# Date 2008-01-16 Time 02:04:27 PST -0800 (1200477867.74 s)
#phil __OFF__

Command line arguments: "../685.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 1274
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 685

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 47.3993, 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: 3.36, per 1000 atoms: 1.19


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.3993, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9529 1.98122
Completeness in resolution range: 0.959728
Completeness with d_max=infinity: 0.956728

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9529
                             d_min =   1.9812

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 47.3993, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9529 1.98122
Completeness in resolution range: 0.959728
Completeness with d_max=infinity: 0.956728

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9533 -  4.2390 [2137/2165]  1925   212   9.9%
  bin  2:  4.2390 -  3.3774 [2056/2075]  1848   208  10.1%
  bin  3:  3.3774 -  2.9542 [2039/2059]  1836   203  10.0%
  bin  4:  2.9542 -  2.6858 [2018/2043]  1820   198   9.8%
  bin  5:  2.6858 -  2.4943 [2008/2027]  1804   204  10.2%
  bin  6:  2.4943 -  2.3478 [1970/2016]  1777   193   9.8%
  bin  7:  2.3478 -  2.2306 [1982/2015]  1782   200  10.1%
  bin  8:  2.2306 -  2.1338 [1988/2023]  1784   204  10.3%
  bin  9:  2.1338 -  2.0519 [1974/2004]  1785   189   9.6%
  bin 10:  2.0519 -  1.9812 [1417/1984]  1269   148  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_685/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: 0.13 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: 19
        2.42 -     3.04: 2184
        3.04 -     3.66: 4697
        3.66 -     4.28: 8991
        4.28 -     4.90: 12403
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 100 " - " O   HOH Z 352 "  2.106 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.151 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  70 " - " O   HOH Z 294 "  2.190 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  2.198 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28289 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_685/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_685/model_refine_001.geo

CPU time processing inputs: 9.11


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 47.3993 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 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4409   r_free= 0.4321   ksol= 0.00   Bsol= 0.00   scale= 0.819    |
|                                                                             |
| 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:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.236122                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9533 -  4.7278 0.99   1386  154 0.3667 0.3446      6.5283      6.4752|
|  2:  4.7278 -  3.7725 0.99   1351  147 0.3397 0.3627      6.6668      6.7012|
|  3:  3.7725 -  3.3015 0.99   1312  153 0.3867 0.3648       6.588      6.5915|
|  4:  3.3015 -  3.0023 0.99   1311  139 0.4141 0.3904      6.4546      6.3713|
|  5:  3.0023 -  2.7886 0.99   1292  144 0.4605 0.4768      6.3314      6.3717|
|  6:  2.7886 -  2.6251 0.98   1292  144 0.4637 0.5201      6.2265      6.2075|
|  7:  2.6251 -  2.4943 0.99   1289  144 0.4780 0.4110      6.2269      6.1013|
|  8:  2.4943 -  2.3861 0.98   1277  145 0.4857 0.4594      6.1562      6.1221|
|  9:  2.3861 -  2.2946 0.98   1285  138 0.4999 0.4969      6.1017       6.123|
| 10:  2.2946 -  2.2157 0.97   1259  142 0.4939 0.5133       6.094      6.1165|
| 11:  2.2157 -  2.1466 0.99   1261  142 0.4999 0.4335      6.0107      6.0008|
| 12:  2.1466 -  2.0854 0.98   1274  138 0.5128 0.5304      5.9787      6.0172|
| 13:  2.0854 -  2.0307 0.97   1252  140 0.5072 0.5113      5.8744      5.8515|
| 14:  2.0307 -  1.9812 0.62    789   89 0.5246 0.4878       5.837      5.7474|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9533 -  4.7278  1386   154  0.73  31.49   0.82     0.75      59977.02|
|  2:  4.7278 -  3.7725  1351   147  0.76  29.60   0.91     0.81      77667.89|
|  3:  3.7725 -  3.3015  1312   153  0.69  36.20   0.86     0.78      81544.41|
|  4:  3.3015 -  3.0023  1311   139  0.63  41.54   0.83     0.70      72269.97|
|  5:  3.0023 -  2.7886  1292   144  0.53  49.53   0.77     0.61      64584.11|
|  6:  2.7886 -  2.6251  1292   144  0.52  50.56   0.76     0.59      56375.70|
|  7:  2.6251 -  2.4943  1289   144  0.53  50.03   0.76     0.58      50830.15|
|  8:  2.4943 -  2.3861  1277   145  0.51  51.13   0.76     0.58      45867.47|
|  9:  2.3861 -  2.2946  1285   138  0.48  53.83   0.74     0.55      43405.91|
| 10:  2.2946 -  2.2157  1259   142  0.46  55.28   0.77     0.53      42122.44|
| 11:  2.2157 -  2.1466  1261   142  0.41  59.19   0.77     0.49      41048.16|
| 12:  2.1466 -  2.0854  1274   138  0.39  60.97   0.77     0.47      39865.23|
| 13:  2.0854 -  2.0307  1252   140  0.36  62.76   0.74     0.45      34808.01|
| 14:  2.0307 -  1.9812   789    89  0.41  59.51   0.73     0.46      27510.92|
|alpha:            min =        0.45 max =            0.81 mean =         0.60|
|beta:             min =    27510.92 max =        81544.41 mean =     53704.32|
|figures of merit: min =        0.00 max =            1.00 mean =         0.54|
|phase err.(work): min =        0.00 max =           89.96 mean =        48.85|
|phase err.(test): min =        0.00 max =           89.94 mean =        48.86|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.576716              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.078   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.720229              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.471   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      164 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      686 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1515 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2617 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3919 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5074 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6570 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7720 |
|-----------------------------------------------------------------------------|
|-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 |       53.768 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.732 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.911)------------------------------------------|
|    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 = 11.911)------------------------------------------|
|    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 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4485   r_free= 0.4393   ksol= 0.00   Bsol= 0.00   scale= 0.788    |
|                                                                             |
| 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:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.240623                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4322   r_free= 0.4233   ksol= 0.34   Bsol= 17.59   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.02,9.71,8.13,0.00,0.00,0.00); trace/3= 8.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.232303                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.986369              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.257   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.713081              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.684   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4322      final r-factor (work) = 0.3275          |
| start r-factor (free) = 0.4233      final r-factor (free) = 0.3532          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 78.7069 = 7.99 * 0.50 * 6.2455 + 1.00 * 53.7676                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.4349 = 7.99 * 0.50 * 6.0880 + 1.00 * 0.1244                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3275      final r-factor (work) = 0.2684          |
| start r-factor (free) = 0.3532      final r-factor (free) = 0.3062          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3556 = 0.71 * 1.00 * 6.0880 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2399 = 0.71 * 1.00 * 5.9288 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.911)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    69.60   10.97    None  None   None       |
|    all(noH): 2823   0      0.00    69.60   10.97    None  None   None       |
|    Sol.    : 438    0      0.00    66.40   27.52    None  None   None       |
|    Mac.    : 2385   0      0.00    69.60   7.93     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.960: 1416   |   5:    34.800 -  41.760:   81        |
|      1:     6.960 -  13.920:  705   |   6:    41.760 -  48.720:   59        |
|      2:    13.920 -  20.880:  250   |   7:    48.720 -  55.680:   23        |
|      3:    20.880 -  27.840:  164   |   8:    55.680 -  62.641:    6        |
|      4:    27.840 -  34.800:  113   |   9:    62.641 -  69.601:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2684 r_free = 0.3062             target_work(ml) = 5.874         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2680 r_free = 0.3061             target_work(ml) = 5.873         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2680   r_free= 0.3061   ksol= 0.34   Bsol= 17.59   scale= 1.087   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.02,9.71,8.13,0.00,0.00,0.00); trace/3= 8.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.873444                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2642   r_free= 0.3008   ksol= 0.32   Bsol= 43.45   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.77,5.91,5.27,0.00,0.00,0.00); trace/3= 4.98                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.873092                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.448100              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.953   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.373928              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.869  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2642      final r-factor (work) = 0.1696          |
| start r-factor (free) = 0.3008      final r-factor (free) = 0.2100          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.2890 = 5.45 * 0.50 * 5.9340 + 1.00 * 0.1244                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.5456 = 5.45 * 0.50 * 5.6805 + 1.00 * 0.0716                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1696      final r-factor (work) = 0.1516          |
| start r-factor (free) = 0.2100      final r-factor (free) = 0.1939          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1364 = 0.37 * 1.00 * 5.6805 + 1.00 * 0.0123                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0383 = 0.37 * 1.00 * 5.4227 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.911)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.97   11.49    None  None   None       |
|    all(noH): 2823   0      0.00    74.97   11.49    None  None   None       |
|    Sol.    : 438    0      0.93    66.39   32.50    None  None   None       |
|    Mac.    : 2385   0      0.00    74.97   7.64     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 -   7.497: 1575   |   5:    37.485 -  44.982:  100        |
|      1:     7.497 -  14.994:  637   |   6:    44.982 -  52.478:   69        |
|      2:    14.994 -  22.491:  178   |   7:    52.478 -  59.975:   26        |
|      3:    22.491 -  29.988:  109   |   8:    59.975 -  67.472:   10        |
|      4:    29.988 -  37.485:  116   |   9:    67.472 -  74.969:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1516 r_free = 0.1939             target_work(ml) = 5.381         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1514 r_free = 0.1938             target_work(ml) = 5.381         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1514   r_free= 0.1938   ksol= 0.32   Bsol= 43.45   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.77,5.91,5.27,0.00,0.00,0.00); trace/3= 4.98                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.380624                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1498   r_free= 0.1924   ksol= 0.32   Bsol= 43.45   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.71,3.92,3.97,0.00,0.00,0.00); trace/3= 3.54                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.380440                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.666876              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.049  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.384800              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.226  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1498      final r-factor (work) = 0.1289          |
| start r-factor (free) = 0.1924      final r-factor (free) = 0.1669          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6020 = 1.67 * 0.50 * 5.4357 + 1.00 * 0.0717                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4838 = 1.67 * 0.50 * 5.3157 + 1.00 * 0.0534                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1289      final r-factor (work) = 0.1247          |
| start r-factor (free) = 0.1669      final r-factor (free) = 0.1628          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0561 = 0.38 * 1.00 * 5.3157 + 1.00 * 0.0106                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0235 = 0.38 * 1.00 * 5.2294 + 1.00 * 0.0112                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.911)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.13   11.72    None  None   None       |
|    all(noH): 2823   0      0.00    78.13   11.72    None  None   None       |
|    Sol.    : 438    0      0.91    66.90   33.94    None  None   None       |
|    Mac.    : 2385   0      0.00    78.13   7.64     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 -   7.813: 1653   |   5:    39.064 -  46.877:   99        |
|      1:     7.813 -  15.626:  587   |   6:    46.877 -  54.689:   80        |
|      2:    15.626 -  23.438:  151   |   7:    54.689 -  62.502:   23        |
|      3:    23.438 -  31.251:  108   |   8:    62.502 -  70.315:    8        |
|      4:    31.251 -  39.064:  110   |   9:    70.315 -  78.127:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1247 r_free = 0.1628             target_work(ml) = 5.219         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1246 r_free = 0.1627             target_work(ml) = 5.218         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1246   r_free= 0.1627   ksol= 0.32   Bsol= 43.45   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.71,3.92,3.97,0.00,0.00,0.00); trace/3= 3.54                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.218249                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1245   r_free= 0.1625   ksol= 0.32   Bsol= 43.45   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.57,3.46,3.73,0.00,0.00,0.00); trace/3= 3.25                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.218002                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.878389              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 132.940  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.694321              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.947  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1245      final r-factor (work) = 0.1153          |
| start r-factor (free) = 0.1625      final r-factor (free) = 0.1572          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9647 = 1.88 * 0.50 * 5.2292 + 1.00 * 0.0534                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9292 = 1.88 * 0.50 * 5.1826 + 1.00 * 0.0617                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1153      final r-factor (work) = 0.1138          |
| start r-factor (free) = 0.1572      final r-factor (free) = 0.1577          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6096 = 0.69 * 1.00 * 5.1826 + 1.00 * 0.0112                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5929 = 0.69 * 1.00 * 5.1561 + 1.00 * 0.0129                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.911)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.10   11.83    None  None   None       |
|    all(noH): 2823   0      0.00    85.10   11.83    None  None   None       |
|    Sol.    : 438    0      0.67    70.29   34.58    None  None   None       |
|    Mac.    : 2385   0      0.00    85.10   7.66     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 -   8.510: 1743   |   5:    42.549 -  51.059:   90        |
|      1:     8.510 -  17.020:  523   |   6:    51.059 -  59.569:   62        |
|      2:    17.020 -  25.529:  154   |   7:    59.569 -  68.078:   16        |
|      3:    25.529 -  34.039:  112   |   8:    68.078 -  76.588:    5        |
|      4:    34.039 -  42.549:  113   |   9:    76.588 -  85.098:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1138 r_free = 0.1577             target_work(ml) = 5.158         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1137 r_free = 0.1577             target_work(ml) = 5.158         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1137   r_free= 0.1577   ksol= 0.32   Bsol= 43.45   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.57,3.46,3.73,0.00,0.00,0.00); trace/3= 3.25                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.158313                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1141   r_free= 0.1584   ksol= 0.32   Bsol= 43.45   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.68,3.41,3.77,0.00,0.00,0.00); trace/3= 3.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.160408                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.303348              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 149.626  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.439972              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 102.496  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1141      final r-factor (work) = 0.1109          |
| start r-factor (free) = 0.1584      final r-factor (free) = 0.1570          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0004 = 2.30 * 0.50 * 5.1566 + 1.00 * 0.0617                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9930 = 2.30 * 0.50 * 5.1486 + 1.00 * 0.0635                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1109      final r-factor (work) = 0.1110          |
| start r-factor (free) = 0.1570      final r-factor (free) = 0.1570          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2806 = 0.44 * 1.00 * 5.1486 + 1.00 * 0.0154                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3326 = 0.44 * 1.00 * 5.1441 + 1.00 * 0.0694                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.911)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.57   11.73    None  None   None       |
|    all(noH): 2823   0      0.00    85.57   11.73    None  None   None       |
|    Sol.    : 438    0      0.77    69.88   34.21    None  None   None       |
|    Mac.    : 2385   0      0.00    85.57   7.60     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.557: 1757   |   5:    42.785 -  51.342:   83        |
|      1:     8.557 -  17.114:  515   |   6:    51.342 -  59.899:   62        |
|      2:    17.114 -  25.671:  156   |   7:    59.899 -  68.456:   17        |
|      3:    25.671 -  34.228:  108   |   8:    68.456 -  77.013:    3        |
|      4:    34.228 -  42.785:  117   |   9:    77.013 -  85.570:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1110 r_free = 0.1570             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1108 r_free = 0.1570             target_work(ml) = 5.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1108   r_free= 0.1570   ksol= 0.32   Bsol= 43.45   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.68,3.41,3.77,0.00,0.00,0.00); trace/3= 3.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.143899                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9533 -  4.7278 0.99   1386  154 0.0990 0.1298      5.3746      5.5116|
|  2:  4.7278 -  3.7725 0.99   1351  147 0.0855 0.1100       5.426      5.6318|
|  3:  3.7725 -  3.3015 0.99   1312  153 0.1032 0.1492      5.4598      5.8449|
|  4:  3.3015 -  3.0023 0.99   1311  139 0.1206 0.1547      5.4501      5.6124|
|  5:  3.0023 -  2.7886 0.99   1292  144 0.1304 0.1697      5.3268      5.5093|
|  6:  2.7886 -  2.6251 0.98   1292  144 0.1220 0.1916      5.2169       5.469|
|  7:  2.6251 -  2.4943 0.99   1289  144 0.1225 0.1631      5.1576      5.3636|
|  8:  2.4943 -  2.3861 0.98   1277  145 0.1164 0.1747      5.0753      5.3277|
|  9:  2.3861 -  2.2946 0.98   1285  138 0.1159 0.1784      5.0313      5.3301|
| 10:  2.2946 -  2.2157 0.97   1259  142 0.1111 0.1689      4.9629      5.2014|
| 11:  2.2157 -  2.1466 0.99   1261  142 0.1143 0.1746      4.9279      5.2777|
| 12:  2.1466 -  2.0854 0.98   1274  138 0.1071 0.1648      4.8635       5.136|
| 13:  2.0854 -  2.0307 0.97   1252  140 0.1158 0.1748      4.8031      5.0811|
| 14:  2.0307 -  1.9812 0.62    789   89 0.1066 0.1774      4.7021       4.929|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9533 -  4.7278  1386   154  0.94   8.83   0.98     0.96       6951.81|
|  2:  4.7278 -  3.7725  1351   147  0.95   7.85   1.01     1.00       8734.72|
|  3:  3.7725 -  3.3015  1312   153  0.94  11.15   1.02     1.02      10297.11|
|  4:  3.3015 -  3.0023  1311   139  0.92  13.57   1.00     0.98      10271.40|
|  5:  3.0023 -  2.7886  1292   144  0.90  16.19   0.99     0.96       8372.43|
|  6:  2.7886 -  2.6251  1292   144  0.90  16.00   0.98     0.95       7232.02|
|  7:  2.6251 -  2.4943  1289   144  0.91  15.43   0.98     0.96       6152.82|
|  8:  2.4943 -  2.3861  1277   145  0.91  15.37   0.99     0.96       5461.40|
|  9:  2.3861 -  2.2946  1285   138  0.91  15.44   1.00     0.97       5034.31|
| 10:  2.2946 -  2.2157  1259   142  0.90  15.62   0.99     0.96       4464.91|
| 11:  2.2157 -  2.1466  1261   142  0.90  16.09   1.00     0.96       4227.14|
| 12:  2.1466 -  2.0854  1274   138  0.92  14.67   1.00     0.98       3837.61|
| 13:  2.0854 -  2.0307  1252   140  0.90  16.56   1.00     0.99       3496.50|
| 14:  2.0307 -  1.9812   789    89  0.91  15.58   0.98     0.94       2815.51|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2815.51 max =        10297.11 mean =      6374.73|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.95 mean =        14.06|
|phase err.(test): min =        0.00 max =           89.78 mean =        13.63|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1108   r_free= 0.1571   ksol= 0.32   Bsol= 46.81   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.59,0.09,0.50,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.143947                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1108   r_free= 0.1571   ksol= 0.32   Bsol= 46.81   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.59,0.09,0.50,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.143947                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9533 -  4.7278 0.99   1386  154 0.0990 0.1299      5.3753      5.5123|
|  2:  4.7278 -  3.7725 0.99   1351  147 0.0855 0.1100      5.4262      5.6317|
|  3:  3.7725 -  3.3015 0.99   1312  153 0.1032 0.1493      5.4599      5.8451|
|  4:  3.3015 -  3.0023 0.99   1311  139 0.1206 0.1547      5.4501      5.6123|
|  5:  3.0023 -  2.7886 0.99   1292  144 0.1304 0.1697      5.3266      5.5091|
|  6:  2.7886 -  2.6251 0.98   1292  144 0.1220 0.1915      5.2168      5.4687|
|  7:  2.6251 -  2.4943 0.99   1289  144 0.1225 0.1632      5.1576      5.3641|
|  8:  2.4943 -  2.3861 0.98   1277  145 0.1164 0.1746      5.0754      5.3275|
|  9:  2.3861 -  2.2946 0.98   1285  138 0.1159 0.1784      5.0313      5.3301|
| 10:  2.2946 -  2.2157 0.97   1259  142 0.1110 0.1690      4.9629      5.2018|
| 11:  2.2157 -  2.1466 0.99   1261  142 0.1143 0.1746      4.9279      5.2775|
| 12:  2.1466 -  2.0854 0.98   1274  138 0.1071 0.1649      4.8634      5.1364|
| 13:  2.0854 -  2.0307 0.97   1252  140 0.1158 0.1747       4.803      5.0809|
| 14:  2.0307 -  1.9812 0.62    789   89 0.1066 0.1773      4.7019      4.9284|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9533 -  4.7278  1386   154  0.94   8.84   0.98     0.96       6962.25|
|  2:  4.7278 -  3.7725  1351   147  0.95   7.85   1.01     1.00       8740.70|
|  3:  3.7725 -  3.3015  1312   153  0.94  11.16   1.03     1.02      10299.60|
|  4:  3.3015 -  3.0023  1311   139  0.92  13.57   1.01     0.99      10270.46|
|  5:  3.0023 -  2.7886  1292   144  0.90  16.18   0.99     0.96       8368.67|
|  6:  2.7886 -  2.6251  1292   144  0.90  16.00   0.98     0.95       7229.05|
|  7:  2.6251 -  2.4943  1289   144  0.91  15.43   0.99     0.96       6152.45|
|  8:  2.4943 -  2.3861  1277   145  0.91  15.37   0.99     0.97       5462.08|
|  9:  2.3861 -  2.2946  1285   138  0.91  15.44   1.01     0.98       5035.51|
| 10:  2.2946 -  2.2157  1259   142  0.90  15.62   1.00     0.96       4465.20|
| 11:  2.2157 -  2.1466  1261   142  0.90  16.09   1.00     0.96       4227.08|
| 12:  2.1466 -  2.0854  1274   138  0.92  14.67   1.00     0.99       3838.28|
| 13:  2.0854 -  2.0307  1252   140  0.90  16.56   1.01     1.00       3495.63|
| 14:  2.0307 -  1.9812   789    89  0.91  15.57   0.98     0.95       2812.99|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2812.99 max =        10299.60 mean =      6375.64|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.06|
|phase err.(test): min =        0.00 max =           89.78 mean =        13.63|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.911)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.36    88.93   15.10    None  None   None       |
|    all(noH): 2823   0      3.36    88.93   15.10    None  None   None       |
|    Sol.    : 438    0      4.14    73.24   37.57    None  None   None       |
|    Mac.    : 2385   0      3.36    88.93   10.97    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.365 -  11.922: 1757   |   5:    46.149 -  54.706:   83        |
|      1:    11.922 -  20.479:  515   |   6:    54.706 -  63.263:   62        |
|      2:    20.479 -  29.035:  156   |   7:    63.263 -  71.820:   17        |
|      3:    29.035 -  37.592:  108   |   8:    71.820 -  80.377:    3        |
|      4:    37.592 -  46.149:  117   |   9:    80.377 -  88.934:    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: 0.361 - 4.599
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 313 from: 320
   mapped sites are within: 0.731 - 4.599

peak=   10.819 closest distance to " CG2 VAL A 230 " =    1.439
peak=    7.390 closest distance to " CG2 VAL A 296 " =    1.115
peak=    6.352 closest distance to " CG  LEU A   5 " =    1.225
peak=    6.028 closest distance to " NH2 ARG A  56 " =    2.260
peak=    5.535 closest distance to " CG  LEU A 228 " =    1.203
peak=    5.442 closest distance to " CB  GLN A 223 " =    1.418
peak=    5.324 closest distance to " CG  PRO A  54 " =    1.273
peak=    5.286 closest distance to " CB  VAL A 296 " =    1.113
peak=    5.134 closest distance to " CB  SER A  63 " =    1.263
peak=    5.022 closest distance to " CB  ARG A 275 " =    0.908
peak=    4.906 closest distance to " CD2 LEU A   5 " =    1.177
peak=    4.792 closest distance to " CB  VAL A 230 " =    1.224
peak=    4.784 closest distance to " O   HOH Z 272 " =    1.894
peak=    4.746 closest distance to " CB  PRO A  54 " =    0.904
peak=    4.735 closest distance to " NE2 GLN A  11 " =    1.100
peak=    4.733 closest distance to " CB  GLN A 183 " =    1.306
peak=    4.686 closest distance to " CG  PRO A 213 " =    1.241
peak=    4.586 closest distance to " O   SER A  87 " =    2.213
peak=    4.504 closest distance to " O   HOH Z 126 " =    1.883
peak=    4.456 closest distance to " C   PRO A 198 " =    1.491
peak=    4.454 closest distance to " O   HOH Z 316 " =    3.043
peak=    4.397 closest distance to " CG  PRO A 198 " =    1.209
peak=    4.385 closest distance to " OD1 ASN A  69 " =    2.600
peak=    4.384 closest distance to " O   HOH Z 423 " =    1.825
peak=    4.382 closest distance to " CB  GLU A 152 " =    1.166
peak=    4.347 closest distance to " O   HOH Z 369 " =    2.127
peak=    4.347 closest distance to " CB  TYR A 169 " =    0.747
peak=    4.342 closest distance to " O   HOH Z 193 " =    1.810
peak=    4.332 closest distance to " CB  SER A   3 " =    1.288
peak=    4.261 closest distance to " O   HOH Z 298 " =    1.841
peak=    4.246 closest distance to " O   HOH Z 236 " =    1.901
peak=    4.234 closest distance to " O   HOH Z 142 " =    1.636
peak=    4.233 closest distance to " CB  GLU A 128 " =    1.070
peak=    4.216 closest distance to " CD2 LEU A 228 " =    1.195
peak=    4.213 closest distance to " O   HOH Z 232 " =    2.330
peak=    4.206 closest distance to " O   HOH Z 368 " =    2.224
peak=    4.202 closest distance to " ND2 ASN A 187 " =    1.541
peak=    4.192 closest distance to " O   HOH Z 403 " =    1.739
peak=    4.190 closest distance to " CB  GLU A 277 " =    3.554
peak=    4.187 closest distance to " CB  ASN A 148 " =    1.308
peak=    4.172 closest distance to " O   HOH Z  48 " =    1.555
peak=    4.150 closest distance to " CG1BVAL A  72 " =    1.670
peak=    4.147 closest distance to " O   HOH Z  78 " =    1.645
peak=    4.144 closest distance to " CG  PRO A 280 " =    0.752
peak=    4.133 closest distance to " O   HOH Z  44 " =    2.309
peak=    4.131 closest distance to " O   HOH Z  97 " =    1.974
peak=    4.118 closest distance to " CB  ARG A  79 " =    1.412
peak=    4.117 closest distance to " CB  TRP A 179 " =    1.377
peak=    4.113 closest distance to " O   HOH Z 234 " =    3.568
peak=    4.113 closest distance to " NH2 ARG A 156 " =    1.123
peak=    4.103 closest distance to " CG  PRO A 243 " =    1.156
peak=    4.102 closest distance to " CA  TYR A  30 " =    0.907
peak=    4.091 closest distance to " O   HOH Z 427 " =    2.964
peak=    4.091 closest distance to " O   HOH Z  80 " =    1.743
peak=    4.089 closest distance to " O   HOH Z 203 " =    1.746
peak=    4.078 closest distance to " CA  ALA A  21 " =    1.190
peak=    4.038 closest distance to " O   HOH Z  15 " =    2.100
peak=    4.014 closest distance to " O   HOH Z 280 " =    2.967
peak=    4.008 closest distance to " O   HOH Z  43 " =    2.080
peak=    3.978 closest distance to " O   HOH Z 303 " =    2.056
peak=    3.958 closest distance to " O   HOH Z 158 " =    3.123
peak=    3.957 closest distance to " O   HOH Z 345 " =    3.149
peak=    3.946 closest distance to " O   HOH Z 371 " =    3.260
peak=    3.936 closest distance to " O   HOH Z 389 " =    1.950
peak=    3.928 closest distance to " O   HOH Z 402 " =    1.462
peak=    3.910 closest distance to " CB  TRP A 266 " =    0.951
peak=    3.903 closest distance to " O   HOH Z  85 " =    1.387
peak=    3.890 closest distance to " O   HOH Z 189 " =    2.665
peak=    3.886 closest distance to " CB  ARG A 139 " =    0.894
peak=    3.884 closest distance to " O   HOH Z  63 " =    1.856
peak=    3.877 closest distance to " CB  ASN A  39 " =    0.838
peak=    3.871 closest distance to " O   TRP A 274 " =    1.913
peak=    3.867 closest distance to " CB  ARG A 190 " =    1.638
peak=    3.861 closest distance to " OD2 ASP A 286 " =    2.833
peak=    3.847 closest distance to " CG2 ILE A  20 " =    1.440
peak=    3.841 closest distance to " O   HOH Z 346 " =    1.545
peak=    3.838 closest distance to " O   HOH Z 261 " =    2.003
peak=    3.823 closest distance to " CB  VAL A 202 " =    1.557
peak=    3.820 closest distance to " O   HOH Z 411 " =    3.750
peak=    3.810 closest distance to " O   HOH Z 124 " =    1.337
peak=    3.808 closest distance to " O   HOH Z  97 " =    2.529
peak=    3.799 closest distance to " CZ  PHE A 218 " =    1.099
peak=    3.796 closest distance to " CB  VAL A 265 " =    1.298
peak=    3.796 closest distance to " O   HOH Z 344 " =    2.844
peak=    3.792 closest distance to " N   ASN A  39 " =    1.246
peak=    3.783 closest distance to " O   HOH Z 128 " =    2.078
peak=    3.778 closest distance to " O   HOH Z  59 " =    2.262
peak=    3.769 closest distance to " O   HOH Z 245 " =    1.414
peak=    3.768 closest distance to " CD  ARG A 159 " =    0.769
peak=    3.765 closest distance to " O   HOH Z  54 " =    1.596
peak=    3.753 closest distance to " CG1 ILE A  33 " =    1.343
peak=    3.752 closest distance to " CB  ALA A 248 " =    1.495
peak=    3.733 closest distance to " O   HOH Z  61 " =    1.628
peak=    3.730 closest distance to " O   HOH Z 273 " =    2.746
peak=    3.730 closest distance to " CA  ALA A  51 " =    1.000
peak=    3.726 closest distance to " OG BSER A 164 " =    2.250
peak=    3.723 closest distance to " CB  LEU A 143 " =    1.170
peak=    3.723 closest distance to " CD1 LEU A 300 " =    1.174
peak=    3.716 closest distance to " CA  LYS A 117 " =    1.284
peak=    3.715 closest distance to " O   HOH Z 426 " =    1.526
peak=    3.707 closest distance to " CA  THR A 221 " =    0.895
peak=    3.696 closest distance to " O   HOH Z 250 " =    1.401
peak=    3.692 closest distance to " O   HOH Z 134 " =    1.468
peak=    3.692 closest distance to " O   HOH Z  40 " =    1.666
peak=    3.687 closest distance to " NZ  LYS A 117 " =    3.215
peak=    3.683 closest distance to " O   HOH Z  48 " =    1.609
peak=    3.672 closest distance to " O   HOH Z 193 " =    2.109
peak=    3.667 closest distance to " O   HOH Z 214 " =    2.281
peak=    3.661 closest distance to " O   HOH Z 197 " =    2.808
peak=    3.660 closest distance to " CB  ALA A 291 " =    1.382
peak=    3.652 closest distance to " CB  ALA A   9 " =    1.613
peak=    3.649 closest distance to " CE1 TYR A 186 " =    1.274
peak=    3.634 closest distance to " CA  THR A 264 " =    0.771
peak=    3.624 closest distance to " CG  ARG A  66 " =    2.804
peak=    3.624 closest distance to " O   HOH Z  20 " =    1.494
peak=    3.621 closest distance to " CD  LYS A 166 " =    1.317
peak=    3.613 closest distance to " CG2 THR A 221 " =    1.182
peak=    3.612 closest distance to " O   HOH Z 128 " =    2.136
peak=    3.594 closest distance to " CD  ARG A 269 " =    0.973
peak=    3.593 closest distance to " O   MET A 105 " =    1.837
peak=    3.583 closest distance to " CA  ASP A 191 " =    0.932
peak=    3.574 closest distance to " O   HOH Z 366 " =    3.005
peak=    3.572 closest distance to " O   HOH Z 126 " =    1.692
peak=    3.570 closest distance to " CB  ARG A  79 " =    0.884
peak=    3.564 closest distance to " O   HOH Z 102 " =    1.266
peak=    3.560 closest distance to " CA  VAL A  41 " =    0.795
peak=    3.556 closest distance to " O   HOH Z 357 " =    1.952
peak=    3.553 closest distance to " OD2 ASP A 298 " =    4.013
peak=    3.542 closest distance to " O   HOH Z 313 " =    1.778
peak=    3.538 closest distance to " CG1 ILE A  49 " =    1.506
peak=    3.530 closest distance to " CB  ASP A 140 " =    0.828
peak=    3.528 closest distance to " O   HOH Z 247 " =    1.305
peak=    3.528 closest distance to " CE1 HIS A 108 " =    1.164
peak=    3.527 closest distance to " O   HOH Z 407 " =    2.688
peak=    3.525 closest distance to " O   HOH Z  88 " =    3.076
peak=    3.515 closest distance to " CB  THR A 157 " =    1.172
peak=    3.505 closest distance to " N   ARG A 190 " =    1.066
peak=    3.503 closest distance to " ND2 ASN A 110 " =    1.661
peak=    3.499 closest distance to " CB  SER A 273 " =    0.842
peak=    3.498 closest distance to " CA  ARG A 195 " =    1.197
peak=    3.497 closest distance to " CA  ALA A 158 " =    1.211
peak=    3.493 closest distance to " O   ALA A 158 " =    1.355
peak=    3.492 closest distance to " O   HOH Z 420 " =    1.984
peak=    3.487 closest distance to " O   HOH Z 126 " =    1.933
peak=    3.486 closest distance to " O   HOH Z 368 " =    3.602
peak=    3.485 closest distance to " CG  GLN A  58 " =    2.733
peak=    3.484 closest distance to " O   HOH Z 261 " =    2.135
peak=    3.480 closest distance to " O   HOH Z 417 " =    2.774
peak=    3.477 closest distance to " CD2 TRP A 179 " =    1.417
peak=    3.476 closest distance to " CA  ASP A 162 " =    1.047
peak=    3.475 closest distance to " O   HOH Z 411 " =    1.789
peak=    3.469 closest distance to " CG1 VAL A 296 " =    1.212
peak=    3.462 closest distance to " O   HOH Z 135 " =    1.870
peak=    3.458 closest distance to " O   HOH Z 227 " =    1.558
peak=    3.455 closest distance to " O   HOH Z 383 " =    2.034
peak=    3.453 closest distance to " NH2 ARG A  79 " =    1.302
peak=    3.449 closest distance to " CG1 VAL A 153 " =    0.965
peak=    3.449 closest distance to " O   HOH Z 419 " =    1.665
peak=    3.446 closest distance to " CB  ASN A 142 " =    1.148
peak=    3.435 closest distance to " NZ  LYS A 166 " =    3.079
peak=    3.434 closest distance to " O   HOH Z 329 " =    3.846
peak=    3.434 closest distance to " O   HOH Z 422 " =    2.709
peak=    3.429 closest distance to " CD BLYS A 290 " =    1.072
peak=    3.427 closest distance to " CG  GLN A  77 " =    2.286
peak=    3.427 closest distance to " CA  ASP A 140 " =    1.211
peak=    3.426 closest distance to " CB  TRP A 150 " =    1.441
peak=    3.425 closest distance to " OE1 GLU A   2 " =    2.084
peak=    3.424 closest distance to " CB  ALA A 295 " =    1.218
peak=    3.422 closest distance to " O   HOH Z 265 " =    2.388
peak=    3.412 closest distance to " O   HOH Z  68 " =    2.073
peak=    3.412 closest distance to " O   HOH Z  68 " =    1.584
peak=    3.410 closest distance to " O   HOH Z 147 " =    1.741
peak=    3.409 closest distance to " CB  SER A 212 " =    1.192
peak=    3.408 closest distance to " CA  ASN A 176 " =    1.141
peak=    3.407 closest distance to " O   HOH Z 263 " =    1.643
peak=    3.400 closest distance to " OD1 ASN A 217 " =    1.703
peak=    3.398 closest distance to " CB  SER A  26 " =    1.670
peak=    3.394 closest distance to " OD1 ASP A 231 " =    1.847
peak=    3.393 closest distance to " OG  SER A  22 " =    2.819
peak=    3.386 closest distance to " O   HOH Z 130 " =    2.236
peak=    3.386 closest distance to " O   HOH Z  21 " =    1.681
peak=    3.386 closest distance to " CB  HIS A 108 " =    0.833
peak=    3.381 closest distance to " CG  LEU A 167 " =    1.133
peak=    3.379 closest distance to " O   HOH Z 133 " =    1.534
peak=    3.378 closest distance to " O   HOH Z 435 " =    1.898
peak=    3.378 closest distance to " CB AVAL A  41 " =    1.133
peak=    3.376 closest distance to " O   HOH Z  49 " =    2.527
peak=    3.375 closest distance to " C   ALA A 299 " =    0.929
peak=    3.374 closest distance to " O   HOH Z 281 " =    4.599
peak=    3.366 closest distance to " CG BARG A 102 " =    1.851
peak=    3.364 closest distance to " O   HOH Z 374 " =    2.638
peak=    3.362 closest distance to " CA  GLY A 267 " =    0.741
peak=    3.362 closest distance to " CB  GLN A 205 " =    1.195
peak=    3.360 closest distance to " CA  GLN A 194 " =    1.216
peak=    3.356 closest distance to " CB  GLN A  88 " =    1.181
peak=    3.355 closest distance to " CD2 HIS A  81 " =    1.104
peak=    3.348 closest distance to " N   SER A 135 " =    1.459
peak=    3.348 closest distance to " O   HOH Z 248 " =    1.681
peak=    3.343 closest distance to " O   HOH Z 421 " =    1.608
peak=    3.340 closest distance to " CD1 ILE A  33 " =    1.622
peak=    3.337 closest distance to " CB  THR A  31 " =    1.684
peak=    3.334 closest distance to " CG  MET A 185 " =    1.194
peak=    3.333 closest distance to " O   HOH Z  10 " =    1.788
peak=    3.327 closest distance to " O   HOH Z 155 " =    3.155
peak=    3.319 closest distance to " O   HOH Z 227 " =    2.111
peak=    3.318 closest distance to " O   HOH Z 250 " =    1.463
peak=    3.317 closest distance to " CA  ALA A 233 " =    1.334
peak=    3.314 closest distance to " O   HOH Z 406 " =    1.537
peak=    3.312 closest distance to " O   HOH Z 180 " =    2.130
peak=    3.312 closest distance to " O   HOH Z 423 " =    3.250
peak=    3.309 closest distance to " CD  ARG A 195 " =    3.436
peak=    3.309 closest distance to " O   ASP A 124 " =    1.227
peak=    3.308 closest distance to " O   HOH Z 392 " =    1.509
peak=    3.307 closest distance to " CB  LEU A 228 " =    1.330
peak=    3.297 closest distance to " OG BSER A 134 " =    2.928
peak=    3.295 closest distance to " CB  MET A  40 " =    0.823
peak=    3.291 closest distance to " O   HOH Z 327 " =    2.560
peak=    3.290 closest distance to " CA  ARG A  36 " =    1.067
peak=    3.289 closest distance to " O   HOH Z 112 " =    1.596
peak=    3.285 closest distance to " OG1 THR A 294 " =    2.321
peak=    3.283 closest distance to " N   VAL A 126 " =    1.408
peak=    3.283 closest distance to " O   ALA A 165 " =    1.431
peak=    3.283 closest distance to " CB  ASN A 187 " =    1.079
peak=    3.282 closest distance to " CA  TYR A 116 " =    1.414
peak=    3.280 closest distance to " O   HOH Z 132 " =    2.794
peak=    3.279 closest distance to " NZ  LYS A  76 " =    1.291
peak=    3.279 closest distance to " ND1 HIS A  81 " =    1.616
peak=    3.279 closest distance to " CB  ALA A 248 " =    1.004
peak=    3.278 closest distance to " O   HOH Z  35 " =    2.476
peak=    3.276 closest distance to " CA  ALA A 295 " =    1.076
peak=    3.275 closest distance to " CG  MET A 185 " =    1.136
peak=    3.267 closest distance to " CB  MET A  47 " =    1.105
peak=    3.264 closest distance to " CB  SER A 141 " =    0.996
peak=    3.264 closest distance to " NH2AARG A 275 " =    3.701
peak=    3.264 closest distance to " CA  VAL A 126 " =    0.929
peak=    3.264 closest distance to " O   HOH Z 166 " =    3.540
peak=    3.263 closest distance to " NH2BARG A 145 " =    2.165
peak=    3.261 closest distance to " O   HOH Z 271 " =    2.519
peak=    3.251 closest distance to " CA  ALA A 291 " =    0.928
peak=    3.248 closest distance to " O   HOH Z 425 " =    2.009
peak=    3.247 closest distance to " CA  ASN A 215 " =    1.216
peak=    3.244 closest distance to " CA  LEU A 282 " =    1.126
peak=    3.243 closest distance to " CA  ILE A 106 " =    0.774
peak=    3.242 closest distance to " O   HOH Z 299 " =    4.354
peak=    3.238 closest distance to " OE1 GLN A  11 " =    1.791
peak=    3.238 closest distance to " O   HOH Z 148 " =    3.185
peak=    3.235 closest distance to " O   HOH Z 163 " =    1.449
peak=    3.235 closest distance to " O   HOH Z 189 " =    2.741
peak=    3.233 closest distance to " CB  GLN A  89 " =    1.162
peak=    3.226 closest distance to " O   HOH Z  46 " =    1.504
peak=    3.224 closest distance to " O   HOH Z 185 " =    1.774
peak=    3.224 closest distance to " O   HOH Z 234 " =    1.737
peak=    3.215 closest distance to " CE  LYS A  76 " =    0.843
peak=    3.213 closest distance to " O   HOH Z 403 " =    1.365
peak=    3.211 closest distance to " O   HOH Z 437 " =    2.102
peak=    3.210 closest distance to " O   HOH Z 367 " =    3.392
peak=    3.209 closest distance to " O   HOH Z 209 " =    2.455
peak=    3.208 closest distance to " O   HOH Z 261 " =    1.622
peak=    3.205 closest distance to " O   HOH Z 133 " =    2.496
peak=    3.203 closest distance to " CG2 ILE A 234 " =    2.058
peak=    3.200 closest distance to " O   GLN A 278 " =    1.324
peak=    3.200 closest distance to " O   HOH Z 116 " =    1.808
peak=    3.198 closest distance to " CD1 ILE A 106 " =    1.063
peak=    3.197 closest distance to " OD2 ASP A 200 " =    1.355
peak=    3.194 closest distance to " O   HOH Z 295 " =    1.503
peak=    3.192 closest distance to " CD  LYS A 119 " =    1.830
peak=    3.188 closest distance to " CB  SER A 216 " =    0.731
peak=    3.188 closest distance to " CB  LYS A 117 " =    1.152
peak=    3.188 closest distance to " O   HOH Z  90 " =    3.334
peak=    3.188 closest distance to " O   HOH Z 286 " =    2.252
peak=    3.188 closest distance to " O   HOH Z 279 " =    2.177
peak=    3.187 closest distance to " O   ALA A   1 " =    1.496
peak=    3.186 closest distance to " O   HOH Z 387 " =    3.065
peak=    3.179 closest distance to " CG2 VAL A 197 " =    1.059
peak=    3.178 closest distance to " O   HOH Z  83 " =    1.546
peak=    3.169 closest distance to " O   HOH Z 353 " =    2.739
peak=    3.169 closest distance to " CG  ARG A  66 " =    0.940
peak=    3.167 closest distance to " CG2 VAL A 202 " =    1.168
peak=    3.167 closest distance to " CA  LYS A 290 " =    1.304
peak=    3.166 closest distance to " O   HOH Z 251 " =    1.694
peak=    3.165 closest distance to " CB  LEU A 255 " =    0.819
peak=    3.164 closest distance to " NH1AARG A 145 " =    0.969
peak=    3.163 closest distance to " O   HOH Z 171 " =    3.795
peak=    3.163 closest distance to " O   HOH Z  44 " =    1.709
peak=    3.155 closest distance to " O   HOH Z 193 " =    1.557
peak=    3.155 closest distance to " O   HOH Z 282 " =    2.013
peak=    3.154 closest distance to " CZ  PHE A 192 " =    0.985
peak=    3.153 closest distance to " O   HOH Z 427 " =    3.035
peak=    3.152 closest distance to " C   TYR A 214 " =    1.435
peak=    3.149 closest distance to " CB  ALA A 100 " =    1.211
peak=    3.144 closest distance to " O   ASN A 217 " =    1.255
peak=    3.142 closest distance to " CA  ALA A  84 " =    1.437
peak=    3.140 closest distance to " OG  SER A 245 " =    1.581
peak=    3.132 closest distance to " O   THR A  31 " =    1.498
peak=    3.132 closest distance to " CG  GLU A 277 " =    2.159
peak=    3.131 closest distance to " O   HOH Z   9 " =    2.097
peak=    3.129 closest distance to " CB  GLN A 278 " =    0.851
peak=    3.129 closest distance to " O   HOH Z 109 " =    2.657
peak=    3.123 closest distance to " O   HOH Z 425 " =    1.255
peak=    3.122 closest distance to " O   HOH Z 291 " =    1.558
peak=    3.114 closest distance to " CD2 TYR A  30 " =    0.908
peak=    3.114 closest distance to " CA  ASN A 217 " =    1.314
peak=    3.108 closest distance to " CA  THR A  52 " =    1.044
peak=    3.104 closest distance to " O   GLY A  91 " =    1.260
peak=    3.094 closest distance to " O   HOH Z 336 " =    1.678
peak=    3.089 closest distance to " O   HOH Z 380 " =    1.960
peak=    3.089 closest distance to " CZ3 TRP A  85 " =    0.965
peak=    3.086 closest distance to " O   HOH Z 292 " =    1.598
peak=    3.071 closest distance to " O   HOH Z 256 " =    2.365
peak=    3.069 closest distance to " CB  ILE A 120 " =    1.439
peak=    3.058 closest distance to " O   HOH Z 357 " =    2.240
peak=    3.055 closest distance to " CG  GLN A  89 " =    1.541
peak=    3.025 closest distance to " O   HOH Z 302 " =    1.807

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 206         
Filter by distance & map next to the model:
   mapped sites are within: 0.770 - 5.534
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 205 from: 206
   mapped sites are within: 0.770 - 5.534

peak=   -5.693 closest distance to " CG2 VAL A 230 " =    0.770
peak=   -4.630 closest distance to " CD  ARG A 156 " =    1.999
peak=   -4.618 closest distance to " SG  CYS A 254 " =    3.280
peak=   -4.449 closest distance to " O   HOH Z 266 " =    4.734
peak=   -4.432 closest distance to " CA  SER A 164 " =    2.174
peak=   -4.202 closest distance to " O   HOH Z 196 " =    2.099
peak=   -4.155 closest distance to " C   HIS A 108 " =    1.178
peak=   -4.115 closest distance to " OE1 GLN A 223 " =    2.084
peak=   -4.074 closest distance to " CB  ALA A 161 " =    2.563
peak=   -4.060 closest distance to " O   HOH Z 351 " =    1.501
peak=   -4.030 closest distance to " OXT GLY A 302 " =    2.824
peak=   -4.013 closest distance to " CG  ASP A 231 " =    0.859
peak=   -4.011 closest distance to " CE2 TYR A  30 " =    2.765
peak=   -3.974 closest distance to " CD1 LEU A 101 " =    2.443
peak=   -3.956 closest distance to " O   HOH Z 290 " =    1.103
peak=   -3.953 closest distance to " CD2 LEU A 300 " =    2.709
peak=   -3.940 closest distance to " OG BSER A 134 " =    1.185
peak=   -3.892 closest distance to " CG2BVAL A  41 " =    2.673
peak=   -3.870 closest distance to " CB  PRO A 243 " =    2.682
peak=   -3.855 closest distance to " CZ3 TRP A 179 " =    1.262
peak=   -3.850 closest distance to " CD1 LEU A  25 " =    2.471
peak=   -3.842 closest distance to " O   HOH Z 231 " =    2.120
peak=   -3.809 closest distance to " O   HOH Z  19 " =    2.159
peak=   -3.796 closest distance to " NH2 ARG A  66 " =    1.654
peak=   -3.796 closest distance to " CG2 VAL A 296 " =    1.285
peak=   -3.783 closest distance to " C   ALA A 158 " =    1.241
peak=   -3.775 closest distance to " O   HOH Z 166 " =    1.460
peak=   -3.774 closest distance to " OG ASER A 134 " =    1.297
peak=   -3.754 closest distance to " ND2 ASN A 187 " =    1.611
peak=   -3.752 closest distance to " NH2AARG A 275 " =    5.076
peak=   -3.747 closest distance to " O   HOH Z 118 " =    3.265
peak=   -3.746 closest distance to " O   HOH Z  52 " =    1.552
peak=   -3.738 closest distance to " O   HOH Z  11 " =    1.942
peak=   -3.738 closest distance to " O   VAL A  67 " =    2.657
peak=   -3.736 closest distance to " CD  GLN A  58 " =    1.161
peak=   -3.728 closest distance to " O   HOH Z 407 " =    3.066
peak=   -3.723 closest distance to " O   HOH Z 353 " =    2.147
peak=   -3.707 closest distance to " O   HOH Z 283 " =    1.992
peak=   -3.703 closest distance to " O   HOH Z  17 " =    1.411
peak=   -3.699 closest distance to " O   HOH Z 292 " =    4.418
peak=   -3.698 closest distance to " CD  LYS A 289 " =    2.481
peak=   -3.685 closest distance to " O   HOH Z 166 " =    1.859
peak=   -3.681 closest distance to " ND2 ASN A  45 " =    1.000
peak=   -3.658 closest distance to " OG  SER A  97 " =    2.268
peak=   -3.650 closest distance to " O   HOH Z 394 " =    1.566
peak=   -3.648 closest distance to " CB  ALA A 248 " =    2.006
peak=   -3.635 closest distance to " CG  LEU A 101 " =    2.443
peak=   -3.635 closest distance to " CE3 TRP A 150 " =    2.027
peak=   -3.622 closest distance to " NE2 GLN A  88 " =    1.936
peak=   -3.620 closest distance to " N   SER A 212 " =    1.955
peak=   -3.619 closest distance to " N   THR A 235 " =    1.302
peak=   -3.617 closest distance to " CD1 PHE A  59 " =    1.855
peak=   -3.604 closest distance to " OG  SER A  62 " =    1.640
peak=   -3.597 closest distance to " CA  ASP A 298 " =    1.039
peak=   -3.596 closest distance to " N   ALA A 226 " =    2.042
peak=   -3.591 closest distance to " N   GLN A  58 " =    1.763
peak=   -3.586 closest distance to " CD2 LEU A 237 " =    2.755
peak=   -3.582 closest distance to " CD  ARG A 139 " =    1.616
peak=   -3.580 closest distance to " N   ALA A  43 " =    2.593
peak=   -3.574 closest distance to " O   HOH Z  37 " =    1.868
peak=   -3.563 closest distance to " O   HOH Z  44 " =    2.185
peak=   -3.552 closest distance to " CB  ALA A 248 " =    2.329
peak=   -3.551 closest distance to " C   ILE A 239 " =    2.188
peak=   -3.546 closest distance to " O   HOH Z 222 " =    1.437
peak=   -3.545 closest distance to " CG2 ILE A 263 " =    2.331
peak=   -3.531 closest distance to " O   HOH Z  13 " =    1.502
peak=   -3.519 closest distance to " CE2 PHE A 218 " =    2.592
peak=   -3.515 closest distance to " CD1 LEU A 228 " =    2.237
peak=   -3.509 closest distance to " O   HOH Z 165 " =    1.923
peak=   -3.501 closest distance to " CG1 VAL A 112 " =    2.551
peak=   -3.496 closest distance to " OD2 ASP A 171 " =    2.240
peak=   -3.488 closest distance to " CE  MET A 105 " =    2.067
peak=   -3.485 closest distance to " NH2 ARG A 159 " =    2.261
peak=   -3.482 closest distance to " OG BSER A 134 " =    1.782
peak=   -3.475 closest distance to " CD1 LEU A 101 " =    2.630
peak=   -3.470 closest distance to " N   THR A 157 " =    1.513
peak=   -3.461 closest distance to " O   HOH Z 185 " =    2.391
peak=   -3.456 closest distance to " CB  PHE A 192 " =    1.941
peak=   -3.450 closest distance to " OD1 ASN A 187 " =    1.654
peak=   -3.448 closest distance to " O   GLY A 196 " =    1.071
peak=   -3.447 closest distance to " O   HOH Z 311 " =    3.601
peak=   -3.446 closest distance to " CB  ASN A  39 " =    2.183
peak=   -3.444 closest distance to " O   HOH Z 234 " =    4.119
peak=   -3.439 closest distance to " CB  PRO A 163 " =    2.604
peak=   -3.437 closest distance to " O   VAL A 189 " =    2.616
peak=   -3.432 closest distance to " OD1 ASN A  39 " =    2.230
peak=   -3.427 closest distance to " O   HOH Z 389 " =    1.759
peak=   -3.423 closest distance to " CG  GLU A  53 " =    1.555
peak=   -3.423 closest distance to " CZ  PHE A  59 " =    1.632
peak=   -3.418 closest distance to " C   MET A 188 " =    1.497
peak=   -3.417 closest distance to " O   SER A  95 " =    1.590
peak=   -3.417 closest distance to " ND2 ASN A  45 " =    1.449
peak=   -3.410 closest distance to " CD1 PHE A  59 " =    2.285
peak=   -3.408 closest distance to " O   HOH Z 426 " =    1.731
peak=   -3.408 closest distance to " O   HOH Z  43 " =    1.680
peak=   -3.403 closest distance to " C   THR A 279 " =    1.165
peak=   -3.401 closest distance to " O   HOH Z 211 " =    1.605
peak=   -3.390 closest distance to " CD2 LEU A 167 " =    1.738
peak=   -3.384 closest distance to " O   VAL A 125 " =    2.247
peak=   -3.360 closest distance to " O   HOH Z 193 " =    1.836
peak=   -3.351 closest distance to " NE2 GLN A 103 " =    1.756
peak=   -3.347 closest distance to " O   HOH Z 136 " =    2.068
peak=   -3.344 closest distance to " CB  ALA A 291 " =    2.185
peak=   -3.341 closest distance to " ND2 ASN A  69 " =    1.704
peak=   -3.336 closest distance to " O   ALA A 161 " =    1.735
peak=   -3.330 closest distance to " CZ  TYR A 169 " =    1.739
peak=   -3.326 closest distance to " CA  GLY A 133 " =    2.253
peak=   -3.325 closest distance to " NE1 TRP A 266 " =    2.341
peak=   -3.324 closest distance to " O   SER A 271 " =    2.049
peak=   -3.320 closest distance to " O   GLY A  80 " =    2.466
peak=   -3.316 closest distance to " CB  ALA A 291 " =    2.269
peak=   -3.315 closest distance to " O   HOH Z  10 " =    1.526
peak=   -3.311 closest distance to " O   HOH Z 102 " =    1.614
peak=   -3.310 closest distance to " CG  TRP A 266 " =    1.870
peak=   -3.309 closest distance to " CG  PHE A 283 " =    2.742
peak=   -3.309 closest distance to " CB  ASN A  69 " =    1.143
peak=   -3.305 closest distance to " CG  ARG A 269 " =    2.359
peak=   -3.302 closest distance to " ND2 ASN A  60 " =    1.490
peak=   -3.300 closest distance to " O   HOH Z  60 " =    2.100
peak=   -3.297 closest distance to " OG  SER A  26 " =    1.316
peak=   -3.295 closest distance to " O   HOH Z 435 " =    2.711
peak=   -3.293 closest distance to " CG1 VAL A 112 " =    2.787
peak=   -3.293 closest distance to " O   HOH Z  38 " =    1.633
peak=   -3.292 closest distance to " N   SER A 276 " =    1.396
peak=   -3.292 closest distance to " CG  GLU A 277 " =    1.150
peak=   -3.281 closest distance to " CG  MET A 105 " =    0.900
peak=   -3.280 closest distance to " CG1 VAL A 296 " =    1.348
peak=   -3.280 closest distance to " O   HOH Z 423 " =    2.228
peak=   -3.279 closest distance to " OG  SER A 206 " =    1.638
peak=   -3.271 closest distance to " O   PRO A 198 " =    1.235
peak=   -3.271 closest distance to " N   ALA A 248 " =    1.643
peak=   -3.270 closest distance to " O   HOH Z 385 " =    1.936
peak=   -3.266 closest distance to " NH2 ARG A  79 " =    1.988
peak=   -3.264 closest distance to " OG  SER A  87 " =    1.453
peak=   -3.258 closest distance to " O   LEU A 167 " =    1.477
peak=   -3.258 closest distance to " CA  GLY A 203 " =    2.348
peak=   -3.254 closest distance to " CA  GLY A 133 " =    2.010
peak=   -3.253 closest distance to " O   HOH Z 175 " =    4.446
peak=   -3.253 closest distance to " N   MET A 105 " =    2.652
peak=   -3.252 closest distance to " O   ILE A 234 " =    1.216
peak=   -3.241 closest distance to " CB  ASP A 132 " =    2.295
peak=   -3.240 closest distance to " C   ASP A 231 " =    2.565
peak=   -3.239 closest distance to " OD1 ASN A 148 " =    1.528
peak=   -3.239 closest distance to " C   SER A 206 " =    1.520
peak=   -3.239 closest distance to " O   HOH Z 150 " =    1.873
peak=   -3.237 closest distance to " O   HOH Z 427 " =    1.402
peak=   -3.234 closest distance to " C   GLN A 205 " =    1.947
peak=   -3.232 closest distance to " OG BSER A 210 " =    2.111
peak=   -3.230 closest distance to " C   ASN A 285 " =    2.386
peak=   -3.229 closest distance to " O   VAL A 197 " =    1.362
peak=   -3.226 closest distance to " CE BMET A  47 " =    1.890
peak=   -3.226 closest distance to " CG1 VAL A 197 " =    2.237
peak=   -3.222 closest distance to " O   PRO A 198 " =    1.319
peak=   -3.221 closest distance to " OD1 ASN A 301 " =    2.056
peak=   -3.220 closest distance to " CG  ASP A  50 " =    2.401
peak=   -3.215 closest distance to " O   HOH Z 191 " =    5.509
peak=   -3.213 closest distance to " O   HOH Z 275 " =    1.461
peak=   -3.211 closest distance to " O   PHE A 218 " =    1.644
peak=   -3.207 closest distance to " OXT GLY A 302 " =    3.409
peak=   -3.203 closest distance to " O   MET A  40 " =    2.711
peak=   -3.202 closest distance to " CB  ALA A  51 " =    1.857
peak=   -3.201 closest distance to " O   HOH Z 431 " =    1.727
peak=   -3.195 closest distance to " O   HOH Z 414 " =    1.783
peak=   -3.194 closest distance to " O   HOH Z  11 " =    2.084
peak=   -3.191 closest distance to " O   HOH Z 262 " =    2.741
peak=   -3.191 closest distance to " CA  VAL A 197 " =    1.022
peak=   -3.190 closest distance to " O   HOH Z 174 " =    2.229
peak=   -3.185 closest distance to " O   HOH Z 151 " =    1.741
peak=   -3.182 closest distance to " CB  ALA A  10 " =    2.246
peak=   -3.177 closest distance to " O   HOH Z 350 " =    1.840
peak=   -3.176 closest distance to " O   HOH Z 252 " =    3.970
peak=   -3.172 closest distance to " CD1 TYR A 247 " =    2.308
peak=   -3.170 closest distance to " N   ASP A 171 " =    2.348
peak=   -3.170 closest distance to " O   HOH Z 123 " =    2.327
peak=   -3.168 closest distance to " CA  GLY A 241 " =    3.015
peak=   -3.167 closest distance to " O   LYS A 117 " =    1.655
peak=   -3.167 closest distance to " OD1 ASP A 200 " =    1.351
peak=   -3.165 closest distance to " CG  LEU A 228 " =    0.979
peak=   -3.164 closest distance to " O   HOH Z 414 " =    1.487
peak=   -3.163 closest distance to " O   HOH Z  71 " =    1.407
peak=   -3.162 closest distance to " CG  GLU A   2 " =    1.839
peak=   -3.160 closest distance to " O   HOH Z 241 " =    1.369
peak=   -3.158 closest distance to " O   HOH Z 412 " =    5.534
peak=   -3.155 closest distance to " O   HOH Z 377 " =    1.629
peak=   -3.143 closest distance to " N   MET A 188 " =    1.927
peak=   -3.143 closest distance to " CB  ASP A 132 " =    2.354
peak=   -3.140 closest distance to " CA  ASN A 127 " =    1.027
peak=   -3.124 closest distance to " O   HOH Z  47 " =    1.529
peak=   -3.124 closest distance to " O   HOH Z 128 " =    2.503
peak=   -3.122 closest distance to " O   HOH Z 372 " =    2.440
peak=   -3.121 closest distance to " CE  LYS A 166 " =    3.046
peak=   -3.121 closest distance to " O   HOH Z  90 " =    1.778
peak=   -3.119 closest distance to " O   HOH Z 422 " =    1.582
peak=   -3.115 closest distance to " O   GLY A  80 " =    2.583
peak=   -3.111 closest distance to " O   HOH Z 353 " =    2.117
peak=   -3.109 closest distance to " CB  PHE A 208 " =    2.295
peak=   -3.108 closest distance to " CG  ARG A 219 " =    2.822
peak=   -3.106 closest distance to " CD1 ILE A 199 " =    2.452
peak=   -3.093 closest distance to " O   HOH Z 113 " =    2.395
peak=   -3.087 closest distance to " O   HOH Z 111 " =    2.491
peak=   -3.081 closest distance to " O   HOH Z 409 " =    4.994
peak=   -3.071 closest distance to " CD  ARG A 195 " =    5.136
peak=   -3.043 closest distance to " CD2 LEU A 237 " =    2.447
peak=   -3.021 closest distance to " O   HOH Z 407 " =    3.198
peak=   -3.001 closest distance to " O   HOH Z  37 " =    2.042

================= 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    :  0.4409 0.4321   6.236122e+00   6.217862e+00
   1_bss:  0.4322 0.4233   6.232303e+00   6.205027e+00
   1_xyz:  0.3275 0.3532   6.037211e+00   6.086877e+00
   1_adp:  0.2684 0.3062   5.874423e+00   5.979313e+00
   1_occ:  0.2680 0.3061   5.873444e+00   5.979286e+00
   2_bss:  0.2642 0.3008   5.873092e+00   5.973906e+00
   2_xyz:  0.1696 0.2100   5.483104e+00   5.666691e+00
   2_adp:  0.1516 0.1939   5.381283e+00   5.582341e+00
   2_occ:  0.1514 0.1938   5.380624e+00   5.581891e+00
   3_bss:  0.1498 0.1924   5.380440e+00   5.581161e+00
   3_xyz:  0.1289 0.1669   5.244685e+00   5.451588e+00
   3_adp:  0.1247 0.1628   5.218729e+00   5.430378e+00
   3_occ:  0.1246 0.1627   5.218249e+00   5.430047e+00
   4_bss:  0.1245 0.1625   5.218002e+00   5.429848e+00
   4_xyz:  0.1153 0.1572   5.163286e+00   5.394793e+00
   4_adp:  0.1138 0.1577   5.158456e+00   5.396676e+00
   4_occ:  0.1137 0.1577   5.158313e+00   5.396712e+00
   5_bss:  0.1141 0.1584   5.160408e+00   5.397734e+00
   5_xyz:  0.1109 0.1570   5.143989e+00   5.389910e+00
   5_adp:  0.1110 0.1570   5.144896e+00   5.390513e+00
   5_occ:  0.1108 0.1570   5.143899e+00   5.390100e+00
   5_bss:  0.1108 0.1571   5.143947e+00   5.390144e+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:  0.335  17.591   7.015   9.712   8.128   0.000   0.000   0.000
   1_xyz:  0.335  17.591   7.015   9.712   8.128   0.000   0.000   0.000
   1_adp:  0.335  17.591   7.015   9.712   8.128   0.000   0.000   0.000
   1_occ:  0.335  17.591   7.015   9.712   8.128   0.000   0.000   0.000
   2_bss:  0.318  43.450   3.765   5.909   5.269   0.000   0.000   0.000
   2_xyz:  0.318  43.450   3.765   5.909   5.269   0.000   0.000   0.000
   2_adp:  0.318  43.450   3.765   5.909   5.269   0.000   0.000   0.000
   2_occ:  0.318  43.450   3.765   5.909   5.269   0.000   0.000   0.000
   3_bss:  0.322  43.450   2.712   3.923   3.973   0.000   0.000   0.000
   3_xyz:  0.322  43.450   2.712   3.923   3.973   0.000   0.000   0.000
   3_adp:  0.322  43.450   2.712   3.923   3.973   0.000   0.000   0.000
   3_occ:  0.322  43.450   2.712   3.923   3.973   0.000   0.000   0.000
   4_bss:  0.324  43.450   2.565   3.462   3.727   0.000   0.000   0.000
   4_xyz:  0.324  43.450   2.565   3.462   3.727   0.000   0.000   0.000
   4_adp:  0.324  43.450   2.565   3.462   3.727   0.000   0.000   0.000
   4_occ:  0.324  43.450   2.565   3.462   3.727   0.000   0.000   0.000
   5_bss:  0.319  43.450   2.676   3.407   3.774   0.000   0.000   0.000
   5_xyz:  0.319  43.450   2.676   3.407   3.774   0.000   0.000   0.000
   5_adp:  0.319  43.450   2.676   3.407   3.774   0.000   0.000   0.000
   5_occ:  0.319  43.450   2.676   3.407   3.774   0.000   0.000   0.000
   5_bss:  0.320  46.815  -0.590   0.089   0.501   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  48.854 0.5358  0.6022    53703.320
   1_bss:  48.760 0.5345  0.7651    51360.494
   1_xyz:  38.394 0.6603  0.9250    33990.416
   1_adp:  31.303 0.7438  1.0251    24633.994
   1_occ:  31.325 0.7435  1.0238    24624.104
   2_bss:  31.015 0.7469  0.9137    24209.388
   2_xyz:  20.554 0.8557  1.0076    11329.449
   2_adp:  18.340 0.8773  1.0221     9529.133
   2_occ:  18.337 0.8773  1.0220     9522.071
   3_bss:  18.295 0.8778  0.9701     9520.536
   3_xyz:  15.313 0.9041  0.9832     7164.579
   3_adp:  14.792 0.9089  0.9861     6891.592
   3_occ:  14.779 0.9090  0.9860     6888.296
   4_bss:  14.770 0.9090  0.9763     6886.255
   4_xyz:  14.083 0.9146  0.9765     6435.296
   4_adp:  14.124 0.9143  0.9732     6456.505
   4_occ:  14.122 0.9144  0.9730     6460.628
   5_bss:  14.175 0.9139  0.9737     6510.743
   5_xyz:  14.031 0.9150  0.9753     6380.157
   5_adp:  14.029 0.9150  0.9728     6374.581
   5_occ:  14.017 0.9151  0.9726     6374.392
   5_bss:  14.018 0.9151  0.9754     6375.293
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.3768e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.3768e+01
   1_xyz:   1.587  0.012  0.105 17.830  0.006  4.111   1.2437e-01
   1_adp:   1.587  0.012  0.105 17.830  0.006  4.111   1.2437e-01
   1_occ:   1.587  0.012  0.105 17.830  0.006  4.111   1.2437e-01
   2_bss:   1.587  0.012  0.105 17.830  0.006  4.111   1.2437e-01
   2_xyz:   1.099  0.008  0.078 16.166  0.004  4.126   7.1599e-02
   2_adp:   1.099  0.008  0.078 16.166  0.004  4.126   7.1599e-02
   2_occ:   1.099  0.008  0.078 16.166  0.004  4.126   7.1599e-02
   3_bss:   1.099  0.008  0.078 16.166  0.004  4.126   7.1599e-02
   3_xyz:   0.924  0.006  0.072 15.322  0.003  4.120   5.3425e-02
   3_adp:   0.924  0.006  0.072 15.322  0.003  4.120   5.3425e-02
   3_occ:   0.924  0.006  0.072 15.322  0.003  4.120   5.3425e-02
   4_bss:   0.924  0.006  0.072 15.322  0.003  4.120   5.3425e-02
   4_xyz:   1.019  0.007  0.083 15.491  0.003  4.124   6.1677e-02
   4_adp:   1.019  0.007  0.083 15.491  0.003  4.124   6.1677e-02
   4_occ:   1.019  0.007  0.083 15.491  0.003  4.124   6.1677e-02
   5_bss:   1.019  0.007  0.083 15.491  0.003  4.124   6.1677e-02
   5_xyz:   1.030  0.008  0.083 15.258  0.004  4.122   6.3464e-02
   5_adp:   1.030  0.008  0.083 15.258  0.004  4.122   6.3464e-02
   5_occ:   1.030  0.008  0.083 15.258  0.004  4.122   6.3464e-02
   5_bss:   1.030  0.008  0.083 15.258  0.004  4.122   6.3464e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9711e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9711e+00
   1_xyz:  13.967  0.151  0.481 89.280  0.047  2.267   9.3923e-02
   1_adp:  13.967  0.151  0.481 89.280  0.047  2.267   9.3923e-02
   1_occ:  13.967  0.151  0.481 89.280  0.047  2.267   9.3923e-02
   2_bss:  13.967  0.151  0.481 89.280  0.047  2.267   9.3923e-02
   2_xyz:   7.310  0.070  0.327 84.608  0.034  2.245   5.9363e-02
   2_adp:   7.310  0.070  0.327 84.608  0.034  2.245   5.9363e-02
   2_occ:   7.310  0.070  0.327 84.608  0.034  2.245   5.9363e-02
   3_bss:   7.310  0.070  0.327 84.608  0.034  2.245   5.9363e-02
   3_xyz:   6.583  0.049  0.444 80.618  0.032  2.357   2.9995e-02
   3_adp:   6.583  0.049  0.444 80.618  0.032  2.357   2.9995e-02
   3_occ:   6.583  0.049  0.444 80.618  0.032  2.357   2.9995e-02
   4_bss:   6.583  0.049  0.444 80.618  0.032  2.357   2.9995e-02
   4_xyz:   7.292  0.039  0.574 83.934  0.029  2.346   3.9229e-02
   4_adp:   7.292  0.039  0.574 83.934  0.029  2.346   3.9229e-02
   4_occ:   7.292  0.039  0.574 83.934  0.029  2.346   3.9229e-02
   5_bss:   7.292  0.039  0.574 83.934  0.029  2.346   3.9229e-02
   5_xyz:   7.199  0.039  0.580 81.289  0.028  2.338   4.4523e-02
   5_adp:   7.199  0.039  0.580 81.289  0.028  2.338   4.4523e-02
   5_occ:   7.199  0.039  0.580 81.289  0.028  2.338   4.4523e-02
   5_bss:   7.199  0.039  0.580 81.289  0.028  2.338   4.4523e-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:  69.60   0.00  10.97  69.60   0.00   7.93  66.40   0.00  27.52
   1_occ:  69.60   0.00  10.97  69.60   0.00   7.93  66.40   0.00  27.52
   2_bss:  69.60   0.00  10.97  69.60   0.00   7.93  66.40   0.00  27.52
   2_xyz:  69.60   0.00  10.97  69.60   0.00   7.93  66.40   0.00  27.52
   2_adp:  74.97   0.00  11.49  74.97   0.00   7.64  66.39   0.93  32.50
   2_occ:  74.97   0.00  11.49  74.97   0.00   7.64  66.39   0.93  32.50
   3_bss:  74.97   0.00  11.49  74.97   0.00   7.64  66.39   0.93  32.50
   3_xyz:  74.97   0.00  11.49  74.97   0.00   7.64  66.39   0.93  32.50
   3_adp:  78.13   0.00  11.72  78.13   0.00   7.64  66.90   0.91  33.94
   3_occ:  78.13   0.00  11.72  78.13   0.00   7.64  66.90   0.91  33.94
   4_bss:  78.13   0.00  11.72  78.13   0.00   7.64  66.90   0.91  33.94
   4_xyz:  78.13   0.00  11.72  78.13   0.00   7.64  66.90   0.91  33.94
   4_adp:  85.10   0.00  11.83  85.10   0.00   7.66  70.29   0.67  34.58
   4_occ:  85.10   0.00  11.83  85.10   0.00   7.66  70.29   0.67  34.58
   5_bss:  85.10   0.00  11.83  85.10   0.00   7.66  70.29   0.67  34.58
   5_xyz:  85.10   0.00  11.83  85.10   0.00   7.66  70.29   0.67  34.58
   5_adp:  85.57   0.00  11.73  85.57   0.00   7.60  69.88   0.77  34.21
   5_occ:  85.57   0.00  11.73  85.57   0.00   7.60  69.88   0.77  34.21
   5_bss:  88.93   3.36  15.10  88.93   3.36  10.97  73.24   4.14  37.57
------------------------------------------------------------------------
 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:    1.179    0.022    0.408
   1_adp:    1.179    0.022    0.408
   1_occ:    1.179    0.022    0.408
   2_bss:    1.179    0.022    0.408
   2_xyz:    1.451    0.034    0.535
   2_adp:    1.451    0.034    0.535
   2_occ:    1.451    0.034    0.535
   3_bss:    1.451    0.034    0.535
   3_xyz:    1.540    0.038    0.562
   3_adp:    1.540    0.038    0.562
   3_occ:    1.540    0.038    0.562
   4_bss:    1.540    0.038    0.562
   4_xyz:    1.621    0.048    0.589
   4_adp:    1.621    0.048    0.589
   4_occ:    1.621    0.048    0.589
   5_bss:    1.621    0.048    0.589
   5_xyz:    1.671    0.061    0.601
   5_adp:    1.671    0.061    0.601
   5_occ:    1.671    0.061    0.601
   5_bss:    1.671    0.061    0.601
------------------------------------------------------------------------

CPU time actual refinement: 342.71


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_685/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_685/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_685/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_685/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_685/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 342.57 
  Macro-tasks:
    bulk solvent and scale       = 44.54  
    individual site refinement   = 144.42 
    weights calculation          = 32.59  
    collect and process          = 6.69   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 228.34 
  Micro-tasks:
    mask                            = 1.66   
    f_calc                          = 105.25 
    alpha_beta                      = 8.56   
    target                          = 1.24   
    gradients_wrt_atomic_parameters = 112.96 
    fmodel                         = 7.83   
    r_factors                      = 0.19   
    phase_errors                   = 11.69  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 249.64 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.700 micro seconds
Total CPU time: 5.93 minutes
from_scatterers_fft:    674 calls, 104.70 s
gradients_fft:          619 calls, 100.26 s

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

# Date 2008-01-16 Time 02:10:24 PST -0800 (1200478224.72 s)
Start R-work = 0.4409, R-free = 0.4321 (no bulk solvent and anisotropic scale)
Final R-work = 0.1279, R-free = 0.1725 (no bulk solvent and anisotropic scale)

Start R-work = 0.4322, R-free = 0.4233
Final R-work = 0.1108, R-free = 0.1571