# Date 2008-01-16 Time 01:22:03 PST -0800 (1200475323.35 s)
#phil __OFF__

Command line arguments: "../391.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 28475
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 391

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.5475, 46.2261, 86.822, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.30, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 46.2261, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.904 1.97209
Completeness in resolution range: 0.964263
Completeness with d_max=infinity: 0.961282

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9040
                             d_min =   1.9721

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 46.2261, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.904 1.97209
Completeness in resolution range: 0.964263
Completeness with d_max=infinity: 0.961282

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9044 -  4.2196 [2142/2166]  1924   218  10.2%
  bin  2:  4.2196 -  3.3619 [2042/2062]  1841   201   9.8%
  bin  3:  3.3619 -  2.9406 [2021/2040]  1819   202  10.0%
  bin  4:  2.9406 -  2.6734 [1995/2025]  1793   202  10.1%
  bin  5:  2.6734 -  2.4828 [2006/2025]  1808   198   9.9%
  bin  6:  2.4828 -  2.3370 [1983/2008]  1781   202  10.2%
  bin  7:  2.3370 -  2.2203 [1962/1990]  1768   194   9.9%
  bin  8:  2.2203 -  2.1240 [1965/2001]  1769   196  10.0%
  bin  9:  2.1240 -  2.0424 [1946/1988]  1755   191   9.8%
  bin 10:  2.0424 -  1.9721 [1527/2010]  1372   155  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_391/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 38
        2.42 -     3.04: 2215
        3.04 -     3.66: 4758
        3.66 -     4.28: 9149
        4.28 -     4.90: 12440
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.847 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.890 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.091 3.040 x,y+1,z
  " O   HOH Z  52 " - " O   HOH Z 183 "  2.115 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28595 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_391/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_391/model_refine_001.geo

CPU time processing inputs: 9.23


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.5475 46.22605 86.82195 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4630   r_free= 0.4575   ksol= 0.00   Bsol= 0.00   scale= 0.810    |
|                                                                             |
| 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:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.264679                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9044 -  4.7062 0.99   1390  152 0.3857 0.3761      6.5651      6.5501|
|  2:  4.7062 -  3.7552 0.99   1330  152 0.3689 0.3513      6.7288      6.7121|
|  3:  3.7552 -  3.2863 0.99   1299  143 0.4053 0.3754       6.632      6.6178|
|  4:  3.2863 -  2.9885 0.99   1307  145 0.4473 0.4331      6.5125      6.4765|
|  5:  2.9885 -  2.7757 0.99   1283  145 0.4900 0.4648      6.3586      6.3739|
|  6:  2.7757 -  2.6130 0.99   1292  141 0.4878 0.5536       6.275      6.2039|
|  7:  2.6130 -  2.4828 0.99   1284  143 0.4984 0.4860      6.2321      6.1842|
|  8:  2.4828 -  2.3751 0.98   1270  137 0.5133 0.4741      6.1878      6.2124|
|  9:  2.3751 -  2.2840 0.98   1262  144 0.5026 0.5491      6.1033      6.1707|
| 10:  2.2840 -  2.2055 1.00   1285  143 0.5281 0.5071      6.1257      6.0507|
| 11:  2.2055 -  2.1367 0.97   1252  137 0.5213 0.4793      6.0327      6.0561|
| 12:  2.1367 -  2.0758 0.98   1249  144 0.5229 0.5142      5.9906      6.0236|
| 13:  2.0758 -  2.0213 0.99   1277  133 0.5151 0.5036      5.8798      5.8321|
| 14:  2.0213 -  1.9721 0.66    850  100 0.5399 0.5572      5.8839      5.7824|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9044 -  4.7062  1390   152  0.70  34.44   0.80     0.74      71524.21|
|  2:  4.7062 -  3.7552  1330   152  0.74  31.95   0.89     0.81      91407.15|
|  3:  3.7552 -  3.2863  1299   143  0.65  39.45   0.88     0.76      96301.41|
|  4:  3.2863 -  2.9885  1307   145  0.56  46.69   0.81     0.65      88535.17|
|  5:  2.9885 -  2.7757  1283   145  0.45  55.50   0.77     0.54      76703.67|
|  6:  2.7757 -  2.6130  1292   141  0.41  58.72   0.73     0.47      70351.14|
|  7:  2.6130 -  2.4828  1284   143  0.36  63.24   0.76     0.42      67208.81|
|  8:  2.4828 -  2.3751  1270   137  0.34  64.54   0.73     0.40      61434.06|
|  9:  2.3751 -  2.2840  1262   144  0.37  62.27   0.75     0.44      54096.92|
| 10:  2.2840 -  2.2055  1285   143  0.41  59.54   0.76     0.47      45415.93|
| 11:  2.2055 -  2.1367  1252   137  0.41  59.55   0.76     0.50      42814.03|
| 12:  2.1367 -  2.0758  1249   144  0.37  62.13   0.78     0.46      40151.82|
| 13:  2.0758 -  2.0213  1277   133  0.34  64.52   0.73     0.42      36092.04|
| 14:  2.0213 -  1.9721   850   100  0.36  63.26   0.74     0.40      29785.03|
|alpha:            min =        0.40 max =            0.81 mean =         0.54|
|beta:             min =    29785.03 max =        96301.41 mean =     63369.96|
|figures of merit: min =        0.00 max =            1.00 mean =         0.47|
|phase err.(work): min =        0.00 max =           90.00 mean =        54.24|
|phase err.(test): min =        0.00 max =           90.00 mean =        54.41|
|-----------------------------------------------------------------------------|

============================== 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 = 11.487812             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.240   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.105862              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.373   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       32 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      174 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      701 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1526 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2653 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     4006 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5103 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6650 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7768 |
|-----------------------------------------------------------------------------|
|-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 |       53.300 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.196 |       1.996 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.632)------------------------------------------|
|    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 = 11.632)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4709   r_free= 0.4584   ksol= 0.00   Bsol= 0.00   scale= 0.778    |
|                                                                             |
| 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:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.267950                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4546   r_free= 0.4418   ksol= 0.36   Bsol= 6.37   scale= 1.020    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.39,10.14,8.58,0.00,0.00,0.00); trace/3= 8.70                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.257907                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.475877              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.844   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.971116              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.546   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4546      final r-factor (work) = 0.3660          |
| start r-factor (free) = 0.4418      final r-factor (free) = 0.3837          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 82.9911 = 9.48 * 0.50 * 6.2666 + 1.00 * 53.3001                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.2977 = 9.48 * 0.50 * 6.1563 + 1.00 * 0.1297                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3660      final r-factor (work) = 0.3159          |
| start r-factor (free) = 0.3837      final r-factor (free) = 0.3641          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.9928 = 0.97 * 1.00 * 6.1563 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8841 = 0.97 * 1.00 * 6.0436 + 1.00 * 0.0150                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.632)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    73.33   12.51    None  None   None       |
|    all(noH): 2823   0      0.00    73.33   12.51    None  None   None       |
|    Sol.    : 438    0      0.00    73.33   25.73    None  None   None       |
|    Mac.    : 2385   0      0.00    67.65   10.09    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.334: 1137   |   5:    36.667 -  44.001:   71        |
|      1:     7.334 -  14.667:  781   |   6:    44.001 -  51.334:   37        |
|      2:    14.667 -  22.000:  436   |   7:    51.334 -  58.668:   13        |
|      3:    22.000 -  29.334:  206   |   8:    58.668 -  66.001:    4        |
|      4:    29.334 -  36.667:  134   |   9:    66.001 -  73.335:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3159 r_free = 0.3641             target_work(ml) = 6.019         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3154 r_free = 0.3640             target_work(ml) = 6.018         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3154   r_free= 0.3640   ksol= 0.36   Bsol= 6.37   scale= 1.120    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.39,10.14,8.58,0.00,0.00,0.00); trace/3= 8.70                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 6.018275                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3104   r_free= 0.3564   ksol= 0.34   Bsol= 31.06   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.63,5.44,4.81,0.00,0.00,0.00); trace/3= 4.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 6.016740                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.315492              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.009   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.459319              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.520  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3104      final r-factor (work) = 0.2333          |
| start r-factor (free) = 0.3564      final r-factor (free) = 0.2853          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.1683 = 4.32 * 0.50 * 6.0427 + 1.00 * 0.1297                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.7745 = 4.32 * 0.50 * 5.8872 + 1.00 * 0.0713                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2333      final r-factor (work) = 0.2139          |
| start r-factor (free) = 0.2853      final r-factor (free) = 0.2682          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7196 = 0.46 * 1.00 * 5.8872 + 1.00 * 0.0155                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6613 = 0.46 * 1.00 * 5.7323 + 1.00 * 0.0283                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.632)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    202.55  12.48    None  None   None       |
|    all(noH): 2823   0      0.00    202.55  12.48    None  None   None       |
|    Sol.    : 438    0      1.59    77.18   29.99    None  None   None       |
|    Mac.    : 2385   0      0.00    202.55  9.27     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  20.255: 2263   |   5:   101.276 - 121.531:    0        |
|      1:    20.255 -  40.510:  459   |   6:   121.531 - 141.786:    0        |
|      2:    40.510 -  60.765:   95   |   7:   141.786 - 162.041:    0        |
|      3:    60.765 -  81.021:    5   |   8:   162.041 - 182.296:    0        |
|      4:    81.021 - 101.276:    0   |   9:   182.296 - 202.551:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2139 r_free = 0.2682             target_work(ml) = 5.704         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2136 r_free = 0.2680             target_work(ml) = 5.704         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2136   r_free= 0.2680   ksol= 0.34   Bsol= 31.06   scale= 1.052   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.63,5.44,4.81,0.00,0.00,0.00); trace/3= 4.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.703547                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2129   r_free= 0.2664   ksol= 0.32   Bsol= 34.99   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.30,3.32,3.83,0.00,0.00,0.00); trace/3= 3.15                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.703472                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.210696              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.087  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.100370              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 105.448  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2129      final r-factor (work) = 0.1549          |
| start r-factor (free) = 0.2664      final r-factor (free) = 0.2040          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.1450 = 4.21 * 0.50 * 5.7349 + 1.00 * 0.0710                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.7848 = 4.21 * 0.50 * 5.5647 + 1.00 * 0.0691                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1549      final r-factor (work) = 0.1372          |
| start r-factor (free) = 0.2040      final r-factor (free) = 0.1897          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 17.2685 = 3.10 * 1.00 * 5.5647 + 1.00 * 0.0158                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 16.6290 = 3.10 * 1.00 * 5.3578 + 1.00 * 0.0179                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.632)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    151.35  13.48    None  None   None       |
|    all(noH): 2823   0      0.00    151.35  13.48    None  None   None       |
|    Sol.    : 438    0      1.71    89.04   38.53    None  None   None       |
|    Mac.    : 2385   0      0.00    151.35  8.88     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 -  15.135: 2113   |   5:    75.675 -  90.810:    6        |
|      1:    15.135 -  30.270:  332   |   6:    90.810 - 105.945:    0        |
|      2:    30.270 -  45.405:  173   |   7:   105.945 - 121.080:    0        |
|      3:    45.405 -  60.540:  144   |   8:   121.080 - 136.216:    0        |
|      4:    60.540 -  75.675:   54   |   9:   136.216 - 151.351:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1372 r_free = 0.1897             target_work(ml) = 5.321         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1372 r_free = 0.1895             target_work(ml) = 5.320         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1372   r_free= 0.1895   ksol= 0.32   Bsol= 34.99   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.30,3.32,3.83,0.00,0.00,0.00); trace/3= 3.15                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.320098                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1370   r_free= 0.1890   ksol= 0.32   Bsol= 45.70   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.98,2.45,3.68,0.00,0.00,0.00); trace/3= 2.70                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.317941                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.684673              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.665  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.766201              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.386  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1370      final r-factor (work) = 0.1257          |
| start r-factor (free) = 0.1890      final r-factor (free) = 0.1758          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5831 = 1.68 * 0.50 * 5.3588 + 1.00 * 0.0691                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5040 = 1.68 * 0.50 * 5.2856 + 1.00 * 0.0518                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1257      final r-factor (work) = 0.1236          |
| start r-factor (free) = 0.1758      final r-factor (free) = 0.1708          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1206 = 0.77 * 1.00 * 5.2856 + 1.00 * 0.0708                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0287 = 0.77 * 1.00 * 5.2401 + 1.00 * 0.0138                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.632)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.37   13.12    None  None   None       |
|    all(noH): 2823   0      0.00    94.37   13.12    None  None   None       |
|    Sol.    : 438    0      1.69    89.86   38.00    None  None   None       |
|    Mac.    : 2385   0      0.00    94.37   8.55     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.438: 1737   |   5:    47.188 -  56.625:   80        |
|      1:     9.438 -  18.875:  536   |   6:    56.625 -  66.062:   51        |
|      2:    18.875 -  28.313:  155   |   7:    66.062 -  75.500:   27        |
|      3:    28.313 -  37.750:  120   |   8:    75.500 -  84.937:    9        |
|      4:    37.750 -  47.188:  105   |   9:    84.937 -  94.375:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1236 r_free = 0.1708             target_work(ml) = 5.224         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1235 r_free = 0.1708             target_work(ml) = 5.223         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1235   r_free= 0.1708   ksol= 0.32   Bsol= 45.70   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.98,2.45,3.68,0.00,0.00,0.00); trace/3= 2.70                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.223145                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1235   r_free= 0.1708   ksol= 0.32   Bsol= 45.70   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.02,2.33,3.78,0.00,0.00,0.00); trace/3= 2.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.222915                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.023380              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 130.183  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.608863              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.287  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1235      final r-factor (work) = 0.1132          |
| start r-factor (free) = 0.1708      final r-factor (free) = 0.1614          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9728 = 3.02 * 0.50 * 5.2398 + 1.00 * 0.0518                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9057 = 3.02 * 0.50 * 5.1859 + 1.00 * 0.0662                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1132      final r-factor (work) = 0.1117          |
| start r-factor (free) = 0.1614      final r-factor (free) = 0.1588          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1712 = 0.61 * 1.00 * 5.1859 + 1.00 * 0.0137                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1498 = 0.61 * 1.00 * 5.1529 + 1.00 * 0.0124                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.632)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.99   12.69    None  None   None       |
|    all(noH): 2823   0      0.00    96.99   12.69    None  None   None       |
|    Sol.    : 438    0      1.37    87.28   36.69    None  None   None       |
|    Mac.    : 2385   0      0.00    96.99   8.29     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.699: 1820   |   5:    48.494 -  58.193:   63        |
|      1:     9.699 -  19.398:  484   |   6:    58.193 -  67.892:   41        |
|      2:    19.398 -  29.097:  150   |   7:    67.892 -  77.591:   17        |
|      3:    29.097 -  38.796:  124   |   8:    77.591 -  87.290:    6        |
|      4:    38.796 -  48.494:  116   |   9:    87.290 -  96.989:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1117 r_free = 0.1588             target_work(ml) = 5.146         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1116 r_free = 0.1588             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1116   r_free= 0.1588   ksol= 0.32   Bsol= 45.70   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.02,2.33,3.78,0.00,0.00,0.00); trace/3= 2.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.145417                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9044 -  4.7062 0.99   1390  152 0.0989 0.1246      5.3749      5.5157|
|  2:  4.7062 -  3.7552 0.99   1330  152 0.0846 0.1126      5.4295      5.6278|
|  3:  3.7552 -  3.2863 0.99   1299  143 0.1059 0.1471      5.4795      5.8483|
|  4:  3.2863 -  2.9885 0.99   1307  145 0.1222 0.1755       5.454      5.6218|
|  5:  2.9885 -  2.7757 0.99   1283  145 0.1293 0.1613      5.3218      5.5284|
|  6:  2.7757 -  2.6130 0.99   1292  141 0.1179 0.2077      5.1937      5.5169|
|  7:  2.6130 -  2.4828 0.99   1284  143 0.1270 0.1590      5.1703      5.3204|
|  8:  2.4828 -  2.3751 0.98   1270  137 0.1184 0.1631      5.0833      5.3463|
|  9:  2.3751 -  2.2840 0.98   1262  144 0.1199 0.1808      5.0519      5.3116|
| 10:  2.2840 -  2.2055 1.00   1285  143 0.1121 0.1723      4.9685      5.2059|
| 11:  2.2055 -  2.1367 0.97   1252  137 0.1136 0.1769      4.9576      5.2833|
| 12:  2.1367 -  2.0758 0.98   1249  144 0.1140 0.1760      4.8968      5.2409|
| 13:  2.0758 -  2.0213 0.99   1277  133 0.1117 0.1701      4.7896      5.0463|
| 14:  2.0213 -  1.9721 0.66    850  100 0.0974 0.1633      4.6391      4.8721|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9044 -  4.7062  1390   152  0.94   9.17   0.98     0.96       7123.79|
|  2:  4.7062 -  3.7552  1330   152  0.95   7.82   1.02     1.01       8984.73|
|  3:  3.7552 -  3.2863  1299   143  0.93  11.22   1.04     1.03      10331.75|
|  4:  3.2863 -  2.9885  1307   145  0.92  13.63   1.02     1.00      10336.99|
|  5:  2.9885 -  2.7757  1283   145  0.90  15.62   1.01     0.99       8305.73|
|  6:  2.7757 -  2.6130  1292   141  0.90  15.94   0.99     0.96       6901.72|
|  7:  2.6130 -  2.4828  1284   143  0.90  15.71   0.99     0.96       6095.02|
|  8:  2.4828 -  2.3751  1270   137  0.91  15.29   1.00     0.98       5356.68|
|  9:  2.3751 -  2.2840  1262   144  0.91  15.38   1.01     0.98       5207.91|
| 10:  2.2840 -  2.2055  1285   143  0.90  16.06   1.01     0.97       4528.05|
| 11:  2.2055 -  2.1367  1252   137  0.90  16.72   1.01     0.97       4685.96|
| 12:  2.1367 -  2.0758  1249   144  0.90  16.25   1.02     1.01       4163.26|
| 13:  2.0758 -  2.0213  1277   133  0.90  15.97   1.01     0.99       3361.74|
| 14:  2.0213 -  1.9721   850   100  0.92  13.48   1.00     0.97       2440.23|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     2440.23 max =        10336.99 mean =      6398.76|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.71 mean =        14.12|
|phase err.(test): min =        0.00 max =           87.84 mean =        13.56|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1116   r_free= 0.1590   ksol= 0.32   Bsol= 45.87   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.68,-0.44,1.12,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.145179                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1116   r_free= 0.1590   ksol= 0.32   Bsol= 45.87   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.68,-0.44,1.12,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.145179                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9044 -  4.7062 0.99   1390  152 0.0977 0.1248      5.3728      5.5117|
|  2:  4.7062 -  3.7552 0.99   1330  152 0.0853 0.1122      5.4311      5.6211|
|  3:  3.7552 -  3.2863 0.99   1299  143 0.1062 0.1465      5.4788      5.8426|
|  4:  3.2863 -  2.9885 0.99   1307  145 0.1220 0.1762      5.4545      5.6263|
|  5:  2.9885 -  2.7757 0.99   1283  145 0.1295 0.1608      5.3224      5.5238|
|  6:  2.7757 -  2.6130 0.99   1292  141 0.1180 0.2081      5.1933      5.5172|
|  7:  2.6130 -  2.4828 0.99   1284  143 0.1268 0.1593      5.1694      5.3205|
|  8:  2.4828 -  2.3751 0.98   1270  137 0.1182 0.1625      5.0816      5.3447|
|  9:  2.3751 -  2.2840 0.98   1262  144 0.1198 0.1803      5.0507        5.31|
| 10:  2.2840 -  2.2055 1.00   1285  143 0.1122 0.1725      4.9681      5.2074|
| 11:  2.2055 -  2.1367 0.97   1252  137 0.1135 0.1776       4.959      5.2855|
| 12:  2.1367 -  2.0758 0.98   1249  144 0.1138 0.1764      4.8973      5.2433|
| 13:  2.0758 -  2.0213 0.99   1277  133 0.1117 0.1701      4.7896      5.0448|
| 14:  2.0213 -  1.9721 0.66    850  100 0.0974 0.1628      4.6385      4.8715|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9044 -  4.7062  1390   152  0.94   9.18   0.98     0.95       7121.08|
|  2:  4.7062 -  3.7552  1330   152  0.95   7.85   1.02     1.01       8947.66|
|  3:  3.7552 -  3.2863  1299   143  0.93  11.19   1.04     1.03      10268.59|
|  4:  3.2863 -  2.9885  1307   145  0.92  13.60   1.02     1.00      10321.41|
|  5:  2.9885 -  2.7757  1283   145  0.90  15.61   1.01     0.99       8288.74|
|  6:  2.7757 -  2.6130  1292   141  0.90  15.93   0.99     0.96       6887.07|
|  7:  2.6130 -  2.4828  1284   143  0.90  15.70   0.99     0.96       6097.23|
|  8:  2.4828 -  2.3751  1270   137  0.91  15.27   1.00     0.98       5339.38|
|  9:  2.3751 -  2.2840  1262   144  0.91  15.35   1.01     0.98       5197.45|
| 10:  2.2840 -  2.2055  1285   143  0.90  16.06   1.01     0.97       4524.40|
| 11:  2.2055 -  2.1367  1252   137  0.90  16.75   1.01     0.97       4705.71|
| 12:  2.1367 -  2.0758  1249   144  0.90  16.28   1.02     1.01       4178.07|
| 13:  2.0758 -  2.0213  1277   133  0.90  15.98   1.01     0.99       3363.64|
| 14:  2.0213 -  1.9721   850   100  0.92  13.46   0.99     0.97       2432.78|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2432.78 max =        10321.41 mean =      6387.76|
|figures of merit: min =        0.01 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.53 mean =        14.11|
|phase err.(test): min =        0.00 max =           89.04 mean =        13.59|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.632)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.70    99.69   15.40    None  None   None       |
|    all(noH): 2823   0      2.70    99.69   15.40    None  None   None       |
|    Sol.    : 438    0      4.07    89.98   39.40    None  None   None       |
|    Mac.    : 2385   0      2.70    99.69   10.99    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.701 -  12.400: 1820   |   5:    51.196 -  60.895:   63        |
|      1:    12.400 -  22.099:  484   |   6:    60.895 -  70.594:   41        |
|      2:    22.099 -  31.798:  150   |   7:    70.594 -  80.292:   17        |
|      3:    31.798 -  41.497:  124   |   8:    80.292 -  89.991:    6        |
|      4:    41.497 -  51.196:  116   |   9:    89.991 -  99.690:    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)= 309         
Filter by distance & map next to the model:
   mapped sites are within: 0.316 - 4.637
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 306 from: 309
   mapped sites are within: 0.704 - 4.637

peak=   11.190 closest distance to " CB  VAL A 230 " =    1.450
peak=   10.421 closest distance to " CB  VAL A 296 " =    1.545
peak=    7.935 closest distance to " O   HOH Z 130 " =    1.413
peak=    6.318 closest distance to " NE2 GLN A  11 " =    1.191
peak=    6.194 closest distance to " CD2 LEU A   5 " =    1.236
peak=    5.874 closest distance to " CG  LEU A   5 " =    1.157
peak=    5.648 closest distance to " O   HOH Z 142 " =    1.994
peak=    5.482 closest distance to " O   HOH Z   9 " =    1.806
peak=    5.444 closest distance to " NH2 ARG A  56 " =    2.082
peak=    5.417 closest distance to " CG  PRO A  54 " =    1.320
peak=    5.326 closest distance to " CG  LEU A 228 " =    1.195
peak=    5.303 closest distance to " CD1AILE A 234 " =    0.974
peak=    5.111 closest distance to " O   HOH Z 427 " =    2.524
peak=    5.004 closest distance to " CB  PRO A  54 " =    0.988
peak=    4.699 closest distance to " CB  ARG A 275 " =    0.953
peak=    4.692 closest distance to " O   HOH Z 369 " =    2.119
peak=    4.688 closest distance to " CB  GLN A 183 " =    1.243
peak=    4.678 closest distance to " O   HOH Z  65 " =    1.080
peak=    4.630 closest distance to " O   HOH Z  78 " =    1.672
peak=    4.600 closest distance to " O   HOH Z 209 " =    2.328
peak=    4.585 closest distance to " O   HOH Z 232 " =    2.324
peak=    4.585 closest distance to " O   HOH Z 126 " =    1.988
peak=    4.555 closest distance to " CB  SER A   3 " =    1.350
peak=    4.549 closest distance to " O   HOH Z 124 " =    1.367
peak=    4.457 closest distance to " O   HOH Z 346 " =    1.595
peak=    4.449 closest distance to " O   HOH Z 425 " =    1.482
peak=    4.433 closest distance to " O   SER A  87 " =    2.387
peak=    4.432 closest distance to " O   HOH Z  68 " =    2.117
peak=    4.417 closest distance to " CB  VAL A 230 " =    1.141
peak=    4.413 closest distance to " CB  GLN A 223 " =    1.569
peak=    4.368 closest distance to " CB  ASN A 148 " =    1.368
peak=    4.365 closest distance to " O   HOH Z 403 " =    1.685
peak=    4.278 closest distance to " O   HOH Z 380 " =    1.779
peak=    4.252 closest distance to " CB  VAL A 265 " =    1.342
peak=    4.232 closest distance to " O   HOH Z 423 " =    1.499
peak=    4.228 closest distance to " O   HOH Z  30 " =    1.691
peak=    4.189 closest distance to " CB  VAL A 202 " =    1.630
peak=    4.183 closest distance to " O   HOH Z 234 " =    3.605
peak=    4.179 closest distance to " CB  GLU A 277 " =    3.455
peak=    4.170 closest distance to " O   HOH Z 193 " =    1.612
peak=    4.153 closest distance to " CG  PRO A 213 " =    1.220
peak=    4.149 closest distance to " O   HOH Z 130 " =    2.350
peak=    4.144 closest distance to " CB  SER A  63 " =    1.234
peak=    4.133 closest distance to " O   HOH Z 112 " =    1.127
peak=    4.129 closest distance to " ND2 ASN A 187 " =    1.671
peak=    4.119 closest distance to " O   HOH Z 272 " =    1.822
peak=    4.113 closest distance to " O   HOH Z   2 " =    1.580
peak=    4.099 closest distance to " O   HOH Z 368 " =    2.053
peak=    4.071 closest distance to " O   PRO A 198 " =    1.564
peak=    4.071 closest distance to " O   HOH Z 417 " =    1.292
peak=    4.068 closest distance to " O   HOH Z  78 " =    1.933
peak=    4.067 closest distance to " O   HOH Z 424 " =    1.368
peak=    4.051 closest distance to " O   HOH Z 261 " =    2.125
peak=    4.024 closest distance to " CB AVAL A  41 " =    1.227
peak=    4.018 closest distance to " OG ASER A 258 " =    2.999
peak=    3.963 closest distance to " O   HOH Z 366 " =    2.855
peak=    3.961 closest distance to " O   HOH Z 203 " =    1.619
peak=    3.961 closest distance to " CB  TRP A 266 " =    1.053
peak=    3.945 closest distance to " O   HOH Z  61 " =    1.605
peak=    3.931 closest distance to " O   HOH Z 419 " =    2.079
peak=    3.926 closest distance to " CB  ARG A  79 " =    1.497
peak=    3.921 closest distance to " O   HOH Z 287 " =    1.808
peak=    3.917 closest distance to " NH2AARG A 190 " =    1.793
peak=    3.913 closest distance to " O   HOH Z  85 " =    1.348
peak=    3.913 closest distance to " OG BSER A 164 " =    2.084
peak=    3.910 closest distance to " NH1 ARG A 138 " =    1.157
peak=    3.910 closest distance to " O   HOH Z 298 " =    1.720
peak=    3.902 closest distance to " O   HOH Z  97 " =    2.509
peak=    3.892 closest distance to " O   HOH Z 353 " =    2.515
peak=    3.885 closest distance to " O   HOH Z  55 " =    2.136
peak=    3.871 closest distance to " O   HOH Z 193 " =    1.711
peak=    3.854 closest distance to " CG  PRO A 243 " =    1.180
peak=    3.850 closest distance to " O   HOH Z   3 " =    2.009
peak=    3.848 closest distance to " O   HOH Z 405 " =    1.315
peak=    3.838 closest distance to " CG  LYS A  76 " =    1.609
peak=    3.829 closest distance to " O   HOH Z 422 " =    2.585
peak=    3.825 closest distance to " O   HOH Z 389 " =    1.241
peak=    3.812 closest distance to " O   HOH Z 189 " =    2.912
peak=    3.801 closest distance to " CB  GLU A 152 " =    1.210
peak=    3.798 closest distance to " CB  ASN A 142 " =    0.973
peak=    3.786 closest distance to " O   HOH Z 303 " =    2.286
peak=    3.784 closest distance to " CB  ASN A  39 " =    0.996
peak=    3.779 closest distance to " CG  LEU A 167 " =    1.223
peak=    3.769 closest distance to " CB  TRP A 179 " =    1.341
peak=    3.767 closest distance to " O   HOH Z  59 " =    1.708
peak=    3.762 closest distance to " O   HOH Z 359 " =    1.223
peak=    3.760 closest distance to " N   PHE A 130 " =    1.284
peak=    3.758 closest distance to " CB  GLU A 128 " =    1.094
peak=    3.757 closest distance to " O   HOH Z  44 " =    1.633
peak=    3.757 closest distance to " O   HOH Z 214 " =    2.354
peak=    3.755 closest distance to " O   HOH Z 411 " =    3.677
peak=    3.755 closest distance to " O   HOH Z 248 " =    1.624
peak=    3.751 closest distance to " CG BARG A 102 " =    1.862
peak=    3.742 closest distance to " CD2 LEU A 228 " =    1.225
peak=    3.727 closest distance to " CG  PRO A 198 " =    1.226
peak=    3.724 closest distance to " O   HOH Z 133 " =    2.540
peak=    3.706 closest distance to " CA  PHE A 283 " =    1.280
peak=    3.699 closest distance to " O   HOH Z 290 " =    0.972
peak=    3.698 closest distance to " O   HOH Z 193 " =    1.851
peak=    3.698 closest distance to " O   PRO A 198 " =    1.306
peak=    3.695 closest distance to " O   HOH Z 258 " =    2.115
peak=    3.691 closest distance to " O   HOH Z  61 " =    1.543
peak=    3.687 closest distance to " O   HOH Z 352 " =    1.302
peak=    3.672 closest distance to " O   HOH Z 236 " =    1.510
peak=    3.667 closest distance to " OG  SER A  62 " =    2.912
peak=    3.666 closest distance to " CB  GLN A  88 " =    1.307
peak=    3.664 closest distance to " O   HOH Z 371 " =    2.803
peak=    3.664 closest distance to " O   HOH Z 423 " =    1.754
peak=    3.663 closest distance to " O   HOH Z 222 " =    2.421
peak=    3.660 closest distance to " O   HOH Z  63 " =    1.257
peak=    3.658 closest distance to " O   HOH Z 117 " =    1.992
peak=    3.643 closest distance to " O   HOH Z 368 " =    3.534
peak=    3.642 closest distance to " CG  MET A 185 " =    1.217
peak=    3.639 closest distance to " O   HOH Z 272 " =    2.163
peak=    3.637 closest distance to " O   HOH Z 305 " =    3.381
peak=    3.630 closest distance to " O   HOH Z 158 " =    3.154
peak=    3.628 closest distance to " O   HOH Z   1 " =    1.664
peak=    3.625 closest distance to " OE2 GLU A  53 " =    1.912
peak=    3.620 closest distance to " O   HOH Z   6 " =    2.055
peak=    3.612 closest distance to " O   HOH Z  40 " =    2.103
peak=    3.597 closest distance to " CD  LYS A 166 " =    1.412
peak=    3.597 closest distance to " CA  LYS A 117 " =    1.177
peak=    3.595 closest distance to " O   HOH Z 435 " =    2.032
peak=    3.592 closest distance to " OG BSER A 210 " =    1.415
peak=    3.591 closest distance to " O   HOH Z  88 " =    2.709
peak=    3.590 closest distance to " O   HOH Z  10 " =    1.706
peak=    3.589 closest distance to " CD1 ILE A  33 " =    1.660
peak=    3.588 closest distance to " O   HOH Z 180 " =    2.062
peak=    3.588 closest distance to " O   HOH Z 425 " =    1.971
peak=    3.584 closest distance to " O  BHOH Z 338 " =    2.461
peak=    3.580 closest distance to " O   HOH Z 146 " =    1.547
peak=    3.577 closest distance to " CD  ARG A 269 " =    1.052
peak=    3.577 closest distance to " O   HOH Z 126 " =    1.521
peak=    3.576 closest distance to " NZ  LYS A 117 " =    2.971
peak=    3.570 closest distance to " CB  ASN A 187 " =    1.148
peak=    3.568 closest distance to " O   HOH Z 427 " =    1.402
peak=    3.567 closest distance to " OG  SER A  62 " =    2.733
peak=    3.551 closest distance to " O   HOH Z 435 " =    1.750
peak=    3.546 closest distance to " CB  ARG A 190 " =    1.601
peak=    3.543 closest distance to " CG  GLN A  88 " =    1.151
peak=    3.541 closest distance to " CB  ALA A 114 " =    1.504
peak=    3.541 closest distance to " CG AARG A 275 " =    1.113
peak=    3.538 closest distance to " CD2 TRP A 179 " =    1.322
peak=    3.533 closest distance to " O   HOH Z  43 " =    1.888
peak=    3.529 closest distance to " O   HOH Z 343 " =    3.217
peak=    3.526 closest distance to " CA  ASN A 215 " =    1.067
peak=    3.514 closest distance to " CE1 TYR A 186 " =    1.323
peak=    3.510 closest distance to " O   HOH Z 116 " =    2.854
peak=    3.510 closest distance to " O   HOH Z  39 " =    1.235
peak=    3.506 closest distance to " CG1BVAL A  72 " =    1.395
peak=    3.505 closest distance to " O   HOH Z 119 " =    1.655
peak=    3.499 closest distance to " O   HOH Z 128 " =    2.142
peak=    3.482 closest distance to " NH2BARG A 145 " =    2.072
peak=    3.482 closest distance to " O   HOH Z 329 " =    3.986
peak=    3.479 closest distance to " O   HOH Z 196 " =    1.476
peak=    3.477 closest distance to " CG2 VAL A 257 " =    0.797
peak=    3.465 closest distance to " O   HOH Z 392 " =    1.248
peak=    3.464 closest distance to " O   HOH Z 273 " =    2.907
peak=    3.460 closest distance to " O   HOH Z 128 " =    1.883
peak=    3.452 closest distance to " NE  ARG A  56 " =    3.440
peak=    3.452 closest distance to " O   HOH Z 261 " =    1.565
peak=    3.451 closest distance to " O   HOH Z 128 " =    2.082
peak=    3.447 closest distance to " CB  SER A 216 " =    0.800
peak=    3.438 closest distance to " CB  ASN A 215 " =    1.125
peak=    3.438 closest distance to " O   HOH Z 109 " =    2.417
peak=    3.437 closest distance to " CA  TYR A  30 " =    0.981
peak=    3.435 closest distance to " CB  SER A  26 " =    1.621
peak=    3.434 closest distance to " CB  THR A 157 " =    1.142
peak=    3.432 closest distance to " O   HOH Z 263 " =    1.663
peak=    3.430 closest distance to " CB  SER A 276 " =    1.142
peak=    3.430 closest distance to " O   HOH Z   1 " =    1.756
peak=    3.429 closest distance to " CB  ARG A 139 " =    0.996
peak=    3.427 closest distance to " OE2 GLU A   2 " =    1.833
peak=    3.420 closest distance to " N   ASN A 127 " =    1.335
peak=    3.416 closest distance to " ND1 HIS A  86 " =    1.828
peak=    3.415 closest distance to " CB  SER A  62 " =    1.192
peak=    3.412 closest distance to " NH1AARG A 145 " =    1.156
peak=    3.402 closest distance to " OD1 ASN A  69 " =    2.569
peak=    3.402 closest distance to " CB  PHE A 204 " =    1.072
peak=    3.395 closest distance to " O   HOH Z 145 " =    3.617
peak=    3.392 closest distance to " O   HOH Z 143 " =    1.405
peak=    3.392 closest distance to " O   HOH Z 437 " =    2.027
peak=    3.384 closest distance to " CH2 TRP A 266 " =    1.027
peak=    3.379 closest distance to " O   HOH Z 145 " =    1.446
peak=    3.375 closest distance to " CB  LYS A 117 " =    1.189
peak=    3.374 closest distance to " O   HOH Z 234 " =    2.061
peak=    3.369 closest distance to " CD  PRO A 243 " =    1.463
peak=    3.365 closest distance to " CA  ALA A  51 " =    0.980
peak=    3.359 closest distance to " CA  ASN A 127 " =    1.061
peak=    3.359 closest distance to " O   HOH Z 371 " =    1.666
peak=    3.357 closest distance to " O   HOH Z 303 " =    1.779
peak=    3.353 closest distance to " O   HOH Z 392 " =    3.117
peak=    3.353 closest distance to " O   HOH Z 175 " =    2.233
peak=    3.352 closest distance to " O   HOH Z  59 " =    2.041
peak=    3.349 closest distance to " O   HOH Z  58 " =    1.721
peak=    3.348 closest distance to " NH1BARG A 145 " =    1.325
peak=    3.347 closest distance to " CB  ASN A 110 " =    1.077
peak=    3.344 closest distance to " CD2 LEU A 297 " =    0.977
peak=    3.341 closest distance to " CG1 VAL A 153 " =    0.876
peak=    3.337 closest distance to " CG2 THR A 221 " =    1.210
peak=    3.332 closest distance to " CA  ALA A 158 " =    1.266
peak=    3.329 closest distance to " O   HOH Z  59 " =    2.121
peak=    3.328 closest distance to " O   HOH Z 145 " =    1.997
peak=    3.325 closest distance to " CG  LYS A 119 " =    1.115
peak=    3.324 closest distance to " CA  SER A  87 " =    0.950
peak=    3.322 closest distance to " CA  LYS A 290 " =    1.305
peak=    3.322 closest distance to " O   HOH Z   9 " =    1.679
peak=    3.321 closest distance to " O   HOH Z 250 " =    1.373
peak=    3.321 closest distance to " CE3 TRP A 150 " =    0.967
peak=    3.318 closest distance to " N   SER A 135 " =    1.279
peak=    3.312 closest distance to " CB  THR A  31 " =    1.624
peak=    3.310 closest distance to " N   ASP A 162 " =    1.160
peak=    3.298 closest distance to " O   HOH Z  89 " =    2.120
peak=    3.298 closest distance to " CG1 ILE A 151 " =    1.102
peak=    3.296 closest distance to " O   HOH Z 357 " =    1.941
peak=    3.295 closest distance to " O   HOH Z 299 " =    4.030
peak=    3.290 closest distance to " CG1 ILE A  33 " =    1.303
peak=    3.290 closest distance to " O   HOH Z 209 " =    2.288
peak=    3.285 closest distance to " CA  MET A 105 " =    0.920
peak=    3.283 closest distance to " O   HOH Z 123 " =    1.103
peak=    3.280 closest distance to " CG2 ILE A  20 " =    1.577
peak=    3.277 closest distance to " O   HOH Z 118 " =    1.245
peak=    3.276 closest distance to " O   HOH Z 301 " =    1.637
peak=    3.274 closest distance to " CB  LEU A 143 " =    1.065
peak=    3.274 closest distance to " CB  GLN A 278 " =    0.896
peak=    3.271 closest distance to " CB  TRP A 150 " =    1.293
peak=    3.271 closest distance to " O   ARG A 145 " =    1.851
peak=    3.269 closest distance to " CB  SER A 212 " =    1.261
peak=    3.269 closest distance to " CE AMET A  47 " =    1.456
peak=    3.265 closest distance to " ND2 ASN A 110 " =    1.662
peak=    3.252 closest distance to " CB  ARG A  79 " =    0.878
peak=    3.250 closest distance to " OG1 THR A 294 " =    2.387
peak=    3.249 closest distance to " CA  ARG A 195 " =    1.149
peak=    3.249 closest distance to " CB  HIS A 108 " =    0.840
peak=    3.249 closest distance to " N   ASN A  39 " =    1.261
peak=    3.248 closest distance to " NE2 GLN A  58 " =    3.982
peak=    3.246 closest distance to " O   HOH Z 251 " =    1.656
peak=    3.238 closest distance to " O   HOH Z 222 " =    2.230
peak=    3.236 closest distance to " ND2 ASN A 249 " =    0.826
peak=    3.232 closest distance to " CB  TYR A  30 " =    1.704
peak=    3.232 closest distance to " O   HOH Z  66 " =    2.176
peak=    3.229 closest distance to " CA  ALA A 248 " =    1.241
peak=    3.228 closest distance to " O   HOH Z 323 " =    1.545
peak=    3.224 closest distance to " CB  ARG A 219 " =    0.971
peak=    3.224 closest distance to " N   GLN A 278 " =    1.261
peak=    3.223 closest distance to " CE  LYS A  76 " =    0.912
peak=    3.223 closest distance to " CB  ALA A   1 " =    4.637
peak=    3.218 closest distance to " OG1 THR A 221 " =    1.311
peak=    3.217 closest distance to " NH1 ARG A  14 " =    1.222
peak=    3.214 closest distance to " NZ  LYS A  48 " =    1.319
peak=    3.210 closest distance to " CA  ALA A 291 " =    0.869
peak=    3.210 closest distance to " CA  ALA A  21 " =    1.224
peak=    3.208 closest distance to " CD1 ILE A 263 " =    1.352
peak=    3.206 closest distance to " CG2 ILE A 234 " =    0.745
peak=    3.203 closest distance to " CA  ALA A  84 " =    1.347
peak=    3.199 closest distance to " CB  SER A  99 " =    0.946
peak=    3.197 closest distance to " O   HOH Z 172 " =    3.193
peak=    3.197 closest distance to " CB  ALA A 291 " =    1.361
peak=    3.196 closest distance to " CG  GLN A  89 " =    1.422
peak=    3.192 closest distance to " O   HOH Z  80 " =    1.528
peak=    3.191 closest distance to " CD1 LEU A 228 " =    1.952
peak=    3.191 closest distance to " O   HOH Z 402 " =    1.336
peak=    3.188 closest distance to " OD1BASN A 224 " =    2.234
peak=    3.187 closest distance to " O   HOH Z 327 " =    1.876
peak=    3.184 closest distance to " O   HOH Z 303 " =    2.863
peak=    3.183 closest distance to " CG2 THR A 294 " =    1.659
peak=    3.181 closest distance to " OG ASER A  99 " =    1.541
peak=    3.178 closest distance to " CA  ILE A 234 " =    1.026
peak=    3.175 closest distance to " CA  GLY A 267 " =    1.021
peak=    3.170 closest distance to " CD  ARG A 195 " =    3.464
peak=    3.169 closest distance to " CD  GLN A 194 " =    1.366
peak=    3.168 closest distance to " O   HOH Z  43 " =    2.629
peak=    3.164 closest distance to " CG1 ILE A 120 " =    1.318
peak=    3.164 closest distance to " NH2BARG A 190 " =    1.509
peak=    3.162 closest distance to " NE2 GLN A 278 " =    3.428
peak=    3.161 closest distance to " CA  ALA A 299 " =    0.968
peak=    3.151 closest distance to " O   HOH Z 432 " =    1.617
peak=    3.150 closest distance to " O   HOH Z   7 " =    1.430
peak=    3.140 closest distance to " O   HOH Z  47 " =    1.718
peak=    3.138 closest distance to " CA  ASN A 217 " =    1.181
peak=    3.137 closest distance to " CA  LEU A 101 " =    1.450
peak=    3.136 closest distance to " O   HOH Z 383 " =    2.242
peak=    3.136 closest distance to " CG1 ILE A 263 " =    1.242
peak=    3.131 closest distance to " CB  LEU A 300 " =    0.886
peak=    3.130 closest distance to " CB  ASP A 124 " =    0.704
peak=    3.129 closest distance to " O   HOH Z 132 " =    1.344
peak=    3.123 closest distance to " N   ALA A 256 " =    0.983
peak=    3.110 closest distance to " O   HOH Z 325 " =    2.153
peak=    3.109 closest distance to " O   HOH Z 344 " =    2.938
peak=    3.108 closest distance to " CD1 LEU A   5 " =    1.631
peak=    3.108 closest distance to " CG1 ILE A  49 " =    1.454
peak=    3.096 closest distance to " O   HOH Z  88 " =    3.029
peak=    3.093 closest distance to " O   HOH Z 273 " =    1.597
peak=    3.092 closest distance to " CG  MET A 113 " =    1.034
peak=    3.091 closest distance to " CG  LEU A 281 " =    0.985
peak=    3.086 closest distance to " O   HOH Z  85 " =    1.925
peak=    3.083 closest distance to " O   HOH Z 148 " =    2.236
peak=    3.079 closest distance to " CA  ILE A 106 " =    0.756
peak=    3.079 closest distance to " CB  MET A  40 " =    0.819
peak=    3.074 closest distance to " O   HOH Z 153 " =    3.686
peak=    3.073 closest distance to " O   HOH Z 173 " =    2.128
peak=    3.051 closest distance to " CA  ALA A 233 " =    0.935
peak=    3.040 closest distance to " O   HOH Z  51 " =    1.085
peak=    3.039 closest distance to " O   HOH Z 433 " =    1.875
peak=    3.035 closest distance to " O   HOH Z 374 " =    2.447
peak=    3.023 closest distance to " O   HOH Z 156 " =    3.223

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 202         
Filter by distance & map next to the model:
   mapped sites are within: 0.716 - 5.999
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 202 from: 202
   mapped sites are within: 0.716 - 5.999

peak=   -4.780 closest distance to " CD  ARG A 156 " =    2.016
peak=   -4.657 closest distance to " CG2 VAL A 230 " =    0.716
peak=   -4.304 closest distance to " O   VAL A  67 " =    2.463
peak=   -4.293 closest distance to " OG BSER A 134 " =    1.266
peak=   -4.249 closest distance to " C   HIS A 108 " =    1.267
peak=   -4.246 closest distance to " O   HOH Z 266 " =    5.062
peak=   -4.129 closest distance to " CD1 LEU A 255 " =    2.761
peak=   -4.125 closest distance to " CG  GLN A 223 " =    1.971
peak=   -4.050 closest distance to " CB  PRO A 243 " =    2.646
peak=   -4.026 closest distance to " CD  ARG A  14 " =    3.199
peak=   -4.011 closest distance to " O   HOH Z 231 " =    1.964
peak=   -3.970 closest distance to " NH2 ARG A  79 " =    2.018
peak=   -3.951 closest distance to " CB  ALA A  43 " =    2.424
peak=   -3.939 closest distance to " O   PRO A 198 " =    1.217
peak=   -3.927 closest distance to " CG2 ILE A  20 " =    2.957
peak=   -3.921 closest distance to " CG  GLN A  58 " =    1.021
peak=   -3.893 closest distance to " O   HOH Z 185 " =    2.122
peak=   -3.888 closest distance to " O   HOH Z 211 " =    1.426
peak=   -3.880 closest distance to " CE2 PHE A 218 " =    2.450
peak=   -3.849 closest distance to " O   HOH Z  11 " =    1.778
peak=   -3.831 closest distance to " O   HOH Z 131 " =    4.104
peak=   -3.815 closest distance to " O   HOH Z 290 " =    1.104
peak=   -3.801 closest distance to " O   HOH Z 351 " =    1.573
peak=   -3.796 closest distance to " O   PRO A 163 " =    2.023
peak=   -3.795 closest distance to " C   ILE A 239 " =    2.100
peak=   -3.785 closest distance to " CD  LYS A 289 " =    2.408
peak=   -3.779 closest distance to " O   HOH Z 313 " =    1.625
peak=   -3.771 closest distance to " CG2 VAL A 296 " =    2.195
peak=   -3.757 closest distance to " O   SER A  22 " =    2.348
peak=   -3.755 closest distance to " CE2 TYR A  30 " =    2.687
peak=   -3.719 closest distance to " O   HOH Z 359 " =    3.301
peak=   -3.709 closest distance to " CZ2 TRP A 274 " =    0.936
peak=   -3.705 closest distance to " CB  ALA A 248 " =    2.058
peak=   -3.701 closest distance to " OD1 ASN A  39 " =    2.119
peak=   -3.693 closest distance to " O   HOH Z  43 " =    1.920
peak=   -3.618 closest distance to " O   HOH Z 140 " =    1.394
peak=   -3.618 closest distance to " O   SER A 135 " =    1.456
peak=   -3.609 closest distance to " CE  MET A 105 " =    2.411
peak=   -3.600 closest distance to " C   MET A 188 " =    1.477
peak=   -3.600 closest distance to " CE  LYS A  76 " =    2.825
peak=   -3.595 closest distance to " O   HOH Z 191 " =    5.444
peak=   -3.591 closest distance to " OD2 ASP A 191 " =    1.294
peak=   -3.587 closest distance to " CE1 PHE A  59 " =    1.982
peak=   -3.586 closest distance to " N   THR A 157 " =    1.399
peak=   -3.586 closest distance to " CB  PHE A 192 " =    1.898
peak=   -3.585 closest distance to " O   HOH Z 362 " =    5.999
peak=   -3.578 closest distance to " O   ARG A 145 " =    1.551
peak=   -3.574 closest distance to " N   GLN A  58 " =    1.954
peak=   -3.573 closest distance to " CE BMET A  47 " =    1.064
peak=   -3.570 closest distance to " O   HOH Z 389 " =    1.499
peak=   -3.569 closest distance to " O   PRO A 243 " =    2.525
peak=   -3.558 closest distance to " O   HOH Z 114 " =    3.023
peak=   -3.545 closest distance to " O   ILE A  49 " =    1.714
peak=   -3.543 closest distance to " N   ALA A  43 " =    2.692
peak=   -3.524 closest distance to " CA  GLY A 133 " =    1.953
peak=   -3.524 closest distance to " N   PRO A 163 " =    1.532
peak=   -3.522 closest distance to " N   ALA A 226 " =    1.992
peak=   -3.520 closest distance to " CG1 VAL A 112 " =    2.838
peak=   -3.518 closest distance to " ND2 ASN A 249 " =    2.380
peak=   -3.517 closest distance to " OD2 ASP A 171 " =    2.146
peak=   -3.515 closest distance to " O   HOH Z 385 " =    2.038
peak=   -3.515 closest distance to " OE2 GLU A 152 " =    1.189
peak=   -3.512 closest distance to " O   ALA A 161 " =    1.736
peak=   -3.502 closest distance to " CG2 VAL A 202 " =    2.702
peak=   -3.498 closest distance to " OG  SER A  87 " =    1.301
peak=   -3.497 closest distance to " OG  SER A  97 " =    2.175
peak=   -3.496 closest distance to " CD2 LEU A   5 " =    1.083
peak=   -3.493 closest distance to " CA  GLY A 203 " =    2.398
peak=   -3.488 closest distance to " O   HOH Z 286 " =    1.570
peak=   -3.485 closest distance to " O   HOH Z 102 " =    1.629
peak=   -3.483 closest distance to " OG  SER A  62 " =    4.371
peak=   -3.482 closest distance to " CG  TRP A 266 " =    1.872
peak=   -3.482 closest distance to " OG  SER A   3 " =    1.635
peak=   -3.476 closest distance to " O   HOH Z  90 " =    2.585
peak=   -3.475 closest distance to " N   ALA A 248 " =    1.606
peak=   -3.468 closest distance to " CB  PRO A 163 " =    2.368
peak=   -3.466 closest distance to " CB  ASN A  39 " =    2.126
peak=   -3.466 closest distance to " O   HOH Z 389 " =    2.149
peak=   -3.463 closest distance to " CZ  TYR A 169 " =    1.737
peak=   -3.462 closest distance to " O   HOH Z  51 " =    1.130
peak=   -3.461 closest distance to " CB  ALA A 131 " =    1.960
peak=   -3.460 closest distance to " O   PRO A 198 " =    1.325
peak=   -3.459 closest distance to " O   HOH Z 427 " =    1.625
peak=   -3.458 closest distance to " CB  ALA A 161 " =    2.472
peak=   -3.456 closest distance to " O   HOH Z 339 " =    1.793
peak=   -3.456 closest distance to " CA  GLY A 241 " =    2.262
peak=   -3.454 closest distance to " O   HOH Z  65 " =    1.104
peak=   -3.449 closest distance to " CG  ASN A 301 " =    2.072
peak=   -3.445 closest distance to " CG1 VAL A 230 " =    1.917
peak=   -3.443 closest distance to " O   HOH Z 394 " =    1.469
peak=   -3.433 closest distance to " O   HOH Z 359 " =    1.716
peak=   -3.432 closest distance to " O   HOH Z  60 " =    2.002
peak=   -3.426 closest distance to " N   VAL A  72 " =    1.649
peak=   -3.417 closest distance to " CD1 LEU A 101 " =    2.201
peak=   -3.415 closest distance to " O   HOH Z 231 " =    1.292
peak=   -3.414 closest distance to " N   MET A 188 " =    1.793
peak=   -3.411 closest distance to " CA  GLY A  35 " =    2.016
peak=   -3.407 closest distance to " O   SER A 210 " =    1.867
peak=   -3.402 closest distance to " ND2 ASN A 187 " =    1.596
peak=   -3.399 closest distance to " CD1 LEU A 228 " =    2.218
peak=   -3.398 closest distance to " O   GLU A 152 " =    1.487
peak=   -3.397 closest distance to " O   HOH Z 350 " =    1.896
peak=   -3.393 closest distance to " CB  ALA A 244 " =    2.113
peak=   -3.392 closest distance to " C   ASP A 231 " =    2.434
peak=   -3.382 closest distance to " O   GLY A  80 " =    2.445
peak=   -3.381 closest distance to " CB  ASP A 132 " =    2.380
peak=   -3.379 closest distance to " O   HOH Z 166 " =    1.878
peak=   -3.368 closest distance to " ND2 ASN A  69 " =    1.798
peak=   -3.366 closest distance to " CB  ALA A 248 " =    2.356
peak=   -3.363 closest distance to " CB  SER A 210 " =    1.222
peak=   -3.360 closest distance to " CB  ALA A  64 " =    2.724
peak=   -3.353 closest distance to " CB  ALA A   7 " =    2.092
peak=   -3.352 closest distance to " C   GLN A 205 " =    1.889
peak=   -3.348 closest distance to " O   ALA A   1 " =    1.656
peak=   -3.346 closest distance to " OH  TYR A 172 " =    1.776
peak=   -3.344 closest distance to " CG  GLN A 278 " =    2.096
peak=   -3.343 closest distance to " CD2 TYR A 293 " =    1.908
peak=   -3.343 closest distance to " CA  ASN A 127 " =    1.348
peak=   -3.340 closest distance to " O   HOH Z 165 " =    2.106
peak=   -3.337 closest distance to " ND2 ASN A 252 " =    1.838
peak=   -3.331 closest distance to " O   VAL A 189 " =    2.562
peak=   -3.329 closest distance to " O   GLN A 240 " =    1.952
peak=   -3.326 closest distance to " O   HOH Z 377 " =    1.041
peak=   -3.324 closest distance to " CD2 LEU A 237 " =    2.592
peak=   -3.323 closest distance to " C   ASN A 285 " =    2.213
peak=   -3.314 closest distance to " O   HOH Z 208 " =    1.918
peak=   -3.302 closest distance to " CB  ALA A 114 " =    2.344
peak=   -3.300 closest distance to " O   HOH Z 111 " =    4.464
peak=   -3.298 closest distance to " CE1 PHE A  59 " =    2.078
peak=   -3.288 closest distance to " OE1 GLN A  88 " =    1.260
peak=   -3.288 closest distance to " O   HOH Z 134 " =    3.836
peak=   -3.287 closest distance to " O   SER A 271 " =    2.059
peak=   -3.284 closest distance to " O   ALA A  10 " =    1.789
peak=   -3.284 closest distance to " CB  ALA A 291 " =    2.325
peak=   -3.280 closest distance to " OG ASER A 134 " =    1.186
peak=   -3.279 closest distance to " O   HOH Z 298 " =    1.175
peak=   -3.278 closest distance to " CA  GLY A  98 " =    1.742
peak=   -3.276 closest distance to " O   HOH Z  89 " =    2.931
peak=   -3.274 closest distance to " NE2 GLN A 278 " =    1.898
peak=   -3.268 closest distance to " CG2 THR A  18 " =    2.825
peak=   -3.268 closest distance to " O   PHE A 218 " =    1.488
peak=   -3.263 closest distance to " CD2 HIS A 207 " =    2.320
peak=   -3.258 closest distance to " ND2BASN A 224 " =    1.632
peak=   -3.256 closest distance to " O   ALA A   8 " =    1.872
peak=   -3.254 closest distance to " OE1 GLN A 183 " =    1.496
peak=   -3.251 closest distance to " O   GLY A 229 " =    1.848
peak=   -3.250 closest distance to " ND2 ASN A  45 " =    2.142
peak=   -3.249 closest distance to " O   HOH Z 407 " =    2.903
peak=   -3.248 closest distance to " O   SER A  95 " =    1.472
peak=   -3.246 closest distance to " OG  SER A  63 " =    1.218
peak=   -3.239 closest distance to " O   HOH Z 392 " =    0.937
peak=   -3.235 closest distance to " CG2 THR A 178 " =    2.180
peak=   -3.233 closest distance to " ND2 ASN A  39 " =    1.353
peak=   -3.231 closest distance to " CB  ALA A 291 " =    2.125
peak=   -3.227 closest distance to " O   HOH Z 152 " =    4.569
peak=   -3.219 closest distance to " CG  GLN A  88 " =    0.925
peak=   -3.216 closest distance to " OG1 THR A 178 " =    1.202
peak=   -3.215 closest distance to " CG  GLU A 152 " =    1.579
peak=   -3.214 closest distance to " CE  MET A 105 " =    2.316
peak=   -3.214 closest distance to " O   HOH Z 346 " =    1.729
peak=   -3.214 closest distance to " CG  PHE A 283 " =    2.543
peak=   -3.205 closest distance to " CG2 THR A  52 " =    2.913
peak=   -3.202 closest distance to " CZ3 TRP A 179 " =    1.286
peak=   -3.200 closest distance to " CA  ASP A  27 " =    2.455
peak=   -3.200 closest distance to " CG1 VAL A 197 " =    2.218
peak=   -3.197 closest distance to " O   HOH Z 384 " =    2.154
peak=   -3.196 closest distance to " ND2 ASN A 285 " =    2.048
peak=   -3.196 closest distance to " O   HOH Z 364 " =    1.297
peak=   -3.186 closest distance to " CG2 THR A  42 " =    1.821
peak=   -3.184 closest distance to " N   THR A 235 " =    1.173
peak=   -3.184 closest distance to " O   HOH Z 198 " =    2.000
peak=   -3.183 closest distance to " NH1 ARG A  66 " =    3.622
peak=   -3.183 closest distance to " O   HOH Z 149 " =    2.159
peak=   -3.182 closest distance to " CA  ASP A 298 " =    1.036
peak=   -3.177 closest distance to " CG1 VAL A 250 " =    2.710
peak=   -3.176 closest distance to " CB  ASP A 286 " =    2.309
peak=   -3.169 closest distance to " O   HOH Z 431 " =    1.525
peak=   -3.165 closest distance to " O   HOH Z 139 " =    3.059
peak=   -3.158 closest distance to " O   HOH Z 158 " =    1.978
peak=   -3.158 closest distance to " O   HOH Z 353 " =    1.885
peak=   -3.158 closest distance to " ND2 ASN A  45 " =    1.197
peak=   -3.153 closest distance to " CG  PRO A  90 " =    1.638
peak=   -3.152 closest distance to " C   ARG A 269 " =    1.343
peak=   -3.150 closest distance to " CE2 TRP A  70 " =    2.223
peak=   -3.150 closest distance to " CG2AVAL A  41 " =    2.900
peak=   -3.149 closest distance to " CD1 TYR A 247 " =    2.645
peak=   -3.145 closest distance to " CG  ASP A 231 " =    0.759
peak=   -3.141 closest distance to " OXT GLY A 302 " =    3.022
peak=   -3.139 closest distance to " CG  MET A 105 " =    0.949
peak=   -3.138 closest distance to " O   HOH Z 130 " =    2.020
peak=   -3.129 closest distance to " O   HOH Z 193 " =    1.630
peak=   -3.129 closest distance to " C   LYS A  76 " =    1.589
peak=   -3.127 closest distance to " O   HOH Z 292 " =    1.685
peak=   -3.124 closest distance to " O   ALA A 256 " =    2.677
peak=   -3.123 closest distance to " O   ALA A  51 " =    1.210
peak=   -3.111 closest distance to " O   ALA A 180 " =    1.212
peak=   -3.110 closest distance to " O   HOH Z 111 " =    2.316
peak=   -3.103 closest distance to " O   LEU A 101 " =    2.757
peak=   -3.087 closest distance to " O   HOH Z 368 " =    2.407
peak=   -3.086 closest distance to " NE2 GLN A 194 " =    1.722
peak=   -3.048 closest distance to " O   HOH Z 132 " =    1.205
peak=   -3.037 closest distance to " OG  SER A   3 " =    1.220

================= 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    :  0.4630 0.4575   6.264679e+00   6.248352e+00
   1_bss:  0.4546 0.4418   6.257907e+00   6.233442e+00
   1_xyz:  0.3660 0.3837   6.121299e+00   6.147307e+00
   1_adp:  0.3159 0.3641   6.018916e+00   6.111220e+00
   1_occ:  0.3154 0.3640   6.018275e+00   6.112248e+00
   2_bss:  0.3104 0.3564   6.016740e+00   6.108216e+00
   2_xyz:  0.2333 0.2853   5.773581e+00   5.921289e+00
   2_adp:  0.2139 0.2682   5.704427e+00   5.867187e+00
   2_occ:  0.2136 0.2680   5.703547e+00   5.866627e+00
   3_bss:  0.2129 0.2664   5.703472e+00   5.864821e+00
   3_xyz:  0.1549 0.2040   5.415745e+00   5.623845e+00
   3_adp:  0.1372 0.1897   5.320702e+00   5.554763e+00
   3_occ:  0.1372 0.1895   5.320098e+00   5.554167e+00
   4_bss:  0.1370 0.1890   5.317941e+00   5.551389e+00
   4_xyz:  0.1257 0.1758   5.246317e+00   5.483413e+00
   4_adp:  0.1236 0.1708   5.223538e+00   5.452990e+00
   4_occ:  0.1235 0.1708   5.223145e+00   5.452370e+00
   5_bss:  0.1235 0.1708   5.222915e+00   5.452169e+00
   5_xyz:  0.1132 0.1614   5.157745e+00   5.405258e+00
   5_adp:  0.1117 0.1588   5.145523e+00   5.392750e+00
   5_occ:  0.1116 0.1588   5.145417e+00   5.392652e+00
   5_bss:  0.1116 0.1590   5.145179e+00   5.391497e+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:  0.358   6.375   7.388  10.142   8.580   0.000   0.000   0.000
   1_xyz:  0.358   6.375   7.388  10.142   8.580   0.000   0.000   0.000
   1_adp:  0.358   6.375   7.388  10.142   8.580   0.000   0.000   0.000
   1_occ:  0.358   6.375   7.388  10.142   8.580   0.000   0.000   0.000
   2_bss:  0.344  31.062   3.635   5.438   4.810   0.000   0.000   0.000
   2_xyz:  0.344  31.062   3.635   5.438   4.810   0.000   0.000   0.000
   2_adp:  0.344  31.062   3.635   5.438   4.810   0.000   0.000   0.000
   2_occ:  0.344  31.062   3.635   5.438   4.810   0.000   0.000   0.000
   3_bss:  0.319  34.985   2.304   3.323   3.833   0.000   0.000   0.000
   3_xyz:  0.319  34.985   2.304   3.323   3.833   0.000   0.000   0.000
   3_adp:  0.319  34.985   2.304   3.323   3.833   0.000   0.000   0.000
   3_occ:  0.319  34.985   2.304   3.323   3.833   0.000   0.000   0.000
   4_bss:  0.321  45.696   1.977   2.452   3.683   0.000   0.000   0.000
   4_xyz:  0.321  45.696   1.977   2.452   3.683   0.000   0.000   0.000
   4_adp:  0.321  45.696   1.977   2.452   3.683   0.000   0.000   0.000
   4_occ:  0.321  45.696   1.977   2.452   3.683   0.000   0.000   0.000
   5_bss:  0.322  45.696   2.020   2.327   3.777   0.000   0.000   0.000
   5_xyz:  0.322  45.696   2.020   2.327   3.777   0.000   0.000   0.000
   5_adp:  0.322  45.696   2.020   2.327   3.777   0.000   0.000   0.000
   5_occ:  0.322  45.696   2.020   2.327   3.777   0.000   0.000   0.000
   5_bss:  0.321  45.867  -0.684  -0.437   1.121  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  54.258 0.4675  0.5403    63370.569
   1_bss:  53.511 0.4751  0.7075    59755.048
   1_xyz:  43.196 0.6030  0.8782    42196.305
   1_adp:  39.183 0.6522  0.9829    37106.766
   1_occ:  39.303 0.6507  0.9795    37182.180
   2_bss:  38.775 0.6569  0.8562    36459.517
   2_xyz:  29.209 0.7660  0.9711    21496.597
   2_adp:  26.514 0.7960  0.9965    18664.170
   2_occ:  26.481 0.7964  0.9963    18622.205
   3_bss:  26.353 0.7976  0.9452    18519.010
   3_xyz:  19.480 0.8664  0.9940    10550.498
   3_adp:  17.787 0.8821  0.9938     9109.088
   3_occ:  17.773 0.8823  0.9937     9091.809
   4_bss:  17.698 0.8829  0.9780     9024.533
   4_xyz:  16.098 0.8973  0.9847     7725.141
   4_adp:  15.339 0.9042  0.9825     7304.067
   4_occ:  15.331 0.9042  0.9824     7288.343
   5_bss:  15.326 0.9043  0.9827     7285.159
   5_xyz:  14.373 0.9119  0.9872     6571.286
   5_adp:  14.060 0.9146  0.9849     6405.454
   5_occ:  14.061 0.9146  0.9848     6398.897
   5_bss:  14.062 0.9145  0.9845     6387.895
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3300e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3300e+01
   1_xyz:   1.621  0.012  0.103 18.036  0.006  4.106   1.2972e-01
   1_adp:   1.621  0.012  0.103 18.036  0.006  4.106   1.2972e-01
   1_occ:   1.621  0.012  0.103 18.036  0.006  4.106   1.2972e-01
   2_bss:   1.621  0.012  0.103 18.036  0.006  4.106   1.2972e-01
   2_xyz:   1.081  0.007  0.078 15.690  0.004  4.116   7.1346e-02
   2_adp:   1.081  0.007  0.078 15.690  0.004  4.116   7.1346e-02
   2_occ:   1.081  0.007  0.078 15.690  0.004  4.116   7.1346e-02
   3_bss:   1.081  0.007  0.078 15.690  0.004  4.116   7.1346e-02
   3_xyz:   1.079  0.007  0.081 15.928  0.004  4.119   6.9123e-02
   3_adp:   1.079  0.007  0.081 15.928  0.004  4.119   6.9123e-02
   3_occ:   1.079  0.007  0.081 15.928  0.004  4.119   6.9123e-02
   4_bss:   1.079  0.007  0.081 15.928  0.004  4.119   6.9123e-02
   4_xyz:   0.882  0.005  0.067 15.548  0.003  4.119   5.1755e-02
   4_adp:   0.882  0.005  0.067 15.548  0.003  4.119   5.1755e-02
   4_occ:   0.882  0.005  0.067 15.548  0.003  4.119   5.1755e-02
   5_bss:   0.882  0.005  0.067 15.548  0.003  4.119   5.1755e-02
   5_xyz:   1.051  0.007  0.080 15.656  0.004  4.108   6.6239e-02
   5_adp:   1.051  0.007  0.080 15.656  0.004  4.108   6.6239e-02
   5_occ:   1.051  0.007  0.080 15.656  0.004  4.108   6.6239e-02
   5_bss:   1.051  0.007  0.080 15.656  0.004  4.108   6.6239e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9085e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9085e+00
   1_xyz:  12.893  0.160  0.397 87.133  0.030  2.188   9.2008e-02
   1_adp:  12.893  0.160  0.397 87.133  0.030  2.188   9.2008e-02
   1_occ:  12.893  0.160  0.397 87.133  0.030  2.188   9.2008e-02
   2_bss:  12.893  0.160  0.397 87.133  0.030  2.188   9.2008e-02
   2_xyz:   6.173  0.070  0.267 84.602  0.027  2.314   5.1682e-02
   2_adp:   6.173  0.070  0.267 84.602  0.027  2.314   5.1682e-02
   2_occ:   6.173  0.070  0.267 84.602  0.027  2.314   5.1682e-02
   3_bss:   6.173  0.070  0.267 84.602  0.027  2.314   5.1682e-02
   3_xyz:   7.950  0.052  0.341 84.619  0.035  2.299   5.6827e-02
   3_adp:   7.950  0.052  0.341 84.619  0.035  2.299   5.6827e-02
   3_occ:   7.950  0.052  0.341 84.619  0.035  2.299   5.6827e-02
   4_bss:   7.950  0.052  0.341 84.619  0.035  2.299   5.6827e-02
   4_xyz:   6.635  0.045  0.246 82.485  0.030  2.356   3.2498e-02
   4_adp:   6.635  0.045  0.246 82.485  0.030  2.356   3.2498e-02
   4_occ:   6.635  0.045  0.246 82.485  0.030  2.356   3.2498e-02
   5_bss:   6.635  0.045  0.246 82.485  0.030  2.356   3.2498e-02
   5_xyz:   7.044  0.051  0.323 84.480  0.039  2.275   5.0386e-02
   5_adp:   7.044  0.051  0.323 84.480  0.039  2.275   5.0386e-02
   5_occ:   7.044  0.051  0.323 84.480  0.039  2.275   5.0386e-02
   5_bss:   7.044  0.051  0.323 84.480  0.039  2.275   5.0386e-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:  73.33   0.00  12.51  67.65   0.00  10.09  73.33   0.00  25.73
   1_occ:  73.33   0.00  12.51  67.65   0.00  10.09  73.33   0.00  25.73
   2_bss:  73.33   0.00  12.51  67.65   0.00  10.09  73.33   0.00  25.73
   2_xyz:  73.33   0.00  12.51  67.65   0.00  10.09  73.33   0.00  25.73
   2_adp: 202.55   0.00  12.48 202.55   0.00   9.27  77.18   1.59  29.99
   2_occ: 202.55   0.00  12.48 202.55   0.00   9.27  77.18   1.59  29.99
   3_bss: 202.55   0.00  12.48 202.55   0.00   9.27  77.18   1.59  29.99
   3_xyz: 202.55   0.00  12.48 202.55   0.00   9.27  77.18   1.59  29.99
   3_adp: 151.35   0.00  13.48 151.35   0.00   8.88  89.04   1.71  38.53
   3_occ: 151.35   0.00  13.48 151.35   0.00   8.88  89.04   1.71  38.53
   4_bss: 151.35   0.00  13.48 151.35   0.00   8.88  89.04   1.71  38.53
   4_xyz: 151.35   0.00  13.48 151.35   0.00   8.88  89.04   1.71  38.53
   4_adp:  94.37   0.00  13.12  94.37   0.00   8.55  89.86   1.69  38.00
   4_occ:  94.37   0.00  13.12  94.37   0.00   8.55  89.86   1.69  38.00
   5_bss:  94.37   0.00  13.12  94.37   0.00   8.55  89.86   1.69  38.00
   5_xyz:  94.37   0.00  13.12  94.37   0.00   8.55  89.86   1.69  38.00
   5_adp:  96.99   0.00  12.69  96.99   0.00   8.29  87.28   1.37  36.69
   5_occ:  96.99   0.00  12.69  96.99   0.00   8.29  87.28   1.37  36.69
   5_bss:  99.69   2.70  15.40  99.69   2.70  10.99  89.98   4.07  39.40
------------------------------------------------------------------------
 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:    1.249    0.035    0.405
   1_adp:    1.249    0.035    0.405
   1_occ:    1.249    0.035    0.405
   2_bss:    1.249    0.035    0.405
   2_xyz:    1.543    0.029    0.537
   2_adp:    1.543    0.029    0.537
   2_occ:    1.543    0.029    0.537
   3_bss:    1.543    0.029    0.537
   3_xyz:    1.455    0.046    0.626
   3_adp:    1.455    0.046    0.626
   3_occ:    1.455    0.046    0.626
   4_bss:    1.455    0.046    0.626
   4_xyz:    1.608    0.024    0.646
   4_adp:    1.608    0.024    0.646
   4_occ:    1.608    0.024    0.646
   5_bss:    1.608    0.024    0.646
   5_xyz:    1.589    0.043    0.666
   5_adp:    1.589    0.043    0.666
   5_occ:    1.589    0.043    0.666
   5_bss:    1.589    0.043    0.666
------------------------------------------------------------------------

CPU time actual refinement: 347.89


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_391/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_391/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_391/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_391/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_391/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 347.74 
  Macro-tasks:
    bulk solvent and scale       = 43.15  
    individual site refinement   = 148.31 
    weights calculation          = 33.35  
    collect and process          = 6.68   
    model show statistics        = 0.15   
    TOTAL for macro-tasks        = 231.64 
  Micro-tasks:
    mask                            = 2.32   
    f_calc                          = 106.91 
    alpha_beta                      = 8.45   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 118.11 
    fmodel                         = 7.57   
    r_factors                      = 0.24   
    phase_errors                   = 10.74  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 255.79 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.842 micro seconds
Total CPU time: 6.02 minutes
from_scatterers_fft:    644 calls, 106.60 s
gradients_fft:          589 calls, 104.07 s

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

# Date 2008-01-16 Time 01:28:03 PST -0800 (1200475683.60 s)
Start R-work = 0.4630, R-free = 0.4575 (no bulk solvent and anisotropic scale)
Final R-work = 0.1292, R-free = 0.1751 (no bulk solvent and anisotropic scale)

Start R-work = 0.4546, R-free = 0.4418
Final R-work = 0.1116, R-free = 0.1590