# Date 2008-01-16 Time 03:15:32 PST -0800 (1200482132.17 s)
#phil __OFF__

Command line arguments: "../1167.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 = 28033
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1167

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.655, 47.3993, 84.6622, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 47.3993, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.124 1.96139
Completeness in resolution range: 0.921445
Completeness with d_max=infinity: 0.918722

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1240
                             d_min =   1.9614

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 47.3993, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.124 1.96139
Completeness in resolution range: 0.921445
Completeness with d_max=infinity: 0.918722

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1245 -  4.1984 [2230/2259]  2010   220   9.9%
  bin  2:  4.1984 -  3.3442 [2135/2158]  1920   215  10.1%
  bin  3:  3.3442 -  2.9250 [2111/2136]  1895   216  10.2%
  bin  4:  2.9250 -  2.6591 [2104/2120]  1899   205   9.7%
  bin  5:  2.6591 -  2.4694 [2065/2104]  1860   205   9.9%
  bin  6:  2.4694 -  2.3244 [2083/2116]  1872   211  10.1%
  bin  7:  2.3244 -  2.2083 [2050/2086]  1840   210  10.2%
  bin  8:  2.2083 -  2.1125 [2043/2085]  1843   200   9.8%
  bin  9:  2.1125 -  2.0313 [2047/2105]  1841   206  10.1%
  bin 10:  2.0313 -  1.9614 [ 721/2090]   650    71   9.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1167/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:
        1.75 -     2.38: 31
        2.38 -     3.01: 1973
        3.01 -     3.64: 4598
        3.64 -     4.27: 9085
        4.27 -     4.90: 12543
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.746 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.763 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.768 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " ND2 ASN A 215 " - " O   HOH Z 203 "  1.872 3.120 -x+1/2,-y+1,z-1/2
  ... (remaining 28225 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_1167/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1167/model_refine_001.geo

CPU time processing inputs: 9.04


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.655 47.3993 84.6622 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4860   r_free= 0.4830   ksol= 0.00   Bsol= 0.00   scale= 0.786    |
|                                                                             |
| 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:   0.82 A                  |
| x-ray target function (ml) for work reflections: 6.287632                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1245 -  4.6834 0.99   1446  165 0.3972 0.3827      6.6026      6.5745|
|  2:  4.6834 -  3.7358 0.99   1392  149 0.4016 0.4236      6.7986      6.8718|
|  3:  3.7358 -  3.2690 0.99   1362  153 0.4493 0.4089      6.6709      6.6506|
|  4:  3.2690 -  2.9726 0.99   1365  149 0.4763 0.4808      6.5113      6.5096|
|  5:  2.9726 -  2.7609 0.98   1339  152 0.5137 0.5473      6.3706      6.3732|
|  6:  2.7609 -  2.5990 0.99   1348  150 0.5181 0.5145       6.278      6.2242|
|  7:  2.5990 -  2.4694 0.99   1332  143 0.5253 0.4408      6.2482      6.1823|
|  8:  2.4694 -  2.3623 0.99   1329  152 0.5379 0.5372      6.1618      6.1918|
|  9:  2.3623 -  2.2717 0.99   1327  153 0.5367 0.5283      6.1457      6.0947|
| 10:  2.2717 -  2.1936 0.98   1326  147 0.5205 0.5371      6.0719      6.1166|
| 11:  2.1936 -  2.1252 0.98   1333  133 0.5217 0.5591      6.0341      6.0192|
| 12:  2.1252 -  2.0646 1.00   1303  156 0.5502 0.5648      5.9435      5.9777|
| 13:  2.0646 -  2.0103 0.83   1117  132 0.5418 0.5230      5.8704      5.8393|
| 14:  2.0103 -  1.9614 0.22    311   25 0.5672 0.5332      5.8199      5.8421|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1245 -  4.6834  1446   165  0.70  33.88   0.79     0.73      69811.38|
|  2:  4.6834 -  3.7358  1392   149  0.69  36.20   0.88     0.76     109396.64|
|  3:  3.7358 -  3.2690  1362   153  0.56  47.20   0.82     0.68     123358.34|
|  4:  3.2690 -  2.9726  1365   149  0.44  56.91   0.79     0.55     115676.75|
|  5:  2.9726 -  2.7609  1339   152  0.35  63.55   0.72     0.44      93388.40|
|  6:  2.7609 -  2.5990  1348   150  0.36  63.28   0.73     0.43      76527.83|
|  7:  2.5990 -  2.4694  1332   143  0.38  61.29   0.73     0.43      62338.44|
|  8:  2.4694 -  2.3623  1329   152  0.36  62.67   0.71     0.44      58102.74|
|  9:  2.3623 -  2.2717  1327   153  0.33  65.60   0.73     0.39      54506.71|
| 10:  2.2717 -  2.1936  1326   147  0.28  69.26   0.75     0.34      54981.63|
| 11:  2.1936 -  2.1252  1333   133  0.22  73.43   0.76     0.28      51562.07|
| 12:  2.1252 -  2.0646  1303   156  0.17  77.27   0.71     0.23      49552.69|
| 13:  2.0646 -  2.0103  1117   132  0.17  77.51   0.71     0.22      42561.20|
| 14:  2.0103 -  1.9614   311    25  0.19  75.94   0.68     0.24      34733.55|
|alpha:            min =        0.22 max =            0.76 mean =         0.46|
|beta:             min =    34733.55 max =       123358.34 mean =     73991.98|
|figures of merit: min =        0.00 max =            1.00 mean =         0.39|
|phase err.(work): min =        0.00 max =           89.99 mean =        60.37|
|phase err.(test): min =        0.00 max =           90.00 mean =        60.41|
|-----------------------------------------------------------------------------|

============================== 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 = 17.408812             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.971   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.526073              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.877   (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:       29 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      164 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      707 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1491 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2642 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3907 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5027 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6547 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7746 |
|-----------------------------------------------------------------------------|
|-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 |       53.822 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.905 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.014)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.014)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4906   r_free= 0.4885   ksol= 0.00   Bsol= 0.00   scale= 0.757    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.288727                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4777   r_free= 0.4720   ksol= 0.32   Bsol= 7.55   scale= 0.986    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.83,8.67,8.47,0.00,0.00,0.00); trace/3= 8.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.87 A                  |
| x-ray target function (ml) for work reflections: 6.286560                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.746646             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.165   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.291459              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.608   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4777      final r-factor (work) = 0.4042          |
| start r-factor (free) = 0.4720      final r-factor (free) = 0.4366          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 97.0227 = 13.75 * 0.50 * 6.2853 + 1.00 * 53.8216                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 42.8007 = 13.75 * 0.50 * 6.2047 + 1.00 * 0.1538                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4042      final r-factor (work) = 0.3676          |
| start r-factor (free) = 0.4366      final r-factor (free) = 0.4243          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.0275 = 1.29 * 1.00 * 6.2047 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.9510 = 1.29 * 1.00 * 6.1443 + 1.00 * 0.0159                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.014)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.00   13.05    None  None   None       |
|    all(noH): 2823   0      0.00    82.00   13.05    None  None   None       |
|    Sol.    : 438    0      0.00    82.00   24.88    None  None   None       |
|    Mac.    : 2385   0      0.00    77.58   10.87    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.200: 1187   |   5:    40.998 -  49.198:   39        |
|      1:     8.200 -  16.399:  857   |   6:    49.198 -  57.398:   27        |
|      2:    16.399 -  24.599:  384   |   7:    57.398 -  65.597:   14        |
|      3:    24.599 -  32.799:  200   |   8:    65.597 -  73.797:    6        |
|      4:    32.799 -  40.998:  104   |   9:    73.797 -  81.997:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3676 r_free = 0.4243             target_work(ml) = 6.128         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3670 r_free = 0.4252             target_work(ml) = 6.128         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3670   r_free= 0.4252   ksol= 0.32   Bsol= 7.55   scale= 1.090    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.83,8.67,8.47,0.00,0.00,0.00); trace/3= 8.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.128091                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3654   r_free= 0.4205   ksol= 0.33   Bsol= 37.34   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.35,5.51,5.90,0.00,0.00,0.00); trace/3= 5.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.127876                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.689124              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.012  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.696156              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.031  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3654      final r-factor (work) = 0.2791          |
| start r-factor (free) = 0.4205      final r-factor (free) = 0.3522          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.8309 = 8.69 * 0.50 * 6.1403 + 1.00 * 0.1538                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.2999 = 8.69 * 0.50 * 6.0344 + 1.00 * 0.0829                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2791      final r-factor (work) = 0.2582          |
| start r-factor (free) = 0.3522      final r-factor (free) = 0.3278          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2170 = 0.70 * 1.00 * 6.0344 + 1.00 * 0.0161                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1229 = 0.70 * 1.00 * 5.9051 + 1.00 * 0.0120                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.014)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.34   13.24    None  None   None       |
|    all(noH): 2823   0      0.00    81.34   13.24    None  None   None       |
|    Sol.    : 438    0      0.00    81.34   31.46    None  None   None       |
|    Mac.    : 2385   0      0.00    71.72   9.89     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.134: 1293   |   5:    40.669 -  48.803:   87        |
|      1:     8.134 -  16.268:  767   |   6:    48.803 -  56.937:   34        |
|      2:    16.268 -  24.402:  313   |   7:    56.937 -  65.071:   18        |
|      3:    24.402 -  32.535:  177   |   8:    65.071 -  73.205:    9        |
|      4:    32.535 -  40.669:  123   |   9:    73.205 -  81.338:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2582 r_free = 0.3278             target_work(ml) = 5.872         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2581 r_free = 0.3276             target_work(ml) = 5.871         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2581   r_free= 0.3276   ksol= 0.33   Bsol= 37.34   scale= 1.061   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.35,5.51,5.90,0.00,0.00,0.00); trace/3= 5.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.871216                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2561   r_free= 0.3239   ksol= 0.31   Bsol= 37.34   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.24,3.30,3.52,0.00,0.00,0.00); trace/3= 3.35                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.869726                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.512281              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.636  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.535709              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.537  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2561      final r-factor (work) = 0.1816          |
| start r-factor (free) = 0.3239      final r-factor (free) = 0.2374          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.3214 = 6.51 * 0.50 * 5.9084 + 1.00 * 0.0829                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.8123 = 6.51 * 0.50 * 5.7540 + 1.00 * 0.0765                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1816      final r-factor (work) = 0.1595          |
| start r-factor (free) = 0.2374      final r-factor (free) = 0.2159          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.8485 = 1.54 * 1.00 * 5.7540 + 1.00 * 0.0120                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.4680 = 1.54 * 1.00 * 5.5040 + 1.00 * 0.0155                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.014)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.12   14.44    None  None   None       |
|    all(noH): 2823   0      0.00    99.12   14.44    None  None   None       |
|    Sol.    : 438    0      0.66    98.49   40.81    None  None   None       |
|    Mac.    : 2385   0      0.00    99.12   9.60     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.912: 1633   |   5:    49.559 -  59.471:   71        |
|      1:     9.912 -  19.824:  616   |   6:    59.471 -  69.383:   62        |
|      2:    19.824 -  29.735:  168   |   7:    69.383 -  79.294:   24        |
|      3:    29.735 -  39.647:  118   |   8:    79.294 -  89.206:    7        |
|      4:    39.647 -  49.559:  118   |   9:    89.206 -  99.118:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1595 r_free = 0.2159             target_work(ml) = 5.461         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1593 r_free = 0.2157             target_work(ml) = 5.460         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1593   r_free= 0.2157   ksol= 0.31   Bsol= 37.34   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.24,3.30,3.52,0.00,0.00,0.00); trace/3= 3.35                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.459874                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1587   r_free= 0.2161   ksol= 0.32   Bsol= 51.14   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.11,2.19,2.23,0.00,0.00,0.00); trace/3= 2.18                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.459863                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.155210              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 111.846  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.410039              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.532  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1587      final r-factor (work) = 0.1330          |
| start r-factor (free) = 0.2161      final r-factor (free) = 0.1847          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.5276 = 4.16 * 0.50 * 5.5115 + 1.00 * 0.0769                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.2813 = 4.16 * 0.50 * 5.3942 + 1.00 * 0.0742                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1330      final r-factor (work) = 0.1278          |
| start r-factor (free) = 0.1847      final r-factor (free) = 0.1771          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2272 = 0.41 * 1.00 * 5.3942 + 1.00 * 0.0153                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1858 = 0.41 * 1.00 * 5.2907 + 1.00 * 0.0164                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.014)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.35  13.88    None  None   None       |
|    all(noH): 2823   0      0.00    100.35  13.88    None  None   None       |
|    Sol.    : 438    0      1.94    90.19   39.11    None  None   None       |
|    Mac.    : 2385   0      0.00    100.35  9.25     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.035: 1708   |   5:    50.174 -  60.209:   67        |
|      1:    10.035 -  20.070:  588   |   6:    60.209 -  70.244:   55        |
|      2:    20.070 -  30.105:  149   |   7:    70.244 -  80.279:   13        |
|      3:    30.105 -  40.140:  121   |   8:    80.279 -  90.314:    6        |
|      4:    40.140 -  50.174:  112   |   9:    90.314 - 100.349:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1278 r_free = 0.1771             target_work(ml) = 5.267         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1276 r_free = 0.1770             target_work(ml) = 5.266         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1276   r_free= 0.1770   ksol= 0.32   Bsol= 51.14   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.11,2.19,2.23,0.00,0.00,0.00); trace/3= 2.18                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.266217                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1281   r_free= 0.1776   ksol= 0.32   Bsol= 51.14   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.78,1.86,2.00,0.00,0.00,0.00); trace/3= 1.88                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.269368                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.898312              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 134.476  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.759409              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.801   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1281      final r-factor (work) = 0.1167          |
| start r-factor (free) = 0.1776      final r-factor (free) = 0.1659          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.3891 = 3.90 * 0.50 * 5.2920 + 1.00 * 0.0742                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2880 = 3.90 * 0.50 * 5.2357 + 1.00 * 0.0829                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1167      final r-factor (work) = 0.1148          |
| start r-factor (free) = 0.1659      final r-factor (free) = 0.1652          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9882 = 0.76 * 1.00 * 5.2357 + 1.00 * 0.0122                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9561 = 0.76 * 1.00 * 5.1929 + 1.00 * 0.0126                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.014)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.97  13.72    None  None   None       |
|    all(noH): 2823   0      0.00    102.97  13.72    None  None   None       |
|    Sol.    : 438    0      1.79    92.89   38.70    None  None   None       |
|    Mac.    : 2385   0      0.00    102.97  9.13     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.297: 1756   |   5:    51.484 -  61.780:   62        |
|      1:    10.297 -  20.594:  558   |   6:    61.780 -  72.077:   46        |
|      2:    20.594 -  30.890:  155   |   7:    72.077 -  82.374:   10        |
|      3:    30.890 -  41.187:  117   |   8:    82.374 -  92.671:    5        |
|      4:    41.187 -  51.484:  109   |   9:    92.671 - 102.967:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1148 r_free = 0.1652             target_work(ml) = 5.192         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1148 r_free = 0.1652             target_work(ml) = 5.192         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1148   r_free= 0.1652   ksol= 0.32   Bsol= 51.14   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.78,1.86,2.00,0.00,0.00,0.00); trace/3= 1.88                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.192430                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1245 -  4.6834 0.99   1446  165 0.0950 0.1288      5.3508       5.543|
|  2:  4.6834 -  3.7358 0.99   1392  149 0.0850 0.1100      5.4276      5.6742|
|  3:  3.7358 -  3.2690 0.99   1362  153 0.1082 0.1761      5.4868      5.9294|
|  4:  3.2690 -  2.9726 0.99   1365  149 0.1323 0.1546      5.5032      5.6285|
|  5:  2.9726 -  2.7609 0.98   1339  152 0.1366 0.1842      5.3774      5.5697|
|  6:  2.7609 -  2.5990 0.99   1348  150 0.1310 0.2020      5.2773      5.5446|
|  7:  2.5990 -  2.4694 0.99   1332  143 0.1294 0.1724      5.2136      5.4328|
|  8:  2.4694 -  2.3623 0.99   1329  152 0.1189 0.1769      5.0933      5.3321|
|  9:  2.3623 -  2.2717 0.99   1327  153 0.1155 0.2031      5.0517      5.3605|
| 10:  2.2717 -  2.1936 0.98   1326  147 0.1172 0.1733      5.0266      5.2665|
| 11:  2.1936 -  2.1252 0.98   1333  133 0.1205 0.2003      4.9832        5.34|
| 12:  2.1252 -  2.0646 1.00   1303  156 0.1165 0.1882      4.9193      5.1558|
| 13:  2.0646 -  2.0103 0.83   1117  132 0.1182 0.1789      4.8056      5.0334|
| 14:  2.0103 -  1.9614 0.22    311   25 0.1062 0.1691      4.6567      4.9464|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1245 -  4.6834  1446   165  0.94   8.73   0.97     0.95       6965.79|
|  2:  4.6834 -  3.7358  1392   149  0.95   8.06   1.01     0.99       8951.68|
|  3:  3.7358 -  3.2690  1362   153  0.93  12.18   1.03     1.02      11082.35|
|  4:  3.2690 -  2.9726  1365   149  0.90  15.88   1.00     0.98      11783.59|
|  5:  2.9726 -  2.7609  1339   152  0.89  17.65   0.99     0.96       9714.53|
|  6:  2.7609 -  2.5990  1348   150  0.89  17.77   0.98     0.96       8394.72|
|  7:  2.5990 -  2.4694  1332   143  0.89  16.94   0.99     0.96       7109.14|
|  8:  2.4694 -  2.3623  1329   152  0.90  16.72   0.98     0.94       5845.47|
|  9:  2.3623 -  2.2717  1327   153  0.89  17.38   1.00     0.97       5586.28|
| 10:  2.2717 -  2.1936  1326   147  0.90  16.77   0.99     0.96       5244.00|
| 11:  2.1936 -  2.1252  1333   133  0.89  17.71   0.99     0.95       4947.01|
| 12:  2.1252 -  2.0646  1303   156  0.89  17.43   1.00     0.99       4578.77|
| 13:  2.0646 -  2.0103  1117   132  0.89  17.52   0.99     0.97       3597.97|
| 14:  2.0103 -  1.9614   311    25  0.89  16.65   0.98     0.96       2713.69|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2713.69 max =        11783.59 mean =      7207.25|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.92 mean =        15.36|
|phase err.(test): min =        0.00 max =           88.81 mean =        14.70|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1147   r_free= 0.1652   ksol= 0.32   Bsol= 53.08   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.07,-0.03,0.10,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.192455                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.12 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1147   r_free= 0.1652   ksol= 0.32   Bsol= 53.08   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.07,-0.03,0.10,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.192455                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1245 -  4.6834 0.99   1446  165 0.0950 0.1288      5.3511      5.5435|
|  2:  4.6834 -  3.7358 0.99   1392  149 0.0850 0.1100      5.4278      5.6744|
|  3:  3.7358 -  3.2690 0.99   1362  153 0.1082 0.1762       5.487      5.9295|
|  4:  3.2690 -  2.9726 0.99   1365  149 0.1323 0.1546      5.5032      5.6284|
|  5:  2.9726 -  2.7609 0.98   1339  152 0.1366 0.1841      5.3773      5.5695|
|  6:  2.7609 -  2.5990 0.99   1348  150 0.1310 0.2020      5.2773      5.5447|
|  7:  2.5990 -  2.4694 0.99   1332  143 0.1294 0.1724      5.2138       5.433|
|  8:  2.4694 -  2.3623 0.99   1329  152 0.1189 0.1769      5.0934      5.3322|
|  9:  2.3623 -  2.2717 0.99   1327  153 0.1155 0.2032      5.0518      5.3606|
| 10:  2.2717 -  2.1936 0.98   1326  147 0.1172 0.1732      5.0266      5.2663|
| 11:  2.1936 -  2.1252 0.98   1333  133 0.1205 0.2002       4.983      5.3396|
| 12:  2.1252 -  2.0646 1.00   1303  156 0.1165 0.1881      4.9189      5.1554|
| 13:  2.0646 -  2.0103 0.83   1117  132 0.1182 0.1788      4.8055      5.0331|
| 14:  2.0103 -  1.9614 0.22    311   25 0.1062 0.1691      4.6566      4.9468|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1245 -  4.6834  1446   165  0.94   8.73   0.97     0.96       6970.76|
|  2:  4.6834 -  3.7358  1392   149  0.95   8.06   1.01     0.99       8957.18|
|  3:  3.7358 -  3.2690  1362   153  0.93  12.19   1.03     1.02      11088.34|
|  4:  3.2690 -  2.9726  1365   149  0.90  15.88   1.00     0.98      11782.43|
|  5:  2.9726 -  2.7609  1339   152  0.89  17.65   0.99     0.96       9714.03|
|  6:  2.7609 -  2.5990  1348   150  0.89  17.78   0.99     0.96       8394.84|
|  7:  2.5990 -  2.4694  1332   143  0.89  16.94   0.99     0.96       7110.04|
|  8:  2.4694 -  2.3623  1329   152  0.90  16.73   0.98     0.94       5846.70|
|  9:  2.3623 -  2.2717  1327   153  0.89  17.39   1.00     0.97       5586.44|
| 10:  2.2717 -  2.1936  1326   147  0.90  16.77   1.00     0.96       5243.85|
| 11:  2.1936 -  2.1252  1333   133  0.89  17.71   0.99     0.95       4944.92|
| 12:  2.1252 -  2.0646  1303   156  0.89  17.42   1.00     0.99       4575.08|
| 13:  2.0646 -  2.0103  1117   132  0.89  17.51   0.99     0.97       3596.31|
| 14:  2.0103 -  1.9614   311    25  0.89  16.64   0.98     0.96       2712.90|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2712.90 max =        11782.43 mean =      7208.05|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.92 mean =        15.36|
|phase err.(test): min =        0.00 max =           88.81 mean =        14.70|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.014)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.94    104.91  15.66    None  None   None       |
|    all(noH): 2823   0      1.94    104.91  15.66    None  None   None       |
|    Sol.    : 438    0      3.73    94.83   40.64    None  None   None       |
|    Mac.    : 2385   0      1.94    104.91  11.07    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.940 -  12.237: 1756   |   5:    53.424 -  63.720:   62        |
|      1:    12.237 -  22.533:  558   |   6:    63.720 -  74.017:   46        |
|      2:    22.533 -  32.830:  155   |   7:    74.017 -  84.314:   10        |
|      3:    32.830 -  43.127:  117   |   8:    84.314 -  94.611:    5        |
|      4:    43.127 -  53.424:  109   |   9:    94.611 - 104.907:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 334         
Filter by distance & map next to the model:
   mapped sites are within: 0.545 - 5.990
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 328 from: 334
   mapped sites are within: 0.776 - 5.990

peak=    9.357 closest distance to " CG2 VAL A 230 " =    1.374
peak=    7.408 closest distance to " CG2 VAL A 296 " =    1.113
peak=    6.211 closest distance to " O   HOH Z 111 " =    2.080
peak=    6.127 closest distance to " O   HOH Z  37 " =    1.398
peak=    6.120 closest distance to " CG  LEU A   5 " =    1.212
peak=    5.704 closest distance to " O   HOH Z 278 " =    1.164
peak=    5.289 closest distance to " CB  SER A  63 " =    1.353
peak=    5.285 closest distance to " CB  GLN A 223 " =    1.459
peak=    5.284 closest distance to " CD2 LEU A   5 " =    1.189
peak=    5.271 closest distance to " CG  LEU A 228 " =    1.209
peak=    5.102 closest distance to " CG  PRO A  54 " =    1.167
peak=    5.043 closest distance to " CB  VAL A 230 " =    1.294
peak=    4.957 closest distance to " O   HOH Z 126 " =    1.671
peak=    4.944 closest distance to " O   HOH Z 124 " =    1.400
peak=    4.942 closest distance to " O   HOH Z 247 " =    1.511
peak=    4.833 closest distance to " O   HOH Z  11 " =    1.288
peak=    4.816 closest distance to " O   HOH Z 277 " =    1.077
peak=    4.792 closest distance to " O   HOH Z  48 " =    1.890
peak=    4.728 closest distance to " CB  GLN A 183 " =    1.223
peak=    4.713 closest distance to " O   HOH Z 186 " =    1.248
peak=    4.595 closest distance to " O   HOH Z 132 " =    1.058
peak=    4.557 closest distance to " CB  PRO A  54 " =    0.783
peak=    4.532 closest distance to " CG  PRO A 213 " =    1.252
peak=    4.488 closest distance to " NE2 GLN A  11 " =    1.129
peak=    4.482 closest distance to " CB  GLU A 152 " =    1.137
peak=    4.480 closest distance to " O   HOH Z  80 " =    1.788
peak=    4.447 closest distance to " O   HOH Z  15 " =    2.258
peak=    4.418 closest distance to " O   HOH Z 403 " =    1.763
peak=    4.402 closest distance to " O   HOH Z 368 " =    2.166
peak=    4.386 closest distance to " O   HOH Z 371 " =    3.440
peak=    4.368 closest distance to " O   HOH Z 112 " =    1.401
peak=    4.344 closest distance to " OD1 ASN A  69 " =    2.564
peak=    4.340 closest distance to " O   HOH Z 128 " =    2.117
peak=    4.334 closest distance to " CB  VAL A 296 " =    1.087
peak=    4.312 closest distance to " O   HOH Z 295 " =    1.575
peak=    4.286 closest distance to " O   HOH Z 260 " =    1.255
peak=    4.285 closest distance to " O   HOH Z 369 " =    2.069
peak=    4.250 closest distance to " O   HOH Z  68 " =    1.904
peak=    4.230 closest distance to " O   HOH Z 280 " =    3.071
peak=    4.218 closest distance to " CB  TYR A 169 " =    0.865
peak=    4.212 closest distance to " CB  SER A   3 " =    1.439
peak=    4.209 closest distance to " O   HOH Z 108 " =    1.548
peak=    4.183 closest distance to " NH1 ARG A  56 " =    1.056
peak=    4.182 closest distance to " CD1 LEU A 300 " =    1.200
peak=    4.180 closest distance to " O   HOH Z  92 " =    1.019
peak=    4.176 closest distance to " O   HOH Z 232 " =    2.276
peak=    4.171 closest distance to " CG2 THR A 221 " =    1.004
peak=    4.151 closest distance to " O   HOH Z 272 " =    1.949
peak=    4.150 closest distance to " O   HOH Z 386 " =    2.155
peak=    4.150 closest distance to " CG1BVAL A  72 " =    1.654
peak=    4.144 closest distance to " O   HOH Z 236 " =    1.843
peak=    4.131 closest distance to " O   HOH Z  63 " =    1.406
peak=    4.129 closest distance to " OG BSER A 164 " =    2.186
peak=    4.122 closest distance to " O   PRO A 198 " =    1.480
peak=    4.119 closest distance to " O   HOH Z  20 " =    2.252
peak=    4.117 closest distance to " CB  ASN A 148 " =    1.268
peak=    4.116 closest distance to " CG  ARG A  66 " =    2.681
peak=    4.098 closest distance to " CA  TYR A  30 " =    0.982
peak=    4.093 closest distance to " O   HOH Z  97 " =    1.913
peak=    4.090 closest distance to " O   SER A  87 " =    2.332
peak=    4.084 closest distance to " O   HOH Z 411 " =    3.555
peak=    4.080 closest distance to " O   HOH Z 423 " =    1.844
peak=    4.060 closest distance to " O   HOH Z 193 " =    1.895
peak=    4.050 closest distance to " CG  PRO A 198 " =    1.439
peak=    4.049 closest distance to " O   HOH Z 303 " =    2.169
peak=    4.028 closest distance to " CA  ALA A  21 " =    1.261
peak=    4.026 closest distance to " NH2 ARG A 156 " =    1.221
peak=    4.012 closest distance to " OD2 ASP A 286 " =    2.883
peak=    4.010 closest distance to " CB  ARG A  79 " =    1.458
peak=    4.008 closest distance to " O   HOH Z  93 " =    2.680
peak=    4.003 closest distance to " O   HOH Z 163 " =    1.559
peak=    3.995 closest distance to " O   HOH Z 298 " =    1.807
peak=    3.987 closest distance to " CB  GLU A 277 " =    3.649
peak=    3.986 closest distance to " CB  VAL A 265 " =    1.262
peak=    3.980 closest distance to " O   HOH Z  78 " =    1.752
peak=    3.970 closest distance to " CD2 LEU A 228 " =    1.201
peak=    3.962 closest distance to " O   HOH Z 427 " =    3.117
peak=    3.962 closest distance to " O   HOH Z 389 " =    1.998
peak=    3.959 closest distance to " O   HOH Z 316 " =    2.864
peak=    3.938 closest distance to " O   HOH Z  54 " =    1.556
peak=    3.932 closest distance to " O   HOH Z 184 " =    1.395
peak=    3.926 closest distance to " O   HOH Z 116 " =    1.759
peak=    3.916 closest distance to " O   HOH Z 120 " =    1.078
peak=    3.911 closest distance to " CG1 ILE A  33 " =    1.243
peak=    3.907 closest distance to " CB  GLU A 128 " =    1.175
peak=    3.893 closest distance to " O   HOH Z 425 " =    1.436
peak=    3.891 closest distance to " O   HOH Z  30 " =    1.372
peak=    3.885 closest distance to " O   ASP A 132 " =    3.814
peak=    3.874 closest distance to " CB  VAL A 202 " =    1.562
peak=    3.871 closest distance to " O   HOH Z 180 " =    2.158
peak=    3.854 closest distance to " O   HOH Z 118 " =    1.715
peak=    3.830 closest distance to " O   ALA A 158 " =    1.368
peak=    3.817 closest distance to " O   HOH Z 271 " =    2.059
peak=    3.805 closest distance to " O   MET A 105 " =    1.899
peak=    3.801 closest distance to " O   HOH Z  88 " =    3.191
peak=    3.797 closest distance to " O   HOH Z  58 " =    1.536
peak=    3.793 closest distance to " CB  LEU A 228 " =    1.303
peak=    3.791 closest distance to " CB  ARG A 275 " =    0.852
peak=    3.787 closest distance to " O   HOH Z 426 " =    1.452
peak=    3.779 closest distance to " O   HOH Z 394 " =    1.702
peak=    3.773 closest distance to " O   HOH Z 313 " =    1.861
peak=    3.771 closest distance to " O   HOH Z  61 " =    1.554
peak=    3.743 closest distance to " CA  THR A 221 " =    0.889
peak=    3.740 closest distance to " CB  ALA A 100 " =    1.334
peak=    3.737 closest distance to " CD ALYS A 290 " =    1.048
peak=    3.730 closest distance to " NH2BARG A 145 " =    2.178
peak=    3.730 closest distance to " O   HOH Z 203 " =    1.679
peak=    3.704 closest distance to " OE1 GLN A  11 " =    1.820
peak=    3.703 closest distance to " O   HOH Z 132 " =    2.154
peak=    3.701 closest distance to " O   HOH Z 189 " =    2.598
peak=    3.698 closest distance to " O   HOH Z 276 " =    1.374
peak=    3.693 closest distance to " O   HOH Z 346 " =    1.465
peak=    3.686 closest distance to " O   HOH Z 281 " =    4.145
peak=    3.682 closest distance to " CB  TRP A 179 " =    1.403
peak=    3.679 closest distance to " CA  LYS A 117 " =    1.291
peak=    3.677 closest distance to " O   HOH Z 183 " =    1.373
peak=    3.672 closest distance to " O   HOH Z 263 " =    1.530
peak=    3.665 closest distance to " OD1 ASN A 217 " =    1.648
peak=    3.654 closest distance to " CG1 VAL A 153 " =    1.046
peak=    3.649 closest distance to " O   HOH Z 136 " =    1.233
peak=    3.648 closest distance to " NZ  LYS A 117 " =    3.271
peak=    3.648 closest distance to " NH2BARG A 102 " =    0.978
peak=    3.645 closest distance to " CA  ALA A 160 " =    0.850
peak=    3.644 closest distance to " CD2 LEU A 255 " =    1.420
peak=    3.637 closest distance to " O   HOH Z  49 " =    2.596
peak=    3.631 closest distance to " CD1 LEU A   5 " =    1.171
peak=    3.626 closest distance to " NZ  LYS A 166 " =    3.093
peak=    3.623 closest distance to " O   HOH Z 344 " =    2.909
peak=    3.622 closest distance to " O   HOH Z 102 " =    1.262
peak=    3.612 closest distance to " CD  ARG A 159 " =    0.874
peak=    3.610 closest distance to " O   HOH Z 355 " =    1.886
peak=    3.603 closest distance to " CZ  PHE A 192 " =    1.036
peak=    3.603 closest distance to " CA  ALA A  51 " =    1.053
peak=    3.603 closest distance to " O   HOH Z 134 " =    1.446
peak=    3.602 closest distance to " O   HOH Z  49 " =    1.944
peak=    3.601 closest distance to " O   HOH Z 126 " =    1.801
peak=    3.593 closest distance to " CA  ASP A 140 " =    1.253
peak=    3.580 closest distance to " CB  TYR A  30 " =    1.475
peak=    3.577 closest distance to " O   HOH Z 131 " =    2.472
peak=    3.572 closest distance to " CA  ALA A 295 " =    1.038
peak=    3.569 closest distance to " O   HOH Z   4 " =    1.886
peak=    3.565 closest distance to " CD  LYS A 119 " =    1.890
peak=    3.562 closest distance to " O   HOH Z  44 " =    2.371
peak=    3.562 closest distance to " O   HOH Z 329 " =    3.821
peak=    3.559 closest distance to " O   HOH Z 197 " =    2.106
peak=    3.559 closest distance to " OE1 GLN A  58 " =    1.206
peak=    3.558 closest distance to " O   HOH Z 243 " =    1.050
peak=    3.550 closest distance to " O   HOH Z 345 " =    3.393
peak=    3.549 closest distance to " N   ASN A  39 " =    1.357
peak=    3.548 closest distance to " O   HOH Z 387 " =    2.704
peak=    3.545 closest distance to " O   HOH Z 374 " =    2.551
peak=    3.536 closest distance to " OE1 GLN A  58 " =    5.835
peak=    3.534 closest distance to " CG AARG A 275 " =    1.079
peak=    3.533 closest distance to " O   HOH Z 420 " =    2.312
peak=    3.531 closest distance to " O   HOH Z 108 " =    2.036
peak=    3.529 closest distance to " CG  PRO A 280 " =    0.782
peak=    3.525 closest distance to " CB  SER A 216 " =    0.802
peak=    3.521 closest distance to " CB  ALA A   9 " =    1.566
peak=    3.512 closest distance to " CB  ALA A 248 " =    1.006
peak=    3.507 closest distance to " CD  ARG A 269 " =    0.865
peak=    3.505 closest distance to " CA  ASN A  74 " =    1.253
peak=    3.493 closest distance to " O   HOH Z 175 " =    3.626
peak=    3.492 closest distance to " O   HOH Z 327 " =    2.392
peak=    3.469 closest distance to " O   TRP A 274 " =    1.860
peak=    3.466 closest distance to " O   GLN A 278 " =    1.187
peak=    3.465 closest distance to " O   HOH Z 128 " =    2.152
peak=    3.462 closest distance to " O   HOH Z  40 " =    1.480
peak=    3.461 closest distance to " CB  ASP A 140 " =    0.801
peak=    3.460 closest distance to " CB  TRP A 266 " =    1.045
peak=    3.455 closest distance to " CG1 ILE A  49 " =    1.672
peak=    3.445 closest distance to " O   HOH Z 261 " =    1.850
peak=    3.444 closest distance to " CG BARG A 102 " =    1.951
peak=    3.441 closest distance to " CB  LEU A 143 " =    1.184
peak=    3.441 closest distance to " CG  GLN A  88 " =    1.047
peak=    3.438 closest distance to " O   HOH Z  21 " =    1.771
peak=    3.436 closest distance to " OD1 ASP A 231 " =    1.829
peak=    3.433 closest distance to " O   HOH Z 133 " =    1.801
peak=    3.429 closest distance to " O   HOH Z 422 " =    2.664
peak=    3.429 closest distance to " O   HOH Z  53 " =    2.546
peak=    3.421 closest distance to " ND1 HIS A  86 " =    1.667
peak=    3.421 closest distance to " O   HOH Z 383 " =    2.191
peak=    3.415 closest distance to " O   HOH Z 114 " =    1.461
peak=    3.413 closest distance to " CG2 THR A 220 " =    0.944
peak=    3.412 closest distance to " O   HOH Z 227 " =    1.859
peak=    3.401 closest distance to " O   HOH Z 214 " =    2.100
peak=    3.400 closest distance to " O   HOH Z 217 " =    1.417
peak=    3.399 closest distance to " O   HOH Z 434 " =    2.947
peak=    3.394 closest distance to " CD  LYS A 166 " =    1.393
peak=    3.393 closest distance to " CA  LEU A 282 " =    1.106
peak=    3.390 closest distance to " O   HOH Z 279 " =    2.304
peak=    3.390 closest distance to " ND1 HIS A  81 " =    1.572
peak=    3.390 closest distance to " O   HOH Z 332 " =    1.568
peak=    3.390 closest distance to " CA  ALA A 158 " =    1.135
peak=    3.389 closest distance to " O   HOH Z 174 " =    2.452
peak=    3.387 closest distance to " O   HOH Z 132 " =    2.716
peak=    3.383 closest distance to " O   HOH Z 437 " =    2.367
peak=    3.383 closest distance to " O   HOH Z 406 " =    1.691
peak=    3.377 closest distance to " CG  GLN A  58 " =    2.590
peak=    3.369 closest distance to " CB  ARG A 139 " =    0.877
peak=    3.361 closest distance to " O   HOH Z  85 " =    1.353
peak=    3.361 closest distance to " CA  MET A  40 " =    1.062
peak=    3.360 closest distance to " O   HOH Z 109 " =    2.623
peak=    3.354 closest distance to " CA  ASP A 191 " =    0.790
peak=    3.353 closest distance to " NH1 ARG A  14 " =    1.036
peak=    3.352 closest distance to " CB  LYS A 117 " =    1.161
peak=    3.346 closest distance to " O   HOH Z 207 " =    2.365
peak=    3.343 closest distance to " O   HOH Z  43 " =    2.319
peak=    3.339 closest distance to " CD2 HIS A  81 " =    1.063
peak=    3.334 closest distance to " O   HOH Z 171 " =    3.825
peak=    3.332 closest distance to " CA  VAL A 126 " =    1.139
peak=    3.331 closest distance to " O   HOH Z  54 " =    2.381
peak=    3.330 closest distance to " O   HOH Z 145 " =    1.899
peak=    3.325 closest distance to " CA  GLY A 267 " =    1.006
peak=    3.324 closest distance to " O   HOH Z 423 " =    3.283
peak=    3.316 closest distance to " CB  ILE A 120 " =    1.497
peak=    3.315 closest distance to " CD  ARG A  14 " =    1.244
peak=    3.313 closest distance to " CD1AILE A 234 " =    0.851
peak=    3.313 closest distance to " CB  LEU A 237 " =    0.886
peak=    3.312 closest distance to " O   HOH Z 184 " =    2.222
peak=    3.306 closest distance to " O   HOH Z 193 " =    1.517
peak=    3.304 closest distance to " O   HOH Z 155 " =    2.857
peak=    3.300 closest distance to " CG2 VAL A 296 " =    1.693
peak=    3.299 closest distance to " CG2 THR A  42 " =    0.894
peak=    3.297 closest distance to " OG  SER A  22 " =    2.910
peak=    3.295 closest distance to " O   HOH Z  48 " =    1.897
peak=    3.295 closest distance to " O   HOH Z 147 " =    1.699
peak=    3.294 closest distance to " O   HOH Z 221 " =    1.192
peak=    3.291 closest distance to " CD  GLU A 152 " =    0.889
peak=    3.289 closest distance to " CG1 VAL A 296 " =    1.133
peak=    3.289 closest distance to " O   ALA A 165 " =    1.290
peak=    3.287 closest distance to " O   HOH Z 211 " =    2.499
peak=    3.285 closest distance to " CG  MET A 188 " =    1.303
peak=    3.284 closest distance to " CA  ALA A 154 " =    1.331
peak=    3.283 closest distance to " CG1 ILE A 151 " =    1.174
peak=    3.278 closest distance to " O   HOH Z  38 " =    1.995
peak=    3.277 closest distance to " CG BARG A 275 " =    1.519
peak=    3.275 closest distance to " O   HOH Z 244 " =    1.636
peak=    3.270 closest distance to " O   HOH Z 328 " =    1.769
peak=    3.270 closest distance to " CA  LEU A 101 " =    1.639
peak=    3.265 closest distance to " O   HOH Z 155 " =    1.538
peak=    3.263 closest distance to " CD1 ILE A  33 " =    1.567
peak=    3.262 closest distance to " O   HOH Z 215 " =    1.557
peak=    3.260 closest distance to " CD1 LEU A 101 " =    1.195
peak=    3.260 closest distance to " CD1 LEU A 228 " =    1.350
peak=    3.259 closest distance to " CG2 VAL A 174 " =    1.344
peak=    3.257 closest distance to " O   HOH Z 407 " =    3.480
peak=    3.256 closest distance to " O   HOH Z 172 " =    5.990
peak=    3.256 closest distance to " NH1AARG A 145 " =    0.967
peak=    3.254 closest distance to " CE  LYS A 166 " =    1.964
peak=    3.252 closest distance to " O   HOH Z 345 " =    1.602
peak=    3.252 closest distance to " CB  GLU A 152 " =    1.456
peak=    3.251 closest distance to " OG  SER A  62 " =    3.058
peak=    3.248 closest distance to " O   HOH Z 277 " =    2.307
peak=    3.246 closest distance to " O   ALA A   1 " =    1.522
peak=    3.245 closest distance to " O   HOH Z  99 " =    2.817
peak=    3.243 closest distance to " O   HOH Z 388 " =    1.842
peak=    3.242 closest distance to " O   HOH Z 149 " =    2.031
peak=    3.240 closest distance to " O   HOH Z 156 " =    2.748
peak=    3.239 closest distance to " CB  MET A  40 " =    0.780
peak=    3.236 closest distance to " O   HOH Z  98 " =    2.132
peak=    3.236 closest distance to " O   HOH Z 361 " =    3.379
peak=    3.234 closest distance to " CA  ASN A 215 " =    1.177
peak=    3.233 closest distance to " CG  PRO A 243 " =    1.212
peak=    3.230 closest distance to " O   ASN A 217 " =    1.326
peak=    3.227 closest distance to " NH2 ARG A  79 " =    1.352
peak=    3.226 closest distance to " CB  ASN A  39 " =    0.777
peak=    3.224 closest distance to " CA  GLY A 211 " =    1.194
peak=    3.224 closest distance to " CB  ARG A 190 " =    1.683
peak=    3.223 closest distance to " O   HOH Z 280 " =    1.595
peak=    3.221 closest distance to " CZ  PHE A 218 " =    1.031
peak=    3.221 closest distance to " CB  ALA A 256 " =    1.318
peak=    3.218 closest distance to " CG  GLN A  55 " =    2.116
peak=    3.217 closest distance to " C   SER A  32 " =    1.041
peak=    3.216 closest distance to " CD  ARG A 195 " =    0.939
peak=    3.216 closest distance to " CA  ARG A 195 " =    1.221
peak=    3.214 closest distance to " CB  ASN A 187 " =    1.085
peak=    3.210 closest distance to " CD1 TRP A 266 " =    1.145
peak=    3.210 closest distance to " N   ALA A 256 " =    0.937
peak=    3.210 closest distance to " OD2 ASP A 298 " =    4.157
peak=    3.208 closest distance to " CB  SER A  62 " =    1.262
peak=    3.206 closest distance to " CB  SER A 141 " =    0.988
peak=    3.200 closest distance to " O   HOH Z 150 " =    3.317
peak=    3.200 closest distance to " O   HOH Z 185 " =    1.777
peak=    3.199 closest distance to " O   HOH Z 350 " =    1.561
peak=    3.195 closest distance to " O   THR A  31 " =    1.500
peak=    3.195 closest distance to " CA  TYR A 116 " =    1.600
peak=    3.191 closest distance to " CA  VAL A  41 " =    0.952
peak=    3.190 closest distance to " O   HOH Z 128 " =    1.936
peak=    3.190 closest distance to " CA  ARG A  36 " =    1.141
peak=    3.184 closest distance to " CB  LYS A 193 " =    1.191
peak=    3.184 closest distance to " O   HOH Z 290 " =    1.050
peak=    3.182 closest distance to " O   TRP A  70 " =    1.401
peak=    3.180 closest distance to " O   HOH Z 144 " =    1.476
peak=    3.178 closest distance to " O   HOH Z  90 " =    3.137
peak=    3.177 closest distance to " CB  THR A 157 " =    1.021
peak=    3.174 closest distance to " O   HOH Z 282 " =    2.063
peak=    3.172 closest distance to " O   HOH Z  66 " =    1.785
peak=    3.170 closest distance to " O   HOH Z 197 " =    2.538
peak=    3.166 closest distance to " CB  THR A  31 " =    1.608
peak=    3.161 closest distance to " CB  THR A 235 " =    0.970
peak=    3.153 closest distance to " CB  ALA A  71 " =    1.293
peak=    3.140 closest distance to " O   HOH Z 395 " =    1.368
peak=    3.138 closest distance to " CA  ILE A  33 " =    1.563
peak=    3.138 closest distance to " O   HOH Z 438 " =    2.197
peak=    3.135 closest distance to " CB  GLN A  89 " =    1.075
peak=    3.135 closest distance to " CD  ARG A 195 " =    3.444
peak=    3.133 closest distance to " CA  SER A  32 " =    1.547
peak=    3.133 closest distance to " O   HOH Z  13 " =    1.478
peak=    3.130 closest distance to " NE2 GLN A  58 " =    4.077
peak=    3.128 closest distance to " C   ALA A 299 " =    0.966
peak=    3.128 closest distance to " CG  LEU A 167 " =    1.158
peak=    3.126 closest distance to " O   HOH Z  64 " =    2.031
peak=    3.126 closest distance to " O   HOH Z  44 " =    1.713
peak=    3.124 closest distance to " CB  ALA A 291 " =    1.445
peak=    3.117 closest distance to " CB  SER A 212 " =    1.155
peak=    3.107 closest distance to " O   HOH Z  10 " =    1.893
peak=    3.102 closest distance to " CD  LYS A 119 " =    2.331
peak=    3.098 closest distance to " O   HOH Z 166 " =    1.545
peak=    3.097 closest distance to " OE1 GLU A   2 " =    2.189
peak=    3.096 closest distance to " O   HOH Z 420 " =    5.668
peak=    3.096 closest distance to " ND2 ASN A 187 " =    1.606
peak=    3.096 closest distance to " CB  THR A  52 " =    1.065
peak=    3.090 closest distance to " CB  LEU A 255 " =    0.776
peak=    3.089 closest distance to " CA  GLY A  75 " =    1.325
peak=    3.077 closest distance to " O   HOH Z  46 " =    1.486
peak=    3.073 closest distance to " CA  THR A 264 " =    0.824
peak=    3.072 closest distance to " O   HOH Z  66 " =    2.189
peak=    3.039 closest distance to " CG2 VAL A 257 " =    0.778

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 205         
Filter by distance & map next to the model:
   mapped sites are within: 0.830 - 5.386
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 204 from: 205
   mapped sites are within: 0.830 - 5.386

peak=   -5.103 closest distance to " CG2 VAL A 230 " =    0.966
peak=   -4.470 closest distance to " O   HOH Z 266 " =    4.353
peak=   -4.421 closest distance to " OG ASER A 134 " =    1.243
peak=   -4.393 closest distance to " O   ILE A 109 " =    2.659
peak=   -4.351 closest distance to " O   HOH Z 231 " =    1.803
peak=   -4.244 closest distance to " O   HOH Z  19 " =    2.069
peak=   -4.225 closest distance to " O   HOH Z  52 " =    1.623
peak=   -4.199 closest distance to " CD  ARG A 156 " =    1.973
peak=   -4.124 closest distance to " O   HOH Z  13 " =    1.349
peak=   -4.054 closest distance to " O   HOH Z 377 " =    1.901
peak=   -4.050 closest distance to " O   HOH Z  17 " =    1.387
peak=   -4.028 closest distance to " O   HOH Z 407 " =    3.439
peak=   -4.018 closest distance to " CD  GLN A  88 " =    2.304
peak=   -4.005 closest distance to " CD2 LEU A 143 " =    2.600
peak=   -4.003 closest distance to " OE2 GLU A   2 " =    1.753
peak=   -3.979 closest distance to " CD  LYS A 289 " =    2.451
peak=   -3.979 closest distance to " NH2 ARG A  66 " =    1.578
peak=   -3.968 closest distance to " O   HOH Z 290 " =    1.160
peak=   -3.964 closest distance to " O   HOH Z 166 " =    1.913
peak=   -3.958 closest distance to " CD2 LEU A 237 " =    2.730
peak=   -3.954 closest distance to " OG1 THR A   4 " =    1.929
peak=   -3.921 closest distance to " O   HOH Z 184 " =    1.247
peak=   -3.897 closest distance to " O   HOH Z 151 " =    1.447
peak=   -3.870 closest distance to " OG  SER A  87 " =    1.542
peak=   -3.834 closest distance to " N   ALA A 226 " =    2.040
peak=   -3.830 closest distance to " CD2 LEU A 300 " =    2.915
peak=   -3.823 closest distance to " O   HOH Z  15 " =    1.646
peak=   -3.810 closest distance to " CG  GLN A 223 " =    2.353
peak=   -3.801 closest distance to " CG1 VAL A 112 " =    2.604
peak=   -3.786 closest distance to " O   HOH Z  11 " =    1.715
peak=   -3.770 closest distance to " OG BSER A 134 " =    1.829
peak=   -3.765 closest distance to " CG2BVAL A  41 " =    2.748
peak=   -3.761 closest distance to " O   HOH Z 275 " =    1.579
peak=   -3.755 closest distance to " CB  CYS A 254 " =    2.371
peak=   -3.753 closest distance to " CD2 TYR A 293 " =    2.080
peak=   -3.747 closest distance to " O   HOH Z 252 " =    4.109
peak=   -3.741 closest distance to " CG  ASP A 231 " =    0.857
peak=   -3.735 closest distance to " CE2 TYR A  30 " =    2.743
peak=   -3.735 closest distance to " CD1 PHE A  59 " =    1.849
peak=   -3.722 closest distance to " O   HOH Z 292 " =    4.463
peak=   -3.721 closest distance to " O   HOH Z 243 " =    1.707
peak=   -3.719 closest distance to " C   HIS A 108 " =    1.155
peak=   -3.715 closest distance to " CG  MET A 105 " =    0.926
peak=   -3.694 closest distance to " CH2 TRP A 179 " =    1.188
peak=   -3.694 closest distance to " O   HOH Z 103 " =    1.914
peak=   -3.690 closest distance to " C   ASN A 187 " =    1.835
peak=   -3.690 closest distance to " O   HOH Z  43 " =    1.560
peak=   -3.687 closest distance to " C   ALA A 158 " =    1.232
peak=   -3.687 closest distance to " CG1 VAL A 296 " =    1.309
peak=   -3.674 closest distance to " O   HOH Z 266 " =    4.783
peak=   -3.659 closest distance to " O   HOH Z 388 " =    1.866
peak=   -3.654 closest distance to " O   HOH Z 234 " =    4.377
peak=   -3.648 closest distance to " CA  SER A 164 " =    2.089
peak=   -3.637 closest distance to " O   HOH Z 353 " =    2.370
peak=   -3.629 closest distance to " CB  PRO A 163 " =    2.712
peak=   -3.627 closest distance to " OG  SER A  26 " =    1.316
peak=   -3.622 closest distance to " CD  ARG A 139 " =    1.595
peak=   -3.600 closest distance to " O   HOH Z 274 " =    2.881
peak=   -3.599 closest distance to " CG2 VAL A 112 " =    2.547
peak=   -3.587 closest distance to " CD2 LEU A 167 " =    1.746
peak=   -3.578 closest distance to " O   HOH Z 189 " =    2.151
peak=   -3.572 closest distance to " O   HOH Z 166 " =    1.627
peak=   -3.571 closest distance to " O   HOH Z 377 " =    1.269
peak=   -3.564 closest distance to " CB  ALA A 248 " =    1.931
peak=   -3.564 closest distance to " O   HOH Z 184 " =    1.447
peak=   -3.558 closest distance to " O   HOH Z 241 " =    1.234
peak=   -3.554 closest distance to " CG  GLU A  53 " =    1.662
peak=   -3.551 closest distance to " CB  TYR A  15 " =    2.236
peak=   -3.544 closest distance to " N   ALA A  43 " =    2.507
peak=   -3.538 closest distance to " O   HOH Z  38 " =    1.423
peak=   -3.536 closest distance to " O   SER A 271 " =    2.266
peak=   -3.533 closest distance to " O   HOH Z 221 " =    1.305
peak=   -3.532 closest distance to " ND2 ASN A  60 " =    1.582
peak=   -3.528 closest distance to " N   GLN A  58 " =    1.626
peak=   -3.525 closest distance to " OD1 ASN A 148 " =    1.630
peak=   -3.521 closest distance to " O   HOH Z 102 " =    1.019
peak=   -3.520 closest distance to " O   GLY A 211 " =    1.513
peak=   -3.497 closest distance to " O   HOH Z  71 " =    1.118
peak=   -3.496 closest distance to " O   HOH Z 385 " =    3.852
peak=   -3.490 closest distance to " SG  CYS A 254 " =    3.190
peak=   -3.481 closest distance to " CD  GLN A  88 " =    0.830
peak=   -3.480 closest distance to " OG  SER A  97 " =    2.269
peak=   -3.468 closest distance to " CG  ASN A  45 " =    1.734
peak=   -3.462 closest distance to " CG  ASP A  50 " =    2.291
peak=   -3.460 closest distance to " OG BSER A 134 " =    1.320
peak=   -3.458 closest distance to " CA  ASN A 127 " =    1.022
peak=   -3.449 closest distance to " CD1 LEU A 228 " =    2.491
peak=   -3.448 closest distance to " N   SER A 276 " =    1.409
peak=   -3.445 closest distance to " NH1 ARG A 195 " =    2.667
peak=   -3.442 closest distance to " O   HOH Z  97 " =    1.716
peak=   -3.441 closest distance to " O   HOH Z 389 " =    1.789
peak=   -3.437 closest distance to " C   GLN A 240 " =    2.263
peak=   -3.434 closest distance to " CG  PRO A 163 " =    2.506
peak=   -3.430 closest distance to " O   HOH Z 165 " =    2.088
peak=   -3.427 closest distance to " O   HOH Z  98 " =    2.006
peak=   -3.427 closest distance to " O   HOH Z 292 " =    2.929
peak=   -3.422 closest distance to " O   HOH Z 113 " =    1.835
peak=   -3.415 closest distance to " O   ASN A 301 " =    1.499
peak=   -3.415 closest distance to " N   THR A 157 " =    1.603
peak=   -3.409 closest distance to " O   HOH Z 426 " =    1.753
peak=   -3.404 closest distance to " O   HOH Z 396 " =    1.613
peak=   -3.402 closest distance to " NH1 ARG A  56 " =    2.438
peak=   -3.401 closest distance to " O   HOH Z 283 " =    1.938
peak=   -3.399 closest distance to " OG  SER A  63 " =    1.455
peak=   -3.396 closest distance to " SG ACYS A 201 " =    2.042
peak=   -3.376 closest distance to " O   HOH Z 120 " =    4.018
peak=   -3.365 closest distance to " NH2AARG A 275 " =    5.386
peak=   -3.363 closest distance to " O   HOH Z  37 " =    1.497
peak=   -3.363 closest distance to " CA  GLY A 203 " =    2.205
peak=   -3.361 closest distance to " O   HOH Z 108 " =    2.293
peak=   -3.359 closest distance to " CG  TRP A 266 " =    1.747
peak=   -3.356 closest distance to " NH1 ARG A 195 " =    2.288
peak=   -3.351 closest distance to " O   VAL A 125 " =    2.193
peak=   -3.345 closest distance to " C   LEU A 143 " =    1.311
peak=   -3.336 closest distance to " CA  ASN A 142 " =    1.335
peak=   -3.335 closest distance to " O   HOH Z  92 " =    1.282
peak=   -3.335 closest distance to " O   HOH Z  90 " =    1.410
peak=   -3.329 closest distance to " CB  ALA A  43 " =    2.519
peak=   -3.329 closest distance to " NH2 ARG A 159 " =    2.471
peak=   -3.328 closest distance to " CG2 VAL A 296 " =    1.433
peak=   -3.328 closest distance to " CB  SER A 245 " =    2.337
peak=   -3.327 closest distance to " N   THR A 235 " =    1.303
peak=   -3.318 closest distance to " CD1 ILE A 263 " =    2.453
peak=   -3.317 closest distance to " CA  ASP A 298 " =    1.076
peak=   -3.313 closest distance to " CA  GLY A 241 " =    2.252
peak=   -3.311 closest distance to " CG  GLU A 152 " =    2.329
peak=   -3.309 closest distance to " CZ  TYR A 172 " =    1.607
peak=   -3.303 closest distance to " C   LEU A 255 " =    1.789
peak=   -3.299 closest distance to " CE1 TYR A 169 " =    2.580
peak=   -3.298 closest distance to " CA  GLY A 133 " =    2.271
peak=   -3.294 closest distance to " CB  ALA A 227 " =    2.347
peak=   -3.281 closest distance to " O   HOH Z 431 " =    1.615
peak=   -3.281 closest distance to " O   HOH Z 147 " =    2.036
peak=   -3.277 closest distance to " CB  GLN A  55 " =    1.486
peak=   -3.276 closest distance to " O   HOH Z 128 " =    2.478
peak=   -3.269 closest distance to " O   ALA A 256 " =    1.611
peak=   -3.268 closest distance to " CG  ARG A  66 " =    2.388
peak=   -3.268 closest distance to " OD1 ASP A 191 " =    1.678
peak=   -3.267 closest distance to " O   HOH Z  10 " =    1.604
peak=   -3.261 closest distance to " CE3 TRP A  70 " =    1.730
peak=   -3.258 closest distance to " CD1 LEU A 101 " =    2.835
peak=   -3.257 closest distance to " N   GLN A 122 " =    1.658
peak=   -3.256 closest distance to " O   HOH Z  98 " =    1.485
peak=   -3.249 closest distance to " O   HOH Z 411 " =    3.492
peak=   -3.248 closest distance to " O   HOH Z 177 " =    1.549
peak=   -3.248 closest distance to " OH  TYR A 169 " =    1.044
peak=   -3.240 closest distance to " O   GLY A 196 " =    1.157
peak=   -3.238 closest distance to " CB  GLN A  11 " =    1.992
peak=   -3.234 closest distance to " CD  ARG A 195 " =    4.976
peak=   -3.233 closest distance to " O   VAL A  67 " =    2.629
peak=   -3.225 closest distance to " C   ASN A 285 " =    2.473
peak=   -3.221 closest distance to " NE  ARG A 138 " =    2.049
peak=   -3.220 closest distance to " O   HOH Z 186 " =    1.394
peak=   -3.218 closest distance to " OD2 ASP A  65 " =    1.598
peak=   -3.216 closest distance to " O   VAL A 197 " =    1.486
peak=   -3.215 closest distance to " ND2 ASN A  60 " =    1.508
peak=   -3.214 closest distance to " CB  PRO A 243 " =    2.661
peak=   -3.209 closest distance to " N   GLY A  23 " =    2.126
peak=   -3.207 closest distance to " CA  GLY A 241 " =    3.059
peak=   -3.202 closest distance to " OD2 ASP A 171 " =    2.279
peak=   -3.200 closest distance to " O   HOH Z 250 " =    1.490
peak=   -3.195 closest distance to " CA  GLY A 133 " =    1.933
peak=   -3.194 closest distance to " CD1 LEU A   5 " =    2.578
peak=   -3.191 closest distance to " O   HOH Z 385 " =    2.169
peak=   -3.187 closest distance to " O   ASP A 191 " =    1.432
peak=   -3.183 closest distance to " OD2 ASP A 171 " =    1.861
peak=   -3.183 closest distance to " O   HOH Z 423 " =    2.253
peak=   -3.181 closest distance to " N   ALA A 248 " =    2.027
peak=   -3.180 closest distance to " O   HOH Z 311 " =    3.799
peak=   -3.172 closest distance to " O   HOH Z 211 " =    1.478
peak=   -3.167 closest distance to " C   ALA A   8 " =    1.485
peak=   -3.163 closest distance to " O   PRO A 198 " =    1.294
peak=   -3.156 closest distance to " O   SER A 135 " =    1.478
peak=   -3.155 closest distance to " O   HOH Z 426 " =    2.374
peak=   -3.153 closest distance to " NE  ARG A 259 " =    1.210
peak=   -3.150 closest distance to " O   HOH Z   9 " =    1.949
peak=   -3.149 closest distance to " O   HOH Z  60 " =    1.703
peak=   -3.148 closest distance to " O   HOH Z  60 " =    2.047
peak=   -3.146 closest distance to " CG  GLN A  58 " =    1.153
peak=   -3.143 closest distance to " CZ  TYR A 169 " =    1.851
peak=   -3.137 closest distance to " OXT GLY A 302 " =    3.408
peak=   -3.126 closest distance to " CG  ARG A 269 " =    2.265
peak=   -3.123 closest distance to " CB  ASP A 286 " =    2.284
peak=   -3.122 closest distance to " CD2 LEU A 237 " =    2.776
peak=   -3.118 closest distance to " OE1 GLN A  88 " =    1.034
peak=   -3.113 closest distance to " ND2 ASN A 173 " =    1.823
peak=   -3.103 closest distance to " O   PRO A 198 " =    1.314
peak=   -3.101 closest distance to " ND2 ASN A 215 " =    2.144
peak=   -3.100 closest distance to " N   PHE A  59 " =    2.120
peak=   -3.097 closest distance to " CG  ARG A 259 " =    2.506
peak=   -3.087 closest distance to " CE  MET A 105 " =    2.051
peak=   -3.084 closest distance to " O   HOH Z 345 " =    2.200
peak=   -3.082 closest distance to " O   HOH Z  48 " =    1.347
peak=   -3.077 closest distance to " O   HOH Z   1 " =    4.019
peak=   -3.073 closest distance to " O   ALA A 158 " =    1.128
peak=   -3.070 closest distance to " O   HOH Z 351 " =    1.459
peak=   -3.060 closest distance to " CB  SER A 258 " =    2.097
peak=   -3.059 closest distance to " CG  LYS A 166 " =    2.198
peak=   -3.058 closest distance to " O   HOH Z 246 " =    1.412
peak=   -3.056 closest distance to " CB  ALA A 100 " =    2.077
peak=   -3.034 closest distance to " O   HOH Z 198 " =    1.790
peak=   -3.033 closest distance to " CB  ALA A 114 " =    2.251
peak=   -3.032 closest distance to " CB  TRP A  85 " =    2.409
peak=   -3.010 closest distance to " ND2 ASN A  45 " =    0.970

================= 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    :  0.4860 0.4830   6.287632e+00   6.281408e+00
   1_bss:  0.4777 0.4720   6.286560e+00   6.277438e+00
   1_xyz:  0.4042 0.4366   6.186439e+00   6.232816e+00
   1_adp:  0.3676 0.4243   6.128162e+00   6.214410e+00
   1_occ:  0.3670 0.4252   6.128091e+00   6.214699e+00
   2_bss:  0.3654 0.4205   6.127876e+00   6.212710e+00
   2_xyz:  0.2791 0.3522   5.935530e+00   6.094174e+00
   2_adp:  0.2582 0.3278   5.872097e+00   6.041979e+00
   2_occ:  0.2581 0.3276   5.871216e+00   6.041440e+00
   3_bss:  0.2561 0.3239   5.869726e+00   6.038256e+00
   3_xyz:  0.1816 0.2374   5.560739e+00   5.771221e+00
   3_adp:  0.1595 0.2159   5.460577e+00   5.690809e+00
   3_occ:  0.1593 0.2157   5.459874e+00   5.690181e+00
   4_bss:  0.1587 0.2161   5.459863e+00   5.690364e+00
   4_xyz:  0.1330 0.1847   5.302850e+00   5.544835e+00
   4_adp:  0.1278 0.1771   5.266681e+00   5.503046e+00
   4_occ:  0.1276 0.1770   5.266217e+00   5.502703e+00
   5_bss:  0.1281 0.1776   5.269368e+00   5.505666e+00
   5_xyz:  0.1167 0.1659   5.199284e+00   5.447829e+00
   5_adp:  0.1148 0.1652   5.192327e+00   5.445490e+00
   5_occ:  0.1148 0.1652   5.192430e+00   5.445873e+00
   5_bss:  0.1147 0.1652   5.192455e+00   5.445870e+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:  0.319   7.555   8.835   8.669   8.467   0.000   0.000   0.000
   1_xyz:  0.319   7.555   8.835   8.669   8.467   0.000   0.000   0.000
   1_adp:  0.319   7.555   8.835   8.669   8.467   0.000   0.000   0.000
   1_occ:  0.319   7.555   8.835   8.669   8.467   0.000   0.000   0.000
   2_bss:  0.329  37.340   5.354   5.512   5.903   0.000   0.000   0.000
   2_xyz:  0.329  37.340   5.354   5.512   5.903   0.000   0.000   0.000
   2_adp:  0.329  37.340   5.354   5.512   5.903   0.000   0.000   0.000
   2_occ:  0.329  37.340   5.354   5.512   5.903   0.000   0.000   0.000
   3_bss:  0.314  37.341   3.240   3.299   3.519   0.000   0.000   0.000
   3_xyz:  0.314  37.341   3.240   3.299   3.519   0.000   0.000   0.000
   3_adp:  0.314  37.341   3.240   3.299   3.519   0.000   0.000   0.000
   3_occ:  0.314  37.341   3.240   3.299   3.519   0.000   0.000   0.000
   4_bss:  0.324  51.137   2.112   2.189   2.231   0.000   0.000   0.000
   4_xyz:  0.324  51.137   2.112   2.189   2.231   0.000   0.000   0.000
   4_adp:  0.324  51.137   2.112   2.189   2.231   0.000   0.000   0.000
   4_occ:  0.324  51.137   2.112   2.189   2.231   0.000   0.000   0.000
   5_bss:  0.324  51.137   1.783   1.862   1.996   0.000   0.000   0.000
   5_xyz:  0.324  51.137   1.783   1.862   1.996   0.000   0.000   0.000
   5_adp:  0.324  51.137   1.783   1.862   1.996   0.000   0.000   0.000
   5_occ:  0.324  51.137   1.783   1.862   1.996   0.000   0.000   0.000
   5_bss:  0.324  53.077  -0.067  -0.029   0.096   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  60.372 0.3881  0.4575    73986.607
   1_bss:  60.976 0.3778  0.5605    71652.177
   1_xyz:  54.597 0.4582  0.6667    58509.046
   1_adp:  50.963 0.5049  0.7785    53674.693
   1_occ:  51.225 0.5015  0.7720    54030.834
   2_bss:  50.737 0.5077  0.7099    53410.591
   2_xyz:  38.745 0.6559  0.9137    35358.533
   2_adp:  35.108 0.6990  0.9659    30024.450
   2_occ:  35.056 0.6996  0.9665    29946.843
   3_bss:  34.823 0.7020  0.8952    29604.331
   3_xyz:  23.662 0.8238  0.9910    14584.713
   3_adp:  21.279 0.8484  0.9976    12302.400
   3_occ:  21.267 0.8485  0.9974    12281.235
   4_bss:  21.253 0.8487  0.9574    12299.703
   4_xyz:  17.653 0.8831  0.9769     8931.636
   4_adp:  16.611 0.8928  0.9788     8228.283
   4_occ:  16.602 0.8930  0.9787     8227.176
   5_bss:  16.660 0.8925  0.9681     8312.358
   5_xyz:  15.369 0.9036  0.9727     7247.920
   5_adp:  15.294 0.9043  0.9686     7201.102
   5_occ:  15.297 0.9043  0.9684     7207.097
   5_bss:  15.298 0.9043  0.9705     7207.895
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.3822e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.3822e+01
   1_xyz:   1.784  0.014  0.111 18.202  0.007  4.110   1.5378e-01
   1_adp:   1.784  0.014  0.111 18.202  0.007  4.110   1.5378e-01
   1_occ:   1.784  0.014  0.111 18.202  0.007  4.110   1.5378e-01
   2_bss:   1.784  0.014  0.111 18.202  0.007  4.110   1.5378e-01
   2_xyz:   1.147  0.008  0.079 16.179  0.005  4.114   8.2918e-02
   2_adp:   1.147  0.008  0.079 16.179  0.005  4.114   8.2918e-02
   2_occ:   1.147  0.008  0.079 16.179  0.005  4.114   8.2918e-02
   3_bss:   1.147  0.008  0.079 16.179  0.005  4.114   8.2918e-02
   3_xyz:   1.162  0.008  0.085 15.635  0.005  4.138   7.6520e-02
   3_adp:   1.162  0.008  0.085 15.635  0.005  4.138   7.6520e-02
   3_occ:   1.162  0.008  0.085 15.635  0.005  4.138   7.6520e-02
   4_bss:   1.162  0.008  0.085 15.635  0.005  4.138   7.6520e-02
   4_xyz:   1.135  0.008  0.085 15.685  0.004  4.126   7.4211e-02
   4_adp:   1.135  0.008  0.085 15.685  0.004  4.126   7.4211e-02
   4_occ:   1.135  0.008  0.085 15.685  0.004  4.126   7.4211e-02
   5_bss:   1.135  0.008  0.085 15.685  0.004  4.126   7.4211e-02
   5_xyz:   1.199  0.010  0.092 15.651  0.004  4.112   8.2881e-02
   5_adp:   1.199  0.010  0.092 15.651  0.004  4.112   8.2881e-02
   5_occ:   1.199  0.010  0.092 15.651  0.004  4.112   8.2881e-02
   5_bss:   1.199  0.010  0.092 15.651  0.004  4.112   8.2881e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9767e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9767e+00
   1_xyz:  15.718  0.179  0.506 85.563  0.055  2.164   1.0644e-01
   1_adp:  15.718  0.179  0.506 85.563  0.055  2.164   1.0644e-01
   1_occ:  15.718  0.179  0.506 85.563  0.055  2.164   1.0644e-01
   2_bss:  15.718  0.179  0.506 85.563  0.055  2.164   1.0644e-01
   2_xyz:   7.104  0.075  0.276 82.335  0.034  2.121   6.7529e-02
   2_adp:   7.104  0.075  0.276 82.335  0.034  2.121   6.7529e-02
   2_occ:   7.104  0.075  0.276 82.335  0.034  2.121   6.7529e-02
   3_bss:   7.104  0.075  0.276 82.335  0.034  2.121   6.7529e-02
   3_xyz:   7.792  0.055  0.392 82.167  0.044  2.312   5.5296e-02
   3_adp:   7.792  0.055  0.392 82.167  0.044  2.312   5.5296e-02
   3_occ:   7.792  0.055  0.392 82.167  0.044  2.312   5.5296e-02
   4_bss:   7.792  0.055  0.392 82.167  0.044  2.312   5.5296e-02
   4_xyz:   7.931  0.049  0.509 82.642  0.031  2.309   5.2139e-02
   4_adp:   7.931  0.049  0.509 82.642  0.031  2.309   5.2139e-02
   4_occ:   7.931  0.049  0.509 82.642  0.031  2.309   5.2139e-02
   5_bss:   7.931  0.049  0.509 82.642  0.031  2.309   5.2139e-02
   5_xyz:   7.746  0.053  0.656 83.222  0.035  2.280   6.2413e-02
   5_adp:   7.746  0.053  0.656 83.222  0.035  2.280   6.2413e-02
   5_occ:   7.746  0.053  0.656 83.222  0.035  2.280   6.2413e-02
   5_bss:   7.746  0.053  0.656 83.222  0.035  2.280   6.2413e-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:  82.00   0.00  13.05  77.58   0.00  10.87  82.00   0.00  24.88
   1_occ:  82.00   0.00  13.05  77.58   0.00  10.87  82.00   0.00  24.88
   2_bss:  82.00   0.00  13.05  77.58   0.00  10.87  82.00   0.00  24.88
   2_xyz:  82.00   0.00  13.05  77.58   0.00  10.87  82.00   0.00  24.88
   2_adp:  81.34   0.00  13.24  71.72   0.00   9.89  81.34   0.00  31.46
   2_occ:  81.34   0.00  13.24  71.72   0.00   9.89  81.34   0.00  31.46
   3_bss:  81.34   0.00  13.24  71.72   0.00   9.89  81.34   0.00  31.46
   3_xyz:  81.34   0.00  13.24  71.72   0.00   9.89  81.34   0.00  31.46
   3_adp:  99.12   0.00  14.44  99.12   0.00   9.60  98.49   0.66  40.81
   3_occ:  99.12   0.00  14.44  99.12   0.00   9.60  98.49   0.66  40.81
   4_bss:  99.12   0.00  14.44  99.12   0.00   9.60  98.49   0.66  40.81
   4_xyz:  99.12   0.00  14.44  99.12   0.00   9.60  98.49   0.66  40.81
   4_adp: 100.35   0.00  13.88 100.35   0.00   9.25  90.19   1.94  39.11
   4_occ: 100.35   0.00  13.88 100.35   0.00   9.25  90.19   1.94  39.11
   5_bss: 100.35   0.00  13.88 100.35   0.00   9.25  90.19   1.94  39.11
   5_xyz: 100.35   0.00  13.88 100.35   0.00   9.25  90.19   1.94  39.11
   5_adp: 102.97   0.00  13.72 102.97   0.00   9.13  92.89   1.79  38.70
   5_occ: 102.97   0.00  13.72 102.97   0.00   9.13  92.89   1.79  38.70
   5_bss: 104.91   1.94  15.66 104.91   1.94  11.07  94.83   3.73  40.64
------------------------------------------------------------------------
 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:    1.221    0.035    0.417
   1_adp:    1.221    0.035    0.417
   1_occ:    1.221    0.035    0.417
   2_bss:    1.221    0.035    0.417
   2_xyz:    1.792    0.054    0.582
   2_adp:    1.792    0.054    0.582
   2_occ:    1.792    0.054    0.582
   3_bss:    1.792    0.054    0.582
   3_xyz:    1.756    0.064    0.712
   3_adp:    1.756    0.064    0.712
   3_occ:    1.756    0.064    0.712
   4_bss:    1.756    0.064    0.712
   4_xyz:    1.719    0.030    0.752
   4_adp:    1.719    0.030    0.752
   4_occ:    1.719    0.030    0.752
   5_bss:    1.719    0.030    0.752
   5_xyz:    1.775    0.034    0.777
   5_adp:    1.775    0.034    0.777
   5_occ:    1.775    0.034    0.777
   5_bss:    1.775    0.034    0.777
------------------------------------------------------------------------

CPU time actual refinement: 346.69


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1167/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_1167/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1167/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1167/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1167/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 346.54 
  Macro-tasks:
    bulk solvent and scale       = 40.67  
    individual site refinement   = 144.41 
    weights calculation          = 32.33  
    collect and process          = 6.30   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 223.82 
  Micro-tasks:
    mask                            = 2.50   
    f_calc                          = 111.29 
    alpha_beta                      = 8.05   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 119.89 
    fmodel                         = 6.83   
    r_factors                      = 0.19   
    phase_errors                   = 10.22  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 260.37 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.928 micro seconds
Total CPU time: 6.00 minutes
from_scatterers_fft:    625 calls, 110.96 s
gradients_fft:          569 calls, 107.21 s

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

# Date 2008-01-16 Time 03:21:31 PST -0800 (1200482491.67 s)
Start R-work = 0.4860, R-free = 0.4830 (no bulk solvent and anisotropic scale)
Final R-work = 0.1310, R-free = 0.1821 (no bulk solvent and anisotropic scale)

Start R-work = 0.4777, R-free = 0.4720
Final R-work = 0.1147, R-free = 0.1652