# Date 2008-01-16 Time 01:32:23 PST -0800 (1200475943.26 s)
#phil __OFF__

Command line arguments: "../454.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 32715
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 454

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.5475, 47.6339, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 47.6339, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.885 1.9805
Completeness in resolution range: 0.962746
Completeness with d_max=infinity: 0.959728

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8850
                             d_min =   1.9805

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 47.6339, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.885 1.9805
Completeness in resolution range: 0.962746
Completeness with d_max=infinity: 0.959728

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8855 -  4.2371 [2137/2165]  1923   214  10.0%
  bin  2:  4.2371 -  3.3760 [2041/2064]  1837   204  10.0%
  bin  3:  3.3760 -  2.9531 [2031/2053]  1827   204  10.0%
  bin  4:  2.9531 -  2.6848 [2000/2019]  1804   196   9.8%
  bin  5:  2.6848 -  2.4933 [1999/2028]  1793   206  10.3%
  bin  6:  2.4933 -  2.3469 [1969/2010]  1777   192   9.8%
  bin  7:  2.3469 -  2.2298 [1973/2009]  1778   195   9.9%
  bin  8:  2.2298 -  2.1330 [1978/2016]  1775   203  10.3%
  bin  9:  2.1330 -  2.0511 [1946/1978]  1755   191   9.8%
  bin 10:  2.0511 -  1.9805 [1515/2005]  1361   154  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_454/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 28
        2.42 -     3.04: 2202
        3.04 -     3.66: 4726
        3.66 -     4.28: 9029
        4.28 -     4.90: 12399
  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  18 " - " O   HOH Z 102 "  1.883 3.040 -x+1,y+1/2,-z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.899 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.986 3.040 -x+1,y+1/2,-z+1/2
  " OG  SER A  95 " - " O   SER A 271 "  2.008 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28379 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_454/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_454/model_refine_001.geo

CPU time processing inputs: 9.19


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.5475 47.63395 85.5261 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: 1.98 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4704   r_free= 0.4585   ksol= 0.00   Bsol= 0.00   scale= 0.803    |
|                                                                             |
| 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:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.271018                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8855 -  4.7256 0.99   1385  155 0.3843 0.3714      6.5624      6.5719|
|  2:  4.7256 -  3.7709 0.99   1339  146 0.3878 0.3989      6.7539      6.7888|
|  3:  3.7709 -  3.3001 0.99   1308  152 0.4228 0.3836      6.6534      6.6485|
|  4:  3.3001 -  3.0011 0.99   1301  133 0.4466 0.4076      6.5034      6.4306|
|  5:  3.0011 -  2.7875 0.98   1279  146 0.4954 0.5041      6.3789      6.4002|
|  6:  2.7875 -  2.6241 0.98   1293  143 0.4950 0.5262      6.2717      6.2298|
|  7:  2.6241 -  2.4933 0.99   1279  149 0.4980 0.4551       6.248      6.1497|
|  8:  2.4933 -  2.3852 0.99   1279  136 0.5182 0.4807       6.183      6.1629|
|  9:  2.3852 -  2.2938 0.98   1285  146 0.5279 0.5441      6.1221      6.1489|
| 10:  2.2938 -  2.2149 0.97   1245  139 0.5196 0.5355      6.1151      6.1164|
| 11:  2.2149 -  2.1458 0.98   1260  143 0.5168 0.4810       6.036       6.067|
| 12:  2.1458 -  2.0847 0.99   1278  134 0.5326 0.5518       5.986      6.0154|
| 13:  2.0847 -  2.0299 0.97   1248  134 0.5289 0.5284      5.8927      5.8866|
| 14:  2.0299 -  1.9805 0.67    851  103 0.5522 0.4671      5.8816      5.7275|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8855 -  4.7256  1385   155  0.68  35.58   0.81     0.71      74338.84|
|  2:  4.7256 -  3.7709  1339   146  0.71  34.29   0.89     0.77      98447.66|
|  3:  3.7709 -  3.3001  1308   152  0.63  41.01   0.85     0.73     102439.72|
|  4:  3.3001 -  3.0011  1301   133  0.56  46.94   0.81     0.64      87722.20|
|  5:  3.0011 -  2.7875  1279   146  0.46  54.95   0.75     0.54      77006.11|
|  6:  2.7875 -  2.6241  1293   143  0.44  56.91   0.74     0.50      66088.30|
|  7:  2.6241 -  2.4933  1279   149  0.43  57.61   0.74     0.48      60751.84|
|  8:  2.4933 -  2.3852  1279   136  0.43  57.94   0.74     0.49      53710.68|
|  9:  2.3852 -  2.2938  1285   146  0.38  61.57   0.73     0.46      51826.65|
| 10:  2.2938 -  2.2149  1245   139  0.37  62.08   0.74     0.43      48715.15|
| 11:  2.2149 -  2.1458  1260   143  0.33  65.68   0.76     0.39      47337.46|
| 12:  2.1458 -  2.0847  1278   134  0.32  66.12   0.75     0.40      44049.20|
| 13:  2.0847 -  2.0299  1248   134  0.34  64.77   0.74     0.42      36447.08|
| 14:  2.0299 -  1.9805   851   103  0.43  57.83   0.72     0.47      25529.00|
|alpha:            min =        0.39 max =            0.77 mean =         0.53|
|beta:             min =    25529.00 max =       102439.72 mean =     63734.42|
|figures of merit: min =        0.00 max =            1.00 mean =         0.47|
|phase err.(work): min =        0.00 max =           90.00 mean =        54.19|
|phase err.(test): min =        0.00 max =           89.58 mean =        54.06|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.839792             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.092   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.019035              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.397   (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:        5 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      169 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      700 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1537 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2628 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3932 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5100 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6573 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7755 |
|-----------------------------------------------------------------------------|
|-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 |       53.588 |
| 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 |       1.945 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.809)------------------------------------------|
|    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 = 11.809)------------------------------------------|
|    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: 1.98 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4766   r_free= 0.4676   ksol= 0.00   Bsol= 0.00   scale= 0.772    |
|                                                                             |
| 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:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.272711                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4627   r_free= 0.4522   ksol= 0.35   Bsol= 20.00   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.90,10.70,7.66,0.00,0.00,0.00); trace/3= 8.42                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.263803                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.307920             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.662   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.048155              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.147   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4627      final r-factor (work) = 0.3716          |
| start r-factor (free) = 0.4522      final r-factor (free) = 0.3916          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 89.0650 = 11.31 * 0.50 * 6.2746 + 1.00 * 53.5884                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.9834 = 11.31 * 0.50 * 6.1620 + 1.00 * 0.1436                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3716      final r-factor (work) = 0.3212          |
| start r-factor (free) = 0.3916      final r-factor (free) = 0.3622          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.4734 = 1.05 * 1.00 * 6.1620 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3622 = 1.05 * 1.00 * 6.0544 + 1.00 * 0.0162                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.809)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.68   12.34    None  None   None       |
|    all(noH): 2823   0      0.00    81.68   12.34    None  None   None       |
|    Sol.    : 438    0      0.00    81.68   26.56    None  None   None       |
|    Mac.    : 2385   0      0.00    76.12   9.72     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 -   8.168: 1356   |   5:    40.839 -  49.006:   63        |
|      1:     8.168 -  16.335:  716   |   6:    49.006 -  57.174:   20        |
|      2:    16.335 -  24.503:  351   |   7:    57.174 -  65.342:   17        |
|      3:    24.503 -  32.671:  182   |   8:    65.342 -  73.509:    2        |
|      4:    32.671 -  40.839:  114   |   9:    73.509 -  81.677:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3212 r_free = 0.3622             target_work(ml) = 6.026         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3207 r_free = 0.3615             target_work(ml) = 6.025         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3207   r_free= 0.3615   ksol= 0.35   Bsol= 20.00   scale= 1.093   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.90,10.70,7.66,0.00,0.00,0.00); trace/3= 8.42                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 6.025460                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3185   r_free= 0.3569   ksol= 0.31   Bsol= 33.90   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.64,6.82,4.84,0.00,0.00,0.00); trace/3= 5.10                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 6.026399                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.611526              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.833   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.431304              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.597  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3185      final r-factor (work) = 0.2302          |
| start r-factor (free) = 0.3569      final r-factor (free) = 0.2749          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.1231 = 5.61 * 0.50 * 6.0520 + 1.00 * 0.1427                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.5762 = 5.61 * 0.50 * 5.8810 + 1.00 * 0.0756                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2302      final r-factor (work) = 0.2083          |
| start r-factor (free) = 0.2749      final r-factor (free) = 0.2563          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5531 = 0.43 * 1.00 * 5.8810 + 1.00 * 0.0166                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4728 = 0.43 * 1.00 * 5.7077 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.809)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.25   12.36    None  None   None       |
|    all(noH): 2823   0      0.00    79.25   12.36    None  None   None       |
|    Sol.    : 438    0      1.49    76.80   31.53    None  None   None       |
|    Mac.    : 2385   0      0.00    79.25   8.85     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 -   7.925: 1439   |   5:    39.624 -  47.549:   99        |
|      1:     7.925 -  15.850:  709   |   6:    47.549 -  55.474:   50        |
|      2:    15.850 -  23.774:  242   |   7:    55.474 -  63.398:   17        |
|      3:    23.774 -  31.699:  146   |   8:    63.398 -  71.323:    9        |
|      4:    31.699 -  39.624:  110   |   9:    71.323 -  79.248:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2083 r_free = 0.2563             target_work(ml) = 5.674         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2080 r_free = 0.2564             target_work(ml) = 5.674         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2080   r_free= 0.2564   ksol= 0.31   Bsol= 33.90   scale= 1.047   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.64,6.82,4.84,0.00,0.00,0.00); trace/3= 5.10                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.673675                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2063   r_free= 0.2560   ksol= 0.31   Bsol= 33.90   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.18,4.32,3.57,0.00,0.00,0.00); trace/3= 3.36                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.673564                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.987675              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.136  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.205662              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.548  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2063      final r-factor (work) = 0.1523          |
| start r-factor (free) = 0.2560      final r-factor (free) = 0.1938          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6105 = 2.99 * 0.50 * 5.7134 + 1.00 * 0.0756                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3499 = 2.99 * 0.50 * 5.5477 + 1.00 * 0.0626                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1523      final r-factor (work) = 0.1433          |
| start r-factor (free) = 0.1938      final r-factor (free) = 0.1813          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1519 = 0.21 * 1.00 * 5.5477 + 1.00 * 0.0110                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1118 = 0.21 * 1.00 * 5.3624 + 1.00 * 0.0089                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.809)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.14   12.30    None  None   None       |
|    all(noH): 2823   0      0.00    76.14   12.30    None  None   None       |
|    Sol.    : 438    0      1.74    68.59   33.11    None  None   None       |
|    Mac.    : 2385   0      0.00    76.14   8.48     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 -   7.614: 1446   |   5:    38.070 -  45.684:  101        |
|      1:     7.614 -  15.228:  745   |   6:    45.684 -  53.297:   66        |
|      2:    15.228 -  22.842:  191   |   7:    53.297 -  60.911:   30        |
|      3:    22.842 -  30.456:  111   |   8:    60.911 -  68.525:    8        |
|      4:    30.456 -  38.070:  121   |   9:    68.525 -  76.139:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1433 r_free = 0.1813             target_work(ml) = 5.331         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1430 r_free = 0.1812             target_work(ml) = 5.331         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1430   r_free= 0.1812   ksol= 0.31   Bsol= 33.90   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.18,4.32,3.57,0.00,0.00,0.00); trace/3= 3.36                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.330877                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1431   r_free= 0.1813   ksol= 0.32   Bsol= 44.23   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.62,3.12,3.03,0.00,0.00,0.00); trace/3= 2.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.331839                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.575714              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.276  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.299615              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.262  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1431      final r-factor (work) = 0.1228          |
| start r-factor (free) = 0.1813      final r-factor (free) = 0.1634          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9738 = 2.58 * 0.50 * 5.3665 + 1.00 * 0.0626                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8424 = 2.58 * 0.50 * 5.2622 + 1.00 * 0.0654                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1228      final r-factor (work) = 0.1192          |
| start r-factor (free) = 0.1634      final r-factor (free) = 0.1610          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5856 = 0.30 * 1.00 * 5.2622 + 1.00 * 0.0089                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5655 = 0.30 * 1.00 * 5.1917 + 1.00 * 0.0099                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.809)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.17   12.42    None  None   None       |
|    all(noH): 2823   0      0.00    77.17   12.42    None  None   None       |
|    Sol.    : 438    0      1.62    66.49   34.35    None  None   None       |
|    Mac.    : 2385   0      0.00    77.17   8.39     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 -   7.717: 1501   |   5:    38.585 -  46.302:  100        |
|      1:     7.717 -  15.434:  706   |   6:    46.302 -  54.019:   70        |
|      2:    15.434 -  23.151:  173   |   7:    54.019 -  61.736:   39        |
|      3:    23.151 -  30.868:  110   |   8:    61.736 -  69.453:    8        |
|      4:    30.868 -  38.585:  112   |   9:    69.453 -  77.170:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1192 r_free = 0.1610             target_work(ml) = 5.185         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1191 r_free = 0.1610             target_work(ml) = 5.184         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1191   r_free= 0.1610   ksol= 0.32   Bsol= 44.23   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.62,3.12,3.03,0.00,0.00,0.00); trace/3= 2.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.184395                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1190   r_free= 0.1609   ksol= 0.33   Bsol= 44.23   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.58,2.78,2.95,0.00,0.00,0.00); trace/3= 2.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.184428                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.112396              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 125.991  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.381490              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 156.127  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1190      final r-factor (work) = 0.1120          |
| start r-factor (free) = 0.1609      final r-factor (free) = 0.1568          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1442 = 3.11 * 0.50 * 5.1914 + 1.00 * 0.0654                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1035 = 3.11 * 0.50 * 5.1584 + 1.00 * 0.0760                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1120      final r-factor (work) = 0.1110          |
| start r-factor (free) = 0.1568      final r-factor (free) = 0.1571          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9777 = 0.38 * 1.00 * 5.1584 + 1.00 * 0.0099                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9725 = 0.38 * 1.00 * 5.1399 + 1.00 * 0.0116                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.809)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.97   12.36    None  None   None       |
|    all(noH): 2823   0      0.00    79.97   12.36    None  None   None       |
|    Sol.    : 438    0      1.35    67.32   34.46    None  None   None       |
|    Mac.    : 2385   0      0.00    79.97   8.30     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 -   7.997: 1578   |   5:    39.986 -  47.983:  101        |
|      1:     7.997 -  15.994:  655   |   6:    47.983 -  55.980:   64        |
|      2:    15.994 -  23.992:  160   |   7:    55.980 -  63.978:   25        |
|      3:    23.992 -  31.989:  119   |   8:    63.978 -  71.975:    9        |
|      4:    31.989 -  39.986:  107   |   9:    71.975 -  79.972:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1110 r_free = 0.1571             target_work(ml) = 5.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1110 r_free = 0.1572             target_work(ml) = 5.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1110   r_free= 0.1572   ksol= 0.33   Bsol= 44.23   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.58,2.78,2.95,0.00,0.00,0.00); trace/3= 2.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.140850                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8855 -  4.7256 0.99   1385  155 0.1021 0.1325      5.3959      5.5362|
|  2:  4.7256 -  3.7709 0.99   1339  146 0.0866 0.1116      5.4458      5.6559|
|  3:  3.7709 -  3.3001 0.99   1308  152 0.1038 0.1507      5.4663      5.8543|
|  4:  3.3001 -  3.0011 0.99   1301  133 0.1209 0.1523      5.4436      5.6173|
|  5:  3.0011 -  2.7875 0.98   1279  146 0.1297 0.1592      5.3247      5.4819|
|  6:  2.7875 -  2.6241 0.98   1293  143 0.1274 0.1936      5.2376      5.4954|
|  7:  2.6241 -  2.4933 0.99   1279  149 0.1198 0.1640      5.1535      5.3905|
|  8:  2.4933 -  2.3852 0.99   1279  136 0.1168 0.1806      5.0831      5.3554|
|  9:  2.3852 -  2.2938 0.98   1285  146 0.1160 0.1832      5.0253       5.315|
| 10:  2.2938 -  2.2149 0.97   1245  139 0.1119 0.1806      4.9707      5.2105|
| 11:  2.2149 -  2.1458 0.98   1260  143 0.1108 0.1617      4.9106      5.2331|
| 12:  2.1458 -  2.0847 0.99   1278  134 0.1057 0.1700      4.8385      5.1394|
| 13:  2.0847 -  2.0299 0.97   1248  134 0.1093 0.1678      4.7738      5.0295|
| 14:  2.0299 -  1.9805 0.67    851  103 0.1061 0.1639      4.6837      4.9005|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8855 -  4.7256  1385   155  0.94   9.08   0.98     0.96       7273.15|
|  2:  4.7256 -  3.7709  1339   146  0.95   8.26   1.02     1.00       9304.75|
|  3:  3.7709 -  3.3001  1308   152  0.93  11.22   1.02     1.01      10507.70|
|  4:  3.3001 -  3.0011  1301   133  0.92  13.61   1.00     0.99      10063.35|
|  5:  3.0011 -  2.7875  1279   146  0.90  15.67   0.99     0.96       8221.41|
|  6:  2.7875 -  2.6241  1293   143  0.90  16.27   0.98     0.95       7336.24|
|  7:  2.6241 -  2.4933  1279   149  0.90  15.57   0.98     0.95       6179.17|
|  8:  2.4933 -  2.3852  1279   136  0.91  15.14   0.99     0.96       5526.95|
|  9:  2.3852 -  2.2938  1285   146  0.90  15.91   1.00     0.98       5032.32|
| 10:  2.2938 -  2.2149  1245   139  0.90  15.82   1.00     0.96       4568.08|
| 11:  2.2149 -  2.1458  1260   143  0.91  15.37   1.00     0.96       4090.70|
| 12:  2.1458 -  2.0847  1278   134  0.92  14.63   1.00     0.99       3666.11|
| 13:  2.0847 -  2.0299  1248   134  0.91  15.39   1.00     0.99       3257.68|
| 14:  2.0299 -  1.9805   851   103  0.91  15.44   0.98     0.94       2673.88|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2673.88 max =        10507.70 mean =      6391.17|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.01|
|phase err.(test): min =        0.00 max =           89.08 mean =        13.47|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1109   r_free= 0.1568   ksol= 0.33   Bsol= 46.74   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.82,0.29,0.54,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.140514                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1109   r_free= 0.1568   ksol= 0.33   Bsol= 46.74   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.82,0.29,0.54,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.140514                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8855 -  4.7256 0.99   1385  155 0.1000 0.1301      5.3867      5.5397|
|  2:  4.7256 -  3.7709 0.99   1339  146 0.0880 0.1116      5.4546      5.6623|
|  3:  3.7709 -  3.3001 0.99   1308  152 0.1040 0.1496      5.4689       5.844|
|  4:  3.3001 -  3.0011 0.99   1301  133 0.1214 0.1521      5.4447      5.6175|
|  5:  3.0011 -  2.7875 0.98   1279  146 0.1297 0.1590      5.3247      5.4796|
|  6:  2.7875 -  2.6241 0.98   1293  143 0.1273 0.1939      5.2374      5.4952|
|  7:  2.6241 -  2.4933 0.99   1279  149 0.1194 0.1637      5.1514      5.3908|
|  8:  2.4933 -  2.3852 0.99   1279  136 0.1163 0.1799      5.0809      5.3549|
|  9:  2.3852 -  2.2938 0.98   1285  146 0.1157 0.1824      5.0239      5.3105|
| 10:  2.2938 -  2.2149 0.97   1245  139 0.1117 0.1813      4.9694      5.2129|
| 11:  2.2149 -  2.1458 0.98   1260  143 0.1107 0.1616      4.9107      5.2317|
| 12:  2.1458 -  2.0847 0.99   1278  134 0.1055 0.1707      4.8383       5.143|
| 13:  2.0847 -  2.0299 0.97   1248  134 0.1093 0.1681      4.7741      5.0297|
| 14:  2.0299 -  1.9805 0.67    851  103 0.1061 0.1632      4.6831      4.8984|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8855 -  4.7256  1385   155  0.94   9.11   0.98     0.96       7235.18|
|  2:  4.7256 -  3.7709  1339   146  0.95   8.39   1.02     1.00       9372.20|
|  3:  3.7709 -  3.3001  1308   152  0.93  11.24   1.02     1.01      10605.39|
|  4:  3.3001 -  3.0011  1301   133  0.92  13.53   1.01     0.99       9996.63|
|  5:  3.0011 -  2.7875  1279   146  0.90  15.65   0.99     0.96       8203.41|
|  6:  2.7875 -  2.6241  1293   143  0.90  16.29   0.98     0.95       7338.69|
|  7:  2.6241 -  2.4933  1279   149  0.91  15.56   0.99     0.96       6176.32|
|  8:  2.4933 -  2.3852  1279   136  0.91  15.12   1.00     0.97       5505.88|
|  9:  2.3852 -  2.2938  1285   146  0.90  15.89   1.01     0.98       5021.43|
| 10:  2.2938 -  2.2149  1245   139  0.90  15.80   1.00     0.97       4555.92|
| 11:  2.2149 -  2.1458  1260   143  0.91  15.37   1.00     0.97       4095.14|
| 12:  2.1458 -  2.0847  1278   134  0.92  14.66   1.01     0.99       3672.74|
| 13:  2.0847 -  2.0299  1248   134  0.91  15.41   1.00     1.00       3261.43|
| 14:  2.0299 -  1.9805   851   103  0.91  15.43   0.98     0.95       2669.18|
|alpha:            min =        0.95 max =            1.01 mean =         0.98|
|beta:             min =     2669.18 max =        10605.39 mean =      6391.96|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.01|
|phase err.(test): min =        0.00 max =           88.86 mean =        13.45|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.809)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.51    82.48   14.88    None  None   None       |
|    all(noH): 2823   0      2.51    82.48   14.88    None  None   None       |
|    Sol.    : 438    0      3.87    69.84   36.98    None  None   None       |
|    Mac.    : 2385   0      2.51    82.48   10.82    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:     2.513 -  10.510: 1578   |   5:    42.499 -  50.496:  101        |
|      1:    10.510 -  18.507:  655   |   6:    50.496 -  58.493:   64        |
|      2:    18.507 -  26.504:  160   |   7:    58.493 -  66.490:   25        |
|      3:    26.504 -  34.502:  119   |   8:    66.490 -  74.488:    9        |
|      4:    34.502 -  42.499:  107   |   9:    74.488 -  82.485:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 320         
Filter by distance & map next to the model:
   mapped sites are within: 0.345 - 4.879
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 314 from: 320
   mapped sites are within: 0.728 - 4.879

peak=   10.604 closest distance to " CB  VAL A 230 " =    1.447
peak=    6.244 closest distance to " CG  LEU A   5 " =    1.221
peak=    6.120 closest distance to " CB  VAL A 296 " =    1.128
peak=    5.906 closest distance to " CG2 VAL A 296 " =    1.020
peak=    5.697 closest distance to " NH2 ARG A  56 " =    2.275
peak=    5.482 closest distance to " O   HOH Z 124 " =    1.577
peak=    5.283 closest distance to " CG  LEU A 228 " =    1.188
peak=    5.197 closest distance to " O   HOH Z 209 " =    2.326
peak=    5.193 closest distance to " O   HOH Z 402 " =    1.583
peak=    5.143 closest distance to " CB  SER A  63 " =    1.170
peak=    5.128 closest distance to " O   HOH Z 403 " =    1.784
peak=    5.036 closest distance to " CB  ARG A 275 " =    0.901
peak=    4.985 closest distance to " CG  PRO A  54 " =    1.215
peak=    4.913 closest distance to " O   HOH Z 272 " =    1.922
peak=    4.848 closest distance to " CB  GLN A 223 " =    1.382
peak=    4.837 closest distance to " O   SER A  87 " =    2.192
peak=    4.810 closest distance to " CB  GLN A 183 " =    1.306
peak=    4.800 closest distance to " O   HOH Z 193 " =    1.822
peak=    4.770 closest distance to " CD1AILE A 234 " =    1.070
peak=    4.570 closest distance to " O   HOH Z 232 " =    2.345
peak=    4.541 closest distance to " O   HOH Z  85 " =    1.447
peak=    4.503 closest distance to " O   HOH Z  80 " =    1.814
peak=    4.487 closest distance to " O   HOH Z  63 " =    2.249
peak=    4.459 closest distance to " CG  PRO A 213 " =    1.198
peak=    4.412 closest distance to " O   HOH Z 414 " =    1.772
peak=    4.401 closest distance to " CB  GLU A 152 " =    1.126
peak=    4.388 closest distance to " O   HOH Z 126 " =    1.859
peak=    4.381 closest distance to " O   HOH Z 368 " =    2.285
peak=    4.359 closest distance to " CB  VAL A 230 " =    1.162
peak=    4.357 closest distance to " C   PRO A 198 " =    1.486
peak=    4.352 closest distance to " O   HOH Z 298 " =    1.845
peak=    4.352 closest distance to " O   HOH Z  97 " =    1.902
peak=    4.339 closest distance to " O   HOH Z 423 " =    1.797
peak=    4.331 closest distance to " O   HOH Z 234 " =    3.603
peak=    4.331 closest distance to " CD2 LEU A   5 " =    1.094
peak=    4.325 closest distance to " CB  PRO A  54 " =    0.824
peak=    4.320 closest distance to " NE2 GLN A  11 " =    1.040
peak=    4.314 closest distance to " CA  TYR A  30 " =    0.956
peak=    4.283 closest distance to " CD2 LEU A 228 " =    1.208
peak=    4.281 closest distance to " CB  SER A   3 " =    1.244
peak=    4.263 closest distance to " O   HOH Z  40 " =    1.770
peak=    4.253 closest distance to " O   HOH Z  59 " =    2.385
peak=    4.228 closest distance to " O   HOH Z  48 " =    1.792
peak=    4.169 closest distance to " O   HOH Z 102 " =    1.336
peak=    4.156 closest distance to " CB  GLU A 277 " =    3.553
peak=    4.150 closest distance to " OD1 ASN A  69 " =    2.552
peak=    4.147 closest distance to " O   HOH Z 142 " =    1.628
peak=    4.141 closest distance to " O   HOH Z 189 " =    2.441
peak=    4.141 closest distance to " CG  ARG A  66 " =    2.856
peak=    4.111 closest distance to " O   HOH Z  54 " =    1.577
peak=    4.060 closest distance to " O   HOH Z 369 " =    2.198
peak=    4.049 closest distance to " CG1 ILE A  33 " =    1.274
peak=    4.042 closest distance to " CB  ARG A 190 " =    1.702
peak=    4.033 closest distance to " O   HOH Z 137 " =    1.737
peak=    4.028 closest distance to " O   HOH Z 303 " =    2.125
peak=    4.022 closest distance to " O   HOH Z 263 " =    1.574
peak=    4.021 closest distance to " O   HOH Z 346 " =    1.491
peak=    4.019 closest distance to " O   HOH Z 214 " =    2.428
peak=    4.015 closest distance to " O   HOH Z 203 " =    1.761
peak=    4.008 closest distance to " CG1BVAL A  72 " =    1.691
peak=    4.008 closest distance to " CB  TRP A 179 " =    1.252
peak=    4.001 closest distance to " O   HOH Z 426 " =    1.509
peak=    3.977 closest distance to " O   HOH Z 134 " =    1.631
peak=    3.964 closest distance to " O   HOH Z 345 " =    2.906
peak=    3.951 closest distance to " O   HOH Z 227 " =    1.632
peak=    3.949 closest distance to " CA  ALA A  51 " =    1.014
peak=    3.939 closest distance to " CB  TYR A 169 " =    0.834
peak=    3.928 closest distance to " O   HOH Z 419 " =    1.801
peak=    3.923 closest distance to " O   HOH Z 245 " =    1.441
peak=    3.915 closest distance to " O   HOH Z 327 " =    1.629
peak=    3.913 closest distance to " O   HOH Z  43 " =    2.261
peak=    3.902 closest distance to " O   HOH Z 247 " =    1.328
peak=    3.896 closest distance to " O   HOH Z 316 " =    2.950
peak=    3.893 closest distance to " O   HOH Z  15 " =    2.009
peak=    3.889 closest distance to " O   HOH Z  61 " =    1.599
peak=    3.887 closest distance to " OG1 THR A 294 " =    2.283
peak=    3.881 closest distance to " ND2 ASN A 187 " =    1.617
peak=    3.872 closest distance to " O   HOH Z 236 " =    1.876
peak=    3.865 closest distance to " CB  ASN A 148 " =    1.328
peak=    3.859 closest distance to " CB  ARG A  79 " =    1.377
peak=    3.852 closest distance to " CD  ARG A 269 " =    1.029
peak=    3.851 closest distance to " O   HOH Z 389 " =    1.968
peak=    3.850 closest distance to " CB  ASN A  39 " =    0.796
peak=    3.837 closest distance to " O   HOH Z 416 " =    2.687
peak=    3.833 closest distance to " O   TRP A 274 " =    1.925
peak=    3.826 closest distance to " OG BSER A 164 " =    2.191
peak=    3.823 closest distance to " CB  SER A  26 " =    1.689
peak=    3.816 closest distance to " OE1 GLU A   2 " =    2.087
peak=    3.815 closest distance to " CA  ALA A  21 " =    1.214
peak=    3.814 closest distance to " CD  LYS A 166 " =    1.348
peak=    3.812 closest distance to " CB  ALA A   9 " =    1.574
peak=    3.811 closest distance to " O   HOH Z 154 " =    1.412
peak=    3.809 closest distance to " O   HOH Z 248 " =    1.669
peak=    3.804 closest distance to " NZ  LYS A 117 " =    3.115
peak=    3.794 closest distance to " O   HOH Z 128 " =    1.925
peak=    3.786 closest distance to " CG  PRO A 198 " =    1.167
peak=    3.785 closest distance to " O   HOH Z 411 " =    3.587
peak=    3.784 closest distance to " O   HOH Z 371 " =    3.320
peak=    3.784 closest distance to " N   ASN A  39 " =    1.245
peak=    3.776 closest distance to " O   ASP A 124 " =    1.441
peak=    3.772 closest distance to " O   HOH Z  78 " =    1.664
peak=    3.759 closest distance to " CB  GLU A 128 " =    1.070
peak=    3.756 closest distance to " O   HOH Z 126 " =    1.872
peak=    3.756 closest distance to " CA  VAL A  41 " =    0.825
peak=    3.755 closest distance to " O   HOH Z 357 " =    1.926
peak=    3.755 closest distance to " CD2 TRP A 179 " =    1.392
peak=    3.750 closest distance to " O   HOH Z 366 " =    2.936
peak=    3.738 closest distance to " O   HOH Z 420 " =    1.947
peak=    3.738 closest distance to " NH2 ARG A 156 " =    1.085
peak=    3.730 closest distance to " O   HOH Z 406 " =    1.567
peak=    3.727 closest distance to " CB  ALA A 100 " =    1.228
peak=    3.726 closest distance to " CG2 ILE A  20 " =    1.412
peak=    3.715 closest distance to " CA  LYS A 117 " =    1.331
peak=    3.714 closest distance to " CG2 THR A 221 " =    1.253
peak=    3.708 closest distance to " O   HOH Z 344 " =    2.895
peak=    3.708 closest distance to " O   HOH Z  66 " =    2.330
peak=    3.703 closest distance to " CB  ARG A 139 " =    0.965
peak=    3.702 closest distance to " NH2BARG A 145 " =    2.117
peak=    3.700 closest distance to " CG  ARG A  66 " =    0.973
peak=    3.689 closest distance to " CB  VAL A 265 " =    1.311
peak=    3.688 closest distance to " CG  PRO A 243 " =    1.184
peak=    3.685 closest distance to " O   HOH Z 261 " =    1.848
peak=    3.671 closest distance to " O   HOH Z 250 " =    1.397
peak=    3.664 closest distance to " O   HOH Z 126 " =    1.587
peak=    3.661 closest distance to " O   HOH Z 197 " =    2.569
peak=    3.660 closest distance to " O   HOH Z 284 " =    2.977
peak=    3.653 closest distance to " O   HOH Z 193 " =    2.116
peak=    3.651 closest distance to " O   HOH Z 128 " =    2.133
peak=    3.642 closest distance to " O   HOH Z 158 " =    2.992
peak=    3.639 closest distance to " O   HOH Z 417 " =    3.202
peak=    3.622 closest distance to " OD2 ASP A 286 " =    2.815
peak=    3.617 closest distance to " O   HOH Z 261 " =    2.197
peak=    3.600 closest distance to " CG  GLN A  58 " =    2.647
peak=    3.596 closest distance to " CB BVAL A  41 " =    1.023
peak=    3.594 closest distance to " O   HOH Z  21 " =    1.868
peak=    3.592 closest distance to " CE  LYS A 119 " =    1.088
peak=    3.586 closest distance to " O   HOH Z  67 " =    1.829
peak=    3.575 closest distance to " O   HOH Z 147 " =    1.836
peak=    3.574 closest distance to " O   HOH Z 128 " =    1.682
peak=    3.572 closest distance to " CB  ARG A  79 " =    0.873
peak=    3.570 closest distance to " CG2AVAL A 121 " =    2.112
peak=    3.569 closest distance to " NH1BARG A 190 " =    2.156
peak=    3.566 closest distance to " O   HOH Z 408 " =    1.611
peak=    3.564 closest distance to " O   HOH Z 383 " =    1.938
peak=    3.564 closest distance to " O   HOH Z 185 " =    1.654
peak=    3.558 closest distance to " O   HOH Z 329 " =    3.869
peak=    3.557 closest distance to " CD  LYS A 119 " =    2.003
peak=    3.553 closest distance to " O   HOH Z 394 " =    1.576
peak=    3.552 closest distance to " CB  TRP A 266 " =    0.993
peak=    3.547 closest distance to " O   HOH Z  97 " =    2.499
peak=    3.544 closest distance to " CA  ASP A 191 " =    0.961
peak=    3.540 closest distance to " O   HOH Z 273 " =    2.779
peak=    3.539 closest distance to " O   HOH Z 265 " =    2.391
peak=    3.530 closest distance to " O   HOH Z 422 " =    2.599
peak=    3.529 closest distance to " CE1 HIS A 108 " =    1.121
peak=    3.524 closest distance to " CB  VAL A 202 " =    1.462
peak=    3.515 closest distance to " CA  ASP A 140 " =    1.201
peak=    3.512 closest distance to " O   HOH Z 130 " =    2.326
peak=    3.512 closest distance to " O   HOH Z 345 " =    1.646
peak=    3.512 closest distance to " CA  ALA A 295 " =    1.008
peak=    3.504 closest distance to " OE1 GLN A  11 " =    1.836
peak=    3.503 closest distance to " CG  GLN A  77 " =    2.289
peak=    3.502 closest distance to " O   HOH Z 257 " =    2.307
peak=    3.497 closest distance to " O   HOH Z 421 " =    1.790
peak=    3.497 closest distance to " O   HOH Z  47 " =    1.550
peak=    3.488 closest distance to " O   HOH Z 427 " =    2.786
peak=    3.484 closest distance to " CG AARG A 275 " =    1.196
peak=    3.476 closest distance to " CE1 TYR A 186 " =    1.241
peak=    3.469 closest distance to " CB  ALA A 248 " =    1.380
peak=    3.451 closest distance to " O   GLY A  91 " =    1.396
peak=    3.446 closest distance to " O   HOH Z 112 " =    1.671
peak=    3.445 closest distance to " O   ALA A 165 " =    1.395
peak=    3.437 closest distance to " CB  SER A 141 " =    1.065
peak=    3.435 closest distance to " CG  MET A 185 " =    1.071
peak=    3.434 closest distance to " OD1 ASP A 286 " =    1.765
peak=    3.429 closest distance to " O   HOH Z 409 " =    3.845
peak=    3.428 closest distance to " CB  ASP A 140 " =    0.846
peak=    3.421 closest distance to " O   HOH Z 387 " =    2.498
peak=    3.420 closest distance to " CG BARG A 102 " =    1.785
peak=    3.417 closest distance to " O   HOH Z   4 " =    1.746
peak=    3.407 closest distance to " CB  ALA A 295 " =    1.245
peak=    3.399 closest distance to " O   HOH Z 163 " =    1.395
peak=    3.397 closest distance to " NH2AARG A 275 " =    3.752
peak=    3.394 closest distance to " O   ALA A   1 " =    1.735
peak=    3.394 closest distance to " O   HOH Z 145 " =    2.500
peak=    3.390 closest distance to " O   HOH Z 423 " =    3.152
peak=    3.390 closest distance to " OG  SER A 276 " =    1.441
peak=    3.388 closest distance to " CB  LEU A   5 " =    1.231
peak=    3.388 closest distance to " O   HOH Z 261 " =    2.122
peak=    3.382 closest distance to " CG1 ILE A  49 " =    1.525
peak=    3.382 closest distance to " O   HOH Z 417 " =    2.501
peak=    3.378 closest distance to " N   SER A 135 " =    1.292
peak=    3.373 closest distance to " CA  ARG A 195 " =    1.116
peak=    3.370 closest distance to " O   HOH Z  40 " =    2.606
peak=    3.363 closest distance to " O   HOH Z 227 " =    2.181
peak=    3.363 closest distance to " CA  ASN A 176 " =    0.980
peak=    3.361 closest distance to " OH  TYR A 116 " =    1.121
peak=    3.361 closest distance to " O   HOH Z 425 " =    2.089
peak=    3.361 closest distance to " CB  ALA A  71 " =    1.291
peak=    3.358 closest distance to " ND2 ASN A 110 " =    1.620
peak=    3.355 closest distance to " O   HOH Z 250 " =    1.534
peak=    3.348 closest distance to " O   HOH Z  46 " =    1.413
peak=    3.343 closest distance to " O   HOH Z   9 " =    2.238
peak=    3.337 closest distance to " CA  ASP A 162 " =    1.141
peak=    3.334 closest distance to " CD1 LEU A  96 " =    0.728
peak=    3.333 closest distance to " CG2 VAL A 197 " =    1.061
peak=    3.328 closest distance to " CB  THR A  31 " =    1.634
peak=    3.326 closest distance to " O   HOH Z 435 " =    1.848
peak=    3.326 closest distance to " O   HOH Z 433 " =    1.423
peak=    3.324 closest distance to " CD BLYS A 290 " =    1.129
peak=    3.320 closest distance to " OD1 ASN A  60 " =    1.636
peak=    3.318 closest distance to " O   HOH Z  44 " =    1.878
peak=    3.312 closest distance to " CZ  PHE A 218 " =    1.162
peak=    3.305 closest distance to " NH2 ARG A  79 " =    1.361
peak=    3.303 closest distance to " O   HOH Z 189 " =    2.663
peak=    3.303 closest distance to " O   HOH Z 358 " =    2.313
peak=    3.300 closest distance to " CG1 VAL A 153 " =    1.000
peak=    3.300 closest distance to " CA  TYR A 116 " =    1.407
peak=    3.300 closest distance to " O   HOH Z 166 " =    1.527
peak=    3.296 closest distance to " O   HOH Z  88 " =    3.111
peak=    3.291 closest distance to " C   ALA A 299 " =    0.932
peak=    3.290 closest distance to " CB  PRO A 198 " =    1.045
peak=    3.287 closest distance to " O   HOH Z 214 " =    2.365
peak=    3.282 closest distance to " OD2 ASP A 298 " =    3.908
peak=    3.275 closest distance to " CG2 ILE A 234 " =    2.070
peak=    3.274 closest distance to " O   HOH Z 299 " =    4.260
peak=    3.271 closest distance to " O   HOH Z  83 " =    1.563
peak=    3.267 closest distance to " NZ  LYS A 166 " =    3.000
peak=    3.264 closest distance to " O   HOH Z 389 " =    1.864
peak=    3.258 closest distance to " O   HOH Z 281 " =    4.615
peak=    3.257 closest distance to " O   HOH Z 280 " =    2.497
peak=    3.253 closest distance to " O   HOH Z 132 " =    2.766
peak=    3.251 closest distance to " CB  ARG A 259 " =    1.881
peak=    3.250 closest distance to " CH2 TRP A 274 " =    1.890
peak=    3.246 closest distance to " O   HOH Z 359 " =    1.782
peak=    3.246 closest distance to " O   HOH Z 417 " =    2.004
peak=    3.245 closest distance to " CD1 LEU A 300 " =    1.127
peak=    3.245 closest distance to " CD2 TYR A  30 " =    0.851
peak=    3.243 closest distance to " OG  SER A  22 " =    2.716
peak=    3.242 closest distance to " CB  THR A  52 " =    1.007
peak=    3.241 closest distance to " CD2 HIS A  81 " =    1.084
peak=    3.240 closest distance to " CA  ARG A  36 " =    1.078
peak=    3.236 closest distance to " O   HOH Z 301 " =    1.913
peak=    3.235 closest distance to " CA  VAL A 126 " =    0.942
peak=    3.233 closest distance to " CD  ARG A 159 " =    0.767
peak=    3.231 closest distance to " O   HOH Z 362 " =    3.487
peak=    3.229 closest distance to " O  BHOH Z  74 " =    1.540
peak=    3.227 closest distance to " O   HOH Z 271 " =    2.393
peak=    3.225 closest distance to " O   HOH Z 197 " =    2.005
peak=    3.224 closest distance to " CG2 ILE A 120 " =    1.284
peak=    3.223 closest distance to " O   HOH Z 336 " =    1.856
peak=    3.222 closest distance to " OG BSER A 258 " =    3.286
peak=    3.221 closest distance to " O   HOH Z 148 " =    3.145
peak=    3.221 closest distance to " O   HOH Z   1 " =    1.895
peak=    3.217 closest distance to " CD  GLN A 194 " =    1.507
peak=    3.217 closest distance to " CB  THR A 279 " =    1.606
peak=    3.216 closest distance to " OG  SER A 245 " =    1.523
peak=    3.212 closest distance to " CB  GLN A 278 " =    0.889
peak=    3.211 closest distance to " O   HOH Z 162 " =    1.817
peak=    3.204 closest distance to " CA  ALA A  84 " =    1.312
peak=    3.201 closest distance to " CA  GLY A  80 " =    0.836
peak=    3.188 closest distance to " C   ILE A 106 " =    1.840
peak=    3.183 closest distance to " O   HOH Z 260 " =    1.501
peak=    3.182 closest distance to " CB  GLU A  46 " =    1.055
peak=    3.175 closest distance to " O   HOH Z  90 " =    3.467
peak=    3.174 closest distance to " CZ  PHE A  38 " =    1.310
peak=    3.171 closest distance to " CG1 VAL A 296 " =    1.121
peak=    3.171 closest distance to " O   HOH Z  88 " =    2.628
peak=    3.170 closest distance to " O   HOH Z 353 " =    2.827
peak=    3.165 closest distance to " ND1 HIS A  81 " =    1.624
peak=    3.163 closest distance to " O   HOH Z 380 " =    2.032
peak=    3.163 closest distance to " N   ASP A 162 " =    1.342
peak=    3.162 closest distance to " NZ  LYS A  76 " =    1.481
peak=    3.162 closest distance to " O   HOH Z  43 " =    1.492
peak=    3.158 closest distance to " O   HOH Z 292 " =    1.597
peak=    3.158 closest distance to " OG  SER A  62 " =    2.856
peak=    3.157 closest distance to " O   HOH Z  66 " =    1.588
peak=    3.156 closest distance to " CD1 ILE A  33 " =    1.629
peak=    3.155 closest distance to " CB  SER A 273 " =    0.803
peak=    3.154 closest distance to " O   THR A  31 " =    1.537
peak=    3.144 closest distance to " O   HOH Z 367 " =    3.358
peak=    3.142 closest distance to " O   HOH Z 437 " =    2.139
peak=    3.139 closest distance to " O   HOH Z 180 " =    2.207
peak=    3.138 closest distance to " O   ALA A 158 " =    1.347
peak=    3.132 closest distance to " O   HOH Z 109 " =    2.389
peak=    3.132 closest distance to " O   HOH Z 374 " =    2.579
peak=    3.131 closest distance to " CZ3 TRP A  85 " =    0.969
peak=    3.129 closest distance to " CB  GLN A 205 " =    1.178
peak=    3.128 closest distance to " O   ILE A  33 " =    1.270
peak=    3.126 closest distance to " O   HOH Z 430 " =    1.737
peak=    3.126 closest distance to " O   HOH Z 334 " =    1.407
peak=    3.122 closest distance to " CB  ALA A 291 " =    1.352
peak=    3.121 closest distance to " CG  MET A 185 " =    0.999
peak=    3.119 closest distance to " NH1AARG A 145 " =    1.095
peak=    3.119 closest distance to " CB  SER A  62 " =    0.795
peak=    3.118 closest distance to " O   HOH Z 251 " =    1.684
peak=    3.114 closest distance to " CG2 THR A  42 " =    0.822
peak=    3.113 closest distance to " O   HOH Z 253 " =    1.634
peak=    3.112 closest distance to " CB  ALA A  34 " =    0.833
peak=    3.111 closest distance to " O   HOH Z 298 " =    4.879
peak=    3.107 closest distance to " O   HOH Z 319 " =    2.349
peak=    3.100 closest distance to " CG  GLN A  89 " =    1.488
peak=    3.098 closest distance to " CB  MET A  47 " =    1.153
peak=    3.097 closest distance to " NH1 ARG A  14 " =    1.182
peak=    3.092 closest distance to " CA  SER A  32 " =    1.607
peak=    3.089 closest distance to " O   HOH Z 123 " =    2.143
peak=    3.084 closest distance to " CA  ARG A  56 " =    1.461
peak=    3.081 closest distance to " C   SER A  32 " =    1.052
peak=    3.077 closest distance to " CB  ASN A 215 " =    1.089
peak=    3.073 closest distance to " O   HOH Z 355 " =    1.783
peak=    3.066 closest distance to " O   HOH Z  63 " =    2.106
peak=    3.063 closest distance to " CB  ASN A 142 " =    1.144
peak=    3.038 closest distance to " CA  LYS A 290 " =    1.145
peak=    3.024 closest distance to " O   HOH Z 286 " =    2.360

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 217         
Filter by distance & map next to the model:
   mapped sites are within: 0.555 - 5.479
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 214 from: 217
   mapped sites are within: 0.759 - 5.479

peak=   -5.407 closest distance to " CG2 VAL A 230 " =    0.759
peak=   -4.779 closest distance to " CD  ARG A 156 " =    2.029
peak=   -4.708 closest distance to " O   PRO A 163 " =    2.105
peak=   -4.670 closest distance to " O   HOH Z 266 " =    4.639
peak=   -4.389 closest distance to " SG  CYS A 254 " =    3.226
peak=   -4.183 closest distance to " O   HOH Z 351 " =    1.567
peak=   -4.182 closest distance to " O   HOH Z 166 " =    1.727
peak=   -4.153 closest distance to " C   HIS A 108 " =    1.233
peak=   -4.073 closest distance to " CD  GLN A  58 " =    1.195
peak=   -4.064 closest distance to " OXT GLY A 302 " =    2.772
peak=   -4.040 closest distance to " O   VAL A  67 " =    2.743
peak=   -4.023 closest distance to " O   HOH Z  13 " =    1.652
peak=   -4.016 closest distance to " O   HOH Z  11 " =    1.857
peak=   -3.998 closest distance to " CB  ALA A 161 " =    2.541
peak=   -3.997 closest distance to " O   HOH Z 196 " =    2.181
peak=   -3.992 closest distance to " O   HOH Z 414 " =    1.838
peak=   -3.984 closest distance to " CD1 LEU A 101 " =    2.463
peak=   -3.980 closest distance to " CE2 TYR A  30 " =    2.752
peak=   -3.952 closest distance to " O   HOH Z 231 " =    2.200
peak=   -3.907 closest distance to " CD2 LEU A 300 " =    2.691
peak=   -3.899 closest distance to " O   HOH Z 290 " =    1.021
peak=   -3.898 closest distance to " O   HOH Z 394 " =    1.562
peak=   -3.868 closest distance to " OG BSER A 134 " =    1.332
peak=   -3.860 closest distance to " CD1 PHE A  59 " =    1.965
peak=   -3.846 closest distance to " OE1 GLN A 223 " =    2.347
peak=   -3.776 closest distance to " O   HOH Z 165 " =    1.972
peak=   -3.766 closest distance to " C   THR A 279 " =    1.188
peak=   -3.750 closest distance to " CG  ASP A 231 " =    0.873
peak=   -3.742 closest distance to " CH2 TRP A 179 " =    1.282
peak=   -3.741 closest distance to " O   HOH Z  44 " =    2.111
peak=   -3.702 closest distance to " NE2 GLN A  88 " =    1.055
peak=   -3.698 closest distance to " CD1 LEU A  25 " =    2.501
peak=   -3.697 closest distance to " CG2BVAL A  41 " =    2.685
peak=   -3.676 closest distance to " CB  PRO A 243 " =    2.620
peak=   -3.675 closest distance to " O   HOH Z  37 " =    1.940
peak=   -3.674 closest distance to " OG ASER A 134 " =    1.278
peak=   -3.656 closest distance to " O   HOH Z 283 " =    1.803
peak=   -3.653 closest distance to " N   THR A 235 " =    1.350
peak=   -3.646 closest distance to " O   HOH Z  60 " =    2.286
peak=   -3.637 closest distance to " CG1 VAL A 250 " =    2.770
peak=   -3.622 closest distance to " N   ALA A 226 " =    2.003
peak=   -3.621 closest distance to " O   HOH Z 136 " =    2.220
peak=   -3.618 closest distance to " O   HOH Z 311 " =    3.584
peak=   -3.613 closest distance to " O   PRO A 198 " =    1.287
peak=   -3.613 closest distance to " O   HOH Z 114 " =    3.310
peak=   -3.612 closest distance to " O   ASN A  45 " =    1.864
peak=   -3.598 closest distance to " ND2 ASN A 187 " =    1.665
peak=   -3.595 closest distance to " O   HOH Z 377 " =    1.721
peak=   -3.593 closest distance to " CD  ARG A 139 " =    1.691
peak=   -3.586 closest distance to " O   HOH Z 150 " =    1.839
peak=   -3.584 closest distance to " C   ALA A 158 " =    1.225
peak=   -3.567 closest distance to " CA  ASP A 298 " =    1.043
peak=   -3.566 closest distance to " NH2 ARG A  66 " =    1.462
peak=   -3.564 closest distance to " O   TRP A  92 " =    1.901
peak=   -3.562 closest distance to " N   GLN A  58 " =    1.830
peak=   -3.561 closest distance to " OG BSER A 134 " =    1.650
peak=   -3.557 closest distance to " N   SER A 276 " =    1.417
peak=   -3.552 closest distance to " O   HOH Z 234 " =    4.102
peak=   -3.551 closest distance to " NE2 GLN A 103 " =    1.649
peak=   -3.545 closest distance to " CB  PHE A 192 " =    1.948
peak=   -3.542 closest distance to " CB  ALA A 248 " =    2.266
peak=   -3.539 closest distance to " ND2 ASN A  45 " =    1.031
peak=   -3.529 closest distance to " O   HOH Z 407 " =    3.024
peak=   -3.519 closest distance to " C   GLY A  80 " =    2.481
peak=   -3.516 closest distance to " N   ALA A 248 " =    1.757
peak=   -3.515 closest distance to " CB  PRO A 163 " =    2.643
peak=   -3.503 closest distance to " CZ  TYR A 169 " =    1.779
peak=   -3.501 closest distance to " OD1 ASN A  39 " =    2.157
peak=   -3.499 closest distance to " CB  ALA A 248 " =    1.963
peak=   -3.489 closest distance to " OG  SER A  97 " =    2.344
peak=   -3.485 closest distance to " O   PHE A 218 " =    1.635
peak=   -3.483 closest distance to " CD  LYS A 289 " =    2.473
peak=   -3.479 closest distance to " ND2 ASN A  69 " =    1.609
peak=   -3.477 closest distance to " O   HOH Z 435 " =    2.641
peak=   -3.477 closest distance to " CB  ALA A 291 " =    2.249
peak=   -3.472 closest distance to " OD1 ASN A 148 " =    1.532
peak=   -3.471 closest distance to " O   HOH Z  20 " =    1.358
peak=   -3.470 closest distance to " O   HOH Z 313 " =    1.172
peak=   -3.470 closest distance to " O   GLY A 196 " =    1.075
peak=   -3.469 closest distance to " O   HOH Z 353 " =    2.184
peak=   -3.453 closest distance to " CD1 TYR A 247 " =    2.376
peak=   -3.449 closest distance to " CB  LEU A  83 " =    2.336
peak=   -3.448 closest distance to " O   ALA A   1 " =    1.821
peak=   -3.447 closest distance to " OG1 THR A  82 " =    1.335
peak=   -3.441 closest distance to " CG  GLU A 277 " =    1.116
peak=   -3.423 closest distance to " CB  PHE A 208 " =    2.271
peak=   -3.423 closest distance to " CB  ASN A  39 " =    2.178
peak=   -3.415 closest distance to " O   ALA A 161 " =    1.644
peak=   -3.413 closest distance to " O   SER A 210 " =    1.896
peak=   -3.409 closest distance to " CG  ASP A  50 " =    2.293
peak=   -3.406 closest distance to " O   HOH Z  17 " =    1.284
peak=   -3.393 closest distance to " CG  GLU A  53 " =    1.538
peak=   -3.389 closest distance to " OG  SER A  62 " =    1.317
peak=   -3.385 closest distance to " O   HOH Z 193 " =    1.657
peak=   -3.381 closest distance to " CE3 TRP A 150 " =    2.294
peak=   -3.381 closest distance to " CD1 PHE A  59 " =    2.163
peak=   -3.381 closest distance to " O   HOH Z 292 " =    4.423
peak=   -3.380 closest distance to " CG1 VAL A 112 " =    2.622
peak=   -3.379 closest distance to " CG2 VAL A 296 " =    1.232
peak=   -3.378 closest distance to " CB  GLN A  11 " =    1.931
peak=   -3.374 closest distance to " NH2AARG A 275 " =    4.866
peak=   -3.373 closest distance to " C   LEU A 143 " =    0.963
peak=   -3.369 closest distance to " CE  LYS A 166 " =    3.057
peak=   -3.365 closest distance to " O   HOH Z 265 " =    2.087
peak=   -3.362 closest distance to " NH2 ARG A  79 " =    1.952
peak=   -3.360 closest distance to " O   HOH Z 423 " =    2.134
peak=   -3.354 closest distance to " OXT GLY A 302 " =    3.454
peak=   -3.351 closest distance to " O   MET A  40 " =    2.764
peak=   -3.349 closest distance to " ND2 ASN A  39 " =    1.106
peak=   -3.349 closest distance to " N   VAL A 189 " =    1.599
peak=   -3.346 closest distance to " OG  SER A  26 " =    1.243
peak=   -3.343 closest distance to " CB  CYS A 254 " =    2.593
peak=   -3.334 closest distance to " CE  MET A 105 " =    2.207
peak=   -3.331 closest distance to " O   HOH Z  19 " =    2.352
peak=   -3.327 closest distance to " CG2 THR A 221 " =    2.254
peak=   -3.324 closest distance to " CD  GLN A 223 " =    0.812
peak=   -3.321 closest distance to " O   HOH Z 191 " =    5.479
peak=   -3.315 closest distance to " CE BMET A  47 " =    1.557
peak=   -3.314 closest distance to " O   HOH Z 151 " =    1.405
peak=   -3.310 closest distance to " CA  GLY A 203 " =    2.310
peak=   -3.306 closest distance to " CG  TRP A 266 " =    1.968
peak=   -3.306 closest distance to " O   SER A  95 " =    1.662
peak=   -3.303 closest distance to " CB  ASP A 132 " =    2.321
peak=   -3.300 closest distance to " CD  ARG A 195 " =    5.057
peak=   -3.294 closest distance to " O   HOH Z 411 " =    1.569
peak=   -3.292 closest distance to " N   ALA A 248 " =    2.491
peak=   -3.290 closest distance to " O   HOH Z 131 " =    4.095
peak=   -3.286 closest distance to " NE2 GLN A 194 " =    1.742
peak=   -3.285 closest distance to " O   HOH Z  15 " =    1.499
peak=   -3.285 closest distance to " O   LYS A 117 " =    1.660
peak=   -3.280 closest distance to " O   HOH Z  71 " =    1.523
peak=   -3.272 closest distance to " O   HOH Z 126 " =    1.878
peak=   -3.270 closest distance to " CG2 ILE A 263 " =    2.258
peak=   -3.266 closest distance to " C   GLY A  91 " =    1.416
peak=   -3.264 closest distance to " OD1 ASN A 301 " =    1.977
peak=   -3.264 closest distance to " CD1 LEU A 228 " =    2.195
peak=   -3.263 closest distance to " O   HOH Z 171 " =    2.073
peak=   -3.257 closest distance to " O   HOH Z  92 " =    1.610
peak=   -3.257 closest distance to " NE2 GLN A  88 " =    1.991
peak=   -3.256 closest distance to " C   GLN A 205 " =    1.919
peak=   -3.252 closest distance to " O   SER A 271 " =    1.993
peak=   -3.252 closest distance to " O   HOH Z 414 " =    2.195
peak=   -3.250 closest distance to " C   SER A 206 " =    1.602
peak=   -3.246 closest distance to " CD2 LEU A 167 " =    1.704
peak=   -3.244 closest distance to " O   ASP A 171 " =    1.966
peak=   -3.240 closest distance to " CB  ASN A  69 " =    1.065
peak=   -3.239 closest distance to " CB  SER A 210 " =    1.317
peak=   -3.236 closest distance to " O   HOH Z 222 " =    1.531
peak=   -3.232 closest distance to " O   HOH Z 388 " =    2.033
peak=   -3.226 closest distance to " O   VAL A 174 " =    2.115
peak=   -3.223 closest distance to " O   HOH Z 339 " =    1.815
peak=   -3.221 closest distance to " CD2 TYR A 293 " =    2.014
peak=   -3.219 closest distance to " N   SER A   3 " =    2.162
peak=   -3.218 closest distance to " O   HOH Z  56 " =    2.533
peak=   -3.217 closest distance to " O   ASN A 187 " =    1.509
peak=   -3.217 closest distance to " O   HOH Z 174 " =    4.290
peak=   -3.213 closest distance to " N   THR A 157 " =    1.498
peak=   -3.212 closest distance to " O   HOH Z 372 " =    2.352
peak=   -3.212 closest distance to " O   HOH Z 422 " =    1.485
peak=   -3.210 closest distance to " O   VAL A 189 " =    2.618
peak=   -3.207 closest distance to " O   GLU A 152 " =    1.690
peak=   -3.206 closest distance to " O   HOH Z 166 " =    1.616
peak=   -3.206 closest distance to " OD1 ASN A 249 " =    1.994
peak=   -3.200 closest distance to " O   HOH Z  52 " =    1.626
peak=   -3.199 closest distance to " ND2 ASN A  45 " =    1.713
peak=   -3.197 closest distance to " O   HOH Z  43 " =    1.943
peak=   -3.195 closest distance to " CG1 VAL A 296 " =    1.252
peak=   -3.194 closest distance to " O   HOH Z 123 " =    2.303
peak=   -3.193 closest distance to " O   HOH Z  10 " =    1.553
peak=   -3.191 closest distance to " O   HOH Z 252 " =    3.924
peak=   -3.191 closest distance to " NZ  LYS A 119 " =    3.556
peak=   -3.189 closest distance to " O   HOH Z 174 " =    2.206
peak=   -3.188 closest distance to " CD2 LEU A 237 " =    2.751
peak=   -3.185 closest distance to " N   LEU A 281 " =    1.824
peak=   -3.182 closest distance to " CG  LEU A  83 " =    1.903
peak=   -3.181 closest distance to " O   HOH Z 211 " =    1.671
peak=   -3.174 closest distance to " CG  ARG A 269 " =    2.208
peak=   -3.172 closest distance to " CD1 TRP A 179 " =    1.110
peak=   -3.171 closest distance to " O   HOH Z 193 " =    1.897
peak=   -3.169 closest distance to " O   SER A   3 " =    1.125
peak=   -3.166 closest distance to " O   HOH Z 377 " =    1.740
peak=   -3.164 closest distance to " O   HOH Z 197 " =    5.154
peak=   -3.164 closest distance to " O   HOH Z 198 " =    2.479
peak=   -3.162 closest distance to " N   GLN A  77 " =    1.528
peak=   -3.155 closest distance to " O   HOH Z 313 " =    2.108
peak=   -3.154 closest distance to " O   HOH Z  47 " =    1.533
peak=   -3.154 closest distance to " NH2 ARG A  66 " =    4.948
peak=   -3.147 closest distance to " O   HOH Z  40 " =    2.304
peak=   -3.147 closest distance to " CG  GLU A 152 " =    1.209
peak=   -3.143 closest distance to " O   HOH Z   6 " =    1.938
peak=   -3.141 closest distance to " CB  ALA A  10 " =    2.252
peak=   -3.138 closest distance to " CB  ALA A 291 " =    2.118
peak=   -3.138 closest distance to " NH1 ARG A 195 " =    2.532
peak=   -3.135 closest distance to " O   HOH Z 407 " =    1.590
peak=   -3.128 closest distance to " O   HOH Z 389 " =    1.714
peak=   -3.123 closest distance to " OD2 ASP A 171 " =    2.321
peak=   -3.117 closest distance to " O   HOH Z 116 " =    1.412
peak=   -3.116 closest distance to " OG  SER A   3 " =    1.612
peak=   -3.112 closest distance to " O   ALA A  51 " =    1.468
peak=   -3.112 closest distance to " OD1 ASP A 191 " =    1.604
peak=   -3.101 closest distance to " O   HOH Z 310 " =    3.382
peak=   -3.100 closest distance to " O   HOH Z 185 " =    2.385
peak=   -3.096 closest distance to " CG2 VAL A 189 " =    2.023
peak=   -3.090 closest distance to " N   SER A 271 " =    1.333
peak=   -3.088 closest distance to " O   HOH Z 139 " =    3.295
peak=   -3.087 closest distance to " O   PRO A 198 " =    1.229
peak=   -3.080 closest distance to " O   HOH Z  97 " =    1.475
peak=   -3.066 closest distance to " CG1 VAL A 230 " =    1.801
peak=   -3.060 closest distance to " O   HOH Z  11 " =    1.905
peak=   -3.054 closest distance to " CE3 TRP A 274 " =    2.407
peak=   -3.048 closest distance to " CD  ARG A 259 " =    2.477
peak=   -3.027 closest distance to " O   HOH Z 350 " =    1.987
peak=   -3.018 closest distance to " O   HOH Z 407 " =    3.618
peak=   -3.015 closest distance to " O   HOH Z 437 " =    1.668

================= 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    :  0.4704 0.4585   6.271018e+00   6.256112e+00
   1_bss:  0.4627 0.4522   6.263803e+00   6.247038e+00
   1_xyz:  0.3716 0.3916   6.127888e+00   6.161720e+00
   1_adp:  0.3212 0.3622   6.026445e+00   6.114121e+00
   1_occ:  0.3207 0.3615   6.025460e+00   6.113904e+00
   2_bss:  0.3185 0.3569   6.026399e+00   6.111966e+00
   2_xyz:  0.2302 0.2749   5.754845e+00   5.907640e+00
   2_adp:  0.2083 0.2563   5.674039e+00   5.839433e+00
   2_occ:  0.2080 0.2564   5.673675e+00   5.839628e+00
   3_bss:  0.2063 0.2560   5.673564e+00   5.837305e+00
   3_xyz:  0.1523 0.1938   5.392558e+00   5.587423e+00
   3_adp:  0.1433 0.1813   5.331367e+00   5.522523e+00
   3_occ:  0.1430 0.1812   5.330877e+00   5.522877e+00
   4_bss:  0.1431 0.1813   5.331839e+00   5.522684e+00
   4_xyz:  0.1228 0.1634   5.206437e+00   5.422445e+00
   4_adp:  0.1192 0.1610   5.184790e+00   5.409715e+00
   4_occ:  0.1191 0.1610   5.184395e+00   5.409690e+00
   5_bss:  0.1190 0.1609   5.184428e+00   5.409870e+00
   5_xyz:  0.1120 0.1568   5.145063e+00   5.387018e+00
   5_adp:  0.1110 0.1571   5.140825e+00   5.387291e+00
   5_occ:  0.1110 0.1572   5.140850e+00   5.387712e+00
   5_bss:  0.1109 0.1568   5.140514e+00   5.387357e+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:  0.345  20.000   6.902  10.698   7.656   0.000   0.000   0.000
   1_xyz:  0.345  20.000   6.902  10.698   7.656   0.000   0.000   0.000
   1_adp:  0.345  20.000   6.902  10.698   7.656   0.000   0.000   0.000
   1_occ:  0.345  20.000   6.902  10.698   7.656   0.000   0.000   0.000
   2_bss:  0.308  33.899   3.643   6.815   4.843   0.000   0.000   0.000
   2_xyz:  0.308  33.899   3.643   6.815   4.843   0.000   0.000   0.000
   2_adp:  0.308  33.899   3.643   6.815   4.843   0.000   0.000   0.000
   2_occ:  0.308  33.899   3.643   6.815   4.843   0.000   0.000   0.000
   3_bss:  0.314  33.899   2.180   4.319   3.568   0.000   0.000   0.000
   3_xyz:  0.314  33.899   2.180   4.319   3.568   0.000   0.000   0.000
   3_adp:  0.314  33.899   2.180   4.319   3.568   0.000   0.000   0.000
   3_occ:  0.314  33.899   2.180   4.319   3.568   0.000   0.000   0.000
   4_bss:  0.317  44.227   1.617   3.120   3.028   0.000   0.000   0.000
   4_xyz:  0.317  44.227   1.617   3.120   3.028   0.000   0.000   0.000
   4_adp:  0.317  44.227   1.617   3.120   3.028   0.000   0.000   0.000
   4_occ:  0.317  44.227   1.617   3.120   3.028   0.000   0.000   0.000
   5_bss:  0.325  44.227   1.584   2.778   2.952   0.000   0.000   0.000
   5_xyz:  0.325  44.227   1.584   2.778   2.952   0.000   0.000   0.000
   5_adp:  0.325  44.227   1.584   2.778   2.952   0.000   0.000   0.000
   5_occ:  0.325  44.227   1.584   2.778   2.952   0.000   0.000   0.000
   5_bss:  0.325  46.739  -0.824   0.288   0.536   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  54.173 0.4691  0.5346    63726.843
   1_bss:  54.253 0.4660  0.6792    61491.122
   1_xyz:  44.595 0.5856  0.8386    43719.158
   1_adp:  39.226 0.6518  0.9548    36628.053
   1_occ:  39.175 0.6524  0.9542    36536.089
   2_bss:  38.935 0.6552  0.8522    36126.651
   2_xyz:  28.942 0.7684  0.9762    20554.229
   2_adp:  25.982 0.8012  1.0024    17456.281
   2_occ:  25.985 0.8012  1.0022    17458.403
   3_bss:  25.915 0.8019  0.9422    17388.618
   3_xyz:  18.590 0.8747  0.9933     9611.658
   3_adp:  16.924 0.8904  1.0031     8436.193
   3_occ:  16.930 0.8904  1.0031     8440.584
   4_bss:  16.917 0.8905  0.9762     8447.763
   4_xyz:  14.796 0.9085  0.9831     6863.843
   4_adp:  14.459 0.9115  0.9814     6711.294
   4_occ:  14.454 0.9116  0.9813     6713.639
   5_bss:  14.453 0.9116  0.9765     6718.799
   5_xyz:  13.956 0.9156  0.9779     6396.764
   5_adp:  13.951 0.9157  0.9737     6383.769
   5_occ:  13.953 0.9157  0.9735     6390.187
   5_bss:  13.956 0.9157  0.9758     6391.030
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3588e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3588e+01
   1_xyz:   1.712  0.014  0.110 18.015  0.007  4.120   1.4362e-01
   1_adp:   1.712  0.014  0.110 18.015  0.007  4.120   1.4362e-01
   1_occ:   1.712  0.014  0.110 18.015  0.007  4.120   1.4362e-01
   2_bss:   1.712  0.014  0.110 18.015  0.007  4.120   1.4362e-01
   2_xyz:   1.151  0.008  0.079 16.207  0.004  4.125   7.5582e-02
   2_adp:   1.151  0.008  0.079 16.207  0.004  4.125   7.5582e-02
   2_occ:   1.151  0.008  0.079 16.207  0.004  4.125   7.5582e-02
   3_bss:   1.151  0.008  0.079 16.207  0.004  4.125   7.5582e-02
   3_xyz:   1.008  0.007  0.074 15.346  0.003  4.110   6.2561e-02
   3_adp:   1.008  0.007  0.074 15.346  0.003  4.110   6.2561e-02
   3_occ:   1.008  0.007  0.074 15.346  0.003  4.110   6.2561e-02
   4_bss:   1.008  0.007  0.074 15.346  0.003  4.110   6.2561e-02
   4_xyz:   1.055  0.007  0.083 15.489  0.004  4.114   6.5376e-02
   4_adp:   1.055  0.007  0.083 15.489  0.004  4.114   6.5376e-02
   4_occ:   1.055  0.007  0.083 15.489  0.004  4.114   6.5376e-02
   5_bss:   1.055  0.007  0.083 15.489  0.004  4.114   6.5376e-02
   5_xyz:   1.138  0.009  0.092 15.664  0.004  4.117   7.6030e-02
   5_adp:   1.138  0.009  0.092 15.664  0.004  4.117   7.6030e-02
   5_occ:   1.138  0.009  0.092 15.664  0.004  4.117   7.6030e-02
   5_bss:   1.138  0.009  0.092 15.664  0.004  4.117   7.6030e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9463e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9463e+00
   1_xyz:  15.727  0.165  0.553 85.795  0.047  2.284   1.0571e-01
   1_adp:  15.727  0.165  0.553 85.795  0.047  2.284   1.0571e-01
   1_occ:  15.727  0.165  0.553 85.795  0.047  2.284   1.0571e-01
   2_bss:  15.727  0.165  0.553 85.795  0.047  2.284   1.0571e-01
   2_xyz:   7.289  0.082  0.260 83.345  0.031  2.156   5.3152e-02
   2_adp:   7.289  0.082  0.260 83.345  0.031  2.156   5.3152e-02
   2_occ:   7.289  0.082  0.260 83.345  0.031  2.156   5.3152e-02
   3_bss:   7.289  0.082  0.260 83.345  0.031  2.156   5.3152e-02
   3_xyz:   6.430  0.053  0.390 80.861  0.024  2.317   9.8707e-02
   3_adp:   6.430  0.053  0.390 80.861  0.024  2.317   9.8707e-02
   3_occ:   6.430  0.053  0.390 80.861  0.024  2.317   9.8707e-02
   4_bss:   6.430  0.053  0.390 80.861  0.024  2.317   9.8707e-02
   4_xyz:   7.181  0.044  0.592 83.771  0.029  2.262   5.5492e-02
   4_adp:   7.181  0.044  0.592 83.771  0.029  2.262   5.5492e-02
   4_occ:   7.181  0.044  0.592 83.771  0.029  2.262   5.5492e-02
   5_bss:   7.181  0.044  0.592 83.771  0.029  2.262   5.5492e-02
   5_xyz:   7.865  0.049  0.733 81.795  0.029  2.289   5.7234e-02
   5_adp:   7.865  0.049  0.733 81.795  0.029  2.289   5.7234e-02
   5_occ:   7.865  0.049  0.733 81.795  0.029  2.289   5.7234e-02
   5_bss:   7.865  0.049  0.733 81.795  0.029  2.289   5.7234e-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:  81.68   0.00  12.34  76.12   0.00   9.72  81.68   0.00  26.56
   1_occ:  81.68   0.00  12.34  76.12   0.00   9.72  81.68   0.00  26.56
   2_bss:  81.68   0.00  12.34  76.12   0.00   9.72  81.68   0.00  26.56
   2_xyz:  81.68   0.00  12.34  76.12   0.00   9.72  81.68   0.00  26.56
   2_adp:  79.25   0.00  12.36  79.25   0.00   8.85  76.80   1.49  31.53
   2_occ:  79.25   0.00  12.36  79.25   0.00   8.85  76.80   1.49  31.53
   3_bss:  79.25   0.00  12.36  79.25   0.00   8.85  76.80   1.49  31.53
   3_xyz:  79.25   0.00  12.36  79.25   0.00   8.85  76.80   1.49  31.53
   3_adp:  76.14   0.00  12.30  76.14   0.00   8.48  68.59   1.74  33.11
   3_occ:  76.14   0.00  12.30  76.14   0.00   8.48  68.59   1.74  33.11
   4_bss:  76.14   0.00  12.30  76.14   0.00   8.48  68.59   1.74  33.11
   4_xyz:  76.14   0.00  12.30  76.14   0.00   8.48  68.59   1.74  33.11
   4_adp:  77.17   0.00  12.42  77.17   0.00   8.39  66.49   1.62  34.35
   4_occ:  77.17   0.00  12.42  77.17   0.00   8.39  66.49   1.62  34.35
   5_bss:  77.17   0.00  12.42  77.17   0.00   8.39  66.49   1.62  34.35
   5_xyz:  77.17   0.00  12.42  77.17   0.00   8.39  66.49   1.62  34.35
   5_adp:  79.97   0.00  12.36  79.97   0.00   8.30  67.32   1.35  34.46
   5_occ:  79.97   0.00  12.36  79.97   0.00   8.30  67.32   1.35  34.46
   5_bss:  82.48   2.51  14.88  82.48   2.51  10.82  69.84   3.87  36.98
------------------------------------------------------------------------
 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:    1.162    0.024    0.415
   1_adp:    1.162    0.024    0.415
   1_occ:    1.162    0.024    0.415
   2_bss:    1.162    0.024    0.415
   2_xyz:    1.654    0.042    0.576
   2_adp:    1.654    0.042    0.576
   2_occ:    1.654    0.042    0.576
   3_bss:    1.654    0.042    0.576
   3_xyz:    1.682    0.062    0.640
   3_adp:    1.682    0.062    0.640
   3_occ:    1.682    0.062    0.640
   4_bss:    1.682    0.062    0.640
   4_xyz:    1.766    0.033    0.688
   4_adp:    1.766    0.033    0.688
   4_occ:    1.766    0.033    0.688
   5_bss:    1.766    0.033    0.688
   5_xyz:    1.809    0.052    0.704
   5_adp:    1.809    0.052    0.704
   5_occ:    1.809    0.052    0.704
   5_bss:    1.809    0.052    0.704
------------------------------------------------------------------------

CPU time actual refinement: 342.02


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_454/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_454/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_454/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_454/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_454/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 341.86 
  Macro-tasks:
    bulk solvent and scale       = 39.33  
    individual site refinement   = 144.59 
    weights calculation          = 32.29  
    collect and process          = 6.51   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 222.83 
  Micro-tasks:
    mask                            = 2.49   
    f_calc                          = 106.86 
    alpha_beta                      = 8.38   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 118.46 
    fmodel                         = 7.21   
    r_factors                      = 0.15   
    phase_errors                   = 10.65  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 255.65 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.736 micro seconds
Total CPU time: 5.93 minutes
from_scatterers_fft:    663 calls, 106.47 s
gradients_fft:          608 calls, 104.28 s

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

# Date 2008-01-16 Time 01:38:18 PST -0800 (1200476298.62 s)
Start R-work = 0.4704, R-free = 0.4585 (no bulk solvent and anisotropic scale)
Final R-work = 0.1284, R-free = 0.1724 (no bulk solvent and anisotropic scale)

Start R-work = 0.4627, R-free = 0.4522
Final R-work = 0.1109, R-free = 0.1568