# Date 2008-01-16 Time 01:12:17 PST -0800 (1200474737.26 s)
#phil __OFF__

Command line arguments: "../326.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 1438
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 326

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 47.3993, 87.2539, 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: 2.76, per 1000 atoms: 0.98


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

F-obs:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA

R-free flags:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.3993, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8679 1.97078
Completeness in resolution range: 0.939205
Completeness with d_max=infinity: 0.936332

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8679
                             d_min =   1.9708

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.3993, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8679 1.97078
Completeness in resolution range: 0.939205
Completeness with d_max=infinity: 0.936332

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8683 -  4.2167 [2195/2223]  1972   223  10.2%
  bin  2:  4.2167 -  3.3596 [2085/2108]  1878   207   9.9%
  bin  3:  3.3596 -  2.9386 [2078/2100]  1872   206   9.9%
  bin  4:  2.9386 -  2.6716 [2073/2092]  1864   209  10.1%
  bin  5:  2.6716 -  2.4811 [2014/2043]  1810   204  10.1%
  bin  6:  2.4811 -  2.3354 [2043/2085]  1844   199   9.7%
  bin  7:  2.3354 -  2.2188 [2009/2045]  1808   201  10.0%
  bin  8:  2.2188 -  2.1225 [2025/2063]  1817   208  10.3%
  bin  9:  2.1225 -  2.0410 [2026/2057]  1832   194   9.6%
  bin 10:  2.0410 -  1.9708 [1041/2041]   933   108  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_326/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: 0.12 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:
        1.62 -     2.28: 13
        2.28 -     2.93: 1549
        2.93 -     3.59: 4475
        3.59 -     4.24: 9184
        4.24 -     4.90: 13043
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.619 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.772 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.780 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.837 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28259 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_326/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_326/model_refine_001.geo

CPU time processing inputs: 7.98


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 47.3993 87.2539 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: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4645   r_free= 0.4471   ksol= 0.00   Bsol= 0.00   scale= 0.804    |
|                                                                             |
| 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:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.263692                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8683 -  4.7029 0.99   1423  158 0.3704 0.3588      6.5559      6.5703|
|  2:  4.7029 -  3.7526 0.99   1376  153 0.3667 0.3965      6.7066      6.7929|
|  3:  3.7526 -  3.2840 0.99   1333  150 0.4254 0.3872      6.6334      6.6069|
|  4:  3.2840 -  2.9864 0.99   1336  140 0.4483 0.4302       6.482      6.4498|
|  5:  2.9864 -  2.7739 0.99   1315  149 0.4949 0.4478      6.3475      6.3587|
|  6:  2.7739 -  2.6112 0.98   1307  150 0.4922 0.5306      6.2722      6.1918|
|  7:  2.6112 -  2.4811 0.99   1306  149 0.4885 0.4860      6.2122       6.144|
|  8:  2.4811 -  2.3735 0.99   1323  140 0.5130 0.4361      6.1771       6.136|
|  9:  2.3735 -  2.2825 0.98   1308  145 0.5236 0.5289      6.1107      6.1556|
| 10:  2.2825 -  2.2040 0.98   1295  141 0.5221 0.4621      6.1096      6.0576|
| 11:  2.2040 -  2.1353 0.98   1308  149 0.5262 0.5198      6.0199      6.0385|
| 12:  2.1353 -  2.0744 0.99   1294  145 0.5264 0.4931      5.9606      5.9581|
| 13:  2.0744 -  2.0199 0.97   1271  135 0.5322 0.5313      5.8854      5.8335|
| 14:  2.0199 -  1.9708 0.33    435   55 0.5292 0.4224       5.901      5.6998|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8683 -  4.7029  1423   158  0.71  33.63   0.81     0.71      66935.29|
|  2:  4.7029 -  3.7526  1376   153  0.72  33.20   0.90     0.77      93584.18|
|  3:  3.7526 -  3.2840  1333   150  0.65  39.93   0.84     0.74      96870.71|
|  4:  3.2840 -  2.9864  1336   140  0.57  45.90   0.81     0.65      82244.59|
|  5:  2.9864 -  2.7739  1315   149  0.49  53.02   0.74     0.57      70834.01|
|  6:  2.7739 -  2.6112  1307   150  0.45  55.73   0.73     0.52      64882.76|
|  7:  2.6112 -  2.4811  1306   149  0.43  57.28   0.76     0.50      60002.32|
|  8:  2.4811 -  2.3735  1323   140  0.45  56.22   0.73     0.52      51118.50|
|  9:  2.3735 -  2.2825  1308   145  0.45  55.78   0.73     0.54      46148.54|
| 10:  2.2825 -  2.2040  1295   141  0.46  55.19   0.73     0.53      41759.48|
| 11:  2.2040 -  2.1353  1308   149  0.40  60.01   0.74     0.51      42586.69|
| 12:  2.1353 -  2.0744  1294   145  0.38  61.84   0.76     0.48      39971.61|
| 13:  2.0744 -  2.0199  1271   135  0.37  62.22   0.72     0.47      34769.50|
| 14:  2.0199 -  1.9708   435    55  0.44  56.65   0.75     0.46      24796.61|
|alpha:            min =        0.46 max =            0.77 mean =         0.58|
|beta:             min =    24796.61 max =        96870.71 mean =     60341.21|
|figures of merit: min =        0.00 max =            1.00 mean =         0.50|
|phase err.(work): min =        0.00 max =           89.99 mean =        51.42|
|phase err.(test): min =        0.00 max =           89.88 mean =        51.58|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.291514             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.152   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.871346              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.464   (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:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      177 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      688 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1505 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2643 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3892 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5076 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6582 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7699 |
|-----------------------------------------------------------------------------|
|-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 |       53.789 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.994 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.888)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.888)------------------------------------------|
|    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: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4703   r_free= 0.4509   ksol= 0.00   Bsol= 0.00   scale= 0.774    |
|                                                                             |
| 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:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.266594                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4558   r_free= 0.4405   ksol= 0.34   Bsol= 20.00   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.45,9.27,9.18,0.00,0.00,0.00); trace/3= 8.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.255006                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.644347              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.577   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.840975              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 75.284   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4558      final r-factor (work) = 0.3550          |
| start r-factor (free) = 0.4405      final r-factor (free) = 0.3746          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 84.0129 = 9.64 * 0.50 * 6.2678 + 1.00 * 53.7885                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.7256 = 9.64 * 0.50 * 6.1361 + 1.00 * 0.1364                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3550      final r-factor (work) = 0.3020          |
| start r-factor (free) = 0.3746      final r-factor (free) = 0.3461          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1746 = 0.84 * 1.00 * 6.1361 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0614 = 0.84 * 1.00 * 6.0015 + 1.00 * 0.0143                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.888)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    70.48   12.13    None  None   None       |
|    all(noH): 2823   0      0.00    70.48   12.13    None  None   None       |
|    Sol.    : 438    0      0.00    70.48   27.75    None  None   None       |
|    Mac.    : 2385   0      0.00    64.86   9.27     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.048: 1218   |   5:    35.238 -  42.286:   72        |
|      1:     7.048 -  14.095:  772   |   6:    42.286 -  49.333:   49        |
|      2:    14.095 -  21.143:  361   |   7:    49.333 -  56.381:   30        |
|      3:    21.143 -  28.190:  182   |   8:    56.381 -  63.428:   13        |
|      4:    28.190 -  35.238:  118   |   9:    63.428 -  70.476:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3020 r_free = 0.3461             target_work(ml) = 5.969         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3016 r_free = 0.3471             target_work(ml) = 5.968         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3016   r_free= 0.3471   ksol= 0.34   Bsol= 20.00   scale= 1.101   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.45,9.27,9.18,0.00,0.00,0.00); trace/3= 8.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.968077                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2972   r_free= 0.3425   ksol= 0.33   Bsol= 40.66   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.81,5.23,5.62,0.00,0.00,0.00); trace/3= 4.89                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.968743                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.003153              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.235   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.348008              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.651  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2972      final r-factor (work) = 0.1946          |
| start r-factor (free) = 0.3425      final r-factor (free) = 0.2353          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.1582 = 6.00 * 0.50 * 6.0041 + 1.00 * 0.1364                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.4741 = 6.00 * 0.50 * 5.7960 + 1.00 * 0.0771                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1946      final r-factor (work) = 0.1712          |
| start r-factor (free) = 0.2353      final r-factor (free) = 0.2121          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0415 = 0.35 * 1.00 * 5.7960 + 1.00 * 0.0244                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9769 = 0.35 * 1.00 * 5.5320 + 1.00 * 0.0517                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.888)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    70.08   12.10    None  None   None       |
|    all(noH): 2823   0      0.00    70.08   12.10    None  None   None       |
|    Sol.    : 438    0      0.62    68.37   32.74    None  None   None       |
|    Mac.    : 2385   0      0.00    70.08   8.31     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 -   7.008: 1360   |   5:    35.039 -  42.046:   91        |
|      1:     7.008 -  14.016:  764   |   6:    42.046 -  49.054:   90        |
|      2:    14.016 -  21.023:  213   |   7:    49.054 -  56.062:   40        |
|      3:    21.023 -  28.031:  132   |   8:    56.062 -  63.070:   23        |
|      4:    28.031 -  35.039:  104   |   9:    63.070 -  70.077:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1712 r_free = 0.2121             target_work(ml) = 5.486         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1710 r_free = 0.2122             target_work(ml) = 5.485         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1710   r_free= 0.2122   ksol= 0.33   Bsol= 40.66   scale= 1.044   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.81,5.23,5.62,0.00,0.00,0.00); trace/3= 4.89                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.485074                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1689   r_free= 0.2123   ksol= 0.32   Bsol= 47.64   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.02,3.37,4.06,0.00,0.00,0.00); trace/3= 3.15                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.483950                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.303632              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.705   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.051781              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.198   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1689      final r-factor (work) = 0.1357          |
| start r-factor (free) = 0.2123      final r-factor (free) = 0.1739          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4651 = 2.30 * 0.50 * 5.5461 + 1.00 * 0.0770                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2718 = 2.30 * 0.50 * 5.3923 + 1.00 * 0.0609                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1357      final r-factor (work) = 0.1283          |
| start r-factor (free) = 0.1739      final r-factor (free) = 0.1692          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6918 = 1.05 * 1.00 * 5.3923 + 1.00 * 0.0202                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5542 = 1.05 * 1.00 * 5.2649 + 1.00 * 0.0167                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.888)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.54   12.91    None  None   None       |
|    all(noH): 2823   0      0.00    87.54   12.91    None  None   None       |
|    Sol.    : 438    0      0.98    78.58   37.42    None  None   None       |
|    Mac.    : 2385   0      0.00    87.54   8.41     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 -   8.754: 1673   |   5:    43.770 -  52.524:   91        |
|      1:     8.754 -  17.508:  572   |   6:    52.524 -  61.278:   53        |
|      2:    17.508 -  26.262:  165   |   7:    61.278 -  70.032:   41        |
|      3:    26.262 -  35.016:  109   |   8:    70.032 -  78.786:   15        |
|      4:    35.016 -  43.770:  101   |   9:    78.786 -  87.540:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1283 r_free = 0.1692             target_work(ml) = 5.252         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1281 r_free = 0.1694             target_work(ml) = 5.252         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1281   r_free= 0.1694   ksol= 0.32   Bsol= 47.64   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.02,3.37,4.06,0.00,0.00,0.00); trace/3= 3.15                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.251534                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1284   r_free= 0.1697   ksol= 0.33   Bsol= 53.55   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.80,2.93,3.86,0.00,0.00,0.00); trace/3= 2.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.252359                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.646886              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 124.430  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.264066              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 101.730  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1284      final r-factor (work) = 0.1142          |
| start r-factor (free) = 0.1697      final r-factor (free) = 0.1606          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6628 = 3.65 * 0.50 * 5.2658 + 1.00 * 0.0609                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5692 = 3.65 * 0.50 * 5.2037 + 1.00 * 0.0806                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1142      final r-factor (work) = 0.1133          |
| start r-factor (free) = 0.1606      final r-factor (free) = 0.1575          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3930 = 0.26 * 1.00 * 5.2037 + 1.00 * 0.0189                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3769 = 0.26 * 1.00 * 5.1717 + 1.00 * 0.0112                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.888)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.05   12.42    None  None   None       |
|    all(noH): 2823   0      0.00    87.05   12.42    None  None   None       |
|    Sol.    : 438    0      1.46    78.35   35.60    None  None   None       |
|    Mac.    : 2385   0      0.00    87.05   8.16     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.705: 1727   |   5:    43.524 -  52.228:   79        |
|      1:     8.705 -  17.409:  542   |   6:    52.228 -  60.933:   53        |
|      2:    17.409 -  26.114:  160   |   7:    60.933 -  69.638:   27        |
|      3:    26.114 -  34.819:  116   |   8:    69.638 -  78.342:   10        |
|      4:    34.819 -  43.524:  105   |   9:    78.342 -  87.047:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1133 r_free = 0.1575             target_work(ml) = 5.160         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1133 r_free = 0.1575             target_work(ml) = 5.160         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1575   ksol= 0.33   Bsol= 53.55   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.80,2.93,3.86,0.00,0.00,0.00); trace/3= 2.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.159702                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1132   r_free= 0.1575   ksol= 0.33   Bsol= 50.11   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.85,2.86,3.91,0.00,0.00,0.00); trace/3= 2.87                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.159790                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.243845              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 153.573  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.217089              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 159.788  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1132      final r-factor (work) = 0.1115          |
| start r-factor (free) = 0.1575      final r-factor (free) = 0.1561          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4684 = 3.24 * 0.50 * 5.1715 + 1.00 * 0.0806                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4349 = 3.24 * 0.50 * 5.1532 + 1.00 * 0.0768                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1115      final r-factor (work) = 0.1118          |
| start r-factor (free) = 0.1561      final r-factor (free) = 0.1556          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1299 = 0.22 * 1.00 * 5.1532 + 1.00 * 0.0111                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1284 = 0.22 * 1.00 * 5.1512 + 1.00 * 0.0101                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.888)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.72   12.08    None  None   None       |
|    all(noH): 2823   0      0.00    85.72   12.08    None  None   None       |
|    Sol.    : 438    0      1.58    77.20   34.16    None  None   None       |
|    Mac.    : 2385   0      0.00    85.72   8.02     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.572: 1718   |   5:    42.861 -  51.434:   89        |
|      1:     8.572 -  17.145:  560   |   6:    51.434 -  60.006:   46        |
|      2:    17.145 -  25.717:  159   |   7:    60.006 -  68.578:   23        |
|      3:    25.717 -  34.289:  119   |   8:    68.578 -  77.150:    8        |
|      4:    34.289 -  42.861:   98   |   9:    77.150 -  85.722:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1118 r_free = 0.1556             target_work(ml) = 5.150         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1117 r_free = 0.1556             target_work(ml) = 5.150         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1117   r_free= 0.1556   ksol= 0.33   Bsol= 50.11   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.85,2.86,3.91,0.00,0.00,0.00); trace/3= 2.87                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.150022                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8683 -  4.7029 0.99   1423  158 0.0996 0.1275      5.3928      5.5572|
|  2:  4.7029 -  3.7526 0.99   1376  153 0.0860 0.1104      5.4356      5.6471|
|  3:  3.7526 -  3.2840 0.99   1333  150 0.1057 0.1494      5.4643      5.8198|
|  4:  3.2840 -  2.9864 0.99   1336  140 0.1213 0.1533      5.4427      5.6006|
|  5:  2.9864 -  2.7739 0.99   1315  149 0.1347 0.1618      5.3324      5.5038|
|  6:  2.7739 -  2.6112 0.98   1307  150 0.1228 0.2058      5.2133       5.505|
|  7:  2.6112 -  2.4811 0.99   1306  149 0.1252 0.1594      5.1762      5.3491|
|  8:  2.4811 -  2.3735 0.99   1323  140 0.1140 0.1708      5.0748      5.3176|
|  9:  2.3735 -  2.2825 0.98   1308  145 0.1187 0.1958      5.0273      5.3624|
| 10:  2.2825 -  2.2040 0.98   1295  141 0.1132 0.1601      4.9572      5.1423|
| 11:  2.2040 -  2.1353 0.98   1308  149 0.1138 0.1720      4.9109      5.2187|
| 12:  2.1353 -  2.0744 0.99   1294  145 0.1105 0.1660      4.8467      5.1174|
| 13:  2.0744 -  2.0199 0.97   1271  135 0.1111 0.1645      4.7679       4.962|
| 14:  2.0199 -  1.9708 0.33    435   55 0.1038 0.1763      4.6801      4.9326|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8683 -  4.7029  1423   158  0.94   9.19   0.98     0.96       7426.20|
|  2:  4.7029 -  3.7526  1376   153  0.95   8.10   1.01     1.00       9039.97|
|  3:  3.7526 -  3.2840  1333   150  0.93  11.33   1.02     1.01      10296.44|
|  4:  3.2840 -  2.9864  1336   140  0.92  13.47   1.00     0.99      10130.91|
|  5:  2.9864 -  2.7739  1315   149  0.90  16.18   0.99     0.96       8422.12|
|  6:  2.7739 -  2.6112  1307   150  0.90  16.44   0.98     0.95       7078.67|
|  7:  2.6112 -  2.4811  1306   149  0.91  15.65   0.99     0.95       6334.22|
|  8:  2.4811 -  2.3735  1323   140  0.91  15.52   1.00     0.97       5553.28|
|  9:  2.3735 -  2.2825  1308   145  0.90  15.92   1.01     0.98       4990.92|
| 10:  2.2825 -  2.2040  1295   141  0.90  15.91   1.00     0.96       4451.30|
| 11:  2.2040 -  2.1353  1308   149  0.90  15.79   1.00     0.97       4133.53|
| 12:  2.1353 -  2.0744  1294   145  0.91  15.41   1.01     1.00       3737.55|
| 13:  2.0744 -  2.0199  1271   135  0.91  15.53   1.00     0.98       3178.70|
| 14:  2.0199 -  1.9708   435    55  0.91  14.84   0.98     0.93       2611.60|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2611.60 max =        10296.44 mean =      6461.98|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.14|
|phase err.(test): min =        0.00 max =           89.48 mean =        13.66|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1117   r_free= 0.1557   ksol= 0.32   Bsol= 51.50   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.02,-0.01,1.04,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.149992                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1117   r_free= 0.1557   ksol= 0.32   Bsol= 51.50   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.02,-0.01,1.04,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.149992                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8683 -  4.7029 0.99   1423  158 0.0993 0.1278      5.3906      5.5562|
|  2:  4.7029 -  3.7526 0.99   1376  153 0.0861 0.1105       5.436      5.6479|
|  3:  3.7526 -  3.2840 0.99   1333  150 0.1057 0.1494      5.4647      5.8197|
|  4:  3.2840 -  2.9864 0.99   1336  140 0.1213 0.1533      5.4428      5.6006|
|  5:  2.9864 -  2.7739 0.99   1315  149 0.1347 0.1618      5.3325       5.504|
|  6:  2.7739 -  2.6112 0.98   1307  150 0.1229 0.2058      5.2134      5.5051|
|  7:  2.6112 -  2.4811 0.99   1306  149 0.1252 0.1594      5.1764      5.3492|
|  8:  2.4811 -  2.3735 0.99   1323  140 0.1140 0.1708       5.075      5.3177|
|  9:  2.3735 -  2.2825 0.98   1308  145 0.1187 0.1958      5.0274      5.3624|
| 10:  2.2825 -  2.2040 0.98   1295  141 0.1132 0.1600      4.9572      5.1423|
| 11:  2.2040 -  2.1353 0.98   1308  149 0.1138 0.1721      4.9109      5.2189|
| 12:  2.1353 -  2.0744 0.99   1294  145 0.1105 0.1660      4.8467      5.1174|
| 13:  2.0744 -  2.0199 0.97   1271  135 0.1111 0.1645       4.768      4.9621|
| 14:  2.0199 -  1.9708 0.33    435   55 0.1038 0.1763      4.6803      4.9329|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8683 -  4.7029  1423   158  0.94   9.15   0.98     0.95       7381.48|
|  2:  4.7029 -  3.7526  1376   153  0.95   8.10   1.01     1.00       9034.71|
|  3:  3.7526 -  3.2840  1333   150  0.93  11.34   1.02     1.01      10311.87|
|  4:  3.2840 -  2.9864  1336   140  0.92  13.47   1.00     0.99      10133.07|
|  5:  2.9864 -  2.7739  1315   149  0.90  16.19   0.99     0.96       8424.94|
|  6:  2.7739 -  2.6112  1307   150  0.90  16.45   0.98     0.95       7081.37|
|  7:  2.6112 -  2.4811  1306   149  0.91  15.66   0.99     0.95       6336.35|
|  8:  2.4811 -  2.3735  1323   140  0.91  15.53   1.00     0.97       5554.68|
|  9:  2.3735 -  2.2825  1308   145  0.90  15.92   1.01     0.98       4992.11|
| 10:  2.2825 -  2.2040  1295   141  0.90  15.91   1.00     0.96       4452.07|
| 11:  2.2040 -  2.1353  1308   149  0.90  15.79   1.00     0.97       4134.20|
| 12:  2.1353 -  2.0744  1294   145  0.91  15.42   1.01     1.00       3737.99|
| 13:  2.0744 -  2.0199  1271   135  0.91  15.53   1.00     0.98       3179.59|
| 14:  2.0199 -  1.9708   435    55  0.91  14.84   0.98     0.93       2613.21|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2613.21 max =        10311.87 mean =      6460.29|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.14|
|phase err.(test): min =        0.00 max =           89.48 mean =        13.65|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.888)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.87    88.60   14.95    None  None   None       |
|    all(noH): 2823   0      2.87    88.60   14.95    None  None   None       |
|    Sol.    : 438    0      4.46    80.08   37.04    None  None   None       |
|    Mac.    : 2385   0      2.87    88.60   10.90    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:     2.875 -  11.447: 1718   |   5:    45.736 -  54.308:   89        |
|      1:    11.447 -  20.019:  560   |   6:    54.308 -  62.880:   46        |
|      2:    20.019 -  28.591:  159   |   7:    62.880 -  71.453:   23        |
|      3:    28.591 -  37.164:  119   |   8:    71.453 -  80.025:    8        |
|      4:    37.164 -  45.736:   98   |   9:    80.025 -  88.597:    3        |
|                               =>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: 0.271 - 4.902
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 307 from: 315
   mapped sites are within: 0.711 - 4.902

peak=   11.228 closest distance to " CB  VAL A 230 " =    1.487
peak=    6.480 closest distance to " CG  LEU A   5 " =    1.243
peak=    6.079 closest distance to " CB  VAL A 296 " =    1.209
peak=    6.005 closest distance to " NH2 ARG A  56 " =    2.229
peak=    5.230 closest distance to " CG  PRO A  54 " =    1.236
peak=    5.204 closest distance to " CG  LEU A 228 " =    1.202
peak=    5.182 closest distance to " CB  ARG A 275 " =    0.907
peak=    5.018 closest distance to " CB  GLN A 223 " =    1.503
peak=    4.978 closest distance to " CG2 VAL A 296 " =    0.995
peak=    4.953 closest distance to " NE2 GLN A  11 " =    1.105
peak=    4.908 closest distance to " O   HOH Z 142 " =    1.730
peak=    4.795 closest distance to " O   HOH Z 232 " =    2.283
peak=    4.760 closest distance to " CB  SER A  63 " =    1.190
peak=    4.746 closest distance to " CG1 VAL A 296 " =    1.166
peak=    4.736 closest distance to " O   HOH Z  85 " =    1.598
peak=    4.736 closest distance to " CD2 LEU A   5 " =    1.166
peak=    4.716 closest distance to " O   HOH Z 209 " =    2.292
peak=    4.629 closest distance to " CB  ARG A  79 " =    1.427
peak=    4.615 closest distance to " O   HOH Z 346 " =    1.547
peak=    4.559 closest distance to " CB  GLN A 183 " =    1.286
peak=    4.552 closest distance to " CB  VAL A 230 " =    1.205
peak=    4.509 closest distance to " CB  GLU A 152 " =    1.172
peak=    4.500 closest distance to " O   HOH Z  61 " =    1.664
peak=    4.499 closest distance to " O   SER A  87 " =    2.209
peak=    4.418 closest distance to " O   HOH Z 154 " =    1.654
peak=    4.391 closest distance to " O   HOH Z 403 " =    1.786
peak=    4.390 closest distance to " O   HOH Z 193 " =    1.821
peak=    4.389 closest distance to " O   HOH Z 272 " =    1.891
peak=    4.379 closest distance to " O   HOH Z 287 " =    1.952
peak=    4.377 closest distance to " CB  PRO A  54 " =    0.939
peak=    4.376 closest distance to " O   HOH Z  63 " =    2.085
peak=    4.358 closest distance to " O   HOH Z 126 " =    1.822
peak=    4.316 closest distance to " C   PRO A 198 " =    1.469
peak=    4.290 closest distance to " O   HOH Z 248 " =    1.422
peak=    4.282 closest distance to " CZ  PHE A 218 " =    1.136
peak=    4.251 closest distance to " CG  PRO A 213 " =    1.197
peak=    4.230 closest distance to " O   HOH Z 265 " =    2.135
peak=    4.222 closest distance to " CG  PRO A 243 " =    1.118
peak=    4.205 closest distance to " ND2 ASN A 187 " =    1.576
peak=    4.204 closest distance to " O   HOH Z  97 " =    1.980
peak=    4.183 closest distance to " CA  TYR A  30 " =    0.934
peak=    4.179 closest distance to " CD2 TRP A 179 " =    1.313
peak=    4.155 closest distance to " O   HOH Z 251 " =    1.468
peak=    4.148 closest distance to " CB  GLU A 277 " =    3.592
peak=    4.076 closest distance to " O   HOH Z 298 " =    1.759
peak=    4.076 closest distance to " O   HOH Z 234 " =    3.620
peak=    4.075 closest distance to " CG  ARG A  66 " =    2.734
peak=    4.071 closest distance to " O   HOH Z 189 " =    2.895
peak=    4.046 closest distance to " O   HOH Z 389 " =    1.937
peak=    4.045 closest distance to " O   HOH Z 369 " =    2.337
peak=    4.039 closest distance to " CA  ALA A  51 " =    0.989
peak=    4.035 closest distance to " O   HOH Z 423 " =    1.905
peak=    4.034 closest distance to " O   HOH Z 402 " =    1.426
peak=    4.021 closest distance to " O   HOH Z 158 " =    3.125
peak=    4.014 closest distance to " CD2 LEU A 228 " =    1.331
peak=    3.997 closest distance to " O   HOH Z  43 " =    2.086
peak=    3.988 closest distance to " N   ALA A   1 " =    3.069
peak=    3.983 closest distance to " O   HOH Z 303 " =    2.156
peak=    3.977 closest distance to " CB  SER A   3 " =    1.267
peak=    3.954 closest distance to " O   HOH Z 126 " =    1.819
peak=    3.953 closest distance to " N   ASN A  39 " =    1.223
peak=    3.953 closest distance to " O   HOH Z 368 " =    2.309
peak=    3.941 closest distance to " O   HOH Z 214 " =    2.596
peak=    3.912 closest distance to " O   HOH Z 427 " =    2.817
peak=    3.898 closest distance to " CB  TRP A 179 " =    1.315
peak=    3.885 closest distance to " CB  ARG A 190 " =    1.711
peak=    3.879 closest distance to " O   HOH Z 411 " =    3.772
peak=    3.871 closest distance to " O   HOH Z 359 " =    1.610
peak=    3.863 closest distance to " OD1 ASN A  69 " =    2.411
peak=    3.859 closest distance to " O   HOH Z 316 " =    3.008
peak=    3.854 closest distance to " O   HOH Z 273 " =    2.853
peak=    3.852 closest distance to " CB  SER A  26 " =    1.867
peak=    3.846 closest distance to " CB  ASN A 148 " =    1.410
peak=    3.841 closest distance to " O   HOH Z  97 " =    2.363
peak=    3.839 closest distance to " CB  ASN A  39 " =    0.802
peak=    3.825 closest distance to " CG2 ILE A  20 " =    1.413
peak=    3.818 closest distance to " O   HOH Z  54 " =    1.645
peak=    3.816 closest distance to " O   HOH Z 261 " =    2.096
peak=    3.800 closest distance to " O   HOH Z 422 " =    2.569
peak=    3.800 closest distance to " CB  ARG A 139 " =    1.017
peak=    3.799 closest distance to " OG BSER A 164 " =    2.212
peak=    3.797 closest distance to " CB  VAL A 265 " =    1.305
peak=    3.781 closest distance to " CB  ALA A   9 " =    1.662
peak=    3.775 closest distance to " O   HOH Z 345 " =    3.053
peak=    3.768 closest distance to " CB  ASN A 187 " =    1.278
peak=    3.764 closest distance to " O   HOH Z 327 " =    1.570
peak=    3.758 closest distance to " CD  LYS A 166 " =    1.338
peak=    3.738 closest distance to " CB  GLU A  46 " =    1.031
peak=    3.731 closest distance to " O   HOH Z  59 " =    2.138
peak=    3.728 closest distance to " O   HOH Z 313 " =    1.776
peak=    3.699 closest distance to " O   HOH Z  88 " =    2.730
peak=    3.693 closest distance to " CB  GLN A  88 " =    1.121
peak=    3.692 closest distance to " O   HOH Z  80 " =    1.794
peak=    3.689 closest distance to " O   HOH Z 126 " =    1.591
peak=    3.685 closest distance to " CB  THR A  31 " =    1.467
peak=    3.682 closest distance to " O   HOH Z 371 " =    3.162
peak=    3.668 closest distance to " O   HOH Z 421 " =    1.739
peak=    3.653 closest distance to " CB  ASN A 142 " =    1.117
peak=    3.652 closest distance to " O   HOH Z 250 " =    1.408
peak=    3.650 closest distance to " CD  ARG A 269 " =    0.931
peak=    3.631 closest distance to " CG  PRO A 198 " =    1.246
peak=    3.626 closest distance to " CB  VAL A 202 " =    1.450
peak=    3.625 closest distance to " O   HOH Z 120 " =    2.629
peak=    3.612 closest distance to " NE2 GLN A  77 " =    3.267
peak=    3.609 closest distance to " CG1 ILE A  49 " =    1.528
peak=    3.588 closest distance to " CZ  PHE A  38 " =    1.167
peak=    3.586 closest distance to " O   HOH Z 145 " =    2.380
peak=    3.582 closest distance to " NZ  LYS A 117 " =    2.740
peak=    3.580 closest distance to " CB  ASP A 140 " =    1.025
peak=    3.579 closest distance to " CA  TYR A 116 " =    1.446
peak=    3.577 closest distance to " O   HOH Z  44 " =    1.901
peak=    3.574 closest distance to " CA  ARG A  36 " =    1.061
peak=    3.572 closest distance to " O   HOH Z 383 " =    1.910
peak=    3.572 closest distance to " O   TRP A 274 " =    1.890
peak=    3.566 closest distance to " CG  MET A 185 " =    1.112
peak=    3.555 closest distance to " O   HOH Z  40 " =    1.822
peak=    3.550 closest distance to " CA  ASN A 215 " =    1.065
peak=    3.546 closest distance to " CG  LEU A 167 " =    1.205
peak=    3.542 closest distance to " CA  VAL A  41 " =    0.770
peak=    3.540 closest distance to " O   HOH Z  21 " =    1.797
peak=    3.536 closest distance to " O   HOH Z 404 " =    2.314
peak=    3.536 closest distance to " CB  TRP A 266 " =    1.007
peak=    3.533 closest distance to " CG2 THR A 221 " =    1.209
peak=    3.517 closest distance to " OD2 ASP A 298 " =    3.900
peak=    3.511 closest distance to " O   HOH Z  48 " =    1.622
peak=    3.509 closest distance to " NZ  LYS A  48 " =    1.162
peak=    3.509 closest distance to " O   HOH Z 426 " =    1.447
peak=    3.506 closest distance to " O   HOH Z 203 " =    1.705
peak=    3.500 closest distance to " O   ASP A 124 " =    1.425
peak=    3.496 closest distance to " O   HOH Z 416 " =    2.809
peak=    3.495 closest distance to " CB AVAL A  41 " =    1.091
peak=    3.494 closest distance to " CD  ARG A 159 " =    0.723
peak=    3.494 closest distance to " OG  SER A 276 " =    1.269
peak=    3.493 closest distance to " O   HOH Z 185 " =    1.814
peak=    3.490 closest distance to " CG  GLN A  58 " =    2.888
peak=    3.484 closest distance to " O   HOH Z 147 " =    1.818
peak=    3.480 closest distance to " CD  LYS A  76 " =    1.884
peak=    3.478 closest distance to " CG2AVAL A  72 " =    1.693
peak=    3.476 closest distance to " O   HOH Z 130 " =    2.304
peak=    3.471 closest distance to " O   HOH Z 234 " =    1.881
peak=    3.469 closest distance to " O   HOH Z 406 " =    1.399
peak=    3.467 closest distance to " CB  GLN A 278 " =    0.809
peak=    3.463 closest distance to " O   HOH Z 180 " =    2.183
peak=    3.458 closest distance to " O   HOH Z 357 " =    1.997
peak=    3.455 closest distance to " O   HOH Z 238 " =    0.767
peak=    3.451 closest distance to " O   HOH Z 193 " =    1.907
peak=    3.450 closest distance to " O   HOH Z  35 " =    2.371
peak=    3.448 closest distance to " N   SER A 135 " =    1.357
peak=    3.447 closest distance to " O   HOH Z 245 " =    1.430
peak=    3.439 closest distance to " CG2 ILE A 120 " =    1.228
peak=    3.435 closest distance to " O   HOH Z 124 " =    1.264
peak=    3.430 closest distance to " CB  PHE A 204 " =    0.802
peak=    3.429 closest distance to " N   GLU A  44 " =    2.165
peak=    3.429 closest distance to " CA  SER A  32 " =    1.642
peak=    3.427 closest distance to " O   HOH Z 437 " =    1.856
peak=    3.426 closest distance to " O   HOH Z 417 " =    3.282
peak=    3.425 closest distance to " NH2BARG A 145 " =    2.124
peak=    3.422 closest distance to " O   HOH Z  68 " =    2.139
peak=    3.415 closest distance to " CA  ALA A 295 " =    1.034
peak=    3.414 closest distance to " O   HOH Z 435 " =    1.899
peak=    3.414 closest distance to " N   PHE A 130 " =    1.309
peak=    3.413 closest distance to " CA  ALA A  21 " =    1.118
peak=    3.413 closest distance to " O  BHOH Z 338 " =    2.389
peak=    3.411 closest distance to " CA  ARG A 195 " =    1.198
peak=    3.404 closest distance to " CB  ARG A 190 " =    1.120
peak=    3.399 closest distance to " CG1 VAL A 153 " =    0.945
peak=    3.399 closest distance to " N   ASP A 162 " =    1.263
peak=    3.398 closest distance to " O   HOH Z 162 " =    2.135
peak=    3.395 closest distance to " CB  PRO A  90 " =    1.091
peak=    3.393 closest distance to " NH2AARG A 275 " =    3.565
peak=    3.388 closest distance to " O   HOH Z 392 " =    2.802
peak=    3.383 closest distance to " O   HOH Z 345 " =    1.575
peak=    3.380 closest distance to " O   HOH Z 128 " =    1.882
peak=    3.380 closest distance to " O   HOH Z 425 " =    1.943
peak=    3.378 closest distance to " CZ3 TRP A  85 " =    0.959
peak=    3.375 closest distance to " O   HOH Z 380 " =    1.885
peak=    3.374 closest distance to " O   HOH Z  63 " =    2.018
peak=    3.370 closest distance to " O   HOH Z 257 " =    2.239
peak=    3.361 closest distance to " O   HOH Z 148 " =    3.266
peak=    3.358 closest distance to " CA  LYS A 117 " =    1.304
peak=    3.356 closest distance to " CG2 VAL A 257 " =    0.836
peak=    3.352 closest distance to " CB  HIS A 108 " =    0.813
peak=    3.351 closest distance to " CB  ALA A 248 " =    1.298
peak=    3.350 closest distance to " CB  THR A  52 " =    0.927
peak=    3.347 closest distance to " O   HOH Z 130 " =    2.641
peak=    3.346 closest distance to " CD1 LEU A  96 " =    0.711
peak=    3.345 closest distance to " CB  TRP A 150 " =    1.439
peak=    3.344 closest distance to " CA  ASN A 176 " =    1.136
peak=    3.343 closest distance to " CG2AVAL A 121 " =    2.173
peak=    3.342 closest distance to " CA  ASP A 191 " =    1.106
peak=    3.338 closest distance to " O   ASN A  74 " =    1.595
peak=    3.332 closest distance to " O   HOH Z 419 " =    1.720
peak=    3.328 closest distance to " CE1 TYR A 186 " =    1.286
peak=    3.325 closest distance to " NH2 ARG A 156 " =    1.078
peak=    3.325 closest distance to " O   HOH Z 116 " =    2.775
peak=    3.323 closest distance to " OE1 GLU A   2 " =    2.098
peak=    3.322 closest distance to " O   HOH Z 325 " =    2.080
peak=    3.322 closest distance to " CA  ILE A 106 " =    0.748
peak=    3.319 closest distance to " CA  ASP A 162 " =    1.046
peak=    3.318 closest distance to " O   HOH Z 298 " =    4.256
peak=    3.317 closest distance to " O   HOH Z 109 " =    2.301
peak=    3.315 closest distance to " O   HOH Z 438 " =    2.416
peak=    3.308 closest distance to " O   HOH Z  78 " =    1.569
peak=    3.307 closest distance to " CB  ARG A 219 " =    1.125
peak=    3.305 closest distance to " CB  ASN A 215 " =    1.148
peak=    3.302 closest distance to " CA  ALA A 158 " =    1.357
peak=    3.300 closest distance to " O   SER A 164 " =    1.128
peak=    3.297 closest distance to " CG2 ILE A  49 " =    1.441
peak=    3.297 closest distance to " O   HOH Z 294 " =    1.539
peak=    3.297 closest distance to " CB  ILE A 120 " =    1.388
peak=    3.296 closest distance to " CG1 ILE A  33 " =    1.253
peak=    3.296 closest distance to " O   HOH Z 368 " =    3.548
peak=    3.295 closest distance to " O   HOH Z 344 " =    2.881
peak=    3.294 closest distance to " O   HOH Z 171 " =    2.769
peak=    3.294 closest distance to " CA  ALA A 233 " =    1.350
peak=    3.293 closest distance to " O   HOH Z 414 " =    1.356
peak=    3.291 closest distance to " O   HOH Z 409 " =    3.532
peak=    3.290 closest distance to " O   HOH Z 128 " =    1.457
peak=    3.288 closest distance to " CE1 HIS A 108 " =    1.138
peak=    3.287 closest distance to " O   HOH Z 299 " =    4.225
peak=    3.283 closest distance to " O   HOH Z 367 " =    3.466
peak=    3.283 closest distance to " CG BARG A 102 " =    1.748
peak=    3.278 closest distance to " O   HOH Z  83 " =    1.578
peak=    3.278 closest distance to " O   HOH Z  15 " =    2.015
peak=    3.278 closest distance to " O   HOH Z  94 " =    2.263
peak=    3.275 closest distance to " OH  TYR A 116 " =    1.173
peak=    3.275 closest distance to " CB  GLU A 128 " =    1.005
peak=    3.274 closest distance to " O   HOH Z 361 " =    3.130
peak=    3.274 closest distance to " CD2 TYR A 186 " =    1.005
peak=    3.270 closest distance to " O   HOH Z 252 " =    1.788
peak=    3.257 closest distance to " O   HOH Z 188 " =    1.882
peak=    3.252 closest distance to " N   TRP A 177 " =    1.814
peak=    3.250 closest distance to " CB  ALA A 295 " =    1.185
peak=    3.245 closest distance to " CD  LYS A 119 " =    1.963
peak=    3.230 closest distance to " CA  LEU A 282 " =    1.193
peak=    3.228 closest distance to " O   HOH Z 285 " =    2.700
peak=    3.228 closest distance to " CA  ALA A 291 " =    0.848
peak=    3.226 closest distance to " CB  ASN A 110 " =    1.074
peak=    3.224 closest distance to " O   HOH Z 355 " =    1.887
peak=    3.219 closest distance to " N   ARG A 190 " =    1.010
peak=    3.217 closest distance to " O   HOH Z 353 " =    2.815
peak=    3.214 closest distance to " CZ2 TRP A 150 " =    1.178
peak=    3.213 closest distance to " O   HOH Z 420 " =    2.314
peak=    3.213 closest distance to " CD1 LEU A 101 " =    1.235
peak=    3.212 closest distance to " NH2 ARG A  79 " =    1.310
peak=    3.209 closest distance to " OG1 THR A 294 " =    1.616
peak=    3.209 closest distance to " CA  LYS A 181 " =    1.065
peak=    3.209 closest distance to " OG1 THR A 221 " =    1.332
peak=    3.206 closest distance to " O   HOH Z 250 " =    1.407
peak=    3.206 closest distance to " OG  SER A  62 " =    2.742
peak=    3.206 closest distance to " O   HOH Z  49 " =    0.939
peak=    3.205 closest distance to " CA  ALA A  84 " =    1.260
peak=    3.202 closest distance to " O   HOH Z 102 " =    1.329
peak=    3.201 closest distance to " O   HOH Z 227 " =    2.118
peak=    3.198 closest distance to " O   HOH Z 227 " =    1.593
peak=    3.197 closest distance to " CG1 VAL A 174 " =    1.199
peak=    3.197 closest distance to " CA  SER A  87 " =    0.984
peak=    3.194 closest distance to " ND2 ASN A 249 " =    0.937
peak=    3.193 closest distance to " CE  LYS A  76 " =    0.874
peak=    3.187 closest distance to " O   HOH Z 366 " =    2.819
peak=    3.187 closest distance to " NH1AARG A 145 " =    1.264
peak=    3.186 closest distance to " N   CYS A 260 " =    0.784
peak=    3.185 closest distance to " CD2 HIS A  81 " =    1.053
peak=    3.182 closest distance to " CB  THR A 279 " =    1.639
peak=    3.180 closest distance to " O   HOH Z 256 " =    2.439
peak=    3.179 closest distance to " O   HOH Z 361 " =    3.609
peak=    3.175 closest distance to " OG  SER A  22 " =    2.683
peak=    3.175 closest distance to " O   HOH Z 188 " =    2.202
peak=    3.172 closest distance to " CA  ASN A 217 " =    1.296
peak=    3.170 closest distance to " OE2 GLU A  53 " =    2.052
peak=    3.163 closest distance to " CA  PHE A  59 " =    0.969
peak=    3.160 closest distance to " CG2 VAL A 197 " =    1.071
peak=    3.158 closest distance to " O   HOH Z 301 " =    1.858
peak=    3.156 closest distance to " O   HOH Z  19 " =    1.724
peak=    3.154 closest distance to " O   HOH Z 171 " =    3.900
peak=    3.154 closest distance to " O   HOH Z 291 " =    1.541
peak=    3.153 closest distance to " CB  LYS A 290 " =    0.974
peak=    3.146 closest distance to " NH2BARG A 190 " =    1.788
peak=    3.141 closest distance to " C   ALA A 299 " =    0.914
peak=    3.136 closest distance to " O   HOH Z  49 " =    3.583
peak=    3.135 closest distance to " CD1 ILE A  33 " =    1.740
peak=    3.134 closest distance to " O   HOH Z 134 " =    1.294
peak=    3.128 closest distance to " ND2 ASN A 110 " =    1.473
peak=    3.126 closest distance to " CA  GLY A 133 " =    3.619
peak=    3.124 closest distance to " O   HOH Z  90 " =    3.419
peak=    3.123 closest distance to " O   LEU A 228 " =    1.801
peak=    3.123 closest distance to " O   HOH Z 152 " =    1.722
peak=    3.118 closest distance to " CB  THR A 235 " =    1.142
peak=    3.110 closest distance to " CB  ALA A 114 " =    1.220
peak=    3.108 closest distance to " CD  ARG A  79 " =    1.766
peak=    3.107 closest distance to " CB  ALA A   1 " =    4.902
peak=    3.104 closest distance to " O   HOH Z 162 " =    1.512
peak=    3.100 closest distance to " O   HOH Z 299 " =    2.303
peak=    3.099 closest distance to " O   HOH Z  88 " =    3.002
peak=    3.097 closest distance to " CG BARG A 275 " =    1.310
peak=    3.096 closest distance to " O   HOH Z 329 " =    4.088
peak=    3.094 closest distance to " O   HOH Z  88 " =    3.170
peak=    3.092 closest distance to " CB  ALA A 242 " =    0.917
peak=    3.090 closest distance to " CB  GLN A 103 " =    0.936
peak=    3.074 closest distance to " OG  SER A 245 " =    1.546
peak=    3.073 closest distance to " CA  LYS A 290 " =    1.201
peak=    3.068 closest distance to " CB  MET A  47 " =    1.093
peak=    3.068 closest distance to " O   HOH Z 316 " =    2.369
peak=    3.057 closest distance to " O   HOH Z 173 " =    2.488
peak=    3.039 closest distance to " CB  TYR A  30 " =    1.047
peak=    3.034 closest distance to " NH1 ARG A 138 " =    1.308
peak=    3.033 closest distance to " O   HOH Z 305 " =    3.526

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 207         
Filter by distance & map next to the model:
   mapped sites are within: 0.629 - 5.745
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 204 from: 207
   mapped sites are within: 0.812 - 5.745

peak=   -4.767 closest distance to " CD  GLN A  58 " =    1.137
peak=   -4.580 closest distance to " SG  CYS A 254 " =    3.377
peak=   -4.475 closest distance to " CG2BVAL A  41 " =    2.565
peak=   -4.420 closest distance to " CD  ARG A 156 " =    2.023
peak=   -4.195 closest distance to " CD1 LEU A 101 " =    2.388
peak=   -4.155 closest distance to " O   HOH Z 166 " =    1.772
peak=   -4.154 closest distance to " CZ3 TRP A 179 " =    1.268
peak=   -4.129 closest distance to " CG  GLN A 223 " =    2.133
peak=   -4.119 closest distance to " O   HOH Z 351 " =    1.570
peak=   -4.099 closest distance to " CB  ALA A 248 " =    2.322
peak=   -4.088 closest distance to " OG BSER A 134 " =    1.339
peak=   -4.078 closest distance to " CB  PRO A 243 " =    2.668
peak=   -4.072 closest distance to " NE2 GLN A  88 " =    1.004
peak=   -4.042 closest distance to " O   PRO A 163 " =    2.189
peak=   -4.016 closest distance to " O   HOH Z 196 " =    2.056
peak=   -4.003 closest distance to " O   HOH Z 266 " =    5.242
peak=   -3.972 closest distance to " CD2 PHE A 192 " =    2.061
peak=   -3.967 closest distance to " OXT GLY A 302 " =    2.776
peak=   -3.938 closest distance to " CB  ALA A 161 " =    2.438
peak=   -3.882 closest distance to " C   HIS A 108 " =    1.207
peak=   -3.874 closest distance to " O   HOH Z 290 " =    1.136
peak=   -3.850 closest distance to " CB  PRO A 163 " =    2.528
peak=   -3.818 closest distance to " CG  ASP A 231 " =    0.812
peak=   -3.816 closest distance to " O   HOH Z 193 " =    1.527
peak=   -3.815 closest distance to " CG1 VAL A 112 " =    2.609
peak=   -3.807 closest distance to " O   HOH Z 394 " =    1.504
peak=   -3.799 closest distance to " O   HOH Z 114 " =    3.261
peak=   -3.792 closest distance to " ND2 ASN A 187 " =    1.617
peak=   -3.785 closest distance to " O   HOH Z 103 " =    1.945
peak=   -3.762 closest distance to " CB  ALA A 291 " =    2.222
peak=   -3.761 closest distance to " CB  ALA A 248 " =    2.080
peak=   -3.759 closest distance to " CA  GLY A 241 " =    2.482
peak=   -3.745 closest distance to " CD2 LEU A 237 " =    2.747
peak=   -3.740 closest distance to " O   PRO A 198 " =    1.220
peak=   -3.740 closest distance to " CZ  TYR A 169 " =    1.763
peak=   -3.733 closest distance to " N   ALA A 248 " =    2.224
peak=   -3.702 closest distance to " CD2 TYR A 293 " =    1.993
peak=   -3.696 closest distance to " O   HOH Z  13 " =    1.737
peak=   -3.692 closest distance to " CE2 TYR A  30 " =    2.722
peak=   -3.692 closest distance to " CD1 PHE A 130 " =    2.252
peak=   -3.678 closest distance to " O   HOH Z 193 " =    2.176
peak=   -3.667 closest distance to " O   HOH Z 165 " =    1.933
peak=   -3.665 closest distance to " CA  ASP A 298 " =    1.088
peak=   -3.661 closest distance to " ND2 ASN A  45 " =    1.108
peak=   -3.637 closest distance to " N   ALA A 226 " =    1.930
peak=   -3.629 closest distance to " CD1 PHE A  59 " =    2.050
peak=   -3.623 closest distance to " N   SER A 276 " =    1.357
peak=   -3.616 closest distance to " CG2 ILE A 263 " =    2.326
peak=   -3.608 closest distance to " CG1 VAL A 112 " =    2.655
peak=   -3.587 closest distance to " CE  MET A 105 " =    2.242
peak=   -3.581 closest distance to " NH2AARG A 275 " =    4.884
peak=   -3.579 closest distance to " O   HOH Z 435 " =    2.513
peak=   -3.558 closest distance to " CA  VAL A  67 " =    2.922
peak=   -3.542 closest distance to " O   HOH Z 283 " =    2.112
peak=   -3.539 closest distance to " CG  GLU A  53 " =    1.605
peak=   -3.537 closest distance to " O   HOH Z  44 " =    2.308
peak=   -3.534 closest distance to " O   HOH Z 211 " =    1.596
peak=   -3.532 closest distance to " CE3 TRP A 150 " =    2.168
peak=   -3.531 closest distance to " O   HOH Z 136 " =    2.461
peak=   -3.520 closest distance to " O   HOH Z 407 " =    2.851
peak=   -3.516 closest distance to " CD  ARG A 139 " =    1.673
peak=   -3.503 closest distance to " CB  ASP A 132 " =    2.313
peak=   -3.500 closest distance to " O   HOH Z 301 " =    2.474
peak=   -3.498 closest distance to " C   ILE A 239 " =    2.031
peak=   -3.489 closest distance to " N   HIS A 115 " =    2.247
peak=   -3.480 closest distance to " O   HOH Z 166 " =    1.675
peak=   -3.479 closest distance to " ND2 ASN A  69 " =    1.825
peak=   -3.478 closest distance to " O   PHE A 218 " =    1.623
peak=   -3.474 closest distance to " O   HOH Z 389 " =    1.857
peak=   -3.473 closest distance to " O   SER A 210 " =    1.977
peak=   -3.472 closest distance to " CD  LYS A 289 " =    2.478
peak=   -3.462 closest distance to " O   GLY A 196 " =    1.156
peak=   -3.459 closest distance to " OD1 ASN A 148 " =    1.539
peak=   -3.459 closest distance to " ND2 ASN A  39 " =    1.086
peak=   -3.450 closest distance to " O   VAL A 189 " =    2.647
peak=   -3.450 closest distance to " OG  SER A  97 " =    2.335
peak=   -3.448 closest distance to " O   HOH Z 131 " =    4.026
peak=   -3.438 closest distance to " O   SER A 271 " =    2.122
peak=   -3.435 closest distance to " NE2 GLN A  88 " =    1.821
peak=   -3.426 closest distance to " CE BMET A  47 " =    1.621
peak=   -3.423 closest distance to " CD  GLN A 223 " =    0.839
peak=   -3.423 closest distance to " C   SER A 206 " =    1.483
peak=   -3.416 closest distance to " N   GLN A  58 " =    1.843
peak=   -3.411 closest distance to " OH  TYR A 247 " =    2.060
peak=   -3.404 closest distance to " O   HOH Z 369 " =    2.311
peak=   -3.404 closest distance to " O   HOH Z 423 " =    2.299
peak=   -3.404 closest distance to " O   HOH Z 426 " =    1.874
peak=   -3.403 closest distance to " O   HOH Z  15 " =    1.522
peak=   -3.398 closest distance to " N   PHE A  59 " =    2.210
peak=   -3.398 closest distance to " N   THR A 157 " =    1.522
peak=   -3.390 closest distance to " CG  LEU A   5 " =    0.878
peak=   -3.388 closest distance to " CG  GLU A 277 " =    1.249
peak=   -3.383 closest distance to " O   VAL A 174 " =    2.201
peak=   -3.377 closest distance to " C   ASP A 231 " =    2.472
peak=   -3.375 closest distance to " O   ALA A   1 " =    1.690
peak=   -3.371 closest distance to " CD2 LEU A 167 " =    1.841
peak=   -3.369 closest distance to " CB  SER A 210 " =    1.211
peak=   -3.369 closest distance to " O   HOH Z   6 " =    1.704
peak=   -3.368 closest distance to " CG1 VAL A 296 " =    1.128
peak=   -3.366 closest distance to " OD2 ASP A 171 " =    2.282
peak=   -3.360 closest distance to " O   SER A 276 " =    1.718
peak=   -3.355 closest distance to " O   ALA A   8 " =    1.973
peak=   -3.346 closest distance to " O   HOH Z 313 " =    1.952
peak=   -3.345 closest distance to " OD1 ASN A 301 " =    2.024
peak=   -3.344 closest distance to " O   GLY A  80 " =    2.443
peak=   -3.343 closest distance to " O   HOH Z 154 " =    1.504
peak=   -3.342 closest distance to " O   ASN A 187 " =    1.602
peak=   -3.335 closest distance to " CG1 VAL A 112 " =    2.728
peak=   -3.327 closest distance to " CB  VAL A 296 " =    0.947
peak=   -3.326 closest distance to " O   HOH Z  11 " =    1.927
peak=   -3.317 closest distance to " OG ASER A 134 " =    1.377
peak=   -3.317 closest distance to " O   HOH Z  52 " =    1.630
peak=   -3.313 closest distance to " CG2 VAL A 296 " =    1.315
peak=   -3.309 closest distance to " O   HOH Z 185 " =    2.539
peak=   -3.306 closest distance to " OD1 ASN A 249 " =    2.310
peak=   -3.298 closest distance to " O   ASN A  45 " =    1.864
peak=   -3.295 closest distance to " O   HOH Z 102 " =    1.614
peak=   -3.294 closest distance to " CG  TRP A 266 " =    1.924
peak=   -3.293 closest distance to " CD1 ILE A 199 " =    2.394
peak=   -3.288 closest distance to " O   HOH Z 191 " =    5.745
peak=   -3.287 closest distance to " O   GLY A  75 " =    1.817
peak=   -3.283 closest distance to " O   HOH Z 295 " =    1.436
peak=   -3.282 closest distance to " OD2 ASP A  50 " =    2.090
peak=   -3.282 closest distance to " O   HOH Z 174 " =    3.912
peak=   -3.279 closest distance to " O   HOH Z  17 " =    1.284
peak=   -3.277 closest distance to " CB  ALA A  43 " =    2.383
peak=   -3.270 closest distance to " O   ILE A 106 " =    1.887
peak=   -3.269 closest distance to " NH2 ARG A  79 " =    2.062
peak=   -3.267 closest distance to " O   HOH Z 353 " =    2.223
peak=   -3.262 closest distance to " O   HOH Z  19 " =    2.217
peak=   -3.262 closest distance to " CB  PHE A 208 " =    2.368
peak=   -3.261 closest distance to " OE1 GLN A 223 " =    1.997
peak=   -3.261 closest distance to " O   ILE A 234 " =    1.224
peak=   -3.256 closest distance to " O   HOH Z 377 " =    1.568
peak=   -3.254 closest distance to " O   HOH Z 177 " =    1.681
peak=   -3.250 closest distance to " CE1 TYR A 247 " =    2.634
peak=   -3.249 closest distance to " N   ALA A 248 " =    1.672
peak=   -3.248 closest distance to " O   HOH Z 252 " =    3.862
peak=   -3.244 closest distance to " CA  GLY A 133 " =    2.330
peak=   -3.243 closest distance to " O   HOH Z  63 " =    1.095
peak=   -3.239 closest distance to " O   HOH Z 264 " =    1.695
peak=   -3.235 closest distance to " CG1 VAL A 230 " =    1.911
peak=   -3.234 closest distance to " CG2 THR A 182 " =    2.230
peak=   -3.234 closest distance to " O   HOH Z 174 " =    2.281
peak=   -3.233 closest distance to " C   ILE A 234 " =    1.318
peak=   -3.232 closest distance to " CA  SER A  62 " =    2.555
peak=   -3.230 closest distance to " C   MET A 188 " =    1.493
peak=   -3.228 closest distance to " N   ALA A  43 " =    2.677
peak=   -3.225 closest distance to " OXT GLY A 302 " =    3.491
peak=   -3.221 closest distance to " CZ  PHE A  38 " =    2.022
peak=   -3.213 closest distance to " C   GLN A 205 " =    1.838
peak=   -3.211 closest distance to " O   HOH Z 244 " =    1.308
peak=   -3.209 closest distance to " C   ALA A 158 " =    1.303
peak=   -3.208 closest distance to " N   ASP A 171 " =    2.303
peak=   -3.207 closest distance to " O   HOH Z 285 " =    1.659
peak=   -3.206 closest distance to " CG  GLU A 152 " =    1.137
peak=   -3.203 closest distance to " OG  SER A  26 " =    1.185
peak=   -3.202 closest distance to " CD  PRO A 243 " =    2.064
peak=   -3.201 closest distance to " O   HOH Z  71 " =    1.870
peak=   -3.198 closest distance to " O   HOH Z  38 " =    1.790
peak=   -3.196 closest distance to " O   ARG A  24 " =    2.003
peak=   -3.184 closest distance to " O   HOH Z 434 " =    1.736
peak=   -3.182 closest distance to " CG1 VAL A 125 " =    2.358
peak=   -3.180 closest distance to " N   THR A  52 " =    1.723
peak=   -3.176 closest distance to " NE  ARG A  66 " =    4.214
peak=   -3.175 closest distance to " C   THR A 279 " =    1.130
peak=   -3.174 closest distance to " N   SER A   3 " =    2.181
peak=   -3.164 closest distance to " CA  GLY A 133 " =    1.942
peak=   -3.163 closest distance to " CG  ARG A  66 " =    2.538
peak=   -3.153 closest distance to " O   PRO A 198 " =    1.271
peak=   -3.152 closest distance to " O   HOH Z 431 " =    1.977
peak=   -3.152 closest distance to " O   TRP A  92 " =    2.010
peak=   -3.145 closest distance to " CB  ASP A 132 " =    2.406
peak=   -3.145 closest distance to " O   HOH Z  60 " =    2.185
peak=   -3.143 closest distance to " CB  TRP A  85 " =    2.626
peak=   -3.140 closest distance to " NE2 GLN A  58 " =    2.418
peak=   -3.140 closest distance to " CG  PHE A 283 " =    2.613
peak=   -3.138 closest distance to " O   HOH Z 203 " =    1.718
peak=   -3.136 closest distance to " O   HOH Z 234 " =    4.080
peak=   -3.125 closest distance to " NE2 GLN A 194 " =    1.810
peak=   -3.122 closest distance to " OG1 THR A  82 " =    1.485
peak=   -3.121 closest distance to " O   HOH Z  90 " =    1.846
peak=   -3.111 closest distance to " O   HOH Z  10 " =    1.506
peak=   -3.108 closest distance to " O   SER A   3 " =    1.107
peak=   -3.107 closest distance to " O   SER A  95 " =    1.600
peak=   -3.103 closest distance to " O   HOH Z 340 " =    1.162
peak=   -3.101 closest distance to " O   HOH Z 252 " =    4.082
peak=   -3.099 closest distance to " O   ASN A 301 " =    1.540
peak=   -3.097 closest distance to " O   HOH Z 216 " =    1.606
peak=   -3.095 closest distance to " O   HOH Z 404 " =    1.408
peak=   -3.083 closest distance to " OD1 ASP A 231 " =    1.131
peak=   -3.078 closest distance to " NH2 ARG A  66 " =    1.845
peak=   -3.076 closest distance to " O   HOH Z 110 " =    1.413
peak=   -3.068 closest distance to " OG BSER A 134 " =    1.841
peak=   -3.065 closest distance to " NE1 TRP A 266 " =    2.494
peak=   -3.064 closest distance to " O   HOH Z 421 " =    3.645
peak=   -3.062 closest distance to " CG  PRO A 163 " =    2.708
peak=   -3.056 closest distance to " CA  GLY A 241 " =    3.129
peak=   -3.050 closest distance to " O   HOH Z 222 " =    1.639
peak=   -3.045 closest distance to " O   HOH Z 422 " =    1.476
peak=   -3.039 closest distance to " CH2 TRP A 150 " =    1.068
peak=   -3.023 closest distance to " O   HOH Z 265 " =    1.377
peak=   -3.018 closest distance to " O   HOH Z  64 " =    2.753
peak=   -3.017 closest distance to " O   HOH Z  11 " =    2.010

================= 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    :  0.4645 0.4471   6.263692e+00   6.244763e+00
   1_bss:  0.4558 0.4405   6.255006e+00   6.237906e+00
   1_xyz:  0.3550 0.3746   6.092245e+00   6.126320e+00
   1_adp:  0.3020 0.3461   5.968731e+00   6.062700e+00
   1_occ:  0.3016 0.3471   5.968077e+00   6.063894e+00
   2_bss:  0.2972 0.3425   5.968743e+00   6.063418e+00
   2_xyz:  0.1946 0.2353   5.596128e+00   5.764916e+00
   2_adp:  0.1712 0.2121   5.485674e+00   5.670353e+00
   2_occ:  0.1710 0.2122   5.485074e+00   5.670826e+00
   3_bss:  0.1689 0.2123   5.483950e+00   5.668563e+00
   3_xyz:  0.1357 0.1739   5.292549e+00   5.491711e+00
   3_adp:  0.1283 0.1692   5.251603e+00   5.464672e+00
   3_occ:  0.1281 0.1694   5.251534e+00   5.465290e+00
   4_bss:  0.1284 0.1697   5.252359e+00   5.464606e+00
   4_xyz:  0.1142 0.1606   5.173552e+00   5.412230e+00
   4_adp:  0.1133 0.1575   5.160047e+00   5.392408e+00
   4_occ:  0.1133 0.1575   5.159702e+00   5.392153e+00
   5_bss:  0.1132 0.1575   5.159790e+00   5.392337e+00
   5_xyz:  0.1115 0.1561   5.149615e+00   5.386675e+00
   5_adp:  0.1118 0.1556   5.150190e+00   5.385284e+00
   5_occ:  0.1117 0.1556   5.150022e+00   5.385289e+00
   5_bss:  0.1117 0.1557   5.149992e+00   5.385344e+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:  0.337  20.002   7.446   9.269   9.185   0.000   0.000   0.000
   1_xyz:  0.337  20.002   7.446   9.269   9.185   0.000   0.000   0.000
   1_adp:  0.337  20.002   7.446   9.269   9.185   0.000   0.000   0.000
   1_occ:  0.337  20.002   7.446   9.269   9.185   0.000   0.000   0.000
   2_bss:  0.328  40.660   3.811   5.231   5.618   0.000   0.000   0.000
   2_xyz:  0.328  40.660   3.811   5.231   5.618   0.000   0.000   0.000
   2_adp:  0.328  40.660   3.811   5.231   5.618   0.000   0.000   0.000
   2_occ:  0.328  40.660   3.811   5.231   5.618   0.000   0.000   0.000
   3_bss:  0.317  47.638   2.020   3.366   4.064   0.000   0.000   0.000
   3_xyz:  0.317  47.638   2.020   3.366   4.064   0.000   0.000   0.000
   3_adp:  0.317  47.638   2.020   3.366   4.064   0.000   0.000   0.000
   3_occ:  0.317  47.638   2.020   3.366   4.064   0.000   0.000   0.000
   4_bss:  0.328  53.551   1.805   2.929   3.858   0.000   0.000   0.000
   4_xyz:  0.328  53.551   1.805   2.929   3.858   0.000   0.000   0.000
   4_adp:  0.328  53.551   1.805   2.929   3.858   0.000   0.000   0.000
   4_occ:  0.328  53.551   1.805   2.929   3.858   0.000   0.000   0.000
   5_bss:  0.326  50.108   1.851   2.861   3.912   0.000   0.000   0.000
   5_xyz:  0.326  50.108   1.851   2.861   3.912   0.000   0.000   0.000
   5_adp:  0.326  50.108   1.851   2.861   3.912   0.000   0.000   0.000
   5_occ:  0.326  50.108   1.851   2.861   3.912   0.000   0.000   0.000
   5_bss:  0.315  51.500  -1.024  -0.014   1.038   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  51.436 0.5041  0.5775    60335.736
   1_bss:  51.187 0.5057  0.7531    58487.466
   1_xyz:  41.083 0.6287  0.9036    38684.374
   1_adp:  36.112 0.6884  1.0039    31907.149
   1_occ:  36.174 0.6877  1.0020    32008.966
   2_bss:  35.973 0.6901  0.8812    31876.372
   2_xyz:  23.749 0.8233  1.0030    14390.160
   2_adp:  20.830 0.8534  1.0235    11780.319
   2_occ:  20.837 0.8533  1.0233    11778.290
   3_bss:  20.742 0.8542  0.9613    11696.484
   3_xyz:  16.475 0.8939  0.9824     7974.736
   3_adp:  15.819 0.8998  0.9824     7547.461
   3_occ:  15.831 0.8997  0.9821     7552.765
   4_bss:  15.828 0.8997  0.9726     7557.094
   4_xyz:  14.753 0.9088  0.9762     6797.140
   4_adp:  14.307 0.9127  0.9756     6576.252
   4_occ:  14.299 0.9128  0.9755     6571.504
   5_bss:  14.303 0.9127  0.9759     6572.120
   5_xyz:  14.161 0.9139  0.9763     6482.807
   5_adp:  14.091 0.9146  0.9740     6462.654
   5_occ:  14.092 0.9146  0.9739     6460.964
   5_bss:  14.090 0.9146  0.9738     6459.279
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3789e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3789e+01
   1_xyz:   1.670  0.013  0.108 17.858  0.007  4.110   1.3635e-01
   1_adp:   1.670  0.013  0.108 17.858  0.007  4.110   1.3635e-01
   1_occ:   1.670  0.013  0.108 17.858  0.007  4.110   1.3635e-01
   2_bss:   1.670  0.013  0.108 17.858  0.007  4.110   1.3635e-01
   2_xyz:   1.141  0.009  0.079 15.960  0.004  4.127   7.7103e-02
   2_adp:   1.141  0.009  0.079 15.960  0.004  4.127   7.7103e-02
   2_occ:   1.141  0.009  0.079 15.960  0.004  4.127   7.7103e-02
   3_bss:   1.141  0.009  0.079 15.960  0.004  4.127   7.7103e-02
   3_xyz:   0.996  0.007  0.076 15.649  0.004  4.125   6.0891e-02
   3_adp:   0.996  0.007  0.076 15.649  0.004  4.125   6.0891e-02
   3_occ:   0.996  0.007  0.076 15.649  0.004  4.125   6.0891e-02
   4_bss:   0.996  0.007  0.076 15.649  0.004  4.125   6.0891e-02
   4_xyz:   1.165  0.010  0.092 15.752  0.004  4.112   8.0610e-02
   4_adp:   1.165  0.010  0.092 15.752  0.004  4.112   8.0610e-02
   4_occ:   1.165  0.010  0.092 15.752  0.004  4.112   8.0610e-02
   5_bss:   1.165  0.010  0.092 15.752  0.004  4.112   8.0610e-02
   5_xyz:   1.133  0.010  0.091 15.583  0.004  4.113   7.6779e-02
   5_adp:   1.133  0.010  0.091 15.583  0.004  4.113   7.6779e-02
   5_occ:   1.133  0.010  0.091 15.583  0.004  4.113   7.6779e-02
   5_bss:   1.133  0.010  0.091 15.583  0.004  4.113   7.6779e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9717e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9717e+00
   1_xyz:  15.394  0.165  0.504 84.972  0.035  2.269   1.0204e-01
   1_adp:  15.394  0.165  0.504 84.972  0.035  2.269   1.0204e-01
   1_occ:  15.394  0.165  0.504 84.972  0.035  2.269   1.0204e-01
   2_bss:  15.394  0.165  0.504 84.972  0.035  2.269   1.0204e-01
   2_xyz:   7.305  0.083  0.291 85.212  0.039  2.182   9.1670e-02
   2_adp:   7.305  0.083  0.291 85.212  0.039  2.182   9.1670e-02
   2_occ:   7.305  0.083  0.291 85.212  0.039  2.182   9.1670e-02
   3_bss:   7.305  0.083  0.291 85.212  0.039  2.182   9.1670e-02
   3_xyz:   6.926  0.046  0.382 80.815  0.046  2.270   4.2448e-02
   3_adp:   6.926  0.046  0.382 80.815  0.046  2.270   4.2448e-02
   3_occ:   6.926  0.046  0.382 80.815  0.046  2.270   4.2448e-02
   4_bss:   6.926  0.046  0.382 80.815  0.046  2.270   4.2448e-02
   4_xyz:   8.031  0.055  0.564 82.433  0.042  2.261   6.1281e-02
   4_adp:   8.031  0.055  0.564 82.433  0.042  2.261   6.1281e-02
   4_occ:   8.031  0.055  0.564 82.433  0.042  2.261   6.1281e-02
   5_bss:   8.031  0.055  0.564 82.433  0.042  2.261   6.1281e-02
   5_xyz:   8.021  0.058  0.559 82.159  0.037  2.287   5.7163e-02
   5_adp:   8.021  0.058  0.559 82.159  0.037  2.287   5.7163e-02
   5_occ:   8.021  0.058  0.559 82.159  0.037  2.287   5.7163e-02
   5_bss:   8.021  0.058  0.559 82.159  0.037  2.287   5.7163e-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:  70.48   0.00  12.13  64.86   0.00   9.27  70.48   0.00  27.75
   1_occ:  70.48   0.00  12.13  64.86   0.00   9.27  70.48   0.00  27.75
   2_bss:  70.48   0.00  12.13  64.86   0.00   9.27  70.48   0.00  27.75
   2_xyz:  70.48   0.00  12.13  64.86   0.00   9.27  70.48   0.00  27.75
   2_adp:  70.08   0.00  12.10  70.08   0.00   8.31  68.37   0.62  32.74
   2_occ:  70.08   0.00  12.10  70.08   0.00   8.31  68.37   0.62  32.74
   3_bss:  70.08   0.00  12.10  70.08   0.00   8.31  68.37   0.62  32.74
   3_xyz:  70.08   0.00  12.10  70.08   0.00   8.31  68.37   0.62  32.74
   3_adp:  87.54   0.00  12.91  87.54   0.00   8.41  78.58   0.98  37.42
   3_occ:  87.54   0.00  12.91  87.54   0.00   8.41  78.58   0.98  37.42
   4_bss:  87.54   0.00  12.91  87.54   0.00   8.41  78.58   0.98  37.42
   4_xyz:  87.54   0.00  12.91  87.54   0.00   8.41  78.58   0.98  37.42
   4_adp:  87.05   0.00  12.42  87.05   0.00   8.16  78.35   1.46  35.60
   4_occ:  87.05   0.00  12.42  87.05   0.00   8.16  78.35   1.46  35.60
   5_bss:  87.05   0.00  12.42  87.05   0.00   8.16  78.35   1.46  35.60
   5_xyz:  87.05   0.00  12.42  87.05   0.00   8.16  78.35   1.46  35.60
   5_adp:  85.72   0.00  12.08  85.72   0.00   8.02  77.20   1.58  34.16
   5_occ:  85.72   0.00  12.08  85.72   0.00   8.02  77.20   1.58  34.16
   5_bss:  88.60   2.87  14.95  88.60   2.87  10.90  80.08   4.46  37.04
------------------------------------------------------------------------
 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:    1.261    0.025    0.413
   1_adp:    1.261    0.025    0.413
   1_occ:    1.261    0.025    0.413
   2_bss:    1.261    0.025    0.413
   2_xyz:    1.664    0.037    0.579
   2_adp:    1.664    0.037    0.579
   2_occ:    1.664    0.037    0.579
   3_bss:    1.664    0.037    0.579
   3_xyz:    1.691    0.012    0.606
   3_adp:    1.691    0.012    0.606
   3_occ:    1.691    0.012    0.606
   4_bss:    1.691    0.012    0.606
   4_xyz:    1.798    0.036    0.640
   4_adp:    1.798    0.036    0.640
   4_occ:    1.798    0.036    0.640
   5_bss:    1.798    0.036    0.640
   5_xyz:    1.861    0.045    0.649
   5_adp:    1.861    0.045    0.649
   5_occ:    1.861    0.045    0.649
   5_bss:    1.861    0.045    0.649
------------------------------------------------------------------------

CPU time actual refinement: 284.37


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_326/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_326/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_326/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_326/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_326/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 284.23 
  Macro-tasks:
    bulk solvent and scale       = 37.22  
    individual site refinement   = 111.88 
    weights calculation          = 27.61  
    collect and process          = 5.61   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 182.42 
  Micro-tasks:
    mask                            = 1.53   
    f_calc                          = 86.97  
    alpha_beta                      = 7.27   
    target                          = 1.03   
    gradients_wrt_atomic_parameters = 94.65  
    fmodel                         = 6.25   
    r_factors                      = 0.32   
    phase_errors                   = 8.83   
    foms                           = 0.24   
    TOTAL for micro-tasks          = 207.09 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.058 micro seconds
Total CPU time: 4.93 minutes
from_scatterers_fft:    639 calls, 86.67 s
gradients_fft:          584 calls, 83.64 s

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

# Date 2008-01-16 Time 01:17:11 PST -0800 (1200475031.95 s)
Start R-work = 0.4645, R-free = 0.4471 (no bulk solvent and anisotropic scale)
Final R-work = 0.1297, R-free = 0.1718 (no bulk solvent and anisotropic scale)

Start R-work = 0.4558, R-free = 0.4405
Final R-work = 0.1117, R-free = 0.1557