# Date 2008-01-16 Time 00:51:02 PST -0800 (1200473462.17 s)
#phil __OFF__

Command line arguments: "../166.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 8195
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 166

-------------------------------------------------------------------------------
  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: (68.845, 46.6953, 84.6622, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, per 1000 atoms: 1.15


================================== 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: (68.845, 46.6953, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6941 1.96047
Completeness in resolution range: 0.97158
Completeness with d_max=infinity: 0.968506

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.6941
                             d_min =   1.9605

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: (68.845, 46.6953, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6941 1.96047
Completeness in resolution range: 0.97158
Completeness with d_max=infinity: 0.968506

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.6945 -  4.1940 [2114/2141]  1903   211  10.0%
  bin  2:  4.1940 -  3.3418 [2031/2047]  1827   204  10.0%
  bin  3:  3.3418 -  2.9232 [2016/2035]  1813   203  10.1%
  bin  4:  2.9232 -  2.6576 [1981/2011]  1789   192   9.7%
  bin  5:  2.6576 -  2.4681 [1970/1989]  1769   201  10.2%
  bin  6:  2.4681 -  2.3232 [1963/1999]  1768   195   9.9%
  bin  7:  2.3232 -  2.2072 [1958/1991]  1764   194   9.9%
  bin  8:  2.2072 -  2.1114 [1944/1979]  1746   198  10.2%
  bin  9:  2.1114 -  2.0304 [1939/1966]  1745   194  10.0%
  bin 10:  2.0304 -  1.9605 [1673/2004]  1506   167  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_166/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.06 -     1.83: 11
        1.83 -     2.60: 98
        2.60 -     3.36: 4230
        3.36 -     4.13: 9627
        4.13 -     4.90: 15041
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.059 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.330 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.503 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.581 3.040 -x+1,y+1/2,-z+1/2
  " OD2 ASP A 107 " - " OG ASER A 216 "  1.655 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 29002 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_166/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_166/model_refine_001.geo

CPU time processing inputs: 9.14


============================ 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 = 68.845 46.69535 84.6622 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4833   r_free= 0.4750   ksol= 0.00   Bsol= 0.00   scale= 0.807    |
|                                                                             |
| 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:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.280271                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6945 -  4.6774 0.99   1374  153 0.3969 0.3931      6.5855      6.6083|
|  2:  4.6774 -  3.7326 0.99   1322  146 0.4093 0.4060      6.7797      6.7954|
|  3:  3.7326 -  3.2667 0.99   1299  146 0.4369 0.4056      6.6783      6.7463|
|  4:  3.2667 -  2.9707 0.99   1285  139 0.4532 0.4748      6.5236      6.4942|
|  5:  2.9707 -  2.7593 0.99   1275  142 0.5014 0.5269      6.3874      6.3737|
|  6:  2.7593 -  2.5975 0.99   1279  146 0.5159 0.5285      6.2981      6.2593|
|  7:  2.5975 -  2.4681 0.99   1267  139 0.5156 0.4964      6.2506       6.167|
|  8:  2.4681 -  2.3611 0.98   1269  142 0.5245 0.5105      6.1998      6.1858|
|  9:  2.3611 -  2.2705 0.98   1264  139 0.5343 0.5219      6.1235      6.1356|
| 10:  2.2705 -  2.1925 0.98   1243  136 0.5360 0.5054      6.1271      6.0861|
| 11:  2.1925 -  2.1241 1.00   1267  147 0.5461 0.5376      6.0546      6.1038|
| 12:  2.1241 -  2.0636 0.97   1252  128 0.5208 0.4694      5.9845      6.0007|
| 13:  2.0636 -  2.0094 0.98   1241  138 0.5489 0.5319      5.9102      5.8913|
| 14:  2.0094 -  1.9605 0.79    993  118 0.5351 0.5245      5.8523      5.7563|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6945 -  4.6774  1374   153  0.66  38.00   0.80     0.68      81988.78|
|  2:  4.6774 -  3.7326  1322   146  0.67  37.87   0.89     0.74     118220.58|
|  3:  3.7326 -  3.2667  1299   146  0.58  45.74   0.87     0.71     124504.09|
|  4:  3.2667 -  2.9707  1285   139  0.51  51.43   0.83     0.62     106317.80|
|  5:  2.9707 -  2.7593  1275   142  0.43  57.21   0.74     0.53      84695.55|
|  6:  2.7593 -  2.5975  1279   146  0.41  59.21   0.73     0.48      70620.37|
|  7:  2.5975 -  2.4681  1267   139  0.39  60.57   0.74     0.45      64868.98|
|  8:  2.4681 -  2.3611  1269   142  0.39  60.60   0.75     0.45      56725.47|
|  9:  2.3611 -  2.2705  1264   139  0.38  61.80   0.73     0.46      52606.06|
| 10:  2.2705 -  2.1925  1243   136  0.40  59.95   0.77     0.48      46138.54|
| 11:  2.1925 -  2.1241  1267   147  0.36  63.10   0.77     0.46      45472.46|
| 12:  2.1241 -  2.0636  1252   128  0.34  64.73   0.75     0.42      43438.09|
| 13:  2.0636 -  2.0094  1241   138  0.28  69.36   0.75     0.36      39468.70|
| 14:  2.0094 -  1.9605   993   118  0.26  70.50   0.74     0.29      31866.43|
|alpha:            min =        0.29 max =            0.74 mean =         0.52|
|beta:             min =    31866.43 max =       124504.09 mean =     70121.36|
|figures of merit: min =        0.00 max =            1.00 mean =         0.44|
|phase err.(work): min =        0.00 max =           89.95 mean =        56.71|
|phase err.(test): min =        0.00 max =           89.83 mean =        57.19|
|-----------------------------------------------------------------------------|

============================== 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 = 14.723042             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.648   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.211098              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 82.664   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  0.684 -  1.106:        1 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.106 -  1.527:        4 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.527 -  1.949:       39 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  1.949 -  2.370:      271 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.370 -  2.792:     1025 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.792 -  3.214:     2232 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.214 -  3.635:     3862 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.635 -  4.057:     5509 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.057 -  4.478:     7230 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.478 -  4.900:     8845 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       52.767 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.086    4.900  0.684 |       2.815 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.345)------------------------------------------|
|    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 = 11.345)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4880   r_free= 0.4808   ksol= 0.00   Bsol= 0.00   scale= 0.775    |
|                                                                             |
| 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:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.282045                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4735   r_free= 0.4639   ksol= 0.38   Bsol= 3.35   scale= 1.011    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.00,8.07,9.42,0.00,0.00,0.00); trace/3= 8.50                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.272909                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.430846             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.876   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.146419              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.538   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4735      final r-factor (work) = 0.3944          |
| start r-factor (free) = 0.4639      final r-factor (free) = 0.4113          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 91.8087 = 12.43 * 0.50 * 6.2815 + 1.00 * 52.7665                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.6239 = 12.43 * 0.50 * 6.1900 + 1.00 * 0.1504                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3944      final r-factor (work) = 0.3476          |
| start r-factor (free) = 0.4113      final r-factor (free) = 0.3965          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1107 = 1.15 * 1.00 * 6.1900 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.0123 = 1.15 * 1.00 * 6.1023 + 1.00 * 0.0165                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.345)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.99   12.94    None  None   None       |
|    all(noH): 2823   0      0.00    72.99   12.94    None  None   None       |
|    Sol.    : 438    0      0.00    68.87   26.19    None  None   None       |
|    Mac.    : 2385   0      0.00    72.99   10.50    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 -   7.299: 1118   |   5:    36.493 -  43.792:   77        |
|      1:     7.299 -  14.597:  747   |   6:    43.792 -  51.090:   36        |
|      2:    14.597 -  21.896:  417   |   7:    51.090 -  58.389:   19        |
|      3:    21.896 -  29.194:  252   |   8:    58.389 -  65.687:    7        |
|      4:    29.194 -  36.493:  145   |   9:    65.687 -  72.986:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3476 r_free = 0.3965             target_work(ml) = 6.083         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3471 r_free = 0.3963             target_work(ml) = 6.082         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3471   r_free= 0.3963   ksol= 0.38   Bsol= 3.35   scale= 1.113    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.00,8.07,9.42,0.00,0.00,0.00); trace/3= 8.50                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.081865                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3429   r_free= 0.3922   ksol= 0.34   Bsol= 22.66   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.26,4.06,5.96,0.00,0.00,0.00); trace/3= 4.76                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.079996                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.432250              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.929   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.543169              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.992  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3429      final r-factor (work) = 0.2452          |
| start r-factor (free) = 0.3922      final r-factor (free) = 0.2952          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.8078 = 7.43 * 0.50 * 6.0971 + 1.00 * 0.1504                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.1961 = 7.43 * 0.50 * 5.9488 + 1.00 * 0.0897                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2452      final r-factor (work) = 0.2185          |
| start r-factor (free) = 0.2952      final r-factor (free) = 0.2690          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2508 = 0.54 * 1.00 * 5.9488 + 1.00 * 0.0196                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1336 = 0.54 * 1.00 * 5.7468 + 1.00 * 0.0121                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.345)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    136.78  12.92    None  None   None       |
|    all(noH): 2823   0      0.00    136.78  12.92    None  None   None       |
|    Sol.    : 438    0      1.16    70.42   32.36    None  None   None       |
|    Mac.    : 2385   0      0.00    136.78  9.35     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 -  13.678: 1969   |   5:    68.389 -  82.067:    4        |
|      1:    13.678 -  27.356:  440   |   6:    82.067 -  95.745:    0        |
|      2:    27.356 -  41.034:  257   |   7:    95.745 - 109.423:    0        |
|      3:    41.034 -  54.711:  126   |   8:   109.423 - 123.101:    0        |
|      4:    54.711 -  68.389:   25   |   9:   123.101 - 136.778:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2185 r_free = 0.2690             target_work(ml) = 5.706         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2181 r_free = 0.2683             target_work(ml) = 5.705         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2181   r_free= 0.2683   ksol= 0.34   Bsol= 22.66   scale= 1.065   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.26,4.06,5.96,0.00,0.00,0.00); trace/3= 4.76                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.704827                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2158   r_free= 0.2670   ksol= 0.33   Bsol= 33.48   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.23,2.64,3.77,0.00,0.00,0.00); trace/3= 2.88                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.701851                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.825320              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.642   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.325646              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.308  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2158      final r-factor (work) = 0.1602          |
| start r-factor (free) = 0.2670      final r-factor (free) = 0.2074          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2164 = 2.83 * 0.50 * 5.7527 + 1.00 * 0.0897                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9440 = 2.83 * 0.50 * 5.5804 + 1.00 * 0.0608                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1602      final r-factor (work) = 0.1482          |
| start r-factor (free) = 0.2074      final r-factor (free) = 0.1938          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8294 = 0.33 * 1.00 * 5.5804 + 1.00 * 0.0121                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7710 = 0.33 * 1.00 * 5.4065 + 1.00 * 0.0104                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.345)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.10   13.07    None  None   None       |
|    all(noH): 2823   0      0.00    99.10   13.07    None  None   None       |
|    Sol.    : 438    0      2.21    75.26   35.56    None  None   None       |
|    Mac.    : 2385   0      0.00    99.10   8.94     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.910: 1743   |   5:    49.550 -  59.460:   63        |
|      1:     9.910 -  19.820:  540   |   6:    59.460 -  69.370:   23        |
|      2:    19.820 -  29.730:  164   |   7:    69.370 -  79.280:    6        |
|      3:    29.730 -  39.640:  145   |   8:    79.280 -  89.190:    0        |
|      4:    39.640 -  49.550:  137   |   9:    89.190 -  99.100:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1482 r_free = 0.1938             target_work(ml) = 5.370         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1480 r_free = 0.1938             target_work(ml) = 5.369         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1480   r_free= 0.1938   ksol= 0.33   Bsol= 33.48   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.23,2.64,3.77,0.00,0.00,0.00); trace/3= 2.88                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.369020                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1476   r_free= 0.1926   ksol= 0.32   Bsol= 29.65   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.48,2.11,2.85,0.00,0.00,0.00); trace/3= 2.15                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.366926                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.858744              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.752  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.150752              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.832  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1476      final r-factor (work) = 0.1208          |
| start r-factor (free) = 0.1926      final r-factor (free) = 0.1654          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.4975 = 3.86 * 0.50 * 5.4094 + 1.00 * 0.0608                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2648 = 3.86 * 0.50 * 5.2822 + 1.00 * 0.0734                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1208      final r-factor (work) = 0.1183          |
| start r-factor (free) = 0.1654      final r-factor (free) = 0.1602          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8066 = 0.15 * 1.00 * 5.2822 + 1.00 * 0.0103                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7900 = 0.15 * 1.00 * 5.1873 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.345)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.31    81.64   12.47    None  None   None       |
|    all(noH): 2823   0      0.31    81.64   12.47    None  None   None       |
|    Sol.    : 438    0      2.63    78.16   33.46    None  None   None       |
|    Mac.    : 2385   0      0.31    81.64   8.61     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:     0.307 -   8.440: 1598   |   5:    40.972 -  49.106:   85        |
|      1:     8.440 -  16.573:  654   |   6:    49.106 -  57.239:   49        |
|      2:    16.573 -  24.706:  157   |   7:    57.239 -  65.372:   16        |
|      3:    24.706 -  32.839:  133   |   8:    65.372 -  73.505:    5        |
|      4:    32.839 -  40.972:  122   |   9:    73.505 -  81.638:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1183 r_free = 0.1602             target_work(ml) = 5.171         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1181 r_free = 0.1600             target_work(ml) = 5.170         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1181   r_free= 0.1600   ksol= 0.32   Bsol= 29.65   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.48,2.11,2.85,0.00,0.00,0.00); trace/3= 2.15                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.170149                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1181   r_free= 0.1593   ksol= 0.32   Bsol= 30.95   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.25,1.91,2.58,0.00,0.00,0.00); trace/3= 1.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.169414                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.402858              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 118.218  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.255361              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 155.941  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1181      final r-factor (work) = 0.1168          |
| start r-factor (free) = 0.1593      final r-factor (free) = 0.1583          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.7114 = 1.40 * 0.50 * 5.1866 + 1.00 * 0.0734                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.6793 = 1.40 * 0.50 * 5.1670 + 1.00 * 0.0550                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1168      final r-factor (work) = 0.1150          |
| start r-factor (free) = 0.1583      final r-factor (free) = 0.1580          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3275 = 0.26 * 1.00 * 5.1670 + 1.00 * 0.0081                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3249 = 0.26 * 1.00 * 5.1530 + 1.00 * 0.0090                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.345)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.38   12.63    None  None   None       |
|    all(noH): 2823   0      0.00    84.38   12.63    None  None   None       |
|    Sol.    : 438    0      2.39    78.53   34.39    None  None   None       |
|    Mac.    : 2385   0      0.00    84.38   8.64     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 -   8.438: 1610   |   5:    42.190 -  50.628:   93        |
|      1:     8.438 -  16.876:  647   |   6:    50.628 -  59.066:   50        |
|      2:    16.876 -  25.314:  155   |   7:    59.066 -  67.504:   14        |
|      3:    25.314 -  33.752:  125   |   8:    67.504 -  75.942:    4        |
|      4:    33.752 -  42.190:  121   |   9:    75.942 -  84.380:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1150 r_free = 0.1580             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1149 r_free = 0.1579             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1149   r_free= 0.1579   ksol= 0.32   Bsol= 30.95   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.25,1.91,2.58,0.00,0.00,0.00); trace/3= 1.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.152525                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6945 -  4.6774 0.99   1374  153 0.1046 0.1286      5.4179      5.5412|
|  2:  4.6774 -  3.7326 0.99   1322  146 0.0914 0.1161      5.4773      5.6596|
|  3:  3.7326 -  3.2667 0.99   1299  146 0.1088 0.1478      5.4853       5.807|
|  4:  3.2667 -  2.9707 0.99   1285  139 0.1257 0.1577      5.4647      5.6152|
|  5:  2.9707 -  2.7593 0.99   1275  142 0.1312 0.1656      5.3217      5.4793|
|  6:  2.7593 -  2.5975 0.99   1279  146 0.1261 0.1791      5.2224      5.4352|
|  7:  2.5975 -  2.4681 0.99   1267  139 0.1228 0.1631      5.1544      5.3519|
|  8:  2.4681 -  2.3611 0.98   1269  142 0.1185 0.1761      5.0895      5.3674|
|  9:  2.3611 -  2.2705 0.98   1264  139 0.1183 0.1788      5.0249       5.262|
| 10:  2.2705 -  2.1925 0.98   1243  136 0.1156 0.1689      4.9726      5.2022|
| 11:  2.1925 -  2.1241 1.00   1267  147 0.1153 0.1674        4.92      5.2671|
| 12:  2.1241 -  2.0636 0.97   1252  128 0.1114 0.1698       4.876      5.1531|
| 13:  2.0636 -  2.0094 0.98   1241  138 0.1175 0.1729      4.8188      5.0583|
| 14:  2.0094 -  1.9605 0.79    993  118 0.1107 0.1879      4.7348      5.0049|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6945 -  4.6774  1374   153  0.94   9.26   0.99     0.97       7444.32|
|  2:  4.6774 -  3.7326  1322   146  0.95   7.89   1.03     1.02       9037.27|
|  3:  3.7326 -  3.2667  1299   146  0.93  11.25   1.04     1.03      10237.58|
|  4:  3.2667 -  2.9707  1285   139  0.93  13.00   1.02     1.01       9866.42|
|  5:  2.9707 -  2.7593  1275   142  0.91  15.11   1.00     0.96       7797.83|
|  6:  2.7593 -  2.5975  1279   146  0.90  15.53   0.99     0.96       6815.96|
|  7:  2.5975 -  2.4681  1267   139  0.91  15.40   0.99     0.96       6036.23|
|  8:  2.4681 -  2.3611  1269   142  0.91  14.99   1.00     0.98       5379.10|
|  9:  2.3611 -  2.2705  1264   139  0.91  15.27   1.02     1.00       4860.76|
| 10:  2.2705 -  2.1925  1243   136  0.91  15.02   1.02     0.99       4297.49|
| 11:  2.1925 -  2.1241  1267   147  0.91  15.19   1.01     0.98       4046.46|
| 12:  2.1241 -  2.0636  1252   128  0.92  14.81   1.02     1.01       3847.73|
| 13:  2.0636 -  2.0094  1241   138  0.90  15.88   1.02     1.01       3470.84|
| 14:  2.0094 -  1.9605   993   118  0.90  15.84   1.01     0.98       2941.22|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2941.22 max =        10237.58 mean =      6236.22|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.95 mean =        13.80|
|phase err.(test): min =        0.00 max =           88.40 mean =        13.40|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1149   r_free= 0.1579   ksol= 0.32   Bsol= 33.66   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.67,-0.00,0.67,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.152446                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1149   r_free= 0.1579   ksol= 0.32   Bsol= 33.66   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.67,-0.00,0.67,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.152446                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6945 -  4.6774 0.99   1374  153 0.1046 0.1286      5.4181      5.5416|
|  2:  4.6774 -  3.7326 0.99   1322  146 0.0915 0.1163      5.4779      5.6605|
|  3:  3.7326 -  3.2667 0.99   1299  146 0.1089 0.1479      5.4857      5.8074|
|  4:  3.2667 -  2.9707 0.99   1285  139 0.1257 0.1577      5.4648      5.6151|
|  5:  2.9707 -  2.7593 0.99   1275  142 0.1312 0.1656      5.3215       5.479|
|  6:  2.7593 -  2.5975 0.99   1279  146 0.1261 0.1791      5.2221      5.4349|
|  7:  2.5975 -  2.4681 0.99   1267  139 0.1227 0.1630       5.154      5.3516|
|  8:  2.4681 -  2.3611 0.98   1269  142 0.1185 0.1760      5.0892      5.3669|
|  9:  2.3611 -  2.2705 0.98   1264  139 0.1183 0.1789      5.0247      5.2619|
| 10:  2.2705 -  2.1925 0.98   1243  136 0.1156 0.1689      4.9724      5.2019|
| 11:  2.1925 -  2.1241 1.00   1267  147 0.1153 0.1673      4.9198       5.267|
| 12:  2.1241 -  2.0636 0.97   1252  128 0.1113 0.1698      4.8758      5.1529|
| 13:  2.0636 -  2.0094 0.98   1241  138 0.1175 0.1729      4.8187      5.0581|
| 14:  2.0094 -  1.9605 0.79    993  118 0.1106 0.1878      4.7343      5.0043|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6945 -  4.6774  1374   153  0.94   9.26   0.99     0.97       7451.08|
|  2:  4.6774 -  3.7326  1322   146  0.95   7.90   1.03     1.02       9046.94|
|  3:  3.7326 -  3.2667  1299   146  0.93  11.26   1.04     1.03      10247.18|
|  4:  3.2667 -  2.9707  1285   139  0.93  13.00   1.02     1.01       9868.15|
|  5:  2.9707 -  2.7593  1275   142  0.91  15.11   1.00     0.96       7795.02|
|  6:  2.7593 -  2.5975  1279   146  0.90  15.52   0.99     0.96       6812.83|
|  7:  2.5975 -  2.4681  1267   139  0.91  15.40   0.99     0.96       6031.11|
|  8:  2.4681 -  2.3611  1269   142  0.91  14.98   1.00     0.98       5374.95|
|  9:  2.3611 -  2.2705  1264   139  0.91  15.27   1.02     1.00       4857.51|
| 10:  2.2705 -  2.1925  1243   136  0.91  15.02   1.02     0.99       4296.06|
| 11:  2.1925 -  2.1241  1267   147  0.91  15.19   1.01     0.98       4045.56|
| 12:  2.1241 -  2.0636  1252   128  0.92  14.80   1.02     1.01       3846.48|
| 13:  2.0636 -  2.0094  1241   138  0.90  15.87   1.02     1.01       3468.68|
| 14:  2.0094 -  1.9605   993   118  0.90  15.83   1.01     0.98       2937.78|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2937.78 max =        10247.18 mean =      6236.37|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.95 mean =        13.80|
|phase err.(test): min =        0.00 max =           88.36 mean =        13.40|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.345)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.91    86.29   14.55    None  None   None       |
|    all(noH): 2823   0      1.91    86.29   14.55    None  None   None       |
|    Sol.    : 438    0      4.31    80.44   36.30    None  None   None       |
|    Mac.    : 2385   0      1.91    86.29   10.55    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.913 -  10.351: 1610   |   5:    44.103 -  52.541:   93        |
|      1:    10.351 -  18.789:  647   |   6:    52.541 -  60.979:   50        |
|      2:    18.789 -  27.227:  155   |   7:    60.979 -  69.417:   14        |
|      3:    27.227 -  35.665:  125   |   8:    69.417 -  77.855:    4        |
|      4:    35.665 -  44.103:  121   |   9:    77.855 -  86.293:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 329         
Filter by distance & map next to the model:
   mapped sites are within: 0.730 - 5.730
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 329 from: 329
   mapped sites are within: 0.730 - 5.730

peak=   11.190 closest distance to " CB  VAL A 230 " =    1.430
peak=   10.801 closest distance to " CG2 VAL A 296 " =    1.580
peak=    5.890 closest distance to " CD2 LEU A   5 " =    1.225
peak=    5.868 closest distance to " CG  LEU A   5 " =    1.220
peak=    5.745 closest distance to " NE2 GLN A  11 " =    1.139
peak=    5.674 closest distance to " O   HOH Z 278 " =    1.584
peak=    5.512 closest distance to " O   HOH Z 142 " =    1.845
peak=    5.466 closest distance to " O   HOH Z 193 " =    1.797
peak=    5.375 closest distance to " O   HOH Z 124 " =    1.571
peak=    5.332 closest distance to " O   HOH Z 126 " =    1.955
peak=    5.260 closest distance to " O   HOH Z 236 " =    1.480
peak=    5.238 closest distance to " CB  ARG A 275 " =    0.998
peak=    5.141 closest distance to " CG  PRO A 213 " =    1.299
peak=    5.096 closest distance to " O   HOH Z 209 " =    2.219
peak=    4.992 closest distance to " O   HOH Z 272 " =    1.904
peak=    4.839 closest distance to " O   HOH Z 232 " =    2.199
peak=    4.825 closest distance to " NH2 ARG A  56 " =    2.051
peak=    4.698 closest distance to " O   HOH Z  85 " =    1.575
peak=    4.683 closest distance to " CB  VAL A 230 " =    1.119
peak=    4.655 closest distance to " CB  GLN A 223 " =    1.497
peak=    4.653 closest distance to " CG  LEU A 228 " =    1.196
peak=    4.592 closest distance to " O   HOH Z 427 " =    2.587
peak=    4.530 closest distance to " O   HOH Z  78 " =    1.666
peak=    4.487 closest distance to " O   HOH Z 403 " =    1.890
peak=    4.485 closest distance to " O   HOH Z 322 " =    2.051
peak=    4.481 closest distance to " O   HOH Z 118 " =    1.816
peak=    4.470 closest distance to " CB  GLN A 183 " =    1.270
peak=    4.463 closest distance to " CG  PRO A 198 " =    1.240
peak=    4.451 closest distance to " O   HOH Z   3 " =    1.976
peak=    4.428 closest distance to " O   HOH Z  97 " =    1.911
peak=    4.406 closest distance to " O   HOH Z 203 " =    1.572
peak=    4.397 closest distance to " O   HOH Z  59 " =    1.865
peak=    4.379 closest distance to " CD2 LEU A 228 " =    1.201
peak=    4.375 closest distance to " O   SER A  87 " =    2.338
peak=    4.375 closest distance to " O   HOH Z 263 " =    1.473
peak=    4.365 closest distance to " CD1AILE A 234 " =    0.938
peak=    4.347 closest distance to " CB  SER A   3 " =    1.276
peak=    4.336 closest distance to " O   HOH Z 411 " =    3.729
peak=    4.293 closest distance to " O   HOH Z 346 " =    1.600
peak=    4.276 closest distance to " C   PRO A 198 " =    1.500
peak=    4.268 closest distance to " CB  GLU A 152 " =    1.140
peak=    4.265 closest distance to " O   HOH Z 192 " =    1.472
peak=    4.258 closest distance to " O   HOH Z 234 " =    3.570
peak=    4.253 closest distance to " O   HOH Z 303 " =    2.080
peak=    4.227 closest distance to " CB  SER A  63 " =    1.210
peak=    4.202 closest distance to " O   HOH Z 402 " =    1.425
peak=    4.200 closest distance to " O   HOH Z  66 " =    2.122
peak=    4.188 closest distance to " CG AARG A 275 " =    1.122
peak=    4.174 closest distance to " O   HOH Z  97 " =    2.253
peak=    4.168 closest distance to " CB  VAL A 265 " =    1.201
peak=    4.168 closest distance to " O   HOH Z 368 " =    2.098
peak=    4.103 closest distance to " O   HOH Z 345 " =    2.947
peak=    4.082 closest distance to " CA  VAL A  41 " =    0.822
peak=    4.080 closest distance to " O   HOH Z 188 " =    1.045
peak=    4.074 closest distance to " CB  SER A  26 " =    1.633
peak=    4.071 closest distance to " CG1BVAL A  72 " =    1.444
peak=    4.070 closest distance to " CG2 VAL A 257 " =    0.856
peak=    4.046 closest distance to " O   HOH Z  61 " =    1.590
peak=    4.027 closest distance to " O   HOH Z 134 " =    1.476
peak=    4.023 closest distance to " O   HOH Z 250 " =    1.350
peak=    3.991 closest distance to " CB  ASN A 148 " =    1.419
peak=    3.988 closest distance to " O   HOH Z 132 " =    1.036
peak=    3.983 closest distance to " O   HOH Z  54 " =    1.574
peak=    3.980 closest distance to " O   TRP A 274 " =    1.938
peak=    3.978 closest distance to " CB  VAL A 202 " =    1.603
peak=    3.978 closest distance to " OE1 GLU A   2 " =    2.196
peak=    3.961 closest distance to " O   HOH Z 227 " =    1.692
peak=    3.953 closest distance to " O   HOH Z 316 " =    2.807
peak=    3.950 closest distance to " O   HOH Z 260 " =    1.422
peak=    3.937 closest distance to " O   HOH Z 128 " =    1.985
peak=    3.917 closest distance to " O   HOH Z 392 " =    2.832
peak=    3.908 closest distance to " O   HOH Z 344 " =    2.683
peak=    3.905 closest distance to " O   HOH Z 406 " =    1.135
peak=    3.901 closest distance to " N   ASN A  39 " =    1.102
peak=    3.900 closest distance to " NZ  LYS A 117 " =    3.155
peak=    3.899 closest distance to " O   HOH Z 199 " =    1.008
peak=    3.896 closest distance to " O   HOH Z 369 " =    2.030
peak=    3.895 closest distance to " CD  ARG A 269 " =    1.124
peak=    3.883 closest distance to " CA  TYR A  30 " =    1.047
peak=    3.883 closest distance to " CG  PRO A 243 " =    1.182
peak=    3.874 closest distance to " O   HOH Z 298 " =    1.780
peak=    3.872 closest distance to " CD  GLN A 194 " =    1.484
peak=    3.871 closest distance to " O   HOH Z 143 " =    1.065
peak=    3.868 closest distance to " O   HOH Z 156 " =    3.122
peak=    3.867 closest distance to " O   HOH Z  95 " =    1.594
peak=    3.860 closest distance to " O   HOH Z 423 " =    1.910
peak=    3.857 closest distance to " O   HOH Z  10 " =    1.702
peak=    3.854 closest distance to " O   HOH Z 118 " =    1.535
peak=    3.853 closest distance to " NE2 GLN A  55 " =    1.371
peak=    3.848 closest distance to " O   HOH Z 291 " =    1.460
peak=    3.847 closest distance to " O   HOH Z 222 " =    2.316
peak=    3.841 closest distance to " CB  TRP A 179 " =    1.235
peak=    3.837 closest distance to " O   HOH Z 366 " =    2.969
peak=    3.836 closest distance to " CA  ALA A  21 " =    1.075
peak=    3.823 closest distance to " O   HOH Z 357 " =    1.763
peak=    3.822 closest distance to " O   HOH Z  43 " =    2.215
peak=    3.819 closest distance to " O   HOH Z 407 " =    2.290
peak=    3.814 closest distance to " O   HOH Z 148 " =    3.191
peak=    3.812 closest distance to " CB  GLN A  88 " =    1.227
peak=    3.808 closest distance to " CB  ASN A 148 " =    2.035
peak=    3.806 closest distance to " O   HOH Z 261 " =    1.718
peak=    3.777 closest distance to " CG2 ILE A  20 " =    1.566
peak=    3.768 closest distance to " O   HOH Z 202 " =    1.136
peak=    3.763 closest distance to " O   HOH Z 251 " =    1.701
peak=    3.754 closest distance to " CE3 TRP A 274 " =    2.466
peak=    3.754 closest distance to " O   HOH Z 287 " =    1.733
peak=    3.752 closest distance to " CB  TYR A 169 " =    0.909
peak=    3.748 closest distance to " CB  ARG A 102 " =    0.751
peak=    3.740 closest distance to " O   HOH Z 374 " =    2.415
peak=    3.739 closest distance to " CB  GLN A 278 " =    0.879
peak=    3.732 closest distance to " O   HOH Z 128 " =    1.951
peak=    3.730 closest distance to " O   HOH Z 248 " =    1.752
peak=    3.725 closest distance to " O   HOH Z 344 " =    1.357
peak=    3.714 closest distance to " CB  ARG A  79 " =    1.385
peak=    3.713 closest distance to " O   HOH Z  89 " =    2.205
peak=    3.711 closest distance to " O   HOH Z 276 " =    1.339
peak=    3.711 closest distance to " CD2 TRP A 179 " =    1.435
peak=    3.711 closest distance to " N   ARG A 156 " =    1.281
peak=    3.706 closest distance to " O   HOH Z 245 " =    1.380
peak=    3.705 closest distance to " O   HOH Z  59 " =    2.155
peak=    3.702 closest distance to " O   HOH Z 249 " =    1.075
peak=    3.700 closest distance to " CB  ALA A   9 " =    1.581
peak=    3.699 closest distance to " CZ AARG A 102 " =    1.598
peak=    3.694 closest distance to " CB  THR A  31 " =    1.635
peak=    3.686 closest distance to " O   HOH Z 327 " =    1.675
peak=    3.680 closest distance to " CB  ALA A 248 " =    1.347
peak=    3.665 closest distance to " O   HOH Z 213 " =    1.672
peak=    3.664 closest distance to " O   HOH Z 334 " =    1.611
peak=    3.662 closest distance to " O   HOH Z 189 " =    2.552
peak=    3.644 closest distance to " CG AARG A 275 " =    1.325
peak=    3.642 closest distance to " CB  GLU A 128 " =    1.005
peak=    3.635 closest distance to " O   HOH Z 261 " =    2.063
peak=    3.632 closest distance to " CB  VAL A 296 " =    0.927
peak=    3.631 closest distance to " CG2 ILE A 120 " =    1.278
peak=    3.631 closest distance to " ND2 ASN A 187 " =    1.575
peak=    3.628 closest distance to " O   HOH Z  15 " =    2.207
peak=    3.626 closest distance to " O   HOH Z 299 " =    4.133
peak=    3.625 closest distance to " OD2 ASP A 286 " =    2.568
peak=    3.608 closest distance to " O   HOH Z 191 " =    1.503
peak=    3.600 closest distance to " O   HOH Z 247 " =    1.256
peak=    3.592 closest distance to " CA  GLY A  80 " =    0.730
peak=    3.585 closest distance to " CA  GLN A 194 " =    1.112
peak=    3.582 closest distance to " NH2BARG A 145 " =    1.436
peak=    3.578 closest distance to " O   HOH Z 435 " =    1.949
peak=    3.573 closest distance to " O   LYS A 290 " =    2.328
peak=    3.567 closest distance to " O   HOH Z 303 " =    1.739
peak=    3.564 closest distance to " CA  ASN A 215 " =    1.046
peak=    3.556 closest distance to " O   HOH Z 427 " =    3.316
peak=    3.554 closest distance to " CE ALYS A 290 " =    1.224
peak=    3.545 closest distance to " OD1 ASN A  69 " =    2.710
peak=    3.541 closest distance to " CA  ALA A  51 " =    1.010
peak=    3.541 closest distance to " O   HOH Z  44 " =    1.896
peak=    3.537 closest distance to " CB  PRO A 198 " =    0.924
peak=    3.531 closest distance to " CD1 ILE A 106 " =    1.322
peak=    3.524 closest distance to " O   HOH Z 273 " =    2.804
peak=    3.517 closest distance to " O   HOH Z 173 " =    2.265
peak=    3.512 closest distance to " O   HOH Z 334 " =    1.321
peak=    3.511 closest distance to " O   HOH Z  61 " =    1.524
peak=    3.504 closest distance to " O   HOH Z 261 " =    2.078
peak=    3.493 closest distance to " CG2 THR A 221 " =    1.195
peak=    3.485 closest distance to " O   HOH Z 417 " =    3.077
peak=    3.470 closest distance to " NZ  LYS A  76 " =    1.391
peak=    3.469 closest distance to " CB  SER A 273 " =    0.876
peak=    3.464 closest distance to " CB  ASN A 110 " =    1.163
peak=    3.461 closest distance to " OG BSER A 210 " =    1.447
peak=    3.458 closest distance to " CB BVAL A  41 " =    1.140
peak=    3.448 closest distance to " O   HOH Z  48 " =    1.620
peak=    3.448 closest distance to " O   HOH Z 137 " =    1.504
peak=    3.446 closest distance to " NH1 ARG A  14 " =    1.017
peak=    3.446 closest distance to " O   HOH Z  80 " =    2.259
peak=    3.444 closest distance to " O   HOH Z 383 " =    1.733
peak=    3.442 closest distance to " CB  LEU A 255 " =    0.801
peak=    3.440 closest distance to " O   HOH Z 130 " =    2.879
peak=    3.438 closest distance to " CD2 TYR A  30 " =    0.837
peak=    3.420 closest distance to " CG  GLN A  88 " =    1.068
peak=    3.420 closest distance to " O   HOH Z 433 " =    1.845
peak=    3.415 closest distance to " O   HOH Z 214 " =    2.220
peak=    3.414 closest distance to " O   HOH Z 109 " =    2.351
peak=    3.412 closest distance to " CB  TRP A 266 " =    1.091
peak=    3.410 closest distance to " N   PHE A 130 " =    1.387
peak=    3.406 closest distance to " O   HOH Z  39 " =    2.723
peak=    3.401 closest distance to " CG  ARG A  66 " =    1.031
peak=    3.399 closest distance to " O   HOH Z 209 " =    2.315
peak=    3.397 closest distance to " OG BSER A 164 " =    2.177
peak=    3.395 closest distance to " CE BMET A  47 " =    1.455
peak=    3.394 closest distance to " CE1 HIS A 108 " =    1.233
peak=    3.393 closest distance to " O   GLN A 194 " =    1.797
peak=    3.393 closest distance to " CB  ARG A 139 " =    0.933
peak=    3.390 closest distance to " O   HOH Z 180 " =    2.169
peak=    3.385 closest distance to " CG1 ILE A  33 " =    1.427
peak=    3.384 closest distance to " NH2 ARG A 156 " =    1.076
peak=    3.383 closest distance to " O   HOH Z 389 " =    1.284
peak=    3.378 closest distance to " NE2 GLN A  58 " =    5.730
peak=    3.376 closest distance to " CB  ALA A 291 " =    1.219
peak=    3.374 closest distance to " CB  TYR A  30 " =    1.643
peak=    3.367 closest distance to " O   HOH Z  88 " =    2.899
peak=    3.363 closest distance to " CG2 THR A 294 " =    1.567
peak=    3.363 closest distance to " O   HOH Z 392 " =    1.841
peak=    3.361 closest distance to " CE1 TYR A 186 " =    1.320
peak=    3.361 closest distance to " O   HOH Z 380 " =    1.731
peak=    3.360 closest distance to " CG  GLN A  77 " =    2.155
peak=    3.360 closest distance to " C   ALA A   1 " =    1.716
peak=    3.360 closest distance to " ND1 HIS A  81 " =    1.434
peak=    3.357 closest distance to " CG  LEU A 167 " =    1.140
peak=    3.356 closest distance to " CA  VAL A 126 " =    0.963
peak=    3.354 closest distance to " O   HOH Z  21 " =    1.837
peak=    3.354 closest distance to " CB  THR A  52 " =    1.249
peak=    3.351 closest distance to " CG1 VAL A 153 " =    0.895
peak=    3.349 closest distance to " CA  ASN A 176 " =    0.985
peak=    3.344 closest distance to " O   ASP A 124 " =    1.245
peak=    3.342 closest distance to " O   HOH Z 193 " =    2.043
peak=    3.342 closest distance to " C   ALA A 299 " =    0.932
peak=    3.340 closest distance to " O   HOH Z  40 " =    1.357
peak=    3.339 closest distance to " O   HOH Z 329 " =    3.463
peak=    3.339 closest distance to " O   HOH Z  89 " =    1.543
peak=    3.336 closest distance to " CA  LEU A 237 " =    1.117
peak=    3.336 closest distance to " O   HOH Z 257 " =    2.162
peak=    3.333 closest distance to " OD1 ASP A 286 " =    1.611
peak=    3.325 closest distance to " O   SER A 164 " =    1.367
peak=    3.323 closest distance to " CA  LEU A 101 " =    1.444
peak=    3.321 closest distance to " CA  PHE A 283 " =    1.097
peak=    3.320 closest distance to " O   GLY A  91 " =    1.706
peak=    3.320 closest distance to " O   HOH Z 281 " =    1.555
peak=    3.319 closest distance to " CB  SER A 216 " =    0.731
peak=    3.318 closest distance to " O   HOH Z 284 " =    2.845
peak=    3.314 closest distance to " O   HOH Z 422 " =    2.525
peak=    3.313 closest distance to " CB  PRO A  54 " =    0.874
peak=    3.303 closest distance to " CA  ARG A  36 " =    0.978
peak=    3.297 closest distance to " O   HOH Z  13 " =    1.626
peak=    3.294 closest distance to " CA  ASN A 284 " =    0.932
peak=    3.291 closest distance to " CA  LYS A 290 " =    1.257
peak=    3.290 closest distance to " O   HOH Z 406 " =    1.290
peak=    3.285 closest distance to " CA  ALA A 158 " =    1.278
peak=    3.283 closest distance to " O   HOH Z  19 " =    2.167
peak=    3.282 closest distance to " O   HOH Z  80 " =    1.744
peak=    3.279 closest distance to " O   HOH Z   9 " =    1.858
peak=    3.276 closest distance to " CG  MET A 185 " =    1.199
peak=    3.271 closest distance to " O   HOH Z 425 " =    1.432
peak=    3.269 closest distance to " O   HOH Z 113 " =    1.823
peak=    3.264 closest distance to " O   HOH Z 424 " =    1.489
peak=    3.262 closest distance to " O   HOH Z 207 " =    1.786
peak=    3.259 closest distance to " O   HOH Z 194 " =    2.108
peak=    3.255 closest distance to " O   HOH Z 292 " =    1.698
peak=    3.253 closest distance to " O   HOH Z 343 " =    1.374
peak=    3.252 closest distance to " O   HOH Z  59 " =    1.862
peak=    3.249 closest distance to " O   HOH Z 233 " =    1.597
peak=    3.249 closest distance to " O   HOH Z 255 " =    1.696
peak=    3.245 closest distance to " NE2 GLN A 223 " =    1.793
peak=    3.244 closest distance to " O   HOH Z 389 " =    1.617
peak=    3.242 closest distance to " CA  LYS A 117 " =    1.244
peak=    3.240 closest distance to " CA  THR A 221 " =    0.886
peak=    3.240 closest distance to " CB  ASN A  39 " =    0.758
peak=    3.236 closest distance to " O   HOH Z 425 " =    1.965
peak=    3.229 closest distance to " O   HOH Z 352 " =    1.320
peak=    3.226 closest distance to " O   HOH Z 417 " =    2.210
peak=    3.225 closest distance to " CA  ASP A 140 " =    1.128
peak=    3.223 closest distance to " O   HOH Z  19 " =    2.257
peak=    3.222 closest distance to " NH1 ARG A 138 " =    1.505
peak=    3.221 closest distance to " N   TYR A  15 " =    1.078
peak=    3.221 closest distance to " O   HOH Z 172 " =    3.789
peak=    3.216 closest distance to " O   HOH Z 438 " =    2.352
peak=    3.215 closest distance to " N   SER A 135 " =    1.242
peak=    3.210 closest distance to " CB  ASN A 215 " =    1.013
peak=    3.209 closest distance to " O   HOH Z 411 " =    1.764
peak=    3.206 closest distance to " CB  GLN A 205 " =    1.164
peak=    3.201 closest distance to " CG  LYS A 119 " =    1.153
peak=    3.200 closest distance to " O   PHE A  38 " =    1.970
peak=    3.198 closest distance to " CD  PRO A 243 " =    1.572
peak=    3.198 closest distance to " O   HOH Z  20 " =    1.495
peak=    3.197 closest distance to " CE  MET A  93 " =    1.494
peak=    3.194 closest distance to " O   HOH Z 153 " =    3.786
peak=    3.192 closest distance to " O   HOH Z 113 " =    1.711
peak=    3.191 closest distance to " O   HOH Z  83 " =    1.563
peak=    3.188 closest distance to " NH2AARG A 190 " =    1.798
peak=    3.188 closest distance to " CG  MET A 188 " =    1.205
peak=    3.188 closest distance to " CB  ALA A   1 " =    4.556
peak=    3.187 closest distance to " O   HOH Z 430 " =    5.727
peak=    3.187 closest distance to " OE1 GLN A  11 " =    1.768
peak=    3.186 closest distance to " CB  PRO A  90 " =    1.242
peak=    3.184 closest distance to " CG  LEU A 281 " =    0.965
peak=    3.184 closest distance to " CB  ALA A 295 " =    1.277
peak=    3.183 closest distance to " O   HOH Z  55 " =    2.252
peak=    3.176 closest distance to " CD2 HIS A  81 " =    1.241
peak=    3.176 closest distance to " CE AMET A  47 " =    1.464
peak=    3.175 closest distance to " CB  HIS A 108 " =    0.912
peak=    3.173 closest distance to " NE1 TRP A 274 " =    0.968
peak=    3.172 closest distance to " CB  ALA A   1 " =    1.174
peak=    3.169 closest distance to " CB  GLU A 277 " =    3.474
peak=    3.168 closest distance to " NH2BARG A 190 " =    2.018
peak=    3.166 closest distance to " CG AARG A 190 " =    1.289
peak=    3.164 closest distance to " CB  LEU A 228 " =    1.449
peak=    3.157 closest distance to " CB  SER A  62 " =    1.229
peak=    3.154 closest distance to " O   HOH Z 151 " =    1.698
peak=    3.148 closest distance to " O   HOH Z 271 " =    2.280
peak=    3.143 closest distance to " O   HOH Z 163 " =    1.832
peak=    3.141 closest distance to " CE2 TRP A 274 " =    2.448
peak=    3.141 closest distance to " O   HOH Z 345 " =    1.578
peak=    3.135 closest distance to " O   HOH Z 266 " =    1.936
peak=    3.135 closest distance to " O   HOH Z 421 " =    1.313
peak=    3.133 closest distance to " O   HOH Z 227 " =    1.487
peak=    3.131 closest distance to " O   HOH Z  88 " =    2.347
peak=    3.130 closest distance to " SD BMET A  47 " =    1.352
peak=    3.128 closest distance to " NH2 ARG A 219 " =    1.975
peak=    3.128 closest distance to " O   HOH Z 148 " =    1.504
peak=    3.122 closest distance to " O   HOH Z 426 " =    1.454
peak=    3.122 closest distance to " CB  ASN A  69 " =    1.398
peak=    3.121 closest distance to " CB  ALA A  21 " =    1.820
peak=    3.120 closest distance to " CD  LYS A 119 " =    1.938
peak=    3.120 closest distance to " N   GLN A 278 " =    1.023
peak=    3.118 closest distance to " O   HOH Z 380 " =    1.981
peak=    3.116 closest distance to " OG BSER A 258 " =    2.794
peak=    3.115 closest distance to " CB  PRO A 198 " =    1.192
peak=    3.113 closest distance to " CZ2 TRP A 274 " =    1.661
peak=    3.112 closest distance to " CB  VAL A 268 " =    0.835
peak=    3.109 closest distance to " O   HOH Z 326 " =    1.351
peak=    3.108 closest distance to " O   GLN A  58 " =    1.361
peak=    3.108 closest distance to " CG1 ILE A 120 " =    1.271
peak=    3.103 closest distance to " OG  SER A  97 " =    2.579
peak=    3.102 closest distance to " O   HOH Z 271 " =    1.686
peak=    3.102 closest distance to " O   HOH Z 215 " =    1.328
peak=    3.099 closest distance to " O   HOH Z 250 " =    1.907
peak=    3.098 closest distance to " O   HOH Z 367 " =    3.583
peak=    3.095 closest distance to " CD1 ILE A  33 " =    1.609
peak=    3.088 closest distance to " CD2 LEU A 261 " =    1.217
peak=    3.073 closest distance to " CA  THR A 264 " =    0.774
peak=    3.066 closest distance to " OD1 ASN A  45 " =    1.158
peak=    3.054 closest distance to " O  BHOH Z  74 " =    1.378
peak=    3.040 closest distance to " CB  ILE A  20 " =    1.413
peak=    3.038 closest distance to " O   HOH Z  59 " =    1.876

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 193         
Filter by distance & map next to the model:
   mapped sites are within: 0.566 - 5.688
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 190 from: 193
   mapped sites are within: 0.714 - 5.688

peak=   -5.006 closest distance to " CG2 VAL A 230 " =    0.714
peak=   -4.623 closest distance to " CD  ARG A 156 " =    2.039
peak=   -4.621 closest distance to " SG  CYS A 254 " =    3.165
peak=   -4.351 closest distance to " O   HOH Z 290 " =    0.996
peak=   -4.253 closest distance to " O   HOH Z  11 " =    1.729
peak=   -4.245 closest distance to " O   PRO A 163 " =    1.974
peak=   -4.172 closest distance to " O   HOH Z 423 " =    2.201
peak=   -4.104 closest distance to " CE2 TYR A  30 " =    2.836
peak=   -4.093 closest distance to " OG  SER A   3 " =    1.249
peak=   -4.067 closest distance to " CD1 LEU A 255 " =    2.696
peak=   -4.064 closest distance to " C   HIS A 108 " =    1.172
peak=   -4.045 closest distance to " OXT GLY A 302 " =    2.702
peak=   -4.018 closest distance to " CA  VAL A  67 " =    2.794
peak=   -3.980 closest distance to " O   PRO A 198 " =    1.225
peak=   -3.980 closest distance to " CB  ALA A 161 " =    2.463
peak=   -3.945 closest distance to " O   ALA A   8 " =    1.862
peak=   -3.945 closest distance to " N   ALA A 248 " =    1.651
peak=   -3.902 closest distance to " O   ALA A 161 " =    1.498
peak=   -3.900 closest distance to " N   HIS A 115 " =    1.988
peak=   -3.887 closest distance to " O   HOH Z 266 " =    4.442
peak=   -3.874 closest distance to " N   GLN A  58 " =    2.002
peak=   -3.874 closest distance to " ND2 ASN A  45 " =    0.950
peak=   -3.872 closest distance to " CG  ASP A 231 " =    0.782
peak=   -3.865 closest distance to " O   HOH Z 191 " =    4.910
peak=   -3.812 closest distance to " CG  PHE A 283 " =    2.665
peak=   -3.766 closest distance to " OD1 ASN A 249 " =    1.133
peak=   -3.762 closest distance to " O   HOH Z  98 " =    1.689
peak=   -3.751 closest distance to " NH2 ARG A  79 " =    1.977
peak=   -3.747 closest distance to " O   HOH Z 362 " =    5.688
peak=   -3.743 closest distance to " O   HOH Z 388 " =    2.073
peak=   -3.732 closest distance to " CB  ALA A 244 " =    2.030
peak=   -3.723 closest distance to " CA  GLY A  23 " =    1.879
peak=   -3.714 closest distance to " CB  ALA A 248 " =    1.995
peak=   -3.701 closest distance to " O   ASN A  45 " =    1.855
peak=   -3.692 closest distance to " O   HOH Z 111 " =    4.480
peak=   -3.689 closest distance to " O   HOH Z 250 " =    1.431
peak=   -3.678 closest distance to " CG  LYS A 193 " =    2.161
peak=   -3.676 closest distance to " OG BSER A 134 " =    1.238
peak=   -3.675 closest distance to " O   VAL A  67 " =    2.599
peak=   -3.666 closest distance to " O   HOH Z 175 " =    4.379
peak=   -3.665 closest distance to " CG2 VAL A 296 " =    1.930
peak=   -3.663 closest distance to " O   HOH Z  56 " =    2.236
peak=   -3.661 closest distance to " CD1 PHE A  59 " =    2.300
peak=   -3.650 closest distance to " O   HOH Z 102 " =    1.730
peak=   -3.642 closest distance to " ND2 ASN A 187 " =    1.629
peak=   -3.642 closest distance to " O   ALA A  51 " =    1.253
peak=   -3.641 closest distance to " CD1 LEU A 101 " =    2.341
peak=   -3.635 closest distance to " O   HOH Z 427 " =    1.528
peak=   -3.626 closest distance to " O   HOH Z 312 " =    1.473
peak=   -3.623 closest distance to " CG  ASP A  50 " =    2.362
peak=   -3.613 closest distance to " OG  SER A 206 " =    1.462
peak=   -3.595 closest distance to " O   HOH Z 166 " =    1.521
peak=   -3.591 closest distance to " CD  GLN A  88 " =    1.078
peak=   -3.583 closest distance to " O   HOH Z 134 " =    2.681
peak=   -3.579 closest distance to " CD  GLN A  58 " =    1.233
peak=   -3.570 closest distance to " O   HOH Z 351 " =    1.404
peak=   -3.566 closest distance to " CG  GLN A 223 " =    1.952
peak=   -3.559 closest distance to " CB  ASN A  39 " =    2.131
peak=   -3.558 closest distance to " O   SER A 146 " =    0.828
peak=   -3.546 closest distance to " CB  ALA A 291 " =    2.345
peak=   -3.546 closest distance to " CG  LEU A 228 " =    1.098
peak=   -3.533 closest distance to " CD  LYS A 289 " =    2.517
peak=   -3.531 closest distance to " C   ASP A 231 " =    2.445
peak=   -3.527 closest distance to " CB  ASP A 132 " =    2.100
peak=   -3.517 closest distance to " OD2 ASP A 191 " =    1.392
peak=   -3.516 closest distance to " CZ  TYR A 169 " =    1.764
peak=   -3.507 closest distance to " CB  ALA A 100 " =    2.512
peak=   -3.505 closest distance to " C   ALA A 158 " =    1.149
peak=   -3.503 closest distance to " CD  ARG A 139 " =    1.510
peak=   -3.496 closest distance to " C   LEU A 143 " =    1.043
peak=   -3.493 closest distance to " O   HOH Z 126 " =    1.883
peak=   -3.487 closest distance to " CZ  PHE A 130 " =    0.929
peak=   -3.486 closest distance to " O   HOH Z 407 " =    2.817
peak=   -3.474 closest distance to " OD2 ASP A  50 " =    1.343
peak=   -3.466 closest distance to " CE2 PHE A 218 " =    2.663
peak=   -3.455 closest distance to " CB  ASP A 132 " =    2.228
peak=   -3.450 closest distance to " O   HOH Z 193 " =    1.685
peak=   -3.447 closest distance to " O   HOH Z 281 " =    3.299
peak=   -3.444 closest distance to " N   GLN A  77 " =    1.526
peak=   -3.439 closest distance to " O   HOH Z 313 " =    1.692
peak=   -3.435 closest distance to " O   HOH Z  69 " =    1.872
peak=   -3.426 closest distance to " O   HOH Z  93 " =    1.387
peak=   -3.418 closest distance to " ND2 ASN A  60 " =    1.790
peak=   -3.414 closest distance to " O   MET A  40 " =    2.633
peak=   -3.406 closest distance to " OG ASER A 134 " =    1.223
peak=   -3.405 closest distance to " CB  TYR A  15 " =    2.140
peak=   -3.403 closest distance to " N   ALA A 226 " =    1.882
peak=   -3.400 closest distance to " CB  PRO A 243 " =    2.619
peak=   -3.399 closest distance to " N   SER A 276 " =    1.147
peak=   -3.386 closest distance to " O   THR A 182 " =    1.198
peak=   -3.384 closest distance to " OXT GLY A 302 " =    3.543
peak=   -3.381 closest distance to " O   HOH Z 295 " =    1.479
peak=   -3.364 closest distance to " O   HOH Z 211 " =    1.462
peak=   -3.362 closest distance to " O   HOH Z 165 " =    2.073
peak=   -3.360 closest distance to " O   HOH Z 406 " =    0.787
peak=   -3.349 closest distance to " NE2 GLN A 278 " =    1.937
peak=   -3.348 closest distance to " CG  GLU A 152 " =    2.473
peak=   -3.346 closest distance to " C   GLN A 205 " =    1.873
peak=   -3.343 closest distance to " CZ3 TRP A 274 " =    1.116
peak=   -3.342 closest distance to " O   HOH Z 256 " =    1.146
peak=   -3.341 closest distance to " CD1 TYR A 247 " =    2.480
peak=   -3.335 closest distance to " CG  GLU A   2 " =    2.058
peak=   -3.332 closest distance to " OE1 GLN A  88 " =    1.089
peak=   -3.331 closest distance to " N   THR A 157 " =    1.412
peak=   -3.329 closest distance to " O   HOH Z 385 " =    2.068
peak=   -3.323 closest distance to " O   HOH Z 114 " =    2.894
peak=   -3.314 closest distance to " C   MET A 188 " =    1.559
peak=   -3.313 closest distance to " N   GLN A 122 " =    1.399
peak=   -3.312 closest distance to " O   SER A 135 " =    1.561
peak=   -3.309 closest distance to " O   HOH Z  11 " =    1.870
peak=   -3.303 closest distance to " O   HOH Z 210 " =    0.893
peak=   -3.301 closest distance to " O   HOH Z 385 " =    1.815
peak=   -3.297 closest distance to " OD1 ASP A 200 " =    1.235
peak=   -3.295 closest distance to " CD2 LEU A 300 " =    2.787
peak=   -3.290 closest distance to " O   HOH Z 185 " =    2.299
peak=   -3.290 closest distance to " O   HOH Z  71 " =    1.008
peak=   -3.289 closest distance to " O   ALA A 256 " =    2.821
peak=   -3.288 closest distance to " CA  GLY A 133 " =    1.849
peak=   -3.286 closest distance to " ND2 ASN A  39 " =    1.097
peak=   -3.277 closest distance to " O   HOH Z 152 " =    5.086
peak=   -3.275 closest distance to " O   HOH Z 344 " =    2.468
peak=   -3.274 closest distance to " O   HOH Z 132 " =    0.756
peak=   -3.265 closest distance to " CD1 LEU A 228 " =    1.981
peak=   -3.264 closest distance to " N   THR A 220 " =    2.180
peak=   -3.261 closest distance to " O   HOH Z  97 " =    1.165
peak=   -3.259 closest distance to " CG  GLU A 152 " =    1.143
peak=   -3.256 closest distance to " C   THR A 279 " =    1.275
peak=   -3.253 closest distance to " C   ASN A  69 " =    1.239
peak=   -3.244 closest distance to " O   HOH Z 346 " =    1.809
peak=   -3.240 closest distance to " O   TYR A 247 " =    2.820
peak=   -3.236 closest distance to " O   ALA A   1 " =    1.747
peak=   -3.235 closest distance to " O   GLN A 205 " =    1.564
peak=   -3.235 closest distance to " O   TRP A  92 " =    1.836
peak=   -3.227 closest distance to " O   HOH Z 350 " =    2.131
peak=   -3.222 closest distance to " O   HOH Z  60 " =    2.271
peak=   -3.221 closest distance to " CZ  PHE A  59 " =    1.375
peak=   -3.217 closest distance to " N   VAL A 230 " =    1.200
peak=   -3.215 closest distance to " O   HOH Z 231 " =    1.940
peak=   -3.214 closest distance to " O   VAL A 197 " =    1.025
peak=   -3.214 closest distance to " N   THR A  52 " =    1.724
peak=   -3.211 closest distance to " CB  ALA A  43 " =    2.137
peak=   -3.207 closest distance to " OD1 ASN A 301 " =    1.936
peak=   -3.206 closest distance to " NZ  LYS A 119 " =    3.225
peak=   -3.205 closest distance to " O   HOH Z 198 " =    1.961
peak=   -3.204 closest distance to " OG BSER A  99 " =    1.286
peak=   -3.203 closest distance to " NH1 ARG A  66 " =    4.678
peak=   -3.203 closest distance to " O   HOH Z 436 " =    1.540
peak=   -3.201 closest distance to " CB  ALA A  64 " =    2.624
peak=   -3.201 closest distance to " C   ARG A 269 " =    1.385
peak=   -3.199 closest distance to " CG2 VAL A 189 " =    2.060
peak=   -3.197 closest distance to " O   HOH Z 414 " =    2.290
peak=   -3.194 closest distance to " CG  MET A 105 " =    0.881
peak=   -3.188 closest distance to " CG2AVAL A  41 " =    3.053
peak=   -3.184 closest distance to " O   HOH Z 377 " =    0.819
peak=   -3.182 closest distance to " O   HOH Z  13 " =    1.448
peak=   -3.181 closest distance to " O   HOH Z 197 " =    4.844
peak=   -3.177 closest distance to " O   HOH Z 341 " =    1.495
peak=   -3.177 closest distance to " O   HOH Z  47 " =    1.594
peak=   -3.173 closest distance to " CB  PRO A 163 " =    2.685
peak=   -3.171 closest distance to " CG1 VAL A 112 " =    2.946
peak=   -3.171 closest distance to " O   ALA A 256 " =    1.498
peak=   -3.169 closest distance to " OG1 THR A 178 " =    1.197
peak=   -3.167 closest distance to " O   LYS A 117 " =    1.511
peak=   -3.162 closest distance to " O   HOH Z 131 " =    3.967
peak=   -3.156 closest distance to " O   ASN A 249 " =    1.619
peak=   -3.153 closest distance to " OD1 ASP A 191 " =    1.355
peak=   -3.144 closest distance to " OG1 THR A  82 " =    1.289
peak=   -3.140 closest distance to " O   HOH Z 426 " =    1.570
peak=   -3.140 closest distance to " CG  PRO A 213 " =    0.919
peak=   -3.139 closest distance to " O   PRO A 198 " =    1.201
peak=   -3.138 closest distance to " CE1 TYR A 169 " =    2.269
peak=   -3.135 closest distance to " ND2 ASN A  60 " =    1.372
peak=   -3.133 closest distance to " C   ASN A 285 " =    2.122
peak=   -3.131 closest distance to " O   HOH Z 192 " =    1.016
peak=   -3.125 closest distance to " O   HOH Z 222 " =    2.979
peak=   -3.120 closest distance to " CA  ASP A 298 " =    1.079
peak=   -3.118 closest distance to " O   HOH Z 404 " =    1.502
peak=   -3.110 closest distance to " CD2 TYR A 293 " =    2.162
peak=   -3.098 closest distance to " CG  GLU A 277 " =    1.160
peak=   -3.092 closest distance to " ND2 ASN A 127 " =    1.687
peak=   -3.092 closest distance to " O   SER A 210 " =    1.759
peak=   -3.091 closest distance to " O   ARG A  56 " =    1.305
peak=   -3.088 closest distance to " O   HOH Z 421 " =    2.996
peak=   -3.086 closest distance to " O   HOH Z 148 " =    1.638
peak=   -3.085 closest distance to " O   HOH Z 139 " =    3.205
peak=   -3.079 closest distance to " CD2 TYR A  30 " =    2.887
peak=   -3.074 closest distance to " CD  PRO A 243 " =    2.074
peak=   -3.046 closest distance to " CD1 ILE A 239 " =    2.471
peak=   -3.043 closest distance to " O   HOH Z 234 " =    3.961
peak=   -3.030 closest distance to " O   HOH Z 407 " =    3.229

================= 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    :  0.4833 0.4750   6.280271e+00   6.270308e+00
   1_bss:  0.4735 0.4639   6.272909e+00   6.258680e+00
   1_xyz:  0.3944 0.4113   6.165025e+00   6.192459e+00
   1_adp:  0.3476 0.3965   6.082788e+00   6.164730e+00
   1_occ:  0.3471 0.3963   6.081865e+00   6.164851e+00
   2_bss:  0.3429 0.3922   6.079996e+00   6.162275e+00
   2_xyz:  0.2452 0.2952   5.802730e+00   5.952476e+00
   2_adp:  0.2185 0.2690   5.705666e+00   5.874977e+00
   2_occ:  0.2181 0.2683   5.704827e+00   5.874157e+00
   3_bss:  0.2158 0.2670   5.701851e+00   5.871299e+00
   3_xyz:  0.1602 0.2074   5.442874e+00   5.651378e+00
   3_adp:  0.1482 0.1938   5.369591e+00   5.581180e+00
   3_occ:  0.1480 0.1938   5.369020e+00   5.580340e+00
   4_bss:  0.1476 0.1926   5.366926e+00   5.576415e+00
   4_xyz:  0.1208 0.1654   5.196475e+00   5.425003e+00
   4_adp:  0.1183 0.1602   5.171231e+00   5.394550e+00
   4_occ:  0.1181 0.1600   5.170149e+00   5.393449e+00
   5_bss:  0.1181 0.1593   5.169414e+00   5.392103e+00
   5_xyz:  0.1168 0.1583   5.161365e+00   5.382834e+00
   5_adp:  0.1150 0.1580   5.153032e+00   5.381723e+00
   5_occ:  0.1149 0.1579   5.152525e+00   5.381073e+00
   5_bss:  0.1149 0.1579   5.152446e+00   5.381000e+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:  0.380   3.353   8.003   8.069   9.424   0.000   0.000   0.000
   1_xyz:  0.380   3.353   8.003   8.069   9.424   0.000   0.000   0.000
   1_adp:  0.380   3.353   8.003   8.069   9.424   0.000   0.000   0.000
   1_occ:  0.380   3.353   8.003   8.069   9.424   0.000   0.000   0.000
   2_bss:  0.341  22.660   4.260   4.063   5.963   0.000   0.000   0.000
   2_xyz:  0.341  22.660   4.260   4.063   5.963   0.000   0.000   0.000
   2_adp:  0.341  22.660   4.260   4.063   5.963   0.000   0.000   0.000
   2_occ:  0.341  22.660   4.260   4.063   5.963   0.000   0.000   0.000
   3_bss:  0.329  33.477   2.234   2.641   3.767   0.000   0.000   0.000
   3_xyz:  0.329  33.477   2.234   2.641   3.767   0.000   0.000   0.000
   3_adp:  0.329  33.477   2.234   2.641   3.767   0.000   0.000   0.000
   3_occ:  0.329  33.477   2.234   2.641   3.767   0.000   0.000   0.000
   4_bss:  0.321  29.650   1.485   2.109   2.846   0.000   0.000   0.000
   4_xyz:  0.321  29.650   1.485   2.109   2.846   0.000   0.000   0.000
   4_adp:  0.321  29.650   1.485   2.109   2.846   0.000   0.000   0.000
   4_occ:  0.321  29.650   1.485   2.109   2.846   0.000   0.000   0.000
   5_bss:  0.322  30.953   1.247   1.912   2.580   0.000   0.000   0.000
   5_xyz:  0.322  30.953   1.247   1.912   2.580   0.000   0.000   0.000
   5_adp:  0.322  30.953   1.247   1.912   2.580   0.000   0.000   0.000
   5_occ:  0.322  30.953   1.247   1.912   2.580   0.000   0.000   0.000
   5_bss:  0.323  33.663  -0.666  -0.001   0.667   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  56.758 0.4365  0.5160    70113.206
   1_bss:  57.070 0.4299  0.6438    66482.559
   1_xyz:  47.489 0.5507  0.8157    49661.388
   1_adp:  43.652 0.5987  0.9234    44770.447
   1_occ:  43.647 0.5987  0.9222    44664.989
   2_bss:  43.213 0.6038  0.8160    44010.059
   2_xyz:  30.549 0.7511  0.9845    22950.693
   2_adp:  26.780 0.7930  1.0254    18678.413
   2_occ:  26.741 0.7934  1.0257    18636.838
   3_bss:  26.593 0.7948  0.9582    18416.951
   3_xyz:  19.823 0.8636  1.0031    10944.859
   3_adp:  17.990 0.8814  1.0130     9592.290
   3_occ:  17.979 0.8814  1.0128     9576.262
   4_bss:  17.903 0.8820  0.9852     9464.231
   4_xyz:  14.849 0.9077  0.9963     6833.382
   4_adp:  14.168 0.9136  0.9991     6468.042
   4_occ:  14.143 0.9138  0.9990     6449.754
   5_bss:  14.117 0.9140  0.9902     6427.297
   5_xyz:  13.798 0.9169  0.9917     6263.397
   5_adp:  13.774 0.9172  0.9908     6242.945
   5_occ:  13.762 0.9173  0.9907     6235.531
   5_bss:  13.759 0.9173  0.9908     6235.686
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.086   5.2767e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.086   5.2767e+01
   1_xyz:   1.733  0.014  0.110 18.376  0.007  4.104   1.5038e-01
   1_adp:   1.733  0.014  0.110 18.376  0.007  4.104   1.5038e-01
   1_occ:   1.733  0.014  0.110 18.376  0.007  4.104   1.5038e-01
   2_bss:   1.733  0.014  0.110 18.376  0.007  4.104   1.5038e-01
   2_xyz:   1.200  0.009  0.083 16.622  0.006  4.108   8.9721e-02
   2_adp:   1.200  0.009  0.083 16.622  0.006  4.108   8.9721e-02
   2_occ:   1.200  0.009  0.083 16.622  0.006  4.108   8.9721e-02
   3_bss:   1.200  0.009  0.083 16.622  0.006  4.108   8.9721e-02
   3_xyz:   0.988  0.006  0.070 15.846  0.004  4.118   6.0823e-02
   3_adp:   0.988  0.006  0.070 15.846  0.004  4.118   6.0823e-02
   3_occ:   0.988  0.006  0.070 15.846  0.004  4.118   6.0823e-02
   4_bss:   0.988  0.006  0.070 15.846  0.004  4.118   6.0823e-02
   4_xyz:   1.122  0.008  0.080 16.105  0.005  4.107   7.3407e-02
   4_adp:   1.122  0.008  0.080 16.105  0.005  4.107   7.3407e-02
   4_occ:   1.122  0.008  0.080 16.105  0.005  4.107   7.3407e-02
   5_bss:   1.122  0.008  0.080 16.105  0.005  4.107   7.3407e-02
   5_xyz:   0.925  0.005  0.068 15.663  0.004  4.107   5.5048e-02
   5_adp:   0.925  0.005  0.068 15.663  0.004  4.107   5.5048e-02
   5_occ:   0.925  0.005  0.068 15.663  0.004  4.107   5.5048e-02
   5_bss:   0.925  0.005  0.068 15.663  0.004  4.107   5.5048e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.684   6.8330e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.684   6.8330e+00
   1_xyz:  15.401  0.174  0.514 86.735  0.043  2.234   1.0376e-01
   1_adp:  15.401  0.174  0.514 86.735  0.043  2.234   1.0376e-01
   1_occ:  15.401  0.174  0.514 86.735  0.043  2.234   1.0376e-01
   2_bss:  15.401  0.174  0.514 86.735  0.043  2.234   1.0376e-01
   2_xyz:   8.007  0.105  0.347 84.521  0.051  2.305   1.1506e-01
   2_adp:   8.007  0.105  0.347 84.521  0.051  2.305   1.1506e-01
   2_occ:   8.007  0.105  0.347 84.521  0.051  2.305   1.1506e-01
   3_bss:   8.007  0.105  0.347 84.521  0.051  2.305   1.1506e-01
   3_xyz:   7.223  0.046  0.330 87.344  0.026  2.324   4.7279e-02
   3_adp:   7.223  0.046  0.330 87.344  0.026  2.324   4.7279e-02
   3_occ:   7.223  0.046  0.330 87.344  0.026  2.324   4.7279e-02
   4_bss:   7.223  0.046  0.330 87.344  0.026  2.324   4.7279e-02
   4_xyz:   6.675  0.050  0.421 84.446  0.034  2.270   8.3964e-02
   4_adp:   6.675  0.050  0.421 84.446  0.034  2.270   8.3964e-02
   4_occ:   6.675  0.050  0.421 84.446  0.034  2.270   8.3964e-02
   5_bss:   6.675  0.050  0.421 84.446  0.034  2.270   8.3964e-02
   5_xyz:   6.507  0.037  0.307 83.758  0.029  2.387   3.2209e-02
   5_adp:   6.507  0.037  0.307 83.758  0.029  2.387   3.2209e-02
   5_occ:   6.507  0.037  0.307 83.758  0.029  2.387   3.2209e-02
   5_bss:   6.507  0.037  0.307 83.758  0.029  2.387   3.2209e-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:  72.99   0.00  12.94  72.99   0.00  10.50  68.87   0.00  26.19
   1_occ:  72.99   0.00  12.94  72.99   0.00  10.50  68.87   0.00  26.19
   2_bss:  72.99   0.00  12.94  72.99   0.00  10.50  68.87   0.00  26.19
   2_xyz:  72.99   0.00  12.94  72.99   0.00  10.50  68.87   0.00  26.19
   2_adp: 136.78   0.00  12.92 136.78   0.00   9.35  70.42   1.16  32.36
   2_occ: 136.78   0.00  12.92 136.78   0.00   9.35  70.42   1.16  32.36
   3_bss: 136.78   0.00  12.92 136.78   0.00   9.35  70.42   1.16  32.36
   3_xyz: 136.78   0.00  12.92 136.78   0.00   9.35  70.42   1.16  32.36
   3_adp:  99.10   0.00  13.07  99.10   0.00   8.94  75.26   2.21  35.56
   3_occ:  99.10   0.00  13.07  99.10   0.00   8.94  75.26   2.21  35.56
   4_bss:  99.10   0.00  13.07  99.10   0.00   8.94  75.26   2.21  35.56
   4_xyz:  99.10   0.00  13.07  99.10   0.00   8.94  75.26   2.21  35.56
   4_adp:  81.64   0.31  12.47  81.64   0.31   8.61  78.16   2.63  33.46
   4_occ:  81.64   0.31  12.47  81.64   0.31   8.61  78.16   2.63  33.46
   5_bss:  81.64   0.31  12.47  81.64   0.31   8.61  78.16   2.63  33.46
   5_xyz:  81.64   0.31  12.47  81.64   0.31   8.61  78.16   2.63  33.46
   5_adp:  84.38   0.00  12.63  84.38   0.00   8.64  78.53   2.39  34.39
   5_occ:  84.38   0.00  12.63  84.38   0.00   8.64  78.53   2.39  34.39
   5_bss:  86.29   1.91  14.55  86.29   1.91  10.55  80.44   4.31  36.30
------------------------------------------------------------------------
 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:    1.262    0.019    0.418
   1_adp:    1.262    0.019    0.418
   1_occ:    1.262    0.019    0.418
   2_bss:    1.262    0.019    0.418
   2_xyz:    1.564    0.047    0.600
   2_adp:    1.564    0.047    0.600
   2_occ:    1.564    0.047    0.600
   3_bss:    1.564    0.047    0.600
   3_xyz:    1.613    0.068    0.658
   3_adp:    1.613    0.068    0.658
   3_occ:    1.613    0.068    0.658
   4_bss:    1.613    0.068    0.658
   4_xyz:    1.641    0.067    0.712
   4_adp:    1.641    0.067    0.712
   4_occ:    1.641    0.067    0.712
   5_bss:    1.641    0.067    0.712
   5_xyz:    1.617    0.061    0.718
   5_adp:    1.617    0.061    0.718
   5_occ:    1.617    0.061    0.718
   5_bss:    1.617    0.061    0.718
------------------------------------------------------------------------

CPU time actual refinement: 344.59


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_166/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_166/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_166/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_166/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_166/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 344.43 
  Macro-tasks:
    bulk solvent and scale       = 47.64  
    individual site refinement   = 143.91 
    weights calculation          = 31.65  
    collect and process          = 6.54   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 229.87 
  Micro-tasks:
    mask                            = 2.39   
    f_calc                          = 103.81 
    alpha_beta                      = 8.26   
    target                          = 1.11   
    gradients_wrt_atomic_parameters = 115.62 
    fmodel                         = 8.12   
    r_factors                      = 0.27   
    phase_errors                   = 10.60  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 250.48 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.766 micro seconds
Total CPU time: 5.97 minutes
from_scatterers_fft:    656 calls, 103.49 s
gradients_fft:          601 calls, 101.61 s

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

# Date 2008-01-16 Time 00:57:00 PST -0800 (1200473820.51 s)
Start R-work = 0.4833, R-free = 0.4750 (no bulk solvent and anisotropic scale)
Final R-work = 0.1327, R-free = 0.1750 (no bulk solvent and anisotropic scale)

Start R-work = 0.4735, R-free = 0.4639
Final R-work = 0.1149, R-free = 0.1579