# Date 2008-01-16 Time 00:47:39 PST -0800 (1200473259.41 s)
#phil __OFF__

Command line arguments: "../164.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 26710
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 164

-------------------------------------------------------------------------------
  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, 46.4607, 88.5498, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 2.76, per 1000 atoms: 0.98


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 46.4607, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9145 1.9609
Completeness in resolution range: 0.93575
Completeness with d_max=infinity: 0.932943

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9145
                             d_min =   1.9609

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, 46.4607, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9145 1.9609
Completeness in resolution range: 0.93575
Completeness with d_max=infinity: 0.932943

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9149 -  4.1962 [2200/2228]  1977   223  10.1%
  bin  2:  4.1962 -  3.3430 [2123/2139]  1910   213  10.0%
  bin  3:  3.3430 -  2.9240 [2089/2108]  1886   203   9.7%
  bin  4:  2.9240 -  2.6583 [2062/2092]  1848   214  10.4%
  bin  5:  2.6583 -  2.4687 [2036/2055]  1834   202   9.9%
  bin  6:  2.4687 -  2.3237 [2048/2073]  1844   204  10.0%
  bin  7:  2.3237 -  2.2077 [2028/2062]  1830   198   9.8%
  bin  8:  2.2077 -  2.1119 [2045/2075]  1838   207  10.1%
  bin  9:  2.1119 -  2.0308 [1974/2054]  1777   197  10.0%
  bin 10:  2.0308 -  1.9609 [ 984/2048]   886    98  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_164/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.12 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.09 -     1.86: 13
        1.86 -     2.62: 89
        2.62 -     3.38: 4260
        3.38 -     4.14: 9431
        4.14 -     4.90: 14723
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.095 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.138 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.206 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  57 " - " O   HOH Z 104 "  1.658 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 176 "  1.680 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28511 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_164/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_164/model_refine_001.geo

CPU time processing inputs: 8.20


============================ 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 46.4607 88.54975 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 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5038   r_free= 0.4960   ksol= 0.00   Bsol= 0.00   scale= 0.779    |
|                                                                             |
| 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:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.299439                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9149 -  4.6804 0.99   1427  157 0.4118 0.3955      6.6247      6.5921|
|  2:  4.6804 -  3.7342 0.99   1378  155 0.4192 0.4631         6.8      6.8969|
|  3:  3.7342 -  3.2678 0.99   1343  149 0.4866 0.4354      6.7125      6.6955|
|  4:  3.2678 -  2.9716 0.99   1343  145 0.5045 0.5041      6.5511      6.5115|
|  5:  2.9716 -  2.7600 0.99   1326  152 0.5277 0.5265      6.3742      6.4408|
|  6:  2.7600 -  2.5982 0.99   1340  148 0.5399 0.5308      6.2946      6.2097|
|  7:  2.5982 -  2.4687 0.99   1298  149 0.5321 0.5110      6.2486      6.1467|
|  8:  2.4687 -  2.3617 0.98   1324  147 0.5470 0.5487      6.1862      6.2076|
|  9:  2.3617 -  2.2711 0.98   1310  142 0.5430 0.5376      6.1305      6.1961|
| 10:  2.2711 -  2.1930 0.99   1324  141 0.5499 0.5341      6.1036      6.0994|
| 11:  2.1930 -  2.1246 0.99   1283  152 0.5484 0.4944      6.0212       6.042|
| 12:  2.1246 -  2.0640 0.97   1310  139 0.5425 0.5268        5.97       5.986|
| 13:  2.0640 -  2.0098 0.88   1164  126 0.5513 0.4871      5.8943      5.8393|
| 14:  2.0098 -  1.9609 0.36    460   57 0.5377 0.5768      5.9018      5.7669|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9149 -  4.6804  1427   157  0.67  37.08   0.78     0.72      84093.68|
|  2:  4.6804 -  3.7342  1378   155  0.65  39.29   0.87     0.73     127383.62|
|  3:  3.7342 -  3.2678  1343   149  0.53  49.74   0.82     0.66     135180.46|
|  4:  3.2678 -  2.9716  1343   145  0.41  59.22   0.77     0.50     124223.03|
|  5:  2.9716 -  2.7600  1326   152  0.29  68.14   0.72     0.36      98673.18|
|  6:  2.7600 -  2.5982  1340   148  0.22  73.14   0.70     0.27      88032.75|
|  7:  2.5982 -  2.4687  1298   149  0.24  72.23   0.72     0.28      75515.08|
|  8:  2.4687 -  2.3617  1324   147  0.26  70.36   0.72     0.32      66229.87|
|  9:  2.3617 -  2.2711  1310   142  0.29  68.24   0.71     0.36      59692.60|
| 10:  2.2711 -  2.1930  1324   141  0.29  68.48   0.72     0.34      52270.11|
| 11:  2.1930 -  2.1246  1283   152  0.23  72.74   0.73     0.31      53770.12|
| 12:  2.1246 -  2.0640  1310   139  0.22  73.79   0.74     0.29      48168.08|
| 13:  2.0640 -  2.0098  1164   126  0.23  73.02   0.72     0.31      42209.99|
| 14:  2.0098 -  1.9609   460    57  0.33  64.98   0.75     0.36      30064.34|
|alpha:            min =        0.27 max =            0.73 mean =         0.42|
|beta:             min =    30064.34 max =       135180.46 mean =     80594.38|
|figures of merit: min =        0.00 max =            1.00 mean =         0.35|
|phase err.(work): min =        0.00 max =           89.98 mean =        63.16|
|phase err.(test): min =        0.00 max =           89.94 mean =        63.53|
|-----------------------------------------------------------------------------|

============================== 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 = 19.387800             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.662   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.926645              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.100   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.159 -  1.533:        7 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.533 -  1.907:       22 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.907 -  2.281:      180 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.281 -  2.655:      678 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.655 -  3.029:     1460 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.029 -  3.403:     2608 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.403 -  3.778:     3985 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.778 -  4.152:     5118 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.152 -  4.526:     6661 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.526 -  4.900:     7816 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.460 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.088    4.900  1.159 |       2.578 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.672)------------------------------------------|
|    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 = 11.672)------------------------------------------|
|    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 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5085   r_free= 0.4996   ksol= 0.00   Bsol= 0.00   scale= 0.749    |
|                                                                             |
| 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:   0.87 A                  |
| x-ray target function (ml) for work reflections: 6.300161                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4945   r_free= 0.4853   ksol= 0.37   Bsol= 20.00   scale= 0.968   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.45,7.23,10.65,0.00,0.00,0.00); trace/3= 8.11                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.292902                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.056978             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.847   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.836703              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.110   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4945      final r-factor (work) = 0.4318          |
| start r-factor (free) = 0.4853      final r-factor (free) = 0.4484          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 103.9936 = 16.06 * 0.50 * 6.2943 + 1.00 * 53.4598                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 50.2716 = 16.06 * 0.50 * 6.2437 + 1.00 * 0.1445                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4318      final r-factor (work) = 0.3884          |
| start r-factor (free) = 0.4484      final r-factor (free) = 0.4458          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.4822 = 1.84 * 1.00 * 6.2437 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.3679 = 1.84 * 1.00 * 6.1769 + 1.00 * 0.0227                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.672)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.77   16.32    None  None   None       |
|    all(noH): 2823   0      0.00    84.77   16.32    None  None   None       |
|    Sol.    : 438    0      0.00    84.77   26.57    None  None   None       |
|    Mac.    : 2385   0      0.00    74.38   14.44    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.477:  979   |   5:    42.383 -  50.859:   76        |
|      1:     8.477 -  16.953:  746   |   6:    50.859 -  59.336:   34        |
|      2:    16.953 -  25.430:  489   |   7:    59.336 -  67.813:   22        |
|      3:    25.430 -  33.906:  303   |   8:    67.813 -  76.289:   12        |
|      4:    33.906 -  42.383:  158   |   9:    76.289 -  84.766:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3884 r_free = 0.4458             target_work(ml) = 6.166         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3886 r_free = 0.4470             target_work(ml) = 6.165         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3886   r_free= 0.4470   ksol= 0.37   Bsol= 20.00   scale= 1.114   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.45,7.23,10.65,0.00,0.00,0.00); trace/3= 8.11                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.164920                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3866   r_free= 0.4459   ksol= 0.35   Bsol= 42.89   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.63,4.01,7.53,0.00,0.00,0.00); trace/3= 5.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.166529                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.579735              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.512   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.619008              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.497  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3866      final r-factor (work) = 0.3200          |
| start r-factor (free) = 0.4459      final r-factor (free) = 0.3831          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.5359 = 7.58 * 0.50 * 6.1721 + 1.00 * 0.1445                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.1781 = 7.58 * 0.50 * 6.0931 + 1.00 * 0.0861                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3200      final r-factor (work) = 0.3012          |
| start r-factor (free) = 0.3831      final r-factor (free) = 0.3680          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7942 = 0.62 * 1.00 * 6.0931 + 1.00 * 0.0225                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7258 = 0.62 * 1.00 * 5.9981 + 1.00 * 0.0129                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.672)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.47   15.69    None  None   None       |
|    all(noH): 2823   0      0.00    87.47   15.69    None  None   None       |
|    Sol.    : 438    0      0.00    87.47   30.98    None  None   None       |
|    Mac.    : 2385   0      0.00    65.87   12.88    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 -   8.747: 1059   |   5:    43.735 -  52.482:   71        |
|      1:     8.747 -  17.494:  801   |   6:    52.482 -  61.229:   32        |
|      2:    17.494 -  26.241:  476   |   7:    61.229 -  69.976:   14        |
|      3:    26.241 -  34.988:  235   |   8:    69.976 -  78.723:    9        |
|      4:    34.988 -  43.735:  125   |   9:    78.723 -  87.469:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3012 r_free = 0.3680             target_work(ml) = 5.979         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3008 r_free = 0.3678             target_work(ml) = 5.979         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3008   r_free= 0.3678   ksol= 0.35   Bsol= 42.89   scale= 1.083   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.63,4.01,7.53,0.00,0.00,0.00); trace/3= 5.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 5.979275                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2993   r_free= 0.3662   ksol= 0.33   Bsol= 42.89   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.39,1.90,4.94,0.00,0.00,0.00); trace/3= 2.74                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 5.979741                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.545958              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.908   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.384574              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.932  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2993      final r-factor (work) = 0.2260          |
| start r-factor (free) = 0.3662      final r-factor (free) = 0.2843          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.7237 = 5.55 * 0.50 * 5.9999 + 1.00 * 0.0861                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.3613 = 5.55 * 0.50 * 5.8718 + 1.00 * 0.0791                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2260      final r-factor (work) = 0.2045          |
| start r-factor (free) = 0.2843      final r-factor (free) = 0.2645          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2713 = 0.38 * 1.00 * 5.8718 + 1.00 * 0.0132                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2076 = 0.38 * 1.00 * 5.7014 + 1.00 * 0.0150                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.672)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.28  15.15    None  None   None       |
|    all(noH): 2823   0      0.00    105.28  15.15    None  None   None       |
|    Sol.    : 438    0      1.44    83.89   35.39    None  None   None       |
|    Mac.    : 2385   0      0.00    105.28  11.44    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.528: 1447   |   5:    52.638 -  63.165:   39        |
|      1:    10.528 -  21.055:  748   |   6:    63.165 -  73.693:   18        |
|      2:    21.055 -  31.583:  257   |   7:    73.693 -  84.220:    4        |
|      3:    31.583 -  42.110:  210   |   8:    84.220 -  94.748:    0        |
|      4:    42.110 -  52.638:   99   |   9:    94.748 - 105.276:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2045 r_free = 0.2645             target_work(ml) = 5.666         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2041 r_free = 0.2639             target_work(ml) = 5.664         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2041   r_free= 0.2639   ksol= 0.33   Bsol= 42.89   scale= 1.052   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.39,1.90,4.94,0.00,0.00,0.00); trace/3= 2.74                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.664033                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2029   r_free= 0.2632   ksol= 0.31   Bsol= 46.53   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.08,0.70,3.04,0.00,0.00,0.00); trace/3= 1.22                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.663968                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.799565              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.659  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.061705              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 108.462  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2029      final r-factor (work) = 0.1556          |
| start r-factor (free) = 0.2632      final r-factor (free) = 0.2114          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.6333 = 5.80 * 0.50 * 5.7088 + 1.00 * 0.0791                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.2063 = 5.80 * 0.50 * 5.5607 + 1.00 * 0.0813                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1556      final r-factor (work) = 0.1412          |
| start r-factor (free) = 0.2114      final r-factor (free) = 0.1989          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.4885 = 2.06 * 1.00 * 5.5607 + 1.00 * 0.0239                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.1268 = 2.06 * 1.00 * 5.3898 + 1.00 * 0.0147                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.672)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.76  16.07    None  None   None       |
|    all(noH): 2823   0      0.00    106.76  16.07    None  None   None       |
|    Sol.    : 438    0      2.88    106.76  43.67    None  None   None       |
|    Mac.    : 2385   0      0.00    96.86   11.00    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:     0.000 -  10.676: 1565   |   5:    53.381 -  64.057:   90        |
|      1:    10.676 -  21.352:  691   |   6:    64.057 -  74.733:   55        |
|      2:    21.352 -  32.028:  168   |   7:    74.733 -  85.409:   27        |
|      3:    32.028 -  42.705:  127   |   8:    85.409 -  96.085:    8        |
|      4:    42.705 -  53.381:   90   |   9:    96.085 - 106.761:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1412 r_free = 0.1989             target_work(ml) = 5.354         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1411 r_free = 0.1988             target_work(ml) = 5.354         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1411   r_free= 0.1988   ksol= 0.31   Bsol= 46.53   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.08,0.70,3.04,0.00,0.00,0.00); trace/3= 1.22                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.353580                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1412   r_free= 0.1992   ksol= 0.32   Bsol= 58.10   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.47,0.27,2.40,0.00,0.00,0.00); trace/3= 0.73                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.353885                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.001085              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.684  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.207040              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.518  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1412      final r-factor (work) = 0.1275          |
| start r-factor (free) = 0.1992      final r-factor (free) = 0.1817          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1723 = 3.00 * 0.50 * 5.3919 + 1.00 * 0.0816                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0448 = 3.00 * 0.50 * 5.3173 + 1.00 * 0.0660                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1275      final r-factor (work) = 0.1255          |
| start r-factor (free) = 0.1817      final r-factor (free) = 0.1750          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1155 = 0.21 * 1.00 * 5.3173 + 1.00 * 0.0146                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1020 = 0.21 * 1.00 * 5.2693 + 1.00 * 0.0111                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.672)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.41    103.76  15.37    None  None   None       |
|    all(noH): 2823   0      0.41    103.76  15.37    None  None   None       |
|    Sol.    : 438    0      3.49    103.76  41.35    None  None   None       |
|    Mac.    : 2385   0      0.41    96.80   10.60    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:     0.412 -  10.747: 1658   |   5:    52.087 -  62.422:   80        |
|      1:    10.747 -  21.082:  637   |   6:    62.422 -  72.757:   52        |
|      2:    21.082 -  31.417:  151   |   7:    72.757 -  83.092:   22        |
|      3:    31.417 -  41.752:  117   |   8:    83.092 -  93.427:    6        |
|      4:    41.752 -  52.087:   98   |   9:    93.427 - 103.763:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1255 r_free = 0.1750             target_work(ml) = 5.249         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1253 r_free = 0.1747             target_work(ml) = 5.248         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1253   r_free= 0.1747   ksol= 0.32   Bsol= 58.10   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.47,0.27,2.40,0.00,0.00,0.00); trace/3= 0.73                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.248076                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9149 -  4.6804 0.99   1427  157 0.1014 0.1367      5.4456      5.6254|
|  2:  4.6804 -  3.7342 0.99   1378  155 0.0915 0.1235      5.5197      5.7322|
|  3:  3.7342 -  3.2678 0.99   1343  149 0.1201 0.1666      5.5809      5.9186|
|  4:  3.2678 -  2.9716 0.99   1343  145 0.1392 0.1874       5.553      5.7438|
|  5:  2.9716 -  2.7600 0.99   1326  152 0.1477 0.1711      5.4455      5.5907|
|  6:  2.7600 -  2.5982 0.99   1340  148 0.1410 0.2391      5.3134        5.64|
|  7:  2.5982 -  2.4687 0.99   1298  149 0.1444 0.1859      5.2819      5.4194|
|  8:  2.4687 -  2.3617 0.98   1324  147 0.1334 0.1914      5.1829      5.4232|
|  9:  2.3617 -  2.2711 0.98   1310  142 0.1391 0.1990      5.1402      5.4159|
| 10:  2.2711 -  2.1930 0.99   1324  141 0.1267 0.1746      5.0524      5.2351|
| 11:  2.1930 -  2.1246 0.99   1283  152 0.1308 0.2184      5.0219      5.4328|
| 12:  2.1246 -  2.0640 0.97   1310  139 0.1308 0.1710      4.9774      5.1807|
| 13:  2.0640 -  2.0098 0.88   1164  126 0.1162 0.1694      4.8071       4.981|
| 14:  2.0098 -  1.9609 0.36    460   57 0.1069 0.1612      4.6808      4.9202|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9149 -  4.6804  1427   157  0.93  10.65   0.97     0.94       8922.33|
|  2:  4.6804 -  3.7342  1378   155  0.94   9.36   1.02     1.01      11051.43|
|  3:  3.7342 -  3.2678  1343   149  0.92  13.49   1.04     1.03      12855.61|
|  4:  3.2678 -  2.9716  1343   145  0.90  15.70   1.02     1.01      12589.39|
|  5:  2.9716 -  2.7600  1326   152  0.88  18.73   1.01     0.98      11188.02|
|  6:  2.7600 -  2.5982  1340   148  0.87  18.88   0.98     0.94       8681.24|
|  7:  2.5982 -  2.4687  1298   149  0.88  18.60   1.00     0.95       7907.98|
|  8:  2.4687 -  2.3617  1324   147  0.89  17.35   1.01     0.98       6702.19|
|  9:  2.3617 -  2.2711  1310   142  0.88  18.15   1.01     0.97       6131.99|
| 10:  2.2711 -  2.1930  1324   141  0.88  17.86   1.01     0.97       5365.21|
| 11:  2.1930 -  2.1246  1283   152  0.88  19.02   1.01     0.98       5439.97|
| 12:  2.1246 -  2.0640  1310   139  0.88  18.18   1.01     1.01       4825.87|
| 13:  2.0640 -  2.0098  1164   126  0.90  16.58   0.99     0.97       3497.83|
| 14:  2.0098 -  1.9609   460    57  0.93  13.03   0.99     0.96       2384.64|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     2384.64 max =        12855.61 mean =      8017.38|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.89 mean =        16.19|
|phase err.(test): min =        0.00 max =           88.71 mean =        15.54|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1253   r_free= 0.1746   ksol= 0.32   Bsol= 53.86   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.16,-0.46,1.61,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.247911                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1253   r_free= 0.1746   ksol= 0.32   Bsol= 53.86   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.16,-0.46,1.61,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.247911                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9149 -  4.6804 0.99   1427  157 0.1012 0.1367      5.4439      5.6223|
|  2:  4.6804 -  3.7342 0.99   1378  155 0.0911 0.1232      5.5165      5.7283|
|  3:  3.7342 -  3.2678 0.99   1343  149 0.1199 0.1664      5.5791      5.9176|
|  4:  3.2678 -  2.9716 0.99   1343  145 0.1394 0.1876      5.5533      5.7445|
|  5:  2.9716 -  2.7600 0.99   1326  152 0.1478 0.1714      5.4463      5.5928|
|  6:  2.7600 -  2.5982 0.99   1340  148 0.1412 0.2392      5.3145      5.6409|
|  7:  2.5982 -  2.4687 0.99   1298  149 0.1445 0.1861      5.2829      5.4204|
|  8:  2.4687 -  2.3617 0.98   1324  147 0.1335 0.1915      5.1836       5.424|
|  9:  2.3617 -  2.2711 0.98   1310  142 0.1391 0.1992      5.1404      5.4164|
| 10:  2.2711 -  2.1930 0.99   1324  141 0.1268 0.1745      5.0528      5.2354|
| 11:  2.1930 -  2.1246 0.99   1283  152 0.1308 0.2183      5.0219      5.4324|
| 12:  2.1246 -  2.0640 0.97   1310  139 0.1309 0.1709      4.9777      5.1804|
| 13:  2.0640 -  2.0098 0.88   1164  126 0.1162 0.1694      4.8071      4.9812|
| 14:  2.0098 -  1.9609 0.36    460   57 0.1070 0.1611      4.6811      4.9201|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9149 -  4.6804  1427   157  0.93  10.62   0.97     0.94       8880.18|
|  2:  4.6804 -  3.7342  1378   155  0.94   9.31   1.02     1.01      10980.26|
|  3:  3.7342 -  3.2678  1343   149  0.92  13.45   1.03     1.03      12790.15|
|  4:  3.2678 -  2.9716  1343   145  0.90  15.69   1.02     1.01      12583.56|
|  5:  2.9716 -  2.7600  1326   152  0.88  18.75   1.00     0.97      11212.88|
|  6:  2.7600 -  2.5982  1340   148  0.87  18.90   0.97     0.93       8704.94|
|  7:  2.5982 -  2.4687  1298   149  0.88  18.63   0.99     0.95       7929.31|
|  8:  2.4687 -  2.3617  1324   147  0.89  17.37   1.01     0.98       6713.65|
|  9:  2.3617 -  2.2711  1310   142  0.88  18.16   1.00     0.96       6140.02|
| 10:  2.2711 -  2.1930  1324   141  0.88  17.86   1.01     0.96       5366.46|
| 11:  2.1930 -  2.1246  1283   152  0.88  19.01   1.01     0.98       5439.56|
| 12:  2.1246 -  2.0640  1310   139  0.88  18.17   1.01     1.00       4823.63|
| 13:  2.0640 -  2.0098  1164   126  0.90  16.57   0.98     0.96       3496.09|
| 14:  2.0098 -  1.9609   460    57  0.93  13.03   0.98     0.96       2383.98|
|alpha:            min =        0.93 max =            1.03 mean =         0.97|
|beta:             min =     2383.98 max =        12790.15 mean =      8009.43|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.96 mean =        16.19|
|phase err.(test): min =        0.00 max =           88.90 mean =        15.54|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.672)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.02    104.37  15.98    None  None   None       |
|    all(noH): 2823   0      1.02    104.37  15.98    None  None   None       |
|    Sol.    : 438    0      4.10    104.37  41.96    None  None   None       |
|    Mac.    : 2385   0      1.02    97.41   11.21    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:     1.023 -  11.358: 1658   |   5:    52.698 -  63.033:   80        |
|      1:    11.358 -  21.693:  637   |   6:    63.033 -  73.368:   52        |
|      2:    21.693 -  32.028:  151   |   7:    73.368 -  83.703:   22        |
|      3:    32.028 -  42.363:  117   |   8:    83.703 -  94.038:    6        |
|      4:    42.363 -  52.698:   98   |   9:    94.038 - 104.373:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 314         
Filter by distance & map next to the model:
   mapped sites are within: 0.495 - 5.393
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 310 from: 314
   mapped sites are within: 0.735 - 5.393

peak=   10.066 closest distance to " CB  VAL A 230 " =    1.502
peak=    8.742 closest distance to " CB  VAL A 296 " =    1.570
peak=    7.451 closest distance to " O   HOH Z 130 " =    1.582
peak=    6.448 closest distance to " CD2 LEU A   5 " =    1.261
peak=    5.691 closest distance to " CG  PRO A  54 " =    1.454
peak=    5.508 closest distance to " NE2 GLN A  11 " =    1.146
peak=    5.502 closest distance to " O   HOH Z 255 " =    0.848
peak=    5.490 closest distance to " NH2AARG A 145 " =    1.184
peak=    5.416 closest distance to " O   HOH Z 246 " =    1.213
peak=    5.112 closest distance to " CB  GLN A 223 " =    1.608
peak=    5.108 closest distance to " O   HOH Z 188 " =    1.553
peak=    5.055 closest distance to " O   HOH Z   9 " =    2.068
peak=    5.031 closest distance to " O   HOH Z 112 " =    1.225
peak=    4.972 closest distance to " O   HOH Z 124 " =    1.322
peak=    4.949 closest distance to " O   HOH Z 103 " =    1.082
peak=    4.933 closest distance to " CB  ARG A 275 " =    0.945
peak=    4.915 closest distance to " CB  ASN A 142 " =    1.079
peak=    4.885 closest distance to " O   HOH Z 232 " =    2.325
peak=    4.875 closest distance to " O   HOH Z 248 " =    1.253
peak=    4.760 closest distance to " O   HOH Z  69 " =    1.090
peak=    4.735 closest distance to " CD1AILE A 234 " =    0.934
peak=    4.703 closest distance to " CG  LEU A 228 " =    1.284
peak=    4.669 closest distance to " O   HOH Z 142 " =    1.791
peak=    4.601 closest distance to " O   HOH Z 369 " =    2.316
peak=    4.601 closest distance to " CG  LEU A   5 " =    1.206
peak=    4.595 closest distance to " CB  ASN A 148 " =    1.391
peak=    4.552 closest distance to " O   HOH Z  49 " =    1.314
peak=    4.547 closest distance to " O   HOH Z 425 " =    1.590
peak=    4.523 closest distance to " O   HOH Z 402 " =    1.429
peak=    4.469 closest distance to " NH2 ARG A  56 " =    2.036
peak=    4.463 closest distance to " O   HOH Z  78 " =    1.656
peak=    4.458 closest distance to " CG  PRO A 243 " =    1.179
peak=    4.440 closest distance to " CB  VAL A 230 " =    1.279
peak=    4.404 closest distance to " CG  GLN A  58 " =    1.215
peak=    4.391 closest distance to " CG  GLN A  11 " =    2.308
peak=    4.359 closest distance to " CG2 ILE A 234 " =    1.195
peak=    4.353 closest distance to " CG  LYS A  76 " =    1.565
peak=    4.348 closest distance to " O   HOH Z 375 " =    1.047
peak=    4.310 closest distance to " O   HOH Z 126 " =    1.629
peak=    4.308 closest distance to " O   HOH Z 251 " =    1.774
peak=    4.305 closest distance to " O   HOH Z  85 " =    1.438
peak=    4.292 closest distance to " O   HOH Z 417 " =    1.439
peak=    4.284 closest distance to " O   HOH Z 143 " =    1.639
peak=    4.282 closest distance to " CB  PRO A  54 " =    0.954
peak=    4.267 closest distance to " O   HOH Z 427 " =    2.841
peak=    4.254 closest distance to " CD2 TRP A 179 " =    1.365
peak=    4.216 closest distance to " O   HOH Z 403 " =    1.661
peak=    4.176 closest distance to " CG  LEU A 167 " =    1.253
peak=    4.164 closest distance to " O   HOH Z 272 " =    1.837
peak=    4.162 closest distance to " O   HOH Z 258 " =    1.233
peak=    4.152 closest distance to " CB BVAL A  41 " =    1.258
peak=    4.150 closest distance to " CA  PHE A 283 " =    1.165
peak=    4.149 closest distance to " O   HOH Z   7 " =    1.221
peak=    4.130 closest distance to " NH2AARG A 190 " =    1.987
peak=    4.130 closest distance to " O   HOH Z 359 " =    1.733
peak=    4.103 closest distance to " O   HOH Z 107 " =    0.977
peak=    4.089 closest distance to " O   HOH Z 236 " =    1.504
peak=    4.079 closest distance to " O   HOH Z  70 " =    0.962
peak=    4.052 closest distance to " O   HOH Z 207 " =    1.245
peak=    4.044 closest distance to " CA  ALA A  51 " =    0.930
peak=    4.043 closest distance to " O   HOH Z 331 " =    1.039
peak=    4.035 closest distance to " O   HOH Z 346 " =    1.547
peak=    4.030 closest distance to " CB  SER A  63 " =    1.209
peak=    4.017 closest distance to " N   ASP A 162 " =    1.142
peak=    4.012 closest distance to " CG AARG A 275 " =    1.319
peak=    4.002 closest distance to " O   HOH Z 193 " =    1.778
peak=    3.987 closest distance to " CZ  PHE A 218 " =    1.171
peak=    3.975 closest distance to " O   HOH Z 123 " =    1.266
peak=    3.975 closest distance to " CG2 VAL A 257 " =    0.902
peak=    3.974 closest distance to " O   HOH Z 203 " =    1.554
peak=    3.966 closest distance to " O   HOH Z 182 " =    1.094
peak=    3.959 closest distance to " O   HOH Z  65 " =    0.862
peak=    3.952 closest distance to " NE AARG A 145 " =    0.947
peak=    3.949 closest distance to " CB  VAL A 265 " =    1.416
peak=    3.945 closest distance to " O   HOH Z  43 " =    1.251
peak=    3.939 closest distance to " CB  SER A   3 " =    1.307
peak=    3.936 closest distance to " CB  GLU A 277 " =    3.634
peak=    3.935 closest distance to " CB  PRO A  90 " =    1.143
peak=    3.930 closest distance to " O   HOH Z 153 " =    3.886
peak=    3.913 closest distance to " ND2 ASN A 249 " =    0.913
peak=    3.912 closest distance to " N   PHE A 130 " =    1.386
peak=    3.910 closest distance to " CB  VAL A 202 " =    1.572
peak=    3.907 closest distance to " O   SER A  87 " =    2.302
peak=    3.903 closest distance to " O   HOH Z 287 " =    1.845
peak=    3.898 closest distance to " CZ3 TRP A 266 " =    1.183
peak=    3.894 closest distance to " O   HOH Z 265 " =    2.022
peak=    3.887 closest distance to " O   HOH Z 238 " =    1.253
peak=    3.878 closest distance to " O   HOH Z 222 " =    1.237
peak=    3.868 closest distance to " CB  ASN A 110 " =    1.171
peak=    3.867 closest distance to " O   HOH Z 380 " =    1.534
peak=    3.866 closest distance to " O   HOH Z  40 " =    1.832
peak=    3.863 closest distance to " O   HOH Z 188 " =    2.255
peak=    3.836 closest distance to " CB  GLN A 183 " =    1.198
peak=    3.828 closest distance to " O   HOH Z 116 " =    1.021
peak=    3.827 closest distance to " O   HOH Z 303 " =    2.156
peak=    3.826 closest distance to " CA  TYR A  30 " =    1.010
peak=    3.825 closest distance to " N   ASN A  39 " =    1.244
peak=    3.821 closest distance to " O   HOH Z 234 " =    3.715
peak=    3.820 closest distance to " CB  SER A  26 " =    1.669
peak=    3.819 closest distance to " O   HOH Z 406 " =    1.547
peak=    3.817 closest distance to " O  BHOH Z 338 " =    2.454
peak=    3.798 closest distance to " O   HOH Z 117 " =    1.304
peak=    3.793 closest distance to " CD  ARG A 269 " =    1.013
peak=    3.792 closest distance to " CB  ARG A 156 " =    1.178
peak=    3.786 closest distance to " O   HOH Z 389 " =    1.631
peak=    3.783 closest distance to " CB  ASN A  39 " =    0.931
peak=    3.779 closest distance to " CB  ARG A  79 " =    1.310
peak=    3.772 closest distance to " O   HOH Z 415 " =    3.405
peak=    3.765 closest distance to " CA  GLN A  58 " =    0.872
peak=    3.761 closest distance to " O   HOH Z 130 " =    2.162
peak=    3.759 closest distance to " O   HOH Z 126 " =    1.897
peak=    3.755 closest distance to " O   HOH Z 422 " =    2.348
peak=    3.754 closest distance to " OG ASER A 258 " =    3.028
peak=    3.754 closest distance to " O   HOH Z 423 " =    1.702
peak=    3.753 closest distance to " CB  ASN A 215 " =    1.085
peak=    3.746 closest distance to " O   HOH Z 411 " =    4.098
peak=    3.746 closest distance to " O   HOH Z 365 " =    2.702
peak=    3.726 closest distance to " ND2 ASN A 187 " =    1.780
peak=    3.722 closest distance to " O   HOH Z 398 " =    1.310
peak=    3.721 closest distance to " O   HOH Z  10 " =    1.720
peak=    3.720 closest distance to " O   HOH Z 324 " =    1.381
peak=    3.712 closest distance to " CG2 ILE A  20 " =    1.651
peak=    3.702 closest distance to " CD2 TYR A 186 " =    1.099
peak=    3.701 closest distance to " CB  THR A  52 " =    0.998
peak=    3.699 closest distance to " O   HOH Z 423 " =    1.463
peak=    3.694 closest distance to " CB  GLU A 152 " =    1.189
peak=    3.691 closest distance to " O   HOH Z 372 " =    1.074
peak=    3.689 closest distance to " O   HOH Z  63 " =    1.848
peak=    3.687 closest distance to " O   HOH Z  39 " =    1.197
peak=    3.682 closest distance to " CD2 LEU A 228 " =    1.193
peak=    3.671 closest distance to " CB  ARG A  79 " =    0.836
peak=    3.670 closest distance to " CB  GLN A  58 " =    0.907
peak=    3.668 closest distance to " CB  TYR A 169 " =    0.954
peak=    3.663 closest distance to " CB  ALA A   9 " =    1.627
peak=    3.661 closest distance to " O   HOH Z  59 " =    1.656
peak=    3.655 closest distance to " CA  ILE A 234 " =    1.133
peak=    3.644 closest distance to " O   HOH Z  88 " =    2.706
peak=    3.639 closest distance to " O   HOH Z 403 " =    1.455
peak=    3.635 closest distance to " O   HOH Z 213 " =    1.936
peak=    3.635 closest distance to " CB  SER A 273 " =    0.913
peak=    3.632 closest distance to " CB  ALA A 114 " =    1.013
peak=    3.626 closest distance to " CB  SER A  62 " =    0.917
peak=    3.626 closest distance to " O   HOH Z 272 " =    2.222
peak=    3.623 closest distance to " CB  LEU A 300 " =    1.069
peak=    3.618 closest distance to " CB  SER A 216 " =    0.902
peak=    3.618 closest distance to " O   TYR A 116 " =    1.185
peak=    3.618 closest distance to " CD1 ILE A 199 " =    1.324
peak=    3.614 closest distance to " CB  ARG A 102 " =    0.780
peak=    3.611 closest distance to " CA  ASP A 162 " =    0.881
peak=    3.609 closest distance to " O   HOH Z 132 " =    2.287
peak=    3.598 closest distance to " O   HOH Z 421 " =    2.333
peak=    3.593 closest distance to " O   HOH Z 211 " =    1.007
peak=    3.592 closest distance to " O   HOH Z  30 " =    1.687
peak=    3.583 closest distance to " O   HOH Z  43 " =    2.219
peak=    3.578 closest distance to " CB  ASP A 107 " =    1.068
peak=    3.574 closest distance to " O   HOH Z 156 " =    2.988
peak=    3.573 closest distance to " O   HOH Z 357 " =    1.997
peak=    3.566 closest distance to " O   HOH Z   6 " =    1.537
peak=    3.566 closest distance to " O   HOH Z 148 " =    1.383
peak=    3.564 closest distance to " O   HOH Z  95 " =    1.136
peak=    3.562 closest distance to " CG  PRO A 198 " =    1.360
peak=    3.559 closest distance to " CA  ARG A 195 " =    1.200
peak=    3.558 closest distance to " CB  GLN A  88 " =    1.262
peak=    3.556 closest distance to " CB  ASP A 124 " =    0.845
peak=    3.556 closest distance to " CE3 TRP A 150 " =    1.116
peak=    3.556 closest distance to " NH1AARG A 145 " =    1.039
peak=    3.550 closest distance to " N   TYR A  15 " =    1.134
peak=    3.550 closest distance to " CA  LEU A 282 " =    1.278
peak=    3.549 closest distance to " O   HOH Z 158 " =    2.942
peak=    3.548 closest distance to " ND2BASN A 224 " =    0.770
peak=    3.545 closest distance to " CG  ARG A 138 " =    1.341
peak=    3.538 closest distance to " O   HOH Z 199 " =    1.284
peak=    3.533 closest distance to " NZ  LYS A 117 " =    1.196
peak=    3.517 closest distance to " CB  ARG A 138 " =    1.006
peak=    3.507 closest distance to " OG  SER A  62 " =    2.876
peak=    3.505 closest distance to " O   HOH Z 353 " =    2.489
peak=    3.505 closest distance to " O   HOH Z 200 " =    1.558
peak=    3.501 closest distance to " CA  ASN A 217 " =    1.144
peak=    3.495 closest distance to " O   PRO A 198 " =    1.577
peak=    3.485 closest distance to " CG2 ILE A 120 " =    1.365
peak=    3.479 closest distance to " O   HOH Z 385 " =    3.838
peak=    3.469 closest distance to " O   HOH Z 193 " =    1.768
peak=    3.462 closest distance to " CB  PHE A 204 " =    0.895
peak=    3.457 closest distance to " OG BSER A 210 " =    1.491
peak=    3.452 closest distance to " CA  ASN A 215 " =    1.043
peak=    3.452 closest distance to " CG  LYS A 119 " =    0.965
peak=    3.447 closest distance to " O   HOH Z 129 " =    1.062
peak=    3.447 closest distance to " O   HOH Z 263 " =    1.645
peak=    3.442 closest distance to " O   HOH Z 162 " =    1.654
peak=    3.438 closest distance to " CD1 LEU A  96 " =    0.830
peak=    3.425 closest distance to " CA  ALA A 100 " =    0.923
peak=    3.417 closest distance to " CB  GLN A  55 " =    0.840
peak=    3.403 closest distance to " O   HOH Z 261 " =    2.064
peak=    3.399 closest distance to " CD  ARG A  66 " =    2.547
peak=    3.393 closest distance to " NZ  LYS A 117 " =    3.054
peak=    3.392 closest distance to " CA  TYR A 116 " =    1.404
peak=    3.391 closest distance to " O   HOH Z 419 " =    1.923
peak=    3.388 closest distance to " O   HOH Z 218 " =    1.903
peak=    3.387 closest distance to " OD1 ASN A  69 " =    2.247
peak=    3.384 closest distance to " O   HOH Z  66 " =    2.223
peak=    3.383 closest distance to " CB  TRP A 179 " =    1.296
peak=    3.383 closest distance to " O   THR A 182 " =    1.485
peak=    3.379 closest distance to " O   HOH Z 329 " =    4.155
peak=    3.375 closest distance to " N   ASN A 127 " =    1.327
peak=    3.366 closest distance to " CB  GLN A  89 " =    1.156
peak=    3.362 closest distance to " CB  GLU A 128 " =    0.952
peak=    3.358 closest distance to " CG  PRO A 213 " =    1.274
peak=    3.354 closest distance to " O   HOH Z  22 " =    1.990
peak=    3.352 closest distance to " O   HOH Z  61 " =    1.537
peak=    3.351 closest distance to " O   HOH Z 128 " =    2.090
peak=    3.351 closest distance to " O   HOH Z 238 " =    3.610
peak=    3.350 closest distance to " CB  ALA A 160 " =    1.465
peak=    3.349 closest distance to " CG  MET A 185 " =    1.315
peak=    3.348 closest distance to " CD1 ILE A  33 " =    1.745
peak=    3.346 closest distance to " O   HOH Z 298 " =    1.692
peak=    3.333 closest distance to " O   HOH Z 196 " =    1.172
peak=    3.329 closest distance to " NH2AARG A 275 " =    3.596
peak=    3.327 closest distance to " CB  GLU A 236 " =    1.247
peak=    3.326 closest distance to " CA  ALA A  21 " =    1.091
peak=    3.321 closest distance to " OG1 THR A 264 " =    0.735
peak=    3.318 closest distance to " CA  VAL A 125 " =    1.083
peak=    3.318 closest distance to " O   HOH Z  80 " =    1.733
peak=    3.315 closest distance to " NE  ARG A  56 " =    3.575
peak=    3.313 closest distance to " O   HOH Z 259 " =    1.458
peak=    3.311 closest distance to " O   HOH Z 368 " =    3.291
peak=    3.310 closest distance to " CZ  PHE A  38 " =    1.100
peak=    3.310 closest distance to " CA  ARG A 102 " =    1.107
peak=    3.307 closest distance to " CD  LYS A 166 " =    1.288
peak=    3.301 closest distance to " O   HOH Z 128 " =    2.005
peak=    3.299 closest distance to " O   PRO A 198 " =    1.512
peak=    3.293 closest distance to " CA  ALA A 160 " =    1.078
peak=    3.289 closest distance to " CA  TRP A 150 " =    0.802
peak=    3.289 closest distance to " CB  TRP A 266 " =    1.100
peak=    3.288 closest distance to " O   HOH Z 293 " =    1.745
peak=    3.285 closest distance to " O   HOH Z   1 " =    1.942
peak=    3.285 closest distance to " O   HOH Z 146 " =    1.378
peak=    3.280 closest distance to " CA  GLY A 267 " =    1.003
peak=    3.276 closest distance to " O   HOH Z 104 " =    1.753
peak=    3.270 closest distance to " O   HOH Z 334 " =    1.508
peak=    3.269 closest distance to " C   PHE A 208 " =    1.075
peak=    3.256 closest distance to " O   HOH Z  59 " =    2.003
peak=    3.253 closest distance to " CB  THR A  31 " =    1.517
peak=    3.249 closest distance to " O   HOH Z 172 " =    3.278
peak=    3.245 closest distance to " CE  LYS A 119 " =    1.169
peak=    3.244 closest distance to " O   HOH Z 425 " =    1.930
peak=    3.241 closest distance to " O   HOH Z 325 " =    2.005
peak=    3.241 closest distance to " CB  ARG A 219 " =    1.290
peak=    3.237 closest distance to " CA  ARG A  36 " =    1.038
peak=    3.236 closest distance to " CA  ARG A 159 " =    1.128
peak=    3.236 closest distance to " O   HOH Z 254 " =    1.357
peak=    3.235 closest distance to " O   HOH Z  61 " =    1.751
peak=    3.233 closest distance to " O   HOH Z 303 " =    1.751
peak=    3.231 closest distance to " O   HOH Z  71 " =    1.544
peak=    3.228 closest distance to " O  BHOH Z  74 " =    1.203
peak=    3.228 closest distance to " CZ3 TRP A 177 " =    1.055
peak=    3.225 closest distance to " CE  LYS A  76 " =    0.922
peak=    3.225 closest distance to " O   HOH Z 379 " =    1.327
peak=    3.223 closest distance to " O   HOH Z 299 " =    4.225
peak=    3.223 closest distance to " NE1 TRP A  92 " =    1.506
peak=    3.218 closest distance to " O   ASP A 124 " =    1.186
peak=    3.214 closest distance to " O   GLN A  88 " =    1.445
peak=    3.214 closest distance to " O   HOH Z 280 " =    2.902
peak=    3.212 closest distance to " O   HOH Z  92 " =    2.044
peak=    3.203 closest distance to " O   ILE A  49 " =    1.033
peak=    3.197 closest distance to " OG BSER A 164 " =    2.126
peak=    3.191 closest distance to " O   HOH Z 305 " =    3.527
peak=    3.189 closest distance to " CG1 VAL A 296 " =    1.232
peak=    3.187 closest distance to " OG1 THR A 221 " =    1.238
peak=    3.183 closest distance to " O   GLY A 211 " =    1.178
peak=    3.182 closest distance to " O   HOH Z 437 " =    2.095
peak=    3.180 closest distance to " O   HOH Z 214 " =    2.764
peak=    3.179 closest distance to " CA  ALA A 295 " =    0.933
peak=    3.178 closest distance to " O   HOH Z 383 " =    2.043
peak=    3.178 closest distance to " CD  ARG A 195 " =    1.114
peak=    3.176 closest distance to " CA  ALA A 154 " =    0.996
peak=    3.173 closest distance to " O   HOH Z 361 " =    3.655
peak=    3.173 closest distance to " O   THR A 220 " =    1.317
peak=    3.164 closest distance to " O   HOH Z 216 " =    3.592
peak=    3.162 closest distance to " O   HOH Z  88 " =    3.271
peak=    3.157 closest distance to " O   HOH Z 222 " =    2.119
peak=    3.154 closest distance to " O   HOH Z 185 " =    1.549
peak=    3.150 closest distance to " O   ASN A  74 " =    1.459
peak=    3.147 closest distance to " CB  SER A 276 " =    1.174
peak=    3.146 closest distance to " N   ARG A 156 " =    1.349
peak=    3.146 closest distance to " O   GLY A  91 " =    1.490
peak=    3.145 closest distance to " CA  ALA A 129 " =    1.245
peak=    3.141 closest distance to " O   HOH Z 285 " =    2.378
peak=    3.139 closest distance to " O   HOH Z 172 " =    5.393
peak=    3.138 closest distance to " CA  GLY A  57 " =    0.903
peak=    3.138 closest distance to " O   HOH Z 350 " =    1.914
peak=    3.133 closest distance to " NE2 GLN A  73 " =    1.580
peak=    3.130 closest distance to " O   PRO A 213 " =    1.225
peak=    3.129 closest distance to " CB  ASP A 191 " =    1.154
peak=    3.126 closest distance to " O   HOH Z 368 " =    2.321
peak=    3.125 closest distance to " O   HOH Z  27 " =    1.027
peak=    3.120 closest distance to " NH1 ARG A  14 " =    1.188
peak=    3.117 closest distance to " CB  PRO A 243 " =    1.228
peak=    3.117 closest distance to " O   ASN A 284 " =    1.883
peak=    3.112 closest distance to " CA  ASN A 127 " =    1.044
peak=    3.112 closest distance to " O   HOH Z 184 " =    1.457
peak=    3.109 closest distance to " O   HOH Z 118 " =    1.408
peak=    3.103 closest distance to " OD1 ASP A 231 " =    1.834
peak=    3.100 closest distance to " CB  ALA A 291 " =    0.761
peak=    3.096 closest distance to " CD  ARG A 195 " =    3.601
peak=    3.095 closest distance to " N   TYR A 247 " =    1.419
peak=    3.087 closest distance to " OE2 GLU A  53 " =    2.040
peak=    3.086 closest distance to " CB  ALA A 114 " =    1.255
peak=    3.075 closest distance to " O   ARG A 275 " =    1.040
peak=    3.049 closest distance to " CB  ASN A 173 " =    0.910
peak=    3.021 closest distance to " O   HOH Z 220 " =    1.509

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 203         
Filter by distance & map next to the model:
   mapped sites are within: 0.556 - 5.695
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 199 from: 203
   mapped sites are within: 0.778 - 5.695

peak=   -4.915 closest distance to " O   HOH Z  69 " =    1.306
peak=   -4.796 closest distance to " O   PRO A 198 " =    1.143
peak=   -4.366 closest distance to " C   HIS A 108 " =    1.181
peak=   -4.318 closest distance to " O   HOH Z 203 " =    1.144
peak=   -4.193 closest distance to " CD  ARG A  14 " =    3.074
peak=   -4.154 closest distance to " CG  GLN A  58 " =    0.947
peak=   -4.105 closest distance to " CD  ARG A 156 " =    1.942
peak=   -4.079 closest distance to " OG BSER A 134 " =    1.424
peak=   -4.074 closest distance to " O   HOH Z 211 " =    0.955
peak=   -4.060 closest distance to " O   VAL A  67 " =    2.278
peak=   -4.019 closest distance to " O   HOH Z 394 " =    1.478
peak=   -4.012 closest distance to " CD  GLN A 223 " =    1.960
peak=   -3.954 closest distance to " O   HOH Z 134 " =    4.327
peak=   -3.950 closest distance to " CZ2 TRP A  92 " =    2.839
peak=   -3.942 closest distance to " CB  ALA A  43 " =    2.425
peak=   -3.892 closest distance to " O   HOH Z 100 " =    0.778
peak=   -3.890 closest distance to " O   HOH Z 131 " =    4.173
peak=   -3.888 closest distance to " CG1 VAL A 250 " =    2.711
peak=   -3.850 closest distance to " NE  ARG A 156 " =    5.582
peak=   -3.805 closest distance to " CB  GLN A  55 " =    1.333
peak=   -3.803 closest distance to " CD  PRO A 213 " =    2.033
peak=   -3.796 closest distance to " CB  ASP A 132 " =    2.426
peak=   -3.793 closest distance to " CD  LYS A 289 " =    2.269
peak=   -3.792 closest distance to " CD1 LEU A 255 " =    2.753
peak=   -3.784 closest distance to " O   HOH Z 116 " =    1.424
peak=   -3.782 closest distance to " OG  SER A  97 " =    2.343
peak=   -3.781 closest distance to " SG BCYS A 201 " =    2.265
peak=   -3.777 closest distance to " CG  TRP A 266 " =    1.791
peak=   -3.777 closest distance to " CD1 LEU A 101 " =    2.289
peak=   -3.732 closest distance to " O   PRO A 163 " =    1.970
peak=   -3.709 closest distance to " O   HOH Z 285 " =    2.134
peak=   -3.677 closest distance to " O   HOH Z 295 " =    1.498
peak=   -3.676 closest distance to " ND2 ASN A 173 " =    1.413
peak=   -3.643 closest distance to " CG2 ILE A  20 " =    2.850
peak=   -3.631 closest distance to " C   ASN A 285 " =    2.146
peak=   -3.622 closest distance to " CD2 TYR A 293 " =    1.992
peak=   -3.615 closest distance to " O   HOH Z 286 " =    1.583
peak=   -3.611 closest distance to " NH2 ARG A  79 " =    2.140
peak=   -3.603 closest distance to " O   HOH Z 276 " =    1.277
peak=   -3.574 closest distance to " O   HOH Z 359 " =    3.097
peak=   -3.574 closest distance to " SD  MET A 105 " =    0.950
peak=   -3.572 closest distance to " CZ  PHE A  38 " =    2.371
peak=   -3.568 closest distance to " CB  ALA A   7 " =    2.154
peak=   -3.566 closest distance to " O   HOH Z 387 " =    2.267
peak=   -3.560 closest distance to " O   SER A 135 " =    1.582
peak=   -3.554 closest distance to " CG1 VAL A 112 " =    3.013
peak=   -3.550 closest distance to " O   HOH Z 126 " =    1.819
peak=   -3.541 closest distance to " NE2 GLN A  55 " =    1.325
peak=   -3.538 closest distance to " CG2 VAL A 202 " =    2.720
peak=   -3.534 closest distance to " NH2BARG A 102 " =    0.892
peak=   -3.521 closest distance to " CD  PRO A 243 " =    1.757
peak=   -3.519 closest distance to " O   HOH Z 429 " =    1.633
peak=   -3.513 closest distance to " OE1 GLN A  88 " =    0.967
peak=   -3.508 closest distance to " CB  VAL A 230 " =    1.021
peak=   -3.506 closest distance to " N   PHE A  59 " =    2.052
peak=   -3.501 closest distance to " CE1 TYR A 247 " =    2.568
peak=   -3.498 closest distance to " CD2 HIS A 207 " =    2.100
peak=   -3.496 closest distance to " O   HOH Z 236 " =    1.424
peak=   -3.495 closest distance to " CA  GLN A  58 " =    1.260
peak=   -3.492 closest distance to " CB  ALA A 161 " =    2.368
peak=   -3.489 closest distance to " O   HOH Z 388 " =    2.284
peak=   -3.487 closest distance to " O   HOH Z 231 " =    2.014
peak=   -3.483 closest distance to " O   HOH Z 166 " =    1.901
peak=   -3.479 closest distance to " O   HOH Z 281 " =    3.064
peak=   -3.477 closest distance to " O   HOH Z  68 " =    1.420
peak=   -3.476 closest distance to " OH  TYR A 172 " =    1.828
peak=   -3.471 closest distance to " NE2 GLN A  11 " =    1.730
peak=   -3.470 closest distance to " OE1 GLN A 183 " =    1.664
peak=   -3.463 closest distance to " CE2 TYR A  30 " =    2.785
peak=   -3.460 closest distance to " CG  ASP A 231 " =    0.795
peak=   -3.448 closest distance to " CZ  TYR A 169 " =    1.851
peak=   -3.447 closest distance to " O   HOH Z 211 " =    1.346
peak=   -3.447 closest distance to " CG  LEU A   5 " =    0.877
peak=   -3.444 closest distance to " OG  SER A  87 " =    1.528
peak=   -3.444 closest distance to " CA  GLY A 241 " =    2.443
peak=   -3.444 closest distance to " O   HOH Z 215 " =    1.662
peak=   -3.435 closest distance to " O   HOH Z 423 " =    2.512
peak=   -3.434 closest distance to " ND2 ASN A 249 " =    2.320
peak=   -3.433 closest distance to " CB  ALA A 248 " =    2.142
peak=   -3.425 closest distance to " CG  GLN A 103 " =    2.339
peak=   -3.422 closest distance to " CG2 VAL A 189 " =    1.944
peak=   -3.421 closest distance to " O   HOH Z 398 " =    1.120
peak=   -3.420 closest distance to " O   HOH Z 113 " =    1.462
peak=   -3.418 closest distance to " CB  SER A 210 " =    1.119
peak=   -3.400 closest distance to " O   HOH Z 351 " =    1.553
peak=   -3.387 closest distance to " O   HOH Z  73 " =    0.848
peak=   -3.379 closest distance to " O   HOH Z 162 " =    2.951
peak=   -3.378 closest distance to " CD1 ILE A 199 " =    2.305
peak=   -3.374 closest distance to " NZ  LYS A 166 " =    1.521
peak=   -3.373 closest distance to " C   MET A 188 " =    1.396
peak=   -3.371 closest distance to " CZ  ARG A 259 " =    0.959
peak=   -3.362 closest distance to " CA  ASP A 298 " =    1.046
peak=   -3.359 closest distance to " O   ASN A 187 " =    1.628
peak=   -3.355 closest distance to " CG2 ILE A 151 " =    2.505
peak=   -3.345 closest distance to " O   HOH Z  60 " =    1.753
peak=   -3.341 closest distance to " O   HOH Z 147 " =    2.119
peak=   -3.333 closest distance to " O   HOH Z 405 " =    1.839
peak=   -3.333 closest distance to " O   HOH Z 377 " =    1.907
peak=   -3.327 closest distance to " O   HOH Z 111 " =    1.526
peak=   -3.319 closest distance to " CB  ALA A 248 " =    2.395
peak=   -3.317 closest distance to " O   HOH Z 140 " =    1.905
peak=   -3.314 closest distance to " O   HOH Z  35 " =    2.478
peak=   -3.311 closest distance to " O   SER A 276 " =    1.647
peak=   -3.307 closest distance to " OG  SER A 271 " =    1.236
peak=   -3.306 closest distance to " O   HOH Z 377 " =    0.958
peak=   -3.301 closest distance to " O   HOH Z  64 " =    1.271
peak=   -3.296 closest distance to " CE1 PHE A 218 " =    1.671
peak=   -3.293 closest distance to " O   HOH Z 106 " =    1.835
peak=   -3.290 closest distance to " CE  MET A 105 " =    2.435
peak=   -3.289 closest distance to " O   HOH Z  26 " =    1.019
peak=   -3.286 closest distance to " O   HOH Z 421 " =    2.983
peak=   -3.283 closest distance to " O   HOH Z 208 " =    2.146
peak=   -3.282 closest distance to " CG2 VAL A 296 " =    2.087
peak=   -3.277 closest distance to " CD  GLN A  88 " =    2.096
peak=   -3.275 closest distance to " O   HOH Z 149 " =    1.731
peak=   -3.273 closest distance to " CB  ALA A 129 " =    2.522
peak=   -3.273 closest distance to " CB  ALA A 114 " =    2.537
peak=   -3.269 closest distance to " O   VAL A 189 " =    2.578
peak=   -3.269 closest distance to " CD2 LEU A   5 " =    1.010
peak=   -3.268 closest distance to " O   HOH Z  40 " =    1.611
peak=   -3.261 closest distance to " N   ALA A 244 " =    1.353
peak=   -3.260 closest distance to " OG  SER A  63 " =    1.082
peak=   -3.256 closest distance to " CG2 THR A 178 " =    2.440
peak=   -3.256 closest distance to " O   HOH Z 177 " =    0.909
peak=   -3.254 closest distance to " N   THR A  52 " =    1.747
peak=   -3.249 closest distance to " CE1 TYR A 186 " =    2.320
peak=   -3.248 closest distance to " O   HOH Z  28 " =    2.367
peak=   -3.243 closest distance to " CD2 LEU A 237 " =    2.147
peak=   -3.243 closest distance to " O   HOH Z  11 " =    1.608
peak=   -3.237 closest distance to " O   HOH Z 235 " =    1.363
peak=   -3.236 closest distance to " O   HOH Z  39 " =    1.328
peak=   -3.235 closest distance to " ND2 ASN A 187 " =    1.522
peak=   -3.234 closest distance to " C   ASP A 124 " =    1.911
peak=   -3.229 closest distance to " O   HOH Z 214 " =    2.676
peak=   -3.221 closest distance to " OG  SER A  87 " =    1.337
peak=   -3.218 closest distance to " O   HOH Z  71 " =    1.078
peak=   -3.215 closest distance to " O   HOH Z 435 " =    3.070
peak=   -3.213 closest distance to " O   HOH Z 384 " =    1.310
peak=   -3.211 closest distance to " O   HOH Z 275 " =    1.675
peak=   -3.207 closest distance to " CB  PRO A 163 " =    2.460
peak=   -3.207 closest distance to " O   HOH Z 183 " =    1.609
peak=   -3.207 closest distance to " O   HOH Z 290 " =    1.133
peak=   -3.205 closest distance to " CA  ASP A  27 " =    2.395
peak=   -3.200 closest distance to " NE2 GLN A  88 " =    1.208
peak=   -3.194 closest distance to " O   HOH Z 427 " =    1.798
peak=   -3.194 closest distance to " O   HOH Z 147 " =    1.252
peak=   -3.193 closest distance to " CG  ARG A 219 " =    2.657
peak=   -3.193 closest distance to " O   HOH Z 117 " =    1.820
peak=   -3.193 closest distance to " O   HOH Z 109 " =    0.869
peak=   -3.191 closest distance to " CB  ALA A  10 " =    2.339
peak=   -3.186 closest distance to " CG  LEU A 281 " =    2.125
peak=   -3.180 closest distance to " ND2 ASN A 209 " =    1.887
peak=   -3.180 closest distance to " NE2 GLN A 240 " =    1.830
peak=   -3.179 closest distance to " N   ASN A 215 " =    1.722
peak=   -3.177 closest distance to " CA  GLY A  57 " =    2.264
peak=   -3.175 closest distance to " O   HOH Z  70 " =    1.025
peak=   -3.173 closest distance to " CB  ALA A  51 " =    1.789
peak=   -3.173 closest distance to " O   LYS A  76 " =    1.796
peak=   -3.169 closest distance to " O   HOH Z 107 " =    0.865
peak=   -3.166 closest distance to " O   HOH Z 293 " =    1.663
peak=   -3.160 closest distance to " O   HOH Z 331 " =    1.118
peak=   -3.158 closest distance to " O   HOH Z 411 " =    1.179
peak=   -3.157 closest distance to " O   HOH Z  36 " =    1.996
peak=   -3.153 closest distance to " O   HOH Z 191 " =    5.695
peak=   -3.147 closest distance to " OD1 ASP A 200 " =    1.043
peak=   -3.146 closest distance to " CG2 THR A  18 " =    2.822
peak=   -3.143 closest distance to " O   GLN A 144 " =    1.326
peak=   -3.143 closest distance to " CG1BVAL A  72 " =    2.621
peak=   -3.141 closest distance to " OG1 THR A  52 " =    2.616
peak=   -3.140 closest distance to " CD2 PHE A 225 " =    1.026
peak=   -3.137 closest distance to " O   HOH Z  52 " =    1.712
peak=   -3.135 closest distance to " C   HIS A 207 " =    1.183
peak=   -3.130 closest distance to " CG  ARG A 269 " =    2.241
peak=   -3.129 closest distance to " O   HOH Z 390 " =    2.446
peak=   -3.127 closest distance to " O   HOH Z 252 " =    3.787
peak=   -3.127 closest distance to " OD2 ASP A 140 " =    0.802
peak=   -3.126 closest distance to " C   ARG A 269 " =    1.251
peak=   -3.122 closest distance to " O   HOH Z 246 " =    1.436
peak=   -3.120 closest distance to " CZ  PHE A  59 " =    1.934
peak=   -3.120 closest distance to " OE2 GLU A 152 " =    1.396
peak=   -3.120 closest distance to " OD2 ASP A 191 " =    1.276
peak=   -3.118 closest distance to " CD2 TYR A 247 " =    2.485
peak=   -3.118 closest distance to " CB  ALA A 161 " =    1.619
peak=   -3.116 closest distance to " O   HOH Z   9 " =    1.282
peak=   -3.114 closest distance to " O   HOH Z 260 " =    1.464
peak=   -3.112 closest distance to " O   HOH Z 185 " =    1.951
peak=   -3.110 closest distance to " O   HOH Z 198 " =    1.000
peak=   -3.101 closest distance to " NE2 GLN A 223 " =    1.818
peak=   -3.099 closest distance to " CD2 LEU A 237 " =    2.725
peak=   -3.099 closest distance to " O   HOH Z 119 " =    2.405
peak=   -3.096 closest distance to " O   PHE A 218 " =    1.544
peak=   -3.096 closest distance to " ND2 ASN A  45 " =    1.370
peak=   -3.089 closest distance to " CA  LEU A   5 " =    2.552
peak=   -3.083 closest distance to " OG BSER A 210 " =    1.700
peak=   -3.082 closest distance to " OE1 GLU A 277 " =    2.147
peak=   -3.070 closest distance to " O   HOH Z 105 " =    2.634
peak=   -3.053 closest distance to " CZ2 TRP A  70 " =    2.384
peak=   -3.027 closest distance to " CB  TRP A  85 " =    2.587
peak=   -3.016 closest distance to " O   HOH Z  88 " =    2.642

================= 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    :  0.5038 0.4960   6.299439e+00   6.292473e+00
   1_bss:  0.4945 0.4853   6.292902e+00   6.284997e+00
   1_xyz:  0.4318 0.4484   6.222554e+00   6.245157e+00
   1_adp:  0.3884 0.4458   6.165858e+00   6.233539e+00
   1_occ:  0.3886 0.4470   6.164920e+00   6.234454e+00
   2_bss:  0.3866 0.4459   6.166529e+00   6.236105e+00
   2_xyz:  0.3200 0.3831   6.020067e+00   6.148160e+00
   2_adp:  0.3012 0.3680   5.979228e+00   6.113003e+00
   2_occ:  0.3008 0.3678   5.979275e+00   6.112941e+00
   3_bss:  0.2993 0.3662   5.979741e+00   6.112822e+00
   3_xyz:  0.2260 0.2843   5.744810e+00   5.925811e+00
   3_adp:  0.2045 0.2645   5.665785e+00   5.858480e+00
   3_occ:  0.2041 0.2639   5.664033e+00   5.856939e+00
   4_bss:  0.2029 0.2632   5.663968e+00   5.856607e+00
   4_xyz:  0.1556 0.2114   5.433287e+00   5.656186e+00
   4_adp:  0.1412 0.1989   5.354221e+00   5.590953e+00
   4_occ:  0.1411 0.1988   5.353580e+00   5.590236e+00
   5_bss:  0.1412 0.1992   5.353885e+00   5.591133e+00
   5_xyz:  0.1275 0.1817   5.273227e+00   5.518323e+00
   5_adp:  0.1255 0.1750   5.248636e+00   5.480888e+00
   5_occ:  0.1253 0.1747   5.248076e+00   5.480754e+00
   5_bss:  0.1253 0.1746   5.247911e+00   5.480534e+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:  0.370  20.000   6.450   7.229  10.647   0.000   0.000   0.000
   1_xyz:  0.370  20.000   6.450   7.229  10.647   0.000   0.000   0.000
   1_adp:  0.370  20.000   6.450   7.229  10.647   0.000   0.000   0.000
   1_occ:  0.370  20.000   6.450   7.229  10.647   0.000   0.000   0.000
   2_bss:  0.346  42.890   3.634   4.013   7.531   0.000   0.000   0.000
   2_xyz:  0.346  42.890   3.634   4.013   7.531   0.000   0.000   0.000
   2_adp:  0.346  42.890   3.634   4.013   7.531   0.000   0.000   0.000
   2_occ:  0.346  42.890   3.634   4.013   7.531   0.000   0.000   0.000
   3_bss:  0.331  42.890   1.390   1.905   4.937   0.000   0.000   0.000
   3_xyz:  0.331  42.890   1.390   1.905   4.937   0.000   0.000   0.000
   3_adp:  0.331  42.890   1.390   1.905   4.937   0.000   0.000   0.000
   3_occ:  0.331  42.890   1.390   1.905   4.937   0.000   0.000   0.000
   4_bss:  0.314  46.534  -0.084   0.699   3.038   0.000   0.000   0.000
   4_xyz:  0.314  46.534  -0.084   0.699   3.038   0.000   0.000   0.000
   4_adp:  0.314  46.534  -0.084   0.699   3.038   0.000   0.000   0.000
   4_occ:  0.314  46.534  -0.084   0.699   3.038   0.000   0.000   0.000
   5_bss:  0.323  58.098  -0.469   0.273   2.396   0.000   0.000   0.000
   5_xyz:  0.323  58.098  -0.469   0.273   2.396   0.000   0.000   0.000
   5_adp:  0.323  58.098  -0.469   0.273   2.396   0.000   0.000   0.000
   5_occ:  0.323  58.098  -0.469   0.273   2.396   0.000   0.000   0.000
   5_bss:  0.321  53.861  -1.156  -0.456   1.612   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  63.201 0.3520  0.4226    80593.288
   1_bss:  63.503 0.3470  0.5240    79090.934
   1_xyz:  53.297 0.4784  0.7100    62060.124
   1_adp:  51.209 0.5050  0.8303    59724.279
   1_occ:  51.270 0.5041  0.8261    59762.277
   2_bss:  51.227 0.5046  0.7454    59915.698
   2_xyz:  41.739 0.6210  0.9004    41417.596
   2_adp:  39.229 0.6513  0.9385    37206.519
   2_occ:  39.284 0.6506  0.9372    37272.973
   3_bss:  39.136 0.6523  0.8649    37091.488
   3_xyz:  29.306 0.7646  0.9827    21628.620
   3_adp:  26.349 0.7975  1.0046    18517.434
   3_occ:  26.310 0.7979  1.0045    18434.295
   4_bss:  26.218 0.7988  0.9511    18366.576
   4_xyz:  20.341 0.8582  0.9885    11483.777
   4_adp:  18.758 0.8733  0.9877    10041.753
   4_occ:  18.740 0.8734  0.9878    10022.052
   5_bss:  18.709 0.8738  0.9714    10043.551
   5_xyz:  16.959 0.8899  0.9798     8580.010
   5_adp:  16.125 0.8974  0.9791     8025.736
   5_occ:  16.128 0.8973  0.9791     8017.333
   5_bss:  16.123 0.8974  0.9748     8009.399
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.3460e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.3460e+01
   1_xyz:   1.715  0.013  0.105 18.353  0.006  4.106   1.4450e-01
   1_adp:   1.715  0.013  0.105 18.353  0.006  4.106   1.4450e-01
   1_occ:   1.715  0.013  0.105 18.353  0.006  4.106   1.4450e-01
   2_bss:   1.715  0.013  0.105 18.353  0.006  4.106   1.4450e-01
   2_xyz:   1.182  0.008  0.079 16.282  0.005  4.107   8.6141e-02
   2_adp:   1.182  0.008  0.079 16.282  0.005  4.107   8.6141e-02
   2_occ:   1.182  0.008  0.079 16.282  0.005  4.107   8.6141e-02
   3_bss:   1.182  0.008  0.079 16.282  0.005  4.107   8.6141e-02
   3_xyz:   1.156  0.009  0.082 15.941  0.004  4.125   7.9070e-02
   3_adp:   1.156  0.009  0.082 15.941  0.004  4.125   7.9070e-02
   3_occ:   1.156  0.009  0.082 15.941  0.004  4.125   7.9070e-02
   4_bss:   1.156  0.009  0.082 15.941  0.004  4.125   7.9070e-02
   4_xyz:   1.146  0.009  0.082 15.826  0.005  4.127   8.1309e-02
   4_adp:   1.146  0.009  0.082 15.826  0.005  4.127   8.1309e-02
   4_occ:   1.146  0.009  0.082 15.826  0.005  4.127   8.1309e-02
   5_bss:   1.146  0.009  0.082 15.826  0.005  4.127   8.1309e-02
   5_xyz:   1.038  0.007  0.075 15.723  0.004  4.118   6.6021e-02
   5_adp:   1.038  0.007  0.075 15.723  0.004  4.118   6.6021e-02
   5_occ:   1.038  0.007  0.075 15.723  0.004  4.118   6.6021e-02
   5_bss:   1.038  0.007  0.075 15.723  0.004  4.118   6.6021e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.159   6.9243e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.159   6.9243e+00
   1_xyz:  13.670  0.172  0.410 84.733  0.049  2.106   9.8093e-02
   1_adp:  13.670  0.172  0.410 84.733  0.049  2.106   9.8093e-02
   1_occ:  13.670  0.172  0.410 84.733  0.049  2.106   9.8093e-02
   2_bss:  13.670  0.172  0.410 84.733  0.049  2.106   9.8093e-02
   2_xyz:   7.247  0.064  0.287 86.915  0.037  2.002   9.7994e-02
   2_adp:   7.247  0.064  0.287 86.915  0.037  2.002   9.7994e-02
   2_occ:   7.247  0.064  0.287 86.915  0.037  2.002   9.7994e-02
   3_bss:   7.247  0.064  0.287 86.915  0.037  2.002   9.7994e-02
   3_xyz:   7.365  0.069  0.309 83.137  0.030  2.262   6.8398e-02
   3_adp:   7.365  0.069  0.309 83.137  0.030  2.262   6.8398e-02
   3_occ:   7.365  0.069  0.309 83.137  0.030  2.262   6.8398e-02
   4_bss:   7.365  0.069  0.309 83.137  0.030  2.262   6.8398e-02
   4_xyz:   8.564  0.078  0.285 84.799  0.040  2.103   1.2601e-01
   4_adp:   8.564  0.078  0.285 84.799  0.040  2.103   1.2601e-01
   4_occ:   8.564  0.078  0.285 84.799  0.040  2.103   1.2601e-01
   5_bss:   8.564  0.078  0.285 84.799  0.040  2.103   1.2601e-01
   5_xyz:   6.506  0.044  0.236 83.702  0.044  2.348   5.0749e-02
   5_adp:   6.506  0.044  0.236 83.702  0.044  2.348   5.0749e-02
   5_occ:   6.506  0.044  0.236 83.702  0.044  2.348   5.0749e-02
   5_bss:   6.506  0.044  0.236 83.702  0.044  2.348   5.0749e-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:  84.77   0.00  16.32  74.38   0.00  14.44  84.77   0.00  26.57
   1_occ:  84.77   0.00  16.32  74.38   0.00  14.44  84.77   0.00  26.57
   2_bss:  84.77   0.00  16.32  74.38   0.00  14.44  84.77   0.00  26.57
   2_xyz:  84.77   0.00  16.32  74.38   0.00  14.44  84.77   0.00  26.57
   2_adp:  87.47   0.00  15.69  65.87   0.00  12.88  87.47   0.00  30.98
   2_occ:  87.47   0.00  15.69  65.87   0.00  12.88  87.47   0.00  30.98
   3_bss:  87.47   0.00  15.69  65.87   0.00  12.88  87.47   0.00  30.98
   3_xyz:  87.47   0.00  15.69  65.87   0.00  12.88  87.47   0.00  30.98
   3_adp: 105.28   0.00  15.15 105.28   0.00  11.44  83.89   1.44  35.39
   3_occ: 105.28   0.00  15.15 105.28   0.00  11.44  83.89   1.44  35.39
   4_bss: 105.28   0.00  15.15 105.28   0.00  11.44  83.89   1.44  35.39
   4_xyz: 105.28   0.00  15.15 105.28   0.00  11.44  83.89   1.44  35.39
   4_adp: 106.76   0.00  16.07  96.86   0.00  11.00 106.76   2.88  43.67
   4_occ: 106.76   0.00  16.07  96.86   0.00  11.00 106.76   2.88  43.67
   5_bss: 106.76   0.00  16.07  96.86   0.00  11.00 106.76   2.88  43.67
   5_xyz: 106.76   0.00  16.07  96.86   0.00  11.00 106.76   2.88  43.67
   5_adp: 103.76   0.41  15.37  96.80   0.41  10.60 103.76   3.49  41.35
   5_occ: 103.76   0.41  15.37  96.80   0.41  10.60 103.76   3.49  41.35
   5_bss: 104.37   1.02  15.98  97.41   1.02  11.21 104.37   4.10  41.96
------------------------------------------------------------------------
 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:    1.277    0.022    0.408
   1_adp:    1.277    0.022    0.408
   1_occ:    1.277    0.022    0.408
   2_bss:    1.277    0.022    0.408
   2_xyz:    1.843    0.033    0.551
   2_adp:    1.843    0.033    0.551
   2_occ:    1.843    0.033    0.551
   3_bss:    1.843    0.033    0.551
   3_xyz:    1.662    0.050    0.694
   3_adp:    1.662    0.050    0.694
   3_occ:    1.662    0.050    0.694
   4_bss:    1.662    0.050    0.694
   4_xyz:    1.702    0.044    0.772
   4_adp:    1.702    0.044    0.772
   4_occ:    1.702    0.044    0.772
   5_bss:    1.702    0.044    0.772
   5_xyz:    1.958    0.010    0.801
   5_adp:    1.958    0.010    0.801
   5_occ:    1.958    0.010    0.801
   5_bss:    1.958    0.010    0.801
------------------------------------------------------------------------

CPU time actual refinement: 286.03


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_164/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_164/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_164/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_164/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_164/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 285.91 
  Macro-tasks:
    bulk solvent and scale       = 34.04  
    individual site refinement   = 116.95 
    weights calculation          = 27.35  
    collect and process          = 5.33   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 183.78 
  Micro-tasks:
    mask                            = 1.99   
    f_calc                          = 89.19  
    alpha_beta                      = 6.98   
    target                          = 0.98   
    gradients_wrt_atomic_parameters = 97.81  
    fmodel                         = 6.06   
    r_factors                      = 0.17   
    phase_errors                   = 8.44   
    foms                           = 0.24   
    TOTAL for micro-tasks          = 211.86 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.025 micro seconds
Total CPU time: 4.96 minutes
from_scatterers_fft:    660 calls, 88.89 s
gradients_fft:          605 calls, 86.30 s

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

# Date 2008-01-16 Time 00:52:35 PST -0800 (1200473555.79 s)
Start R-work = 0.5038, R-free = 0.4960 (no bulk solvent and anisotropic scale)
Final R-work = 0.1428, R-free = 0.1894 (no bulk solvent and anisotropic scale)

Start R-work = 0.4945, R-free = 0.4853
Final R-work = 0.1253, R-free = 0.1746