# Date 2008-01-16 Time 02:57:06 PST -0800 (1200481026.61 s)
#phil __OFF__

Command line arguments: "../1038.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 15320
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1038

-------------------------------------------------------------------------------
  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: (71.3037, 47.1647, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.28, 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: (71.3037, 47.1647, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1358 1.9911
Completeness in resolution range: 0.958976
Completeness with d_max=infinity: 0.956074

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1358
                             d_min =   1.9911

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.1647, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1358 1.9911
Completeness in resolution range: 0.958976
Completeness with d_max=infinity: 0.956074

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1362 -  4.2608 [2140/2169]  1929   211   9.9%
  bin  2:  4.2608 -  3.3945 [2052/2068]  1845   207  10.1%
  bin  3:  3.3945 -  2.9691 [2039/2058]  1833   206  10.1%
  bin  4:  2.9691 -  2.6993 [2028/2058]  1827   201   9.9%
  bin  5:  2.6993 -  2.5067 [1999/2018]  1803   196   9.8%
  bin  6:  2.5067 -  2.3595 [2000/2025]  1794   206  10.3%
  bin  7:  2.3595 -  2.2417 [1956/1989]  1761   195  10.0%
  bin  8:  2.2417 -  2.1444 [1990/2021]  1792   198   9.9%
  bin  9:  2.1444 -  2.0621 [1984/2026]  1784   200  10.1%
  bin 10:  2.0621 -  1.9911 [1401/1995]  1262   139   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1038/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 12
        2.42 -     3.04: 2181
        3.04 -     3.66: 4634
        3.66 -     4.28: 8978
        4.28 -     4.90: 12281
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.806 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.253 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 208 " - " O   HOH Z 342 "  2.340 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28081 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_1038/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1038/model_refine_001.geo

CPU time processing inputs: 9.27


============================ 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 = 71.30375 47.16465 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4322   r_free= 0.4201   ksol= 0.00   Bsol= 0.00   scale= 0.818    |
|                                                                             |
| 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:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.227898                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1362 -  4.7524 0.99   1388  155 0.3669 0.3472      6.5305      6.4561|
|  2:  4.7524 -  3.7917 0.99   1347  146 0.3276 0.3463      6.6466      6.6721|
|  3:  3.7917 -  3.3181 0.99   1316  147 0.3745 0.3461      6.5544      6.5654|
|  4:  3.3181 -  3.0174 0.99   1313  153 0.4062 0.3744      6.4504      6.3511|
|  5:  3.0174 -  2.8026 0.99   1294  139 0.4492 0.4658      6.3131      6.3709|
|  6:  2.8026 -  2.6382 0.99   1287  146 0.4600 0.4670      6.2288      6.1982|
|  7:  2.6382 -  2.5067 0.99   1292  135 0.4845 0.4688      6.2255      6.1944|
|  8:  2.5067 -  2.3981 0.98   1268  150 0.4801 0.4553      6.1339      6.1145|
|  9:  2.3981 -  2.3061 0.98   1270  142 0.4733 0.4824      6.0954      6.1038|
| 10:  2.3061 -  2.2267 0.99   1282  136 0.4859 0.4813       6.084      6.0509|
| 11:  2.2267 -  2.1573 0.99   1282  144 0.4836 0.4580      6.0206      6.0199|
| 12:  2.1573 -  2.0958 0.97   1246  139 0.4916 0.5025      5.9637       6.009|
| 13:  2.0958 -  2.0408 0.99   1270  141 0.5125 0.4880      5.8794       5.829|
| 14:  2.0408 -  1.9911 0.60    775   86 0.5014 0.4288      5.8349      5.6994|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1362 -  4.7524  1388   155  0.74  30.66   0.81     0.77      56770.28|
|  2:  4.7524 -  3.7917  1347   146  0.78  28.19   0.91     0.82      72468.76|
|  3:  3.7917 -  3.3181  1316   147  0.70  35.07   0.86     0.79      76938.57|
|  4:  3.3181 -  3.0174  1313   153  0.64  40.72   0.84     0.71      71993.87|
|  5:  3.0174 -  2.8026  1294   139  0.54  48.77   0.76     0.63      64137.05|
|  6:  2.8026 -  2.6382  1287   146  0.51  51.18   0.76     0.58      57703.09|
|  7:  2.6382 -  2.5067  1292   135  0.51  51.34   0.75     0.56      51971.44|
|  8:  2.5067 -  2.3981  1268   150  0.49  52.77   0.74     0.57      47491.81|
|  9:  2.3981 -  2.3061  1270   142  0.50  51.79   0.75     0.56      42010.18|
| 10:  2.3061 -  2.2267  1282   136  0.49  52.90   0.78     0.56      39168.27|
| 11:  2.2267 -  2.1573  1282   144  0.47  54.65   0.78     0.53      36685.19|
| 12:  2.1573 -  2.0958  1246   139  0.45  56.55   0.77     0.52      36483.79|
| 13:  2.0958 -  2.0408  1270   141  0.44  56.97   0.73     0.52      30715.36|
| 14:  2.0408 -  1.9911   775    86  0.53  49.98   0.73     0.57      22389.77|
|alpha:            min =        0.52 max =            0.82 mean =         0.62|
|beta:             min =    22389.77 max =        76938.57 mean =     51573.00|
|figures of merit: min =        0.00 max =            1.00 mean =         0.56|
|phase err.(work): min =        0.00 max =           90.00 mean =        46.94|
|phase err.(test): min =        0.00 max =           89.97 mean =        46.89|
|-----------------------------------------------------------------------------|

============================== 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 = 8.564056              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 74.744   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.630358              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 75.769   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       22 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      162 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      676 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1503 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2609 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3870 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5020 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6564 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7636 |
|-----------------------------------------------------------------------------|
|-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 |       54.105 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.631 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.108)------------------------------------------|
|    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 = 12.108)------------------------------------------|
|    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 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4401   r_free= 0.4276   ksol= 0.00   Bsol= 0.00   scale= 0.787    |
|                                                                             |
| 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:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.231809                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4243   r_free= 0.4097   ksol= 0.30   Bsol= 20.00   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.59,8.15,7.60,0.00,0.00,0.00); trace/3= 8.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.223891                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.954102              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.727   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.638181              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.401   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4243      final r-factor (work) = 0.3157          |
| start r-factor (free) = 0.4097      final r-factor (free) = 0.3469          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 78.9105 = 7.95 * 0.50 * 6.2372 + 1.00 * 54.1049                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.2521 = 7.95 * 0.50 * 6.0672 + 1.00 * 0.1224                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3157      final r-factor (work) = 0.2553          |
| start r-factor (free) = 0.3469      final r-factor (free) = 0.2951          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8867 = 0.64 * 1.00 * 6.0672 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7783 = 0.64 * 1.00 * 5.9027 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.108)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    54.63   9.99     None  None   None       |
|    all(noH): 2823   0      0.00    54.63   9.99     None  None   None       |
|    Sol.    : 438    0      0.00    54.63   26.24    None  None   None       |
|    Mac.    : 2385   0      0.00    49.60   7.01     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   5.463: 1244   |   5:    27.313 -  32.776:  107        |
|      1:     5.463 -  10.925:  763   |   6:    32.776 -  38.238:   76        |
|      2:    10.925 -  16.388:  294   |   7:    38.238 -  43.701:   51        |
|      3:    16.388 -  21.850:  138   |   8:    43.701 -  49.163:   28        |
|      4:    21.850 -  27.313:  115   |   9:    49.163 -  54.626:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2553 r_free = 0.2951             target_work(ml) = 5.837         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2547 r_free = 0.2950             target_work(ml) = 5.836         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2547   r_free= 0.2950   ksol= 0.30   Bsol= 20.00   scale= 1.068   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.59,8.15,7.60,0.00,0.00,0.00); trace/3= 8.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.835656                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2516   r_free= 0.2885   ksol= 0.33   Bsol= 50.12   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.43,4.93,5.17,0.00,0.00,0.00); trace/3= 5.17                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.835058                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.644301              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.701   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.363186              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 118.704  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2516      final r-factor (work) = 0.1661          |
| start r-factor (free) = 0.2885      final r-factor (free) = 0.2104          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.8397 = 4.64 * 0.50 * 5.9073 + 1.00 * 0.1221                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.2174 = 4.64 * 0.50 * 5.6611 + 1.00 * 0.0714                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1661      final r-factor (work) = 0.1507          |
| start r-factor (free) = 0.2104      final r-factor (free) = 0.1955          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0773 = 0.36 * 1.00 * 5.6611 + 1.00 * 0.0212                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0291 = 0.36 * 1.00 * 5.4218 + 1.00 * 0.0599                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 12     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.108)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.16   10.68    None  None   None       |
|    all(noH): 2823   0      0.00    86.16   10.68    None  None   None       |
|    Sol.    : 438    0      0.57    55.98   30.37    None  None   None       |
|    Mac.    : 2385   0      0.00    86.16   7.06     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.616: 1799   |   5:    43.082 -  51.698:   57        |
|      1:     8.616 -  17.233:  499   |   6:    51.698 -  60.315:   11        |
|      2:    17.233 -  25.849:  160   |   7:    60.315 -  68.931:    0        |
|      3:    25.849 -  34.466:  147   |   8:    68.931 -  77.547:    0        |
|      4:    34.466 -  43.082:  149   |   9:    77.547 -  86.164:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1507 r_free = 0.1955             target_work(ml) = 5.385         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1506 r_free = 0.1955             target_work(ml) = 5.384         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1506   r_free= 0.1955   ksol= 0.33   Bsol= 50.12   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.43,4.93,5.17,0.00,0.00,0.00); trace/3= 5.17                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.384440                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1496   r_free= 0.1935   ksol= 0.33   Bsol= 50.12   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.73,3.63,4.24,0.00,0.00,0.00); trace/3= 3.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.384093                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.162946              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.171  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.097088              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.183   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1496      final r-factor (work) = 0.1248          |
| start r-factor (free) = 0.1935      final r-factor (free) = 0.1690          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6626 = 3.16 * 0.50 * 5.4324 + 1.00 * 0.0714                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4635 = 3.16 * 0.50 * 5.3064 + 1.00 * 0.0716                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1248      final r-factor (work) = 0.1187          |
| start r-factor (free) = 0.1690      final r-factor (free) = 0.1647          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8362 = 1.10 * 1.00 * 5.3064 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7311 = 1.10 * 1.00 * 5.2114 + 1.00 * 0.0137                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.108)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.20   11.61    None  None   None       |
|    all(noH): 2823   0      0.00    72.20   11.61    None  None   None       |
|    Sol.    : 438    0      0.34    70.80   34.73    None  None   None       |
|    Mac.    : 2385   0      0.00    72.20   7.37     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.220: 1606   |   5:    36.102 -  43.322:   80        |
|      1:     7.220 -  14.441:  584   |   6:    43.322 -  50.542:   89        |
|      2:    14.441 -  21.661:  175   |   7:    50.542 -  57.763:   60        |
|      3:    21.661 -  28.881:  101   |   8:    57.763 -  64.983:   22        |
|      4:    28.881 -  36.102:   94   |   9:    64.983 -  72.203:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1187 r_free = 0.1647             target_work(ml) = 5.199         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1187 r_free = 0.1647             target_work(ml) = 5.199         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1187   r_free= 0.1647   ksol= 0.33   Bsol= 50.12   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.73,3.63,4.24,0.00,0.00,0.00); trace/3= 3.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.198786                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1189   r_free= 0.1651   ksol= 0.32   Bsol= 50.12   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.42,3.43,4.12,0.00,0.00,0.00); trace/3= 3.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.199723                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.676865              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 136.694  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.251137              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.411  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1189      final r-factor (work) = 0.1175          |
| start r-factor (free) = 0.1651      final r-factor (free) = 0.1634          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4411 = 1.68 * 0.50 * 5.2115 + 1.00 * 0.0716                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4159 = 1.68 * 0.50 * 5.1964 + 1.00 * 0.0591                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1175      final r-factor (work) = 0.1181          |
| start r-factor (free) = 0.1634      final r-factor (free) = 0.1612          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3197 = 0.25 * 1.00 * 5.1964 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6286 = 0.25 * 1.00 * 5.1943 + 1.00 * 0.3241                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.108)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    73.36   11.36    None  None   None       |
|    all(noH): 2823   0      0.00    73.36   11.36    None  None   None       |
|    Sol.    : 438    0      0.77    70.41   33.59    None  None   None       |
|    Mac.    : 2385   0      0.00    73.36   7.27     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.336: 1652   |   5:    36.680 -  44.016:   78        |
|      1:     7.336 -  14.672:  563   |   6:    44.016 -  51.352:   80        |
|      2:    14.672 -  22.008:  174   |   7:    51.352 -  58.688:   49        |
|      3:    22.008 -  29.344:   97   |   8:    58.688 -  66.024:   14        |
|      4:    29.344 -  36.680:  105   |   9:    66.024 -  73.360:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1181 r_free = 0.1612             target_work(ml) = 5.186         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1180 r_free = 0.1612             target_work(ml) = 5.186         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1180   r_free= 0.1612   ksol= 0.32   Bsol= 50.12   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.42,3.43,4.12,0.00,0.00,0.00); trace/3= 3.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.186021                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1180   r_free= 0.1611   ksol= 0.32   Bsol= 50.12   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.28,3.37,4.09,0.00,0.00,0.00); trace/3= 3.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.186011                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.212367              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 154.977  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 6.493063              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.633   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1180      final r-factor (work) = 0.1135          |
| start r-factor (free) = 0.1611      final r-factor (free) = 0.1584          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8042 = 2.21 * 0.50 * 5.1936 + 1.00 * 0.0591                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7859 = 2.21 * 0.50 * 5.1681 + 1.00 * 0.0690                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1135      final r-factor (work) = 0.1122          |
| start r-factor (free) = 0.1584      final r-factor (free) = 0.1601          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 33.6660 = 6.49 * 1.00 * 5.1681 + 1.00 * 0.1092                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 33.4725 = 6.49 * 1.00 * 5.1528 + 1.00 * 0.0149                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.108)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.94   11.79    None  None   None       |
|    all(noH): 2823   0      0.00    88.94   11.79    None  None   None       |
|    Sol.    : 438    0      0.51    81.76   35.46    None  None   None       |
|    Mac.    : 2385   0      0.00    88.94   7.44     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.894: 1806   |   5:    44.470 -  53.364:   92        |
|      1:     8.894 -  17.788:  476   |   6:    53.364 -  62.257:   56        |
|      2:    17.788 -  26.682:  151   |   7:    62.257 -  71.151:   13        |
|      3:    26.682 -  35.576:  111   |   8:    71.151 -  80.045:   10        |
|      4:    35.576 -  44.470:  102   |   9:    80.045 -  88.939:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1122 r_free = 0.1601             target_work(ml) = 5.161         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1122 r_free = 0.1603             target_work(ml) = 5.161         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1122   r_free= 0.1603   ksol= 0.32   Bsol= 50.12   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.28,3.37,4.09,0.00,0.00,0.00); trace/3= 3.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.161320                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1362 -  4.7524 0.99   1388  155 0.0967 0.1302      5.3642      5.5162|
|  2:  4.7524 -  3.7917 0.99   1347  146 0.0855 0.1105      5.4309      5.6265|
|  3:  3.7917 -  3.3181 0.99   1316  147 0.1054 0.1525      5.4738      5.8702|
|  4:  3.3181 -  3.0174 0.99   1313  153 0.1185 0.1542      5.4579        5.58|
|  5:  3.0174 -  2.8026 0.99   1294  139 0.1343 0.1844      5.3443       5.579|
|  6:  2.8026 -  2.6382 0.99   1287  146 0.1224 0.1844      5.2266      5.4916|
|  7:  2.6382 -  2.5067 0.99   1292  135 0.1280 0.1670       5.196      5.3947|
|  8:  2.5067 -  2.3981 0.98   1268  150 0.1177 0.1778      5.0884      5.3679|
|  9:  2.3981 -  2.3061 0.98   1270  142 0.1197 0.1871       5.074      5.3721|
| 10:  2.3061 -  2.2267 0.99   1282  136 0.1126 0.1760      4.9812      5.2243|
| 11:  2.2267 -  2.1573 0.99   1282  144 0.1172 0.1839      4.9689      5.3336|
| 12:  2.1573 -  2.0958 0.97   1246  139 0.1098 0.1589      4.8842      5.0983|
| 13:  2.0958 -  2.0408 0.99   1270  141 0.1187 0.1828      4.8206       5.107|
| 14:  2.0408 -  1.9911 0.60    775   86 0.1083 0.1758      4.7069      4.9487|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1362 -  4.7524  1388   155  0.94   8.80   0.97     0.95       6916.27|
|  2:  4.7524 -  3.7917  1347   146  0.95   7.79   1.01     0.99       8857.80|
|  3:  3.7917 -  3.3181  1316   147  0.93  11.46   1.02     1.01      10458.90|
|  4:  3.3181 -  3.0174  1313   153  0.92  13.80   1.00     0.99      10612.26|
|  5:  3.0174 -  2.8026  1294   139  0.89  16.55   0.99     0.96       8686.95|
|  6:  2.8026 -  2.6382  1287   146  0.90  16.30   0.98     0.95       7513.35|
|  7:  2.6382 -  2.5067  1292   135  0.90  15.94   0.98     0.95       6580.44|
|  8:  2.5067 -  2.3981  1268   150  0.90  16.03   0.98     0.96       5759.51|
|  9:  2.3981 -  2.3061  1270   142  0.90  16.16   1.00     0.97       5524.20|
| 10:  2.3061 -  2.2267  1282   136  0.90  15.96   0.98     0.94       4597.77|
| 11:  2.2267 -  2.1573  1282   144  0.89  17.03   0.99     0.95       4687.78|
| 12:  2.1573 -  2.0958  1246   139  0.92  14.86   0.99     0.97       4034.31|
| 13:  2.0958 -  2.0408  1270   141  0.89  17.26   0.99     0.97       3641.47|
| 14:  2.0408 -  1.9911   775    86  0.90  15.89   0.97     0.93       2858.65|
|alpha:            min =        0.93 max =            1.01 mean =         0.96|
|beta:             min =     2858.65 max =        10612.26 mean =      6621.17|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.91 mean =        14.45|
|phase err.(test): min =        0.00 max =           88.26 mean =        13.93|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1122   r_free= 0.1603   ksol= 0.32   Bsol= 53.83   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.28,-0.22,0.50,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.161242                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1122   r_free= 0.1603   ksol= 0.32   Bsol= 53.83   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.28,-0.22,0.50,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.161242                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1362 -  4.7524 0.99   1388  155 0.0965 0.1305      5.3629      5.5168|
|  2:  4.7524 -  3.7917 0.99   1347  146 0.0856 0.1106      5.4319      5.6275|
|  3:  3.7917 -  3.3181 0.99   1316  147 0.1054 0.1525      5.4742      5.8702|
|  4:  3.3181 -  3.0174 0.99   1313  153 0.1185 0.1542      5.4577        5.58|
|  5:  3.0174 -  2.8026 0.99   1294  139 0.1343 0.1843       5.344      5.5785|
|  6:  2.8026 -  2.6382 0.99   1287  146 0.1224 0.1844      5.2264      5.4914|
|  7:  2.6382 -  2.5067 0.99   1292  135 0.1280 0.1670       5.196      5.3948|
|  8:  2.5067 -  2.3981 0.98   1268  150 0.1177 0.1778      5.0884      5.3678|
|  9:  2.3981 -  2.3061 0.98   1270  142 0.1197 0.1871       5.074      5.3722|
| 10:  2.3061 -  2.2267 0.99   1282  136 0.1126 0.1760      4.9813      5.2242|
| 11:  2.2267 -  2.1573 0.99   1282  144 0.1172 0.1839      4.9688      5.3335|
| 12:  2.1573 -  2.0958 0.97   1246  139 0.1097 0.1590       4.884      5.0983|
| 13:  2.0958 -  2.0408 0.99   1270  141 0.1187 0.1828      4.8205      5.1066|
| 14:  2.0408 -  1.9911 0.60    775   86 0.1083 0.1757      4.7069      4.9486|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1362 -  4.7524  1388   155  0.94   8.82   0.97     0.95       6913.05|
|  2:  4.7524 -  3.7917  1347   146  0.95   7.80   1.01     0.99       8869.32|
|  3:  3.7917 -  3.3181  1316   147  0.93  11.47   1.02     1.01      10472.22|
|  4:  3.3181 -  3.0174  1313   153  0.92  13.80   1.01     0.99      10608.55|
|  5:  3.0174 -  2.8026  1294   139  0.89  16.54   0.99     0.97       8682.04|
|  6:  2.8026 -  2.6382  1287   146  0.90  16.30   0.98     0.96       7509.18|
|  7:  2.6382 -  2.5067  1292   135  0.90  15.94   0.99     0.95       6578.88|
|  8:  2.5067 -  2.3981  1268   150  0.90  16.03   0.99     0.96       5758.33|
|  9:  2.3981 -  2.3061  1270   142  0.90  16.16   1.00     0.97       5524.33|
| 10:  2.3061 -  2.2267  1282   136  0.90  15.96   0.99     0.94       4596.60|
| 11:  2.2267 -  2.1573  1282   144  0.89  17.03   1.00     0.96       4686.98|
| 12:  2.1573 -  2.0958  1246   139  0.92  14.85   1.00     0.98       4032.09|
| 13:  2.0958 -  2.0408  1270   141  0.89  17.26   1.00     0.98       3640.34|
| 14:  2.0408 -  1.9911   775    86  0.90  15.89   0.97     0.94       2858.77|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2858.77 max =        10608.55 mean =      6621.29|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.91 mean =        14.45|
|phase err.(test): min =        0.00 max =           88.25 mean =        13.94|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.108)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.72    92.66   15.50    None  None   None       |
|    all(noH): 2823   0      3.72    92.66   15.50    None  None   None       |
|    Sol.    : 438    0      4.23    85.48   39.18    None  None   None       |
|    Mac.    : 2385   0      3.72    92.66   11.16    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.719 -  12.613: 1806   |   5:    48.189 -  57.083:   92        |
|      1:    12.613 -  21.507:  476   |   6:    57.083 -  65.977:   56        |
|      2:    21.507 -  30.401:  151   |   7:    65.977 -  74.871:   13        |
|      3:    30.401 -  39.295:  111   |   8:    74.871 -  83.765:   10        |
|      4:    39.295 -  48.189:  102   |   9:    83.765 -  92.659:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 315         
Filter by distance & map next to the model:
   mapped sites are within: 0.339 - 4.700
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 306 from: 315
   mapped sites are within: 0.713 - 4.700

peak=   10.355 closest distance to " CG2 VAL A 230 " =    1.315
peak=    6.933 closest distance to " CG2 VAL A 296 " =    1.107
peak=    6.263 closest distance to " CG  LEU A   5 " =    1.153
peak=    6.232 closest distance to " NH2 ARG A  56 " =    2.262
peak=    5.669 closest distance to " CB  GLN A 223 " =    1.450
peak=    5.584 closest distance to " CG  LEU A 228 " =    1.150
peak=    5.245 closest distance to " CD2 LEU A   5 " =    1.125
peak=    5.118 closest distance to " CB  VAL A 230 " =    1.166
peak=    5.003 closest distance to " CB  GLN A 183 " =    1.311
peak=    4.882 closest distance to " O   HOH Z 232 " =    2.315
peak=    4.843 closest distance to " CB  VAL A 296 " =    1.068
peak=    4.833 closest distance to " CB  SER A  63 " =    1.326
peak=    4.767 closest distance to " NE2 GLN A  11 " =    1.092
peak=    4.602 closest distance to " OD1 ASN A  69 " =    2.658
peak=    4.601 closest distance to " CG  PRO A 213 " =    1.196
peak=    4.563 closest distance to " O   HOH Z 369 " =    2.194
peak=    4.547 closest distance to " C   PRO A 198 " =    1.518
peak=    4.504 closest distance to " O   HOH Z 298 " =    1.801
peak=    4.473 closest distance to " O   HOH Z 427 " =    3.074
peak=    4.456 closest distance to " O   HOH Z 316 " =    3.085
peak=    4.407 closest distance to " CG  PRO A 198 " =    1.204
peak=    4.396 closest distance to " O   HOH Z 126 " =    1.980
peak=    4.373 closest distance to " CB  TYR A 169 " =    0.720
peak=    4.365 closest distance to " CB  ARG A 275 " =    0.863
peak=    4.301 closest distance to " O   HOH Z 368 " =    2.279
peak=    4.298 closest distance to " CB  GLU A 128 " =    1.073
peak=    4.267 closest distance to " CB  TRP A 266 " =    0.985
peak=    4.245 closest distance to " CB  ASN A 148 " =    1.320
peak=    4.227 closest distance to " CG  PRO A 243 " =    1.160
peak=    4.221 closest distance to " O   HOH Z 142 " =    1.528
peak=    4.203 closest distance to " O   HOH Z 403 " =    1.706
peak=    4.201 closest distance to " CD2 LEU A 228 " =    1.138
peak=    4.197 closest distance to " O   HOH Z  54 " =    2.372
peak=    4.197 closest distance to " O   HOH Z 158 " =    3.034
peak=    4.127 closest distance to " CA  TYR A  30 " =    0.945
peak=    4.109 closest distance to " O   HOH Z 303 " =    2.076
peak=    4.106 closest distance to " CB  ASP A 140 " =    1.012
peak=    4.103 closest distance to " CB  GLU A 152 " =    1.190
peak=    4.088 closest distance to " O   HOH Z 423 " =    1.724
peak=    4.087 closest distance to " O   HOH Z 272 " =    1.872
peak=    4.074 closest distance to " O   HOH Z  78 " =    1.720
peak=    4.053 closest distance to " O   HOH Z 425 " =    1.361
peak=    4.035 closest distance to " CD  ARG A  66 " =    2.634
peak=    4.020 closest distance to " CB  GLU A 277 " =    3.660
peak=    4.011 closest distance to " CB  PRO A  54 " =    0.747
peak=    4.000 closest distance to " O   HOH Z 203 " =    1.770
peak=    3.997 closest distance to " CB  SER A   3 " =    1.350
peak=    3.991 closest distance to " O   HOH Z  61 " =    1.668
peak=    3.976 closest distance to " CB  VAL A 265 " =    1.268
peak=    3.966 closest distance to " NH2 ARG A 156 " =    1.095
peak=    3.956 closest distance to " CB  LEU A 228 " =    1.264
peak=    3.949 closest distance to " CB  ARG A  79 " =    1.483
peak=    3.949 closest distance to " O   HOH Z 280 " =    2.949
peak=    3.939 closest distance to " O   HOH Z 236 " =    1.892
peak=    3.936 closest distance to " CZ  PHE A 218 " =    1.069
peak=    3.935 closest distance to " O   HOH Z 261 " =    1.958
peak=    3.926 closest distance to " O   HOH Z  15 " =    2.241
peak=    3.901 closest distance to " CD ALYS A 290 " =    0.973
peak=    3.891 closest distance to " O   HOH Z  63 " =    1.869
peak=    3.887 closest distance to " O   MET A 105 " =    1.823
peak=    3.886 closest distance to " O   SER A  87 " =    2.314
peak=    3.874 closest distance to " CB BVAL A  41 " =    1.204
peak=    3.869 closest distance to " CA  THR A 264 " =    0.713
peak=    3.867 closest distance to " NH1AARG A 145 " =    1.112
peak=    3.867 closest distance to " CG2 THR A 221 " =    1.189
peak=    3.867 closest distance to " O   HOH Z 189 " =    2.846
peak=    3.866 closest distance to " CB  ARG A 190 " =    1.641
peak=    3.837 closest distance to " O   HOH Z  43 " =    1.984
peak=    3.827 closest distance to " O   HOH Z 234 " =    3.695
peak=    3.825 closest distance to " O   HOH Z 411 " =    3.699
peak=    3.818 closest distance to " CA  ALA A  51 " =    1.030
peak=    3.811 closest distance to " CB  LEU A 143 " =    1.193
peak=    3.804 closest distance to " O   HOH Z  88 " =    3.288
peak=    3.796 closest distance to " O   HOH Z  97 " =    2.052
peak=    3.778 closest distance to " CG  MET A 185 " =    1.221
peak=    3.777 closest distance to " CA  THR A 221 " =    0.941
peak=    3.774 closest distance to " CG1 ILE A  33 " =    1.223
peak=    3.774 closest distance to " ND2 ASN A 187 " =    1.442
peak=    3.773 closest distance to " O   HOH Z  80 " =    1.702
peak=    3.772 closest distance to " ND1 HIS A  81 " =    1.708
peak=    3.767 closest distance to " O   HOH Z  44 " =    2.213
peak=    3.749 closest distance to " CD  ARG A 159 " =    0.802
peak=    3.740 closest distance to " O   HOH Z 112 " =    1.687
peak=    3.733 closest distance to " O   HOH Z 193 " =    2.093
peak=    3.733 closest distance to " O   HOH Z 214 " =    2.179
peak=    3.730 closest distance to " O   HOH Z 193 " =    1.801
peak=    3.723 closest distance to " O   HOH Z 425 " =    2.030
peak=    3.719 closest distance to " CD2 LEU A   5 " =    0.713
peak=    3.719 closest distance to " O   HOH Z 290 " =    0.911
peak=    3.717 closest distance to " CB  ALA A 161 " =    0.869
peak=    3.715 closest distance to " ND2 ASN A 249 " =    1.884
peak=    3.709 closest distance to " OG BSER A 164 " =    2.194
peak=    3.706 closest distance to " O   HOH Z 247 " =    1.305
peak=    3.704 closest distance to " CD  ARG A 269 " =    0.944
peak=    3.703 closest distance to " CB  TRP A 179 " =    1.436
peak=    3.702 closest distance to " OD2 ASP A 286 " =    2.843
peak=    3.693 closest distance to " O   HOH Z 134 " =    1.372
peak=    3.692 closest distance to " CA  MET A  40 " =    1.151
peak=    3.690 closest distance to " O   HOH Z 263 " =    1.639
peak=    3.680 closest distance to " CB  VAL A 202 " =    1.604
peak=    3.679 closest distance to " CA  ALA A  21 " =    1.229
peak=    3.675 closest distance to " CB  ASN A  39 " =    0.909
peak=    3.675 closest distance to " CZ  PHE A 192 " =    0.992
peak=    3.669 closest distance to " O   HOH Z  19 " =    2.403
peak=    3.660 closest distance to " CD1 LEU A 300 " =    1.165
peak=    3.654 closest distance to " CA  LYS A 117 " =    1.261
peak=    3.653 closest distance to " CA  ASN A 215 " =    1.256
peak=    3.652 closest distance to " CB  ALA A   9 " =    1.602
peak=    3.650 closest distance to " CG1BVAL A  72 " =    1.646
peak=    3.647 closest distance to " CB  SER A 212 " =    1.087
peak=    3.644 closest distance to " CB  SER A 216 " =    0.900
peak=    3.641 closest distance to " CB  ASN A 187 " =    1.222
peak=    3.639 closest distance to " O   HOH Z 437 " =    1.807
peak=    3.639 closest distance to " O   HOH Z  20 " =    1.789
peak=    3.633 closest distance to " CA  ALA A 158 " =    1.203
peak=    3.625 closest distance to " O   HOH Z 346 " =    1.603
peak=    3.619 closest distance to " O   HOH Z 180 " =    2.078
peak=    3.619 closest distance to " O   HOH Z 197 " =    2.945
peak=    3.617 closest distance to " O   HOH Z 135 " =    1.905
peak=    3.612 closest distance to " O   HOH Z  97 " =    2.676
peak=    3.609 closest distance to " O   HOH Z 245 " =    1.350
peak=    3.607 closest distance to " CB  ARG A 139 " =    0.887
peak=    3.602 closest distance to " CA  ARG A 195 " =    1.225
peak=    3.602 closest distance to " O   HOH Z 133 " =    1.706
peak=    3.598 closest distance to " CE1 TYR A 186 " =    1.306
peak=    3.591 closest distance to " O   HOH Z 371 " =    3.315
peak=    3.588 closest distance to " CA  ALA A 295 " =    1.092
peak=    3.573 closest distance to " O   GLN A 278 " =    1.339
peak=    3.562 closest distance to " OG  SER A  97 " =    2.689
peak=    3.559 closest distance to " O   HOH Z 147 " =    1.708
peak=    3.553 closest distance to " CG  LEU A 167 " =    1.188
peak=    3.550 closest distance to " O   TRP A 274 " =    1.882
peak=    3.549 closest distance to " NZ  LYS A 117 " =    3.218
peak=    3.543 closest distance to " CB  THR A  82 " =    1.399
peak=    3.542 closest distance to " CA  ARG A  36 " =    1.107
peak=    3.539 closest distance to " O   HOH Z 193 " =    1.672
peak=    3.533 closest distance to " O   HOH Z 126 " =    1.599
peak=    3.532 closest distance to " CA  ALA A 291 " =    0.939
peak=    3.516 closest distance to " O   ALA A 158 " =    1.425
peak=    3.512 closest distance to " O   HOH Z 133 " =    2.377
peak=    3.510 closest distance to " CG1 VAL A 153 " =    0.980
peak=    3.508 closest distance to " N   VAL A 126 " =    1.394
peak=    3.507 closest distance to " O   HOH Z 172 " =    3.657
peak=    3.506 closest distance to " O   HOH Z 329 " =    3.877
peak=    3.502 closest distance to " O   HOH Z 285 " =    3.132
peak=    3.498 closest distance to " CB  THR A 157 " =    1.155
peak=    3.493 closest distance to " O   ALA A 165 " =    1.440
peak=    3.493 closest distance to " O   HOH Z 273 " =    2.667
peak=    3.491 closest distance to " O   HOH Z  68 " =    2.177
peak=    3.490 closest distance to " CG  GLN A  88 " =    1.059
peak=    3.481 closest distance to " CB  ALA A 291 " =    1.429
peak=    3.479 closest distance to " O   HOH Z 383 " =    2.108
peak=    3.474 closest distance to " CE  LYS A  76 " =    0.836
peak=    3.473 closest distance to " O   ASP A 124 " =    1.077
peak=    3.473 closest distance to " CG2 VAL A 257 " =    0.855
peak=    3.470 closest distance to " CD2 LEU A 255 " =    1.575
peak=    3.465 closest distance to " OG  SER A  22 " =    2.888
peak=    3.463 closest distance to " O   HOH Z 344 " =    2.986
peak=    3.462 closest distance to " CD  LYS A 166 " =    1.292
peak=    3.458 closest distance to " CB  MET A  40 " =    0.829
peak=    3.453 closest distance to " CB  THR A  31 " =    1.719
peak=    3.452 closest distance to " CB  ALA A 248 " =    1.475
peak=    3.451 closest distance to " O   HOH Z 128 " =    2.117
peak=    3.449 closest distance to " CB  MET A  47 " =    1.069
peak=    3.435 closest distance to " O   HOH Z 402 " =    1.460
peak=    3.434 closest distance to " CD1 LEU A   5 " =    1.337
peak=    3.432 closest distance to " CD  ARG A  66 " =    2.442
peak=    3.431 closest distance to " O   HOH Z 368 " =    3.586
peak=    3.431 closest distance to " CA  LEU A 282 " =    1.044
peak=    3.429 closest distance to " O   HOH Z 132 " =    2.649
peak=    3.429 closest distance to " O   HOH Z 345 " =    3.460
peak=    3.426 closest distance to " CG1 ILE A  49 " =    1.493
peak=    3.425 closest distance to " CD1 ILE A  33 " =    1.595
peak=    3.416 closest distance to " O   HOH Z 116 " =    1.816
peak=    3.411 closest distance to " CB  ASN A 110 " =    1.287
peak=    3.410 closest distance to " CB  TRP A 150 " =    1.356
peak=    3.406 closest distance to " O   HOH Z  21 " =    1.665
peak=    3.404 closest distance to " O   HOH Z 163 " =    1.520
peak=    3.398 closest distance to " O   HOH Z 227 " =    1.665
peak=    3.394 closest distance to " O   HOH Z 426 " =    1.548
peak=    3.393 closest distance to " O   HOH Z 305 " =    3.581
peak=    3.391 closest distance to " O   HOH Z 171 " =    2.341
peak=    3.386 closest distance to " OG1 THR A 294 " =    2.354
peak=    3.380 closest distance to " CA  VAL A  41 " =    0.881
peak=    3.379 closest distance to " O   HOH Z 248 " =    1.729
peak=    3.376 closest distance to " CB  LYS A 117 " =    1.148
peak=    3.375 closest distance to " O   HOH Z  63 " =    1.272
peak=    3.375 closest distance to " O   HOH Z 171 " =    3.856
peak=    3.368 closest distance to " N   ASN A  39 " =    1.262
peak=    3.362 closest distance to " CB  ASN A 142 " =    1.134
peak=    3.362 closest distance to " CB  VAL A 268 " =    0.856
peak=    3.358 closest distance to " CB  GLN A  88 " =    1.262
peak=    3.356 closest distance to " O   HOH Z 422 " =    2.658
peak=    3.354 closest distance to " CG2 THR A 220 " =    0.962
peak=    3.354 closest distance to " CA  ASP A 140 " =    1.197
peak=    3.351 closest distance to " O   HOH Z 271 " =    2.552
peak=    3.349 closest distance to " CD1 ILE A 106 " =    0.956
peak=    3.349 closest distance to " O   HOH Z 145 " =    1.967
peak=    3.346 closest distance to " ND1 HIS A  86 " =    1.714
peak=    3.342 closest distance to " O   HOH Z 295 " =    1.468
peak=    3.339 closest distance to " O   HOH Z 420 " =    1.948
peak=    3.331 closest distance to " O   HOH Z 128 " =    2.189
peak=    3.324 closest distance to " N   ASN A 127 " =    1.230
peak=    3.324 closest distance to " CB  HIS A 108 " =    0.825
peak=    3.321 closest distance to " OE1 GLU A 152 " =    0.864
peak=    3.321 closest distance to " ND2 ASN A 110 " =    1.676
peak=    3.319 closest distance to " CA  SER A 146 " =    1.776
peak=    3.319 closest distance to " O   HOH Z  10 " =    1.812
peak=    3.318 closest distance to " O   HOH Z 102 " =    1.263
peak=    3.312 closest distance to " N   SER A 135 " =    1.489
peak=    3.311 closest distance to " CD2 HIS A  81 " =    0.949
peak=    3.309 closest distance to " NH2 ARG A  79 " =    1.415
peak=    3.308 closest distance to " O   HOH Z 271 " =    2.065
peak=    3.304 closest distance to " CG BARG A 275 " =    1.470
peak=    3.293 closest distance to " O   HOH Z 353 " =    2.764
peak=    3.284 closest distance to " O   HOH Z  48 " =    1.696
peak=    3.283 closest distance to " O   HOH Z 423 " =    2.938
peak=    3.281 closest distance to " OH  TYR A 214 " =    1.229
peak=    3.280 closest distance to " CG1 ILE A 151 " =    1.014
peak=    3.277 closest distance to " NH2 ARG A 219 " =    1.834
peak=    3.277 closest distance to " N   PHE A 130 " =    1.255
peak=    3.274 closest distance to " O   HOH Z 250 " =    1.354
peak=    3.269 closest distance to " NZ  LYS A  48 " =    1.438
peak=    3.269 closest distance to " CB  ALA A  34 " =    0.773
peak=    3.267 closest distance to " CG2 ILE A  20 " =    1.420
peak=    3.267 closest distance to " O   HOH Z 281 " =    4.700
peak=    3.265 closest distance to " O   HOH Z 250 " =    1.313
peak=    3.265 closest distance to " CD1 LEU A 228 " =    1.811
peak=    3.259 closest distance to " O   HOH Z 155 " =    3.283
peak=    3.259 closest distance to " CE  LYS A  48 " =    1.067
peak=    3.258 closest distance to " C   SER A  32 " =    1.047
peak=    3.255 closest distance to " CG1 VAL A 296 " =    1.228
peak=    3.243 closest distance to " CG2 ILE A 234 " =    0.898
peak=    3.240 closest distance to " NE2 HIS A 207 " =    1.426
peak=    3.239 closest distance to " CG BARG A 102 " =    1.812
peak=    3.237 closest distance to " O   HOH Z 299 " =    4.273
peak=    3.236 closest distance to " CB  LEU A 255 " =    0.762
peak=    3.234 closest distance to " OG BSER A 210 " =    1.225
peak=    3.232 closest distance to " O   HOH Z  58 " =    1.226
peak=    3.229 closest distance to " O   HOH Z 174 " =    2.624
peak=    3.228 closest distance to " CA  SER A  87 " =    0.992
peak=    3.226 closest distance to " O   HOH Z 409 " =    3.313
peak=    3.225 closest distance to " CB  ALA A 100 " =    1.257
peak=    3.225 closest distance to " O   HOH Z 435 " =    2.012
peak=    3.224 closest distance to " O   HOH Z 213 " =    1.771
peak=    3.223 closest distance to " CA  ASP A 191 " =    0.763
peak=    3.223 closest distance to " O  BHOH Z 338 " =    2.373
peak=    3.222 closest distance to " O   ARG A  56 " =    2.798
peak=    3.216 closest distance to " CA  ALA A 154 " =    1.173
peak=    3.212 closest distance to " CA  ASN A 176 " =    1.145
peak=    3.209 closest distance to " O   HOH Z  59 " =    2.251
peak=    3.208 closest distance to " O   HOH Z 236 " =    1.654
peak=    3.206 closest distance to " OD1 ASP A 231 " =    1.901
peak=    3.205 closest distance to " O   HOH Z 189 " =    3.059
peak=    3.202 closest distance to " O   HOH Z 403 " =    1.406
peak=    3.201 closest distance to " O   HOH Z 327 " =    1.832
peak=    3.201 closest distance to " O   HOH Z 313 " =    1.789
peak=    3.201 closest distance to " O   HOH Z 302 " =    1.965
peak=    3.199 closest distance to " CA  GLY A 211 " =    1.309
peak=    3.194 closest distance to " O   HOH Z 109 " =    2.604
peak=    3.190 closest distance to " CA  LYS A 290 " =    1.289
peak=    3.185 closest distance to " O   HOH Z  68 " =    1.485
peak=    3.181 closest distance to " O   HOH Z 407 " =    2.337
peak=    3.179 closest distance to " CB  SER A 273 " =    0.833
peak=    3.175 closest distance to " O   HOH Z 411 " =    1.828
peak=    3.174 closest distance to " CD2 TRP A 179 " =    1.416
peak=    3.170 closest distance to " CG  MET A 185 " =    1.127
peak=    3.169 closest distance to " O   HOH Z   1 " =    2.141
peak=    3.166 closest distance to " O   ALA A   1 " =    1.594
peak=    3.163 closest distance to " CA  TYR A 116 " =    1.456
peak=    3.162 closest distance to " CB  ILE A 120 " =    1.385
peak=    3.161 closest distance to " CB  ALA A 104 " =    0.773
peak=    3.158 closest distance to " CG2 VAL A 197 " =    1.072
peak=    3.155 closest distance to " NE  ARG A  79 " =    1.212
peak=    3.155 closest distance to " OD1 ASN A 217 " =    1.638
peak=    3.153 closest distance to " O   HOH Z 391 " =    2.991
peak=    3.151 closest distance to " CA  ALA A 233 " =    1.487
peak=    3.151 closest distance to " CB  TYR A 116 " =    0.892
peak=    3.151 closest distance to " O   HOH Z 201 " =    3.146
peak=    3.149 closest distance to " O   HOH Z  62 " =    2.373
peak=    3.148 closest distance to " CB  ALA A 242 " =    0.884
peak=    3.146 closest distance to " CB  GLN A 205 " =    1.076
peak=    3.142 closest distance to " CG  GLU A  37 " =    0.828
peak=    3.141 closest distance to " O   HOH Z 187 " =    2.292
peak=    3.140 closest distance to " O   HOH Z 325 " =    2.323
peak=    3.138 closest distance to " O   HOH Z 291 " =    1.586
peak=    3.133 closest distance to " O   HOH Z  48 " =    1.350
peak=    3.132 closest distance to " CD  LYS A 119 " =    1.617
peak=    3.126 closest distance to " O   HOH Z 365 " =    3.021
peak=    3.126 closest distance to " CD2 TYR A  30 " =    1.274
peak=    3.119 closest distance to " O   HOH Z 313 " =    1.739
peak=    3.116 closest distance to " O   HOH Z 341 " =    1.926
peak=    3.114 closest distance to " O   THR A  31 " =    1.527
peak=    3.112 closest distance to " CA  VAL A 126 " =    0.912
peak=    3.112 closest distance to " NH1 ARG A  56 " =    1.049
peak=    3.110 closest distance to " O   HOH Z 128 " =    1.835
peak=    3.107 closest distance to " CB  ASN A 215 " =    1.157
peak=    3.103 closest distance to " CA  ALA A 299 " =    0.958
peak=    3.093 closest distance to " O   HOH Z  61 " =    1.618
peak=    3.091 closest distance to " OE2 GLU A  53 " =    2.028
peak=    3.087 closest distance to " CA  ILE A 106 " =    0.795
peak=    3.085 closest distance to " CA  ARG A 102 " =    1.179
peak=    3.072 closest distance to " O   HOH Z 213 " =    2.565
peak=    3.061 closest distance to " O   GLU A   2 " =    1.736
peak=    3.020 closest distance to " O   HOH Z  49 " =    2.556
peak=    3.019 closest distance to " CA  THR A 221 " =    1.432

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 210         
Filter by distance & map next to the model:
   mapped sites are within: 0.784 - 5.544
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 209 from: 210
   mapped sites are within: 0.784 - 5.544

peak=   -4.933 closest distance to " CG2 VAL A 230 " =    0.937
peak=   -4.531 closest distance to " CD  ARG A 156 " =    1.977
peak=   -4.516 closest distance to " O   HOH Z 266 " =    4.932
peak=   -4.268 closest distance to " SG  CYS A 254 " =    3.274
peak=   -4.066 closest distance to " CB  ALA A 161 " =    2.634
peak=   -4.042 closest distance to " O   HOH Z  52 " =    1.613
peak=   -4.018 closest distance to " OE1 GLN A 223 " =    2.153
peak=   -3.997 closest distance to " O   HOH Z 231 " =    1.979
peak=   -3.985 closest distance to " CE2 TYR A  30 " =    2.761
peak=   -3.943 closest distance to " CG2 VAL A 296 " =    1.381
peak=   -3.935 closest distance to " CB  PRO A 243 " =    2.653
peak=   -3.921 closest distance to " CA  ASP A 298 " =    1.039
peak=   -3.903 closest distance to " CG2BVAL A  41 " =    2.586
peak=   -3.889 closest distance to " C   HIS A 108 " =    1.150
peak=   -3.888 closest distance to " NH2AARG A 275 " =    5.341
peak=   -3.887 closest distance to " O   PRO A 163 " =    2.106
peak=   -3.865 closest distance to " OG BSER A 134 " =    1.109
peak=   -3.854 closest distance to " O   HOH Z 196 " =    2.234
peak=   -3.837 closest distance to " CD2 LEU A 300 " =    2.829
peak=   -3.830 closest distance to " O   HOH Z 118 " =    3.119
peak=   -3.824 closest distance to " CG1 VAL A 250 " =    2.714
peak=   -3.792 closest distance to " CG1 VAL A 112 " =    2.637
peak=   -3.782 closest distance to " CG1 VAL A 112 " =    2.959
peak=   -3.774 closest distance to " C   ALA A 158 " =    1.259
peak=   -3.773 closest distance to " CD1 LEU A 228 " =    2.351
peak=   -3.756 closest distance to " O   HOH Z 426 " =    1.662
peak=   -3.749 closest distance to " O   HOH Z 394 " =    1.538
peak=   -3.745 closest distance to " CG  ASP A 231 " =    0.784
peak=   -3.721 closest distance to " CD  GLN A  58 " =    1.125
peak=   -3.713 closest distance to " OG  SER A  97 " =    2.212
peak=   -3.711 closest distance to " N   ALA A 226 " =    2.122
peak=   -3.700 closest distance to " CD1 LEU A 101 " =    2.553
peak=   -3.699 closest distance to " O   HOH Z  73 " =    2.165
peak=   -3.687 closest distance to " O   HOH Z 166 " =    1.949
peak=   -3.685 closest distance to " O   HOH Z 290 " =    1.274
peak=   -3.684 closest distance to " OD1 ASN A 148 " =    1.502
peak=   -3.684 closest distance to " O   HOH Z 292 " =    4.573
peak=   -3.674 closest distance to " SD BMET A  47 " =    0.884
peak=   -3.671 closest distance to " CG  ARG A 269 " =    2.459
peak=   -3.671 closest distance to " O   HOH Z 389 " =    1.918
peak=   -3.666 closest distance to " OXT GLY A 302 " =    3.042
peak=   -3.664 closest distance to " O   HOH Z  11 " =    1.937
peak=   -3.657 closest distance to " O   HOH Z  43 " =    1.638
peak=   -3.655 closest distance to " CG  LEU A 101 " =    2.521
peak=   -3.647 closest distance to " O   HOH Z 350 " =    1.647
peak=   -3.644 closest distance to " CB  ALA A  43 " =    2.570
peak=   -3.642 closest distance to " O   HOH Z  13 " =    1.437
peak=   -3.636 closest distance to " O   HOH Z 351 " =    1.495
peak=   -3.627 closest distance to " CG2 ILE A  49 " =    2.778
peak=   -3.623 closest distance to " OG  SER A  87 " =    1.516
peak=   -3.622 closest distance to " ND2 ASN A  45 " =    1.082
peak=   -3.615 closest distance to " NE2 GLN A  88 " =    2.130
peak=   -3.609 closest distance to " O   VAL A  67 " =    2.718
peak=   -3.609 closest distance to " O   HOH Z 377 " =    2.099
peak=   -3.607 closest distance to " O   HOH Z  17 " =    1.573
peak=   -3.602 closest distance to " O   HOH Z 103 " =    1.858
peak=   -3.602 closest distance to " CG2 ILE A 263 " =    2.414
peak=   -3.600 closest distance to " CZ3 TRP A 179 " =    1.178
peak=   -3.592 closest distance to " CB  PRO A 163 " =    2.586
peak=   -3.590 closest distance to " O   HOH Z 435 " =    2.751
peak=   -3.588 closest distance to " CD  ARG A 139 " =    1.619
peak=   -3.586 closest distance to " CG1 VAL A 296 " =    1.363
peak=   -3.582 closest distance to " CG  TRP A 266 " =    1.821
peak=   -3.579 closest distance to " OD1 ASN A 187 " =    1.622
peak=   -3.567 closest distance to " CA  GLY A 241 " =    3.101
peak=   -3.563 closest distance to " ND2 ASN A  45 " =    1.466
peak=   -3.562 closest distance to " O   HOH Z  19 " =    2.286
peak=   -3.561 closest distance to " OG ASER A 134 " =    1.236
peak=   -3.560 closest distance to " CB  ALA A 291 " =    2.185
peak=   -3.559 closest distance to " OG  SER A  26 " =    1.342
peak=   -3.552 closest distance to " CD2 LEU A 167 " =    1.699
peak=   -3.548 closest distance to " O   SER A 271 " =    2.202
peak=   -3.537 closest distance to " O   HOH Z 353 " =    2.145
peak=   -3.536 closest distance to " CA  GLY A 203 " =    2.411
peak=   -3.517 closest distance to " N   ALA A  43 " =    2.631
peak=   -3.508 closest distance to " CD  LYS A 289 " =    2.518
peak=   -3.504 closest distance to " O   HOH Z  60 " =    2.181
peak=   -3.502 closest distance to " O   HOH Z 102 " =    1.654
peak=   -3.488 closest distance to " O   HOH Z 185 " =    2.343
peak=   -3.488 closest distance to " CE  MET A 105 " =    2.241
peak=   -3.487 closest distance to " NH2 ARG A  66 " =    1.891
peak=   -3.484 closest distance to " O   VAL A 189 " =    2.599
peak=   -3.482 closest distance to " C   ASN A 187 " =    1.789
peak=   -3.475 closest distance to " CB  PHE A 192 " =    1.854
peak=   -3.467 closest distance to " O   HOH Z  10 " =    1.534
peak=   -3.465 closest distance to " O   HOH Z 311 " =    3.843
peak=   -3.464 closest distance to " N   THR A 157 " =    1.490
peak=   -3.456 closest distance to " CG  HIS A  86 " =    0.890
peak=   -3.456 closest distance to " O   HOH Z  38 " =    1.530
peak=   -3.455 closest distance to " CE3 TRP A 150 " =    2.175
peak=   -3.455 closest distance to " OG  SER A  62 " =    1.759
peak=   -3.453 closest distance to " O   HOH Z 166 " =    1.514
peak=   -3.434 closest distance to " ND2 ASN A 187 " =    1.708
peak=   -3.432 closest distance to " CD  PRO A 213 " =    2.207
peak=   -3.430 closest distance to " CD1 LEU A 101 " =    2.927
peak=   -3.420 closest distance to " N   THR A 235 " =    1.323
peak=   -3.418 closest distance to " O   HOH Z 407 " =    3.155
peak=   -3.414 closest distance to " CB  PHE A 283 " =    2.988
peak=   -3.411 closest distance to " NH2 ARG A  79 " =    1.986
peak=   -3.408 closest distance to " O   GLY A 211 " =    1.471
peak=   -3.402 closest distance to " O   LEU A 167 " =    1.509
peak=   -3.401 closest distance to " OG BSER A 134 " =    1.774
peak=   -3.396 closest distance to " CE2 PHE A 218 " =    2.587
peak=   -3.383 closest distance to " CE BMET A  47 " =    1.849
peak=   -3.382 closest distance to " CB  ASP A 132 " =    2.297
peak=   -3.382 closest distance to " O   HOH Z 198 " =    1.594
peak=   -3.381 closest distance to " CG2 VAL A 112 " =    2.518
peak=   -3.380 closest distance to " OH  TYR A 169 " =    0.960
peak=   -3.380 closest distance to " N   SER A 276 " =    1.328
peak=   -3.375 closest distance to " O   HOH Z 241 " =    1.290
peak=   -3.373 closest distance to " CD1 PHE A  59 " =    1.921
peak=   -3.361 closest distance to " NE2 GLN A 103 " =    1.755
peak=   -3.361 closest distance to " CG  GLU A 277 " =    1.118
peak=   -3.358 closest distance to " O   HOH Z 184 " =    1.469
peak=   -3.352 closest distance to " O   HOH Z 128 " =    2.559
peak=   -3.350 closest distance to " CG  PRO A 163 " =    2.527
peak=   -3.348 closest distance to " CD2 TYR A 293 " =    2.079
peak=   -3.344 closest distance to " CG1 VAL A 197 " =    2.344
peak=   -3.342 closest distance to " O   HOH Z 211 " =    1.619
peak=   -3.339 closest distance to " CG  LYS A 193 " =    2.383
peak=   -3.337 closest distance to " C   GLY A  17 " =    1.315
peak=   -3.335 closest distance to " O   HOH Z 388 " =    2.042
peak=   -3.331 closest distance to " C   ASN A 285 " =    2.508
peak=   -3.327 closest distance to " C   ALA A   8 " =    1.578
peak=   -3.327 closest distance to " O   GLY A  80 " =    2.608
peak=   -3.327 closest distance to " ND2 ASN A  60 " =    1.455
peak=   -3.323 closest distance to " O   HOH Z 275 " =    1.501
peak=   -3.319 closest distance to " O   PRO A 198 " =    1.381
peak=   -3.319 closest distance to " CB  ALA A 291 " =    2.347
peak=   -3.317 closest distance to " O   PRO A 198 " =    1.245
peak=   -3.306 closest distance to " CB  ASN A  39 " =    2.194
peak=   -3.305 closest distance to " C   LEU A 143 " =    1.092
peak=   -3.302 closest distance to " CB  ALA A 248 " =    2.065
peak=   -3.298 closest distance to " CG  ASP A  50 " =    2.512
peak=   -3.290 closest distance to " O   GLY A 203 " =    2.359
peak=   -3.285 closest distance to " CB  VAL A 230 " =    1.042
peak=   -3.284 closest distance to " O   HOH Z  44 " =    2.118
peak=   -3.279 closest distance to " O   HOH Z 310 " =    1.826
peak=   -3.275 closest distance to " O   HOH Z 243 " =    1.989
peak=   -3.268 closest distance to " O   VAL A 125 " =    2.312
peak=   -3.253 closest distance to " NH1 ARG A 195 " =    2.621
peak=   -3.252 closest distance to " O   HOH Z 111 " =    2.230
peak=   -3.251 closest distance to " CD2 PHE A  61 " =    2.436
peak=   -3.249 closest distance to " O   HOH Z 191 " =    5.544
peak=   -3.248 closest distance to " CE1 TYR A 169 " =    2.409
peak=   -3.247 closest distance to " CA  GLY A 133 " =    2.253
peak=   -3.246 closest distance to " CG  GLU A  53 " =    1.491
peak=   -3.239 closest distance to " OD2 ASP A 171 " =    1.788
peak=   -3.239 closest distance to " N   GLN A  58 " =    1.550
peak=   -3.237 closest distance to " O   HOH Z 139 " =    2.993
peak=   -3.234 closest distance to " NE2 GLN A 194 " =    1.820
peak=   -3.231 closest distance to " OH  TYR A 214 " =    1.268
peak=   -3.228 closest distance to " NZ  LYS A 119 " =    3.498
peak=   -3.224 closest distance to " O   HOH Z 417 " =    2.822
peak=   -3.223 closest distance to " CH2 TRP A 177 " =    2.141
peak=   -3.222 closest distance to " O   HOH Z 149 " =    2.237
peak=   -3.215 closest distance to " CA  ASN A 127 " =    1.075
peak=   -3.214 closest distance to " O   HOH Z 177 " =    1.680
peak=   -3.213 closest distance to " O   GLY A 196 " =    1.114
peak=   -3.206 closest distance to " OG1 THR A 178 " =    1.298
peak=   -3.204 closest distance to " CD1 ILE A 199 " =    2.576
peak=   -3.196 closest distance to " CG  GLU A   2 " =    1.898
peak=   -3.196 closest distance to " CG  MET A 105 " =    0.956
peak=   -3.194 closest distance to " O   ASN A 301 " =    1.388
peak=   -3.193 closest distance to " O   HOH Z  98 " =    2.145
peak=   -3.192 closest distance to " CZ  PHE A  59 " =    1.635
peak=   -3.192 closest distance to " CB  ALA A 248 " =    2.405
peak=   -3.189 closest distance to " O   HOH Z 431 " =    1.711
peak=   -3.185 closest distance to " O   HOH Z 189 " =    1.902
peak=   -3.184 closest distance to " CB  TYR A  15 " =    2.260
peak=   -3.181 closest distance to " CA  GLY A 241 " =    2.276
peak=   -3.177 closest distance to " O   HOH Z 193 " =    1.710
peak=   -3.174 closest distance to " O   HOH Z 113 " =    2.125
peak=   -3.172 closest distance to " O   HOH Z 165 " =    1.935
peak=   -3.172 closest distance to " C   LEU A 222 " =    0.824
peak=   -3.170 closest distance to " O   HOH Z 184 " =    1.688
peak=   -3.169 closest distance to " CB  ALA A  10 " =    2.266
peak=   -3.158 closest distance to " CD  ARG A 195 " =    5.118
peak=   -3.158 closest distance to " O   LYS A 117 " =    1.713
peak=   -3.157 closest distance to " OE1 GLN A  88 " =    1.060
peak=   -3.155 closest distance to " O   THR A  18 " =    1.537
peak=   -3.154 closest distance to " ND2BASN A 224 " =    1.706
peak=   -3.154 closest distance to " O   HOH Z 222 " =    1.576
peak=   -3.153 closest distance to " O   HOH Z  90 " =    1.546
peak=   -3.152 closest distance to " CZ  PHE A  38 " =    2.311
peak=   -3.152 closest distance to " N   SER A 212 " =    2.069
peak=   -3.147 closest distance to " O   HOH Z 396 " =    1.737
peak=   -3.146 closest distance to " CB  ASP A 132 " =    2.314
peak=   -3.138 closest distance to " CZ  TYR A 169 " =    1.699
peak=   -3.137 closest distance to " O   HOH Z 252 " =    4.072
peak=   -3.136 closest distance to " CE3 TRP A  70 " =    1.807
peak=   -3.136 closest distance to " O   HOH Z   6 " =    1.782
peak=   -3.130 closest distance to " O   HOH Z 423 " =    2.081
peak=   -3.128 closest distance to " O   HOH Z  60 " =    1.939
peak=   -3.124 closest distance to " O   HOH Z 174 " =    2.443
peak=   -3.117 closest distance to " OD1 ASP A 191 " =    1.580
peak=   -3.115 closest distance to " O   HOH Z 380 " =    4.835
peak=   -3.110 closest distance to " O   SER A 276 " =    1.668
peak=   -3.104 closest distance to " OG  SER A 206 " =    1.769
peak=   -3.101 closest distance to " O   HOH Z 234 " =    4.257
peak=   -3.099 closest distance to " CD1 TYR A 247 " =    2.330
peak=   -3.088 closest distance to " O   HOH Z 262 " =    2.849
peak=   -3.087 closest distance to " O   HOH Z 281 " =    2.473
peak=   -3.076 closest distance to " C   ASP A 231 " =    2.592
peak=   -3.076 closest distance to " CD1 ILE A 151 " =    2.298
peak=   -3.065 closest distance to " C   MET A 188 " =    1.417
peak=   -3.057 closest distance to " CE  MET A  93 " =    1.246
peak=   -3.055 closest distance to " OG1 THR A 246 " =    1.369
peak=   -3.010 closest distance to " CB  TRP A  85 " =    2.420

================= 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    :  0.4322 0.4201   6.227898e+00   6.206926e+00
   1_bss:  0.4243 0.4097   6.223891e+00   6.197929e+00
   1_xyz:  0.3157 0.3469   6.013202e+00   6.080006e+00
   1_adp:  0.2553 0.2951   5.836854e+00   5.960387e+00
   1_occ:  0.2547 0.2950   5.835656e+00   5.960815e+00
   2_bss:  0.2516 0.2885   5.835058e+00   5.956503e+00
   2_xyz:  0.1661 0.2104   5.470625e+00   5.661199e+00
   2_adp:  0.1507 0.1955   5.384978e+00   5.589571e+00
   2_occ:  0.1506 0.1955   5.384440e+00   5.589507e+00
   3_bss:  0.1496 0.1935   5.384093e+00   5.587711e+00
   3_xyz:  0.1248 0.1690   5.232964e+00   5.463597e+00
   3_adp:  0.1187 0.1647   5.198951e+00   5.439091e+00
   3_occ:  0.1187 0.1647   5.198786e+00   5.439132e+00
   4_bss:  0.1189 0.1651   5.199723e+00   5.439325e+00
   4_xyz:  0.1175 0.1634   5.190242e+00   5.427865e+00
   4_adp:  0.1181 0.1612   5.186285e+00   5.414838e+00
   4_occ:  0.1180 0.1612   5.186021e+00   5.414863e+00
   5_bss:  0.1180 0.1611   5.186011e+00   5.414830e+00
   5_xyz:  0.1135 0.1584   5.159115e+00   5.399574e+00
   5_adp:  0.1122 0.1601   5.160979e+00   5.410151e+00
   5_occ:  0.1122 0.1603   5.161320e+00   5.410708e+00
   5_bss:  0.1122 0.1603   5.161242e+00   5.410738e+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:  0.300  20.000   8.588   8.147   7.603   0.000   0.000   0.000
   1_xyz:  0.300  20.000   8.588   8.147   7.603   0.000   0.000   0.000
   1_adp:  0.300  20.000   8.588   8.147   7.603   0.000   0.000   0.000
   1_occ:  0.300  20.000   8.588   8.147   7.603   0.000   0.000   0.000
   2_bss:  0.331  50.115   5.429   4.927   5.166   0.000   0.000   0.000
   2_xyz:  0.331  50.115   5.429   4.927   5.166   0.000   0.000   0.000
   2_adp:  0.331  50.115   5.429   4.927   5.166   0.000   0.000   0.000
   2_occ:  0.331  50.115   5.429   4.927   5.166   0.000   0.000   0.000
   3_bss:  0.331  50.115   3.725   3.630   4.239   0.000   0.000   0.000
   3_xyz:  0.331  50.115   3.725   3.630   4.239   0.000   0.000   0.000
   3_adp:  0.331  50.115   3.725   3.630   4.239   0.000   0.000   0.000
   3_occ:  0.331  50.115   3.725   3.630   4.239   0.000   0.000   0.000
   4_bss:  0.324  50.115   3.424   3.433   4.120   0.000   0.000   0.000
   4_xyz:  0.324  50.115   3.424   3.433   4.120   0.000   0.000   0.000
   4_adp:  0.324  50.115   3.424   3.433   4.120   0.000   0.000   0.000
   4_occ:  0.324  50.115   3.424   3.433   4.120   0.000   0.000   0.000
   5_bss:  0.324  50.115   3.284   3.365   4.087   0.000   0.000   0.000
   5_xyz:  0.324  50.115   3.284   3.365   4.087   0.000   0.000   0.000
   5_adp:  0.324  50.115   3.284   3.365   4.087   0.000   0.000   0.000
   5_occ:  0.324  50.115   3.284   3.365   4.087   0.000   0.000   0.000
   5_bss:  0.319  53.834  -0.280  -0.221   0.501  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  46.936 0.5603  0.6240    51575.841
   1_bss:  46.945 0.5581  0.7912    49555.241
   1_xyz:  37.875 0.6667  0.9207    33489.812
   1_adp:  30.260 0.7554  1.0100    23219.326
   1_occ:  30.270 0.7552  1.0099    23227.880
   2_bss:  30.047 0.7576  0.9127    22959.520
   2_xyz:  20.272 0.8589  0.9970    11284.338
   2_adp:  18.338 0.8777  1.0126     9693.014
   2_occ:  18.338 0.8777  1.0123     9688.964
   3_bss:  18.275 0.8783  0.9655     9642.873
   3_xyz:  15.524 0.9024  0.9770     7418.950
   3_adp:  15.031 0.9067  0.9789     7057.698
   3_occ:  15.029 0.9067  0.9788     7056.776
   4_bss:  15.034 0.9066  0.9706     7058.802
   4_xyz:  14.734 0.9093  0.9704     6835.725
   4_adp:  14.409 0.9121  0.9713     6685.802
   4_occ:  14.409 0.9121  0.9711     6683.313
   5_bss:  14.409 0.9121  0.9683     6682.098
   5_xyz:  14.138 0.9142  0.9693     6499.079
   5_adp:  14.391 0.9121  0.9650     6614.443
   5_occ:  14.400 0.9121  0.9649     6622.045
   5_bss:  14.402 0.9120  0.9696     6622.157
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4105e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4105e+01
   1_xyz:   1.554  0.012  0.102 17.923  0.006  4.125   1.2245e-01
   1_adp:   1.554  0.012  0.102 17.923  0.006  4.125   1.2245e-01
   1_occ:   1.554  0.012  0.102 17.923  0.006  4.125   1.2245e-01
   2_bss:   1.554  0.012  0.102 17.923  0.006  4.125   1.2245e-01
   2_xyz:   1.066  0.008  0.076 16.435  0.004  4.129   7.1421e-02
   2_adp:   1.066  0.008  0.076 16.435  0.004  4.129   7.1421e-02
   2_occ:   1.066  0.008  0.076 16.435  0.004  4.129   7.1421e-02
   3_bss:   1.066  0.008  0.076 16.435  0.004  4.129   7.1421e-02
   3_xyz:   1.075  0.009  0.086 16.123  0.004  4.115   7.1646e-02
   3_adp:   1.075  0.009  0.086 16.123  0.004  4.115   7.1646e-02
   3_occ:   1.075  0.009  0.086 16.123  0.004  4.115   7.1646e-02
   4_bss:   1.075  0.009  0.086 16.123  0.004  4.115   7.1646e-02
   4_xyz:   0.955  0.007  0.077 15.801  0.003  4.116   5.9110e-02
   4_adp:   0.955  0.007  0.077 15.801  0.003  4.116   5.9110e-02
   4_occ:   0.955  0.007  0.077 15.801  0.003  4.116   5.9110e-02
   5_bss:   0.955  0.007  0.077 15.801  0.003  4.116   5.9110e-02
   5_xyz:   1.062  0.008  0.085 15.764  0.004  4.119   6.9033e-02
   5_adp:   1.062  0.008  0.085 15.764  0.004  4.119   6.9033e-02
   5_occ:   1.062  0.008  0.085 15.764  0.004  4.119   6.9033e-02
   5_bss:   1.062  0.008  0.085 15.764  0.004  4.119   6.9033e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0156e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0156e+00
   1_xyz:  13.560  0.146  0.442 86.470  0.040  2.270   9.2576e-02
   1_adp:  13.560  0.146  0.442 86.470  0.040  2.270   9.2576e-02
   1_occ:  13.560  0.146  0.442 86.470  0.040  2.270   9.2576e-02
   2_bss:  13.560  0.146  0.442 86.470  0.040  2.270   9.2576e-02
   2_xyz:   7.486  0.090  0.282 83.748  0.041  2.340   6.3324e-02
   2_adp:   7.486  0.090  0.282 83.748  0.041  2.340   6.3324e-02
   2_occ:   7.486  0.090  0.282 83.748  0.041  2.340   6.3324e-02
   3_bss:   7.486  0.090  0.282 83.748  0.041  2.340   6.3324e-02
   3_xyz:   7.423  0.045  0.568 83.907  0.041  2.351   5.1490e-02
   3_adp:   7.423  0.045  0.568 83.907  0.041  2.351   5.1490e-02
   3_occ:   7.423  0.045  0.568 83.907  0.041  2.351   5.1490e-02
   4_bss:   7.423  0.045  0.568 83.907  0.041  2.351   5.1490e-02
   4_xyz:   7.648  0.039  0.468 82.840  0.039  2.374   3.4247e-02
   4_adp:   7.648  0.039  0.468 82.840  0.039  2.374   3.4247e-02
   4_occ:   7.648  0.039  0.468 82.840  0.039  2.374   3.4247e-02
   5_bss:   7.648  0.039  0.468 82.840  0.039  2.374   3.4247e-02
   5_xyz:   7.648  0.043  0.583 83.798  0.040  2.325   4.3126e-02
   5_adp:   7.648  0.043  0.583 83.798  0.040  2.325   4.3126e-02
   5_occ:   7.648  0.043  0.583 83.798  0.040  2.325   4.3126e-02
   5_bss:   7.648  0.043  0.583 83.798  0.040  2.325   4.3126e-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:  54.63   0.00   9.99  49.60   0.00   7.01  54.63   0.00  26.24
   1_occ:  54.63   0.00   9.99  49.60   0.00   7.01  54.63   0.00  26.24
   2_bss:  54.63   0.00   9.99  49.60   0.00   7.01  54.63   0.00  26.24
   2_xyz:  54.63   0.00   9.99  49.60   0.00   7.01  54.63   0.00  26.24
   2_adp:  86.16   0.00  10.68  86.16   0.00   7.06  55.98   0.57  30.37
   2_occ:  86.16   0.00  10.68  86.16   0.00   7.06  55.98   0.57  30.37
   3_bss:  86.16   0.00  10.68  86.16   0.00   7.06  55.98   0.57  30.37
   3_xyz:  86.16   0.00  10.68  86.16   0.00   7.06  55.98   0.57  30.37
   3_adp:  72.20   0.00  11.61  72.20   0.00   7.37  70.80   0.34  34.73
   3_occ:  72.20   0.00  11.61  72.20   0.00   7.37  70.80   0.34  34.73
   4_bss:  72.20   0.00  11.61  72.20   0.00   7.37  70.80   0.34  34.73
   4_xyz:  72.20   0.00  11.61  72.20   0.00   7.37  70.80   0.34  34.73
   4_adp:  73.36   0.00  11.36  73.36   0.00   7.27  70.41   0.77  33.59
   4_occ:  73.36   0.00  11.36  73.36   0.00   7.27  70.41   0.77  33.59
   5_bss:  73.36   0.00  11.36  73.36   0.00   7.27  70.41   0.77  33.59
   5_xyz:  73.36   0.00  11.36  73.36   0.00   7.27  70.41   0.77  33.59
   5_adp:  88.94   0.00  11.79  88.94   0.00   7.44  81.76   0.51  35.46
   5_occ:  88.94   0.00  11.79  88.94   0.00   7.44  81.76   0.51  35.46
   5_bss:  92.66   3.72  15.50  92.66   3.72  11.16  85.48   4.23  39.18
------------------------------------------------------------------------
 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:    1.184    0.021    0.407
   1_adp:    1.184    0.021    0.407
   1_occ:    1.184    0.021    0.407
   2_bss:    1.184    0.021    0.407
   2_xyz:    1.395    0.004    0.517
   2_adp:    1.395    0.004    0.517
   2_occ:    1.395    0.004    0.517
   3_bss:    1.395    0.004    0.517
   3_xyz:    1.424    0.043    0.557
   3_adp:    1.424    0.043    0.557
   3_occ:    1.424    0.043    0.557
   4_bss:    1.424    0.043    0.557
   4_xyz:    1.515    0.022    0.565
   4_adp:    1.515    0.022    0.565
   4_occ:    1.515    0.022    0.565
   5_bss:    1.515    0.022    0.565
   5_xyz:    1.566    0.017    0.575
   5_adp:    1.566    0.017    0.575
   5_occ:    1.566    0.017    0.575
   5_bss:    1.566    0.017    0.575
------------------------------------------------------------------------

CPU time actual refinement: 328.71


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1038/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_1038/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1038/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1038/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1038/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 328.54 
  Macro-tasks:
    bulk solvent and scale       = 42.83  
    individual site refinement   = 134.00 
    weights calculation          = 33.71  
    collect and process          = 6.84   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 217.52 
  Micro-tasks:
    mask                            = 1.75   
    f_calc                          = 97.31  
    alpha_beta                      = 8.39   
    target                          = 1.22   
    gradients_wrt_atomic_parameters = 108.30 
    fmodel                         = 8.01   
    r_factors                      = 0.27   
    phase_errors                   = 11.09  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 236.64 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.645 micro seconds
Total CPU time: 5.70 minutes
from_scatterers_fft:    632 calls, 96.77 s
gradients_fft:          577 calls, 94.84 s

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

# Date 2008-01-16 Time 03:02:48 PST -0800 (1200481368.15 s)
Start R-work = 0.4322, R-free = 0.4201 (no bulk solvent and anisotropic scale)
Final R-work = 0.1287, R-free = 0.1758 (no bulk solvent and anisotropic scale)

Start R-work = 0.4243, R-free = 0.4097
Final R-work = 0.1122, R-free = 0.1603