# Date 2008-01-16 Time 01:03:26 PST -0800 (1200474206.55 s)
#phil __OFF__

Command line arguments: "../257.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 27599
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 257

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 45.9914, 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: (69.1963, 45.9914, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8093 1.962
Completeness in resolution range: 0.968985
Completeness with d_max=infinity: 0.965975

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8093
                             d_min =   1.9620

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 45.9914, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8093 1.962
Completeness in resolution range: 0.968985
Completeness with d_max=infinity: 0.965975

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8097 -  4.1979 [2128/2152]  1914   214  10.1%
  bin  2:  4.1979 -  3.3446 [2031/2051]  1829   202   9.9%
  bin  3:  3.3446 -  2.9256 [2017/2036]  1814   203  10.1%
  bin  4:  2.9256 -  2.6598 [1984/2014]  1786   198  10.0%
  bin  5:  2.6598 -  2.4701 [1990/2009]  1788   202  10.2%
  bin  6:  2.4701 -  2.3250 [1974/1999]  1779   195   9.9%
  bin  7:  2.3250 -  2.2090 [1953/1981]  1757   196  10.0%
  bin  8:  2.2090 -  2.1131 [1968/2004]  1776   192   9.8%
  bin  9:  2.1131 -  2.0320 [1927/1969]  1730   197  10.2%
  bin 10:  2.0320 -  1.9620 [1617/2001]  1457   160   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_257/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.55 -     2.22: 26
        2.22 -     2.89: 1377
        2.89 -     3.56: 4583
        3.56 -     4.23: 9425
        4.23 -     4.90: 13490
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.547 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.665 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.678 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 302 " - " O   HOH Z  70 "  1.678 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 112 " - " O   HOH Z 408 "  1.772 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28896 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_257/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_257/model_refine_001.geo

CPU time processing inputs: 9.26


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 45.9914 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: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4879   r_free= 0.4837   ksol= 0.00   Bsol= 0.00   scale= 0.798    |
|                                                                             |
| 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:   0.84 A                  |
| x-ray target function (ml) for work reflections: 6.289826                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8097 -  4.6820 0.99   1383  152 0.4100 0.4084      6.6068      6.6408|
|  2:  4.6820 -  3.7359 0.99   1318  152 0.4163 0.3795      6.8129      6.7785|
|  3:  3.7359 -  3.2694 0.99   1299  141 0.4479 0.4323      6.7013      6.7278|
|  4:  3.2694 -  2.9731 0.99   1300  143 0.4745 0.4309      6.5513      6.4779|
|  5:  2.9731 -  2.7615 0.99   1273  144 0.5133 0.5101       6.388      6.4163|
|  6:  2.7615 -  2.5996 0.99   1291  141 0.5168 0.5550      6.2942      6.2218|
|  7:  2.5996 -  2.4701 0.99   1267  146 0.5194 0.4902       6.259      6.1949|
|  8:  2.4701 -  2.3630 0.98   1277  135 0.5363 0.5175      6.1948      6.2196|
|  9:  2.3630 -  2.2723 0.98   1257  141 0.5197 0.5916      6.1268      6.1819|
| 10:  2.2723 -  2.1942 1.00   1280  144 0.5300 0.5395      6.1243      6.1137|
| 11:  2.1942 -  2.1258 0.97   1239  138 0.5259 0.5119      6.0417       6.069|
| 12:  2.1258 -  2.0652 0.98   1254  136 0.5175 0.5177       5.993      6.0426|
| 13:  2.0652 -  2.0110 0.99   1261  138 0.5519 0.5369      5.9027      5.8593|
| 14:  2.0110 -  1.9620 0.73    931  108 0.5376 0.5197      5.8736      5.7944|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8097 -  4.6820  1383   152  0.63  40.10   0.79     0.69      92346.35|
|  2:  4.6820 -  3.7359  1318   152  0.68  37.28   0.87     0.76     118091.82|
|  3:  3.7359 -  3.2694  1299   141  0.58  45.32   0.86     0.71     121515.83|
|  4:  3.2694 -  2.9731  1300   143  0.49  52.68   0.80     0.59     107160.45|
|  5:  2.9731 -  2.7615  1273   144  0.38  61.67   0.75     0.46      88982.35|
|  6:  2.7615 -  2.5996  1291   141  0.33  65.47   0.72     0.38      79025.42|
|  7:  2.5996 -  2.4701  1267   146  0.24  71.84   0.75     0.29      75956.95|
|  8:  2.4701 -  2.3630  1277   135  0.21  74.41   0.73     0.25      69920.86|
|  9:  2.3630 -  2.2723  1257   141  0.21  74.06   0.73     0.26      64356.82|
| 10:  2.2723 -  2.1942  1280   144  0.26  70.65   0.76     0.31      54407.78|
| 11:  2.1942 -  2.1258  1239   138  0.25  71.20   0.77     0.32      52250.12|
| 12:  2.1258 -  2.0652  1254   136  0.25  71.26   0.80     0.32      46914.81|
| 13:  2.0652 -  2.0110  1261   138  0.26  70.79   0.73     0.33      40286.44|
| 14:  2.0110 -  1.9620   931   108  0.36  63.03   0.73     0.41      29528.61|
|alpha:            min =        0.25 max =            0.76 mean =         0.44|
|beta:             min =    29528.61 max =       121515.83 mean =     75651.75|
|figures of merit: min =        0.00 max =            1.00 mean =         0.37|
|phase err.(work): min =        0.00 max =           90.00 mean =        61.83|
|phase err.(test): min =        0.00 max =           89.95 mean =        61.87|
|-----------------------------------------------------------------------------|

============================== 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 = 19.155152             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.551   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.772989              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.678   (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 |  1.114 -  1.493:        5 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.493 -  1.871:       20 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.871 -  2.250:      152 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.250 -  2.628:      633 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.628 -  3.007:     1473 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.007 -  3.386:     2590 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.386 -  3.764:     4058 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.764 -  4.143:     5234 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.143 -  4.521:     6772 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.521 -  4.900:     7983 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       52.890 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.086    4.900  1.114 |       2.528 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.398)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.398)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4933   r_free= 0.4855   ksol= 0.00   Bsol= 0.00   scale= 0.767    |
|                                                                             |
| 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:   0.83 A                  |
| x-ray target function (ml) for work reflections: 6.290871                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4795   r_free= 0.4723   ksol= 0.40   Bsol= 20.00   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.77,9.81,7.10,0.00,0.00,0.00); trace/3= 7.89                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.83 A                  |
| x-ray target function (ml) for work reflections: 6.282865                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.754304             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.632   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.669530              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.290   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4795      final r-factor (work) = 0.4099          |
| start r-factor (free) = 0.4723      final r-factor (free) = 0.4317          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 99.2740 = 14.75 * 0.50 * 6.2876 + 1.00 * 52.8897                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 46.0364 = 14.75 * 0.50 * 6.2207 + 1.00 * 0.1457                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4099      final r-factor (work) = 0.3650          |
| start r-factor (free) = 0.4317      final r-factor (free) = 0.4195          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.4000 = 1.67 * 1.00 * 6.2207 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.2899 = 1.67 * 1.00 * 6.1506 + 1.00 * 0.0213                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.398)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.40   14.42    None  None   None       |
|    all(noH): 2823   0      0.00    85.40   14.42    None  None   None       |
|    Sol.    : 438    0      0.00    80.64   25.18    None  None   None       |
|    Mac.    : 2385   0      0.00    85.40   12.44    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 -   8.540: 1117   |   5:    42.699 -  51.239:   56        |
|      1:     8.540 -  17.080:  797   |   6:    51.239 -  59.779:   31        |
|      2:    17.080 -  25.620:  421   |   7:    59.779 -  68.319:    7        |
|      3:    25.620 -  34.160:  261   |   8:    68.319 -  76.859:    4        |
|      4:    34.160 -  42.699:  125   |   9:    76.859 -  85.399:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3650 r_free = 0.4195             target_work(ml) = 6.137         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3643 r_free = 0.4195             target_work(ml) = 6.136         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3643   r_free= 0.4195   ksol= 0.40   Bsol= 20.00   scale= 1.104   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.77,9.81,7.10,0.00,0.00,0.00); trace/3= 7.89                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.136362                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3625   r_free= 0.4160   ksol= 0.37   Bsol= 40.26   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.93,5.90,4.59,0.00,0.00,0.00); trace/3= 4.80                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.136559                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.284122              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.259  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.711572              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.140  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3625      final r-factor (work) = 0.2995          |
| start r-factor (free) = 0.4160      final r-factor (free) = 0.3623          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.5273 = 7.28 * 0.50 * 6.1453 + 1.00 * 0.1457                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.1579 = 7.28 * 0.50 * 6.0618 + 1.00 * 0.0803                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2995      final r-factor (work) = 0.2808          |
| start r-factor (free) = 0.3623      final r-factor (free) = 0.3472          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3583 = 0.71 * 1.00 * 6.0618 + 1.00 * 0.0448                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3363 = 0.71 * 1.00 * 5.9661 + 1.00 * 0.0910                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.398)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.69   13.98    None  None   None       |
|    all(noH): 2823   0      0.00    88.69   13.98    None  None   None       |
|    Sol.    : 438    0      0.00    86.54   29.38    None  None   None       |
|    Mac.    : 2385   0      0.00    88.69   11.15    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.869: 1251   |   5:    44.343 -  53.211:   53        |
|      1:     8.869 -  17.737:  793   |   6:    53.211 -  62.080:   17        |
|      2:    17.737 -  26.606:  359   |   7:    62.080 -  70.948:   11        |
|      3:    26.606 -  35.474:  232   |   8:    70.948 -  79.817:    3        |
|      4:    35.474 -  44.343:  102   |   9:    79.817 -  88.685:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2808 r_free = 0.3472             target_work(ml) = 5.947         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2806 r_free = 0.3476             target_work(ml) = 5.947         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2806   r_free= 0.3476   ksol= 0.37   Bsol= 40.26   scale= 1.066   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.93,5.90,4.59,0.00,0.00,0.00); trace/3= 4.80                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.946540                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2802   r_free= 0.3464   ksol= 0.34   Bsol= 40.26   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.27,3.67,3.34,0.00,0.00,0.00); trace/3= 3.09                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.946822                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.694302              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.576  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.832208              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.748   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2802      final r-factor (work) = 0.2160          |
| start r-factor (free) = 0.3464      final r-factor (free) = 0.2705          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.0822 = 4.69 * 0.50 * 5.9656 + 1.00 * 0.0800                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.7800 = 4.69 * 0.50 * 5.8397 + 1.00 * 0.0733                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2160      final r-factor (work) = 0.1917          |
| start r-factor (free) = 0.2705      final r-factor (free) = 0.2572          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 22.4065 = 3.83 * 1.00 * 5.8397 + 1.00 * 0.0274                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 21.6605 = 3.83 * 1.00 * 5.6472 + 1.00 * 0.0192                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.398)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.02  15.14    None  None   None       |
|    all(noH): 2823   0      0.00    107.02  15.14    None  None   None       |
|    Sol.    : 438    0      0.29    101.55  40.13    None  None   None       |
|    Mac.    : 2385   0      0.00    107.02  10.55    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.702: 1598   |   5:    53.509 -  64.211:   68        |
|      1:    10.702 -  21.404:  596   |   6:    64.211 -  74.913:   41        |
|      2:    21.404 -  32.105:  225   |   7:    74.913 -  85.614:   11        |
|      3:    32.105 -  42.807:  140   |   8:    85.614 -  96.316:    1        |
|      4:    42.807 -  53.509:  141   |   9:    96.316 - 107.018:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1917 r_free = 0.2572             target_work(ml) = 5.620         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1916 r_free = 0.2571             target_work(ml) = 5.620         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1916   r_free= 0.2571   ksol= 0.34   Bsol= 40.26   scale= 1.048   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.27,3.67,3.34,0.00,0.00,0.00); trace/3= 3.09                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.619627                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1911   r_free= 0.2563   ksol= 0.33   Bsol= 40.26   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.63,2.32,2.93,0.00,0.00,0.00); trace/3= 2.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.616968                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.361426              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.220  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.349588              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.503  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1911      final r-factor (work) = 0.1577          |
| start r-factor (free) = 0.2563      final r-factor (free) = 0.2181          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7420 = 2.36 * 0.50 * 5.6481 + 1.00 * 0.0733                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5902 = 2.36 * 0.50 * 5.5371 + 1.00 * 0.0524                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1577      final r-factor (work) = 0.1493          |
| start r-factor (free) = 0.2181      final r-factor (free) = 0.2033          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9545 = 0.35 * 1.00 * 5.5371 + 1.00 * 0.0188                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9171 = 0.35 * 1.00 * 5.4305 + 1.00 * 0.0187                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.398)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.91  14.27    None  None   None       |
|    all(noH): 2823   0      0.00    105.91  14.27    None  None   None       |
|    Sol.    : 438    0      1.70    100.21  39.33    None  None   None       |
|    Mac.    : 2385   0      0.00    105.91  9.67     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.591: 1773   |   5:    52.953 -  63.544:   69        |
|      1:    10.591 -  21.181:  488   |   6:    63.544 -  74.134:   38        |
|      2:    21.181 -  31.772:  175   |   7:    74.134 -  84.725:   14        |
|      3:    31.772 -  42.362:  145   |   8:    84.725 -  95.315:    0        |
|      4:    42.362 -  52.953:  119   |   9:    95.315 - 105.906:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1493 r_free = 0.2033             target_work(ml) = 5.390         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1490 r_free = 0.2027             target_work(ml) = 5.388         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1490   r_free= 0.2027   ksol= 0.33   Bsol= 40.26   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.63,2.32,2.93,0.00,0.00,0.00); trace/3= 2.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.387646                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1492   r_free= 0.2026   ksol= 0.32   Bsol= 40.26   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.38,1.70,2.86,0.00,0.00,0.00); trace/3= 1.98                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.386517                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.817986              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.873  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.830657              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.091   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1492      final r-factor (work) = 0.1261          |
| start r-factor (free) = 0.2026      final r-factor (free) = 0.1775          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.4182 = 3.82 * 0.50 * 5.4300 + 1.00 * 0.0524                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2170 = 3.82 * 0.50 * 5.3161 + 1.00 * 0.0685                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1261      final r-factor (work) = 0.1209          |
| start r-factor (free) = 0.1775      final r-factor (free) = 0.1710          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4310 = 0.83 * 1.00 * 5.3161 + 1.00 * 0.0151                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3835 = 0.83 * 1.00 * 5.2260 + 1.00 * 0.0426                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.398)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    116.54  13.98    None  None   None       |
|    all(noH): 2823   0      0.00    116.54  13.98    None  None   None       |
|    Sol.    : 438    0      0.00    98.82   39.48    None  None   None       |
|    Mac.    : 2385   0      0.00    116.54  9.30     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.654: 1902   |   5:    58.269 -  69.923:   56        |
|      1:    11.654 -  23.308:  444   |   6:    69.923 -  81.577:   18        |
|      2:    23.308 -  34.962:  142   |   7:    81.577 -  93.231:    4        |
|      3:    34.962 -  46.616:  139   |   8:    93.231 - 104.885:    1        |
|      4:    46.616 -  58.269:  115   |   9:   104.885 - 116.539:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1209 r_free = 0.1710             target_work(ml) = 5.205         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1204 r_free = 0.1704             target_work(ml) = 5.202         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1204   r_free= 0.1704   ksol= 0.32   Bsol= 40.26   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.38,1.70,2.86,0.00,0.00,0.00); trace/3= 1.98                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.202239                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8097 -  4.6820 0.99   1383  152 0.0997 0.1367      5.4066      5.5734|
|  2:  4.6820 -  3.7359 0.99   1318  152 0.0880 0.1246      5.4843        5.73|
|  3:  3.7359 -  3.2694 0.99   1299  141 0.1166 0.1532       5.566      5.8922|
|  4:  3.2694 -  2.9731 0.99   1300  143 0.1329 0.1924      5.5338      5.7278|
|  5:  2.9731 -  2.7615 0.99   1273  144 0.1408 0.1801      5.3953       5.587|
|  6:  2.7615 -  2.5996 0.99   1291  141 0.1290 0.2072        5.27      5.5115|
|  7:  2.5996 -  2.4701 0.99   1267  146 0.1373 0.1802      5.2243      5.4409|
|  8:  2.4701 -  2.3630 0.98   1277  135 0.1322 0.1771       5.153      5.3996|
|  9:  2.3630 -  2.2723 0.98   1257  141 0.1272 0.1801      5.0934      5.3139|
| 10:  2.2723 -  2.1942 1.00   1280  144 0.1227 0.1861      5.0337      5.2695|
| 11:  2.1942 -  2.1258 0.97   1239  138 0.1237 0.1881      5.0129       5.307|
| 12:  2.1258 -  2.0652 0.98   1254  136 0.1238 0.1898      4.9643      5.3106|
| 13:  2.0652 -  2.0110 0.99   1261  138 0.1200 0.1842      4.8324      5.1033|
| 14:  2.0110 -  1.9620 0.73    931  108 0.1040 0.1637      4.6604       4.939|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8097 -  4.6820  1383   152  0.93  10.10   0.98     0.96       8195.67|
|  2:  4.6820 -  3.7359  1318   152  0.95   8.91   1.04     1.02      10459.20|
|  3:  3.7359 -  3.2694  1299   141  0.92  12.76   1.06     1.04      12431.66|
|  4:  3.2694 -  2.9731  1300   143  0.91  15.24   1.03     1.01      12132.44|
|  5:  2.9731 -  2.7615  1273   144  0.89  16.84   1.02     0.98       9396.62|
|  6:  2.7615 -  2.5996  1291   141  0.89  17.30   1.00     0.96       7931.53|
|  7:  2.5996 -  2.4701  1267   146  0.89  17.49   1.01     0.97       7035.63|
|  8:  2.4701 -  2.3630  1277   135  0.90  16.58   1.01     1.00       6132.96|
|  9:  2.3630 -  2.2723  1257   141  0.90  16.56   1.02     0.98       5620.69|
| 10:  2.2723 -  2.1942  1280   144  0.89  16.77   1.01     0.97       5044.45|
| 11:  2.1942 -  2.1258  1239   138  0.89  17.92   1.02     0.98       5156.91|
| 12:  2.1258 -  2.0652  1254   136  0.89  17.35   1.03     1.03       4733.76|
| 13:  2.0652 -  2.0110  1261   138  0.90  16.78   1.03     1.01       3584.89|
| 14:  2.0110 -  1.9620   931   108  0.92  13.61   1.02     0.99       2477.33|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     2477.33 max =        12431.66 mean =      7297.94|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.90 mean =        15.27|
|phase err.(test): min =        0.00 max =           89.37 mean =        14.69|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1207   r_free= 0.1707   ksol= 0.32   Bsol= 42.24   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.60,-0.28,0.88,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.203841                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.81 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1207   r_free= 0.1707   ksol= 0.32   Bsol= 42.24   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.60,-0.28,0.88,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.203841                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8097 -  4.6820 0.99   1383  152 0.0998 0.1370      5.4131      5.5814|
|  2:  4.6820 -  3.7359 0.99   1318  152 0.0895 0.1242      5.4951      5.7314|
|  3:  3.7359 -  3.2694 0.99   1299  141 0.1170 0.1534      5.5685      5.8908|
|  4:  3.2694 -  2.9731 0.99   1300  143 0.1333 0.1931      5.5347      5.7287|
|  5:  2.9731 -  2.7615 0.99   1273  144 0.1409 0.1803      5.3966      5.5898|
|  6:  2.7615 -  2.5996 0.99   1291  141 0.1289 0.2075      5.2699      5.5134|
|  7:  2.5996 -  2.4701 0.99   1267  146 0.1371 0.1801      5.2239      5.4401|
|  8:  2.4701 -  2.3630 0.98   1277  135 0.1321 0.1771      5.1515      5.3965|
|  9:  2.3630 -  2.2723 0.98   1257  141 0.1270 0.1798      5.0932      5.3139|
| 10:  2.2723 -  2.1942 1.00   1280  144 0.1228 0.1861      5.0343      5.2701|
| 11:  2.1942 -  2.1258 0.97   1239  138 0.1235 0.1883      5.0133      5.3091|
| 12:  2.1258 -  2.0652 0.98   1254  136 0.1237 0.1899      4.9645      5.3101|
| 13:  2.0652 -  2.0110 0.99   1261  138 0.1199 0.1843      4.8323      5.1038|
| 14:  2.0110 -  1.9620 0.73    931  108 0.1041 0.1637      4.6608      4.9402|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8097 -  4.6820  1383   152  0.93  10.12   0.98     0.96       8311.16|
|  2:  4.6820 -  3.7359  1318   152  0.95   8.98   1.04     1.02      10525.36|
|  3:  3.7359 -  3.2694  1299   141  0.92  12.80   1.06     1.04      12478.09|
|  4:  3.2694 -  2.9731  1300   143  0.91  15.29   1.03     1.01      12171.84|
|  5:  2.9731 -  2.7615  1273   144  0.89  16.89   1.02     0.98       9428.35|
|  6:  2.7615 -  2.5996  1291   141  0.89  17.30   1.00     0.96       7935.07|
|  7:  2.5996 -  2.4701  1267   146  0.89  17.49   1.01     0.97       7037.36|
|  8:  2.4701 -  2.3630  1277   135  0.90  16.58   1.01     1.00       6117.65|
|  9:  2.3630 -  2.2723  1257   141  0.90  16.55   1.02     0.98       5618.01|
| 10:  2.2723 -  2.1942  1280   144  0.89  16.78   1.01     0.97       5044.95|
| 11:  2.1942 -  2.1258  1239   138  0.89  17.94   1.02     0.98       5166.41|
| 12:  2.1258 -  2.0652  1254   136  0.89  17.37   1.03     1.03       4741.46|
| 13:  2.0652 -  2.0110  1261   138  0.90  16.78   1.03     1.01       3588.34|
| 14:  2.0110 -  1.9620   931   108  0.92  13.61   1.02     0.99       2478.65|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     2478.65 max =        12478.09 mean =      7321.22|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.73 mean =        15.29|
|phase err.(test): min =        0.00 max =           89.77 mean =        14.70|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.398)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.98    118.52  15.96    None  None   None       |
|    all(noH): 2823   0      1.98    118.52  15.96    None  None   None       |
|    Sol.    : 438    0      1.98    100.80  41.46    None  None   None       |
|    Mac.    : 2385   0      1.98    118.52  11.28    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.979 -  13.633: 1902   |   5:    60.249 -  71.902:   56        |
|      1:    13.633 -  25.287:  444   |   6:    71.902 -  83.556:   18        |
|      2:    25.287 -  36.941:  142   |   7:    83.556 -  95.210:    4        |
|      3:    36.941 -  48.595:  139   |   8:    95.210 - 106.864:    1        |
|      4:    48.595 -  60.249:  115   |   9:   106.864 - 118.518:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 331         
Filter by distance & map next to the model:
   mapped sites are within: 0.255 - 5.692
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 328 from: 331
   mapped sites are within: 0.759 - 5.692

peak=   10.479 closest distance to " CB  VAL A 296 " =    1.520
peak=    9.894 closest distance to " CB  VAL A 230 " =    1.395
peak=    8.018 closest distance to " O   HOH Z 130 " =    1.755
peak=    7.492 closest distance to " CG  ARG A 138 " =    1.139
peak=    6.768 closest distance to " CD1AILE A 234 " =    1.081
peak=    6.587 closest distance to " CD2 LEU A   5 " =    1.287
peak=    6.183 closest distance to " O   HOH Z 385 " =    1.164
peak=    5.978 closest distance to " O   HOH Z  65 " =    1.607
peak=    5.947 closest distance to " O   HOH Z 124 " =    1.584
peak=    5.899 closest distance to " NE2 GLN A  11 " =    1.103
peak=    5.863 closest distance to " O   HOH Z 424 " =    1.458
peak=    5.627 closest distance to " O   HOH Z 375 " =    1.175
peak=    5.395 closest distance to " O   HOH Z 142 " =    1.973
peak=    5.342 closest distance to " O   HOH Z   9 " =    1.622
peak=    5.263 closest distance to " CG  LEU A   5 " =    1.181
peak=    5.122 closest distance to " CB  ARG A 275 " =    1.087
peak=    5.117 closest distance to " O   HOH Z 112 " =    1.459
peak=    5.095 closest distance to " O   HOH Z 422 " =    0.915
peak=    5.093 closest distance to " CB  PRO A  54 " =    1.082
peak=    5.083 closest distance to " O   HOH Z 193 " =    1.579
peak=    4.956 closest distance to " O   HOH Z   7 " =    1.604
peak=    4.947 closest distance to " O   HOH Z 427 " =    2.165
peak=    4.941 closest distance to " O   HOH Z  78 " =    1.696
peak=    4.899 closest distance to " O   HOH Z 427 " =    1.142
peak=    4.854 closest distance to " O   HOH Z 369 " =    2.293
peak=    4.835 closest distance to " O   HOH Z 418 " =    1.077
peak=    4.803 closest distance to " O   HOH Z 423 " =    1.651
peak=    4.797 closest distance to " NH2 ARG A  56 " =    1.909
peak=    4.784 closest distance to " O   HOH Z 236 " =    1.467
peak=    4.745 closest distance to " O   HOH Z 417 " =    1.399
peak=    4.714 closest distance to " O   HOH Z 390 " =    1.080
peak=    4.704 closest distance to " CB  VAL A 230 " =    1.216
peak=    4.695 closest distance to " O   HOH Z  91 " =    2.467
peak=    4.652 closest distance to " CD2 LEU A 228 " =    1.184
peak=    4.539 closest distance to " CG  PRO A  54 " =    1.325
peak=    4.539 closest distance to " O   HOH Z 126 " =    1.904
peak=    4.505 closest distance to " CB  SER A   3 " =    1.300
peak=    4.495 closest distance to " O   HOH Z  11 " =    2.037
peak=    4.477 closest distance to " O   HOH Z  39 " =    1.659
peak=    4.457 closest distance to " O   HOH Z 347 " =    0.855
peak=    4.389 closest distance to " O   HOH Z  59 " =    1.611
peak=    4.389 closest distance to " CB  GLN A 223 " =    1.599
peak=    4.369 closest distance to " O   HOH Z  63 " =    1.493
peak=    4.364 closest distance to " CG  LEU A 228 " =    1.010
peak=    4.359 closest distance to " O   HOH Z 232 " =    2.342
peak=    4.335 closest distance to " O   HOH Z 123 " =    1.287
peak=    4.335 closest distance to " O   HOH Z 389 " =    1.406
peak=    4.324 closest distance to " O   HOH Z 380 " =    1.993
peak=    4.315 closest distance to " NE1 TRP A 274 " =    1.055
peak=    4.314 closest distance to " O   HOH Z 410 " =    1.354
peak=    4.307 closest distance to " O   HOH Z  51 " =    1.713
peak=    4.295 closest distance to " O   HOH Z 366 " =    2.705
peak=    4.284 closest distance to " O   HOH Z 371 " =    3.001
peak=    4.276 closest distance to " CB  GLN A 183 " =    1.202
peak=    4.255 closest distance to " O   HOH Z 419 " =    1.936
peak=    4.243 closest distance to " O   HOH Z 344 " =    1.223
peak=    4.226 closest distance to " O   HOH Z 214 " =    1.296
peak=    4.221 closest distance to " O   HOH Z  30 " =    1.811
peak=    4.209 closest distance to " CA  PHE A 283 " =    1.239
peak=    4.183 closest distance to " NH1 ARG A 138 " =    0.986
peak=    4.110 closest distance to " O   HOH Z 222 " =    1.178
peak=    4.098 closest distance to " O   HOH Z 145 " =    1.814
peak=    4.092 closest distance to " O   HOH Z 414 " =    1.247
peak=    4.078 closest distance to " O   HOH Z 193 " =    1.762
peak=    4.073 closest distance to " O   HOH Z 298 " =    1.750
peak=    4.073 closest distance to " O   HOH Z 425 " =    1.473
peak=    4.061 closest distance to " O   HOH Z 405 " =    1.596
peak=    4.050 closest distance to " O   HOH Z 425 " =    2.038
peak=    4.027 closest distance to " O   PRO A 198 " =    1.278
peak=    4.026 closest distance to " CA  ASN A 127 " =    1.111
peak=    4.024 closest distance to " O   HOH Z 426 " =    1.090
peak=    4.022 closest distance to " OG  SER A  62 " =    2.970
peak=    4.019 closest distance to " O   HOH Z 316 " =    2.980
peak=    4.008 closest distance to " CB  SER A  63 " =    1.274
peak=    4.002 closest distance to " CB  ASN A 148 " =    1.368
peak=    3.986 closest distance to " NH2BARG A 145 " =    1.303
peak=    3.984 closest distance to " O   HOH Z 258 " =    2.161
peak=    3.976 closest distance to " O   HOH Z 384 " =    1.325
peak=    3.976 closest distance to " O   HOH Z  85 " =    1.379
peak=    3.973 closest distance to " O   HOH Z 130 " =    1.800
peak=    3.965 closest distance to " CB  SER A 276 " =    1.208
peak=    3.929 closest distance to " O   HOH Z 272 " =    1.855
peak=    3.927 closest distance to " O   HOH Z 392 " =    1.227
peak=    3.917 closest distance to " O   HOH Z  28 " =    1.388
peak=    3.910 closest distance to " O   HOH Z 139 " =    1.186
peak=    3.903 closest distance to " CB  VAL A 202 " =    1.676
peak=    3.900 closest distance to " CE AMET A  47 " =    1.435
peak=    3.884 closest distance to " OD1 ASN A  45 " =    1.127
peak=    3.883 closest distance to " O   HOH Z  69 " =    1.123
peak=    3.870 closest distance to " O   HOH Z 290 " =    0.999
peak=    3.852 closest distance to " CG  GLN A  11 " =    2.104
peak=    3.850 closest distance to " O   HOH Z 403 " =    1.769
peak=    3.833 closest distance to " CB BVAL A  41 " =    1.270
peak=    3.831 closest distance to " CB  GLU A 277 " =    3.464
peak=    3.831 closest distance to " O   HOH Z 143 " =    1.398
peak=    3.826 closest distance to " CB  VAL A 265 " =    1.317
peak=    3.826 closest distance to " O   HOH Z  68 " =    2.097
peak=    3.824 closest distance to " NE2 GLN A  73 " =    1.523
peak=    3.820 closest distance to " O   HOH Z 287 " =    1.745
peak=    3.807 closest distance to " O   HOH Z 303 " =    2.267
peak=    3.806 closest distance to " O   HOH Z  69 " =    2.170
peak=    3.805 closest distance to " ND1 HIS A  81 " =    1.425
peak=    3.803 closest distance to " O   HOH Z 423 " =    1.578
peak=    3.796 closest distance to " O   HOH Z 346 " =    1.618
peak=    3.790 closest distance to " NE2 GLN A  58 " =    3.788
peak=    3.780 closest distance to " NH1AARG A 275 " =    1.007
peak=    3.771 closest distance to " O   HOH Z 176 " =    1.646
peak=    3.768 closest distance to " O   HOH Z   4 " =    1.220
peak=    3.765 closest distance to " NZ  LYS A 117 " =    3.227
peak=    3.753 closest distance to " CE  MET A  93 " =    1.572
peak=    3.728 closest distance to " O   HOH Z 422 " =    2.203
peak=    3.725 closest distance to " CB  TRP A 179 " =    1.342
peak=    3.715 closest distance to " O   HOH Z   1 " =    1.624
peak=    3.713 closest distance to " OD2 ASP A 286 " =    2.441
peak=    3.706 closest distance to " O   HOH Z 358 " =    1.318
peak=    3.703 closest distance to " CG  PRO A 213 " =    1.187
peak=    3.699 closest distance to " O   HOH Z 132 " =    1.049
peak=    3.697 closest distance to " O   HOH Z 213 " =    1.549
peak=    3.691 closest distance to " O   HOH Z 211 " =    1.134
peak=    3.683 closest distance to " O   HOH Z 303 " =    1.706
peak=    3.679 closest distance to " O   HOH Z 128 " =    2.008
peak=    3.675 closest distance to " O   HOH Z 327 " =    1.616
peak=    3.671 closest distance to " O   HOH Z 222 " =    2.220
peak=    3.669 closest distance to " CB  ALA A   1 " =    0.900
peak=    3.661 closest distance to " O   HOH Z 118 " =    1.780
peak=    3.658 closest distance to " CG2 THR A 221 " =    1.218
peak=    3.657 closest distance to " O   HOH Z 244 " =    1.677
peak=    3.646 closest distance to " O   HOH Z 415 " =    1.112
peak=    3.643 closest distance to " O   HOH Z  55 " =    1.811
peak=    3.643 closest distance to " O   HOH Z  61 " =    1.508
peak=    3.638 closest distance to " N   PHE A 130 " =    1.253
peak=    3.634 closest distance to " CG  LEU A 167 " =    1.219
peak=    3.619 closest distance to " O   HOH Z 435 " =    2.079
peak=    3.618 closest distance to " CE3 TRP A 150 " =    0.960
peak=    3.611 closest distance to " O   HOH Z 352 " =    1.323
peak=    3.609 closest distance to " O   HOH Z 234 " =    3.331
peak=    3.607 closest distance to " NH2BARG A 190 " =    1.443
peak=    3.601 closest distance to " O   HOH Z  47 " =    1.514
peak=    3.598 closest distance to " O   HOH Z 305 " =    3.214
peak=    3.596 closest distance to " OG1 THR A 221 " =    1.317
peak=    3.594 closest distance to " O   HOH Z 119 " =    1.491
peak=    3.589 closest distance to " O   HOH Z 293 " =    1.528
peak=    3.585 closest distance to " CG  PRO A 243 " =    1.196
peak=    3.582 closest distance to " C   ALA A 299 " =    1.047
peak=    3.576 closest distance to " O   HOH Z 227 " =    1.880
peak=    3.574 closest distance to " CG2 ILE A  20 " =    1.821
peak=    3.564 closest distance to " O   HOH Z  58 " =    1.811
peak=    3.562 closest distance to " O   HOH Z 356 " =    1.350
peak=    3.559 closest distance to " O   HOH Z  93 " =    2.171
peak=    3.552 closest distance to " O   HOH Z  48 " =    1.501
peak=    3.543 closest distance to " O   HOH Z 371 " =    1.965
peak=    3.539 closest distance to " O   HOH Z 106 " =    2.561
peak=    3.533 closest distance to " CG  LYS A  76 " =    1.534
peak=    3.532 closest distance to " O   HOH Z 148 " =    1.568
peak=    3.529 closest distance to " O   HOH Z 189 " =    2.493
peak=    3.527 closest distance to " CG2 ILE A 234 " =    0.832
peak=    3.524 closest distance to " O   HOH Z 368 " =    2.020
peak=    3.524 closest distance to " CG BARG A 102 " =    1.869
peak=    3.518 closest distance to " O   HOH Z 366 " =    2.158
peak=    3.512 closest distance to " O   HOH Z 334 " =    1.420
peak=    3.512 closest distance to " OE2 GLU A   2 " =    1.953
peak=    3.510 closest distance to " CG  PRO A 198 " =    1.271
peak=    3.510 closest distance to " CA  ARG A 195 " =    1.279
peak=    3.506 closest distance to " O   HOH Z 362 " =    2.111
peak=    3.502 closest distance to " O   HOH Z 203 " =    1.589
peak=    3.498 closest distance to " CD1 ILE A  33 " =    1.826
peak=    3.492 closest distance to " O   HOH Z 126 " =    1.536
peak=    3.489 closest distance to " CB  ALA A 248 " =    1.416
peak=    3.489 closest distance to " CB  MET A  40 " =    0.918
peak=    3.489 closest distance to " CA  ILE A 234 " =    0.993
peak=    3.485 closest distance to " O   HOH Z 166 " =    1.252
peak=    3.477 closest distance to " O   HOH Z 108 " =    2.333
peak=    3.470 closest distance to " CH2 TRP A 266 " =    1.074
peak=    3.469 closest distance to " CB  ARG A  79 " =    1.445
peak=    3.465 closest distance to " CB  ALA A 114 " =    1.593
peak=    3.457 closest distance to " NH2AARG A 145 " =    0.991
peak=    3.452 closest distance to " NH1AARG A 145 " =    1.263
peak=    3.445 closest distance to " OG BSER A 164 " =    2.284
peak=    3.441 closest distance to " O   HOH Z  44 " =    1.762
peak=    3.439 closest distance to " O   HOH Z 129 " =    0.759
peak=    3.432 closest distance to " O   HOH Z 278 " =    0.824
peak=    3.422 closest distance to " O   HOH Z 326 " =    1.366
peak=    3.420 closest distance to " OE1 GLU A   2 " =    2.170
peak=    3.420 closest distance to " O   HOH Z 158 " =    3.003
peak=    3.417 closest distance to " OG BSER A 212 " =    2.827
peak=    3.416 closest distance to " N   ALA A   1 " =    2.982
peak=    3.412 closest distance to " O   HOH Z 128 " =    2.217
peak=    3.411 closest distance to " O   HOH Z 109 " =    2.405
peak=    3.407 closest distance to " CB  THR A  31 " =    1.575
peak=    3.402 closest distance to " O   HOH Z 276 " =    1.252
peak=    3.400 closest distance to " O   HOH Z  11 " =    1.149
peak=    3.396 closest distance to " O   HOH Z  59 " =    2.249
peak=    3.395 closest distance to " O   HOH Z 263 " =    1.687
peak=    3.391 closest distance to " CG1 ILE A 120 " =    1.357
peak=    3.390 closest distance to " OG BSER A 210 " =    1.399
peak=    3.389 closest distance to " O   HOH Z 410 " =    3.188
peak=    3.384 closest distance to " O   HOH Z 392 " =    1.846
peak=    3.383 closest distance to " O  BHOH Z  74 " =    1.337
peak=    3.379 closest distance to " O   HOH Z  88 " =    3.188
peak=    3.379 closest distance to " O   HOH Z 406 " =    1.236
peak=    3.369 closest distance to " O   HOH Z 361 " =    1.275
peak=    3.360 closest distance to " CB  TYR A  30 " =    1.783
peak=    3.359 closest distance to " CD  GLN A 194 " =    1.399
peak=    3.355 closest distance to " O   HOH Z 424 " =    2.000
peak=    3.355 closest distance to " OD1 ASN A  45 " =    1.104
peak=    3.348 closest distance to " CB  ASN A 110 " =    1.084
peak=    3.347 closest distance to " O   HOH Z 144 " =    2.337
peak=    3.347 closest distance to " O   HOH Z 368 " =    3.635
peak=    3.344 closest distance to " O   HOH Z 250 " =    1.428
peak=    3.343 closest distance to " OG BSER A  99 " =    2.125
peak=    3.342 closest distance to " O   HOH Z 388 " =    1.954
peak=    3.339 closest distance to " CD1 ILE A 263 " =    1.343
peak=    3.338 closest distance to " O   HOH Z 128 " =    1.990
peak=    3.334 closest distance to " O   HOH Z 345 " =    3.087
peak=    3.332 closest distance to " N   GLU A   2 " =    1.281
peak=    3.329 closest distance to " O   HOH Z   9 " =    1.875
peak=    3.326 closest distance to " CB  LEU A 300 " =    0.890
peak=    3.325 closest distance to " O   HOH Z 402 " =    1.362
peak=    3.325 closest distance to " O   HOH Z 329 " =    3.623
peak=    3.323 closest distance to " O   HOH Z 272 " =    2.174
peak=    3.321 closest distance to " CD  LYS A 166 " =    1.418
peak=    3.320 closest distance to " CG  GLN A  88 " =    1.114
peak=    3.315 closest distance to " O   HOH Z 323 " =    1.581
peak=    3.313 closest distance to " NH2 ARG A 156 " =    1.125
peak=    3.313 closest distance to " CG1 ILE A  33 " =    1.311
peak=    3.311 closest distance to " O   HOH Z  26 " =    1.529
peak=    3.310 closest distance to " O   HOH Z 212 " =    1.394
peak=    3.301 closest distance to " O   PRO A 198 " =    1.506
peak=    3.300 closest distance to " O   HOH Z  32 " =    2.209
peak=    3.299 closest distance to " O   HOH Z 173 " =    2.153
peak=    3.294 closest distance to " N   ASN A 148 " =    1.082
peak=    3.293 closest distance to " N   ALA A   1 " =    1.059
peak=    3.292 closest distance to " CB  GLU A 152 " =    1.296
peak=    3.289 closest distance to " CG1AVAL A 121 " =    0.921
peak=    3.289 closest distance to " O   HOH Z 214 " =    2.215
peak=    3.288 closest distance to " CB  TRP A 266 " =    1.098
peak=    3.275 closest distance to " CA  LEU A 282 " =    1.149
peak=    3.271 closest distance to " OH  TYR A 116 " =    1.154
peak=    3.271 closest distance to " NZ  LYS A 117 " =    1.043
peak=    3.265 closest distance to " CA  ALA A  21 " =    1.160
peak=    3.263 closest distance to " NZ BLYS A 290 " =    0.979
peak=    3.260 closest distance to " O   HOH Z 248 " =    2.272
peak=    3.255 closest distance to " CD1 LEU A   5 " =    1.757
peak=    3.253 closest distance to " NZ  LYS A  76 " =    1.476
peak=    3.252 closest distance to " O   HOH Z  59 " =    2.031
peak=    3.248 closest distance to " O   HOH Z  65 " =    1.545
peak=    3.248 closest distance to " O   HOH Z  61 " =    1.682
peak=    3.247 closest distance to " CB  ARG A 138 " =    0.918
peak=    3.246 closest distance to " CB  ASN A 215 " =    1.078
peak=    3.245 closest distance to " OG ASER A 134 " =    1.374
peak=    3.244 closest distance to " CB  SER A 216 " =    0.904
peak=    3.243 closest distance to " CA  ALA A 158 " =    1.253
peak=    3.243 closest distance to " O   HOH Z 326 " =    1.841
peak=    3.240 closest distance to " O   HOH Z  89 " =    2.034
peak=    3.239 closest distance to " CD  ARG A 269 " =    0.944
peak=    3.238 closest distance to " O   HOH Z 117 " =    1.912
peak=    3.235 closest distance to " CB  ARG A 219 " =    0.878
peak=    3.235 closest distance to " O   HOH Z 147 " =    1.459
peak=    3.233 closest distance to " ND2 ASN A 187 " =    1.622
peak=    3.233 closest distance to " O   HOH Z 220 " =    1.388
peak=    3.232 closest distance to " O   HOH Z 130 " =    1.598
peak=    3.230 closest distance to " O   HOH Z 357 " =    1.869
peak=    3.225 closest distance to " CG2 ILE A  20 " =    1.131
peak=    3.217 closest distance to " O   HOH Z 406 " =    1.478
peak=    3.216 closest distance to " O   HOH Z 365 " =    5.382
peak=    3.215 closest distance to " O   HOH Z 313 " =    1.578
peak=    3.215 closest distance to " CB  ASN A 142 " =    1.092
peak=    3.213 closest distance to " CB  PHE A 204 " =    0.889
peak=    3.210 closest distance to " CB  MET A 188 " =    1.689
peak=    3.207 closest distance to " CD  ARG A 138 " =    0.913
peak=    3.207 closest distance to " NH1 ARG A  14 " =    1.071
peak=    3.200 closest distance to " O   HOH Z 411 " =    1.767
peak=    3.198 closest distance to " O   HOH Z 222 " =    2.205
peak=    3.197 closest distance to " O   HOH Z 153 " =    3.474
peak=    3.188 closest distance to " OE1 GLN A  58 " =    3.945
peak=    3.182 closest distance to " O   HOH Z 181 " =    2.167
peak=    3.181 closest distance to " C   LYS A 290 " =    1.435
peak=    3.181 closest distance to " CG  ARG A 156 " =    1.154
peak=    3.178 closest distance to " NH2AARG A 190 " =    1.743
peak=    3.176 closest distance to " O   HOH Z 233 " =    1.614
peak=    3.174 closest distance to " CB  ALA A 291 " =    1.339
peak=    3.166 closest distance to " CG1 VAL A 153 " =    0.771
peak=    3.164 closest distance to " O   HOH Z 191 " =    2.010
peak=    3.164 closest distance to " O   HOH Z 152 " =    2.114
peak=    3.162 closest distance to " O   HOH Z 411 " =    3.776
peak=    3.161 closest distance to " CB  PRO A  90 " =    1.209
peak=    3.159 closest distance to " CB  LYS A 117 " =    1.164
peak=    3.158 closest distance to " OG1 THR A 246 " =    1.229
peak=    3.155 closest distance to " O   HOH Z  40 " =    2.184
peak=    3.152 closest distance to " O   HOH Z 412 " =    1.633
peak=    3.150 closest distance to " CG  MET A 185 " =    1.152
peak=    3.148 closest distance to " O   HOH Z  64 " =    1.986
peak=    3.148 closest distance to " O   HOH Z 359 " =    1.158
peak=    3.143 closest distance to " O   HOH Z 413 " =    1.666
peak=    3.139 closest distance to " O   HOH Z  71 " =    1.018
peak=    3.137 closest distance to " O   HOH Z 200 " =    1.627
peak=    3.130 closest distance to " CB  ALA A 248 " =    1.044
peak=    3.130 closest distance to " CB  PHE A 225 " =    1.337
peak=    3.125 closest distance to " O   HOH Z 145 " =    2.122
peak=    3.123 closest distance to " O   HOH Z 353 " =    1.898
peak=    3.122 closest distance to " CB  LEU A 255 " =    0.774
peak=    3.119 closest distance to " NH1BARG A 145 " =    1.600
peak=    3.116 closest distance to " O   HOH Z 194 " =    2.073
peak=    3.115 closest distance to " CG AARG A 275 " =    1.061
peak=    3.115 closest distance to " ND2 ASN A 249 " =    0.851
peak=    3.113 closest distance to " CE  LYS A  48 " =    1.004
peak=    3.112 closest distance to " CB  GLU A 128 " =    0.989
peak=    3.112 closest distance to " O   HOH Z 273 " =    2.828
peak=    3.107 closest distance to " O   HOH Z  95 " =    1.141
peak=    3.103 closest distance to " O   HOH Z 302 " =    1.599
peak=    3.102 closest distance to " NE2 GLN A 278 " =    3.660
peak=    3.100 closest distance to " O   HOH Z  33 " =    1.766
peak=    3.097 closest distance to " O   HOH Z 438 " =    2.500
peak=    3.097 closest distance to " O   HOH Z 193 " =    1.851
peak=    3.095 closest distance to " O   HOH Z 158 " =    3.249
peak=    3.090 closest distance to " CB  ASN A 187 " =    1.085
peak=    3.088 closest distance to " O   HOH Z 128 " =    2.234
peak=    3.079 closest distance to " C   VAL A 265 " =    1.356
peak=    3.071 closest distance to " CA  MET A 105 " =    0.808
peak=    3.061 closest distance to " OE2 GLU A  53 " =    2.063
peak=    3.059 closest distance to " O   HOH Z  57 " =    1.896
peak=    3.052 closest distance to " CG1BVAL A  72 " =    0.873
peak=    3.047 closest distance to " N   VAL A 126 " =    1.258
peak=    3.045 closest distance to " O   PRO A 198 " =    1.882
peak=    3.031 closest distance to " NE2 GLN A  58 " =    5.692
peak=    3.030 closest distance to " CB  ASN A 148 " =    1.906
peak=    3.023 closest distance to " O   HOH Z 189 " =    4.276
peak=    3.009 closest distance to " CG2 VAL A 232 " =    1.108

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.521 - 5.391
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 204
   mapped sites are within: 0.812 - 5.391

peak=   -4.899 closest distance to " CG2 VAL A 230 " =    0.812
peak=   -4.593 closest distance to " O   HOH Z 385 " =    1.252
peak=   -4.414 closest distance to " OG BSER A 134 " =    1.320
peak=   -4.331 closest distance to " CD  ARG A 156 " =    1.920
peak=   -4.254 closest distance to " O   PRO A 198 " =    1.162
peak=   -4.235 closest distance to " O   HOH Z  69 " =    1.845
peak=   -4.198 closest distance to " O   HOH Z 131 " =    3.989
peak=   -4.194 closest distance to " NH2 ARG A  79 " =    2.036
peak=   -4.171 closest distance to " CG  ARG A 138 " =    0.850
peak=   -4.113 closest distance to " O   HOH Z 412 " =    5.330
peak=   -4.052 closest distance to " CE2 PHE A 218 " =    2.465
peak=   -4.025 closest distance to " O   SER A 135 " =    1.609
peak=   -4.018 closest distance to " C   HIS A 108 " =    1.241
peak=   -3.994 closest distance to " CD1 LEU A 255 " =    2.774
peak=   -3.991 closest distance to " CA  GLY A 133 " =    2.020
peak=   -3.978 closest distance to " CD  ARG A  14 " =    3.030
peak=   -3.962 closest distance to " CA  GLY A  98 " =    1.790
peak=   -3.942 closest distance to " O   ALA A 292 " =    2.220
peak=   -3.891 closest distance to " O   HOH Z 407 " =    2.654
peak=   -3.873 closest distance to " O   HOH Z 103 " =    1.467
peak=   -3.862 closest distance to " CD  ARG A 138 " =    1.350
peak=   -3.835 closest distance to " OD1 ASN A  39 " =    2.075
peak=   -3.832 closest distance to " CD2 LEU A   5 " =    0.990
peak=   -3.811 closest distance to " CA  GLY A  23 " =    2.020
peak=   -3.768 closest distance to " CB  ALA A 248 " =    2.039
peak=   -3.767 closest distance to " O   HOH Z 185 " =    1.928
peak=   -3.767 closest distance to " O   HOH Z  60 " =    2.163
peak=   -3.750 closest distance to " OG  SER A  87 " =    1.334
peak=   -3.742 closest distance to " O   HOH Z 427 " =    1.598
peak=   -3.739 closest distance to " O   VAL A  67 " =    2.902
peak=   -3.734 closest distance to " N   ALA A   1 " =    1.284
peak=   -3.698 closest distance to " N   SER A 276 " =    1.140
peak=   -3.679 closest distance to " OD2 ASP A  50 " =    1.344
peak=   -3.675 closest distance to " CD2 LEU A 237 " =    2.720
peak=   -3.675 closest distance to " N   VAL A  72 " =    1.824
peak=   -3.665 closest distance to " O   HOH Z 298 " =    1.125
peak=   -3.660 closest distance to " O   HOH Z  11 " =    1.813
peak=   -3.643 closest distance to " CB  ASN A  39 " =    2.130
peak=   -3.628 closest distance to " OE2 GLU A 152 " =    1.049
peak=   -3.627 closest distance to " ND2 ASN A 187 " =    1.574
peak=   -3.626 closest distance to " O   HOH Z 234 " =    3.855
peak=   -3.622 closest distance to " CB  ASP A  27 " =    2.322
peak=   -3.622 closest distance to " CE2 TYR A 116 " =    3.007
peak=   -3.620 closest distance to " O   SER A  22 " =    2.336
peak=   -3.616 closest distance to " O   PRO A 243 " =    2.495
peak=   -3.616 closest distance to " O   HOH Z 100 " =    1.193
peak=   -3.613 closest distance to " CD  LYS A 289 " =    2.396
peak=   -3.610 closest distance to " O   SER A 271 " =    1.959
peak=   -3.604 closest distance to " CB  ALA A  43 " =    2.169
peak=   -3.596 closest distance to " O   HOH Z  24 " =    1.086
peak=   -3.596 closest distance to " O   HOH Z   9 " =    1.550
peak=   -3.595 closest distance to " O   HOH Z 191 " =    5.391
peak=   -3.590 closest distance to " O   HOH Z 359 " =    1.731
peak=   -3.585 closest distance to " O   HOH Z 183 " =    1.644
peak=   -3.584 closest distance to " O   HOH Z 211 " =    1.227
peak=   -3.584 closest distance to " CG  GLN A  58 " =    1.051
peak=   -3.574 closest distance to " ND2 ASN A 209 " =    1.957
peak=   -3.573 closest distance to " O   HOH Z 359 " =    3.435
peak=   -3.568 closest distance to " O   HOH Z 286 " =    1.776
peak=   -3.565 closest distance to " O   TRP A 179 " =    1.593
peak=   -3.562 closest distance to " N   GLN A  58 " =    1.303
peak=   -3.558 closest distance to " C   ILE A 239 " =    2.076
peak=   -3.544 closest distance to " O   HOH Z 377 " =    1.058
peak=   -3.543 closest distance to " O   HOH Z 134 " =    2.789
peak=   -3.543 closest distance to " CG  GLN A 223 " =    1.975
peak=   -3.539 closest distance to " CD1 LEU A 101 " =    2.199
peak=   -3.533 closest distance to " CB  PRO A 243 " =    2.623
peak=   -3.530 closest distance to " C   GLN A 205 " =    1.900
peak=   -3.524 closest distance to " O   HOH Z 125 " =    3.501
peak=   -3.508 closest distance to " O   PRO A 163 " =    1.914
peak=   -3.508 closest distance to " NH1 ARG A  56 " =    2.481
peak=   -3.504 closest distance to " O   HOH Z 347 " =    0.992
peak=   -3.500 closest distance to " O   HOH Z 130 " =    2.152
peak=   -3.491 closest distance to " OD2 ASP A 191 " =    1.414
peak=   -3.489 closest distance to " CZ2 TRP A 274 " =    0.959
peak=   -3.479 closest distance to " N   ALA A 248 " =    1.607
peak=   -3.477 closest distance to " O   HOH Z 339 " =    1.848
peak=   -3.474 closest distance to " O   HOH Z 415 " =    1.114
peak=   -3.472 closest distance to " O   HOH Z 137 " =    1.491
peak=   -3.470 closest distance to " C   ALA A 158 " =    1.341
peak=   -3.468 closest distance to " O   HOH Z 313 " =    1.506
peak=   -3.468 closest distance to " CG  PRO A 163 " =    2.615
peak=   -3.466 closest distance to " O   HOH Z 404 " =    1.502
peak=   -3.452 closest distance to " O   HOH Z 231 " =    1.957
peak=   -3.452 closest distance to " O   HOH Z 414 " =    2.306
peak=   -3.446 closest distance to " O   HOH Z 388 " =    1.918
peak=   -3.441 closest distance to " O   HOH Z 426 " =    2.248
peak=   -3.438 closest distance to " C   ASN A 285 " =    2.060
peak=   -3.436 closest distance to " O   MET A  40 " =    2.754
peak=   -3.433 closest distance to " CE2 TYR A  30 " =    2.751
peak=   -3.429 closest distance to " O   HOH Z 193 " =    1.678
peak=   -3.428 closest distance to " O   HOH Z  63 " =    2.181
peak=   -3.420 closest distance to " OG ASER A 134 " =    1.143
peak=   -3.408 closest distance to " O   HOH Z  65 " =    1.021
peak=   -3.407 closest distance to " CE1 TYR A 247 " =    2.527
peak=   -3.407 closest distance to " O   HOH Z 414 " =    2.363
peak=   -3.405 closest distance to " O   ARG A 145 " =    1.561
peak=   -3.401 closest distance to " CA  TYR A  30 " =    2.814
peak=   -3.389 closest distance to " N   MET A 188 " =    1.874
peak=   -3.383 closest distance to " N   HIS A 115 " =    2.052
peak=   -3.382 closest distance to " O   HOH Z 423 " =    2.425
peak=   -3.371 closest distance to " N   PRO A 163 " =    1.483
peak=   -3.371 closest distance to " OG  SER A  97 " =    2.192
peak=   -3.366 closest distance to " O   HOH Z 102 " =    1.545
peak=   -3.365 closest distance to " O   ALA A 161 " =    1.854
peak=   -3.359 closest distance to " O   HOH Z 406 " =    0.900
peak=   -3.358 closest distance to " CZ  PHE A  59 " =    1.448
peak=   -3.357 closest distance to " OD2 ASP A 270 " =    1.408
peak=   -3.352 closest distance to " N   THR A 157 " =    1.403
peak=   -3.347 closest distance to " O   HOH Z  60 " =    1.905
peak=   -3.346 closest distance to " O   ASN A 301 " =    1.321
peak=   -3.343 closest distance to " O   HOH Z  88 " =    2.082
peak=   -3.342 closest distance to " CE3 TRP A 274 " =    2.259
peak=   -3.341 closest distance to " O   HOH Z  56 " =    1.928
peak=   -3.338 closest distance to " CD1 TRP A 274 " =    1.249
peak=   -3.336 closest distance to " CG  PHE A 283 " =    2.495
peak=   -3.335 closest distance to " CD2 PHE A  61 " =    2.012
peak=   -3.335 closest distance to " O   ARG A  24 " =    1.902
peak=   -3.334 closest distance to " O   GLN A 240 " =    1.923
peak=   -3.333 closest distance to " O   HOH Z  53 " =    1.618
peak=   -3.331 closest distance to " CG  GLN A  11 " =    2.078
peak=   -3.330 closest distance to " CD2 TYR A 293 " =    1.766
peak=   -3.327 closest distance to " O   HOH Z 266 " =    4.568
peak=   -3.326 closest distance to " CD1 TRP A 179 " =    1.189
peak=   -3.320 closest distance to " CB  PRO A 163 " =    2.420
peak=   -3.317 closest distance to " C   ARG A 269 " =    1.275
peak=   -3.315 closest distance to " CA  GLY A  35 " =    1.983
peak=   -3.305 closest distance to " O   VAL A  67 " =    2.576
peak=   -3.299 closest distance to " O   ILE A  49 " =    1.673
peak=   -3.298 closest distance to " O   HOH Z 430 " =    1.993
peak=   -3.296 closest distance to " OE1 GLU A 277 " =    2.184
peak=   -3.294 closest distance to " ND2 ASN A  45 " =    2.123
peak=   -3.286 closest distance to " O   HOH Z 350 " =    2.461
peak=   -3.279 closest distance to " CB  GLN A  55 " =    1.190
peak=   -3.273 closest distance to " CB  VAL A 230 " =    1.024
peak=   -3.273 closest distance to " O   HOH Z 208 " =    2.010
peak=   -3.271 closest distance to " CG  MET A 105 " =    0.917
peak=   -3.264 closest distance to " OG  SER A 245 " =    1.327
peak=   -3.258 closest distance to " CG1 ILE A 263 " =    2.105
peak=   -3.257 closest distance to " N   PHE A  59 " =    2.122
peak=   -3.257 closest distance to " O   HOH Z 351 " =    1.509
peak=   -3.257 closest distance to " O   HOH Z 426 " =    1.644
peak=   -3.250 closest distance to " O   HOH Z 274 " =    3.065
peak=   -3.246 closest distance to " O   HOH Z 368 " =    2.541
peak=   -3.240 closest distance to " CG  ARG A 219 " =    2.723
peak=   -3.236 closest distance to " O   HOH Z 290 " =    1.128
peak=   -3.236 closest distance to " OD1 ASP A 200 " =    1.509
peak=   -3.234 closest distance to " O   HOH Z  52 " =    1.116
peak=   -3.233 closest distance to " OG  SER A   3 " =    1.188
peak=   -3.233 closest distance to " CG  ASP A 231 " =    0.820
peak=   -3.231 closest distance to " CD1 LEU A 228 " =    1.917
peak=   -3.229 closest distance to " CB  ALA A 114 " =    2.215
peak=   -3.217 closest distance to " O   HOH Z  54 " =    0.876
peak=   -3.215 closest distance to " CE2 TRP A  70 " =    2.377
peak=   -3.214 closest distance to " CZ  TYR A 169 " =    1.872
peak=   -3.208 closest distance to " O   HOH Z 140 " =    1.329
peak=   -3.208 closest distance to " OD2 ASP A 171 " =    1.887
peak=   -3.207 closest distance to " O   GLN A  11 " =    1.490
peak=   -3.207 closest distance to " O   HOH Z  65 " =    1.360
peak=   -3.207 closest distance to " O   HOH Z  51 " =    0.893
peak=   -3.202 closest distance to " O   HOH Z 192 " =    1.068
peak=   -3.197 closest distance to " O   VAL A 189 " =    2.438
peak=   -3.195 closest distance to " O   HOH Z 435 " =    2.408
peak=   -3.194 closest distance to " O   HOH Z 316 " =    1.910
peak=   -3.192 closest distance to " CE BMET A  47 " =    1.133
peak=   -3.192 closest distance to " CG1BVAL A  72 " =    2.096
peak=   -3.187 closest distance to " CB  ALA A 291 " =    2.096
peak=   -3.182 closest distance to " CG2AVAL A  41 " =    3.002
peak=   -3.181 closest distance to " CB  PHE A 192 " =    1.864
peak=   -3.174 closest distance to " CG  ASN A 301 " =    1.997
peak=   -3.165 closest distance to " CG  TRP A 266 " =    1.728
peak=   -3.162 closest distance to " O   HOH Z 165 " =    2.192
peak=   -3.146 closest distance to " CD  GLU A 277 " =    0.987
peak=   -3.140 closest distance to " O   HOH Z 134 " =    3.689
peak=   -3.140 closest distance to " O   HOH Z 189 " =    1.478
peak=   -3.139 closest distance to " O   HOH Z 256 " =    1.400
peak=   -3.132 closest distance to " CB  SER A 210 " =    1.256
peak=   -3.129 closest distance to " OG  SER A  87 " =    1.674
peak=   -3.128 closest distance to " CG  LEU A 228 " =    1.065
peak=   -3.123 closest distance to " N   GLN A  58 " =    2.123
peak=   -3.121 closest distance to " O   GLY A  80 " =    2.464
peak=   -3.116 closest distance to " O   HOH Z 298 " =    2.647
peak=   -3.115 closest distance to " O   ALA A   1 " =    1.313
peak=   -3.104 closest distance to " CG  GLN A  88 " =    1.071
peak=   -3.103 closest distance to " O   ASP A 270 " =    1.667
peak=   -3.103 closest distance to " CB  ALA A 129 " =    2.506
peak=   -3.101 closest distance to " NH2 ARG A 219 " =    1.786
peak=   -3.095 closest distance to " NE2 GLN A  55 " =    1.018
peak=   -3.094 closest distance to " O   HOH Z 367 " =    4.536
peak=   -3.093 closest distance to " O   HOH Z 235 " =    1.157
peak=   -3.092 closest distance to " CZ3 TRP A 123 " =    1.919
peak=   -3.088 closest distance to " CG  ASN A  45 " =    1.743
peak=   -3.087 closest distance to " O   HOH Z 385 " =    1.782
peak=   -3.087 closest distance to " O   HOH Z 414 " =    2.046
peak=   -3.084 closest distance to " O   HOH Z 213 " =    1.359
peak=   -3.079 closest distance to " CE  LYS A 166 " =    1.112
peak=   -3.076 closest distance to " O   HOH Z 128 " =    1.890
peak=   -3.075 closest distance to " CB  ASP A 132 " =    2.337
peak=   -3.059 closest distance to " O   HOH Z  52 " =    2.081
peak=   -3.058 closest distance to " O   HOH Z 166 " =    1.748
peak=   -3.051 closest distance to " O   HOH Z 210 " =    2.003
peak=   -3.041 closest distance to " N   GLN A 223 " =    1.496
peak=   -3.027 closest distance to " OXT GLY A 302 " =    2.972

================= 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    :  0.4879 0.4837   6.289826e+00   6.281648e+00
   1_bss:  0.4795 0.4723   6.282865e+00   6.269858e+00
   1_xyz:  0.4099 0.4317   6.197663e+00   6.225538e+00
   1_adp:  0.3650 0.4195   6.136860e+00   6.214334e+00
   1_occ:  0.3643 0.4195   6.136362e+00   6.215213e+00
   2_bss:  0.3625 0.4160   6.136559e+00   6.213051e+00
   2_xyz:  0.2995 0.3623   5.989633e+00   6.115766e+00
   2_adp:  0.2808 0.3472   5.946532e+00   6.080581e+00
   2_occ:  0.2806 0.3476   5.946540e+00   6.081061e+00
   3_bss:  0.2802 0.3464   5.946822e+00   6.079967e+00
   3_xyz:  0.2160 0.2705   5.707470e+00   5.879242e+00
   3_adp:  0.1917 0.2572   5.620187e+00   5.830364e+00
   3_occ:  0.1916 0.2571   5.619627e+00   5.830216e+00
   4_bss:  0.1911 0.2563   5.616968e+00   5.827357e+00
   4_xyz:  0.1577 0.2181   5.451104e+00   5.685936e+00
   4_adp:  0.1493 0.2033   5.389704e+00   5.615107e+00
   4_occ:  0.1490 0.2027   5.387646e+00   5.612250e+00
   5_bss:  0.1492 0.2026   5.386517e+00   5.611221e+00
   5_xyz:  0.1261 0.1775   5.244070e+00   5.488762e+00
   5_adp:  0.1209 0.1710   5.205043e+00   5.451509e+00
   5_occ:  0.1204 0.1704   5.202239e+00   5.448343e+00
   5_bss:  0.1207 0.1707   5.203841e+00   5.449353e+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:  0.401  20.000   6.766   9.807   7.096   0.000   0.000   0.000
   1_xyz:  0.401  20.000   6.766   9.807   7.096   0.000   0.000   0.000
   1_adp:  0.401  20.000   6.766   9.807   7.096   0.000   0.000   0.000
   1_occ:  0.401  20.000   6.766   9.807   7.096   0.000   0.000   0.000
   2_bss:  0.369  40.260   3.929   5.897   4.588   0.000   0.000   0.000
   2_xyz:  0.369  40.260   3.929   5.897   4.588   0.000   0.000   0.000
   2_adp:  0.369  40.260   3.929   5.897   4.588   0.000   0.000   0.000
   2_occ:  0.369  40.260   3.929   5.897   4.588   0.000   0.000   0.000
   3_bss:  0.342  40.260   2.267   3.668   3.340   0.000   0.000   0.000
   3_xyz:  0.342  40.260   2.267   3.668   3.340   0.000   0.000   0.000
   3_adp:  0.342  40.260   2.267   3.668   3.340   0.000   0.000   0.000
   3_occ:  0.342  40.260   2.267   3.668   3.340   0.000   0.000   0.000
   4_bss:  0.328  40.260   1.634   2.320   2.927   0.000   0.000   0.000
   4_xyz:  0.328  40.260   1.634   2.320   2.927   0.000   0.000   0.000
   4_adp:  0.328  40.260   1.634   2.320   2.927   0.000   0.000   0.000
   4_occ:  0.328  40.260   1.634   2.320   2.927   0.000   0.000   0.000
   5_bss:  0.322  40.260   1.378   1.701   2.859   0.000   0.000   0.000
   5_xyz:  0.322  40.260   1.378   1.701   2.859   0.000   0.000   0.000
   5_adp:  0.322  40.260   1.378   1.701   2.859   0.000   0.000   0.000
   5_occ:  0.322  40.260   1.378   1.701   2.859   0.000   0.000   0.000
   5_bss:  0.318  42.239  -0.601  -0.279   0.880   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  61.834 0.3699  0.4378    75650.530
   1_bss:  61.120 0.3776  0.5576    72142.766
   1_xyz:  51.824 0.4964  0.7273    57501.061
   1_adp:  49.241 0.5294  0.8262    54717.571
   1_occ:  49.341 0.5281  0.8225    54831.744
   2_bss:  48.938 0.5330  0.7450    54101.562
   2_xyz:  39.567 0.6476  0.8959    38109.608
   2_adp:  36.796 0.6809  0.9380    34175.078
   2_occ:  36.835 0.6804  0.9372    34221.104
   3_bss:  36.692 0.6819  0.8821    34005.939
   3_xyz:  27.125 0.7889  0.9859    19119.293
   3_adp:  25.173 0.8098  0.9928    16907.234
   3_occ:  25.157 0.8100  0.9930    16895.965
   4_bss:  25.032 0.8112  0.9651    16721.851
   4_xyz:  21.003 0.8514  0.9888    11961.242
   4_adp:  18.945 0.8720  0.9925    10354.220
   4_occ:  18.886 0.8725  0.9924    10273.917
   5_bss:  18.852 0.8727  0.9810    10218.618
   5_xyz:  16.144 0.8969  0.9949     7868.173
   5_adp:  15.265 0.9046  0.9934     7352.171
   5_occ:  15.215 0.9050  0.9931     7297.429
   5_bss:  15.233 0.9049  0.9927     7320.711
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.086   5.2890e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.086   5.2890e+01
   1_xyz:   1.713  0.013  0.107 18.182  0.007  4.104   1.4574e-01
   1_adp:   1.713  0.013  0.107 18.182  0.007  4.104   1.4574e-01
   1_occ:   1.713  0.013  0.107 18.182  0.007  4.104   1.4574e-01
   2_bss:   1.713  0.013  0.107 18.182  0.007  4.104   1.4574e-01
   2_xyz:   1.125  0.008  0.076 15.891  0.005  4.113   8.0321e-02
   2_adp:   1.125  0.008  0.076 15.891  0.005  4.113   8.0321e-02
   2_occ:   1.125  0.008  0.076 15.891  0.005  4.113   8.0321e-02
   3_bss:   1.125  0.008  0.076 15.891  0.005  4.113   8.0321e-02
   3_xyz:   1.114  0.008  0.077 15.837  0.004  4.115   7.3259e-02
   3_adp:   1.114  0.008  0.077 15.837  0.004  4.115   7.3259e-02
   3_occ:   1.114  0.008  0.077 15.837  0.004  4.115   7.3259e-02
   4_bss:   1.114  0.008  0.077 15.837  0.004  4.115   7.3259e-02
   4_xyz:   0.879  0.005  0.064 15.221  0.003  4.108   5.2444e-02
   4_adp:   0.879  0.005  0.064 15.221  0.003  4.108   5.2444e-02
   4_occ:   0.879  0.005  0.064 15.221  0.003  4.108   5.2444e-02
   5_bss:   0.879  0.005  0.064 15.221  0.003  4.108   5.2444e-02
   5_xyz:   1.089  0.007  0.078 15.689  0.004  4.110   6.8546e-02
   5_adp:   1.089  0.007  0.078 15.689  0.004  4.110   6.8546e-02
   5_occ:   1.089  0.007  0.078 15.689  0.004  4.110   6.8546e-02
   5_bss:   1.089  0.007  0.078 15.689  0.004  4.110   6.8546e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.114   6.8513e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.114   6.8513e+00
   1_xyz:  14.719  0.172  0.462 89.794  0.037  2.075   9.8503e-02
   1_adp:  14.719  0.172  0.462 89.794  0.037  2.075   9.8503e-02
   1_occ:  14.719  0.172  0.462 89.794  0.037  2.075   9.8503e-02
   2_bss:  14.719  0.172  0.462 89.794  0.037  2.075   9.8503e-02
   2_xyz:   6.956  0.074  0.299 86.575  0.044  2.096   7.5393e-02
   2_adp:   6.956  0.074  0.299 86.575  0.044  2.096   7.5393e-02
   2_occ:   6.956  0.074  0.299 86.575  0.044  2.096   7.5393e-02
   3_bss:   6.956  0.074  0.299 86.575  0.044  2.096   7.5393e-02
   3_xyz:   7.478  0.047  0.301 87.037  0.021  2.311   6.7365e-02
   3_adp:   7.478  0.047  0.301 87.037  0.021  2.311   6.7365e-02
   3_occ:   7.478  0.047  0.301 87.037  0.021  2.311   6.7365e-02
   4_bss:   7.478  0.047  0.301 87.037  0.021  2.311   6.7365e-02
   4_xyz:   7.327  0.043  0.234 82.268  0.027  2.422   6.2481e-02
   4_adp:   7.327  0.043  0.234 82.268  0.027  2.422   6.2481e-02
   4_occ:   7.327  0.043  0.234 82.268  0.027  2.422   6.2481e-02
   5_bss:   7.327  0.043  0.234 82.268  0.027  2.422   6.2481e-02
   5_xyz:   8.833  0.058  0.282 83.013  0.030  2.296   6.4758e-02
   5_adp:   8.833  0.058  0.282 83.013  0.030  2.296   6.4758e-02
   5_occ:   8.833  0.058  0.282 83.013  0.030  2.296   6.4758e-02
   5_bss:   8.833  0.058  0.282 83.013  0.030  2.296   6.4758e-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:  85.40   0.00  14.42  85.40   0.00  12.44  80.64   0.00  25.18
   1_occ:  85.40   0.00  14.42  85.40   0.00  12.44  80.64   0.00  25.18
   2_bss:  85.40   0.00  14.42  85.40   0.00  12.44  80.64   0.00  25.18
   2_xyz:  85.40   0.00  14.42  85.40   0.00  12.44  80.64   0.00  25.18
   2_adp:  88.69   0.00  13.98  88.69   0.00  11.15  86.54   0.00  29.38
   2_occ:  88.69   0.00  13.98  88.69   0.00  11.15  86.54   0.00  29.38
   3_bss:  88.69   0.00  13.98  88.69   0.00  11.15  86.54   0.00  29.38
   3_xyz:  88.69   0.00  13.98  88.69   0.00  11.15  86.54   0.00  29.38
   3_adp: 107.02   0.00  15.14 107.02   0.00  10.55 101.55   0.29  40.13
   3_occ: 107.02   0.00  15.14 107.02   0.00  10.55 101.55   0.29  40.13
   4_bss: 107.02   0.00  15.14 107.02   0.00  10.55 101.55   0.29  40.13
   4_xyz: 107.02   0.00  15.14 107.02   0.00  10.55 101.55   0.29  40.13
   4_adp: 105.91   0.00  14.27 105.91   0.00   9.67 100.21   1.70  39.33
   4_occ: 105.91   0.00  14.27 105.91   0.00   9.67 100.21   1.70  39.33
   5_bss: 105.91   0.00  14.27 105.91   0.00   9.67 100.21   1.70  39.33
   5_xyz: 105.91   0.00  14.27 105.91   0.00   9.67 100.21   1.70  39.33
   5_adp: 116.54   0.00  13.98 116.54   0.00   9.30  98.82   0.00  39.48
   5_occ: 116.54   0.00  13.98 116.54   0.00   9.30  98.82   0.00  39.48
   5_bss: 118.52   1.98  15.96 118.52   1.98  11.28 100.80   1.98  41.46
------------------------------------------------------------------------
 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:    1.253    0.025    0.413
   1_adp:    1.253    0.025    0.413
   1_occ:    1.253    0.025    0.413
   2_bss:    1.253    0.025    0.413
   2_xyz:    1.535    0.034    0.547
   2_adp:    1.535    0.034    0.547
   2_occ:    1.535    0.034    0.547
   3_bss:    1.535    0.034    0.547
   3_xyz:    1.532    0.031    0.682
   3_adp:    1.532    0.031    0.682
   3_occ:    1.532    0.031    0.682
   4_bss:    1.532    0.031    0.682
   4_xyz:    1.743    0.043    0.743
   4_adp:    1.743    0.043    0.743
   4_occ:    1.743    0.043    0.743
   5_bss:    1.743    0.043    0.743
   5_xyz:    1.776    0.057    0.789
   5_adp:    1.776    0.057    0.789
   5_occ:    1.776    0.057    0.789
   5_bss:    1.776    0.057    0.789
------------------------------------------------------------------------

CPU time actual refinement: 344.97


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_257/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_257/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_257/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_257/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_257/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 344.81 
  Macro-tasks:
    bulk solvent and scale       = 42.41  
    individual site refinement   = 145.44 
    weights calculation          = 32.50  
    collect and process          = 6.45   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 226.92 
  Micro-tasks:
    mask                            = 2.94   
    f_calc                          = 106.57 
    alpha_beta                      = 8.27   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 117.48 
    fmodel                         = 7.38   
    r_factors                      = 0.20   
    phase_errors                   = 10.28  
    foms                           = 0.31   
    TOTAL for micro-tasks          = 254.56 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.806 micro seconds
Total CPU time: 5.98 minutes
from_scatterers_fft:    657 calls, 106.21 s
gradients_fft:          601 calls, 103.96 s

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

# Date 2008-01-16 Time 01:09:24 PST -0800 (1200474564.26 s)
Start R-work = 0.4879, R-free = 0.4837 (no bulk solvent and anisotropic scale)
Final R-work = 0.1369, R-free = 0.1832 (no bulk solvent and anisotropic scale)

Start R-work = 0.4795, R-free = 0.4723
Final R-work = 0.1207, R-free = 0.1707