# Date 2008-01-16 Time 02:02:20 PST -0800 (1200477740.99 s)
#phil __OFF__

Command line arguments: "../662.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 18141
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 662

-------------------------------------------------------------------------------
  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: (70.25, 46.93, 85.0941, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 2.75, per 1000 atoms: 0.97


================================== 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: (70.25, 46.93, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.932 1.97116
Completeness in resolution range: 0.958132
Completeness with d_max=infinity: 0.955188

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9320
                             d_min =   1.9712

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: (70.25, 46.93, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.932 1.97116
Completeness in resolution range: 0.958132
Completeness with d_max=infinity: 0.955188

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9324 -  4.2178 [2141/2169]  1929   212   9.9%
  bin  2:  4.2178 -  3.3604 [2056/2072]  1848   208  10.1%
  bin  3:  3.3604 -  2.9393 [2035/2054]  1831   204  10.0%
  bin  4:  2.9393 -  2.6722 [2023/2053]  1826   197   9.7%
  bin  5:  2.6722 -  2.4816 [2010/2029]  1808   202  10.0%
  bin  6:  2.4816 -  2.3359 [1980/2016]  1782   198  10.0%
  bin  7:  2.3359 -  2.2193 [1970/2003]  1770   200  10.2%
  bin  8:  2.2193 -  2.1230 [1991/2025]  1792   199  10.0%
  bin  9:  2.1230 -  2.0414 [1980/2008]  1783   197   9.9%
  bin 10:  2.0414 -  1.9712 [1403/2016]  1261   142  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_662/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.12 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 21
        2.42 -     3.04: 2211
        3.04 -     3.66: 4728
        3.66 -     4.28: 9067
        4.28 -     4.90: 12453
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.970 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.996 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  2.149 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  2.153 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28475 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_662/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_662/model_refine_001.geo

CPU time processing inputs: 7.83


============================ 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 = 70.25 46.93 85.09415 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4306   r_free= 0.4260   ksol= 0.00   Bsol= 0.00   scale= 0.828    |
|                                                                             |
| 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:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.223108                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9324 -  4.7043 0.99   1386  154 0.3653 0.3466      6.5191      6.4715|
|  2:  4.7043 -  3.7535 0.99   1353  147 0.3315 0.3354       6.644      6.6657|
|  3:  3.7535 -  3.2848 0.99   1307  150 0.3781 0.3532      6.5618      6.5965|
|  4:  3.2848 -  2.9871 0.99   1309  145 0.3985 0.4030      6.4353       6.386|
|  5:  2.9871 -  2.7744 0.99   1306  143 0.4396 0.4622      6.3067      6.3363|
|  6:  2.7744 -  2.6118 0.99   1286  145 0.4528 0.4904      6.2184      6.2286|
|  7:  2.6118 -  2.4816 0.99   1295  139 0.4787 0.4370       6.222      6.1408|
|  8:  2.4816 -  2.3740 0.98   1273  149 0.4795 0.4699      6.1375      6.1281|
|  9:  2.3740 -  2.2830 0.98   1278  142 0.4788 0.4575      6.0847      6.0584|
| 10:  2.2830 -  2.2044 0.98   1270  134 0.4876 0.5159      6.0908      6.0929|
| 11:  2.2044 -  2.1357 1.00   1267  146 0.4982 0.4529       6.026      6.0142|
| 12:  2.1357 -  2.0748 0.97   1264  135 0.4776 0.4986      5.9485      5.9938|
| 13:  2.0748 -  2.0203 0.98   1267  145 0.5037 0.5312      5.8714      5.8289|
| 14:  2.0203 -  1.9712 0.59    769   85 0.5120 0.4846      5.8256      5.7394|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9324 -  4.7043  1386   154  0.73  31.88   0.82     0.75      60724.16|
|  2:  4.7043 -  3.7535  1353   147  0.77  29.22   0.92     0.83      76201.27|
|  3:  3.7535 -  3.2848  1307   150  0.69  36.09   0.88     0.80      80306.91|
|  4:  3.2848 -  2.9871  1309   145  0.63  41.17   0.85     0.71      72672.51|
|  5:  2.9871 -  2.7744  1306   143  0.53  49.18   0.78     0.62      65332.90|
|  6:  2.7744 -  2.6118  1286   145  0.51  51.24   0.77     0.58      57542.55|
|  7:  2.6118 -  2.4816  1295   139  0.51  51.26   0.76     0.57      52177.08|
|  8:  2.4816 -  2.3740  1273   149  0.50  51.96   0.76     0.58      46632.40|
|  9:  2.3740 -  2.2830  1278   142  0.51  51.20   0.76     0.58      41225.33|
| 10:  2.2830 -  2.2044  1270   134  0.51  51.71   0.79     0.59      37938.50|
| 11:  2.2044 -  2.1357  1267   146  0.48  53.64   0.78     0.57      35880.79|
| 12:  2.1357 -  2.0748  1264   135  0.43  57.55   0.79     0.52      37345.38|
| 13:  2.0748 -  2.0203  1267   145  0.37  62.51   0.76     0.45      34333.40|
| 14:  2.0203 -  1.9712   769    85  0.35  63.63   0.74     0.39      29056.49|
|alpha:            min =        0.39 max =            0.83 mean =         0.62|
|beta:             min =    29056.49 max =        80306.91 mean =     52920.51|
|figures of merit: min =        0.00 max =            1.00 mean =         0.55|
|phase err.(work): min =        0.00 max =           90.00 mean =        48.06|
|phase err.(test): min =        0.00 max =           89.90 mean =        48.28|
|-----------------------------------------------------------------------------|

============================== 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 = 8.132504              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 75.186   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.678028              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.684   (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:       26 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      162 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      697 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1524 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2653 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3960 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5110 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6569 |
| 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 |       53.463 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.747 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.754)------------------------------------------|
|    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 = 11.754)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4399   r_free= 0.4354   ksol= 0.00   Bsol= 0.00   scale= 0.795    |
|                                                                             |
| 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:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.229657                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4223   r_free= 0.4176   ksol= 0.35   Bsol= 12.78   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.26,8.16,9.21,0.00,0.00,0.00); trace/3= 8.21                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.219467                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.219765              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.351   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.665744              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.281   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4223      final r-factor (work) = 0.3194          |
| start r-factor (free) = 0.4176      final r-factor (free) = 0.3444          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 75.9679 = 7.22 * 0.50 * 6.2343 + 1.00 * 53.4630                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.0538 = 7.22 * 0.50 * 6.0766 + 1.00 * 0.1179                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3194      final r-factor (work) = 0.2548          |
| start r-factor (free) = 0.3444      final r-factor (free) = 0.2975          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0602 = 0.67 * 1.00 * 6.0766 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9402 = 0.67 * 1.00 * 5.9007 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.754)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    64.08   10.83    None  None   None       |
|    all(noH): 2823   0      0.00    64.08   10.83    None  None   None       |
|    Sol.    : 438    0      0.00    64.08   27.93    None  None   None       |
|    Mac.    : 2385   0      0.00    63.47   7.69     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 -   6.408: 1349   |   5:    32.038 -  38.446:  108        |
|      1:     6.408 -  12.815:  729   |   6:    38.446 -  44.853:   68        |
|      2:    12.815 -  19.223:  250   |   7:    44.853 -  51.261:   30        |
|      3:    19.223 -  25.630:  159   |   8:    51.261 -  57.668:    7        |
|      4:    25.630 -  32.038:  116   |   9:    57.668 -  64.076:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2548 r_free = 0.2975             target_work(ml) = 5.840         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2543 r_free = 0.2975             target_work(ml) = 5.839         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2543   r_free= 0.2975   ksol= 0.35   Bsol= 12.78   scale= 1.097   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.26,8.16,9.21,0.00,0.00,0.00); trace/3= 8.21                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.839028                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2488   r_free= 0.2913   ksol= 0.33   Bsol= 31.71   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.84,4.28,6.02,0.00,0.00,0.00); trace/3= 4.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.836009                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.063472              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.602   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.340274              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 116.972  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2488      final r-factor (work) = 0.1673          |
| start r-factor (free) = 0.2913      final r-factor (free) = 0.2127          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.1219 = 4.06 * 0.50 * 5.9086 + 1.00 * 0.1172                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.5642 = 4.06 * 0.50 * 5.6609 + 1.00 * 0.0626                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1673      final r-factor (work) = 0.1496          |
| start r-factor (free) = 0.2127      final r-factor (free) = 0.1954          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9379 = 0.34 * 1.00 * 5.6609 + 1.00 * 0.0116                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8559 = 0.34 * 1.00 * 5.4246 + 1.00 * 0.0101                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.754)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    68.76   11.31    None  None   None       |
|    all(noH): 2823   0      0.00    68.76   11.31    None  None   None       |
|    Sol.    : 438    0      1.57    63.35   31.90    None  None   None       |
|    Mac.    : 2385   0      0.00    68.76   7.53     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 -   6.876: 1502   |   5:    34.382 -  41.258:  124        |
|      1:     6.876 -  13.753:  650   |   6:    41.258 -  48.134:   80        |
|      2:    13.753 -  20.629:  201   |   7:    48.134 -  55.010:   38        |
|      3:    20.629 -  27.505:  107   |   8:    55.010 -  61.887:    7        |
|      4:    27.505 -  34.382:  109   |   9:    61.887 -  68.763:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1496 r_free = 0.1954             target_work(ml) = 5.380         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1494 r_free = 0.1950             target_work(ml) = 5.379         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1494   r_free= 0.1950   ksol= 0.33   Bsol= 31.71   scale= 1.038   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.84,4.28,6.02,0.00,0.00,0.00); trace/3= 4.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.378532                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1485   r_free= 0.1933   ksol= 0.32   Bsol= 31.71   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.89,3.26,4.20,0.00,0.00,0.00); trace/3= 3.45                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.375464                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.908878              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.681  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.729876              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.127  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1485      final r-factor (work) = 0.1220          |
| start r-factor (free) = 0.1933      final r-factor (free) = 0.1627          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9665 = 2.91 * 0.50 * 5.4343 + 1.00 * 0.0626                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7591 = 2.91 * 0.50 * 5.2912 + 1.00 * 0.0634                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1220      final r-factor (work) = 0.1164          |
| start r-factor (free) = 0.1627      final r-factor (free) = 0.1593          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8719 = 0.73 * 1.00 * 5.2912 + 1.00 * 0.0100                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7930 = 0.73 * 1.00 * 5.1803 + 1.00 * 0.0120                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.754)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.30   11.72    None  None   None       |
|    all(noH): 2823   0      0.00    78.30   11.72    None  None   None       |
|    Sol.    : 438    0      0.96    70.48   34.27    None  None   None       |
|    Mac.    : 2385   0      0.00    78.30   7.57     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.830: 1655   |   5:    39.150 -  46.980:  101        |
|      1:     7.830 -  15.660:  578   |   6:    46.980 -  54.810:   72        |
|      2:    15.660 -  23.490:  157   |   7:    54.810 -  62.640:   33        |
|      3:    23.490 -  31.320:  109   |   8:    62.640 -  70.470:    7        |
|      4:    31.320 -  39.150:  106   |   9:    70.470 -  78.300:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1164 r_free = 0.1593             target_work(ml) = 5.169         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1163 r_free = 0.1591             target_work(ml) = 5.169         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1163   r_free= 0.1591   ksol= 0.32   Bsol= 31.71   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.89,3.26,4.20,0.00,0.00,0.00); trace/3= 3.45                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.169025                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1166   r_free= 0.1590   ksol= 0.32   Bsol= 37.93   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.79,3.12,3.82,0.00,0.00,0.00); trace/3= 3.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.169300                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.799233              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 132.518  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.199770              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.032  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1166      final r-factor (work) = 0.1130          |
| start r-factor (free) = 0.1590      final r-factor (free) = 0.1571          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7237 = 1.80 * 0.50 * 5.1804 + 1.00 * 0.0633                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6966 = 1.80 * 0.50 * 5.1586 + 1.00 * 0.0559                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1130      final r-factor (work) = 0.1135          |
| start r-factor (free) = 0.1571      final r-factor (free) = 0.1564          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0424 = 0.20 * 1.00 * 5.1586 + 1.00 * 0.0119                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0412 = 0.20 * 1.00 * 5.1559 + 1.00 * 0.0112                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.754)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.36   11.40    None  None   None       |
|    all(noH): 2823   0      0.00    78.36   11.40    None  None   None       |
|    Sol.    : 438    0      1.03    67.29   32.75    None  None   None       |
|    Mac.    : 2385   0      0.00    78.36   7.48     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.836: 1679   |   5:    39.181 -  47.017:   92        |
|      1:     7.836 -  15.672:  576   |   6:    47.017 -  54.853:   66        |
|      2:    15.672 -  23.508:  154   |   7:    54.853 -  62.689:   21        |
|      3:    23.508 -  31.345:  116   |   8:    62.689 -  70.525:    7        |
|      4:    31.345 -  39.181:  108   |   9:    70.525 -  78.361:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1135 r_free = 0.1564             target_work(ml) = 5.151         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1134 r_free = 0.1563             target_work(ml) = 5.151         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1134   r_free= 0.1563   ksol= 0.32   Bsol= 37.93   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.79,3.12,3.82,0.00,0.00,0.00); trace/3= 3.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.150676                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1134   r_free= 0.1563   ksol= 0.32   Bsol= 37.93   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.79,3.12,3.82,0.00,0.00,0.00); trace/3= 3.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.150676                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.985178              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 141.901  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.576643              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.649   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1134      final r-factor (work) = 0.1083          |
| start r-factor (free) = 0.1563      final r-factor (free) = 0.1541          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7511 = 2.99 * 0.50 * 5.1556 + 1.00 * 0.0559                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7285 = 2.99 * 0.50 * 5.1292 + 1.00 * 0.0727                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1083      final r-factor (work) = 0.1076          |
| start r-factor (free) = 0.1541      final r-factor (free) = 0.1551          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9695 = 0.58 * 1.00 * 5.1292 + 1.00 * 0.0117                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9831 = 0.58 * 1.00 * 5.1172 + 1.00 * 0.0323                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.754)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.08   11.49    None  None   None       |
|    all(noH): 2823   0      0.00    80.08   11.49    None  None   None       |
|    Sol.    : 438    0      1.07    67.18   33.18    None  None   None       |
|    Mac.    : 2385   0      0.00    80.08   7.51     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.008: 1692   |   5:    40.042 -  48.050:   91        |
|      1:     8.008 -  16.017:  563   |   6:    48.050 -  56.058:   62        |
|      2:    16.017 -  24.025:  151   |   7:    56.058 -  64.067:   18        |
|      3:    24.025 -  32.033:  121   |   8:    64.067 -  72.075:    7        |
|      4:    32.033 -  40.042:  114   |   9:    72.075 -  80.083:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1076 r_free = 0.1551             target_work(ml) = 5.124         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1073 r_free = 0.1551             target_work(ml) = 5.122         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1073   r_free= 0.1551   ksol= 0.32   Bsol= 37.93   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.79,3.12,3.82,0.00,0.00,0.00); trace/3= 3.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.121989                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9324 -  4.7043 0.99   1386  154 0.0980 0.1291      5.3741      5.5236|
|  2:  4.7043 -  3.7535 0.99   1353  147 0.0833 0.1101       5.414      5.6254|
|  3:  3.7535 -  3.2848 0.99   1307  150 0.1019 0.1500      5.4489      5.8419|
|  4:  3.2848 -  2.9871 0.99   1309  145 0.1167 0.1520        5.43       5.572|
|  5:  2.9871 -  2.7744 0.99   1306  143 0.1235 0.1677      5.2913      5.5126|
|  6:  2.7744 -  2.6118 0.99   1286  145 0.1146 0.1749      5.1741       5.436|
|  7:  2.6118 -  2.4816 0.99   1295  139 0.1189 0.1600      5.1335      5.3531|
|  8:  2.4816 -  2.3740 0.98   1273  149 0.1116 0.1742      5.0398      5.3205|
|  9:  2.3740 -  2.2830 0.98   1278  142 0.1139 0.1816      5.0233      5.3312|
| 10:  2.2830 -  2.2044 0.98   1270  134 0.1049 0.1731      4.9332      5.2001|
| 11:  2.2044 -  2.1357 1.00   1267  146 0.1084 0.1697       4.922      5.2743|
| 12:  2.1357 -  2.0748 0.97   1264  135 0.1052 0.1638      4.8484      5.1055|
| 13:  2.0748 -  2.0203 0.98   1267  145 0.1107 0.1730      4.7751       5.066|
| 14:  2.0203 -  1.9712 0.59    769   85 0.1012 0.1659      4.6422      4.8836|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9324 -  4.7043  1386   154  0.94   8.89   0.98     0.96       7025.97|
|  2:  4.7043 -  3.7535  1353   147  0.96   7.69   1.02     1.01       8742.38|
|  3:  3.7535 -  3.2848  1307   150  0.93  11.15   1.03     1.02      10084.28|
|  4:  3.2848 -  2.9871  1309   145  0.92  13.52   1.01     0.99      10112.42|
|  5:  2.9871 -  2.7744  1306   143  0.90  15.55   0.99     0.96       7886.08|
|  6:  2.7744 -  2.6118  1286   145  0.90  15.54   0.98     0.96       6789.60|
|  7:  2.6118 -  2.4816  1295   139  0.91  14.88   0.99     0.96       5886.81|
|  8:  2.4816 -  2.3740  1273   149  0.91  15.14   0.99     0.97       5174.56|
|  9:  2.3740 -  2.2830  1278   142  0.91  15.24   1.01     0.99       5013.16|
| 10:  2.2830 -  2.2044  1270   134  0.90  15.38   1.00     0.97       4332.40|
| 11:  2.2044 -  2.1357  1267   146  0.90  16.41   1.00     0.97       4369.22|
| 12:  2.1357 -  2.0748  1264   135  0.92  14.53   1.01     0.98       3786.67|
| 13:  2.0748 -  2.0203  1267   145  0.90  16.25   1.02     1.01       3330.55|
| 14:  2.0203 -  1.9712   769    85  0.91  14.48   0.99     0.96       2455.95|
|alpha:            min =        0.96 max =            1.02 mean =         0.98|
|beta:             min =     2455.95 max =        10112.42 mean =      6214.67|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.83 mean =        13.82|
|phase err.(test): min =        0.00 max =           89.56 mean =        13.38|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1073   r_free= 0.1551   ksol= 0.32   Bsol= 42.44   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.42,-0.11,0.53,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.121813                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1073   r_free= 0.1551   ksol= 0.32   Bsol= 42.44   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.42,-0.11,0.53,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.121813                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9324 -  4.7043 0.99   1386  154 0.0980 0.1293      5.3743      5.5244|
|  2:  4.7043 -  3.7535 0.99   1353  147 0.0835 0.1103      5.4151      5.6265|
|  3:  3.7535 -  3.2848 0.99   1307  150 0.1020 0.1501      5.4495      5.8423|
|  4:  3.2848 -  2.9871 0.99   1309  145 0.1167 0.1520      5.4299      5.5718|
|  5:  2.9871 -  2.7744 0.99   1306  143 0.1234 0.1676      5.2907      5.5115|
|  6:  2.7744 -  2.6118 0.99   1286  145 0.1145 0.1750      5.1735      5.4361|
|  7:  2.6118 -  2.4816 0.99   1295  139 0.1189 0.1599      5.1333      5.3531|
|  8:  2.4816 -  2.3740 0.98   1273  149 0.1116 0.1741      5.0396      5.3199|
|  9:  2.3740 -  2.2830 0.98   1278  142 0.1139 0.1817      5.0231      5.3316|
| 10:  2.2830 -  2.2044 0.98   1270  134 0.1049 0.1730      4.9328       5.199|
| 11:  2.2044 -  2.1357 1.00   1267  146 0.1083 0.1694      4.9215      5.2735|
| 12:  2.1357 -  2.0748 0.97   1264  135 0.1052 0.1638      4.8478       5.105|
| 13:  2.0748 -  2.0203 0.98   1267  145 0.1107 0.1727      4.7746      5.0647|
| 14:  2.0203 -  1.9712 0.59    769   85 0.1012 0.1659      4.6417      4.8839|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9324 -  4.7043  1386   154  0.94   8.90   0.98     0.96       7034.71|
|  2:  4.7043 -  3.7535  1353   147  0.95   7.69   1.02     1.01       8756.42|
|  3:  3.7535 -  3.2848  1307   150  0.93  11.16   1.03     1.03      10098.72|
|  4:  3.2848 -  2.9871  1309   145  0.92  13.51   1.01     0.99      10106.66|
|  5:  2.9871 -  2.7744  1306   143  0.90  15.55   0.99     0.96       7880.69|
|  6:  2.7744 -  2.6118  1286   145  0.90  15.54   0.99     0.96       6783.31|
|  7:  2.6118 -  2.4816  1295   139  0.91  14.88   0.99     0.96       5884.76|
|  8:  2.4816 -  2.3740  1273   149  0.91  15.13   0.99     0.97       5170.95|
|  9:  2.3740 -  2.2830  1278   142  0.91  15.24   1.01     0.99       5010.85|
| 10:  2.2830 -  2.2044  1270   134  0.90  15.37   1.00     0.97       4328.54|
| 11:  2.2044 -  2.1357  1267   146  0.90  16.40   1.01     0.98       4363.88|
| 12:  2.1357 -  2.0748  1264   135  0.92  14.51   1.01     0.99       3780.21|
| 13:  2.0748 -  2.0203  1267   145  0.90  16.23   1.02     1.02       3324.94|
| 14:  2.0203 -  1.9712   769    85  0.91  14.47   0.99     0.96       2452.67|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     2452.67 max =        10106.66 mean =      6213.97|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.93 mean =        13.82|
|phase err.(test): min =        0.00 max =           89.57 mean =        13.37|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.754)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.28    83.37   14.78    None  None   None       |
|    all(noH): 2823   0      3.28    83.37   14.78    None  None   None       |
|    Sol.    : 438    0      4.35    70.46   36.46    None  None   None       |
|    Mac.    : 2385   0      3.28    83.37   10.79    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:     3.283 -  11.292: 1692   |   5:    43.325 -  51.333:   91        |
|      1:    11.292 -  19.300:  563   |   6:    51.333 -  59.342:   62        |
|      2:    19.300 -  27.308:  151   |   7:    59.342 -  67.350:   18        |
|      3:    27.308 -  35.317:  121   |   8:    67.350 -  75.358:    7        |
|      4:    35.317 -  43.325:  114   |   9:    75.358 -  83.367:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 316         
Filter by distance & map next to the model:
   mapped sites are within: 0.417 - 5.781
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 312 from: 316
   mapped sites are within: 0.737 - 5.781

peak=   10.652 closest distance to " CG2 VAL A 230 " =    1.377
peak=    6.550 closest distance to " CG2 VAL A 296 " =    1.095
peak=    6.314 closest distance to " CG  LEU A   5 " =    1.201
peak=    5.592 closest distance to " CG  LEU A 228 " =    1.151
peak=    5.567 closest distance to " NH2 ARG A  56 " =    2.178
peak=    5.548 closest distance to " CB  VAL A 296 " =    1.069
peak=    5.454 closest distance to " NE2 GLN A  11 " =    1.136
peak=    5.372 closest distance to " O   HOH Z 126 " =    1.906
peak=    5.169 closest distance to " CD2 LEU A   5 " =    1.153
peak=    5.069 closest distance to " CG  PRO A  54 " =    1.165
peak=    5.011 closest distance to " CB  SER A  63 " =    1.237
peak=    5.001 closest distance to " CB  GLN A 223 " =    1.478
peak=    4.989 closest distance to " CB  VAL A 230 " =    1.184
peak=    4.927 closest distance to " O   HOH Z 193 " =    1.702
peak=    4.906 closest distance to " CB  GLN A 183 " =    1.294
peak=    4.853 closest distance to " O   HOH Z 142 " =    1.705
peak=    4.772 closest distance to " O   HOH Z 232 " =    2.342
peak=    4.766 closest distance to " O   HOH Z 272 " =    1.836
peak=    4.682 closest distance to " CB  ARG A 275 " =    0.878
peak=    4.663 closest distance to " C   PRO A 198 " =    1.491
peak=    4.632 closest distance to " O   HOH Z 427 " =    2.910
peak=    4.598 closest distance to " CB  GLU A 152 " =    1.179
peak=    4.570 closest distance to " OD1 ASN A  69 " =    2.639
peak=    4.485 closest distance to " O   HOH Z 236 " =    1.904
peak=    4.431 closest distance to " O   HOH Z 316 " =    2.960
peak=    4.427 closest distance to " CB  TYR A 169 " =    0.788
peak=    4.404 closest distance to " O   HOH Z 368 " =    2.091
peak=    4.387 closest distance to " O   HOH Z 298 " =    1.788
peak=    4.355 closest distance to " CB  PRO A  54 " =    0.897
peak=    4.345 closest distance to " CB  SER A   3 " =    1.304
peak=    4.307 closest distance to " O   HOH Z  59 " =    2.105
peak=    4.295 closest distance to " O   SER A  87 " =    2.272
peak=    4.294 closest distance to " O   HOH Z 203 " =    1.660
peak=    4.265 closest distance to " CB  TRP A 179 " =    1.331
peak=    4.252 closest distance to " CB  ASN A 148 " =    1.350
peak=    4.242 closest distance to " O   HOH Z 303 " =    1.996
peak=    4.212 closest distance to " O   HOH Z  78 " =    1.733
peak=    4.178 closest distance to " O   HOH Z 369 " =    2.039
peak=    4.140 closest distance to " O   HOH Z 124 " =    1.382
peak=    4.118 closest distance to " CG  PRO A 213 " =    1.183
peak=    4.087 closest distance to " CD2 LEU A 228 " =    1.199
peak=    4.084 closest distance to " O   HOH Z 158 " =    3.085
peak=    4.079 closest distance to " OD2 ASP A 286 " =    2.775
peak=    4.073 closest distance to " O   HOH Z 403 " =    1.693
peak=    4.051 closest distance to " CB  ARG A  79 " =    1.420
peak=    4.047 closest distance to " O   HOH Z  61 " =    1.634
peak=    4.014 closest distance to " O   HOH Z 234 " =    3.592
peak=    4.000 closest distance to " CB  ARG A 139 " =    0.984
peak=    3.992 closest distance to " OG BSER A 164 " =    2.162
peak=    3.992 closest distance to " CA  ALA A  21 " =    1.136
peak=    3.992 closest distance to " O   HOH Z 197 " =    3.106
peak=    3.989 closest distance to " CG1BVAL A  72 " =    1.581
peak=    3.989 closest distance to " ND2 ASN A 187 " =    1.488
peak=    3.985 closest distance to " O   HOH Z 209 " =    2.362
peak=    3.983 closest distance to " O   HOH Z 128 " =    2.067
peak=    3.972 closest distance to " CB  GLU A 128 " =    1.054
peak=    3.970 closest distance to " O   HOH Z 371 " =    3.135
peak=    3.969 closest distance to " O   HOH Z 389 " =    1.873
peak=    3.969 closest distance to " O   HOH Z 423 " =    1.834
peak=    3.966 closest distance to " O   HOH Z  15 " =    2.147
peak=    3.965 closest distance to " O   HOH Z 263 " =    1.658
peak=    3.959 closest distance to " O   HOH Z  54 " =    1.612
peak=    3.935 closest distance to " CB  VAL A 265 " =    1.311
peak=    3.925 closest distance to " O   HOH Z  97 " =    2.632
peak=    3.915 closest distance to " O   HOH Z  48 " =    1.473
peak=    3.907 closest distance to " O   HOH Z 425 " =    2.085
peak=    3.907 closest distance to " CB  GLU A 277 " =    3.500
peak=    3.907 closest distance to " CA  TYR A  30 " =    0.943
peak=    3.906 closest distance to " O   HOH Z  97 " =    1.933
peak=    3.902 closest distance to " O   HOH Z 193 " =    1.939
peak=    3.898 closest distance to " CA  ASN A 215 " =    1.188
peak=    3.890 closest distance to " O   HOH Z 265 " =    2.428
peak=    3.881 closest distance to " O   HOH Z 411 " =    3.767
peak=    3.868 closest distance to " O   HOH Z 346 " =    1.548
peak=    3.834 closest distance to " O   HOH Z 248 " =    1.716
peak=    3.825 closest distance to " O   HOH Z 280 " =    2.940
peak=    3.822 closest distance to " O   HOH Z  43 " =    2.013
peak=    3.818 closest distance to " O   HOH Z 144 " =    2.282
peak=    3.818 closest distance to " O   HOH Z 145 " =    2.109
peak=    3.809 closest distance to " O   HOH Z 344 " =    2.848
peak=    3.785 closest distance to " O   HOH Z 299 " =    4.254
peak=    3.748 closest distance to " O   TRP A 274 " =    1.884
peak=    3.736 closest distance to " O   HOH Z  66 " =    2.189
peak=    3.729 closest distance to " CB  GLN A  88 " =    1.260
peak=    3.719 closest distance to " O   HOH Z 407 " =    2.512
peak=    3.717 closest distance to " CB  ASP A 140 " =    0.930
peak=    3.716 closest distance to " CB  TRP A 266 " =    0.969
peak=    3.704 closest distance to " O   HOH Z 273 " =    2.627
peak=    3.701 closest distance to " CB  TYR A 169 " =    0.737
peak=    3.697 closest distance to " CB  ASN A  39 " =    0.878
peak=    3.692 closest distance to " O   HOH Z  10 " =    1.847
peak=    3.688 closest distance to " CA  THR A 221 " =    0.952
peak=    3.676 closest distance to " CB  VAL A 202 " =    1.597
peak=    3.673 closest distance to " OE1 GLU A   2 " =    2.170
peak=    3.665 closest distance to " O   HOH Z 250 " =    1.328
peak=    3.660 closest distance to " O   HOH Z 426 " =    1.528
peak=    3.658 closest distance to " CB  ASN A 148 " =    1.899
peak=    3.656 closest distance to " O   HOH Z 402 " =    1.449
peak=    3.654 closest distance to " O   HOH Z  88 " =    3.105
peak=    3.640 closest distance to " NH2 ARG A 156 " =    1.091
peak=    3.630 closest distance to " CD BLYS A 290 " =    1.174
peak=    3.627 closest distance to " O   HOH Z 322 " =    2.007
peak=    3.613 closest distance to " O   HOH Z 227 " =    2.118
peak=    3.609 closest distance to " CG  ARG A  66 " =    2.736
peak=    3.604 closest distance to " O   MET A 105 " =    1.813
peak=    3.603 closest distance to " CA  ALA A 248 " =    1.370
peak=    3.592 closest distance to " CA  VAL A  41 " =    0.862
peak=    3.589 closest distance to " O   HOH Z 279 " =    2.144
peak=    3.587 closest distance to " CB  ARG A 190 " =    1.686
peak=    3.587 closest distance to " O   HOH Z 128 " =    2.100
peak=    3.581 closest distance to " CE1 TYR A 186 " =    1.318
peak=    3.580 closest distance to " O   HOH Z 154 " =    2.078
peak=    3.580 closest distance to " O   HOH Z 147 " =    1.656
peak=    3.577 closest distance to " O   HOH Z 189 " =    2.608
peak=    3.573 closest distance to " CD1 ILE A 106 " =    1.135
peak=    3.568 closest distance to " CA  VAL A 126 " =    0.912
peak=    3.565 closest distance to " CG2 THR A 221 " =    1.235
peak=    3.564 closest distance to " O   HOH Z 175 " =    2.125
peak=    3.559 closest distance to " O   HOH Z 207 " =    1.778
peak=    3.559 closest distance to " O   HOH Z 345 " =    3.233
peak=    3.554 closest distance to " CA  ALA A  51 " =    1.005
peak=    3.554 closest distance to " O   HOH Z 108 " =    2.378
peak=    3.554 closest distance to " CA  LYS A 117 " =    1.234
peak=    3.551 closest distance to " CG  PRO A 243 " =    1.127
peak=    3.547 closest distance to " O   HOH Z  61 " =    1.602
peak=    3.541 closest distance to " CG1 ILE A  33 " =    1.294
peak=    3.539 closest distance to " O   HOH Z 329 " =    3.858
peak=    3.538 closest distance to " O   HOH Z 112 " =    1.605
peak=    3.529 closest distance to " O   HOH Z 411 " =    1.788
peak=    3.526 closest distance to " CG  MET A 185 " =    1.123
peak=    3.521 closest distance to " O   HOH Z 180 " =    2.114
peak=    3.516 closest distance to " CA  THR A 264 " =    0.786
peak=    3.509 closest distance to " CA  ALA A 158 " =    1.203
peak=    3.507 closest distance to " CG2 ILE A 120 " =    1.272
peak=    3.507 closest distance to " O   HOH Z 366 " =    2.955
peak=    3.507 closest distance to " O   HOH Z  44 " =    1.727
peak=    3.503 closest distance to " OG  SER A  22 " =    2.792
peak=    3.500 closest distance to " O   HOH Z 245 " =    1.388
peak=    3.498 closest distance to " CB  LEU A 228 " =    1.322
peak=    3.495 closest distance to " O   HOH Z 132 " =    2.652
peak=    3.494 closest distance to " O   HOH Z 214 " =    2.085
peak=    3.492 closest distance to " CB  SER A 216 " =    0.785
peak=    3.487 closest distance to " CB  ALA A   9 " =    1.577
peak=    3.485 closest distance to " O   HOH Z 291 " =    1.546
peak=    3.483 closest distance to " CG  MET A 185 " =    1.179
peak=    3.482 closest distance to " O   HOH Z 374 " =    2.566
peak=    3.479 closest distance to " CG2 ILE A  20 " =    1.504
peak=    3.478 closest distance to " N   VAL A 126 " =    1.313
peak=    3.462 closest distance to " O   HOH Z   9 " =    2.029
peak=    3.456 closest distance to " O   HOH Z 286 " =    2.311
peak=    3.452 closest distance to " O   HOH Z 422 " =    2.694
peak=    3.448 closest distance to " N   PHE A 130 " =    1.359
peak=    3.441 closest distance to " CG  LEU A 167 " =    1.189
peak=    3.441 closest distance to " O   HOH Z 425 " =    1.248
peak=    3.434 closest distance to " NZ  LYS A 117 " =    3.098
peak=    3.430 closest distance to " O   HOH Z 151 " =    1.671
peak=    3.430 closest distance to " O   HOH Z 423 " =    2.976
peak=    3.428 closest distance to " O   HOH Z 189 " =    2.778
peak=    3.425 closest distance to " CD2 TRP A 179 " =    1.382
peak=    3.425 closest distance to " O   HOH Z 172 " =    3.788
peak=    3.424 closest distance to " CB  SER A  26 " =    1.616
peak=    3.422 closest distance to " CG1 ILE A  49 " =    1.365
peak=    3.411 closest distance to " CG  GLN A  77 " =    2.085
peak=    3.409 closest distance to " O   HOH Z 368 " =    3.610
peak=    3.409 closest distance to " CA  PHE A 283 " =    1.225
peak=    3.404 closest distance to " CB  GLN A 278 " =    0.852
peak=    3.402 closest distance to " O   HOH Z  71 " =    2.094
peak=    3.401 closest distance to " O   HOH Z 251 " =    1.576
peak=    3.400 closest distance to " CB  TRP A 150 " =    1.436
peak=    3.399 closest distance to " CB  LEU A 143 " =    1.146
peak=    3.399 closest distance to " O   HOH Z 163 " =    1.821
peak=    3.395 closest distance to " CA  ALA A 233 " =    1.200
peak=    3.393 closest distance to " CA  ARG A 195 " =    1.220
peak=    3.389 closest distance to " CD1 LEU A 300 " =    1.237
peak=    3.381 closest distance to " CB  THR A  31 " =    1.725
peak=    3.380 closest distance to " CA  ALA A 291 " =    0.958
peak=    3.374 closest distance to " N   SER A 135 " =    1.409
peak=    3.373 closest distance to " CG BARG A 102 " =    1.789
peak=    3.372 closest distance to " CB  ALA A   1 " =    1.225
peak=    3.369 closest distance to " O   HOH Z  40 " =    1.866
peak=    3.366 closest distance to " O   HOH Z 135 " =    1.697
peak=    3.365 closest distance to " CA  ASP A 140 " =    1.183
peak=    3.358 closest distance to " O   HOH Z 258 " =    1.655
peak=    3.358 closest distance to " CB  ASN A 142 " =    1.065
peak=    3.357 closest distance to " O   HOH Z 130 " =    2.329
peak=    3.356 closest distance to " OG1 THR A 294 " =    2.363
peak=    3.353 closest distance to " O   HOH Z 145 " =    3.649
peak=    3.348 closest distance to " NH2 ARG A  79 " =    1.360
peak=    3.346 closest distance to " CZ2 TRP A 179 " =    1.666
peak=    3.346 closest distance to " O   HOH Z 337 " =    3.649
peak=    3.343 closest distance to " CA  ASP A 162 " =    1.069
peak=    3.336 closest distance to " CB  ALA A 291 " =    1.415
peak=    3.336 closest distance to " O   HOH Z 227 " =    1.694
peak=    3.323 closest distance to " O   HOH Z 133 " =    1.517
peak=    3.318 closest distance to " O   ALA A 158 " =    1.364
peak=    3.314 closest distance to " CB BVAL A  41 " =    1.269
peak=    3.313 closest distance to " NE2 GLN A  58 " =    5.781
peak=    3.302 closest distance to " O   HOH Z 193 " =    1.632
peak=    3.301 closest distance to " O   ALA A   1 " =    1.740
peak=    3.291 closest distance to " O   HOH Z 419 " =    1.615
peak=    3.291 closest distance to " O   HOH Z 227 " =    1.529
peak=    3.290 closest distance to " O   ASP A 124 " =    1.172
peak=    3.289 closest distance to " O   HOH Z  21 " =    1.725
peak=    3.288 closest distance to " O   HOH Z 151 " =    1.793
peak=    3.287 closest distance to " O   HOH Z  48 " =    1.712
peak=    3.287 closest distance to " CG1 ILE A 151 " =    1.109
peak=    3.286 closest distance to " O   HOH Z 409 " =    3.362
peak=    3.283 closest distance to " O   HOH Z 134 " =    1.397
peak=    3.281 closest distance to " CD  LYS A 119 " =    1.512
peak=    3.277 closest distance to " O   HOH Z 406 " =    1.561
peak=    3.276 closest distance to " CB  THR A 157 " =    1.104
peak=    3.274 closest distance to " O   HOH Z  35 " =    2.505
peak=    3.273 closest distance to " O   HOH Z   1 " =    1.878
peak=    3.268 closest distance to " O   HOH Z 164 " =    2.081
peak=    3.267 closest distance to " O   HOH Z  80 " =    1.578
peak=    3.266 closest distance to " O   HOH Z 171 " =    2.328
peak=    3.262 closest distance to " O   HOH Z 367 " =    3.411
peak=    3.259 closest distance to " CB  ASN A 224 " =    1.067
peak=    3.259 closest distance to " O   HOH Z 128 " =    2.006
peak=    3.256 closest distance to " O   HOH Z 280 " =    1.723
peak=    3.255 closest distance to " CD2 TYR A  30 " =    0.957
peak=    3.252 closest distance to " CB  GLN A 205 " =    1.229
peak=    3.252 closest distance to " CB  LEU A 255 " =    0.757
peak=    3.251 closest distance to " CZ  PHE A 218 " =    1.093
peak=    3.250 closest distance to " CD2 LEU A 255 " =    1.460
peak=    3.250 closest distance to " CB  GLU A  46 " =    1.106
peak=    3.249 closest distance to " O   HOH Z 286 " =    2.486
peak=    3.247 closest distance to " CG  GLN A  88 " =    1.025
peak=    3.246 closest distance to " CB  ALA A  71 " =    1.395
peak=    3.244 closest distance to " O   HOH Z 216 " =    2.566
peak=    3.244 closest distance to " N   ASN A  39 " =    1.176
peak=    3.241 closest distance to " ND1 HIS A  81 " =    1.616
peak=    3.236 closest distance to " O   HOH Z 250 " =    1.381
peak=    3.233 closest distance to " O   HOH Z 359 " =    3.694
peak=    3.233 closest distance to " O   HOH Z  62 " =    2.269
peak=    3.232 closest distance to " O   THR A  31 " =    1.502
peak=    3.231 closest distance to " CB  VAL A 268 " =    0.849
peak=    3.228 closest distance to " CD  LYS A 166 " =    1.305
peak=    3.227 closest distance to " O   HOH Z  40 " =    2.400
peak=    3.225 closest distance to " O   HOH Z 417 " =    2.004
peak=    3.221 closest distance to " O   GLN A 278 " =    1.259
peak=    3.220 closest distance to " OE2 GLU A  53 " =    2.045
peak=    3.216 closest distance to " CA  ARG A  36 " =    1.038
peak=    3.216 closest distance to " O   HOH Z 327 " =    1.523
peak=    3.216 closest distance to " O   HOH Z 148 " =    3.219
peak=    3.212 closest distance to " O   HOH Z 209 " =    2.305
peak=    3.207 closest distance to " ND1 HIS A  86 " =    1.705
peak=    3.205 closest distance to " CD  ARG A 195 " =    3.589
peak=    3.203 closest distance to " OD1BASN A 224 " =    2.208
peak=    3.202 closest distance to " O   HOH Z  85 " =    1.353
peak=    3.201 closest distance to " O   HOH Z 392 " =    1.521
peak=    3.200 closest distance to " CG2 THR A 294 " =    1.688
peak=    3.199 closest distance to " OD1 ASP A 286 " =    1.724
peak=    3.195 closest distance to " O   HOH Z 437 " =    2.055
peak=    3.194 closest distance to " CB  ASN A 215 " =    1.109
peak=    3.193 closest distance to " CD  ARG A 159 " =    0.757
peak=    3.192 closest distance to " O   HOH Z 187 " =    2.244
peak=    3.192 closest distance to " O   HOH Z 116 " =    1.724
peak=    3.189 closest distance to " O   HOH Z 302 " =    1.868
peak=    3.188 closest distance to " OD1 ASN A 217 " =    1.749
peak=    3.184 closest distance to " O   HOH Z 261 " =    1.483
peak=    3.182 closest distance to " O   HOH Z 128 " =    1.614
peak=    3.181 closest distance to " O   HOH Z  50 " =    1.432
peak=    3.178 closest distance to " CD1 ILE A  33 " =    1.591
peak=    3.176 closest distance to " CA  SER A 146 " =    1.781
peak=    3.175 closest distance to " OE1 GLU A 236 " =    1.678
peak=    3.175 closest distance to " CB  SER A 212 " =    1.151
peak=    3.174 closest distance to " O   GLN A  58 " =    1.515
peak=    3.172 closest distance to " CB  LYS A 117 " =    1.139
peak=    3.170 closest distance to " O   HOH Z 334 " =    1.468
peak=    3.169 closest distance to " O   HOH Z 303 " =    1.712
peak=    3.165 closest distance to " CB  ILE A  20 " =    1.449
peak=    3.164 closest distance to " CA  GLN A 194 " =    1.342
peak=    3.164 closest distance to " O   HOH Z 305 " =    3.535
peak=    3.162 closest distance to " CB  ALA A 248 " =    0.960
peak=    3.157 closest distance to " NH2BARG A 145 " =    2.019
peak=    3.154 closest distance to " CB  TYR A  30 " =    1.117
peak=    3.149 closest distance to " CG  GLN A  89 " =    1.494
peak=    3.137 closest distance to " CB  ASN A 110 " =    1.166
peak=    3.135 closest distance to " N   ARG A 156 " =    1.320
peak=    3.133 closest distance to " CD2 HIS A  81 " =    0.978
peak=    3.133 closest distance to " O   HOH Z  49 " =    2.442
peak=    3.128 closest distance to " O   HOH Z 427 " =    3.134
peak=    3.125 closest distance to " O   HOH Z 173 " =    2.209
peak=    3.122 closest distance to " CA  ASN A 176 " =    1.129
peak=    3.116 closest distance to " O   HOH Z 285 " =    3.050
peak=    3.115 closest distance to " OE1 GLU A   2 " =    2.138
peak=    3.114 closest distance to " N   ASN A 127 " =    1.268
peak=    3.114 closest distance to " O   ALA A   1 " =    1.525
peak=    3.113 closest distance to " CD1 LEU A   5 " =    1.324
peak=    3.113 closest distance to " O   HOH Z 357 " =    1.795
peak=    3.113 closest distance to " O   HOH Z 336 " =    1.719
peak=    3.109 closest distance to " CA  LYS A 290 " =    1.320
peak=    3.106 closest distance to " O   HOH Z 163 " =    1.971
peak=    3.106 closest distance to " NH1AARG A 145 " =    0.854
peak=    3.102 closest distance to " O   HOH Z 271 " =    1.984
peak=    3.100 closest distance to " O   HOH Z 281 " =    4.573
peak=    3.096 closest distance to " CB  ALA A 100 " =    1.163
peak=    3.095 closest distance to " O   GLU A   2 " =    1.800
peak=    3.094 closest distance to " CA  LEU A 282 " =    1.140
peak=    3.087 closest distance to " O   HOH Z 250 " =    1.758
peak=    3.086 closest distance to " CA  THR A  52 " =    1.043
peak=    3.082 closest distance to " CB  ILE A 120 " =    1.436
peak=    3.070 closest distance to " O   HOH Z  85 " =    2.123
peak=    3.066 closest distance to " NZ  LYS A  76 " =    1.290
peak=    3.065 closest distance to " CA  ASP A 191 " =    0.812
peak=    3.059 closest distance to " CA  ILE A 106 " =    0.766
peak=    3.059 closest distance to " O   HOH Z  59 " =    2.291
peak=    3.059 closest distance to " C   ALA A 299 " =    0.967
peak=    3.056 closest distance to " O   HOH Z 213 " =    2.214
peak=    3.044 closest distance to " N   ASP A 162 " =    1.332
peak=    3.042 closest distance to " O   SER A 164 " =    1.178

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 208         
Filter by distance & map next to the model:
   mapped sites are within: 0.567 - 5.446
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 205 from: 208
   mapped sites are within: 0.738 - 5.446

peak=   -5.529 closest distance to " CG2 VAL A 230 " =    0.831
peak=   -4.684 closest distance to " SG  CYS A 254 " =    3.125
peak=   -4.633 closest distance to " CD  ARG A 156 " =    2.015
peak=   -4.506 closest distance to " O   HOH Z 266 " =    4.578
peak=   -4.203 closest distance to " OG BSER A 134 " =    1.117
peak=   -4.192 closest distance to " O   ILE A 109 " =    2.578
peak=   -4.119 closest distance to " O   HOH Z 290 " =    1.087
peak=   -4.102 closest distance to " CD2 LEU A 300 " =    2.829
peak=   -4.092 closest distance to " CB  PRO A 243 " =    2.586
peak=   -4.059 closest distance to " O   PRO A 163 " =    2.107
peak=   -4.055 closest distance to " CG  GLN A 223 " =    1.991
peak=   -4.052 closest distance to " C   HIS A 108 " =    1.215
peak=   -3.971 closest distance to " N   GLN A  58 " =    1.501
peak=   -3.962 closest distance to " CD  ARG A 139 " =    1.575
peak=   -3.945 closest distance to " CG2 VAL A 296 " =    1.277
peak=   -3.911 closest distance to " OXT GLY A 302 " =    2.771
peak=   -3.876 closest distance to " O   HOH Z  11 " =    1.878
peak=   -3.867 closest distance to " CG2BVAL A  41 " =    2.622
peak=   -3.833 closest distance to " CB  ALA A 248 " =    1.975
peak=   -3.826 closest distance to " CE2 TYR A  30 " =    2.786
peak=   -3.792 closest distance to " O   HOH Z 198 " =    2.387
peak=   -3.779 closest distance to " O   HOH Z 231 " =    1.942
peak=   -3.778 closest distance to " OG BSER A 134 " =    1.653
peak=   -3.772 closest distance to " CG  ASP A 231 " =    0.798
peak=   -3.749 closest distance to " CG  PHE A 283 " =    2.814
peak=   -3.746 closest distance to " O   HOH Z 389 " =    1.831
peak=   -3.739 closest distance to " CB  ASP A 132 " =    2.310
peak=   -3.737 closest distance to " CD1 PHE A  59 " =    1.931
peak=   -3.737 closest distance to " CE  MET A 105 " =    2.061
peak=   -3.734 closest distance to " CB  PRO A 280 " =    2.127
peak=   -3.733 closest distance to " CG1 VAL A 112 " =    2.731
peak=   -3.727 closest distance to " O   HOH Z 407 " =    3.049
peak=   -3.720 closest distance to " OG  SER A  97 " =    2.220
peak=   -3.715 closest distance to " CZ  TYR A 169 " =    1.632
peak=   -3.713 closest distance to " CG1 VAL A 250 " =    2.748
peak=   -3.711 closest distance to " CD1 LEU A 101 " =    2.426
peak=   -3.692 closest distance to " CZ3 TRP A 179 " =    1.248
peak=   -3.685 closest distance to " CB  ALA A 291 " =    2.313
peak=   -3.679 closest distance to " O   HOH Z 166 " =    1.438
peak=   -3.676 closest distance to " CB  PRO A 163 " =    2.571
peak=   -3.670 closest distance to " O   VAL A  67 " =    2.708
peak=   -3.669 closest distance to " NH2AARG A 275 " =    5.129
peak=   -3.656 closest distance to " N   ALA A 248 " =    1.590
peak=   -3.653 closest distance to " O   HOH Z  13 " =    1.465
peak=   -3.653 closest distance to " C   ALA A 158 " =    1.267
peak=   -3.646 closest distance to " O   HOH Z 126 " =    1.901
peak=   -3.645 closest distance to " O   HOH Z 211 " =    1.643
peak=   -3.644 closest distance to " NE2 GLN A  88 " =    2.004
peak=   -3.641 closest distance to " CB  PHE A 192 " =    1.856
peak=   -3.634 closest distance to " O   HOH Z 114 " =    3.035
peak=   -3.631 closest distance to " CA  ASP A 298 " =    1.041
peak=   -3.631 closest distance to " O   PRO A 198 " =    1.266
peak=   -3.618 closest distance to " O   HOH Z  43 " =    1.774
peak=   -3.611 closest distance to " CB  TYR A  15 " =    2.197
peak=   -3.597 closest distance to " CE2 PHE A 218 " =    2.643
peak=   -3.595 closest distance to " CZ  PHE A  59 " =    1.587
peak=   -3.594 closest distance to " N   THR A 157 " =    1.486
peak=   -3.591 closest distance to " CD  LYS A 289 " =    2.552
peak=   -3.588 closest distance to " CG  LEU A 228 " =    1.036
peak=   -3.585 closest distance to " N   HIS A 115 " =    2.032
peak=   -3.585 closest distance to " NH2 ARG A  79 " =    1.902
peak=   -3.577 closest distance to " N   ALA A 226 " =    2.034
peak=   -3.575 closest distance to " O   HOH Z  52 " =    1.476
peak=   -3.557 closest distance to " O   HOH Z 351 " =    1.500
peak=   -3.555 closest distance to " O   HOH Z 196 " =    2.107
peak=   -3.546 closest distance to " ND2 ASN A  45 " =    1.046
peak=   -3.543 closest distance to " O   HOH Z 103 " =    1.782
peak=   -3.536 closest distance to " N   ALA A  43 " =    2.481
peak=   -3.528 closest distance to " C   GLN A 205 " =    1.955
peak=   -3.524 closest distance to " N   SER A 276 " =    1.278
peak=   -3.521 closest distance to " OG  SER A  26 " =    1.188
peak=   -3.519 closest distance to " CG  TRP A 266 " =    1.840
peak=   -3.510 closest distance to " OG  SER A   3 " =    1.704
peak=   -3.507 closest distance to " O   HOH Z 435 " =    2.761
peak=   -3.494 closest distance to " CA  GLY A  98 " =    1.882
peak=   -3.493 closest distance to " O   HOH Z 166 " =    1.886
peak=   -3.485 closest distance to " O   HOH Z  47 " =    1.517
peak=   -3.483 closest distance to " O   HOH Z 185 " =    2.295
peak=   -3.477 closest distance to " NZ  LYS A 119 " =    3.426
peak=   -3.468 closest distance to " C   ASP A 231 " =    2.581
peak=   -3.461 closest distance to " CB  ASP A 132 " =    2.233
peak=   -3.454 closest distance to " O   HOH Z 311 " =    3.653
peak=   -3.453 closest distance to " CG  ASP A  50 " =    2.337
peak=   -3.446 closest distance to " C   MET A 188 " =    1.435
peak=   -3.445 closest distance to " CD1 LEU A 228 " =    2.147
peak=   -3.442 closest distance to " ND2 ASN A 187 " =    1.587
peak=   -3.437 closest distance to " CD1 LEU A 101 " =    2.761
peak=   -3.433 closest distance to " O   ALA A 161 " =    1.651
peak=   -3.431 closest distance to " OG  SER A  62 " =    1.576
peak=   -3.421 closest distance to " CD  GLN A  58 " =    1.204
peak=   -3.416 closest distance to " O   HOH Z 198 " =    1.437
peak=   -3.416 closest distance to " CG  LYS A 193 " =    2.255
peak=   -3.414 closest distance to " CA  GLY A 133 " =    2.209
peak=   -3.413 closest distance to " OG  SER A  87 " =    1.399
peak=   -3.399 closest distance to " O   GLY A 196 " =    1.109
peak=   -3.393 closest distance to " OXT GLY A 302 " =    3.495
peak=   -3.382 closest distance to " O   HOH Z 353 " =    2.089
peak=   -3.381 closest distance to " CA  GLY A 133 " =    2.022
peak=   -3.367 closest distance to " N   THR A 235 " =    1.355
peak=   -3.367 closest distance to " O   VAL A 197 " =    1.286
peak=   -3.366 closest distance to " CG1 VAL A 112 " =    2.612
peak=   -3.364 closest distance to " O   HOH Z 436 " =    1.500
peak=   -3.364 closest distance to " O   VAL A 174 " =    1.999
peak=   -3.363 closest distance to " O   HOH Z 292 " =    4.443
peak=   -3.359 closest distance to " O   HOH Z  90 " =    2.778
peak=   -3.358 closest distance to " NH2 ARG A  66 " =    1.856
peak=   -3.358 closest distance to " CB  ASN A  39 " =    2.082
peak=   -3.356 closest distance to " OG ASER A 134 " =    1.269
peak=   -3.354 closest distance to " CB  GLN A  11 " =    1.912
peak=   -3.353 closest distance to " O   HOH Z  38 " =    1.690
peak=   -3.349 closest distance to " O   HOH Z 339 " =    1.882
peak=   -3.341 closest distance to " O   HOH Z 102 " =    1.681
peak=   -3.338 closest distance to " O   HOH Z 394 " =    1.537
peak=   -3.333 closest distance to " O   PHE A 218 " =    1.713
peak=   -3.332 closest distance to " CD  ARG A 195 " =    5.200
peak=   -3.327 closest distance to " OG  SER A 206 " =    1.667
peak=   -3.323 closest distance to " O   VAL A 125 " =    2.288
peak=   -3.315 closest distance to " O   HOH Z  19 " =    2.328
peak=   -3.314 closest distance to " N   ASP A 171 " =    2.345
peak=   -3.314 closest distance to " O   HOH Z 222 " =    1.528
peak=   -3.314 closest distance to " N   PHE A  59 " =    2.099
peak=   -3.313 closest distance to " C   LEU A 143 " =    1.006
peak=   -3.312 closest distance to " OD2 ASP A 171 " =    2.248
peak=   -3.310 closest distance to " CG1 VAL A 296 " =    1.329
peak=   -3.308 closest distance to " O   HOH Z 191 " =    5.446
peak=   -3.307 closest distance to " O   HOH Z 389 " =    4.662
peak=   -3.307 closest distance to " OH  TYR A 214 " =    1.272
peak=   -3.305 closest distance to " OD1 ASN A 148 " =    1.523
peak=   -3.300 closest distance to " O   PRO A 198 " =    1.332
peak=   -3.298 closest distance to " O   HOH Z 174 " =    2.277
peak=   -3.297 closest distance to " CG  ARG A 269 " =    2.318
peak=   -3.293 closest distance to " CA  GLY A 203 " =    2.233
peak=   -3.290 closest distance to " CD2 LEU A 237 " =    2.685
peak=   -3.289 closest distance to " CG2 ILE A 263 " =    2.315
peak=   -3.286 closest distance to " SD BMET A  47 " =    2.871
peak=   -3.274 closest distance to " O   MET A  40 " =    2.674
peak=   -3.270 closest distance to " O   HOH Z 385 " =    1.962
peak=   -3.269 closest distance to " O   HOH Z 134 " =    2.675
peak=   -3.268 closest distance to " O   HOH Z 165 " =    1.966
peak=   -3.267 closest distance to " OG1 THR A 178 " =    1.261
peak=   -3.266 closest distance to " CG  GLU A   2 " =    1.902
peak=   -3.261 closest distance to " O   HOH Z 388 " =    2.067
peak=   -3.259 closest distance to " CA  TYR A  30 " =    2.867
peak=   -3.259 closest distance to " O   HOH Z 369 " =    2.109
peak=   -3.253 closest distance to " CG  GLU A  53 " =    1.492
peak=   -3.252 closest distance to " CE3 TRP A 150 " =    1.979
peak=   -3.251 closest distance to " O   HOH Z 234 " =    4.095
peak=   -3.250 closest distance to " CG  PRO A 163 " =    2.707
peak=   -3.250 closest distance to " O   HOH Z 417 " =    2.798
peak=   -3.247 closest distance to " O   HOH Z 193 " =    1.646
peak=   -3.245 closest distance to " CD1 TYR A 247 " =    2.398
peak=   -3.242 closest distance to " O   ALA A  51 " =    1.342
peak=   -3.241 closest distance to " CE BMET A  47 " =    1.905
peak=   -3.241 closest distance to " CG1 VAL A 230 " =    1.776
peak=   -3.240 closest distance to " O   HOH Z 283 " =    1.842
peak=   -3.239 closest distance to " O   HOH Z 148 " =    1.782
peak=   -3.235 closest distance to " CG2 ILE A  20 " =    2.783
peak=   -3.231 closest distance to " O   TRP A  70 " =    1.498
peak=   -3.228 closest distance to " N   ALA A 248 " =    1.874
peak=   -3.223 closest distance to " O   HOH Z 244 " =    2.054
peak=   -3.223 closest distance to " O   SER A  95 " =    1.572
peak=   -3.222 closest distance to " O   HOH Z 359 " =    3.122
peak=   -3.218 closest distance to " O   HOH Z 385 " =    2.110
peak=   -3.217 closest distance to " O   HOH Z 313 " =    1.837
peak=   -3.215 closest distance to " CB  ASN A  69 " =    1.124
peak=   -3.211 closest distance to " CG  GLU A 277 " =    1.143
peak=   -3.209 closest distance to " CA  GLY A 241 " =    3.072
peak=   -3.209 closest distance to " O   HOH Z 139 " =    3.029
peak=   -3.203 closest distance to " O   HOH Z 148 " =    3.054
peak=   -3.199 closest distance to " C   LEU A 222 " =    0.738
peak=   -3.198 closest distance to " O   HOH Z 411 " =    3.826
peak=   -3.198 closest distance to " CB  ALA A  51 " =    1.857
peak=   -3.190 closest distance to " CD2 TYR A 247 " =    2.473
peak=   -3.189 closest distance to " N   GLN A  77 " =    1.592
peak=   -3.189 closest distance to " O   HOH Z 423 " =    2.082
peak=   -3.185 closest distance to " O   SER A 210 " =    1.921
peak=   -3.184 closest distance to " SG ACYS A 201 " =    2.059
peak=   -3.184 closest distance to " CB  ALA A  43 " =    2.367
peak=   -3.180 closest distance to " NH1 ARG A 195 " =    2.576
peak=   -3.179 closest distance to " O   HOH Z 123 " =    2.310
peak=   -3.169 closest distance to " N   MET A 105 " =    2.634
peak=   -3.169 closest distance to " CZ  ARG A 259 " =    0.855
peak=   -3.164 closest distance to " O   HOH Z 292 " =    2.827
peak=   -3.162 closest distance to " CG1 VAL A 197 " =    2.221
peak=   -3.146 closest distance to " O   LYS A 117 " =    1.633
peak=   -3.145 closest distance to " O   VAL A 189 " =    2.583
peak=   -3.144 closest distance to " CD2 TYR A 293 " =    2.093
peak=   -3.135 closest distance to " O   LEU A 167 " =    1.513
peak=   -3.129 closest distance to " O   HOH Z 295 " =    1.480
peak=   -3.121 closest distance to " CG2 VAL A 189 " =    1.983
peak=   -3.120 closest distance to " O   HOH Z 150 " =    1.892
peak=   -3.114 closest distance to " O   HOH Z  44 " =    2.115
peak=   -3.113 closest distance to " O   HOH Z 210 " =    1.173
peak=   -3.113 closest distance to " ND2 ASN A 249 " =    2.362
peak=   -3.110 closest distance to " O   HOH Z  97 " =    1.694
peak=   -3.105 closest distance to " O   HOH Z 407 " =    3.212
peak=   -3.101 closest distance to " O   HOH Z  11 " =    2.003
peak=   -3.091 closest distance to " NE2 GLN A 103 " =    1.676
peak=   -3.085 closest distance to " O   HOH Z 350 " =    1.800
peak=   -3.071 closest distance to " OD1 ASP A 200 " =    1.331
peak=   -3.039 closest distance to " CB  ALA A 291 " =    2.130
peak=   -3.034 closest distance to " NE2 GLN A  58 " =    1.200
peak=   -3.032 closest distance to " O   SER A  22 " =    2.231
peak=   -3.031 closest distance to " NH2BARG A 145 " =    2.391
peak=   -3.022 closest distance to " O   HOH Z 175 " =    4.342

================= 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    :  0.4306 0.4260   6.223108e+00   6.209707e+00
   1_bss:  0.4223 0.4176   6.219467e+00   6.195230e+00
   1_xyz:  0.3194 0.3444   6.021964e+00   6.068386e+00
   1_adp:  0.2548 0.2975   5.839816e+00   5.956609e+00
   1_occ:  0.2543 0.2975   5.839028e+00   5.957407e+00
   2_bss:  0.2488 0.2913   5.836009e+00   5.951194e+00
   2_xyz:  0.1673 0.2127   5.478374e+00   5.670216e+00
   2_adp:  0.1496 0.1954   5.379681e+00   5.586615e+00
   2_occ:  0.1494 0.1950   5.378532e+00   5.585345e+00
   3_bss:  0.1485 0.1933   5.375464e+00   5.580046e+00
   3_xyz:  0.1220 0.1627   5.201089e+00   5.424670e+00
   3_adp:  0.1164 0.1593   5.169156e+00   5.401872e+00
   3_occ:  0.1163 0.1591   5.169025e+00   5.401843e+00
   4_bss:  0.1166 0.1590   5.169300e+00   5.401434e+00
   4_xyz:  0.1130 0.1571   5.152731e+00   5.392847e+00
   4_adp:  0.1135 0.1564   5.151145e+00   5.386312e+00
   4_occ:  0.1134 0.1563   5.150676e+00   5.385903e+00
   5_bss:  0.1134 0.1563   5.150676e+00   5.385903e+00
   5_xyz:  0.1083 0.1541   5.120817e+00   5.371330e+00
   5_adp:  0.1076 0.1551   5.123904e+00   5.380358e+00
   5_occ:  0.1073 0.1551   5.121989e+00   5.379243e+00
   5_bss:  0.1073 0.1551   5.121813e+00   5.379069e+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:  0.354  12.782   7.261   8.164   9.210   0.000   0.000   0.000
   1_xyz:  0.354  12.782   7.261   8.164   9.210   0.000   0.000   0.000
   1_adp:  0.354  12.782   7.261   8.164   9.210   0.000   0.000   0.000
   1_occ:  0.354  12.782   7.261   8.164   9.210   0.000   0.000   0.000
   2_bss:  0.334  31.706   3.836   4.281   6.018   0.000   0.000   0.000
   2_xyz:  0.334  31.706   3.836   4.281   6.018   0.000   0.000   0.000
   2_adp:  0.334  31.706   3.836   4.281   6.018   0.000   0.000   0.000
   2_occ:  0.334  31.706   3.836   4.281   6.018   0.000   0.000   0.000
   3_bss:  0.324  31.706   2.887   3.264   4.202   0.000   0.000   0.000
   3_xyz:  0.324  31.706   2.887   3.264   4.202   0.000   0.000   0.000
   3_adp:  0.324  31.706   2.887   3.264   4.202   0.000   0.000   0.000
   3_occ:  0.324  31.706   2.887   3.264   4.202   0.000   0.000   0.000
   4_bss:  0.323  37.935   2.786   3.124   3.815   0.000   0.000   0.000
   4_xyz:  0.323  37.935   2.786   3.124   3.815   0.000   0.000   0.000
   4_adp:  0.323  37.935   2.786   3.124   3.815   0.000   0.000   0.000
   4_occ:  0.323  37.935   2.786   3.124   3.815   0.000   0.000   0.000
   5_bss:  0.323  37.935   2.786   3.124   3.815   0.000   0.000   0.000
   5_xyz:  0.323  37.935   2.786   3.124   3.815   0.000   0.000   0.000
   5_adp:  0.323  37.935   2.786   3.124   3.815   0.000   0.000   0.000
   5_occ:  0.323  37.935   2.786   3.124   3.815   0.000   0.000   0.000
   5_bss:  0.323  42.439  -0.423  -0.109   0.532   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  48.086 0.5455  0.6201    52921.458
   1_bss:  48.305 0.5398  0.7791    50314.622
   1_xyz:  37.300 0.6732  0.9524    32462.290
   1_adp:  30.414 0.7533  1.0465    23264.703
   1_occ:  30.453 0.7529  1.0455    23283.308
   2_bss:  30.127 0.7562  0.9257    22833.489
   2_xyz:  20.542 0.8561  1.0069    11385.033
   2_adp:  18.287 0.8782  1.0231     9589.411
   2_occ:  18.259 0.8784  1.0230     9555.068
   3_bss:  18.118 0.8795  0.9768     9412.804
   3_xyz:  14.771 0.9085  0.9893     6771.012
   3_adp:  14.309 0.9125  0.9893     6500.463
   3_occ:  14.304 0.9125  0.9891     6497.145
   4_bss:  14.303 0.9126  0.9817     6517.920
   4_xyz:  14.022 0.9151  0.9819     6373.725
   4_adp:  13.830 0.9168  0.9825     6297.739
   4_occ:  13.819 0.9169  0.9824     6292.672
   5_bss:  13.819 0.9169  0.9824     6292.672
   5_xyz:  13.610 0.9183  0.9832     6131.071
   5_adp:  13.801 0.9168  0.9803     6228.423
   5_occ:  13.780 0.9170  0.9802     6214.985
   5_bss:  13.775 0.9170  0.9818     6214.285
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3463e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3463e+01
   1_xyz:   1.523  0.011  0.101 17.868  0.006  4.119   1.1788e-01
   1_adp:   1.523  0.011  0.101 17.868  0.006  4.119   1.1788e-01
   1_occ:   1.523  0.011  0.101 17.868  0.006  4.119   1.1788e-01
   2_bss:   1.523  0.011  0.101 17.868  0.006  4.119   1.1788e-01
   2_xyz:   1.000  0.007  0.074 15.939  0.004  4.121   6.2647e-02
   2_adp:   1.000  0.007  0.074 15.939  0.004  4.121   6.2647e-02
   2_occ:   1.000  0.007  0.074 15.939  0.004  4.121   6.2647e-02
   3_bss:   1.000  0.007  0.074 15.939  0.004  4.121   6.2647e-02
   3_xyz:   1.031  0.007  0.082 15.741  0.004  4.124   6.3379e-02
   3_adp:   1.031  0.007  0.082 15.741  0.004  4.124   6.3379e-02
   3_occ:   1.031  0.007  0.082 15.741  0.004  4.124   6.3379e-02
   4_bss:   1.031  0.007  0.082 15.741  0.004  4.124   6.3379e-02
   4_xyz:   0.942  0.006  0.076 15.452  0.004  4.112   5.5886e-02
   4_adp:   0.942  0.006  0.076 15.452  0.004  4.112   5.5886e-02
   4_occ:   0.942  0.006  0.076 15.452  0.004  4.112   5.5886e-02
   5_bss:   0.942  0.006  0.076 15.452  0.004  4.112   5.5886e-02
   5_xyz:   1.111  0.008  0.091 15.746  0.004  4.113   7.2683e-02
   5_adp:   1.111  0.008  0.091 15.746  0.004  4.113   7.2683e-02
   5_occ:   1.111  0.008  0.091 15.746  0.004  4.113   7.2683e-02
   5_bss:   1.111  0.008  0.091 15.746  0.004  4.113   7.2683e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9315e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9315e+00
   1_xyz:  12.806  0.139  0.429 88.416  0.045  2.244   8.6723e-02
   1_adp:  12.806  0.139  0.429 88.416  0.045  2.244   8.6723e-02
   1_occ:  12.806  0.139  0.429 88.416  0.045  2.244   8.6723e-02
   2_bss:  12.806  0.139  0.429 88.416  0.045  2.244   8.6723e-02
   2_xyz:   6.670  0.069  0.322 82.581  0.031  2.321   4.7792e-02
   2_adp:   6.670  0.069  0.322 82.581  0.031  2.321   4.7792e-02
   2_occ:   6.670  0.069  0.322 82.581  0.031  2.321   4.7792e-02
   3_bss:   6.670  0.069  0.322 82.581  0.031  2.321   4.7792e-02
   3_xyz:   6.548  0.044  0.573 83.098  0.037  2.309   4.4996e-02
   3_adp:   6.548  0.044  0.573 83.098  0.037  2.309   4.4996e-02
   3_occ:   6.548  0.044  0.573 83.098  0.037  2.309   4.4996e-02
   4_bss:   6.548  0.044  0.573 83.098  0.037  2.309   4.4996e-02
   4_xyz:   6.530  0.037  0.503 83.444  0.037  2.371   3.8430e-02
   4_adp:   6.530  0.037  0.503 83.444  0.037  2.371   3.8430e-02
   4_occ:   6.530  0.037  0.503 83.444  0.037  2.371   3.8430e-02
   5_bss:   6.530  0.037  0.503 83.444  0.037  2.371   3.8430e-02
   5_xyz:   7.039  0.047  0.696 82.650  0.040  2.219   5.5991e-02
   5_adp:   7.039  0.047  0.696 82.650  0.040  2.219   5.5991e-02
   5_occ:   7.039  0.047  0.696 82.650  0.040  2.219   5.5991e-02
   5_bss:   7.039  0.047  0.696 82.650  0.040  2.219   5.5991e-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:  64.08   0.00  10.83  63.47   0.00   7.69  64.08   0.00  27.93
   1_occ:  64.08   0.00  10.83  63.47   0.00   7.69  64.08   0.00  27.93
   2_bss:  64.08   0.00  10.83  63.47   0.00   7.69  64.08   0.00  27.93
   2_xyz:  64.08   0.00  10.83  63.47   0.00   7.69  64.08   0.00  27.93
   2_adp:  68.76   0.00  11.31  68.76   0.00   7.53  63.35   1.57  31.90
   2_occ:  68.76   0.00  11.31  68.76   0.00   7.53  63.35   1.57  31.90
   3_bss:  68.76   0.00  11.31  68.76   0.00   7.53  63.35   1.57  31.90
   3_xyz:  68.76   0.00  11.31  68.76   0.00   7.53  63.35   1.57  31.90
   3_adp:  78.30   0.00  11.72  78.30   0.00   7.57  70.48   0.96  34.27
   3_occ:  78.30   0.00  11.72  78.30   0.00   7.57  70.48   0.96  34.27
   4_bss:  78.30   0.00  11.72  78.30   0.00   7.57  70.48   0.96  34.27
   4_xyz:  78.30   0.00  11.72  78.30   0.00   7.57  70.48   0.96  34.27
   4_adp:  78.36   0.00  11.40  78.36   0.00   7.48  67.29   1.03  32.75
   4_occ:  78.36   0.00  11.40  78.36   0.00   7.48  67.29   1.03  32.75
   5_bss:  78.36   0.00  11.40  78.36   0.00   7.48  67.29   1.03  32.75
   5_xyz:  78.36   0.00  11.40  78.36   0.00   7.48  67.29   1.03  32.75
   5_adp:  80.08   0.00  11.49  80.08   0.00   7.51  67.18   1.07  33.18
   5_occ:  80.08   0.00  11.49  80.08   0.00   7.51  67.18   1.07  33.18
   5_bss:  83.37   3.28  14.78  83.37   3.28  10.79  70.46   4.35  36.46
------------------------------------------------------------------------
 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:    1.175    0.015    0.402
   1_adp:    1.175    0.015    0.402
   1_occ:    1.175    0.015    0.402
   2_bss:    1.175    0.015    0.402
   2_xyz:    1.387    0.037    0.514
   2_adp:    1.387    0.037    0.514
   2_occ:    1.387    0.037    0.514
   3_bss:    1.387    0.037    0.514
   3_xyz:    1.393    0.057    0.543
   3_adp:    1.393    0.057    0.543
   3_occ:    1.393    0.057    0.543
   4_bss:    1.393    0.057    0.543
   4_xyz:    1.488    0.047    0.558
   4_adp:    1.488    0.047    0.558
   4_occ:    1.488    0.047    0.558
   5_bss:    1.488    0.047    0.558
   5_xyz:    1.535    0.060    0.566
   5_adp:    1.535    0.060    0.566
   5_occ:    1.535    0.060    0.566
   5_bss:    1.535    0.060    0.566
------------------------------------------------------------------------

CPU time actual refinement: 270.71


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_662/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_662/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_662/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_662/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_662/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 270.59 
  Macro-tasks:
    bulk solvent and scale       = 34.75  
    individual site refinement   = 109.40 
    weights calculation          = 26.60  
    collect and process          = 5.40   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 176.24 
  Micro-tasks:
    mask                            = 1.41   
    f_calc                          = 82.22  
    alpha_beta                      = 7.15   
    target                          = 0.99   
    gradients_wrt_atomic_parameters = 91.35  
    fmodel                         = 5.77   
    r_factors                      = 0.16   
    phase_errors                   = 8.83   
    foms                           = 0.20   
    TOTAL for micro-tasks          = 198.08 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 3.823 micro seconds
Total CPU time: 4.70 minutes
from_scatterers_fft:    647 calls, 81.89 s
gradients_fft:          592 calls, 80.16 s

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

# Date 2008-01-16 Time 02:07:01 PST -0800 (1200478021.85 s)
Start R-work = 0.4306, R-free = 0.4260 (no bulk solvent and anisotropic scale)
Final R-work = 0.1248, R-free = 0.1712 (no bulk solvent and anisotropic scale)

Start R-work = 0.4223, R-free = 0.4176
Final R-work = 0.1073, R-free = 0.1551