# Date 2008-01-16 Time 01:09:51 PST -0800 (1200474591.41 s)
#phil __OFF__

Command line arguments: "../308.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 22375
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 308

-------------------------------------------------------------------------------
  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, 47.1647, 84.2302, 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, 47.1647, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7288 1.95134
Completeness in resolution range: 0.949908
Completeness with d_max=infinity: 0.946969

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7288
                             d_min =   1.9513

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, 47.1647, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7288 1.95134
Completeness in resolution range: 0.949908
Completeness with d_max=infinity: 0.946969

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7292 -  4.1751 [2168/2196]  1950   218  10.1%
  bin  2:  4.1751 -  3.3265 [2075/2098]  1867   208  10.0%
  bin  3:  3.3265 -  2.9097 [2046/2071]  1840   206  10.1%
  bin  4:  2.9097 -  2.6453 [2047/2063]  1847   200   9.8%
  bin  5:  2.6453 -  2.4566 [2016/2054]  1810   206  10.2%
  bin  6:  2.4566 -  2.3124 [2006/2039]  1817   189   9.4%
  bin  7:  2.3124 -  2.1970 [1994/2031]  1793   201  10.1%
  bin  8:  2.1970 -  2.1016 [1993/2035]  1788   205  10.3%
  bin  9:  2.1016 -  2.0209 [1984/2022]  1790   194   9.8%
  bin 10:  2.0209 -  1.9513 [1260/2013]  1128   132  10.5%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_308/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:
        1.29 -     2.01: 24
        2.01 -     2.73: 245
        2.73 -     3.46: 4696
        3.46 -     4.18: 9552
        4.18 -     4.90: 14306
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.290 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.352 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.644 3.040 -x+1/2,-y+1,z+1/2
  " O   SER A  95 " - " O   HOH Z 404 "  1.703 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.712 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28818 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_308/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_308/model_refine_001.geo

CPU time processing inputs: 9.21


============================ 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 47.16465 84.23025 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: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4821   r_free= 0.4818   ksol= 0.00   Bsol= 0.00   scale= 0.802    |
|                                                                             |
| 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:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.283314                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7292 -  4.6566 0.99   1402  158 0.3983 0.3920      6.5961      6.6202|
|  2:  4.6566 -  3.7156 0.99   1363  145 0.4050 0.3879      6.7834      6.7922|
|  3:  3.7156 -  3.2517 0.99   1317  154 0.4380 0.4376      6.6791      6.7607|
|  4:  3.2517 -  2.9570 0.99   1329  144 0.4537 0.4983      6.5146      6.5096|
|  5:  2.9570 -  2.7465 0.98   1307  147 0.5077 0.5182      6.3851      6.3765|
|  6:  2.7465 -  2.5855 0.99   1301  143 0.5013 0.5665      6.2703       6.225|
|  7:  2.5855 -  2.4566 0.99   1295  147 0.5275 0.4607      6.2572       6.166|
|  8:  2.4566 -  2.3501 0.99   1300  144 0.5273 0.5331      6.1781      6.1791|
|  9:  2.3501 -  2.2600 0.99   1284  136 0.5294 0.5287      6.1246      6.1526|
| 10:  2.2600 -  2.1823 0.98   1280  146 0.5432 0.5034      6.1143      6.0915|
| 11:  2.1823 -  2.1142 0.98   1280  142 0.5340 0.5663      6.0382      6.0455|
| 12:  2.1142 -  2.0540 1.00   1274  143 0.5238 0.5409       5.969       6.001|
| 13:  2.0540 -  2.0000 0.96   1264  139 0.5487 0.5324      5.8837      5.8762|
| 14:  2.0000 -  1.9513 0.49    634   71 0.5446 0.4813      5.8814      5.7121|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7292 -  4.6566  1402   158  0.67  37.12   0.80     0.69      79471.51|
|  2:  4.6566 -  3.7156  1363   145  0.67  38.08   0.88     0.74     118046.55|
|  3:  3.7156 -  3.2517  1317   154  0.56  46.92   0.85     0.69     127469.45|
|  4:  3.2517 -  2.9570  1329   144  0.48  53.75   0.82     0.59     110924.11|
|  5:  2.9570 -  2.7465  1307   147  0.40  60.13   0.74     0.49      89149.99|
|  6:  2.7465 -  2.5855  1301   143  0.38  61.10   0.75     0.45      72632.20|
|  7:  2.5855 -  2.4566  1295   147  0.38  61.36   0.74     0.44      64899.78|
|  8:  2.4566 -  2.3501  1300   144  0.37  62.46   0.73     0.44      58213.23|
|  9:  2.3501 -  2.2600  1284   136  0.34  64.91   0.74     0.41      55717.15|
| 10:  2.2600 -  2.1823  1280   146  0.31  67.07   0.76     0.38      52151.22|
| 11:  2.1823 -  2.1142  1280   142  0.25  71.11   0.76     0.32      51355.14|
| 12:  2.1142 -  2.0540  1274   143  0.25  71.04   0.76     0.33      47633.31|
| 13:  2.0540 -  2.0000  1264   139  0.28  69.07   0.74     0.37      38688.74|
| 14:  2.0000 -  1.9513   634    71  0.43  57.95   0.72     0.48      25956.04|
|alpha:            min =        0.32 max =            0.74 mean =         0.49|
|beta:             min =    25956.04 max =       127469.45 mean =     73081.13|
|figures of merit: min =        0.00 max =            1.00 mean =         0.41|
|phase err.(work): min =        0.00 max =           89.99 mean =        58.46|
|phase err.(test): min =        0.00 max =           89.91 mean =        58.96|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.166626             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.419   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.266146              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 83.486   (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 |  0.706 -  1.126:        1 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.126 -  1.545:        6 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.545 -  1.964:       34 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  1.964 -  2.384:      282 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.384 -  2.803:     1037 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.803 -  3.222:     2258 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.222 -  3.642:     3862 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.642 -  4.061:     5403 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.061 -  4.481:     7215 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.481 -  4.900:     8773 |
|-----------------------------------------------------------------------------|
|-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 |       52.962 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.087    4.900  0.706 |       2.545 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.458)------------------------------------------|
|    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 = 11.458)------------------------------------------|
|    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: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4881   r_free= 0.4867   ksol= 0.00   Bsol= 0.00   scale= 0.771    |
|                                                                             |
| 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:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.284723                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4742   r_free= 0.4725   ksol= 0.38   Bsol= 20.00   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.02,7.66,9.33,0.00,0.00,0.00); trace/3= 8.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.279134                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.863873             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.098   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.290034              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.281   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4742      final r-factor (work) = 0.4011          |
| start r-factor (free) = 0.4725      final r-factor (free) = 0.4251          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 93.3719 = 12.86 * 0.50 * 6.2827 + 1.00 * 52.9623                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 40.0497 = 12.86 * 0.50 * 6.2036 + 1.00 * 0.1482                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4011      final r-factor (work) = 0.3556          |
| start r-factor (free) = 0.4251      final r-factor (free) = 0.4052          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.0172 = 1.29 * 1.00 * 6.2036 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.9225 = 1.29 * 1.00 * 6.1278 + 1.00 * 0.0174                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.458)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.44   13.61    None  None   None       |
|    all(noH): 2823   0      0.00    82.44   13.61    None  None   None       |
|    Sol.    : 438    0      0.00    82.44   26.44    None  None   None       |
|    Mac.    : 2385   0      0.00    70.60   11.26    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 -   8.244: 1201   |   5:    41.219 -  49.463:   54        |
|      1:     8.244 -  16.488:  745   |   6:    49.463 -  57.706:   34        |
|      2:    16.488 -  24.731:  418   |   7:    57.706 -  65.950:   15        |
|      3:    24.731 -  32.975:  205   |   8:    65.950 -  74.194:    5        |
|      4:    32.975 -  41.219:  144   |   9:    74.194 -  82.438:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3556 r_free = 0.4052             target_work(ml) = 6.110         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3550 r_free = 0.4049             target_work(ml) = 6.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3550   r_free= 0.4049   ksol= 0.38   Bsol= 20.00   scale= 1.103   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.02,7.66,9.33,0.00,0.00,0.00); trace/3= 8.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.109273                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3518   r_free= 0.4029   ksol= 0.33   Bsol= 30.52   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.56,4.16,6.34,0.00,0.00,0.00); trace/3= 4.69                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.109354                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.910677              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.474   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.583341              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.723  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3518      final r-factor (work) = 0.2702          |
| start r-factor (free) = 0.4029      final r-factor (free) = 0.3277          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.3657 = 7.91 * 0.50 * 6.1227 + 1.00 * 0.1482                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.8362 = 7.91 * 0.50 * 6.0057 + 1.00 * 0.0815                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2702      final r-factor (work) = 0.2482          |
| start r-factor (free) = 0.3277      final r-factor (free) = 0.3035          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5229 = 0.58 * 1.00 * 6.0057 + 1.00 * 0.0195                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4298 = 0.58 * 1.00 * 5.8584 + 1.00 * 0.0124                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.458)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.86   13.77    None  None   None       |
|    all(noH): 2823   0      0.00    85.86   13.77    None  None   None       |
|    Sol.    : 438    0      0.00    85.86   31.85    None  None   None       |
|    Mac.    : 2385   0      0.00    80.08   10.44    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 -   8.586: 1343   |   5:    42.930 -  51.516:   76        |
|      1:     8.586 -  17.172:  723   |   6:    51.516 -  60.102:   37        |
|      2:    17.172 -  25.758:  303   |   7:    60.102 -  68.688:   13        |
|      3:    25.758 -  34.344:  173   |   8:    68.688 -  77.274:    5        |
|      4:    34.344 -  42.930:  147   |   9:    77.274 -  85.860:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2482 r_free = 0.3035             target_work(ml) = 5.827         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2480 r_free = 0.3037             target_work(ml) = 5.826         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2480   r_free= 0.3037   ksol= 0.33   Bsol= 30.52   scale= 1.066   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.56,4.16,6.34,0.00,0.00,0.00); trace/3= 4.69                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.826128                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2462   r_free= 0.3019   ksol= 0.32   Bsol= 33.45   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.82,2.75,3.85,0.00,0.00,0.00); trace/3= 2.80                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.824426                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.510818              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.190  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.306154              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 118.427  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2462      final r-factor (work) = 0.1780          |
| start r-factor (free) = 0.3019      final r-factor (free) = 0.2341          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.2995 = 4.51 * 0.50 * 5.8606 + 1.00 * 0.0815                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.9209 = 4.51 * 0.50 * 5.6969 + 1.00 * 0.0720                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1780      final r-factor (work) = 0.1593          |
| start r-factor (free) = 0.2341      final r-factor (free) = 0.2086          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7565 = 0.31 * 1.00 * 5.6969 + 1.00 * 0.0124                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6956 = 0.31 * 1.00 * 5.5023 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.458)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.66   13.51    None  None   None       |
|    all(noH): 2823   0      0.00    86.66   13.51    None  None   None       |
|    Sol.    : 438    0      3.18    86.66   35.20    None  None   None       |
|    Mac.    : 2385   0      0.00    77.26   9.52     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 -   8.666: 1476   |   5:    43.330 -  51.996:   89        |
|      1:     8.666 -  17.332:  727   |   6:    51.996 -  60.662:   53        |
|      2:    17.332 -  25.998:  186   |   7:    60.662 -  69.328:   17        |
|      3:    25.998 -  34.664:  139   |   8:    69.328 -  77.994:    4        |
|      4:    34.664 -  43.330:  131   |   9:    77.994 -  86.660:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1593 r_free = 0.2086             target_work(ml) = 5.439         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1590 r_free = 0.2088             target_work(ml) = 5.438         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1590   r_free= 0.2088   ksol= 0.32   Bsol= 33.45   scale= 1.041   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.82,2.75,3.85,0.00,0.00,0.00); trace/3= 2.80                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.438124                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1580   r_free= 0.2069   ksol= 0.31   Bsol= 31.58   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.84,1.76,2.16,0.00,0.00,0.00); trace/3= 1.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.434378                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.917819              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.381  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.185239              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 101.654  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1580      final r-factor (work) = 0.1275          |
| start r-factor (free) = 0.2069      final r-factor (free) = 0.1719          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.8643 = 3.92 * 0.50 * 5.5093 + 1.00 * 0.0720                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.5419 = 3.92 * 0.50 * 5.3463 + 1.00 * 0.0690                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1275      final r-factor (work) = 0.1227          |
| start r-factor (free) = 0.1719      final r-factor (free) = 0.1660          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0009 = 0.19 * 1.00 * 5.3463 + 1.00 * 0.0106                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9767 = 0.19 * 1.00 * 5.2281 + 1.00 * 0.0082                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.458)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.93   13.28    None  None   None       |
|    all(noH): 2823   0      0.00    80.93   13.28    None  None   None       |
|    Sol.    : 438    0      2.91    80.45   35.12    None  None   None       |
|    Mac.    : 2385   0      0.00    80.93   9.27     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 -   8.094: 1403   |   5:    40.467 -  48.561:   95        |
|      1:     8.094 -  16.187:  796   |   6:    48.561 -  56.654:   61        |
|      2:    16.187 -  24.280:  184   |   7:    56.654 -  64.748:   24        |
|      3:    24.280 -  32.374:  127   |   8:    64.748 -  72.841:    9        |
|      4:    32.374 -  40.467:  120   |   9:    72.841 -  80.935:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1227 r_free = 0.1660             target_work(ml) = 5.209         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1225 r_free = 0.1658             target_work(ml) = 5.207         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1225   r_free= 0.1658   ksol= 0.31   Bsol= 31.58   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.84,1.76,2.16,0.00,0.00,0.00); trace/3= 1.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.207204                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1227   r_free= 0.1664   ksol= 0.32   Bsol= 33.26   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.65,1.52,1.78,0.00,0.00,0.00); trace/3= 1.32                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.209632                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.818374              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 127.165  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.306025              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 154.435  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1227      final r-factor (work) = 0.1180          |
| start r-factor (free) = 0.1664      final r-factor (free) = 0.1624          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8228 = 1.82 * 0.50 * 5.2286 + 1.00 * 0.0690                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7815 = 1.82 * 0.50 * 5.1963 + 1.00 * 0.0571                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1180      final r-factor (work) = 0.1160          |
| start r-factor (free) = 0.1624      final r-factor (free) = 0.1625          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5984 = 0.31 * 1.00 * 5.1963 + 1.00 * 0.0082                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5931 = 0.31 * 1.00 * 5.1760 + 1.00 * 0.0091                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.458)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.01   13.32    None  None   None       |
|    all(noH): 2823   0      0.00    82.01   13.32    None  None   None       |
|    Sol.    : 438    0      2.10    78.53   35.44    None  None   None       |
|    Mac.    : 2385   0      0.00    82.01   9.25     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 -   8.201: 1441   |   5:    41.007 -  49.208:   94        |
|      1:     8.201 -  16.403:  761   |   6:    49.208 -  57.410:   60        |
|      2:    16.403 -  24.604:  183   |   7:    57.410 -  65.611:   25        |
|      3:    24.604 -  32.806:  129   |   8:    65.611 -  73.813:    8        |
|      4:    32.806 -  41.007:  118   |   9:    73.813 -  82.014:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1160 r_free = 0.1625             target_work(ml) = 5.176         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1160 r_free = 0.1625             target_work(ml) = 5.176         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1160   r_free= 0.1625   ksol= 0.32   Bsol= 33.26   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.65,1.52,1.78,0.00,0.00,0.00); trace/3= 1.32                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.176053                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7292 -  4.6566 0.99   1402  158 0.1011 0.1304      5.4014       5.563|
|  2:  4.6566 -  3.7156 0.99   1363  145 0.0911 0.1158      5.4727      5.6723|
|  3:  3.7156 -  3.2517 0.99   1317  154 0.1097 0.1551      5.4948      5.8219|
|  4:  3.2517 -  2.9570 0.99   1329  144 0.1275 0.1618      5.4784      5.6511|
|  5:  2.9570 -  2.7465 0.98   1307  147 0.1355 0.1621      5.3416      5.4446|
|  6:  2.7465 -  2.5855 0.99   1301  143 0.1276 0.2124      5.2451      5.5546|
|  7:  2.5855 -  2.4566 0.99   1295  147 0.1264 0.1628      5.1742      5.4019|
|  8:  2.4566 -  2.3501 0.99   1300  144 0.1188 0.1720      5.1019      5.3034|
|  9:  2.3501 -  2.2600 0.99   1284  136 0.1213 0.1855      5.0518      5.3335|
| 10:  2.2600 -  2.1823 0.98   1280  146 0.1181 0.1853      5.0141      5.2453|
| 11:  2.1823 -  2.1142 0.98   1280  142 0.1188 0.1819      4.9556      5.3004|
| 12:  2.1142 -  2.0540 1.00   1274  143 0.1136 0.1847      4.8889       5.164|
| 13:  2.0540 -  2.0000 0.96   1264  139 0.1176 0.1847      4.8137      5.0779|
| 14:  2.0000 -  1.9513 0.49    634   71 0.1114 0.1720      4.7401      4.9191|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7292 -  4.6566  1402   158  0.94   9.05   0.98     0.97       7384.53|
|  2:  4.6566 -  3.7156  1363   145  0.95   8.30   1.03     1.01       9320.41|
|  3:  3.7156 -  3.2517  1317   154  0.93  11.77   1.03     1.03      10904.50|
|  4:  3.2517 -  2.9570  1329   144  0.92  14.07   1.01     1.00      10585.98|
|  5:  2.9570 -  2.7465  1307   147  0.90  16.03   0.99     0.96       8252.80|
|  6:  2.7465 -  2.5855  1301   143  0.90  16.28   0.98     0.96       7524.30|
|  7:  2.5855 -  2.4566  1295   147  0.90  15.61   0.99     0.96       6204.15|
|  8:  2.4566 -  2.3501  1300   144  0.90  16.07   1.01     0.98       5875.54|
|  9:  2.3501 -  2.2600  1284   136  0.90  15.92   1.01     0.99       5215.35|
| 10:  2.2600 -  2.1823  1280   146  0.90  16.36   1.01     0.98       4928.31|
| 11:  2.1823 -  2.1142  1280   142  0.90  16.57   1.00     0.96       4416.33|
| 12:  2.1142 -  2.0540  1274   143  0.91  15.37   1.01     1.00       4023.97|
| 13:  2.0540 -  2.0000  1264   139  0.89  17.07   1.02     1.01       3576.33|
| 14:  2.0000 -  1.9513   634    71  0.90  15.87   1.00     0.96       2954.66|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2954.66 max =        10904.50 mean =      6688.19|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.48|
|phase err.(test): min =        0.00 max =           88.75 mean =        14.11|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1160   r_free= 0.1625   ksol= 0.32   Bsol= 35.23   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.65,0.25,0.40,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.175961                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1160   r_free= 0.1625   ksol= 0.32   Bsol= 35.23   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.65,0.25,0.40,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.175961                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7292 -  4.6566 0.99   1402  158 0.1012 0.1304      5.4019      5.5638|
|  2:  4.6566 -  3.7156 0.99   1363  145 0.0911 0.1159      5.4731      5.6727|
|  3:  3.7156 -  3.2517 0.99   1317  154 0.1097 0.1552       5.495      5.8222|
|  4:  3.2517 -  2.9570 0.99   1329  144 0.1275 0.1618      5.4785      5.6514|
|  5:  2.9570 -  2.7465 0.98   1307  147 0.1354 0.1620      5.3415      5.4445|
|  6:  2.7465 -  2.5855 0.99   1301  143 0.1275 0.2125       5.245      5.5553|
|  7:  2.5855 -  2.4566 0.99   1295  147 0.1265 0.1627      5.1743       5.402|
|  8:  2.4566 -  2.3501 0.99   1300  144 0.1189 0.1718      5.1017      5.3031|
|  9:  2.3501 -  2.2600 0.99   1284  136 0.1213 0.1855      5.0516       5.333|
| 10:  2.2600 -  2.1823 0.98   1280  146 0.1181 0.1852      5.0136      5.2444|
| 11:  2.1823 -  2.1142 0.98   1280  142 0.1188 0.1819      4.9552         5.3|
| 12:  2.1142 -  2.0540 1.00   1274  143 0.1136 0.1845      4.8882      5.1632|
| 13:  2.0540 -  2.0000 0.96   1264  139 0.1175 0.1843      4.8131      5.0767|
| 14:  2.0000 -  1.9513 0.49    634   71 0.1114 0.1721        4.74      4.9203|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7292 -  4.6566  1402   158  0.94   9.06   0.98     0.97       7400.64|
|  2:  4.6566 -  3.7156  1363   145  0.95   8.31   1.03     1.01       9332.15|
|  3:  3.7156 -  3.2517  1317   154  0.93  11.78   1.03     1.03      10912.66|
|  4:  3.2517 -  2.9570  1329   144  0.92  14.07   1.01     1.00      10587.96|
|  5:  2.9570 -  2.7465  1307   147  0.90  16.03   0.99     0.96       8260.61|
|  6:  2.7465 -  2.5855  1301   143  0.90  16.29   0.98     0.96       7527.68|
|  7:  2.5855 -  2.4566  1295   147  0.90  15.62   0.99     0.96       6207.33|
|  8:  2.4566 -  2.3501  1300   144  0.90  16.07   1.01     0.98       5871.01|
|  9:  2.3501 -  2.2600  1284   136  0.90  15.91   1.01     0.99       5211.67|
| 10:  2.2600 -  2.1823  1280   146  0.90  16.35   1.01     0.98       4921.13|
| 11:  2.1823 -  2.1142  1280   142  0.90  16.56   1.00     0.96       4412.32|
| 12:  2.1142 -  2.0540  1274   143  0.91  15.35   1.01     1.00       4015.87|
| 13:  2.0540 -  2.0000  1264   139  0.89  17.06   1.02     1.01       3572.75|
| 14:  2.0000 -  1.9513   634    71  0.90  15.87   1.00     0.96       2954.89|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2954.89 max =        10912.66 mean =      6689.95|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.81 mean =        14.48|
|phase err.(test): min =        0.00 max =           88.67 mean =        14.11|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.458)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.32    83.33   14.63    None  None   None       |
|    all(noH): 2823   0      1.32    83.33   14.63    None  None   None       |
|    Sol.    : 438    0      3.42    79.84   36.76    None  None   None       |
|    Mac.    : 2385   0      1.32    83.33   10.57    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:     1.315 -   9.517: 1441   |   5:    42.322 -  50.524:   94        |
|      1:     9.517 -  17.718:  761   |   6:    50.524 -  58.725:   60        |
|      2:    17.718 -  25.920:  183   |   7:    58.725 -  66.927:   25        |
|      3:    25.920 -  34.121:  129   |   8:    66.927 -  75.128:    8        |
|      4:    34.121 -  42.322:  118   |   9:    75.128 -  83.329:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 330         
Filter by distance & map next to the model:
   mapped sites are within: 0.680 - 5.925
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 328 from: 330
   mapped sites are within: 0.724 - 5.925

peak=   11.035 closest distance to " CB  VAL A 230 " =    1.438
peak=    8.332 closest distance to " CG2 VAL A 296 " =    1.223
peak=    7.348 closest distance to " O   HOH Z 199 " =    1.465
peak=    6.051 closest distance to " O   HOH Z 279 " =    1.211
peak=    6.025 closest distance to " O   HOH Z 278 " =    1.634
peak=    5.870 closest distance to " CG  LEU A   5 " =    1.277
peak=    5.753 closest distance to " O   HOH Z 120 " =    1.066
peak=    5.688 closest distance to " NH2 ARG A  56 " =    2.130
peak=    5.605 closest distance to " O   HOH Z 142 " =    1.789
peak=    5.496 closest distance to " CD2 LEU A   5 " =    1.267
peak=    5.314 closest distance to " O   HOH Z 132 " =    1.644
peak=    5.312 closest distance to " O   HOH Z 193 " =    1.719
peak=    5.279 closest distance to " O   HOH Z 124 " =    1.537
peak=    5.024 closest distance to " CB  VAL A 296 " =    1.036
peak=    4.987 closest distance to " NE2 GLN A  11 " =    1.070
peak=    4.979 closest distance to " O   HOH Z 126 " =    2.014
peak=    4.960 closest distance to " CG  PRO A 213 " =    1.275
peak=    4.911 closest distance to " CB  GLN A 223 " =    1.436
peak=    4.909 closest distance to " CB  ARG A 275 " =    0.967
peak=    4.900 closest distance to " O   HOH Z 272 " =    1.852
peak=    4.861 closest distance to " CD2 LEU A 228 " =    1.209
peak=    4.797 closest distance to " CG  PRO A  54 " =    1.298
peak=    4.669 closest distance to " O   HOH Z 234 " =    3.713
peak=    4.648 closest distance to " CB  SER A  63 " =    1.165
peak=    4.640 closest distance to " O   HOH Z 411 " =    3.712
peak=    4.597 closest distance to " O   HOH Z 232 " =    2.195
peak=    4.591 closest distance to " O   HOH Z 403 " =    1.879
peak=    4.447 closest distance to " O   HOH Z 368 " =    2.076
peak=    4.438 closest distance to " CD1AILE A 234 " =    0.965
peak=    4.429 closest distance to " O   HOH Z 277 " =    1.030
peak=    4.424 closest distance to " O   HOH Z 402 " =    1.412
peak=    4.423 closest distance to " O   HOH Z 108 " =    1.431
peak=    4.420 closest distance to " CA  ALA A  21 " =    1.154
peak=    4.410 closest distance to " O   HOH Z 128 " =    2.105
peak=    4.360 closest distance to " O   HOH Z 427 " =    2.630
peak=    4.354 closest distance to " CA  VAL A  41 " =    0.836
peak=    4.354 closest distance to " O   HOH Z 263 " =    1.442
peak=    4.338 closest distance to " O   SER A  87 " =    2.289
peak=    4.338 closest distance to " CG1BVAL A  72 " =    1.550
peak=    4.328 closest distance to " C   PRO A 198 " =    1.541
peak=    4.319 closest distance to " CG  LEU A 228 " =    1.206
peak=    4.302 closest distance to " O   HOH Z  59 " =    2.049
peak=    4.273 closest distance to " O   HOH Z 316 " =    2.700
peak=    4.254 closest distance to " CB  GLU A 152 " =    1.097
peak=    4.234 closest distance to " CB  SER A   3 " =    1.281
peak=    4.215 closest distance to " O   HOH Z  97 " =    2.456
peak=    4.205 closest distance to " CG  PRO A 198 " =    1.255
peak=    4.186 closest distance to " O   HOH Z  78 " =    1.678
peak=    4.184 closest distance to " O   HOH Z 423 " =    1.932
peak=    4.175 closest distance to " NZ  LYS A 119 " =    1.809
peak=    4.173 closest distance to " O   HOH Z 209 " =    2.343
peak=    4.171 closest distance to " O   HOH Z 322 " =    2.092
peak=    4.148 closest distance to " O   HOH Z 203 " =    1.630
peak=    4.122 closest distance to " CA  TYR A  30 " =    1.013
peak=    4.119 closest distance to " O   HOH Z   3 " =    1.723
peak=    4.115 closest distance to " O   HOH Z 327 " =    1.733
peak=    4.111 closest distance to " CB  GLN A 183 " =    1.330
peak=    4.105 closest distance to " O   HOH Z 247 " =    1.255
peak=    4.102 closest distance to " CB  VAL A 230 " =    1.159
peak=    4.096 closest distance to " O   HOH Z 346 " =    1.502
peak=    4.072 closest distance to " CB  PRO A  54 " =    0.903
peak=    4.067 closest distance to " O   HOH Z  85 " =    1.613
peak=    4.048 closest distance to " O   HOH Z 128 " =    1.889
peak=    4.043 closest distance to " OE1 GLU A   2 " =    2.178
peak=    4.026 closest distance to " CB  TRP A 179 " =    1.250
peak=    4.013 closest distance to " O   HOH Z 371 " =    3.196
peak=    4.012 closest distance to " O   HOH Z 209 " =    2.204
peak=    4.006 closest distance to " O   HOH Z 134 " =    1.692
peak=    3.997 closest distance to " O   HOH Z 303 " =    2.056
peak=    3.988 closest distance to " O   HOH Z  54 " =    1.543
peak=    3.986 closest distance to " O   HOH Z  97 " =    1.821
peak=    3.983 closest distance to " CB  ASN A 148 " =    1.408
peak=    3.982 closest distance to " CD  ARG A 269 " =    1.063
peak=    3.973 closest distance to " O   HOH Z 227 " =    1.651
peak=    3.966 closest distance to " O   HOH Z 344 " =    2.616
peak=    3.944 closest distance to " O   HOH Z 392 " =    2.428
peak=    3.942 closest distance to " O   HOH Z 261 " =    2.195
peak=    3.941 closest distance to " O   HOH Z 192 " =    1.892
peak=    3.937 closest distance to " O   HOH Z 155 " =    1.739
peak=    3.932 closest distance to " O   HOH Z 334 " =    1.513
peak=    3.912 closest distance to " ND2 ASN A 187 " =    1.635
peak=    3.898 closest distance to " O   HOH Z 188 " =    1.060
peak=    3.897 closest distance to " O   HOH Z 389 " =    1.716
peak=    3.883 closest distance to " O   HOH Z 260 " =    1.425
peak=    3.879 closest distance to " O   HOH Z 214 " =    2.226
peak=    3.876 closest distance to " O   HOH Z 276 " =    1.355
peak=    3.867 closest distance to " O   HOH Z 345 " =    2.688
peak=    3.855 closest distance to " C   ALA A 299 " =    0.934
peak=    3.853 closest distance to " O   HOH Z  61 " =    1.567
peak=    3.852 closest distance to " CB  GLU A 128 " =    1.157
peak=    3.850 closest distance to " O   HOH Z 287 " =    1.784
peak=    3.845 closest distance to " CG2 THR A 221 " =    1.136
peak=    3.833 closest distance to " CB  VAL A 265 " =    1.169
peak=    3.833 closest distance to " NE2 GLN A  58 " =    4.216
peak=    3.829 closest distance to " O   HOH Z 426 " =    1.390
peak=    3.829 closest distance to " O   HOH Z 236 " =    1.568
peak=    3.825 closest distance to " O   HOH Z 191 " =    1.451
peak=    3.814 closest distance to " O   HOH Z 366 " =    2.827
peak=    3.814 closest distance to " O   HOH Z 189 " =    2.451
peak=    3.804 closest distance to " O   HOH Z 334 " =    1.804
peak=    3.801 closest distance to " CB  PRO A 198 " =    1.049
peak=    3.798 closest distance to " OD2 ASP A 286 " =    2.621
peak=    3.791 closest distance to " O   HOH Z 118 " =    1.528
peak=    3.781 closest distance to " NZ  LYS A 117 " =    3.183
peak=    3.781 closest distance to " O   HOH Z 227 " =    1.541
peak=    3.780 closest distance to " O   HOH Z 407 " =    2.519
peak=    3.779 closest distance to " O   HOH Z  43 " =    2.313
peak=    3.772 closest distance to " O   HOH Z 118 " =    1.702
peak=    3.768 closest distance to " CB  TYR A 169 " =    0.761
peak=    3.765 closest distance to " O   HOH Z 249 " =    0.996
peak=    3.761 closest distance to " O   HOH Z 283 " =    1.925
peak=    3.761 closest distance to " O   HOH Z 280 " =    2.863
peak=    3.757 closest distance to " CG  PRO A 243 " =    1.225
peak=    3.746 closest distance to " CB  VAL A 202 " =    1.619
peak=    3.740 closest distance to " CB  ALA A   9 " =    1.559
peak=    3.733 closest distance to " O   HOH Z 298 " =    1.847
peak=    3.732 closest distance to " CG AARG A 275 " =    1.111
peak=    3.723 closest distance to " CB  SER A  62 " =    1.177
peak=    3.720 closest distance to " O   HOH Z 369 " =    2.078
peak=    3.714 closest distance to " O   HOH Z 374 " =    2.405
peak=    3.709 closest distance to " O   HOH Z 217 " =    1.574
peak=    3.699 closest distance to " O   TRP A 274 " =    1.958
peak=    3.698 closest distance to " CB  ALA A 248 " =    1.376
peak=    3.685 closest distance to " CB  GLU A 277 " =    3.477
peak=    3.676 closest distance to " CB  SER A  26 " =    1.638
peak=    3.669 closest distance to " O   HOH Z  48 " =    1.717
peak=    3.654 closest distance to " O   HOH Z 357 " =    1.931
peak=    3.650 closest distance to " CA  LYS A 117 " =    1.293
peak=    3.647 closest distance to " CB  ARG A 102 " =    0.774
peak=    3.646 closest distance to " NH1 ARG A  14 " =    0.994
peak=    3.642 closest distance to " CG  ARG A  66 " =    1.062
peak=    3.639 closest distance to " CA  THR A 221 " =    0.911
peak=    3.632 closest distance to " O   HOH Z  15 " =    2.023
peak=    3.631 closest distance to " O   HOH Z  80 " =    1.657
peak=    3.629 closest distance to " CG  GLN A  77 " =    2.198
peak=    3.628 closest distance to " O   HOH Z 261 " =    1.687
peak=    3.627 closest distance to " O   HOH Z 419 " =    1.616
peak=    3.621 closest distance to " CD  GLN A 194 " =    1.465
peak=    3.617 closest distance to " O   HOH Z 406 " =    1.481
peak=    3.616 closest distance to " CG2 ILE A  20 " =    1.579
peak=    3.613 closest distance to " O   HOH Z 345 " =    1.697
peak=    3.603 closest distance to " CB  ARG A 275 " =    1.026
peak=    3.601 closest distance to " O   HOH Z 245 " =    1.376
peak=    3.600 closest distance to " O   HOH Z 154 " =    1.433
peak=    3.598 closest distance to " CA  ALA A  51 " =    1.021
peak=    3.594 closest distance to " CB BVAL A  41 " =    1.110
peak=    3.593 closest distance to " O   HOH Z  55 " =    2.260
peak=    3.587 closest distance to " O   HOH Z 326 " =    1.417
peak=    3.585 closest distance to " O   HOH Z 315 " =    1.888
peak=    3.580 closest distance to " O   HOH Z 414 " =    1.344
peak=    3.562 closest distance to " O   HOH Z 417 " =    3.171
peak=    3.551 closest distance to " O   HOH Z 148 " =    3.006
peak=    3.551 closest distance to " O   HOH Z 163 " =    1.987
peak=    3.550 closest distance to " CD  LYS A 166 " =    1.396
peak=    3.541 closest distance to " OD1 ASP A 286 " =    1.787
peak=    3.540 closest distance to " O   HOH Z 278 " =    1.338
peak=    3.540 closest distance to " OD1 ASN A  69 " =    2.723
peak=    3.538 closest distance to " CB  ALA A 100 " =    1.181
peak=    3.537 closest distance to " CG2 VAL A 257 " =    0.800
peak=    3.535 closest distance to " O   HOH Z 193 " =    2.065
peak=    3.525 closest distance to " CA  ARG A  36 " =    0.991
peak=    3.524 closest distance to " C   ILE A 106 " =    1.882
peak=    3.519 closest distance to " O   HOH Z 303 " =    1.592
peak=    3.517 closest distance to " CB  ARG A 190 " =    1.744
peak=    3.515 closest distance to " CD2 TRP A 179 " =    1.378
peak=    3.513 closest distance to " O   HOH Z 344 " =    1.601
peak=    3.512 closest distance to " NE2 GLN A  58 " =    5.925
peak=    3.509 closest distance to " O   HOH Z 342 " =    0.898
peak=    3.503 closest distance to " NZ  LYS A  76 " =    1.389
peak=    3.502 closest distance to " O   HOH Z  30 " =    2.189
peak=    3.501 closest distance to " CG  MET A  93 " =    1.036
peak=    3.497 closest distance to " O   HOH Z 108 " =    1.853
peak=    3.493 closest distance to " O   HOH Z  49 " =    2.296
peak=    3.492 closest distance to " OG  SER A 276 " =    1.437
peak=    3.491 closest distance to " CD2 HIS A  81 " =    1.233
peak=    3.491 closest distance to " CA  ASP A 140 " =    1.182
peak=    3.481 closest distance to " O   SER A 164 " =    1.341
peak=    3.475 closest distance to " O   HOH Z  47 " =    1.666
peak=    3.475 closest distance to " NH2BARG A 145 " =    2.201
peak=    3.474 closest distance to " O   HOH Z 280 " =    1.365
peak=    3.468 closest distance to " O   HOH Z 144 " =    2.457
peak=    3.463 closest distance to " O   HOH Z  68 " =    1.704
peak=    3.460 closest distance to " O   HOH Z 112 " =    1.635
peak=    3.455 closest distance to " CA  ASN A 176 " =    0.984
peak=    3.454 closest distance to " N   ASN A  39 " =    1.129
peak=    3.453 closest distance to " OG1 THR A 294 " =    2.336
peak=    3.452 closest distance to " CB  ASN A  39 " =    0.755
peak=    3.450 closest distance to " O   HOH Z 102 " =    1.216
peak=    3.439 closest distance to " O   HOH Z 394 " =    1.566
peak=    3.437 closest distance to " CB  GLN A  88 " =    1.243
peak=    3.433 closest distance to " O   HOH Z 406 " =    1.055
peak=    3.430 closest distance to " O   HOH Z 136 " =    1.214
peak=    3.423 closest distance to " CG  GLN A  58 " =    2.641
peak=    3.422 closest distance to " O   HOH Z  88 " =    3.101
peak=    3.422 closest distance to " CG1 ILE A  33 " =    1.298
peak=    3.420 closest distance to " CZ2 TRP A 274 " =    1.583
peak=    3.419 closest distance to " CD1 LEU A  96 " =    0.768
peak=    3.418 closest distance to " OG  SER A  22 " =    2.646
peak=    3.417 closest distance to " O   HOH Z 420 " =    1.981
peak=    3.416 closest distance to " CZ AARG A 102 " =    1.642
peak=    3.414 closest distance to " O   HOH Z 143 " =    1.109
peak=    3.411 closest distance to " CG  MET A 188 " =    1.330
peak=    3.407 closest distance to " CA  GLY A  80 " =    0.774
peak=    3.402 closest distance to " O   HOH Z 164 " =    1.963
peak=    3.399 closest distance to " CZ2 TRP A 179 " =    1.791
peak=    3.396 closest distance to " CB  GLN A 205 " =    1.232
peak=    3.392 closest distance to " O   HOH Z 421 " =    1.467
peak=    3.391 closest distance to " CG1 VAL A 153 " =    1.026
peak=    3.389 closest distance to " O   HOH Z 273 " =    2.788
peak=    3.386 closest distance to " O   HOH Z  63 " =    2.525
peak=    3.386 closest distance to " C   ALA A   1 " =    1.715
peak=    3.385 closest distance to " OD2 ASP A 298 " =    4.023
peak=    3.382 closest distance to " O   HOH Z 425 " =    1.373
peak=    3.380 closest distance to " O   HOH Z 266 " =    2.102
peak=    3.379 closest distance to " O   HOH Z 244 " =    1.638
peak=    3.379 closest distance to " O   HOH Z 250 " =    1.374
peak=    3.377 closest distance to " O   HOH Z 180 " =    2.133
peak=    3.376 closest distance to " CB  ARG A 139 " =    0.892
peak=    3.372 closest distance to " CD BLYS A 290 " =    1.113
peak=    3.372 closest distance to " CE AMET A  47 " =    1.597
peak=    3.369 closest distance to " O   HOH Z  39 " =    2.625
peak=    3.367 closest distance to " O   HOH Z 422 " =    2.605
peak=    3.366 closest distance to " CB  TYR A  30 " =    1.507
peak=    3.362 closest distance to " OG BSER A 164 " =    2.280
peak=    3.362 closest distance to " CG  MET A 185 " =    1.240
peak=    3.361 closest distance to " O   HOH Z  59 " =    2.101
peak=    3.357 closest distance to " CB  SER A 273 " =    0.853
peak=    3.357 closest distance to " CD1 ILE A  33 " =    1.631
peak=    3.353 closest distance to " O   HOH Z 367 " =    3.627
peak=    3.352 closest distance to " CB  LEU A 228 " =    1.379
peak=    3.347 closest distance to " O   HOH Z 291 " =    1.729
peak=    3.346 closest distance to " CG2 ILE A 120 " =    1.272
peak=    3.343 closest distance to " O   HOH Z  66 " =    2.097
peak=    3.341 closest distance to " CA  ASP A 191 " =    0.933
peak=    3.340 closest distance to " NH2BARG A 190 " =    1.935
peak=    3.339 closest distance to " N   ARG A 156 " =    1.310
peak=    3.338 closest distance to " CG2 THR A 294 " =    1.620
peak=    3.337 closest distance to " O   HOH Z 408 " =    1.510
peak=    3.336 closest distance to " O   HOH Z 261 " =    1.968
peak=    3.335 closest distance to " CD2 LEU A 255 " =    1.079
peak=    3.335 closest distance to " CA  ASN A 215 " =    1.167
peak=    3.332 closest distance to " CB  GLN A 278 " =    0.840
peak=    3.324 closest distance to " O   HOH Z  48 " =    1.644
peak=    3.322 closest distance to " O   HOH Z 353 " =    2.607
peak=    3.321 closest distance to " O   HOH Z 280 " =    2.320
peak=    3.321 closest distance to " CB  GLN A 103 " =    1.002
peak=    3.317 closest distance to " O   HOH Z 277 " =    2.211
peak=    3.313 closest distance to " O   HOH Z 438 " =    2.242
peak=    3.310 closest distance to " O   HOH Z  10 " =    1.699
peak=    3.300 closest distance to " O   HOH Z 155 " =    2.580
peak=    3.292 closest distance to " CB  ARG A 139 " =    0.728
peak=    3.290 closest distance to " CG1 VAL A 296 " =    1.114
peak=    3.286 closest distance to " CB  ARG A  79 " =    1.173
peak=    3.286 closest distance to " O   HOH Z  63 " =    1.452
peak=    3.282 closest distance to " O   HOH Z 380 " =    2.030
peak=    3.276 closest distance to " O   SER A 271 " =    1.774
peak=    3.267 closest distance to " CB  THR A  31 " =    1.662
peak=    3.266 closest distance to " OE1 GLN A  11 " =    1.787
peak=    3.258 closest distance to " CG2 VAL A 126 " =    1.830
peak=    3.257 closest distance to " O   HOH Z 329 " =    3.215
peak=    3.256 closest distance to " CA  VAL A 126 " =    0.970
peak=    3.253 closest distance to " CZ  ARG A 269 " =    1.163
peak=    3.251 closest distance to " CG  ARG A  66 " =    2.960
peak=    3.248 closest distance to " O   HOH Z 361 " =    3.482
peak=    3.244 closest distance to " O   HOH Z 411 " =    1.732
peak=    3.240 closest distance to " CA  ALA A 295 " =    1.070
peak=    3.237 closest distance to " O   HOH Z  20 " =    1.348
peak=    3.236 closest distance to " CD  LYS A 119 " =    1.421
peak=    3.235 closest distance to " O   HOH Z 313 " =    1.695
peak=    3.231 closest distance to " CG2 ILE A 234 " =    2.068
peak=    3.227 closest distance to " NE2 GLN A  58 " =    2.634
peak=    3.226 closest distance to " O   HOH Z 211 " =    2.304
peak=    3.224 closest distance to " O   HOH Z  40 " =    1.399
peak=    3.214 closest distance to " CE  LYS A 119 " =    1.005
peak=    3.214 closest distance to " O   PHE A  38 " =    1.892
peak=    3.211 closest distance to " O   HOH Z  89 " =    1.414
peak=    3.210 closest distance to " CE BLYS A 290 " =    1.156
peak=    3.210 closest distance to " O   HOH Z  40 " =    1.877
peak=    3.207 closest distance to " OG BSER A 210 " =    1.401
peak=    3.205 closest distance to " O   HOH Z 248 " =    1.712
peak=    3.199 closest distance to " CB  SER A 141 " =    1.073
peak=    3.198 closest distance to " O   HOH Z 435 " =    1.957
peak=    3.197 closest distance to " O   HOH Z 194 " =    2.377
peak=    3.197 closest distance to " O   HOH Z 425 " =    2.074
peak=    3.197 closest distance to " CB  ALA A 291 " =    1.262
peak=    3.196 closest distance to " CB  ALA A  34 " =    0.886
peak=    3.195 closest distance to " CG  LEU A 167 " =    1.146
peak=    3.194 closest distance to " NH1 ARG A 269 " =    0.841
peak=    3.190 closest distance to " O   HOH Z 350 " =    1.803
peak=    3.187 closest distance to " O   HOH Z 383 " =    1.836
peak=    3.187 closest distance to " CG  PRO A 280 " =    0.925
peak=    3.183 closest distance to " O   HOH Z 430 " =    1.725
peak=    3.178 closest distance to " C   LYS A 290 " =    1.268
peak=    3.176 closest distance to " NH2AARG A 190 " =    1.473
peak=    3.172 closest distance to " CG2 ILE A 106 " =    0.867
peak=    3.172 closest distance to " N   GLY A  57 " =    1.385
peak=    3.167 closest distance to " O   HOH Z 428 " =    3.836
peak=    3.166 closest distance to " CG  GLU A 277 " =    2.188
peak=    3.166 closest distance to " O   HOH Z 263 " =    1.998
peak=    3.164 closest distance to " OE1 GLU A 277 " =    1.949
peak=    3.158 closest distance to " O   HOH Z   4 " =    1.638
peak=    3.155 closest distance to " OG  SER A  97 " =    2.506
peak=    3.154 closest distance to " O   HOH Z  50 " =    1.379
peak=    3.151 closest distance to " O   HOH Z 109 " =    2.585
peak=    3.151 closest distance to " CB  LEU A 255 " =    0.755
peak=    3.139 closest distance to " CB  ALA A   1 " =    1.242
peak=    3.133 closest distance to " O   HOH Z 426 " =    2.995
peak=    3.132 closest distance to " OD1 ASN A  60 " =    1.367
peak=    3.129 closest distance to " O   HOH Z 359 " =    2.100
peak=    3.129 closest distance to " CA  GLN A 194 " =    1.103
peak=    3.125 closest distance to " O   HOH Z 281 " =    4.551
peak=    3.121 closest distance to " O   HOH Z  61 " =    1.546
peak=    3.117 closest distance to " O   HOH Z  63 " =    1.958
peak=    3.117 closest distance to " O   HOH Z 217 " =    2.126
peak=    3.115 closest distance to " OD1 ASP A 238 " =    0.756
peak=    3.113 closest distance to " CA  THR A 264 " =    0.724
peak=    3.108 closest distance to " O   HOH Z   9 " =    2.025
peak=    3.108 closest distance to " CB  ALA A 295 " =    1.217
peak=    3.103 closest distance to " CA  ARG A  66 " =    0.912
peak=    3.101 closest distance to " O   THR A  31 " =    1.543
peak=    3.098 closest distance to " CG2 THR A  82 " =    0.810
peak=    3.098 closest distance to " CB  GLN A  73 " =    1.225
peak=    3.098 closest distance to " CA  TYR A 186 " =    1.281
peak=    3.083 closest distance to " O   HOH Z 250 " =    1.532
peak=    3.079 closest distance to " CB  ALA A  71 " =    1.242
peak=    3.048 closest distance to " N   ASP A 162 " =    1.388
peak=    3.040 closest distance to " O   HOH Z 420 " =    3.901
peak=    3.011 closest distance to " CA  ALA A 248 " =    1.113

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 191         
Filter by distance & map next to the model:
   mapped sites are within: 0.623 - 5.801
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 188 from: 191
   mapped sites are within: 0.705 - 5.801

peak=   -5.175 closest distance to " CG2 VAL A 230 " =    0.718
peak=   -4.504 closest distance to " SG  CYS A 254 " =    3.145
peak=   -4.289 closest distance to " OXT GLY A 302 " =    2.729
peak=   -4.257 closest distance to " O   HOH Z 266 " =    4.274
peak=   -4.254 closest distance to " CD  ARG A 156 " =    2.016
peak=   -4.193 closest distance to " CA  SER A 164 " =    2.039
peak=   -4.192 closest distance to " O   HOH Z 290 " =    0.849
peak=   -4.163 closest distance to " CD1 LEU A 101 " =    2.495
peak=   -4.117 closest distance to " O   HOH Z  11 " =    1.781
peak=   -4.089 closest distance to " OG ASER A 134 " =    1.170
peak=   -4.088 closest distance to " ND2 ASN A  45 " =    1.002
peak=   -4.071 closest distance to " CB  ALA A 161 " =    2.474
peak=   -3.972 closest distance to " CE2 TYR A  30 " =    2.863
peak=   -3.961 closest distance to " O   HOH Z 423 " =    2.267
peak=   -3.952 closest distance to " CG  ASP A  50 " =    2.366
peak=   -3.940 closest distance to " N   ALA A 248 " =    1.612
peak=   -3.920 closest distance to " O   ALA A 161 " =    1.463
peak=   -3.903 closest distance to " C   HIS A 108 " =    1.168
peak=   -3.896 closest distance to " NH2 ARG A  79 " =    1.905
peak=   -3.859 closest distance to " O   HOH Z 250 " =    1.435
peak=   -3.837 closest distance to " N   HIS A 115 " =    1.897
peak=   -3.826 closest distance to " O   HOH Z 166 " =    1.955
peak=   -3.824 closest distance to " O   HOH Z  98 " =    1.468
peak=   -3.821 closest distance to " CD  ARG A 139 " =    1.587
peak=   -3.819 closest distance to " ND2 ASN A  39 " =    1.105
peak=   -3.818 closest distance to " O   HOH Z 362 " =    5.801
peak=   -3.774 closest distance to " O   HOH Z 155 " =    1.503
peak=   -3.772 closest distance to " O   HOH Z 191 " =    4.929
peak=   -3.760 closest distance to " O   PRO A 198 " =    1.263
peak=   -3.746 closest distance to " CG  LYS A 193 " =    2.113
peak=   -3.742 closest distance to " CZ  TYR A 169 " =    1.864
peak=   -3.740 closest distance to " CB  ALA A  51 " =    1.877
peak=   -3.712 closest distance to " N   GLN A  58 " =    1.781
peak=   -3.710 closest distance to " O   HOH Z  63 " =    0.945
peak=   -3.704 closest distance to " OD1 ASN A 249 " =    1.130
peak=   -3.703 closest distance to " OXT GLY A 302 " =    3.408
peak=   -3.700 closest distance to " CD1 LEU A 255 " =    2.707
peak=   -3.690 closest distance to " O   HOH Z  43 " =    1.845
peak=   -3.674 closest distance to " O   HOH Z 407 " =    2.740
peak=   -3.671 closest distance to " CD2 LEU A 300 " =    2.695
peak=   -3.668 closest distance to " C   ALA A 158 " =    1.124
peak=   -3.665 closest distance to " CG  ASN A 110 " =    1.126
peak=   -3.658 closest distance to " O   ASN A 187 " =    1.431
peak=   -3.657 closest distance to " CG  ASP A 231 " =    0.786
peak=   -3.641 closest distance to " OD1 ASP A 200 " =    1.158
peak=   -3.639 closest distance to " OG BSER A 134 " =    1.634
peak=   -3.635 closest distance to " O   MET A  40 " =    2.737
peak=   -3.617 closest distance to " O   HOH Z 211 " =    1.500
peak=   -3.603 closest distance to " O   HOH Z  92 " =    1.663
peak=   -3.600 closest distance to " O   HOH Z   3 " =    2.040
peak=   -3.595 closest distance to " O   ALA A   8 " =    1.839
peak=   -3.584 closest distance to " CB  ASP A 162 " =    2.672
peak=   -3.579 closest distance to " N   SER A 276 " =    1.172
peak=   -3.570 closest distance to " O   HOH Z 231 " =    1.800
peak=   -3.567 closest distance to " N   ALA A 226 " =    1.918
peak=   -3.565 closest distance to " O   VAL A  67 " =    2.342
peak=   -3.563 closest distance to " O   HOH Z  11 " =    1.756
peak=   -3.559 closest distance to " O   VAL A  67 " =    2.514
peak=   -3.553 closest distance to " O   HOH Z 388 " =    2.136
peak=   -3.546 closest distance to " ND2 ASN A 187 " =    1.543
peak=   -3.544 closest distance to " N   GLN A 122 " =    1.562
peak=   -3.541 closest distance to " NE2 GLN A  88 " =    1.110
peak=   -3.538 closest distance to " O   HOH Z 166 " =    1.622
peak=   -3.517 closest distance to " O   HOH Z 113 " =    2.266
peak=   -3.514 closest distance to " O   HOH Z  56 " =    2.121
peak=   -3.505 closest distance to " O   HOH Z 313 " =    1.889
peak=   -3.504 closest distance to " CB  TYR A  15 " =    2.183
peak=   -3.504 closest distance to " CG  GLU A 277 " =    1.139
peak=   -3.492 closest distance to " O   HOH Z 103 " =    1.863
peak=   -3.484 closest distance to " O   PRO A 198 " =    1.257
peak=   -3.482 closest distance to " CB  ALA A 248 " =    1.926
peak=   -3.480 closest distance to " OG1 THR A  82 " =    1.316
peak=   -3.477 closest distance to " O   GLY A 196 " =    0.993
peak=   -3.473 closest distance to " CG  LEU A 228 " =    1.083
peak=   -3.465 closest distance to " O   HOH Z 292 " =    4.237
peak=   -3.463 closest distance to " O   HOH Z 165 " =    2.124
peak=   -3.461 closest distance to " O   ALA A  51 " =    1.391
peak=   -3.461 closest distance to " CD  LYS A 289 " =    2.500
peak=   -3.456 closest distance to " N   MET A 188 " =    1.896
peak=   -3.447 closest distance to " CG  GLU A  53 " =    1.314
peak=   -3.443 closest distance to " C   ASP A 231 " =    2.410
peak=   -3.441 closest distance to " O   HOH Z 138 " =    0.868
peak=   -3.437 closest distance to " OG BSER A 134 " =    1.317
peak=   -3.436 closest distance to " CZ2 TRP A 179 " =    1.253
peak=   -3.435 closest distance to " NH1 ARG A  56 " =    2.559
peak=   -3.415 closest distance to " O   HOH Z 377 " =    1.177
peak=   -3.412 closest distance to " CD1 PHE A  59 " =    1.861
peak=   -3.408 closest distance to " O   HOH Z 431 " =    1.695
peak=   -3.408 closest distance to " CB  ALA A 291 " =    2.268
peak=   -3.407 closest distance to " O   HOH Z 234 " =    4.111
peak=   -3.399 closest distance to " N   GLY A 133 " =    1.855
peak=   -3.394 closest distance to " O   HOH Z 175 " =    4.453
peak=   -3.389 closest distance to " CG  MET A 105 " =    0.874
peak=   -3.385 closest distance to " O   HOH Z 360 " =    2.466
peak=   -3.383 closest distance to " O   HOH Z 311 " =    3.433
peak=   -3.377 closest distance to " NH2 ARG A  66 " =    1.612
peak=   -3.376 closest distance to " O   HOH Z 427 " =    1.405
peak=   -3.373 closest distance to " CG  ARG A 219 " =    2.352
peak=   -3.372 closest distance to " O   VAL A 174 " =    1.748
peak=   -3.354 closest distance to " OG  SER A  97 " =    2.201
peak=   -3.353 closest distance to " CD2 LEU A 167 " =    1.761
peak=   -3.351 closest distance to " ND2 ASN A  60 " =    1.967
peak=   -3.350 closest distance to " O   HOH Z 419 " =    1.055
peak=   -3.339 closest distance to " CB  ASP A 132 " =    2.228
peak=   -3.339 closest distance to " CE  LYS A 166 " =    2.971
peak=   -3.337 closest distance to " O   HOH Z  60 " =    2.075
peak=   -3.337 closest distance to " C   THR A 279 " =    1.185
peak=   -3.336 closest distance to " C   ASN A  69 " =    1.229
peak=   -3.334 closest distance to " C   GLY A  80 " =    2.374
peak=   -3.331 closest distance to " CD2 TYR A 293 " =    2.139
peak=   -3.327 closest distance to " O   HOH Z  17 " =    1.292
peak=   -3.322 closest distance to " OG  SER A 206 " =    1.590
peak=   -3.319 closest distance to " N   VAL A 189 " =    1.613
peak=   -3.311 closest distance to " O   ILE A 120 " =    1.218
peak=   -3.308 closest distance to " N   VAL A 230 " =    1.181
peak=   -3.299 closest distance to " O   HOH Z 389 " =    4.546
peak=   -3.299 closest distance to " CG2 VAL A 296 " =    1.623
peak=   -3.295 closest distance to " O   ALA A 160 " =    1.291
peak=   -3.294 closest distance to " O   ALA A 256 " =    1.359
peak=   -3.289 closest distance to " O   HOH Z 193 " =    2.058
peak=   -3.282 closest distance to " C   ARG A 269 " =    1.452
peak=   -3.274 closest distance to " CD  GLU A 152 " =    2.313
peak=   -3.273 closest distance to " NH2AARG A 275 " =    4.995
peak=   -3.273 closest distance to " N   THR A 157 " =    1.505
peak=   -3.258 closest distance to " C   LEU A 143 " =    1.162
peak=   -3.258 closest distance to " O   LEU A 228 " =    2.311
peak=   -3.257 closest distance to " N   SER A 206 " =    1.861
peak=   -3.256 closest distance to " CG  PHE A 283 " =    2.714
peak=   -3.248 closest distance to " CG2 THR A 182 " =    2.330
peak=   -3.244 closest distance to " CE  MET A 105 " =    1.786
peak=   -3.243 closest distance to " CD  GLN A  88 " =    2.166
peak=   -3.243 closest distance to " C   VAL A 189 " =    1.786
peak=   -3.238 closest distance to " ND2 ASN A 252 " =    1.675
peak=   -3.232 closest distance to " O   HOH Z 134 " =    2.644
peak=   -3.232 closest distance to " CD1 LEU A 228 " =    2.173
peak=   -3.226 closest distance to " CD2 TRP A 274 " =    1.034
peak=   -3.224 closest distance to " O   HOH Z 100 " =    0.964
peak=   -3.223 closest distance to " C   ASN A 285 " =    2.151
peak=   -3.222 closest distance to " CD2 LEU A 237 " =    2.867
peak=   -3.222 closest distance to " CE3 TRP A 150 " =    1.851
peak=   -3.220 closest distance to " O   HOH Z 210 " =    0.932
peak=   -3.220 closest distance to " CB  ASN A  39 " =    1.957
peak=   -3.212 closest distance to " CG  PHE A  59 " =    2.079
peak=   -3.206 closest distance to " O   HOH Z 197 " =    5.024
peak=   -3.206 closest distance to " O   SER A  95 " =    1.507
peak=   -3.197 closest distance to " O   HOH Z 198 " =    2.148
peak=   -3.191 closest distance to " CG  GLU A 152 " =    1.240
peak=   -3.188 closest distance to " CG  ASP A 132 " =    2.140
peak=   -3.187 closest distance to " O   HOH Z  44 " =    2.053
peak=   -3.186 closest distance to " N   GLN A  77 " =    1.503
peak=   -3.186 closest distance to " O   HOH Z 351 " =    1.475
peak=   -3.184 closest distance to " CG  PRO A 213 " =    0.846
peak=   -3.183 closest distance to " CG2AVAL A  41 " =    3.014
peak=   -3.179 closest distance to " NH2 ARG A  79 " =    1.740
peak=   -3.178 closest distance to " CG1 VAL A 112 " =    2.760
peak=   -3.174 closest distance to " OG1 THR A 178 " =    1.204
peak=   -3.168 closest distance to " CB  PHE A 208 " =    2.219
peak=   -3.162 closest distance to " CB  ASP A 124 " =    1.959
peak=   -3.156 closest distance to " CA  ASP A 298 " =    1.067
peak=   -3.155 closest distance to " O   HOH Z  15 " =    1.644
peak=   -3.151 closest distance to " CA  ARG A  66 " =    1.657
peak=   -3.150 closest distance to " O   VAL A 197 " =    1.179
peak=   -3.148 closest distance to " O   HOH Z 256 " =    1.187
peak=   -3.146 closest distance to " CD2 LEU A 237 " =    2.490
peak=   -3.144 closest distance to " OG  SER A   3 " =    1.194
peak=   -3.143 closest distance to " O   HOH Z 126 " =    1.207
peak=   -3.136 closest distance to " NE2 GLN A 278 " =    1.912
peak=   -3.135 closest distance to " CZ3 TRP A 274 " =    1.152
peak=   -3.134 closest distance to " CD  GLN A  11 " =    0.705
peak=   -3.133 closest distance to " CD  GLN A  88 " =    0.917
peak=   -3.131 closest distance to " C   ARG A 102 " =    1.549
peak=   -3.117 closest distance to " CB  PRO A 243 " =    2.488
peak=   -3.115 closest distance to " O   SER A 210 " =    1.858
peak=   -3.101 closest distance to " O   SER A 135 " =    1.558
peak=   -3.101 closest distance to " O   HOH Z 151 " =    1.498
peak=   -3.099 closest distance to " CG  ARG A 269 " =    2.128
peak=   -3.092 closest distance to " O   GLY A  80 " =    2.556
peak=   -3.084 closest distance to " OD1 ASP A 191 " =    1.460
peak=   -3.083 closest distance to " O   HOH Z  60 " =    0.974
peak=   -3.080 closest distance to " OD1 ASP A 191 " =    1.499
peak=   -3.077 closest distance to " O   HOH Z 407 " =    3.357
peak=   -3.072 closest distance to " O   HOH Z 339 " =    1.654
peak=   -3.072 closest distance to " C   GLN A 144 " =    1.000
peak=   -3.069 closest distance to " CB  CYS A 254 " =    2.591
peak=   -3.066 closest distance to " O   HOH Z 111 " =    3.418
peak=   -3.064 closest distance to " O   HOH Z  97 " =    1.401
peak=   -3.063 closest distance to " CG2 VAL A 296 " =    1.104
peak=   -3.037 closest distance to " O   HOH Z 297 " =    2.740

================= 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    :  0.4821 0.4818   6.283314e+00   6.277783e+00
   1_bss:  0.4742 0.4725   6.279134e+00   6.266200e+00
   1_xyz:  0.4011 0.4251   6.181858e+00   6.215451e+00
   1_adp:  0.3556 0.4052   6.109664e+00   6.190684e+00
   1_occ:  0.3550 0.4049   6.109273e+00   6.190918e+00
   2_bss:  0.3518 0.4029   6.109354e+00   6.189496e+00
   2_xyz:  0.2702 0.3277   5.895427e+00   6.036394e+00
   2_adp:  0.2482 0.3035   5.826626e+00   5.978367e+00
   2_occ:  0.2480 0.3037   5.826128e+00   5.978372e+00
   3_bss:  0.2462 0.3019   5.824426e+00   5.976403e+00
   3_xyz:  0.1780 0.2341   5.553402e+00   5.756837e+00
   3_adp:  0.1593 0.2086   5.438615e+00   5.647980e+00
   3_occ:  0.1590 0.2088   5.438124e+00   5.648180e+00
   4_bss:  0.1580 0.2069   5.434378e+00   5.642886e+00
   4_xyz:  0.1275 0.1719   5.244982e+00   5.468888e+00
   4_adp:  0.1227 0.1660   5.208696e+00   5.431902e+00
   4_occ:  0.1225 0.1658   5.207204e+00   5.430661e+00
   5_bss:  0.1227 0.1664   5.209632e+00   5.432736e+00
   5_xyz:  0.1180 0.1624   5.183810e+00   5.411277e+00
   5_adp:  0.1160 0.1625   5.176411e+00   5.411863e+00
   5_occ:  0.1160 0.1625   5.176053e+00   5.411726e+00
   5_bss:  0.1160 0.1625   5.175961e+00   5.411657e+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:  0.384  20.000   7.023   7.665   9.327   0.000   0.000   0.000
   1_xyz:  0.384  20.000   7.023   7.665   9.327   0.000   0.000   0.000
   1_adp:  0.384  20.000   7.023   7.665   9.327   0.000   0.000   0.000
   1_occ:  0.384  20.000   7.023   7.665   9.327   0.000   0.000   0.000
   2_bss:  0.328  30.520   3.561   4.161   6.341   0.000   0.000   0.000
   2_xyz:  0.328  30.520   3.561   4.161   6.341   0.000   0.000   0.000
   2_adp:  0.328  30.520   3.561   4.161   6.341   0.000   0.000   0.000
   2_occ:  0.328  30.520   3.561   4.161   6.341   0.000   0.000   0.000
   3_bss:  0.315  33.453   1.820   2.745   3.846   0.000   0.000   0.000
   3_xyz:  0.315  33.453   1.820   2.745   3.846   0.000   0.000   0.000
   3_adp:  0.315  33.453   1.820   2.745   3.846   0.000   0.000   0.000
   3_occ:  0.315  33.453   1.820   2.745   3.846   0.000   0.000   0.000
   4_bss:  0.314  31.579   0.842   1.760   2.156   0.000   0.000   0.000
   4_xyz:  0.314  31.579   0.842   1.760   2.156   0.000   0.000   0.000
   4_adp:  0.314  31.579   0.842   1.760   2.156   0.000   0.000   0.000
   4_occ:  0.314  31.579   0.842   1.760   2.156   0.000   0.000   0.000
   5_bss:  0.319  33.256   0.651   1.518   1.785   0.000   0.000   0.000
   5_xyz:  0.319  33.256   0.651   1.518   1.785   0.000   0.000   0.000
   5_adp:  0.319  33.256   0.651   1.518   1.785   0.000   0.000   0.000
   5_occ:  0.319  33.256   0.651   1.518   1.785   0.000   0.000   0.000
   5_bss:  0.321  35.232  -0.650   0.246   0.404   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  58.511 0.4135  0.4917    73083.241
   1_bss:  58.508 0.4110  0.6119    69255.375
   1_xyz:  50.531 0.5119  0.7514    54033.990
   1_adp:  46.804 0.5590  0.8665    49156.551
   1_occ:  46.816 0.5589  0.8656    49238.660
   2_bss:  46.519 0.5625  0.7751    48771.089
   2_xyz:  35.237 0.6972  0.9439    29311.407
   2_adp:  31.614 0.7393  0.9947    24677.943
   2_occ:  31.606 0.7394  0.9947    24672.371
   3_bss:  31.408 0.7415  0.9306    24450.807
   3_xyz:  23.163 0.8299  1.0014    14133.652
   3_adp:  19.886 0.8631  1.0230    11176.855
   3_occ:  19.894 0.8630  1.0225    11183.108
   4_bss:  19.730 0.8644  0.9773    10961.416
   4_xyz:  15.897 0.8987  0.9920     7501.374
   4_adp:  15.027 0.9064  0.9951     6973.252
   4_occ:  14.996 0.9066  0.9951     6955.253
   5_bss:  15.055 0.9062  0.9852     7034.778
   5_xyz:  14.470 0.9114  0.9869     6687.256
   5_adp:  14.450 0.9117  0.9853     6688.499
   5_occ:  14.442 0.9118  0.9851     6688.458
   5_bss:  14.441 0.9118  0.9850     6690.222
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.087   5.2962e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.087   5.2962e+01
   1_xyz:   1.715  0.014  0.109 18.292  0.007  4.107   1.4823e-01
   1_adp:   1.715  0.014  0.109 18.292  0.007  4.107   1.4823e-01
   1_occ:   1.715  0.014  0.109 18.292  0.007  4.107   1.4823e-01
   2_bss:   1.715  0.014  0.109 18.292  0.007  4.107   1.4823e-01
   2_xyz:   1.139  0.008  0.081 16.515  0.005  4.108   8.1521e-02
   2_adp:   1.139  0.008  0.081 16.515  0.005  4.108   8.1521e-02
   2_occ:   1.139  0.008  0.081 16.515  0.005  4.108   8.1521e-02
   3_bss:   1.139  0.008  0.081 16.515  0.005  4.108   8.1521e-02
   3_xyz:   1.129  0.007  0.080 15.876  0.004  4.122   7.1988e-02
   3_adp:   1.129  0.007  0.080 15.876  0.004  4.122   7.1988e-02
   3_occ:   1.129  0.007  0.080 15.876  0.004  4.122   7.1988e-02
   4_bss:   1.129  0.007  0.080 15.876  0.004  4.122   7.1988e-02
   4_xyz:   1.090  0.007  0.081 15.752  0.004  4.109   6.8960e-02
   4_adp:   1.090  0.007  0.081 15.752  0.004  4.109   6.8960e-02
   4_occ:   1.090  0.007  0.081 15.752  0.004  4.109   6.8960e-02
   5_bss:   1.090  0.007  0.081 15.752  0.004  4.109   6.8960e-02
   5_xyz:   0.967  0.006  0.073 15.380  0.004  4.109   5.7074e-02
   5_adp:   0.967  0.006  0.073 15.380  0.004  4.109   5.7074e-02
   5_occ:   0.967  0.006  0.073 15.380  0.004  4.109   5.7074e-02
   5_bss:   0.967  0.006  0.073 15.380  0.004  4.109   5.7074e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.706   6.8604e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.706   6.8604e+00
   1_xyz:  15.203  0.189  0.478 88.194  0.054  2.149   1.0172e-01
   1_adp:  15.203  0.189  0.478 88.194  0.054  2.149   1.0172e-01
   1_occ:  15.203  0.189  0.478 88.194  0.054  2.149   1.0172e-01
   2_bss:  15.203  0.189  0.478 88.194  0.054  2.149   1.0172e-01
   2_xyz:   6.771  0.084  0.337 84.167  0.057  2.215   6.9290e-02
   2_adp:   6.771  0.084  0.337 84.167  0.057  2.215   6.9290e-02
   2_occ:   6.771  0.084  0.337 84.167  0.057  2.215   6.9290e-02
   3_bss:   6.771  0.084  0.337 84.167  0.057  2.215   6.9290e-02
   3_xyz:   7.293  0.062  0.467 82.862  0.033  2.252   5.2882e-02
   3_adp:   7.293  0.062  0.467 82.862  0.033  2.252   5.2882e-02
   3_occ:   7.293  0.062  0.467 82.862  0.033  2.252   5.2882e-02
   4_bss:   7.293  0.062  0.467 82.862  0.033  2.252   5.2882e-02
   4_xyz:   6.641  0.043  0.550 83.179  0.036  2.273   6.1176e-02
   4_adp:   6.641  0.043  0.550 83.179  0.036  2.273   6.1176e-02
   4_occ:   6.641  0.043  0.550 83.179  0.036  2.273   6.1176e-02
   5_bss:   6.641  0.043  0.550 83.179  0.036  2.273   6.1176e-02
   5_xyz:   6.279  0.039  0.458 82.940  0.035  2.363   3.9605e-02
   5_adp:   6.279  0.039  0.458 82.940  0.035  2.363   3.9605e-02
   5_occ:   6.279  0.039  0.458 82.940  0.035  2.363   3.9605e-02
   5_bss:   6.279  0.039  0.458 82.940  0.035  2.363   3.9605e-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:  82.44   0.00  13.61  70.60   0.00  11.26  82.44   0.00  26.44
   1_occ:  82.44   0.00  13.61  70.60   0.00  11.26  82.44   0.00  26.44
   2_bss:  82.44   0.00  13.61  70.60   0.00  11.26  82.44   0.00  26.44
   2_xyz:  82.44   0.00  13.61  70.60   0.00  11.26  82.44   0.00  26.44
   2_adp:  85.86   0.00  13.77  80.08   0.00  10.44  85.86   0.00  31.85
   2_occ:  85.86   0.00  13.77  80.08   0.00  10.44  85.86   0.00  31.85
   3_bss:  85.86   0.00  13.77  80.08   0.00  10.44  85.86   0.00  31.85
   3_xyz:  85.86   0.00  13.77  80.08   0.00  10.44  85.86   0.00  31.85
   3_adp:  86.66   0.00  13.51  77.26   0.00   9.52  86.66   3.18  35.20
   3_occ:  86.66   0.00  13.51  77.26   0.00   9.52  86.66   3.18  35.20
   4_bss:  86.66   0.00  13.51  77.26   0.00   9.52  86.66   3.18  35.20
   4_xyz:  86.66   0.00  13.51  77.26   0.00   9.52  86.66   3.18  35.20
   4_adp:  80.93   0.00  13.28  80.93   0.00   9.27  80.45   2.91  35.12
   4_occ:  80.93   0.00  13.28  80.93   0.00   9.27  80.45   2.91  35.12
   5_bss:  80.93   0.00  13.28  80.93   0.00   9.27  80.45   2.91  35.12
   5_xyz:  80.93   0.00  13.28  80.93   0.00   9.27  80.45   2.91  35.12
   5_adp:  82.01   0.00  13.32  82.01   0.00   9.25  78.53   2.10  35.44
   5_occ:  82.01   0.00  13.32  82.01   0.00   9.25  78.53   2.10  35.44
   5_bss:  83.33   1.32  14.63  83.33   1.32  10.57  79.84   3.42  36.76
------------------------------------------------------------------------
 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:    1.263    0.034    0.414
   1_adp:    1.263    0.034    0.414
   1_occ:    1.263    0.034    0.414
   2_bss:    1.263    0.034    0.414
   2_xyz:    1.717    0.032    0.579
   2_adp:    1.717    0.032    0.579
   2_occ:    1.717    0.032    0.579
   3_bss:    1.717    0.032    0.579
   3_xyz:    1.632    0.043    0.690
   3_adp:    1.632    0.043    0.690
   3_occ:    1.632    0.043    0.690
   4_bss:    1.632    0.043    0.690
   4_xyz:    1.734    0.052    0.732
   4_adp:    1.734    0.052    0.732
   4_occ:    1.734    0.052    0.732
   5_bss:    1.734    0.052    0.732
   5_xyz:    1.932    0.041    0.745
   5_adp:    1.932    0.041    0.745
   5_occ:    1.932    0.041    0.745
   5_bss:    1.932    0.041    0.745
------------------------------------------------------------------------

CPU time actual refinement: 359.42


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_308/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_308/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_308/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_308/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_308/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 359.27 
  Macro-tasks:
    bulk solvent and scale       = 41.57  
    individual site refinement   = 153.95 
    weights calculation          = 32.73  
    collect and process          = 6.63   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 235.01 
  Micro-tasks:
    mask                            = 2.47   
    f_calc                          = 112.62 
    alpha_beta                      = 8.28   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 124.63 
    fmodel                         = 7.91   
    r_factors                      = 0.17   
    phase_errors                   = 10.56  
    foms                           = 0.20   
    TOTAL for micro-tasks          = 268.03 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.936 micro seconds
Total CPU time: 6.22 minutes
from_scatterers_fft:    680 calls, 112.11 s
gradients_fft:          625 calls, 110.12 s

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

# Date 2008-01-16 Time 01:16:03 PST -0800 (1200474963.23 s)
Start R-work = 0.4821, R-free = 0.4818 (no bulk solvent and anisotropic scale)
Final R-work = 0.1337, R-free = 0.1797 (no bulk solvent and anisotropic scale)

Start R-work = 0.4742, R-free = 0.4725
Final R-work = 0.1160, R-free = 0.1625