# Date 2008-01-16 Time 01:46:17 PST -0800 (1200476777.50 s)
#phil __OFF__

Command line arguments: "../559.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 932
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 559

-------------------------------------------------------------------------------
  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: (69.8988, 47.1647, 88.1178, 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: 3.27, per 1000 atoms: 1.16


================================== 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: (69.8988, 47.1647, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0179 1.99073
Completeness in resolution range: 0.953329
Completeness with d_max=infinity: 0.950369

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0179
                             d_min =   1.9907

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: (69.8988, 47.1647, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0179 1.99073
Completeness in resolution range: 0.953329
Completeness with d_max=infinity: 0.950369

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0183 -  4.2593 [2161/2188]  1942   219  10.1%
  bin  2:  4.2593 -  3.3936 [2068/2084]  1864   204   9.9%
  bin  3:  3.3936 -  2.9684 [2050/2069]  1845   205  10.0%
  bin  4:  2.9684 -  2.6987 [2024/2054]  1819   205  10.1%
  bin  5:  2.6987 -  2.5062 [2002/2021]  1804   198   9.9%
  bin  6:  2.5062 -  2.3591 [2017/2042]  1814   203  10.1%
  bin  7:  2.3591 -  2.2413 [2003/2037]  1809   194   9.7%
  bin  8:  2.2413 -  2.1440 [1977/2007]  1772   205  10.4%
  bin  9:  2.1440 -  2.0617 [1976/2018]  1785   191   9.7%
  bin 10:  2.0617 -  1.9907 [1311/2028]  1176   135  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_559/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.58 -     2.25: 12
        2.25 -     2.91: 1417
        2.91 -     3.57: 4403
        3.57 -     4.24: 9089
        4.24 -     4.90: 13077
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.584 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.687 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.805 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.905 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 27993 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_559/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_559/model_refine_001.geo

CPU time processing inputs: 9.32


============================ 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 = 69.89875 47.16465 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4565   r_free= 0.4406   ksol= 0.00   Bsol= 0.00   scale= 0.801    |
|                                                                             |
| 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:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.259127                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.7505 0.99   1401  154 0.3719 0.3445      6.5637      6.4835|
|  2:  4.7505 -  3.7906 0.99   1348  154 0.3576 0.4053      6.7011      6.8479|
|  3:  3.7906 -  3.3173 0.99   1322  145 0.4145 0.3748      6.6318      6.5786|
|  4:  3.3173 -  3.0167 0.99   1312  140 0.4392 0.4154      6.4926       6.428|
|  5:  3.0167 -  2.8019 0.99   1313  147 0.4791 0.4574      6.3423      6.3468|
|  6:  2.8019 -  2.6377 0.99   1297  148 0.4838 0.5595      6.2616       6.239|
|  7:  2.6377 -  2.5062 0.99   1281  143 0.4896 0.4433       6.211      6.1168|
|  8:  2.5062 -  2.3976 0.98   1294  143 0.5166 0.4436      6.1908       6.127|
|  9:  2.3976 -  2.3056 0.98   1288  144 0.5033 0.4958      6.0951      6.1421|
| 10:  2.3056 -  2.2263 0.98   1277  138 0.5256 0.4274      6.1246      6.0051|
| 11:  2.2263 -  2.1569 0.99   1284  147 0.5006 0.5150      6.0228      6.0615|
| 12:  2.1569 -  2.0954 0.97   1268  138 0.5135 0.4923       5.951      6.0033|
| 13:  2.0954 -  2.0404 0.99   1270  137 0.5146 0.5246       5.883      5.8402|
| 14:  2.0404 -  1.9907 0.52    675   81 0.5181 0.4197        5.92      5.6754|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0183 -  4.7505  1401   154  0.73  31.18   0.81     0.75      59917.19|
|  2:  4.7505 -  3.7906  1348   154  0.74  31.30   0.89     0.79      87437.70|
|  3:  3.7906 -  3.3173  1322   145  0.66  38.66   0.84     0.75      92766.10|
|  4:  3.3173 -  3.0167  1312   140  0.58  45.05   0.81     0.65      82749.06|
|  5:  3.0167 -  2.8019  1313   147  0.49  52.74   0.75     0.56      71122.84|
|  6:  2.8019 -  2.6377  1297   148  0.45  55.70   0.73     0.51      64496.55|
|  7:  2.6377 -  2.5062  1281   143  0.45  55.79   0.75     0.51      57305.33|
|  8:  2.5062 -  2.3976  1294   143  0.48  53.77   0.73     0.54      48160.71|
|  9:  2.3976 -  2.3056  1288   144  0.49  52.92   0.72     0.57      43428.53|
| 10:  2.3056 -  2.2263  1277   138  0.48  54.14   0.74     0.55      40723.87|
| 11:  2.2263 -  2.1569  1284   147  0.42  58.11   0.75     0.51      41729.51|
| 12:  2.1569 -  2.0954  1268   138  0.40  59.94   0.76     0.50      38873.45|
| 13:  2.0954 -  2.0404  1270   137  0.42  58.26   0.72     0.51      32093.22|
| 14:  2.0404 -  1.9907   675    81  0.53  49.93   0.74     0.53      21357.27|
|alpha:            min =        0.50 max =            0.79 mean =         0.59|
|beta:             min =    21357.27 max =        92766.10 mean =     57388.83|
|figures of merit: min =        0.00 max =            1.00 mean =         0.53|
|phase err.(work): min =        0.00 max =           89.98 mean =        49.59|
|phase err.(test): min =        0.00 max =           89.91 mean =        49.88|
|-----------------------------------------------------------------------------|

============================== 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 = 10.123678             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.814   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.764812              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.671   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       28 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      161 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      682 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1488 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2588 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3883 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5005 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6561 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7624 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.178 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.783 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.079)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.079)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4636   r_free= 0.4407   ksol= 0.00   Bsol= 0.00   scale= 0.772    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.264846                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4471   r_free= 0.4277   ksol= 0.33   Bsol= 12.43   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.83,7.99,11.77,0.00,0.00,0.00); trace/3= 8.86                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.251655                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.127614              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.173   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.741988              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 75.352   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4471      final r-factor (work) = 0.3472          |
| start r-factor (free) = 0.4277      final r-factor (free) = 0.3695          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 82.7642 = 9.13 * 0.50 * 6.2637 + 1.00 * 54.1780                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.0703 = 9.13 * 0.50 * 6.1213 + 1.00 * 0.1340                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3472      final r-factor (work) = 0.2957          |
| start r-factor (free) = 0.3695      final r-factor (free) = 0.3339          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5563 = 0.74 * 1.00 * 6.1213 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4590 = 0.74 * 1.00 * 5.9923 + 1.00 * 0.0128                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 34     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.079)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    63.23   11.69    None  None   None       |
|    all(noH): 2823   0      0.00    63.23   11.69    None  None   None       |
|    Sol.    : 438    0      0.00    63.23   26.45    None  None   None       |
|    Mac.    : 2385   0      0.00    55.52   8.98     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.323: 1108   |   5:    31.614 -  37.937:  101        |
|      1:     6.323 -  12.646:  797   |   6:    37.937 -  44.260:   45        |
|      2:    12.646 -  18.969:  377   |   7:    44.260 -  50.583:   39        |
|      3:    18.969 -  25.292:  203   |   8:    50.583 -  56.906:   11        |
|      4:    25.292 -  31.614:  134   |   9:    56.906 -  63.229:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2957 r_free = 0.3339             target_work(ml) = 5.956         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2951 r_free = 0.3355             target_work(ml) = 5.955         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2951   r_free= 0.3355   ksol= 0.33   Bsol= 12.43   scale= 1.097   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.83,7.99,11.77,0.00,0.00,0.00); trace/3= 8.86                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.955362                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2904   r_free= 0.3316   ksol= 0.33   Bsol= 44.10   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.10,4.11,7.61,0.00,0.00,0.00); trace/3= 4.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.954530                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.652537              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.815   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.400219              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.064  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2904      final r-factor (work) = 0.2113          |
| start r-factor (free) = 0.3316      final r-factor (free) = 0.2557          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.0822 = 3.65 * 0.50 * 5.9949 + 1.00 * 0.1340                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.6700 = 3.65 * 0.50 * 5.8060 + 1.00 * 0.0668                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2113      final r-factor (work) = 0.1916          |
| start r-factor (free) = 0.2557      final r-factor (free) = 0.2394          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3367 = 0.40 * 1.00 * 5.8060 + 1.00 * 0.0130                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2633 = 0.40 * 1.00 * 5.6276 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.079)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    66.74   11.89    None  None   None       |
|    all(noH): 2823   0      0.00    66.74   11.89    None  None   None       |
|    Sol.    : 438    0      0.00    66.74   32.00    None  None   None       |
|    Mac.    : 2385   0      0.00    60.02   8.20     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.674: 1322   |   5:    33.369 -  40.043:  102        |
|      1:     6.674 -  13.348:  729   |   6:    40.043 -  46.716:   88        |
|      2:    13.348 -  20.021:  275   |   7:    46.716 -  53.390:   42        |
|      3:    20.021 -  26.695:  124   |   8:    53.390 -  60.064:   19        |
|      4:    26.695 -  33.369:  117   |   9:    60.064 -  66.737:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1916 r_free = 0.2394             target_work(ml) = 5.601         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1914 r_free = 0.2394             target_work(ml) = 5.601         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1914   r_free= 0.2394   ksol= 0.33   Bsol= 44.10   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.10,4.11,7.61,0.00,0.00,0.00); trace/3= 4.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.600872                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1904   r_free= 0.2400   ksol= 0.32   Bsol= 56.76   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.22,3.20,5.29,0.00,0.00,0.00); trace/3= 3.57                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.601218                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.540952              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.619  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.743242              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.766  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1904      final r-factor (work) = 0.1463          |
| start r-factor (free) = 0.2400      final r-factor (free) = 0.1910          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2229 = 2.54 * 0.50 * 5.6326 + 1.00 * 0.0668                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0324 = 2.54 * 0.50 * 5.4855 + 1.00 * 0.0632                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1463      final r-factor (work) = 0.1376          |
| start r-factor (free) = 0.1910      final r-factor (free) = 0.1826          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0881 = 0.74 * 1.00 * 5.4855 + 1.00 * 0.0110                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9768 = 0.74 * 1.00 * 5.3332 + 1.00 * 0.0129                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.079)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    69.50   12.14    None  None   None       |
|    all(noH): 2823   0      0.00    69.50   12.14    None  None   None       |
|    Sol.    : 438    0      0.66    69.50   34.62    None  None   None       |
|    Mac.    : 2385   0      0.00    64.40   8.02     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.950: 1425   |   5:    34.750 -  41.699:  103        |
|      1:     6.950 -  13.900:  680   |   6:    41.699 -  48.649:  105        |
|      2:    13.900 -  20.850:  230   |   7:    48.649 -  55.599:   48        |
|      3:    20.850 -  27.800:  103   |   8:    55.599 -  62.549:   25        |
|      4:    27.800 -  34.750:   97   |   9:    62.549 -  69.499:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1376 r_free = 0.1826             target_work(ml) = 5.314         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1375 r_free = 0.1824             target_work(ml) = 5.313         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1375   r_free= 0.1824   ksol= 0.32   Bsol= 56.76   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.22,3.20,5.29,0.00,0.00,0.00); trace/3= 3.57                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.313468                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1376   r_free= 0.1824   ksol= 0.33   Bsol= 56.76   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.09,2.88,4.58,0.00,0.00,0.00); trace/3= 3.18                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.313190                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.845894              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 114.000  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.309952              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.728  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1376      final r-factor (work) = 0.1212          |
| start r-factor (free) = 0.1824      final r-factor (free) = 0.1670          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6535 = 2.85 * 0.50 * 5.3342 + 1.00 * 0.0632                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5604 = 2.85 * 0.50 * 5.2609 + 1.00 * 0.0744                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1212      final r-factor (work) = 0.1177          |
| start r-factor (free) = 0.1670      final r-factor (free) = 0.1657          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 17.4260 = 3.31 * 1.00 * 5.2609 + 1.00 * 0.0128                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 17.2511 = 3.31 * 1.00 * 5.2051 + 1.00 * 0.0226                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.079)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.59   12.56    None  None   None       |
|    all(noH): 2823   0      0.00    89.59   12.56    None  None   None       |
|    Sol.    : 438    0      0.34    89.59   37.13    None  None   None       |
|    Mac.    : 2385   0      0.00    79.83   8.05     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 -   8.959: 1736   |   5:    44.793 -  53.752:   98        |
|      1:     8.959 -  17.917:  522   |   6:    53.752 -  62.710:   63        |
|      2:    17.917 -  26.876:  164   |   7:    62.710 -  71.669:   32        |
|      3:    26.876 -  35.835:  108   |   8:    71.669 -  80.628:    7        |
|      4:    35.835 -  44.793:   92   |   9:    80.628 -  89.586:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1177 r_free = 0.1657             target_work(ml) = 5.201         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1176 r_free = 0.1657             target_work(ml) = 5.201         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1176   r_free= 0.1657   ksol= 0.33   Bsol= 56.76   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.09,2.88,4.58,0.00,0.00,0.00); trace/3= 3.18                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.200882                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1175   r_free= 0.1657   ksol= 0.33   Bsol= 56.76   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.39,3.04,4.60,0.00,0.00,0.00); trace/3= 3.35                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.201008                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.707187              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 146.288  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.073331              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.364   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1175      final r-factor (work) = 0.1188          |
| start r-factor (free) = 0.1657      final r-factor (free) = 0.1650          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5181 = 1.71 * 0.50 * 5.2059 + 1.00 * 0.0744                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5018 = 1.71 * 0.50 * 5.2059 + 1.00 * 0.0581                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1188      final r-factor (work) = 0.1186          |
| start r-factor (free) = 0.1650      final r-factor (free) = 0.1645          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6041 = 1.07 * 1.00 * 5.2059 + 1.00 * 0.0164                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6178 = 1.07 * 1.00 * 5.2042 + 1.00 * 0.0320                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.079)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.36   12.42    None  None   None       |
|    all(noH): 2823   0      0.00    90.36   12.42    None  None   None       |
|    Sol.    : 438    0      0.32    90.36   36.86    None  None   None       |
|    Mac.    : 2385   0      0.00    80.60   7.93     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.036: 1765   |   5:    45.178 -  54.213:   88        |
|      1:     9.036 -  18.071:  499   |   6:    54.213 -  63.249:   67        |
|      2:    18.071 -  27.107:  163   |   7:    63.249 -  72.284:   26        |
|      3:    27.107 -  36.142:  111   |   8:    72.284 -  81.320:    7        |
|      4:    36.142 -  45.178:   96   |   9:    81.320 -  90.355:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1186 r_free = 0.1645             target_work(ml) = 5.203         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1185 r_free = 0.1647             target_work(ml) = 5.203         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1185   r_free= 0.1647   ksol= 0.33   Bsol= 56.76   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.39,3.04,4.60,0.00,0.00,0.00); trace/3= 3.35                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.202690                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.7505 0.99   1401  154 0.1035 0.1347      5.4369      5.5744|
|  2:  4.7505 -  3.7906 0.99   1348  154 0.0872 0.1092      5.4576      5.6459|
|  3:  3.7906 -  3.3173 0.99   1322  145 0.1095 0.1551      5.4968      5.8681|
|  4:  3.3173 -  3.0167 0.99   1312  140 0.1241 0.1629      5.4746       5.633|
|  5:  3.0167 -  2.8019 0.99   1313  147 0.1379 0.1699      5.3745      5.5633|
|  6:  2.8019 -  2.6377 0.99   1297  148 0.1323 0.2155      5.2731      5.5754|
|  7:  2.6377 -  2.5062 0.99   1281  143 0.1373 0.1717       5.246      5.3875|
|  8:  2.5062 -  2.3976 0.98   1294  143 0.1242 0.1782      5.1457      5.3813|
|  9:  2.3976 -  2.3056 0.98   1288  144 0.1288 0.2084      5.0941      5.4378|
| 10:  2.3056 -  2.2263 0.98   1277  138 0.1216 0.1559      5.0256      5.1715|
| 11:  2.2263 -  2.1569 0.99   1284  147 0.1247 0.1915      5.0049      5.3144|
| 12:  2.1569 -  2.0954 0.97   1268  138 0.1228 0.1780      4.9417      5.2431|
| 13:  2.0954 -  2.0404 0.99   1270  137 0.1217 0.1811      4.8492      5.0651|
| 14:  2.0404 -  1.9907 0.52    675   81 0.1086 0.1830      4.7346      4.9995|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0183 -  4.7505  1401   154  0.93  10.01   0.97     0.94       8312.76|
|  2:  4.7505 -  3.7906  1348   154  0.95   8.31   1.01     0.99       9508.63|
|  3:  3.7906 -  3.3173  1322   145  0.93  11.49   1.02     1.02      10629.85|
|  4:  3.3173 -  3.0167  1312   140  0.92  13.69   1.01     0.99      10659.27|
|  5:  3.0167 -  2.8019  1313   147  0.90  16.54   1.00     0.97       9049.29|
|  6:  2.8019 -  2.6377  1297   148  0.89  17.53   0.98     0.95       8101.77|
|  7:  2.6377 -  2.5062  1281   143  0.90  16.70   0.98     0.95       7094.92|
|  8:  2.5062 -  2.3976  1294   143  0.90  16.64   0.99     0.96       6287.89|
|  9:  2.3976 -  2.3056  1288   144  0.90  16.89   1.00     0.96       5722.64|
| 10:  2.3056 -  2.2263  1277   138  0.89  17.13   0.99     0.94       5013.45|
| 11:  2.2263 -  2.1569  1284   147  0.89  17.72   0.99     0.95       5010.02|
| 12:  2.1569 -  2.0954  1268   138  0.90  16.77   1.00     0.98       4489.33|
| 13:  2.0954 -  2.0404  1270   137  0.89  17.31   0.98     0.96       3782.69|
| 14:  2.0404 -  1.9907   675    81  0.91  15.24   0.96     0.92       2869.96|
|alpha:            min =        0.92 max =            1.02 mean =         0.96|
|beta:             min =     2869.96 max =        10659.27 mean =      7076.33|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.92 mean =        15.07|
|phase err.(test): min =        0.00 max =           89.28 mean =        14.56|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1185   r_free= 0.1646   ksol= 0.33   Bsol= 60.20   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.93,-0.30,1.22,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.202779                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1185   r_free= 0.1646   ksol= 0.33   Bsol= 60.20   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.93,-0.30,1.22,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.202779                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.7505 0.99   1401  154 0.1035 0.1347      5.4372      5.5749|
|  2:  4.7505 -  3.7906 0.99   1348  154 0.0872 0.1093      5.4579      5.6459|
|  3:  3.7906 -  3.3173 0.99   1322  145 0.1095 0.1552      5.4969      5.8684|
|  4:  3.3173 -  3.0167 0.99   1312  140 0.1241 0.1629      5.4746      5.6331|
|  5:  3.0167 -  2.8019 0.99   1313  147 0.1378 0.1698      5.3744       5.563|
|  6:  2.8019 -  2.6377 0.99   1297  148 0.1323 0.2156      5.2731      5.5756|
|  7:  2.6377 -  2.5062 0.99   1281  143 0.1373 0.1717      5.2461      5.3877|
|  8:  2.5062 -  2.3976 0.98   1294  143 0.1242 0.1782       5.146      5.3815|
|  9:  2.3976 -  2.3056 0.98   1288  144 0.1287 0.2084      5.0941      5.4379|
| 10:  2.3056 -  2.2263 0.98   1277  138 0.1216 0.1559      5.0256      5.1715|
| 11:  2.2263 -  2.1569 0.99   1284  147 0.1247 0.1913      5.0047      5.3139|
| 12:  2.1569 -  2.0954 0.97   1268  138 0.1228 0.1779      4.9416      5.2425|
| 13:  2.0954 -  2.0404 0.99   1270  137 0.1217 0.1813      4.8493      5.0658|
| 14:  2.0404 -  1.9907 0.52    675   81 0.1086 0.1829      4.7351      4.9994|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0183 -  4.7505  1401   154  0.93  10.02   0.97     0.94       8321.47|
|  2:  4.7505 -  3.7906  1348   154  0.95   8.32   1.01     0.99       9515.11|
|  3:  3.7906 -  3.3173  1322   145  0.93  11.50   1.02     1.02      10635.05|
|  4:  3.3173 -  3.0167  1312   140  0.92  13.69   1.01     1.00      10660.53|
|  5:  3.0167 -  2.8019  1313   147  0.90  16.54   1.00     0.97       9050.73|
|  6:  2.8019 -  2.6377  1297   148  0.89  17.53   0.98     0.96       8100.89|
|  7:  2.6377 -  2.5062  1281   143  0.90  16.70   0.99     0.95       7097.38|
|  8:  2.5062 -  2.3976  1294   143  0.90  16.64   0.99     0.96       6291.78|
|  9:  2.3976 -  2.3056  1288   144  0.90  16.89   1.01     0.97       5725.02|
| 10:  2.3056 -  2.2263  1277   138  0.89  17.12   0.99     0.94       5011.45|
| 11:  2.2263 -  2.1569  1284   147  0.89  17.71   0.99     0.95       5006.26|
| 12:  2.1569 -  2.0954  1268   138  0.90  16.77   1.00     0.99       4487.49|
| 13:  2.0954 -  2.0404  1270   137  0.89  17.31   0.99     0.96       3783.62|
| 14:  2.0404 -  1.9907   675    81  0.91  15.25   0.97     0.92       2872.09|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     2872.09 max =        10660.53 mean =      7078.28|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.92 mean =        15.07|
|phase err.(test): min =        0.00 max =           89.28 mean =        14.56|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.079)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.43    93.79   15.85    None  None   None       |
|    all(noH): 2823   0      3.43    93.79   15.85    None  None   None       |
|    Sol.    : 438    0      3.75    93.79   40.29    None  None   None       |
|    Mac.    : 2385   0      3.43    84.03   11.37    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.433 -  12.468: 1765   |   5:    48.610 -  57.646:   88        |
|      1:    12.468 -  21.504:  499   |   6:    57.646 -  66.681:   67        |
|      2:    21.504 -  30.539:  163   |   7:    66.681 -  75.717:   26        |
|      3:    30.539 -  39.575:  111   |   8:    75.717 -  84.752:    7        |
|      4:    39.575 -  48.610:   96   |   9:    84.752 -  93.787:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 301         
Filter by distance & map next to the model:
   mapped sites are within: 0.227 - 4.430
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 292 from: 301
   mapped sites are within: 0.723 - 4.430

peak=   10.895 closest distance to " CB  VAL A 230 " =    1.457
peak=    5.896 closest distance to " CG  LEU A   5 " =    1.222
peak=    5.659 closest distance to " NH2 ARG A  56 " =    2.152
peak=    5.610 closest distance to " CG2 VAL A 296 " =    1.075
peak=    5.452 closest distance to " CB  GLN A 223 " =    1.485
peak=    5.413 closest distance to " CG  PRO A  54 " =    1.353
peak=    5.371 closest distance to " CG  LEU A 228 " =    1.225
peak=    5.342 closest distance to " CD2 LEU A   5 " =    1.171
peak=    5.238 closest distance to " CB  VAL A 296 " =    1.078
peak=    4.973 closest distance to " O   HOH Z 142 " =    1.795
peak=    4.954 closest distance to " NE2 GLN A  11 " =    1.080
peak=    4.863 closest distance to " CG  PRO A 198 " =    1.265
peak=    4.829 closest distance to " CB  PRO A  54 " =    1.039
peak=    4.801 closest distance to " CB  ARG A 275 " =    0.934
peak=    4.743 closest distance to " CG1 VAL A 296 " =    1.188
peak=    4.675 closest distance to " CZ  PHE A 218 " =    1.139
peak=    4.631 closest distance to " O   HOH Z 232 " =    2.298
peak=    4.554 closest distance to " O   HOH Z 265 " =    2.117
peak=    4.553 closest distance to " CG  PRO A 243 " =    1.163
peak=    4.507 closest distance to " CB  ARG A 190 " =    1.680
peak=    4.488 closest distance to " O   HOH Z 248 " =    1.235
peak=    4.459 closest distance to " CB  ASN A 148 " =    1.432
peak=    4.369 closest distance to " CB  GLN A 183 " =    1.257
peak=    4.350 closest distance to " O   HOH Z 402 " =    1.447
peak=    4.348 closest distance to " CB  ASN A 142 " =    1.191
peak=    4.319 closest distance to " CG  PRO A 213 " =    1.236
peak=    4.279 closest distance to " O   SER A  87 " =    2.373
peak=    4.275 closest distance to " CA  TYR A  30 " =    0.981
peak=    4.269 closest distance to " O   HOH Z 346 " =    1.547
peak=    4.262 closest distance to " O   HOH Z 126 " =    1.545
peak=    4.249 closest distance to " O   HOH Z 313 " =    1.845
peak=    4.248 closest distance to " CB  SER A  63 " =    1.187
peak=    4.248 closest distance to " O   HOH Z  78 " =    1.664
peak=    4.232 closest distance to " O   HOH Z 427 " =    3.027
peak=    4.231 closest distance to " O   HOH Z  43 " =    2.072
peak=    4.168 closest distance to " O   HOH Z 251 " =    1.618
peak=    4.137 closest distance to " CD2 TRP A 179 " =    1.295
peak=    4.117 closest distance to " O   HOH Z 188 " =    2.862
peak=    4.113 closest distance to " CZ3 TRP A 266 " =    1.144
peak=    4.108 closest distance to " CB  GLU A 277 " =    3.721
peak=    4.105 closest distance to " CA  ARG A  36 " =    1.053
peak=    4.099 closest distance to " O   HOH Z 369 " =    2.327
peak=    4.087 closest distance to " O   PRO A 198 " =    1.582
peak=    4.071 closest distance to " O   HOH Z 359 " =    1.635
peak=    4.070 closest distance to " CA  VAL A 230 " =    1.233
peak=    4.070 closest distance to " ND2 ASN A 187 " =    1.652
peak=    4.060 closest distance to " CA  ALA A  51 " =    0.968
peak=    4.060 closest distance to " CG  ARG A 138 " =    1.274
peak=    4.039 closest distance to " CE  LYS A  76 " =    0.898
peak=    4.028 closest distance to " ND2 ASN A 249 " =    0.910
peak=    4.027 closest distance to " O   HOH Z 411 " =    3.911
peak=    3.991 closest distance to " O   HOH Z 287 " =    2.072
peak=    3.991 closest distance to " CD2 LEU A 228 " =    1.232
peak=    3.988 closest distance to " O   HOH Z 126 " =    1.983
peak=    3.970 closest distance to " CB  ASN A  39 " =    0.930
peak=    3.963 closest distance to " O   HOH Z 303 " =    2.127
peak=    3.962 closest distance to " CZ  PHE A  38 " =    1.166
peak=    3.954 closest distance to " O   HOH Z 261 " =    2.233
peak=    3.949 closest distance to " CB  ARG A  79 " =    1.407
peak=    3.946 closest distance to " O   HOH Z 298 " =    1.760
peak=    3.945 closest distance to " O   HOH Z  61 " =    1.773
peak=    3.942 closest distance to " CB  ASP A 124 " =    0.825
peak=    3.937 closest distance to " CA  ARG A 195 " =    1.214
peak=    3.934 closest distance to " N   ASN A  39 " =    1.216
peak=    3.924 closest distance to " CB  VAL A 265 " =    1.245
peak=    3.920 closest distance to " O   HOH Z 425 " =    1.440
peak=    3.899 closest distance to " O   HOH Z 214 " =    2.659
peak=    3.891 closest distance to " CB  VAL A 202 " =    1.626
peak=    3.890 closest distance to " O  BHOH Z  74 " =    1.251
peak=    3.883 closest distance to " O   HOH Z 316 " =    3.081
peak=    3.873 closest distance to " CB  GLU A 128 " =    1.101
peak=    3.872 closest distance to " CG  MET A 185 " =    1.249
peak=    3.838 closest distance to " CD  ARG A 269 " =    0.990
peak=    3.828 closest distance to " CG1 ILE A  49 " =    1.630
peak=    3.824 closest distance to " O   HOH Z 130 " =    2.723
peak=    3.820 closest distance to " O   HOH Z 422 " =    2.654
peak=    3.804 closest distance to " CB  GLU A 152 " =    1.112
peak=    3.790 closest distance to " O   HOH Z 368 " =    2.348
peak=    3.789 closest distance to " O   HOH Z  19 " =    2.179
peak=    3.788 closest distance to " CD1 LEU A  96 " =    0.770
peak=    3.781 closest distance to " O   HOH Z 209 " =    2.298
peak=    3.776 closest distance to " O  BHOH Z 338 " =    2.344
peak=    3.768 closest distance to " CG  LEU A 167 " =    1.199
peak=    3.762 closest distance to " O   HOH Z 128 " =    1.245
peak=    3.761 closest distance to " O   HOH Z 353 " =    2.634
peak=    3.759 closest distance to " CB  TRP A 266 " =    1.060
peak=    3.756 closest distance to " CB  GLU A  46 " =    0.953
peak=    3.748 closest distance to " O   HOH Z  80 " =    1.889
peak=    3.746 closest distance to " O   HOH Z 371 " =    2.890
peak=    3.746 closest distance to " NH1AARG A 145 " =    1.291
peak=    3.736 closest distance to " CD  ARG A 159 " =    0.737
peak=    3.735 closest distance to " O   HOH Z  59 " =    2.248
peak=    3.735 closest distance to " O   HOH Z 234 " =    3.725
peak=    3.729 closest distance to " CB BVAL A  41 " =    1.275
peak=    3.728 closest distance to " O   HOH Z 273 " =    2.993
peak=    3.726 closest distance to " CA  ALA A 160 " =    0.954
peak=    3.721 closest distance to " CB  TRP A 179 " =    1.375
peak=    3.710 closest distance to " O   HOH Z 423 " =    1.760
peak=    3.703 closest distance to " O   HOH Z 403 " =    1.606
peak=    3.701 closest distance to " CA  ALA A 295 " =    1.056
peak=    3.699 closest distance to " CD  LYS A 166 " =    1.334
peak=    3.691 closest distance to " O   HOH Z 280 " =    2.965
peak=    3.688 closest distance to " OG BSER A 164 " =    2.260
peak=    3.686 closest distance to " CB  GLN A  89 " =    1.275
peak=    3.682 closest distance to " CB  ASN A 110 " =    1.142
peak=    3.680 closest distance to " O   HOH Z   9 " =    1.219
peak=    3.678 closest distance to " CG1 VAL A 153 " =    0.967
peak=    3.664 closest distance to " CB  THR A  31 " =    1.521
peak=    3.662 closest distance to " CG2 VAL A 257 " =    0.912
peak=    3.662 closest distance to " O   HOH Z 272 " =    1.840
peak=    3.659 closest distance to " CE1 TYR A 186 " =    1.266
peak=    3.644 closest distance to " CB  ASP A 140 " =    1.178
peak=    3.639 closest distance to " CB  ARG A  79 " =    0.934
peak=    3.634 closest distance to " CA  SER A  87 " =    1.013
peak=    3.627 closest distance to " O   HOH Z 365 " =    2.812
peak=    3.616 closest distance to " CB  ALA A 248 " =    1.363
peak=    3.610 closest distance to " CD1 ILE A 199 " =    1.037
peak=    3.604 closest distance to " CB  ALA A   9 " =    1.621
peak=    3.598 closest distance to " CD2 LEU A 297 " =    0.904
peak=    3.596 closest distance to " O   HOH Z 290 " =    1.083
peak=    3.595 closest distance to " CG  GLU A  37 " =    0.924
peak=    3.595 closest distance to " CB  LYS A 117 " =    1.196
peak=    3.588 closest distance to " CA  VAL A  41 " =    0.739
peak=    3.586 closest distance to " OE1 GLN A  55 " =    1.467
peak=    3.585 closest distance to " CG  GLN A  58 " =    0.844
peak=    3.573 closest distance to " O   HOH Z 158 " =    3.165
peak=    3.568 closest distance to " NZ  LYS A  48 " =    1.139
peak=    3.565 closest distance to " OD1 ASN A  69 " =    2.474
peak=    3.558 closest distance to " CD  LYS A  76 " =    2.084
peak=    3.557 closest distance to " O   HOH Z 368 " =    3.453
peak=    3.557 closest distance to " CB  THR A  52 " =    0.790
peak=    3.553 closest distance to " O   HOH Z  97 " =    2.311
peak=    3.544 closest distance to " O   ASN A  74 " =    1.476
peak=    3.542 closest distance to " CB  SER A   3 " =    1.315
peak=    3.539 closest distance to " NE2 GLN A  77 " =    3.278
peak=    3.530 closest distance to " O   HOH Z   4 " =    1.556
peak=    3.530 closest distance to " O   HOH Z 145 " =    2.337
peak=    3.523 closest distance to " NE2 HIS A 207 " =    1.121
peak=    3.518 closest distance to " O   HOH Z 247 " =    1.326
peak=    3.506 closest distance to " CB  ASN A 173 " =    1.083
peak=    3.503 closest distance to " CA  TYR A  30 " =    1.077
peak=    3.497 closest distance to " CB  PRO A  90 " =    1.111
peak=    3.496 closest distance to " NZ  LYS A 117 " =    3.127
peak=    3.496 closest distance to " NH2AARG A 145 " =    1.165
peak=    3.493 closest distance to " O   HOH Z  97 " =    2.122
peak=    3.493 closest distance to " N   GLY A 133 " =    3.728
peak=    3.491 closest distance to " OG  SER A 276 " =    1.348
peak=    3.489 closest distance to " CA  PHE A 283 " =    1.118
peak=    3.488 closest distance to " O   HOH Z 193 " =    1.445
peak=    3.486 closest distance to " CB  SER A 273 " =    0.945
peak=    3.478 closest distance to " CG2AVAL A 121 " =    2.306
peak=    3.478 closest distance to " O   HOH Z 285 " =    2.355
peak=    3.477 closest distance to " O   HOH Z 172 " =    3.818
peak=    3.476 closest distance to " CB  PRO A 243 " =    1.302
peak=    3.471 closest distance to " CA  MET A 105 " =    1.027
peak=    3.471 closest distance to " CA  ALA A 154 " =    1.009
peak=    3.470 closest distance to " CA  ALA A 291 " =    0.894
peak=    3.468 closest distance to " O   ASP A 124 " =    1.151
peak=    3.463 closest distance to " N   ALA A 256 " =    1.122
peak=    3.462 closest distance to " CA  ASP A 191 " =    1.208
peak=    3.457 closest distance to " O   HOH Z  40 " =    1.774
peak=    3.456 closest distance to " CB  SER A 210 " =    0.776
peak=    3.451 closest distance to " O   HOH Z 258 " =    2.009
peak=    3.451 closest distance to " N   PHE A 130 " =    1.259
peak=    3.446 closest distance to " O   GLN A  88 " =    1.634
peak=    3.445 closest distance to " O   HOH Z  63 " =    1.819
peak=    3.441 closest distance to " O   HOH Z 130 " =    2.265
peak=    3.440 closest distance to " O   HOH Z 171 " =    3.964
peak=    3.438 closest distance to " O   HOH Z 406 " =    1.497
peak=    3.438 closest distance to " O   HOH Z  68 " =    2.195
peak=    3.436 closest distance to " CA  ASN A 127 " =    1.113
peak=    3.434 closest distance to " CA  LEU A 282 " =    1.119
peak=    3.431 closest distance to " CB  ALA A 104 " =    0.723
peak=    3.430 closest distance to " O   HOH Z 180 " =    2.151
peak=    3.429 closest distance to " CB  ASN A 215 " =    1.194
peak=    3.429 closest distance to " CB  SER A  26 " =    1.861
peak=    3.425 closest distance to " CG  MET A 185 " =    0.979
peak=    3.423 closest distance to " CD2 LEU A   5 " =    0.741
peak=    3.409 closest distance to " CG AARG A 275 " =    1.242
peak=    3.403 closest distance to " OE2 GLU A  53 " =    1.901
peak=    3.401 closest distance to " O   HOH Z 102 " =    1.237
peak=    3.395 closest distance to " CA  ILE A 106 " =    0.755
peak=    3.390 closest distance to " CA  GLY A 211 " =    1.363
peak=    3.384 closest distance to " O   HOH Z 389 " =    1.867
peak=    3.374 closest distance to " CA  ASN A 215 " =    1.052
peak=    3.362 closest distance to " O   HOH Z  21 " =    1.745
peak=    3.362 closest distance to " CA  ALA A  21 " =    1.099
peak=    3.358 closest distance to " CD BLYS A 290 " =    0.997
peak=    3.358 closest distance to " CG  PHE A 204 " =    1.027
peak=    3.353 closest distance to " O   HOH Z  76 " =    1.019
peak=    3.352 closest distance to " CB  ASN A 187 " =    1.283
peak=    3.352 closest distance to " O   HOH Z 187 " =    2.343
peak=    3.349 closest distance to " O   THR A 182 " =    1.393
peak=    3.339 closest distance to " O   PRO A 213 " =    1.370
peak=    3.339 closest distance to " CA  LYS A 117 " =    1.308
peak=    3.338 closest distance to " O   HOH Z 299 " =    4.235
peak=    3.335 closest distance to " O   ALA A 165 " =    1.539
peak=    3.333 closest distance to " CA  TYR A 116 " =    1.515
peak=    3.329 closest distance to " CG2 ILE A 120 " =    1.202
peak=    3.328 closest distance to " O   HOH Z 238 " =    2.219
peak=    3.326 closest distance to " CE  LYS A  48 " =    1.168
peak=    3.323 closest distance to " N   SER A 135 " =    1.521
peak=    3.320 closest distance to " O   HOH Z 294 " =    1.528
peak=    3.320 closest distance to " CA  THR A 264 " =    0.764
peak=    3.317 closest distance to " O   HOH Z 392 " =    2.776
peak=    3.315 closest distance to " CE3 TRP A 150 " =    1.105
peak=    3.312 closest distance to " O   HOH Z 417 " =    3.147
peak=    3.309 closest distance to " CB  PHE A 204 " =    0.929
peak=    3.296 closest distance to " O   HOH Z 147 " =    1.758
peak=    3.293 closest distance to " CA  LYS A 290 " =    1.093
peak=    3.291 closest distance to " O   HOH Z 435 " =    2.056
peak=    3.289 closest distance to " CB  VAL A 268 " =    0.810
peak=    3.288 closest distance to " CB  SER A 212 " =    1.333
peak=    3.287 closest distance to " O   HOH Z 329 " =    4.181
peak=    3.286 closest distance to " O   HOH Z 130 " =    2.427
peak=    3.279 closest distance to " CG2AVAL A  72 " =    1.846
peak=    3.279 closest distance to " O   MET A 105 " =    1.911
peak=    3.277 closest distance to " CA  ASN A  74 " =    1.158
peak=    3.275 closest distance to " N   ASP A 162 " =    1.251
peak=    3.274 closest distance to " O   HOH Z 250 " =    1.275
peak=    3.273 closest distance to " CG2 ILE A 234 " =    0.990
peak=    3.271 closest distance to " CG1 ILE A  20 " =    1.253
peak=    3.270 closest distance to " CA  GLY A 267 " =    0.736
peak=    3.268 closest distance to " CB  ARG A 138 " =    0.783
peak=    3.268 closest distance to " CD1 ILE A  33 " =    1.713
peak=    3.267 closest distance to " CG2 ILE A  20 " =    1.497
peak=    3.266 closest distance to " CB  ALA A 227 " =    1.083
peak=    3.255 closest distance to " O   HOH Z   9 " =    1.941
peak=    3.252 closest distance to " CD1 LEU A 300 " =    1.126
peak=    3.248 closest distance to " CB  PRO A 198 " =    1.128
peak=    3.245 closest distance to " O   HOH Z  85 " =    1.231
peak=    3.245 closest distance to " O   HOH Z 361 " =    3.648
peak=    3.239 closest distance to " CG1 ILE A 151 " =    1.073
peak=    3.235 closest distance to " O   HOH Z 171 " =    2.520
peak=    3.234 closest distance to " CA  ASN A 217 " =    1.188
peak=    3.234 closest distance to " CA  ARG A 102 " =    1.166
peak=    3.228 closest distance to " CZ3 TRP A  85 " =    0.912
peak=    3.227 closest distance to " CB  SER A  62 " =    0.904
peak=    3.223 closest distance to " CD  LYS A 119 " =    2.001
peak=    3.223 closest distance to " CA  ARG A 139 " =    1.088
peak=    3.218 closest distance to " O   HOH Z 203 " =    1.760
peak=    3.217 closest distance to " O   HOH Z 345 " =    3.385
peak=    3.212 closest distance to " CB  ARG A 145 " =    0.882
peak=    3.212 closest distance to " O   HOH Z 166 " =    3.982
peak=    3.211 closest distance to " CB  ASP A 298 " =    1.216
peak=    3.210 closest distance to " CB  THR A 235 " =    1.434
peak=    3.206 closest distance to " O   HOH Z 337 " =    1.794
peak=    3.206 closest distance to " O   GLY A  91 " =    1.336
peak=    3.206 closest distance to " O   HOH Z  48 " =    1.609
peak=    3.204 closest distance to " CB  TRP A 150 " =    1.374
peak=    3.198 closest distance to " CZ3 TRP A 274 " =    4.430
peak=    3.198 closest distance to " OG  SER A 245 " =    1.539
peak=    3.187 closest distance to " CG2 ILE A 263 " =    1.014
peak=    3.185 closest distance to " O   HOH Z 293 " =    1.924
peak=    3.184 closest distance to " CA  GLU A 152 " =    0.899
peak=    3.182 closest distance to " O   ASP A 200 " =    1.665
peak=    3.177 closest distance to " O   PHE A  61 " =    1.354
peak=    3.176 closest distance to " CB  ALA A  43 " =    0.845
peak=    3.174 closest distance to " CA  ALA A 129 " =    1.455
peak=    3.172 closest distance to " O   ASN A 284 " =    1.815
peak=    3.170 closest distance to " O   HOH Z   3 " =    1.757
peak=    3.169 closest distance to " O   HOH Z 383 " =    1.911
peak=    3.167 closest distance to " CB  ALA A 242 " =    0.778
peak=    3.163 closest distance to " CA  ASP A 162 " =    0.966
peak=    3.157 closest distance to " O   HOH Z 394 " =    3.800
peak=    3.155 closest distance to " C   ALA A 299 " =    0.882
peak=    3.149 closest distance to " O   HOH Z 380 " =    1.865
peak=    3.145 closest distance to " CB  ALA A 114 " =    0.778
peak=    3.142 closest distance to " O   HOH Z 263 " =    1.640
peak=    3.133 closest distance to " O   HOH Z  10 " =    1.736
peak=    3.133 closest distance to " O   TRP A 274 " =    1.823
peak=    3.132 closest distance to " O   SER A 164 " =    1.311
peak=    3.131 closest distance to " CG BARG A 102 " =    1.841
peak=    3.126 closest distance to " O   HOH Z 337 " =    3.550
peak=    3.125 closest distance to " CB  TYR A 247 " =    0.979
peak=    3.113 closest distance to " CB  SER A 216 " =    0.846
peak=    3.109 closest distance to " O   PHE A 192 " =    1.398
peak=    3.107 closest distance to " CB  ARG A 219 " =    1.019
peak=    3.107 closest distance to " CB  ALA A 295 " =    1.337
peak=    3.098 closest distance to " CB  ALA A 291 " =    1.207
peak=    3.095 closest distance to " CB  HIS A 108 " =    0.817
peak=    3.089 closest distance to " CG2 THR A 220 " =    0.761
peak=    3.072 closest distance to " O   HOH Z 128 " =    2.362
peak=    3.068 closest distance to " CA  ILE A 234 " =    0.910
peak=    3.067 closest distance to " CG  LEU A 281 " =    1.057
peak=    3.067 closest distance to " CB  TYR A 172 " =    0.880
peak=    3.065 closest distance to " O   HOH Z 148 " =    3.424
peak=    3.048 closest distance to " CG1AVAL A 121 " =    0.766
peak=    3.047 closest distance to " CA  ASP A 253 " =    1.387
peak=    3.046 closest distance to " O   HOH Z 344 " =    2.929
peak=    3.041 closest distance to " O   HOH Z 109 " =    2.691
peak=    3.038 closest distance to " NH2BARG A 190 " =    1.890

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 213         
Filter by distance & map next to the model:
   mapped sites are within: 0.760 - 5.642
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 213 from: 213
   mapped sites are within: 0.760 - 5.642

peak=   -4.875 closest distance to " CD  ARG A  14 " =    3.328
peak=   -4.710 closest distance to " CD  GLN A  58 " =    1.055
peak=   -4.629 closest distance to " CG2 VAL A 230 " =    0.760
peak=   -4.574 closest distance to " CB  PRO A 243 " =    2.746
peak=   -4.388 closest distance to " CD  ARG A 156 " =    2.086
peak=   -4.265 closest distance to " C   HIS A 108 " =    1.170
peak=   -4.236 closest distance to " OG BSER A 134 " =    1.389
peak=   -4.194 closest distance to " O   VAL A  67 " =    2.617
peak=   -4.119 closest distance to " CZ2 TRP A  92 " =    2.838
peak=   -4.109 closest distance to " O   HOH Z 231 " =    2.185
peak=   -4.102 closest distance to " CG1 VAL A 112 " =    2.687
peak=   -4.093 closest distance to " CA  ASP A 298 " =    1.081
peak=   -4.093 closest distance to " CB  PHE A 192 " =    1.991
peak=   -4.090 closest distance to " O   HOH Z 166 " =    1.809
peak=   -4.080 closest distance to " CG1 VAL A 112 " =    2.768
peak=   -4.076 closest distance to " O   HOH Z 196 " =    2.245
peak=   -4.061 closest distance to " CG1 VAL A 296 " =    1.107
peak=   -4.013 closest distance to " CD2 TYR A 293 " =    1.962
peak=   -4.008 closest distance to " O   HOH Z 267 " =    5.642
peak=   -3.991 closest distance to " O   HOH Z 211 " =    1.324
peak=   -3.979 closest distance to " O   SER A 271 " =    2.122
peak=   -3.954 closest distance to " OE1 GLN A 223 " =    2.263
peak=   -3.948 closest distance to " CE3 TRP A 150 " =    2.245
peak=   -3.942 closest distance to " CG1 VAL A 250 " =    2.744
peak=   -3.932 closest distance to " O   PRO A 198 " =    1.168
peak=   -3.930 closest distance to " O   HOH Z 193 " =    1.150
peak=   -3.929 closest distance to " CE2 TYR A  30 " =    2.696
peak=   -3.906 closest distance to " O   HOH Z 394 " =    1.628
peak=   -3.855 closest distance to " O   HOH Z 103 " =    1.873
peak=   -3.849 closest distance to " CA  VAL A  67 " =    2.991
peak=   -3.824 closest distance to " CD1 LEU A 101 " =    2.388
peak=   -3.793 closest distance to " O   PRO A 163 " =    2.180
peak=   -3.788 closest distance to " CE2 TRP A  70 " =    2.109
peak=   -3.779 closest distance to " CB  ALA A 161 " =    2.578
peak=   -3.733 closest distance to " O   HOH Z 351 " =    1.528
peak=   -3.722 closest distance to " OG  SER A  97 " =    2.348
peak=   -3.687 closest distance to " O   HOH Z 216 " =    1.079
peak=   -3.686 closest distance to " OXT GLY A 302 " =    2.958
peak=   -3.682 closest distance to " O   HOH Z 198 " =    2.096
peak=   -3.621 closest distance to " O   HOH Z  73 " =    2.333
peak=   -3.614 closest distance to " ND2 ASN A  45 " =    1.139
peak=   -3.612 closest distance to " CG  ARG A 269 " =    2.281
peak=   -3.608 closest distance to " O   HOH Z 128 " =    2.365
peak=   -3.599 closest distance to " CB  ALA A 248 " =    2.292
peak=   -3.598 closest distance to " CA  GLY A 241 " =    2.386
peak=   -3.597 closest distance to " O   HOH Z  44 " =    2.444
peak=   -3.595 closest distance to " CG1 VAL A  67 " =    2.901
peak=   -3.581 closest distance to " NE  ARG A  66 " =    4.249
peak=   -3.572 closest distance to " OD1 ASN A 148 " =    1.363
peak=   -3.571 closest distance to " N   ALA A  43 " =    2.645
peak=   -3.558 closest distance to " CB  ALA A  10 " =    2.286
peak=   -3.552 closest distance to " OD1 ASN A 249 " =    2.525
peak=   -3.550 closest distance to " NE2 GLN A  11 " =    1.709
peak=   -3.547 closest distance to " O   HOH Z 359 " =    2.910
peak=   -3.546 closest distance to " CG  TRP A 266 " =    1.747
peak=   -3.546 closest distance to " CD1 ILE A 199 " =    2.451
peak=   -3.545 closest distance to " O   ASN A 252 " =    1.378
peak=   -3.543 closest distance to " O   HOH Z 357 " =    2.121
peak=   -3.534 closest distance to " CG2 VAL A 296 " =    1.278
peak=   -3.534 closest distance to " O   HOH Z 435 " =    2.809
peak=   -3.527 closest distance to " CZ3 TRP A 179 " =    1.246
peak=   -3.525 closest distance to " CG  GLU A 277 " =    1.262
peak=   -3.514 closest distance to " O   HOH Z 133 " =    1.297
peak=   -3.510 closest distance to " CB  ALA A  43 " =    2.584
peak=   -3.508 closest distance to " O   HOH Z 102 " =    1.664
peak=   -3.502 closest distance to " O   HOH Z  52 " =    1.693
peak=   -3.493 closest distance to " NE2 GLN A  88 " =    1.066
peak=   -3.489 closest distance to " CG  ASP A 231 " =    0.907
peak=   -3.489 closest distance to " NE2 GLN A 194 " =    1.917
peak=   -3.486 closest distance to " O   HOH Z 285 " =    1.950
peak=   -3.485 closest distance to " O   HOH Z 431 " =    1.978
peak=   -3.480 closest distance to " CG1 VAL A 125 " =    1.949
peak=   -3.475 closest distance to " CE BMET A  47 " =    1.364
peak=   -3.474 closest distance to " O   ALA A 227 " =    1.451
peak=   -3.473 closest distance to " CD  PRO A 243 " =    1.922
peak=   -3.473 closest distance to " ND2 ASN A 249 " =    2.397
peak=   -3.470 closest distance to " O   ILE A 106 " =    1.876
peak=   -3.465 closest distance to " CB  HIS A  86 " =    1.157
peak=   -3.462 closest distance to " N   ALA A 226 " =    2.012
peak=   -3.461 closest distance to " O   HOH Z 114 " =    3.079
peak=   -3.458 closest distance to " O   HOH Z 377 " =    2.026
peak=   -3.453 closest distance to " O   HOH Z 185 " =    2.455
peak=   -3.452 closest distance to " CE2 PHE A  61 " =    2.660
peak=   -3.447 closest distance to " CE  MET A 105 " =    2.410
peak=   -3.444 closest distance to " O   HOH Z  10 " =    1.505
peak=   -3.436 closest distance to " O   HOH Z  13 " =    1.841
peak=   -3.435 closest distance to " O   HOH Z 177 " =    1.785
peak=   -3.425 closest distance to " O   HOH Z 106 " =    1.847
peak=   -3.423 closest distance to " CE3 TRP A  70 " =    1.732
peak=   -3.414 closest distance to " N   THR A  52 " =    1.631
peak=   -3.406 closest distance to " O   GLY A  17 " =    1.252
peak=   -3.401 closest distance to " NE2 GLN A  88 " =    2.076
peak=   -3.400 closest distance to " CA  GLY A 241 " =    3.167
peak=   -3.396 closest distance to " O   HOH Z 252 " =    3.800
peak=   -3.395 closest distance to " O   HOH Z 136 " =    2.554
peak=   -3.394 closest distance to " O   HOH Z 371 " =    2.325
peak=   -3.394 closest distance to " O   HOH Z 290 " =    1.188
peak=   -3.390 closest distance to " O   HOH Z 191 " =    5.587
peak=   -3.381 closest distance to " CB  ALA A 248 " =    2.179
peak=   -3.377 closest distance to " O   HOH Z   9 " =    1.648
peak=   -3.373 closest distance to " O   HOH Z 128 " =    1.214
peak=   -3.361 closest distance to " O   HOH Z 165 " =    1.886
peak=   -3.360 closest distance to " O   PHE A 218 " =    1.443
peak=   -3.357 closest distance to " O   HOH Z 265 " =    2.414
peak=   -3.352 closest distance to " CG2 VAL A 189 " =    2.018
peak=   -3.343 closest distance to " O   HOH Z 174 " =    2.404
peak=   -3.340 closest distance to " O   HOH Z 295 " =    1.586
peak=   -3.338 closest distance to " O   HOH Z 154 " =    1.677
peak=   -3.335 closest distance to " ND2 ASN A 187 " =    1.512
peak=   -3.334 closest distance to " CA  GLY A 133 " =    2.344
peak=   -3.332 closest distance to " O   HOH Z 421 " =    3.184
peak=   -3.331 closest distance to " ND2 ASN A  45 " =    1.883
peak=   -3.331 closest distance to " O   HOH Z 251 " =    4.981
peak=   -3.330 closest distance to " O   HOH Z 275 " =    1.852
peak=   -3.329 closest distance to " CG  PRO A 243 " =    1.589
peak=   -3.326 closest distance to " CD2 PHE A  61 " =    2.107
peak=   -3.326 closest distance to " OG  SER A  87 " =    1.539
peak=   -3.325 closest distance to " O   HOH Z 131 " =    4.081
peak=   -3.324 closest distance to " OG1 THR A  82 " =    1.356
peak=   -3.322 closest distance to " CA  GLY A 203 " =    2.465
peak=   -3.322 closest distance to " O   SER A 210 " =    1.842
peak=   -3.319 closest distance to " C   MET A 188 " =    1.404
peak=   -3.316 closest distance to " O   ASP A  27 " =    2.103
peak=   -3.309 closest distance to " CD1 ILE A 239 " =    2.234
peak=   -3.309 closest distance to " O   MET A  40 " =    2.797
peak=   -3.305 closest distance to " CG  LYS A 193 " =    2.730
peak=   -3.304 closest distance to " O   HOH Z  38 " =    1.723
peak=   -3.295 closest distance to " CD  LYS A 289 " =    2.458
peak=   -3.295 closest distance to " CB  VAL A 230 " =    1.139
peak=   -3.292 closest distance to " O   HOH Z 123 " =    2.366
peak=   -3.288 closest distance to " CG1 VAL A 265 " =    2.389
peak=   -3.287 closest distance to " O   HOH Z 191 " =    3.437
peak=   -3.285 closest distance to " O   HOH Z  19 " =    2.319
peak=   -3.283 closest distance to " OG1 THR A  82 " =    1.540
peak=   -3.280 closest distance to " O   HOH Z   6 " =    2.219
peak=   -3.270 closest distance to " O   HOH Z 111 " =    1.669
peak=   -3.266 closest distance to " O   HOH Z 407 " =    2.987
peak=   -3.265 closest distance to " CG1BVAL A  72 " =    2.414
peak=   -3.260 closest distance to " C   ALA A 158 " =    1.286
peak=   -3.259 closest distance to " O   HOH Z  11 " =    1.862
peak=   -3.259 closest distance to " NH2AARG A 275 " =    5.086
peak=   -3.250 closest distance to " NE  ARG A  79 " =    1.130
peak=   -3.246 closest distance to " O   HOH Z  43 " =    1.690
peak=   -3.244 closest distance to " O   HOH Z 340 " =    1.799
peak=   -3.237 closest distance to " N   TRP A 274 " =    1.049
peak=   -3.236 closest distance to " OG  SER A  63 " =    1.156
peak=   -3.230 closest distance to " CE3 TRP A 274 " =    2.403
peak=   -3.228 closest distance to " CB  SER A 210 " =    1.011
peak=   -3.223 closest distance to " CB  ALA A  51 " =    1.943
peak=   -3.217 closest distance to " O   HOH Z 149 " =    2.130
peak=   -3.214 closest distance to " CB  ASP A 171 " =    2.199
peak=   -3.211 closest distance to " C   LEU A 143 " =    1.071
peak=   -3.209 closest distance to " O   HOH Z 238 " =    1.012
peak=   -3.208 closest distance to " CA  VAL A 296 " =    0.956
peak=   -3.207 closest distance to " O   HOH Z 423 " =    2.215
peak=   -3.207 closest distance to " SD BMET A  47 " =    1.211
peak=   -3.206 closest distance to " N   SER A 276 " =    1.412
peak=   -3.205 closest distance to " ND2 ASN A  69 " =    1.937
peak=   -3.202 closest distance to " CB  TRP A  85 " =    2.585
peak=   -3.197 closest distance to " CD2 HIS A 207 " =    2.242
peak=   -3.191 closest distance to " O   HOH Z 389 " =    2.084
peak=   -3.187 closest distance to " O   HOH Z 236 " =    1.522
peak=   -3.179 closest distance to " O   HOH Z 243 " =    2.076
peak=   -3.179 closest distance to " O   HOH Z 139 " =    3.096
peak=   -3.174 closest distance to " O   SER A 276 " =    1.759
peak=   -3.174 closest distance to " OE1 GLN A  88 " =    1.034
peak=   -3.172 closest distance to " NH2 ARG A  79 " =    1.534
peak=   -3.170 closest distance to " CG  LEU A   5 " =    0.957
peak=   -3.170 closest distance to " N   ALA A 248 " =    2.445
peak=   -3.170 closest distance to " CG  LEU A   5 " =    1.426
peak=   -3.167 closest distance to " O   HOH Z   6 " =    1.593
peak=   -3.167 closest distance to " CG1 VAL A  78 " =    2.743
peak=   -3.167 closest distance to " O   TRP A  70 " =    1.586
peak=   -3.166 closest distance to " CD  PRO A 213 " =    2.084
peak=   -3.163 closest distance to " CD2 PHE A 225 " =    1.070
peak=   -3.163 closest distance to " CB  ALA A 291 " =    2.266
peak=   -3.162 closest distance to " O   ALA A 180 " =    1.428
peak=   -3.157 closest distance to " O   GLY A 196 " =    1.228
peak=   -3.154 closest distance to " N   ALA A 248 " =    1.858
peak=   -3.148 closest distance to " CZ  PHE A  38 " =    2.463
peak=   -3.142 closest distance to " CH2 TRP A 150 " =    1.178
peak=   -3.139 closest distance to " ND2BASN A 224 " =    1.854
peak=   -3.138 closest distance to " N   ASP A 191 " =    1.147
peak=   -3.137 closest distance to " O   HOH Z 119 " =    2.645
peak=   -3.136 closest distance to " SG BCYS A 201 " =    2.400
peak=   -3.134 closest distance to " CE  LYS A  76 " =    2.561
peak=   -3.127 closest distance to " CG  ARG A 269 " =    2.037
peak=   -3.126 closest distance to " OD1 ASN A  39 " =    1.284
peak=   -3.124 closest distance to " NE2 GLN A 278 " =    1.850
peak=   -3.119 closest distance to " O   HOH Z  68 " =    1.323
peak=   -3.116 closest distance to " O   HOH Z 348 " =    2.273
peak=   -3.116 closest distance to " CG  PRO A 163 " =    2.576
peak=   -3.113 closest distance to " NE2 GLN A 240 " =    1.677
peak=   -3.111 closest distance to " OD2 ASP A  50 " =    2.155
peak=   -3.108 closest distance to " CB  PRO A 163 " =    2.495
peak=   -3.102 closest distance to " O   HOH Z  64 " =    1.701
peak=   -3.101 closest distance to " O   HOH Z 110 " =    1.441
peak=   -3.101 closest distance to " CZ  TYR A 169 " =    1.773
peak=   -3.099 closest distance to " CA  GLY A 133 " =    1.942
peak=   -3.095 closest distance to " CD  GLN A 223 " =    1.382
peak=   -3.092 closest distance to " CE1 TYR A 247 " =    2.611
peak=   -3.092 closest distance to " CG1 VAL A 197 " =    2.263
peak=   -3.090 closest distance to " O   HOH Z 231 " =    1.989
peak=   -3.088 closest distance to " O   HOH Z 166 " =    1.803
peak=   -3.088 closest distance to " CD  GLU A 236 " =    1.159
peak=   -3.087 closest distance to " N   LYS A 289 " =    1.611
peak=   -3.087 closest distance to " CD2 LEU A 237 " =    2.847
peak=   -3.084 closest distance to " O   HOH Z 139 " =    5.178
peak=   -3.079 closest distance to " OD1 ASN A 173 " =    1.383
peak=   -3.070 closest distance to " O   HOH Z 140 " =    1.168
peak=   -3.065 closest distance to " CA  SER A  62 " =    2.513
peak=   -3.054 closest distance to " O   HOH Z 326 " =    5.048
peak=   -3.018 closest distance to " ND2 ASN A 249 " =    2.239

================= 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    :  0.4565 0.4406   6.259127e+00   6.231022e+00
   1_bss:  0.4471 0.4277   6.251655e+00   6.218523e+00
   1_xyz:  0.3472 0.3695   6.083306e+00   6.118942e+00
   1_adp:  0.2957 0.3339   5.956078e+00   6.048363e+00
   1_occ:  0.2951 0.3355   5.955362e+00   6.050432e+00
   2_bss:  0.2904 0.3316   5.954530e+00   6.048114e+00
   2_xyz:  0.2113 0.2557   5.675237e+00   5.826723e+00
   2_adp:  0.1916 0.2394   5.600730e+00   5.771063e+00
   2_occ:  0.1914 0.2394   5.600872e+00   5.771982e+00
   3_bss:  0.1904 0.2400   5.601218e+00   5.772456e+00
   3_xyz:  0.1463 0.1910   5.362927e+00   5.565205e+00
   3_adp:  0.1376 0.1826   5.314007e+00   5.528447e+00
   3_occ:  0.1375 0.1824   5.313468e+00   5.528053e+00
   4_bss:  0.1376 0.1824   5.313190e+00   5.526382e+00
   4_xyz:  0.1212 0.1670   5.218181e+00   5.451691e+00
   4_adp:  0.1177 0.1657   5.200977e+00   5.441213e+00
   4_occ:  0.1176 0.1657   5.200882e+00   5.441195e+00
   5_bss:  0.1175 0.1657   5.201008e+00   5.441434e+00
   5_xyz:  0.1188 0.1650   5.205632e+00   5.440507e+00
   5_adp:  0.1186 0.1645   5.202953e+00   5.436619e+00
   5_occ:  0.1185 0.1647   5.202690e+00   5.436787e+00
   5_bss:  0.1185 0.1646   5.202779e+00   5.436861e+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:  0.327  12.430   6.828   7.989  11.770   0.000   0.000   0.000
   1_xyz:  0.327  12.430   6.828   7.989  11.770   0.000   0.000   0.000
   1_adp:  0.327  12.430   6.828   7.989  11.770   0.000   0.000   0.000
   1_occ:  0.327  12.430   6.828   7.989  11.770   0.000   0.000   0.000
   2_bss:  0.329  44.102   3.101   4.112   7.606   0.000   0.000   0.000
   2_xyz:  0.329  44.102   3.101   4.112   7.606   0.000   0.000   0.000
   2_adp:  0.329  44.102   3.101   4.112   7.606   0.000   0.000   0.000
   2_occ:  0.329  44.102   3.101   4.112   7.606   0.000   0.000   0.000
   3_bss:  0.317  56.763   2.216   3.198   5.286   0.000   0.000   0.000
   3_xyz:  0.317  56.763   2.216   3.198   5.286   0.000   0.000   0.000
   3_adp:  0.317  56.763   2.216   3.198   5.286   0.000   0.000   0.000
   3_occ:  0.317  56.763   2.216   3.198   5.286   0.000   0.000   0.000
   4_bss:  0.330  56.763   2.087   2.885   4.579   0.000   0.000   0.000
   4_xyz:  0.330  56.763   2.087   2.885   4.579   0.000   0.000   0.000
   4_adp:  0.330  56.763   2.087   2.885   4.579   0.000   0.000   0.000
   4_occ:  0.330  56.763   2.087   2.885   4.579   0.000   0.000   0.000
   5_bss:  0.330  56.763   2.394   3.039   4.602   0.000   0.000   0.000
   5_xyz:  0.330  56.763   2.394   3.039   4.602   0.000   0.000   0.000
   5_adp:  0.330  56.763   2.394   3.039   4.602   0.000   0.000   0.000
   5_occ:  0.330  56.763   2.394   3.039   4.602   0.000   0.000   0.000
   5_bss:  0.330  60.196  -0.925  -0.298   1.223   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  49.616 0.5269  0.5936    57382.967
   1_bss:  48.762 0.5365  0.7898    55084.749
   1_xyz:  40.407 0.6371  0.9070    37724.190
   1_adp:  35.222 0.6991  1.0006    30526.087
   1_occ:  35.313 0.6981  0.9982    30698.917
   2_bss:  35.029 0.7014  0.8751    30409.439
   2_xyz:  25.663 0.8045  0.9749    16958.645
   2_adp:  23.498 0.8276  0.9904    14916.463
   2_occ:  23.536 0.8272  0.9900    14945.020
   3_bss:  23.457 0.8281  0.9433    14962.174
   3_xyz:  18.113 0.8795  0.9750     9420.329
   3_adp:  17.114 0.8889  0.9744     8713.062
   3_occ:  17.103 0.8890  0.9745     8703.474
   4_bss:  17.061 0.8893  0.9617     8662.219
   4_xyz:  15.425 0.9033  0.9694     7324.122
   4_adp:  15.173 0.9056  0.9637     7159.004
   4_occ:  15.172 0.9057  0.9636     7155.536
   5_bss:  15.174 0.9056  0.9693     7161.265
   5_xyz:  15.100 0.9065  0.9693     7124.613
   5_adp:  15.012 0.9072  0.9646     7074.820
   5_occ:  15.018 0.9072  0.9644     7075.377
   5_bss:  15.020 0.9072  0.9674     7077.326
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.4178e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.4178e+01
   1_xyz:   1.647  0.013  0.106 17.954  0.006  4.113   1.3397e-01
   1_adp:   1.647  0.013  0.106 17.954  0.006  4.113   1.3397e-01
   1_occ:   1.647  0.013  0.106 17.954  0.006  4.113   1.3397e-01
   2_bss:   1.647  0.013  0.106 17.954  0.006  4.113   1.3397e-01
   2_xyz:   1.047  0.007  0.073 15.983  0.004  4.127   6.6768e-02
   2_adp:   1.047  0.007  0.073 15.983  0.004  4.127   6.6768e-02
   2_occ:   1.047  0.007  0.073 15.983  0.004  4.127   6.6768e-02
   3_bss:   1.047  0.007  0.073 15.983  0.004  4.127   6.6768e-02
   3_xyz:   1.017  0.007  0.078 15.841  0.004  4.130   6.3233e-02
   3_adp:   1.017  0.007  0.078 15.841  0.004  4.130   6.3233e-02
   3_occ:   1.017  0.007  0.078 15.841  0.004  4.130   6.3233e-02
   4_bss:   1.017  0.007  0.078 15.841  0.004  4.130   6.3233e-02
   4_xyz:   1.107  0.010  0.087 15.661  0.004  4.114   7.4426e-02
   4_adp:   1.107  0.010  0.087 15.661  0.004  4.114   7.4426e-02
   4_occ:   1.107  0.010  0.087 15.661  0.004  4.114   7.4426e-02
   5_bss:   1.107  0.010  0.087 15.661  0.004  4.114   7.4426e-02
   5_xyz:   0.960  0.007  0.077 15.272  0.003  4.115   5.8073e-02
   5_adp:   0.960  0.007  0.077 15.272  0.003  4.115   5.8073e-02
   5_occ:   0.960  0.007  0.077 15.272  0.003  4.115   5.8073e-02
   5_bss:   0.960  0.007  0.077 15.272  0.003  4.115   5.8073e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0237e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0237e+00
   1_xyz:  13.915  0.156  0.440 88.210  0.041  2.224   1.0191e-01
   1_adp:  13.915  0.156  0.440 88.210  0.041  2.224   1.0191e-01
   1_occ:  13.915  0.156  0.440 88.210  0.041  2.224   1.0191e-01
   2_bss:  13.915  0.156  0.440 88.210  0.041  2.224   1.0191e-01
   2_xyz:   6.975  0.057  0.280 82.889  0.027  2.311   6.1189e-02
   2_adp:   6.975  0.057  0.280 82.889  0.027  2.311   6.1189e-02
   2_occ:   6.975  0.057  0.280 82.889  0.027  2.311   6.1189e-02
   3_bss:   6.975  0.057  0.280 82.889  0.027  2.311   6.1189e-02
   3_xyz:   7.091  0.050  0.306 83.582  0.042  2.331   5.1837e-02
   3_adp:   7.091  0.050  0.306 83.582  0.042  2.331   5.1837e-02
   3_occ:   7.091  0.050  0.306 83.582  0.042  2.331   5.1837e-02
   4_bss:   7.091  0.050  0.306 83.582  0.042  2.331   5.1837e-02
   4_xyz:   7.315  0.055  0.499 82.911  0.041  2.363   5.2063e-02
   4_adp:   7.315  0.055  0.499 82.911  0.041  2.363   5.2063e-02
   4_occ:   7.315  0.055  0.499 82.911  0.041  2.363   5.2063e-02
   5_bss:   7.315  0.055  0.499 82.911  0.041  2.363   5.2063e-02
   5_xyz:   6.446  0.047  0.376 81.170  0.038  2.384   3.2907e-02
   5_adp:   6.446  0.047  0.376 81.170  0.038  2.384   3.2907e-02
   5_occ:   6.446  0.047  0.376 81.170  0.038  2.384   3.2907e-02
   5_bss:   6.446  0.047  0.376 81.170  0.038  2.384   3.2907e-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:  63.23   0.00  11.69  55.52   0.00   8.98  63.23   0.00  26.45
   1_occ:  63.23   0.00  11.69  55.52   0.00   8.98  63.23   0.00  26.45
   2_bss:  63.23   0.00  11.69  55.52   0.00   8.98  63.23   0.00  26.45
   2_xyz:  63.23   0.00  11.69  55.52   0.00   8.98  63.23   0.00  26.45
   2_adp:  66.74   0.00  11.89  60.02   0.00   8.20  66.74   0.00  32.00
   2_occ:  66.74   0.00  11.89  60.02   0.00   8.20  66.74   0.00  32.00
   3_bss:  66.74   0.00  11.89  60.02   0.00   8.20  66.74   0.00  32.00
   3_xyz:  66.74   0.00  11.89  60.02   0.00   8.20  66.74   0.00  32.00
   3_adp:  69.50   0.00  12.14  64.40   0.00   8.02  69.50   0.66  34.62
   3_occ:  69.50   0.00  12.14  64.40   0.00   8.02  69.50   0.66  34.62
   4_bss:  69.50   0.00  12.14  64.40   0.00   8.02  69.50   0.66  34.62
   4_xyz:  69.50   0.00  12.14  64.40   0.00   8.02  69.50   0.66  34.62
   4_adp:  89.59   0.00  12.56  79.83   0.00   8.05  89.59   0.34  37.13
   4_occ:  89.59   0.00  12.56  79.83   0.00   8.05  89.59   0.34  37.13
   5_bss:  89.59   0.00  12.56  79.83   0.00   8.05  89.59   0.34  37.13
   5_xyz:  89.59   0.00  12.56  79.83   0.00   8.05  89.59   0.34  37.13
   5_adp:  90.36   0.00  12.42  80.60   0.00   7.93  90.36   0.32  36.86
   5_occ:  90.36   0.00  12.42  80.60   0.00   7.93  90.36   0.32  36.86
   5_bss:  93.79   3.43  15.85  84.03   3.43  11.37  93.79   3.75  40.29
------------------------------------------------------------------------
 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:    1.264    0.010    0.412
   1_adp:    1.264    0.010    0.412
   1_occ:    1.264    0.010    0.412
   2_bss:    1.264    0.010    0.412
   2_xyz:    1.802    0.013    0.532
   2_adp:    1.802    0.013    0.532
   2_occ:    1.802    0.013    0.532
   3_bss:    1.802    0.013    0.532
   3_xyz:    1.764    0.042    0.589
   3_adp:    1.764    0.042    0.589
   3_occ:    1.764    0.042    0.589
   4_bss:    1.764    0.042    0.589
   4_xyz:    1.842    0.033    0.624
   4_adp:    1.842    0.033    0.624
   4_occ:    1.842    0.033    0.624
   5_bss:    1.842    0.033    0.624
   5_xyz:    1.935    0.048    0.630
   5_adp:    1.935    0.048    0.630
   5_occ:    1.935    0.048    0.630
   5_bss:    1.935    0.048    0.630
------------------------------------------------------------------------

CPU time actual refinement: 330.71


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_559/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_559/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_559/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_559/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_559/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 330.55 
  Macro-tasks:
    bulk solvent and scale       = 41.20  
    individual site refinement   = 134.36 
    weights calculation          = 32.68  
    collect and process          = 6.57   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 214.93 
  Micro-tasks:
    mask                            = 1.83   
    f_calc                          = 100.14 
    alpha_beta                      = 8.31   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 110.95 
    fmodel                         = 7.51   
    r_factors                      = 0.25   
    phase_errors                   = 10.62  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 241.07 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.663 micro seconds
Total CPU time: 5.74 minutes
from_scatterers_fft:    649 calls, 99.71 s
gradients_fft:          594 calls, 97.50 s

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

# Date 2008-01-16 Time 01:52:00 PST -0800 (1200477120.51 s)
Start R-work = 0.4565, R-free = 0.4406 (no bulk solvent and anisotropic scale)
Final R-work = 0.1355, R-free = 0.1808 (no bulk solvent and anisotropic scale)

Start R-work = 0.4471, R-free = 0.4277
Final R-work = 0.1185, R-free = 0.1646