# Date 2008-01-16 Time 02:32:09 PST -0800 (1200479529.22 s)
#phil __OFF__

Command line arguments: "../870.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 29125
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 870

-------------------------------------------------------------------------------
  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: (70.9525, 46.2261, 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: 3.28, per 1000 atoms: 1.16


================================== 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: (70.9525, 46.2261, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0179 1.96103
Completeness in resolution range: 0.953607
Completeness with d_max=infinity: 0.950738

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0179
                             d_min =   1.9610

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: (70.9525, 46.2261, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0179 1.96103
Completeness in resolution range: 0.953607
Completeness with d_max=infinity: 0.950738

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0183 -  4.1971 [2155/2181]  1943   212   9.8%
  bin  2:  4.1971 -  3.3434 [2080/2099]  1871   209  10.0%
  bin  3:  3.3434 -  2.9243 [2035/2054]  1829   206  10.1%
  bin  4:  2.9243 -  2.6586 [2024/2054]  1826   198   9.8%
  bin  5:  2.6586 -  2.4689 [2037/2056]  1831   206  10.1%
  bin  6:  2.4689 -  2.3239 [1990/2015]  1786   204  10.3%
  bin  7:  2.3239 -  2.2079 [1998/2026]  1801   197   9.9%
  bin  8:  2.2079 -  2.1121 [1984/2020]  1791   193   9.7%
  bin  9:  2.1121 -  2.0310 [1976/2018]  1776   200  10.1%
  bin 10:  2.0310 -  1.9610 [1310/2019]  1176   134  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_870/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: 0.17 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:
        1.72 -     2.35: 34
        2.35 -     2.99: 1886
        2.99 -     3.63: 4681
        3.63 -     4.26: 9266
        4.26 -     4.90: 12793
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.716 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 206 " - " O   HOH Z 341 "  1.835 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.900 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.969 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28655 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_870/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_870/model_refine_001.geo

CPU time processing inputs: 9.20


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 46.22605 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 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4927   r_free= 0.4800   ksol= 0.00   Bsol= 0.00   scale= 0.792    |
|                                                                             |
| 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:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.289199                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.6816 0.99   1400  158 0.4114 0.4301      6.6041      6.6531|
|  2:  4.6816 -  3.7348 0.99   1349  143 0.4213 0.3944      6.8264      6.7717|
|  3:  3.7348 -  3.2682 0.99   1315  147 0.4541 0.4196      6.6852      6.7657|
|  4:  3.2682 -  2.9719 0.99   1329  157 0.4827 0.4392      6.5551      6.4926|
|  5:  2.9719 -  2.7603 0.99   1297  139 0.5209 0.5209      6.3772      6.3563|
|  6:  2.7603 -  2.5985 0.99   1298  148 0.5184 0.5327      6.2862       6.295|
|  7:  2.5985 -  2.4689 0.99   1312  139 0.5274 0.4553      6.2653      6.1691|
|  8:  2.4689 -  2.3619 0.98   1263  145 0.5432 0.4975      6.1737      6.1736|
|  9:  2.3619 -  2.2713 0.98   1291  149 0.5201 0.5169       6.129       6.138|
| 10:  2.2713 -  2.1931 0.99   1282  137 0.5338 0.5683      6.1047      6.1187|
| 11:  2.1931 -  2.1248 0.98   1280  137 0.5284 0.5099      6.0454      6.0501|
| 12:  2.1248 -  2.0642 0.97   1257  144 0.5233 0.5645       5.972      6.0256|
| 13:  2.0642 -  2.0100 0.99   1273  142 0.5517 0.5337      5.8834      5.8182|
| 14:  2.0100 -  1.9610 0.52    684   74 0.5730 0.5516      5.8476      5.8035|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0183 -  4.6816  1400   158  0.64  39.34   0.79     0.70      88391.53|
|  2:  4.6816 -  3.7348  1349   143  0.68  37.03   0.87     0.77     118970.31|
|  3:  3.7348 -  3.2682  1315   147  0.57  46.01   0.84     0.72     123549.77|
|  4:  3.2682 -  2.9719  1329   157  0.50  52.22   0.80     0.61     108452.42|
|  5:  2.9719 -  2.7603  1297   139  0.38  61.09   0.74     0.47      87401.18|
|  6:  2.7603 -  2.5985  1298   148  0.37  62.36   0.72     0.43      76254.17|
|  7:  2.5985 -  2.4689  1312   139  0.36  63.14   0.74     0.41      65928.21|
|  8:  2.4689 -  2.3619  1263   145  0.35  63.36   0.71     0.44      59831.95|
|  9:  2.3619 -  2.2713  1291   149  0.36  63.03   0.74     0.41      53657.50|
| 10:  2.2713 -  2.1931  1282   137  0.32  65.81   0.75     0.40      51685.34|
| 11:  2.1931 -  2.1248  1280   137  0.28  69.15   0.77     0.35      50207.18|
| 12:  2.1248 -  2.0642  1257   144  0.25  71.29   0.77     0.32      46923.02|
| 13:  2.0642 -  2.0100  1273   142  0.21  74.10   0.73     0.28      40883.88|
| 14:  2.0100 -  1.9610   684    74  0.21  74.76   0.69     0.24      34013.38|
|alpha:            min =        0.24 max =            0.77 mean =         0.48|
|beta:             min =    34013.38 max =       123549.77 mean =     73700.13|
|figures of merit: min =        0.00 max =            1.00 mean =         0.40|
|phase err.(work): min =        0.00 max =           90.00 mean =        59.40|
|phase err.(test): min =        0.00 max =           89.98 mean =        59.49|
|-----------------------------------------------------------------------------|

============================== 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 = 17.709210             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.343   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.588470              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.135   (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:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       30 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      173 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      712 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1544 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2659 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3992 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5117 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6653 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7792 |
|-----------------------------------------------------------------------------|
|-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 |       53.212 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.088    4.900  1.196 |       1.962 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.620)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.620)------------------------------------------|
|    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 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4964   r_free= 0.4831   ksol= 0.00   Bsol= 0.00   scale= 0.762    |
|                                                                             |
| 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:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.290993                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4831   r_free= 0.4674   ksol= 0.39   Bsol= 20.00   scale= 0.965   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.19,8.07,7.62,0.00,0.00,0.00); trace/3= 7.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.284114                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.782387             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.505   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.351780              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.377   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4831      final r-factor (work) = 0.4095          |
| start r-factor (free) = 0.4674      final r-factor (free) = 0.4321          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 96.5208 = 13.78 * 0.50 * 6.2846 + 1.00 * 53.2122                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 42.9717 = 13.78 * 0.50 * 6.2146 + 1.00 * 0.1456                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4095      final r-factor (work) = 0.3705          |
| start r-factor (free) = 0.4321      final r-factor (free) = 0.4275          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.4151 = 1.35 * 1.00 * 6.2146 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.3277 = 1.35 * 1.00 * 6.1477 + 1.00 * 0.0173                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.620)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.13   14.08    None  None   None       |
|    all(noH): 2823   0      0.00    96.13   14.08    None  None   None       |
|    Sol.    : 438    0      0.00    91.25   25.29    None  None   None       |
|    Mac.    : 2385   0      0.00    96.13   12.02    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.613: 1267   |   5:    48.065 -  57.678:   38        |
|      1:     9.613 -  19.226:  846   |   6:    57.678 -  67.291:   12        |
|      2:    19.226 -  28.839:  387   |   7:    67.291 -  76.904:    2        |
|      3:    28.839 -  38.452:  174   |   8:    76.904 -  86.517:    2        |
|      4:    38.452 -  48.065:   90   |   9:    86.517 -  96.130:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3705 r_free = 0.4275             target_work(ml) = 6.138         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3703 r_free = 0.4274             target_work(ml) = 6.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3703   r_free= 0.4274   ksol= 0.39   Bsol= 20.00   scale= 1.085   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.19,8.07,7.62,0.00,0.00,0.00); trace/3= 7.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.137295                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3689   r_free= 0.4235   ksol= 0.35   Bsol= 38.28   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.58,4.57,5.19,0.00,0.00,0.00); trace/3= 4.45                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.137481                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.804958              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.025   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.574400              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.218  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3689      final r-factor (work) = 0.2873          |
| start r-factor (free) = 0.4235      final r-factor (free) = 0.3403          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.1227 = 7.80 * 0.50 * 6.1441 + 1.00 * 0.1456                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.6645 = 7.80 * 0.50 * 6.0415 + 1.00 * 0.0877                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2873      final r-factor (work) = 0.2639          |
| start r-factor (free) = 0.3403      final r-factor (free) = 0.3270          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4876 = 0.57 * 1.00 * 6.0415 + 1.00 * 0.0173                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4159 = 0.57 * 1.00 * 5.8987 + 1.00 * 0.0277                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.620)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.58   14.15    None  None   None       |
|    all(noH): 2823   0      0.00    94.58   14.15    None  None   None       |
|    Sol.    : 438    0      0.00    91.57   30.71    None  None   None       |
|    Mac.    : 2385   0      0.00    94.58   11.10    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 -   9.458: 1327   |   5:    47.289 -  56.746:   38        |
|      1:     9.458 -  18.916:  778   |   6:    56.746 -  66.204:   14        |
|      2:    18.916 -  28.373:  349   |   7:    66.204 -  75.662:    0        |
|      3:    28.373 -  37.831:  201   |   8:    75.662 -  85.120:    2        |
|      4:    37.831 -  47.289:  109   |   9:    85.120 -  94.577:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2639 r_free = 0.3270             target_work(ml) = 5.879         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2636 r_free = 0.3272             target_work(ml) = 5.878         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2636   r_free= 0.3272   ksol= 0.35   Bsol= 38.28   scale= 1.067   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.58,4.57,5.19,0.00,0.00,0.00); trace/3= 4.45                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.878327                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2623   r_free= 0.3252   ksol= 0.33   Bsol= 38.28   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.06,2.25,3.00,0.00,0.00,0.00); trace/3= 2.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.877909                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.530398              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.208  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.176470              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.514   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2623      final r-factor (work) = 0.1922          |
| start r-factor (free) = 0.3252      final r-factor (free) = 0.2476          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.4534 = 4.53 * 0.50 * 5.9005 + 1.00 * 0.0877                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.1217 = 4.53 * 0.50 * 5.7607 + 1.00 * 0.0726                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1922      final r-factor (work) = 0.1682          |
| start r-factor (free) = 0.2476      final r-factor (free) = 0.2296          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.7909 = 1.18 * 1.00 * 5.7607 + 1.00 * 0.0136                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5463 = 1.18 * 1.00 * 5.5527 + 1.00 * 0.0137                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 34     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.620)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.92   14.61    None  None   None       |
|    all(noH): 2823   0      0.00    97.92   14.61    None  None   None       |
|    Sol.    : 438    0      1.94    96.34   38.76    None  None   None       |
|    Mac.    : 2385   0      0.00    97.92   10.18    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 -   9.792: 1559   |   5:    48.959 -  58.751:   94        |
|      1:     9.792 -  19.584:  636   |   6:    58.751 -  68.543:   33        |
|      2:    19.584 -  29.376:  204   |   7:    68.543 -  78.335:    9        |
|      3:    29.376 -  39.167:  139   |   8:    78.335 -  88.127:    1        |
|      4:    39.167 -  48.959:  143   |   9:    88.127 -  97.918:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1682 r_free = 0.2296             target_work(ml) = 5.507         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1680 r_free = 0.2291             target_work(ml) = 5.506         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1680   r_free= 0.2291   ksol= 0.33   Bsol= 38.28   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.06,2.25,3.00,0.00,0.00,0.00); trace/3= 2.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.505779                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1677   r_free= 0.2277   ksol= 0.32   Bsol= 38.28   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.50,1.15,2.11,0.00,0.00,0.00); trace/3= 1.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.502256                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.091067              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.463   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.681185              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.868  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1677      final r-factor (work) = 0.1437          |
| start r-factor (free) = 0.2277      final r-factor (free) = 0.1958          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8820 = 2.09 * 0.50 * 5.5564 + 1.00 * 0.0726                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7409 = 2.09 * 0.50 * 5.4408 + 1.00 * 0.0524                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1437      final r-factor (work) = 0.1368          |
| start r-factor (free) = 0.1958      final r-factor (free) = 0.1894          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.6013 = 2.68 * 1.00 * 5.4408 + 1.00 * 0.0135                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 14.3316 = 2.68 * 1.00 * 5.3398 + 1.00 * 0.0147                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.620)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.99  15.01    None  None   None       |
|    all(noH): 2823   0      0.00    109.99  15.01    None  None   None       |
|    Sol.    : 438    0      3.06    100.03  42.34    None  None   None       |
|    Mac.    : 2385   0      0.00    109.99  9.99     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.999: 1746   |   5:    54.996 -  65.995:   84        |
|      1:    10.999 -  21.998:  539   |   6:    65.995 -  76.994:   41        |
|      2:    21.998 -  32.998:  165   |   7:    76.994 -  87.993:    9        |
|      3:    32.998 -  43.997:  117   |   8:    87.993 -  98.993:    6        |
|      4:    43.997 -  54.996:  113   |   9:    98.993 - 109.992:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1368 r_free = 0.1894             target_work(ml) = 5.323         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1367 r_free = 0.1892             target_work(ml) = 5.322         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1367   r_free= 0.1892   ksol= 0.32   Bsol= 38.28   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.50,1.15,2.11,0.00,0.00,0.00); trace/3= 1.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.322121                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1371   r_free= 0.1901   ksol= 0.32   Bsol= 44.45   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.34,0.93,1.83,0.00,0.00,0.00); trace/3= 1.37                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.322855                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.722937              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 122.923  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.689173              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.624  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1371      final r-factor (work) = 0.1258          |
| start r-factor (free) = 0.1901      final r-factor (free) = 0.1767          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6526 = 1.72 * 0.50 * 5.3399 + 1.00 * 0.0524                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6082 = 1.72 * 0.50 * 5.2875 + 1.00 * 0.0532                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1258      final r-factor (work) = 0.1233          |
| start r-factor (free) = 0.1767      final r-factor (free) = 0.1710          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6586 = 0.69 * 1.00 * 5.2875 + 1.00 * 0.0146                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6248 = 0.69 * 1.00 * 5.2412 + 1.00 * 0.0127                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.620)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.91  14.55    None  None   None       |
|    all(noH): 2823   0      0.00    110.91  14.55    None  None   None       |
|    Sol.    : 438    0      2.84    97.18   40.59    None  None   None       |
|    Mac.    : 2385   0      0.00    110.91  9.77     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 -  11.091: 1790   |   5:    55.453 -  66.544:   57        |
|      1:    11.091 -  22.181:  529   |   6:    66.544 -  77.635:   36        |
|      2:    22.181 -  33.272:  153   |   7:    77.635 -  88.725:    9        |
|      3:    33.272 -  44.363:  123   |   8:    88.725 -  99.816:    8        |
|      4:    44.363 -  55.453:  116   |   9:    99.816 - 110.906:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1233 r_free = 0.1710             target_work(ml) = 5.223         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1232 r_free = 0.1707             target_work(ml) = 5.222         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1232   r_free= 0.1707   ksol= 0.32   Bsol= 44.45   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.34,0.93,1.83,0.00,0.00,0.00); trace/3= 1.37                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.222380                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.6816 0.99   1400  158 0.1007 0.1329      5.3957       5.567|
|  2:  4.6816 -  3.7348 0.99   1349  143 0.0912 0.1258      5.4938      5.7486|
|  3:  3.7348 -  3.2682 0.99   1315  147 0.1176 0.1571      5.5646      5.8713|
|  4:  3.2682 -  2.9719 0.99   1329  157 0.1368 0.1795      5.5516      5.7049|
|  5:  2.9719 -  2.7603 0.99   1297  139 0.1462 0.1867      5.3961      5.5835|
|  6:  2.7603 -  2.5985 0.99   1298  148 0.1336 0.1873      5.2861      5.5317|
|  7:  2.5985 -  2.4689 0.99   1312  139 0.1400 0.1826      5.2568       5.432|
|  8:  2.4689 -  2.3619 0.98   1263  145 0.1309 0.1907      5.1341      5.4454|
|  9:  2.3619 -  2.2713 0.98   1291  149 0.1282 0.1983      5.1062      5.3983|
| 10:  2.2713 -  2.1931 0.99   1282  137 0.1241 0.1867      5.0242      5.2347|
| 11:  2.1931 -  2.1248 0.98   1280  137 0.1285 0.1966       5.034      5.3904|
| 12:  2.1248 -  2.0642 0.97   1257  144 0.1205 0.1725      4.9591      5.1668|
| 13:  2.0642 -  2.0100 0.99   1273  142 0.1334 0.1918       4.883      5.1292|
| 14:  2.0100 -  1.9610 0.52    684   74 0.1182 0.1778        4.74      4.9977|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0183 -  4.6816  1400   158  0.94   9.33   0.98     0.96       7537.40|
|  2:  4.6816 -  3.7348  1349   143  0.95   8.79   1.03     1.01      10176.97|
|  3:  3.7348 -  3.2682  1315   147  0.92  12.77   1.04     1.04      12339.45|
|  4:  3.2682 -  2.9719  1329   157  0.91  15.36   1.02     0.99      12167.67|
|  5:  2.9719 -  2.7603  1297   139  0.89  17.17   1.00     0.97       9246.79|
|  6:  2.7603 -  2.5985  1298   148  0.89  17.51   0.99     0.96       8322.38|
|  7:  2.5985 -  2.4689  1312   139  0.89  17.40   1.00     0.97       7499.64|
|  8:  2.4689 -  2.3619  1263   145  0.89  17.19   0.99     0.95       5861.53|
|  9:  2.3619 -  2.2713  1291   149  0.90  16.28   1.01     1.00       5734.43|
| 10:  2.2713 -  2.1931  1282   137  0.89  16.62   1.01     0.98       4955.22|
| 11:  2.1931 -  2.1248  1280   137  0.88  18.24   1.00     0.97       5267.01|
| 12:  2.1248 -  2.0642  1257   144  0.90  16.74   1.02     1.01       4730.67|
| 13:  2.0642 -  2.0100  1273   142  0.89  17.98   1.00     0.99       3902.82|
| 14:  2.0100 -  1.9610   684    74  0.90  16.25   1.00     0.98       2980.26|
|alpha:            min =        0.95 max =            1.04 mean =         0.98|
|beta:             min =     2980.26 max =        12339.45 mean =      7383.28|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.90 mean =        15.45|
|phase err.(test): min =        0.00 max =           89.85 mean =        14.78|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1232   r_free= 0.1707   ksol= 0.32   Bsol= 45.82   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.03,-0.44,0.47,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.222382                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1232   r_free= 0.1707   ksol= 0.32   Bsol= 45.82   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.03,-0.44,0.47,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.222382                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.6816 0.99   1400  158 0.1007 0.1329      5.3957       5.567|
|  2:  4.6816 -  3.7348 0.99   1349  143 0.0912 0.1258      5.4938      5.7485|
|  3:  3.7348 -  3.2682 0.99   1315  147 0.1176 0.1571      5.5645      5.8713|
|  4:  3.2682 -  2.9719 0.99   1329  157 0.1368 0.1795      5.5516      5.7049|
|  5:  2.9719 -  2.7603 0.99   1297  139 0.1462 0.1867      5.3961      5.5835|
|  6:  2.7603 -  2.5985 0.99   1298  148 0.1336 0.1873      5.2861      5.5317|
|  7:  2.5985 -  2.4689 0.99   1312  139 0.1400 0.1826      5.2568       5.432|
|  8:  2.4689 -  2.3619 0.98   1263  145 0.1309 0.1907      5.1341      5.4454|
|  9:  2.3619 -  2.2713 0.98   1291  149 0.1282 0.1983      5.1062      5.3983|
| 10:  2.2713 -  2.1931 0.99   1282  137 0.1241 0.1867      5.0242      5.2347|
| 11:  2.1931 -  2.1248 0.98   1280  137 0.1285 0.1966       5.034      5.3904|
| 12:  2.1248 -  2.0642 0.97   1257  144 0.1205 0.1725      4.9591      5.1668|
| 13:  2.0642 -  2.0100 0.99   1273  142 0.1334 0.1918       4.883      5.1292|
| 14:  2.0100 -  1.9610 0.52    684   74 0.1182 0.1778        4.74      4.9977|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0183 -  4.6816  1400   158  0.94   9.33   0.98     0.96       7537.92|
|  2:  4.6816 -  3.7348  1349   143  0.95   8.79   1.03     1.01      10177.06|
|  3:  3.7348 -  3.2682  1315   147  0.92  12.77   1.04     1.04      12339.18|
|  4:  3.2682 -  2.9719  1329   157  0.91  15.36   1.02     0.99      12167.62|
|  5:  2.9719 -  2.7603  1297   139  0.89  17.17   1.00     0.97       9246.82|
|  6:  2.7603 -  2.5985  1298   148  0.89  17.51   0.99     0.96       8322.41|
|  7:  2.5985 -  2.4689  1312   139  0.89  17.40   1.00     0.97       7499.67|
|  8:  2.4689 -  2.3619  1263   145  0.89  17.19   0.99     0.95       5861.55|
|  9:  2.3619 -  2.2713  1291   149  0.90  16.28   1.01     1.00       5734.44|
| 10:  2.2713 -  2.1931  1282   137  0.89  16.62   1.01     0.98       4955.23|
| 11:  2.1931 -  2.1248  1280   137  0.88  18.24   1.00     0.97       5267.02|
| 12:  2.1248 -  2.0642  1257   144  0.90  16.74   1.02     1.01       4730.67|
| 13:  2.0642 -  2.0100  1273   142  0.89  17.98   1.00     0.99       3902.82|
| 14:  2.0100 -  1.9610   684    74  0.90  16.25   1.00     0.98       2980.26|
|alpha:            min =        0.95 max =            1.04 mean =         0.98|
|beta:             min =     2980.26 max =        12339.18 mean =      7383.32|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.90 mean =        15.45|
|phase err.(test): min =        0.00 max =           89.85 mean =        14.78|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.620)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.37    112.27  15.91    None  None   None       |
|    all(noH): 2823   0      1.37    112.27  15.91    None  None   None       |
|    Sol.    : 438    0      4.21    98.54   41.96    None  None   None       |
|    Mac.    : 2385   0      1.37    112.27  11.13    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:     1.366 -  12.457: 1790   |   5:    56.819 -  67.910:   57        |
|      1:    12.457 -  23.547:  529   |   6:    67.910 -  79.001:   36        |
|      2:    23.547 -  34.638:  153   |   7:    79.001 -  90.091:    9        |
|      3:    34.638 -  45.729:  123   |   8:    90.091 - 101.182:    8        |
|      4:    45.729 -  56.819:  116   |   9:   101.182 - 112.273:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 322         
Filter by distance & map next to the model:
   mapped sites are within: 0.421 - 5.352
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 319 from: 322
   mapped sites are within: 0.715 - 5.352

peak=   10.469 closest distance to " CB  VAL A 230 " =    1.465
peak=    8.691 closest distance to " CG2 VAL A 296 " =    1.244
peak=    7.255 closest distance to " CG  ARG A 138 " =    1.180
peak=    6.142 closest distance to " CD1AILE A 234 " =    1.114
peak=    6.014 closest distance to " O   HOH Z 278 " =    1.535
peak=    5.963 closest distance to " CD2 LEU A   5 " =    1.254
peak=    5.820 closest distance to " O   HOH Z   7 " =    1.737
peak=    5.575 closest distance to " O   HOH Z 132 " =    1.360
peak=    5.540 closest distance to " NH2 ARG A  56 " =    2.143
peak=    5.504 closest distance to " O   HOH Z 130 " =    0.957
peak=    5.388 closest distance to " CG  PRO A 213 " =    1.303
peak=    5.377 closest distance to " O   HOH Z 214 " =    1.381
peak=    5.375 closest distance to " O   HOH Z 124 " =    1.814
peak=    5.338 closest distance to " O   HOH Z  37 " =    1.391
peak=    5.334 closest distance to " NE2 GLN A  11 " =    1.197
peak=    5.095 closest distance to " O   HOH Z 144 " =    1.961
peak=    4.978 closest distance to " O   HOH Z 427 " =    2.669
peak=    4.965 closest distance to " CB  ASN A 148 " =    1.348
peak=    4.916 closest distance to " CG  PRO A 198 " =    1.283
peak=    4.896 closest distance to " O   HOH Z 344 " =    1.331
peak=    4.886 closest distance to " CG  LEU A   5 " =    1.250
peak=    4.830 closest distance to " CB  VAL A 230 " =    1.100
peak=    4.819 closest distance to " O   HOH Z 202 " =    1.365
peak=    4.755 closest distance to " O   HOH Z 316 " =    2.774
peak=    4.707 closest distance to " CD2 LEU A 228 " =    1.227
peak=    4.685 closest distance to " NH1 ARG A 138 " =    0.995
peak=    4.665 closest distance to " O   HOH Z 134 " =    1.564
peak=    4.623 closest distance to " O   HOH Z 247 " =    1.315
peak=    4.578 closest distance to " O   HOH Z  97 " =    1.267
peak=    4.574 closest distance to " O   HOH Z 147 " =    1.384
peak=    4.561 closest distance to " NH2BARG A 102 " =    0.945
peak=    4.534 closest distance to " CB  SER A   3 " =    1.455
peak=    4.508 closest distance to " O   HOH Z 427 " =    1.251
peak=    4.488 closest distance to " O   PRO A 198 " =    1.275
peak=    4.487 closest distance to " CB  ARG A 275 " =    0.940
peak=    4.431 closest distance to " CG  LEU A 167 " =    1.140
peak=    4.427 closest distance to " O   HOH Z 260 " =    1.407
peak=    4.423 closest distance to " O   HOH Z 232 " =    2.192
peak=    4.418 closest distance to " O   HOH Z 126 " =    1.890
peak=    4.417 closest distance to " O   HOH Z 183 " =    1.394
peak=    4.409 closest distance to " O   HOH Z 287 " =    1.955
peak=    4.401 closest distance to " CG  LEU A 228 " =    1.258
peak=    4.399 closest distance to " O   HOH Z 143 " =    1.197
peak=    4.370 closest distance to " O   HOH Z 236 " =    1.653
peak=    4.366 closest distance to " CB  GLN A 223 " =    1.372
peak=    4.358 closest distance to " O   HOH Z  65 " =    0.868
peak=    4.330 closest distance to " O   HOH Z 411 " =    3.578
peak=    4.316 closest distance to " O   HOH Z 373 " =    2.216
peak=    4.299 closest distance to " O   HOH Z 117 " =    1.837
peak=    4.279 closest distance to " CB  GLN A 183 " =    1.220
peak=    4.277 closest distance to " O   HOH Z 425 " =    1.446
peak=    4.211 closest distance to " O   HOH Z 133 " =    1.593
peak=    4.196 closest distance to " CB  SER A  63 " =    1.367
peak=    4.196 closest distance to " CG  PRO A 280 " =    0.897
peak=    4.175 closest distance to " O   HOH Z 108 " =    1.576
peak=    4.172 closest distance to " NH1 ARG A  56 " =    1.026
peak=    4.157 closest distance to " O   HOH Z 369 " =    2.047
peak=    4.150 closest distance to " CB  PRO A  54 " =    0.887
peak=    4.142 closest distance to " CG2 THR A 221 " =    1.327
peak=    4.121 closest distance to " O   HOH Z 126 " =    1.535
peak=    4.117 closest distance to " O   HOH Z 298 " =    1.766
peak=    4.112 closest distance to " O   HOH Z 222 " =    2.206
peak=    4.111 closest distance to " O   HOH Z  97 " =    1.648
peak=    4.086 closest distance to " CB  TYR A 169 " =    0.896
peak=    4.032 closest distance to " O   HOH Z 193 " =    1.767
peak=    4.029 closest distance to " CB  SER A 216 " =    1.006
peak=    4.026 closest distance to " O   HOH Z 227 " =    1.636
peak=    4.016 closest distance to " O   HOH Z 263 " =    1.456
peak=    4.012 closest distance to " CD  ARG A 138 " =    0.951
peak=    4.004 closest distance to " O   SER A  87 " =    2.372
peak=    3.998 closest distance to " CB  TRP A 179 " =    1.389
peak=    3.980 closest distance to " O   HOH Z 186 " =    1.146
peak=    3.971 closest distance to " CB  GLU A 128 " =    1.114
peak=    3.968 closest distance to " O   HOH Z 284 " =    1.607
peak=    3.951 closest distance to " CB  VAL A 296 " =    1.153
peak=    3.950 closest distance to " O   HOH Z 371 " =    2.628
peak=    3.941 closest distance to " O   HOH Z 272 " =    1.899
peak=    3.941 closest distance to " O   HOH Z 193 " =    1.683
peak=    3.928 closest distance to " NH1AARG A 145 " =    1.001
peak=    3.926 closest distance to " O   HOH Z   9 " =    1.972
peak=    3.923 closest distance to " O   HOH Z  11 " =    1.567
peak=    3.919 closest distance to " O   HOH Z 326 " =    1.364
peak=    3.915 closest distance to " CG2 VAL A 257 " =    0.929
peak=    3.909 closest distance to " ND2 ASN A  60 " =    3.200
peak=    3.908 closest distance to " O   HOH Z 350 " =    1.322
peak=    3.886 closest distance to " OD2 ASP A 286 " =    2.695
peak=    3.882 closest distance to " OD1 ASN A 217 " =    1.631
peak=    3.868 closest distance to " CB  VAL A 202 " =    1.597
peak=    3.866 closest distance to " O   HOH Z 217 " =    3.123
peak=    3.855 closest distance to " O   HOH Z 424 " =    1.078
peak=    3.844 closest distance to " O   HOH Z 280 " =    3.011
peak=    3.842 closest distance to " O   HOH Z  78 " =    1.691
peak=    3.840 closest distance to " O   HOH Z 410 " =    1.463
peak=    3.840 closest distance to " CE3 TRP A 274 " =    2.368
peak=    3.832 closest distance to " CB  VAL A 265 " =    1.190
peak=    3.831 closest distance to " O   HOH Z 126 " =    1.609
peak=    3.831 closest distance to " O   HOH Z  59 " =    1.566
peak=    3.823 closest distance to " O   HOH Z  48 " =    1.502
peak=    3.813 closest distance to " NH1 ARG A  14 " =    1.051
peak=    3.800 closest distance to " CG  GLN A  88 " =    1.027
peak=    3.795 closest distance to " O   HOH Z 148 " =    1.650
peak=    3.795 closest distance to " CB  MET A  40 " =    0.912
peak=    3.793 closest distance to " O   HOH Z 116 " =    1.295
peak=    3.784 closest distance to " CB  LEU A 143 " =    1.086
peak=    3.777 closest distance to " CB  GLU A 152 " =    1.394
peak=    3.775 closest distance to " O   HOH Z 290 " =    0.999
peak=    3.761 closest distance to " O   HOH Z 371 " =    1.859
peak=    3.760 closest distance to " NZ  LYS A 117 " =    1.089
peak=    3.760 closest distance to " O   HOH Z 180 " =    2.126
peak=    3.758 closest distance to " O   HOH Z 184 " =    1.265
peak=    3.757 closest distance to " O   HOH Z 423 " =    1.529
peak=    3.755 closest distance to " O   HOH Z  63 " =    1.316
peak=    3.741 closest distance to " O   HOH Z 171 " =    2.960
peak=    3.740 closest distance to " O   HOH Z 207 " =    2.147
peak=    3.739 closest distance to " O   HOH Z 392 " =    1.196
peak=    3.728 closest distance to " CA  TYR A  30 " =    1.053
peak=    3.724 closest distance to " CD  ARG A 269 " =    1.037
peak=    3.722 closest distance to " CA  ASN A 127 " =    1.068
peak=    3.716 closest distance to " O   HOH Z 368 " =    1.958
peak=    3.716 closest distance to " O   HOH Z 357 " =    1.317
peak=    3.712 closest distance to " CA  ILE A 234 " =    0.950
peak=    3.707 closest distance to " NH2BARG A 190 " =    1.566
peak=    3.693 closest distance to " O   HOH Z 209 " =    1.031
peak=    3.676 closest distance to " O   HOH Z  22 " =    2.047
peak=    3.671 closest distance to " OD1 ASN A  69 " =    2.682
peak=    3.661 closest distance to " O   HOH Z 234 " =    3.573
peak=    3.654 closest distance to " O   HOH Z 132 " =    2.297
peak=    3.646 closest distance to " N   GLN A 278 " =    0.982
peak=    3.646 closest distance to " CA  LEU A 101 " =    1.608
peak=    3.639 closest distance to " CG1 VAL A 153 " =    0.905
peak=    3.635 closest distance to " CD2 TRP A 179 " =    2.278
peak=    3.634 closest distance to " O   HOH Z 220 " =    1.384
peak=    3.628 closest distance to " O   HOH Z 209 " =    2.121
peak=    3.624 closest distance to " CA  ALA A 248 " =    1.266
peak=    3.620 closest distance to " O   HOH Z   1 " =    1.824
peak=    3.620 closest distance to " CG1BVAL A 121 " =    1.155
peak=    3.616 closest distance to " O   HOH Z 389 " =    1.720
peak=    3.614 closest distance to " O   HOH Z 345 " =    3.229
peak=    3.599 closest distance to " CA  ASP A  50 " =    1.031
peak=    3.598 closest distance to " CA  ALA A  21 " =    1.118
peak=    3.597 closest distance to " CG  ARG A  66 " =    2.704
peak=    3.592 closest distance to " CB  ILE A 234 " =    0.950
peak=    3.570 closest distance to " O   HOH Z 403 " =    1.201
peak=    3.570 closest distance to " O   HOH Z  89 " =    1.521
peak=    3.565 closest distance to " O   ALA A 165 " =    1.221
peak=    3.555 closest distance to " CA  LEU A 282 " =    1.165
peak=    3.554 closest distance to " O   HOH Z 305 " =    3.177
peak=    3.551 closest distance to " O   HOH Z  49 " =    1.537
peak=    3.547 closest distance to " CD1 LEU A 300 " =    1.189
peak=    3.545 closest distance to " NE2 GLN A  58 " =    5.352
peak=    3.544 closest distance to " O   HOH Z 280 " =    1.601
peak=    3.538 closest distance to " O   HOH Z 189 " =    2.340
peak=    3.535 closest distance to " O   HOH Z 359 " =    1.247
peak=    3.532 closest distance to " O   HOH Z 276 " =    1.407
peak=    3.531 closest distance to " O   HOH Z  92 " =    0.805
peak=    3.525 closest distance to " N   PHE A 130 " =    1.322
peak=    3.521 closest distance to " O   HOH Z 128 " =    1.854
peak=    3.521 closest distance to " CA  ALA A 295 " =    1.020
peak=    3.519 closest distance to " CB  LEU A 228 " =    1.342
peak=    3.519 closest distance to " O   HOH Z 145 " =    1.809
peak=    3.517 closest distance to " O   HOH Z  58 " =    1.729
peak=    3.516 closest distance to " CB BVAL A  41 " =    1.335
peak=    3.513 closest distance to " O   HOH Z 419 " =    1.952
peak=    3.508 closest distance to " CH2 TRP A 150 " =    1.008
peak=    3.508 closest distance to " CG BARG A 102 " =    1.904
peak=    3.506 closest distance to " CB  LEU A 237 " =    0.976
peak=    3.505 closest distance to " CB  ARG A 102 " =    0.762
peak=    3.503 closest distance to " O   HOH Z 181 " =    2.292
peak=    3.498 closest distance to " O   HOH Z 193 " =    1.712
peak=    3.489 closest distance to " CB  ARG A 138 " =    1.630
peak=    3.487 closest distance to " CB  ASN A 187 " =    1.120
peak=    3.484 closest distance to " O   ASN A 301 " =    2.431
peak=    3.483 closest distance to " O   HOH Z 133 " =    2.289
peak=    3.479 closest distance to " CA  ALA A  51 " =    1.056
peak=    3.474 closest distance to " CB  ASP A 124 " =    0.899
peak=    3.471 closest distance to " O   HOH Z  39 " =    1.142
peak=    3.465 closest distance to " O   HOH Z  43 " =    1.787
peak=    3.465 closest distance to " O   HOH Z 119 " =    1.498
peak=    3.465 closest distance to " O   HOH Z 289 " =    1.403
peak=    3.464 closest distance to " CB  GLU A 277 " =    3.509
peak=    3.463 closest distance to " O   HOH Z 380 " =    1.728
peak=    3.461 closest distance to " CA  VAL A 126 " =    1.276
peak=    3.454 closest distance to " OD1 ASP A 238 " =    0.922
peak=    3.449 closest distance to " CA  ASN A  74 " =    1.242
peak=    3.445 closest distance to " O   PRO A 198 " =    1.549
peak=    3.442 closest distance to " CB  LYS A 117 " =    1.210
peak=    3.439 closest distance to " O   HOH Z 222 " =    1.142
peak=    3.434 closest distance to " O   HOH Z  64 " =    2.259
peak=    3.434 closest distance to " CD BLYS A 290 " =    1.000
peak=    3.433 closest distance to " O   HOH Z 426 " =    3.238
peak=    3.432 closest distance to " O   HOH Z  59 " =    2.191
peak=    3.432 closest distance to " O   HOH Z 281 " =    4.417
peak=    3.424 closest distance to " NE AARG A 275 " =    1.333
peak=    3.424 closest distance to " O   HOH Z 112 " =    1.038
peak=    3.421 closest distance to " CB  LEU A 255 " =    0.819
peak=    3.413 closest distance to " O   HOH Z 225 " =    1.422
peak=    3.412 closest distance to " ND1 HIS A  86 " =    1.831
peak=    3.409 closest distance to " O   HOH Z 146 " =    1.569
peak=    3.403 closest distance to " O   SER A  26 " =    1.550
peak=    3.402 closest distance to " C   LYS A 290 " =    1.260
peak=    3.396 closest distance to " CG1 ILE A 151 " =    1.078
peak=    3.395 closest distance to " OG  SER A  62 " =    2.785
peak=    3.393 closest distance to " CG  LYS A  76 " =    1.453
peak=    3.386 closest distance to " CG1 ILE A  33 " =    1.320
peak=    3.384 closest distance to " CA  ALA A 154 " =    1.092
peak=    3.382 closest distance to " CA  ALA A 158 " =    1.146
peak=    3.379 closest distance to " O   HOH Z  61 " =    1.534
peak=    3.375 closest distance to " O   HOH Z 189 " =    3.000
peak=    3.374 closest distance to " O   HOH Z 153 " =    3.476
peak=    3.374 closest distance to " CA  GLY A 267 " =    1.154
peak=    3.373 closest distance to " O   HOH Z 172 " =    3.367
peak=    3.364 closest distance to " O   HOH Z 302 " =    1.594
peak=    3.363 closest distance to " O   HOH Z 108 " =    1.681
peak=    3.358 closest distance to " CA  PHE A 283 " =    1.217
peak=    3.356 closest distance to " CD1 ILE A  33 " =    1.641
peak=    3.356 closest distance to " OE2 GLU A  53 " =    2.093
peak=    3.356 closest distance to " OE1 GLU A   2 " =    1.977
peak=    3.355 closest distance to " CG  PRO A 243 " =    1.136
peak=    3.352 closest distance to " CB  THR A 157 " =    0.961
peak=    3.349 closest distance to " C   GLU A 277 " =    1.227
peak=    3.347 closest distance to " N   ARG A 156 " =    1.283
peak=    3.343 closest distance to " NH2BARG A 145 " =    2.092
peak=    3.341 closest distance to " O   HOH Z 151 " =    1.532
peak=    3.341 closest distance to " O   HOH Z 374 " =    1.051
peak=    3.338 closest distance to " O   MET A 105 " =    1.642
peak=    3.336 closest distance to " O   HOH Z 158 " =    2.419
peak=    3.329 closest distance to " CG2 THR A 220 " =    1.012
peak=    3.322 closest distance to " CB  TRP A 266 " =    0.986
peak=    3.321 closest distance to " O   HOH Z  59 " =    2.151
peak=    3.319 closest distance to " CA  LYS A  48 " =    1.458
peak=    3.314 closest distance to " O   HOH Z 361 " =    1.484
peak=    3.314 closest distance to " CB  MET A  47 " =    1.068
peak=    3.312 closest distance to " O   HOH Z  96 " =    1.762
peak=    3.311 closest distance to " O   HOH Z 329 " =    3.415
peak=    3.310 closest distance to " O   HOH Z 166 " =    2.002
peak=    3.306 closest distance to " O   CYS A 168 " =    1.366
peak=    3.302 closest distance to " C   ALA A 299 " =    0.930
peak=    3.302 closest distance to " CB  SER A 276 " =    1.098
peak=    3.301 closest distance to " CG  ARG A 159 " =    0.880
peak=    3.301 closest distance to " CA  SER A  87 " =    0.968
peak=    3.291 closest distance to " O   HOH Z 250 " =    1.368
peak=    3.288 closest distance to " O   HOH Z 205 " =    0.918
peak=    3.283 closest distance to " O   HOH Z 195 " =    1.405
peak=    3.281 closest distance to " CB  ARG A 139 " =    1.010
peak=    3.278 closest distance to " O   HOH Z 271 " =    1.882
peak=    3.276 closest distance to " CA  VAL A  41 " =    0.922
peak=    3.275 closest distance to " NH1BARG A 275 " =    1.481
peak=    3.272 closest distance to " O   HOH Z 303 " =    1.743
peak=    3.270 closest distance to " O   HOH Z  68 " =    2.056
peak=    3.269 closest distance to " O   HOH Z 109 " =    2.515
peak=    3.264 closest distance to " CA  ALA A 160 " =    0.796
peak=    3.259 closest distance to " CB  SER A 210 " =    0.926
peak=    3.257 closest distance to " O   HOH Z 145 " =    1.694
peak=    3.257 closest distance to " O   HOH Z 244 " =    1.557
peak=    3.254 closest distance to " CB  GLN A  88 " =    1.409
peak=    3.253 closest distance to " NH2 ARG A 219 " =    1.798
peak=    3.249 closest distance to " N   TYR A  15 " =    0.996
peak=    3.249 closest distance to " O   HOH Z 373 " =    1.499
peak=    3.246 closest distance to " ND2 ASN A 187 " =    1.711
peak=    3.245 closest distance to " NH2 ARG A 269 " =    0.824
peak=    3.245 closest distance to " O   HOH Z  61 " =    1.622
peak=    3.240 closest distance to " O   HOH Z 258 " =    2.189
peak=    3.239 closest distance to " CB  ALA A  34 " =    1.003
peak=    3.238 closest distance to " O   HOH Z 158 " =    1.285
peak=    3.236 closest distance to " CB  SER A 273 " =    0.841
peak=    3.236 closest distance to " CH2 TRP A 274 " =    2.387
peak=    3.235 closest distance to " O   HOH Z 313 " =    1.810
peak=    3.234 closest distance to " O   HOH Z 204 " =    1.588
peak=    3.234 closest distance to " CE  MET A  93 " =    1.479
peak=    3.230 closest distance to " O   HOH Z 278 " =    1.133
peak=    3.229 closest distance to " O   HOH Z  32 " =    2.427
peak=    3.228 closest distance to " CA  ASN A 217 " =    1.228
peak=    3.226 closest distance to " CB  PHE A  16 " =    1.022
peak=    3.224 closest distance to " O   HOH Z 285 " =    1.957
peak=    3.219 closest distance to " NE2 GLN A  58 " =    2.915
peak=    3.218 closest distance to " O   HOH Z 411 " =    2.047
peak=    3.218 closest distance to " O   HOH Z 344 " =    2.871
peak=    3.217 closest distance to " CD  PRO A 243 " =    1.779
peak=    3.214 closest distance to " O   HOH Z  44 " =    1.717
peak=    3.208 closest distance to " CB  ALA A 291 " =    1.504
peak=    3.207 closest distance to " O   HOH Z 424 " =    2.700
peak=    3.204 closest distance to " O   HOH Z  18 " =    1.745
peak=    3.201 closest distance to " CB  PRO A 198 " =    1.006
peak=    3.199 closest distance to " CB  VAL A 121 " =    0.994
peak=    3.195 closest distance to " O   HOH Z 130 " =    2.048
peak=    3.195 closest distance to " CA  THR A 264 " =    0.776
peak=    3.192 closest distance to " O   HOH Z 414 " =    1.240
peak=    3.192 closest distance to " O   HOH Z 383 " =    2.459
peak=    3.191 closest distance to " O   HOH Z 334 " =    1.490
peak=    3.191 closest distance to " O   HOH Z  93 " =    2.485
peak=    3.185 closest distance to " OE1 GLN A 240 " =    1.569
peak=    3.179 closest distance to " CG2 VAL A 112 " =    1.284
peak=    3.178 closest distance to " OG BSER A 134 " =    2.917
peak=    3.172 closest distance to " OD1 ASN A  45 " =    1.404
peak=    3.172 closest distance to " CB  TYR A  30 " =    1.660
peak=    3.171 closest distance to " CA  GLU A 152 " =    1.051
peak=    3.170 closest distance to " O   ALA A  10 " =    1.564
peak=    3.168 closest distance to " O   HOH Z 120 " =    1.012
peak=    3.168 closest distance to " O   HOH Z 129 " =    0.715
peak=    3.158 closest distance to " O   HOH Z 115 " =    2.178
peak=    3.157 closest distance to " O   HOH Z 405 " =    1.486
peak=    3.153 closest distance to " O   HOH Z 145 " =    3.289
peak=    3.150 closest distance to " O   HOH Z 175 " =    2.266
peak=    3.141 closest distance to " CB  ALA A 161 " =    0.928
peak=    3.138 closest distance to " NZ BLYS A 290 " =    1.066
peak=    3.119 closest distance to " O   HOH Z 302 " =    1.379
peak=    3.119 closest distance to " O   HOH Z 110 " =    1.676
peak=    3.108 closest distance to " O   HOH Z 211 " =    2.304
peak=    3.104 closest distance to " O   HOH Z 122 " =    1.509
peak=    3.103 closest distance to " O   HOH Z  30 " =    1.506
peak=    3.099 closest distance to " CG  MET A 188 " =    1.434
peak=    3.098 closest distance to " OE2 GLU A   2 " =    1.778
peak=    3.075 closest distance to " O   HOH Z 358 " =    1.503
peak=    3.074 closest distance to " CZ  PHE A 192 " =    1.056
peak=    3.068 closest distance to " OG BSER A 164 " =    2.197
peak=    3.065 closest distance to " CB  ALA A 104 " =    0.815
peak=    3.063 closest distance to " O   HOH Z 139 " =    2.491
peak=    3.061 closest distance to " NZ  LYS A  48 " =    1.959
peak=    3.035 closest distance to " O   HOH Z  37 " =    2.633

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 191         
Filter by distance & map next to the model:
   mapped sites are within: 0.637 - 5.410
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 189 from: 191
   mapped sites are within: 0.736 - 5.410

peak=   -5.155 closest distance to " CG2 VAL A 230 " =    0.838
peak=   -4.763 closest distance to " CD  ARG A 138 " =    1.185
peak=   -4.405 closest distance to " OG ASER A 134 " =    1.086
peak=   -4.388 closest distance to " O   PRO A 198 " =    1.282
peak=   -4.346 closest distance to " O   HOH Z  43 " =    1.741
peak=   -4.322 closest distance to " O   HOH Z 231 " =    1.557
peak=   -4.297 closest distance to " CD  ARG A 156 " =    1.900
peak=   -4.293 closest distance to " O   HOH Z 198 " =    2.352
peak=   -4.282 closest distance to " O   HOH Z 388 " =    1.893
peak=   -4.230 closest distance to " O   HOH Z 266 " =    4.524
peak=   -4.127 closest distance to " CG  ARG A 138 " =    0.888
peak=   -4.099 closest distance to " O   HOH Z 298 " =    1.098
peak=   -4.074 closest distance to " O   HOH Z 377 " =    1.643
peak=   -4.056 closest distance to " OE1 GLN A  88 " =    1.087
peak=   -4.054 closest distance to " CD  LYS A 289 " =    2.566
peak=   -4.024 closest distance to " O   HOH Z 166 " =    1.417
peak=   -3.993 closest distance to " OE1 GLU A 277 " =    2.184
peak=   -3.974 closest distance to " CD  ARG A  14 " =    3.163
peak=   -3.937 closest distance to " CB  ASP A  27 " =    2.421
peak=   -3.933 closest distance to " O   HOH Z  98 " =    1.902
peak=   -3.932 closest distance to " CB  TYR A  15 " =    2.089
peak=   -3.916 closest distance to " CA  GLY A 133 " =    1.905
peak=   -3.869 closest distance to " OG BSER A 134 " =    1.203
peak=   -3.857 closest distance to " NH2AARG A 275 " =    5.410
peak=   -3.841 closest distance to " CD  GLN A  88 " =    0.934
peak=   -3.825 closest distance to " O   HOH Z  92 " =    1.514
peak=   -3.799 closest distance to " C   ASN A 285 " =    2.153
peak=   -3.797 closest distance to " CE2 TYR A  30 " =    2.946
peak=   -3.790 closest distance to " O   HOH Z 111 " =    4.211
peak=   -3.781 closest distance to " NH2 ARG A  79 " =    1.980
peak=   -3.740 closest distance to " CB  ALA A   7 " =    2.070
peak=   -3.734 closest distance to " CD1 LEU A 255 " =    2.858
peak=   -3.731 closest distance to " O   HOH Z 407 " =    3.087
peak=   -3.729 closest distance to " OG  SER A 206 " =    1.596
peak=   -3.726 closest distance to " CG2 THR A   4 " =    1.981
peak=   -3.724 closest distance to " O   HOH Z 365 " =    1.154
peak=   -3.711 closest distance to " CG  MET A 105 " =    0.876
peak=   -3.699 closest distance to " CD  LYS A 166 " =    2.552
peak=   -3.693 closest distance to " CE2 PHE A 218 " =    2.562
peak=   -3.689 closest distance to " O   HOH Z  65 " =    0.995
peak=   -3.684 closest distance to " O   VAL A 197 " =    1.493
peak=   -3.683 closest distance to " OD2 ASP A  50 " =    1.536
peak=   -3.678 closest distance to " CB  PRO A 243 " =    2.657
peak=   -3.678 closest distance to " O   HOH Z 290 " =    1.128
peak=   -3.677 closest distance to " CB  PRO A 163 " =    2.503
peak=   -3.653 closest distance to " O   ALA A   1 " =    1.183
peak=   -3.652 closest distance to " NH1 ARG A  56 " =    2.492
peak=   -3.648 closest distance to " CD1 LEU A 101 " =    2.444
peak=   -3.634 closest distance to " O   HOH Z 359 " =    1.739
peak=   -3.627 closest distance to " O   HOH Z 111 " =    0.929
peak=   -3.626 closest distance to " O   HOH Z 389 " =    1.846
peak=   -3.614 closest distance to " O   ALA A  51 " =    1.507
peak=   -3.601 closest distance to " O   GLY A  80 " =    2.365
peak=   -3.588 closest distance to " O   HOH Z 205 " =    0.936
peak=   -3.579 closest distance to " O   HOH Z 207 " =    1.798
peak=   -3.562 closest distance to " CG  PRO A 163 " =    2.563
peak=   -3.553 closest distance to " O   HOH Z  13 " =    1.353
peak=   -3.551 closest distance to " N   SER A 276 " =    1.156
peak=   -3.549 closest distance to " O   PRO A 163 " =    1.819
peak=   -3.547 closest distance to " O   ILE A  49 " =    1.754
peak=   -3.542 closest distance to " O   HOH Z 350 " =    1.999
peak=   -3.542 closest distance to " O   HOH Z 427 " =    1.729
peak=   -3.539 closest distance to " CD2 LEU A   5 " =    1.050
peak=   -3.498 closest distance to " O   HOH Z 124 " =    3.022
peak=   -3.496 closest distance to " CG  ASP A 231 " =    0.783
peak=   -3.494 closest distance to " CG  ARG A 219 " =    2.340
peak=   -3.489 closest distance to " CZ  PHE A  59 " =    1.568
peak=   -3.486 closest distance to " CG1 VAL A 268 " =    2.701
peak=   -3.482 closest distance to " O   SER A 135 " =    1.597
peak=   -3.478 closest distance to " O   HOH Z 435 " =    1.742
peak=   -3.471 closest distance to " C   HIS A 108 " =    1.169
peak=   -3.468 closest distance to " OG  SER A   3 " =    1.576
peak=   -3.449 closest distance to " C   ALA A 158 " =    1.114
peak=   -3.444 closest distance to " O   PRO A 163 " =    1.080
peak=   -3.444 closest distance to " O   HOH Z  93 " =    2.172
peak=   -3.439 closest distance to " O   GLY A  98 " =    2.019
peak=   -3.436 closest distance to " CB  ALA A 227 " =    2.341
peak=   -3.436 closest distance to " O   THR A  18 " =    1.690
peak=   -3.435 closest distance to " O   HOH Z  47 " =    1.435
peak=   -3.426 closest distance to " C   LEU A 143 " =    1.413
peak=   -3.421 closest distance to " O   HOH Z  44 " =    1.964
peak=   -3.417 closest distance to " N   GLN A  58 " =    1.229
peak=   -3.414 closest distance to " CB  VAL A 230 " =    1.033
peak=   -3.414 closest distance to " O   HOH Z  52 " =    1.861
peak=   -3.411 closest distance to " CG  PHE A 283 " =    2.547
peak=   -3.405 closest distance to " CB  ASN A  39 " =    2.098
peak=   -3.404 closest distance to " C   ASN A 187 " =    1.871
peak=   -3.392 closest distance to " O   HOH Z 189 " =    2.963
peak=   -3.390 closest distance to " CA  GLY A  35 " =    2.029
peak=   -3.378 closest distance to " O   HOH Z 139 " =    3.299
peak=   -3.378 closest distance to " O   HOH Z 143 " =    0.740
peak=   -3.376 closest distance to " O   HOH Z 213 " =    1.416
peak=   -3.368 closest distance to " O   ALA A 161 " =    1.875
peak=   -3.367 closest distance to " O   HOH Z  88 " =    4.507
peak=   -3.363 closest distance to " OD1 ASP A 200 " =    1.317
peak=   -3.361 closest distance to " NE2 GLN A 194 " =    2.871
peak=   -3.356 closest distance to " OG  SER A 245 " =    1.300
peak=   -3.347 closest distance to " OG  SER A  87 " =    1.353
peak=   -3.341 closest distance to " CE  MET A 105 " =    2.094
peak=   -3.338 closest distance to " CD  PRO A 198 " =    1.371
peak=   -3.326 closest distance to " O   HOH Z 392 " =    0.736
peak=   -3.324 closest distance to " CB  ALA A   9 " =    2.536
peak=   -3.320 closest distance to " O   HOH Z 221 " =    1.323
peak=   -3.319 closest distance to " CG1 ILE A  20 " =    2.416
peak=   -3.317 closest distance to " OG  SER A  87 " =    1.652
peak=   -3.309 closest distance to " O   HOH Z 231 " =    1.111
peak=   -3.306 closest distance to " OE1 GLN A  73 " =    2.197
peak=   -3.304 closest distance to " CA  ARG A  56 " =    1.297
peak=   -3.300 closest distance to " O   HOH Z   9 " =    1.572
peak=   -3.296 closest distance to " O   HOH Z 426 " =    1.664
peak=   -3.296 closest distance to " N   ALA A  84 " =    1.686
peak=   -3.295 closest distance to " CZ  PHE A  16 " =    1.370
peak=   -3.287 closest distance to " CG2 VAL A 296 " =    1.689
peak=   -3.285 closest distance to " O   GLY A 211 " =    1.247
peak=   -3.285 closest distance to " O   MET A  40 " =    2.782
peak=   -3.277 closest distance to " O   HOH Z 351 " =    1.474
peak=   -3.275 closest distance to " O   GLN A 194 " =    1.290
peak=   -3.274 closest distance to " O   GLY A 203 " =    2.770
peak=   -3.272 closest distance to " O   VAL A  67 " =    2.731
peak=   -3.270 closest distance to " CG2 VAL A 112 " =    2.529
peak=   -3.269 closest distance to " O   HOH Z 134 " =    2.430
peak=   -3.269 closest distance to " O   TRP A  70 " =    1.478
peak=   -3.269 closest distance to " O   SER A  22 " =    2.594
peak=   -3.267 closest distance to " C   GLY A  23 " =    2.013
peak=   -3.266 closest distance to " O   HOH Z 275 " =    1.535
peak=   -3.257 closest distance to " CB  TYR A 172 " =    2.216
peak=   -3.254 closest distance to " C   ARG A 190 " =    1.034
peak=   -3.252 closest distance to " O   GLN A 183 " =    1.275
peak=   -3.248 closest distance to " O   HOH Z 168 " =    1.865
peak=   -3.243 closest distance to " N   ALA A 248 " =    1.631
peak=   -3.242 closest distance to " CG2 VAL A 257 " =    2.913
peak=   -3.236 closest distance to " O   HOH Z 158 " =    2.072
peak=   -3.233 closest distance to " CB  ALA A   1 " =    1.433
peak=   -3.232 closest distance to " O   HOH Z 274 " =    2.827
peak=   -3.231 closest distance to " OG1 THR A 178 " =    1.057
peak=   -3.230 closest distance to " CE2 TYR A 116 " =    2.997
peak=   -3.229 closest distance to " CB  ALA A 248 " =    1.947
peak=   -3.224 closest distance to " CG  TRP A 266 " =    1.634
peak=   -3.219 closest distance to " N   HIS A 115 " =    1.998
peak=   -3.210 closest distance to " NH2 ARG A  66 " =    3.059
peak=   -3.206 closest distance to " CB  ALA A  43 " =    2.422
peak=   -3.204 closest distance to " O   HOH Z 438 " =    0.860
peak=   -3.200 closest distance to " N   LYS A 166 " =    1.963
peak=   -3.193 closest distance to " CD1 LEU A   5 " =    2.546
peak=   -3.190 closest distance to " O   ILE A 109 " =    2.601
peak=   -3.188 closest distance to " N   PHE A 283 " =    1.742
peak=   -3.185 closest distance to " CD1 PHE A  59 " =    2.052
peak=   -3.184 closest distance to " N   GLN A  58 " =    1.939
peak=   -3.182 closest distance to " O   HOH Z  63 " =    1.029
peak=   -3.176 closest distance to " N   ALA A   9 " =    1.481
peak=   -3.176 closest distance to " CD2 LEU A 237 " =    2.770
peak=   -3.175 closest distance to " OD2 ASP A 171 " =    1.712
peak=   -3.172 closest distance to " CG  LYS A 193 " =    2.415
peak=   -3.170 closest distance to " CB  TRP A  85 " =    2.369
peak=   -3.167 closest distance to " O   HOH Z 368 " =    2.239
peak=   -3.166 closest distance to " O   HOH Z 256 " =    1.347
peak=   -3.165 closest distance to " O   HOH Z 130 " =    1.021
peak=   -3.160 closest distance to " O   HOH Z  56 " =    0.888
peak=   -3.156 closest distance to " OG BSER A 134 " =    1.796
peak=   -3.153 closest distance to " N   TYR A 293 " =    2.321
peak=   -3.153 closest distance to " C   ASP A 124 " =    1.087
peak=   -3.150 closest distance to " CD1 LEU A 228 " =    2.171
peak=   -3.149 closest distance to " CG2 VAL A 202 " =    2.628
peak=   -3.148 closest distance to " O   ASP A  50 " =    1.250
peak=   -3.146 closest distance to " O   HOH Z 385 " =    1.019
peak=   -3.146 closest distance to " CE  LYS A  76 " =    2.960
peak=   -3.146 closest distance to " OD1 ASP A 191 " =    1.971
peak=   -3.144 closest distance to " O   VAL A  67 " =    2.776
peak=   -3.140 closest distance to " O   HOH Z 430 " =    1.816
peak=   -3.138 closest distance to " O   HOH Z 152 " =    4.730
peak=   -3.135 closest distance to " CZ2 TRP A 179 " =    2.156
peak=   -3.135 closest distance to " O   HOH Z  28 " =    1.745
peak=   -3.132 closest distance to " OD1 ASN A 148 " =    1.708
peak=   -3.128 closest distance to " OE2 GLU A 152 " =    1.013
peak=   -3.121 closest distance to " CB  CYS A 254 " =    1.877
peak=   -3.120 closest distance to " NE BARG A 102 " =    1.932
peak=   -3.118 closest distance to " O   HOH Z 417 " =    2.509
peak=   -3.116 closest distance to " ND2 ASN A  60 " =    1.390
peak=   -3.116 closest distance to " OG  SER A  26 " =    1.095
peak=   -3.115 closest distance to " CB  GLN A  55 " =    1.191
peak=   -3.114 closest distance to " O   GLY A  57 " =    1.257
peak=   -3.114 closest distance to " O   HOH Z 103 " =    1.776
peak=   -3.098 closest distance to " O   HOH Z  97 " =    1.483
peak=   -3.087 closest distance to " O   HOH Z  60 " =    2.228
peak=   -3.086 closest distance to " C   LYS A  76 " =    1.421
peak=   -3.081 closest distance to " OD1 ASN A 249 " =    1.344
peak=   -3.070 closest distance to " NH1 ARG A 269 " =    1.584
peak=   -3.064 closest distance to " N   THR A 235 " =    1.051
peak=   -3.042 closest distance to " O   VAL A 197 " =    1.022

================= 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    :  0.4927 0.4800   6.289199e+00   6.281937e+00
   1_bss:  0.4831 0.4674   6.284114e+00   6.274784e+00
   1_xyz:  0.4095 0.4321   6.194069e+00   6.225261e+00
   1_adp:  0.3705 0.4275   6.137837e+00   6.215704e+00
   1_occ:  0.3703 0.4274   6.137295e+00   6.215389e+00
   2_bss:  0.3689 0.4235   6.137481e+00   6.213147e+00
   2_xyz:  0.2873 0.3403   5.934451e+00   6.069927e+00
   2_adp:  0.2639 0.3270   5.878793e+00   6.035931e+00
   2_occ:  0.2636 0.3272   5.878327e+00   6.036012e+00
   3_bss:  0.2623 0.3252   5.877909e+00   6.035121e+00
   3_xyz:  0.1922 0.2476   5.613672e+00   5.809796e+00
   3_adp:  0.1682 0.2296   5.507050e+00   5.731820e+00
   3_occ:  0.1680 0.2291   5.505779e+00   5.730267e+00
   4_bss:  0.1677 0.2277   5.502256e+00   5.725486e+00
   4_xyz:  0.1437 0.1958   5.360161e+00   5.593805e+00
   4_adp:  0.1368 0.1894   5.322755e+00   5.559282e+00
   4_occ:  0.1367 0.1892   5.322121e+00   5.558221e+00
   5_bss:  0.1371 0.1901   5.322855e+00   5.559939e+00
   5_xyz:  0.1258 0.1767   5.247933e+00   5.493984e+00
   5_adp:  0.1233 0.1710   5.223301e+00   5.464471e+00
   5_occ:  0.1232 0.1707   5.222380e+00   5.462988e+00
   5_bss:  0.1232 0.1707   5.222382e+00   5.462988e+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:  0.390  19.999   6.195   8.067   7.618   0.000   0.000   0.000
   1_xyz:  0.390  19.999   6.195   8.067   7.618   0.000   0.000   0.000
   1_adp:  0.390  19.999   6.195   8.067   7.618   0.000   0.000   0.000
   1_occ:  0.390  19.999   6.195   8.067   7.618   0.000   0.000   0.000
   2_bss:  0.351  38.278   3.585   4.574   5.188   0.000   0.000   0.000
   2_xyz:  0.351  38.278   3.585   4.574   5.188   0.000   0.000   0.000
   2_adp:  0.351  38.278   3.585   4.574   5.188   0.000   0.000   0.000
   2_occ:  0.351  38.278   3.585   4.574   5.188   0.000   0.000   0.000
   3_bss:  0.331  38.278   2.055   2.250   3.002   0.000   0.000   0.000
   3_xyz:  0.331  38.278   2.055   2.250   3.002   0.000   0.000   0.000
   3_adp:  0.331  38.278   2.055   2.250   3.002   0.000   0.000   0.000
   3_occ:  0.331  38.278   2.055   2.250   3.002   0.000   0.000   0.000
   4_bss:  0.320  38.278   1.496   1.155   2.106   0.000   0.000   0.000
   4_xyz:  0.320  38.278   1.496   1.155   2.106   0.000   0.000   0.000
   4_adp:  0.320  38.278   1.496   1.155   2.106   0.000   0.000   0.000
   4_occ:  0.320  38.278   1.496   1.155   2.106   0.000   0.000   0.000
   5_bss:  0.319  44.455   1.341   0.926   1.832   0.000   0.000   0.000
   5_xyz:  0.319  44.455   1.341   0.926   1.832   0.000   0.000   0.000
   5_adp:  0.319  44.455   1.341   0.926   1.832   0.000   0.000   0.000
   5_occ:  0.319  44.455   1.341   0.926   1.832   0.000   0.000   0.000
   5_bss:  0.319  45.821  -0.025  -0.440   0.465   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  59.413 0.4015  0.4800    73705.063
   1_bss:  59.280 0.4016  0.5861    70796.452
   1_xyz:  51.399 0.5013  0.7192    56418.396
   1_adp:  49.500 0.5253  0.8105    54266.369
   1_occ:  49.559 0.5246  0.8092    54345.313
   2_bss:  49.194 0.5290  0.7408    53720.071
   2_xyz:  37.044 0.6759  0.9243    32145.084
   2_adp:  34.496 0.7063  0.9670    29095.073
   2_occ:  34.517 0.7060  0.9663    29091.060
   3_bss:  34.371 0.7075  0.8997    28890.634
   3_xyz:  24.828 0.8132  0.9886    16150.737
   3_adp:  22.209 0.8404  0.9988    13537.641
   3_occ:  22.166 0.8408  0.9987    13470.222
   4_bss:  21.998 0.8422  0.9688    13242.644
   4_xyz:  18.501 0.8757  0.9875     9713.599
   4_adp:  17.622 0.8843  0.9852     9097.618
   4_occ:  17.598 0.8845  0.9852     9070.489
   5_bss:  17.636 0.8842  0.9771     9133.106
   5_xyz:  16.140 0.8971  0.9850     7854.664
   5_adp:  15.411 0.9036  0.9849     7410.569
   5_occ:  15.383 0.9038  0.9849     7384.649
   5_bss:  15.383 0.9038  0.9849     7384.684
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.3212e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.3212e+01
   1_xyz:   1.711  0.013  0.107 18.539  0.006  4.106   1.4555e-01
   1_adp:   1.711  0.013  0.107 18.539  0.006  4.106   1.4555e-01
   1_occ:   1.711  0.013  0.107 18.539  0.006  4.106   1.4555e-01
   2_bss:   1.711  0.013  0.107 18.539  0.006  4.106   1.4555e-01
   2_xyz:   1.171  0.008  0.082 16.673  0.005  4.106   8.7652e-02
   2_adp:   1.171  0.008  0.082 16.673  0.005  4.106   8.7652e-02
   2_occ:   1.171  0.008  0.082 16.673  0.005  4.106   8.7652e-02
   3_bss:   1.171  0.008  0.082 16.673  0.005  4.106   8.7652e-02
   3_xyz:   1.049  0.008  0.075 15.987  0.004  4.120   7.2584e-02
   3_adp:   1.049  0.008  0.075 15.987  0.004  4.120   7.2584e-02
   3_occ:   1.049  0.008  0.075 15.987  0.004  4.120   7.2584e-02
   4_bss:   1.049  0.008  0.075 15.987  0.004  4.120   7.2584e-02
   4_xyz:   0.878  0.005  0.066 15.474  0.003  4.109   5.2396e-02
   4_adp:   0.878  0.005  0.066 15.474  0.003  4.109   5.2396e-02
   4_occ:   0.878  0.005  0.066 15.474  0.003  4.109   5.2396e-02
   5_bss:   0.878  0.005  0.066 15.474  0.003  4.109   5.2396e-02
   5_xyz:   0.911  0.005  0.069 15.484  0.003  4.111   5.3215e-02
   5_adp:   0.911  0.005  0.069 15.484  0.003  4.111   5.3215e-02
   5_occ:   0.911  0.005  0.069 15.484  0.003  4.111   5.3215e-02
   5_bss:   0.911  0.005  0.069 15.484  0.003  4.111   5.3215e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.8974e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.8974e+00
   1_xyz:  13.822  0.170  0.462 85.713  0.045  2.208   1.0028e-01
   1_adp:  13.822  0.170  0.462 85.713  0.045  2.208   1.0028e-01
   1_occ:  13.822  0.170  0.462 85.713  0.045  2.208   1.0028e-01
   2_bss:  13.822  0.170  0.462 85.713  0.045  2.208   1.0028e-01
   2_xyz:   7.036  0.070  0.318 86.084  0.038  2.198   5.8203e-02
   2_adp:   7.036  0.070  0.318 86.084  0.038  2.198   5.8203e-02
   2_occ:   7.036  0.070  0.318 86.084  0.038  2.198   5.8203e-02
   3_bss:   7.036  0.070  0.318 86.084  0.038  2.198   5.8203e-02
   3_xyz:   7.769  0.064  0.325 86.168  0.049  2.358   1.4193e-01
   3_adp:   7.769  0.064  0.325 86.168  0.049  2.358   1.4193e-01
   3_occ:   7.769  0.064  0.325 86.168  0.049  2.358   1.4193e-01
   4_bss:   7.769  0.064  0.325 86.168  0.049  2.358   1.4193e-01
   4_xyz:   6.597  0.039  0.344 81.174  0.026  2.409   3.5994e-02
   4_adp:   6.597  0.039  0.344 81.174  0.026  2.409   3.5994e-02
   4_occ:   6.597  0.039  0.344 81.174  0.026  2.409   3.5994e-02
   5_bss:   6.597  0.039  0.344 81.174  0.026  2.409   3.5994e-02
   5_xyz:   7.382  0.049  0.363 84.258  0.029  2.326   3.3580e-02
   5_adp:   7.382  0.049  0.363 84.258  0.029  2.326   3.3580e-02
   5_occ:   7.382  0.049  0.363 84.258  0.029  2.326   3.3580e-02
   5_bss:   7.382  0.049  0.363 84.258  0.029  2.326   3.3580e-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:  96.13   0.00  14.08  96.13   0.00  12.02  91.25   0.00  25.29
   1_occ:  96.13   0.00  14.08  96.13   0.00  12.02  91.25   0.00  25.29
   2_bss:  96.13   0.00  14.08  96.13   0.00  12.02  91.25   0.00  25.29
   2_xyz:  96.13   0.00  14.08  96.13   0.00  12.02  91.25   0.00  25.29
   2_adp:  94.58   0.00  14.15  94.58   0.00  11.10  91.57   0.00  30.71
   2_occ:  94.58   0.00  14.15  94.58   0.00  11.10  91.57   0.00  30.71
   3_bss:  94.58   0.00  14.15  94.58   0.00  11.10  91.57   0.00  30.71
   3_xyz:  94.58   0.00  14.15  94.58   0.00  11.10  91.57   0.00  30.71
   3_adp:  97.92   0.00  14.61  97.92   0.00  10.18  96.34   1.94  38.76
   3_occ:  97.92   0.00  14.61  97.92   0.00  10.18  96.34   1.94  38.76
   4_bss:  97.92   0.00  14.61  97.92   0.00  10.18  96.34   1.94  38.76
   4_xyz:  97.92   0.00  14.61  97.92   0.00  10.18  96.34   1.94  38.76
   4_adp: 109.99   0.00  15.01 109.99   0.00   9.99 100.03   3.06  42.34
   4_occ: 109.99   0.00  15.01 109.99   0.00   9.99 100.03   3.06  42.34
   5_bss: 109.99   0.00  15.01 109.99   0.00   9.99 100.03   3.06  42.34
   5_xyz: 109.99   0.00  15.01 109.99   0.00   9.99 100.03   3.06  42.34
   5_adp: 110.91   0.00  14.55 110.91   0.00   9.77  97.18   2.84  40.59
   5_occ: 110.91   0.00  14.55 110.91   0.00   9.77  97.18   2.84  40.59
   5_bss: 112.27   1.37  15.91 112.27   1.37  11.13  98.54   4.21  41.96
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.251    0.008    0.411
   1_adp:    1.251    0.008    0.411
   1_occ:    1.251    0.008    0.411
   2_bss:    1.251    0.008    0.411
   2_xyz:    1.560    0.061    0.590
   2_adp:    1.560    0.061    0.590
   2_occ:    1.560    0.061    0.590
   3_bss:    1.560    0.061    0.590
   3_xyz:    1.600    0.040    0.695
   3_adp:    1.600    0.040    0.695
   3_occ:    1.600    0.040    0.695
   4_bss:    1.600    0.040    0.695
   4_xyz:    1.917    0.050    0.742
   4_adp:    1.917    0.050    0.742
   4_occ:    1.917    0.050    0.742
   5_bss:    1.917    0.050    0.742
   5_xyz:    2.017    0.075    0.769
   5_adp:    2.017    0.075    0.769
   5_occ:    2.017    0.075    0.769
   5_bss:    2.017    0.075    0.769
------------------------------------------------------------------------

CPU time actual refinement: 367.22


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_870/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_870/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_870/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_870/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_870/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 367.07 
  Macro-tasks:
    bulk solvent and scale       = 42.47  
    individual site refinement   = 154.83 
    weights calculation          = 33.31  
    collect and process          = 6.64   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 237.38 
  Micro-tasks:
    mask                            = 2.48   
    f_calc                          = 117.24 
    alpha_beta                      = 8.44   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 127.78 
    fmodel                         = 7.64   
    r_factors                      = 0.25   
    phase_errors                   = 10.30  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 275.60 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.103 micro seconds
Total CPU time: 6.35 minutes
from_scatterers_fft:    669 calls, 116.87 s
gradients_fft:          615 calls, 113.99 s

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

# Date 2008-01-16 Time 02:38:30 PST -0800 (1200479910.23 s)
Start R-work = 0.4927, R-free = 0.4800 (no bulk solvent and anisotropic scale)
Final R-work = 0.1389, R-free = 0.1866 (no bulk solvent and anisotropic scale)

Start R-work = 0.4831, R-free = 0.4674
Final R-work = 0.1232, R-free = 0.1707