# Date 2008-01-16 Time 01:28:38 PST -0800 (1200475718.40 s)
#phil __OFF__

Command line arguments: "../446.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 = 24340
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 446

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.5475, 47.3993, 86.822, 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: 3.32, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 47.3993, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.904 1.98067
Completeness in resolution range: 0.954351
Completeness with d_max=infinity: 0.951384

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9040
                             d_min =   1.9807

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 47.3993, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.904 1.98067
Completeness in resolution range: 0.954351
Completeness with d_max=infinity: 0.951384

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9044 -  4.2376 [2165/2193]  1947   218  10.1%
  bin  2:  4.2376 -  3.3764 [2058/2077]  1855   203   9.9%
  bin  3:  3.3764 -  2.9533 [2050/2070]  1845   205  10.0%
  bin  4:  2.9533 -  2.6850 [2022/2047]  1821   201   9.9%
  bin  5:  2.6850 -  2.4935 [2015/2035]  1806   209  10.4%
  bin  6:  2.4935 -  2.3471 [1999/2045]  1804   195   9.8%
  bin  7:  2.3471 -  2.2300 [1992/2025]  1796   196   9.8%
  bin  8:  2.2300 -  2.1332 [1996/2031]  1791   205  10.3%
  bin  9:  2.1332 -  2.0513 [1953/1983]  1755   198  10.1%
  bin 10:  2.0513 -  1.9807 [1339/2020]  1210   129   9.6%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_446/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: 2187
        3.04 -     3.66: 4662
        3.66 -     4.28: 9024
        4.28 -     4.90: 12352
  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 109 " - " O   HOH Z 417 "  1.950 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  2.004 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  2.051 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  2.101 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28239 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_446/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_446/model_refine_001.geo

CPU time processing inputs: 9.02


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.5475 47.3993 86.82195 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 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4453   r_free= 0.4295   ksol= 0.00   Bsol= 0.00   scale= 0.815    |
|                                                                             |
| 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: 6.242070                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9044 -  4.7261 0.99   1401  157 0.3600 0.3458      6.5218      6.5198|
|  2:  4.7261 -  3.7713 0.99   1346  151 0.3433 0.3714      6.6676      6.7379|
|  3:  3.7713 -  3.3005 0.99   1324  148 0.3952 0.3576      6.5938      6.5681|
|  4:  3.3005 -  3.0014 0.99   1310  135 0.4253 0.3840      6.4597       6.363|
|  5:  3.0014 -  2.7878 0.99   1306  150 0.4720 0.4600      6.3375      6.3644|
|  6:  2.7878 -  2.6243 0.98   1298  143 0.4680 0.5275      6.2427       6.198|
|  7:  2.6243 -  2.4935 0.99   1289  152 0.4808 0.4537      6.2104      6.1146|
|  8:  2.4935 -  2.3855 0.98   1308  136 0.4909 0.4329      6.1647       6.138|
|  9:  2.3855 -  2.2940 0.98   1282  146 0.4991 0.5122      6.0938      6.1294|
| 10:  2.2940 -  2.2151 0.97   1257  139 0.5145 0.4472      6.1199      6.0554|
| 11:  2.2151 -  2.1460 0.99   1287  146 0.5062 0.4528      6.0132      6.0016|
| 12:  2.1460 -  2.0848 0.98   1279  140 0.5134 0.5164      5.9619      5.9916|
| 13:  2.0848 -  2.0301 0.97   1252  135 0.5077 0.5152      5.8817      5.8216|
| 14:  2.0301 -  1.9807 0.54    691   81 0.5260 0.4527      5.8788      5.7452|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9044 -  4.7261  1401   157  0.72  32.10   0.82     0.73      61645.22|
|  2:  4.7261 -  3.7713  1346   151  0.76  30.14   0.91     0.80      80476.05|
|  3:  3.7713 -  3.3005  1324   148  0.69  36.25   0.86     0.78      82381.83|
|  4:  3.3005 -  3.0014  1310   135  0.64  40.67   0.82     0.70      69338.64|
|  5:  3.0014 -  2.7878  1306   150  0.54  48.71   0.76     0.61      62600.35|
|  6:  2.7878 -  2.6243  1298   143  0.51  51.62   0.75     0.57      57563.66|
|  7:  2.6243 -  2.4935  1289   152  0.48  53.64   0.76     0.54      54494.77|
|  8:  2.4935 -  2.3855  1308   136  0.50  52.35   0.76     0.57      47239.64|
|  9:  2.3855 -  2.2940  1282   146  0.50  52.10   0.73     0.58      42487.38|
| 10:  2.2940 -  2.2151  1257   139  0.50  52.16   0.76     0.58      38453.57|
| 11:  2.2151 -  2.1460  1287   146  0.47  54.84   0.74     0.55      37925.04|
| 12:  2.1460 -  2.0848  1279   140  0.43  57.95   0.79     0.53      37052.69|
| 13:  2.0848 -  2.0301  1252   135  0.42  58.70   0.74     0.50      32316.45|
| 14:  2.0301 -  1.9807   691    81  0.46  55.69   0.73     0.48      23504.08|
|alpha:            min =        0.48 max =            0.80 mean =         0.61|
|beta:             min =    23504.08 max =        82381.83 mean =     53250.49|
|figures of merit: min =        0.00 max =            1.00 mean =         0.55|
|phase err.(work): min =        0.00 max =           89.99 mean =        47.88|
|phase err.(test): min =        0.00 max =           89.98 mean =        47.98|
|-----------------------------------------------------------------------------|

============================== 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 = 8.247681              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.201   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.701407              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.916   (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:       24 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      162 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      694 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1496 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2637 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3888 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5070 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6578 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7694 |
|-----------------------------------------------------------------------------|
|-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 |       53.840 |
| 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 |       1.791 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.926)------------------------------------------|
|    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 = 11.926)------------------------------------------|
|    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 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4524   r_free= 0.4339   ksol= 0.00   Bsol= 0.00   scale= 0.784    |
|                                                                             |
| 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: 6.246866                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4369   r_free= 0.4208   ksol= 0.34   Bsol= 20.00   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.91,9.33,8.22,0.00,0.00,0.00); trace/3= 8.16                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.234043                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.931645              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.771   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.665458              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 75.580   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4369      final r-factor (work) = 0.3278          |
| start r-factor (free) = 0.4208      final r-factor (free) = 0.3468          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 78.6324 = 7.93 * 0.50 * 6.2516 + 1.00 * 53.8395                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.2661 = 7.93 * 0.50 * 6.0874 + 1.00 * 0.1246                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3278      final r-factor (work) = 0.2669          |
| start r-factor (free) = 0.3468      final r-factor (free) = 0.3033          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0653 = 0.67 * 1.00 * 6.0874 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9523 = 0.67 * 1.00 * 5.9210 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.926)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    63.12   11.06    None  None   None       |
|    all(noH): 2823   0      0.00    63.12   11.06    None  None   None       |
|    Sol.    : 438    0      0.00    63.12   27.04    None  None   None       |
|    Mac.    : 2385   0      0.00    59.52   8.12     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 -   6.312: 1262   |   5:    31.559 -  37.871:  106        |
|      1:     6.312 -  12.624:  738   |   6:    37.871 -  44.183:   64        |
|      2:    12.624 -  18.936:  319   |   7:    44.183 -  50.495:   36        |
|      3:    18.936 -  25.247:  174   |   8:    50.495 -  56.807:   15        |
|      4:    25.247 -  31.559:  104   |   9:    56.807 -  63.118:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2669 r_free = 0.3033             target_work(ml) = 5.868         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2664 r_free = 0.3038             target_work(ml) = 5.867         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2664   r_free= 0.3038   ksol= 0.34   Bsol= 20.00   scale= 1.085   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.91,9.33,8.22,0.00,0.00,0.00); trace/3= 8.16                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.867395                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2627   r_free= 0.2994   ksol= 0.33   Bsol= 40.74   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.65,5.56,5.11,0.00,0.00,0.00); trace/3= 4.77                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.867873                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.378004              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.247   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.298306              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.118  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2627      final r-factor (work) = 0.1797          |
| start r-factor (free) = 0.2994      final r-factor (free) = 0.2164          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1369 = 3.38 * 0.50 * 5.9279 + 1.00 * 0.1246                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6800 = 3.38 * 0.50 * 5.6933 + 1.00 * 0.0640                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1797      final r-factor (work) = 0.1639          |
| start r-factor (free) = 0.2164      final r-factor (free) = 0.2010          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7129 = 0.30 * 1.00 * 5.6933 + 1.00 * 0.0146                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6580 = 0.30 * 1.00 * 5.4817 + 1.00 * 0.0228                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.926)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    65.99   11.30    None  None   None       |
|    all(noH): 2823   0      0.00    65.99   11.30    None  None   None       |
|    Sol.    : 438    0      0.93    64.10   31.29    None  None   None       |
|    Mac.    : 2385   0      0.00    65.99   7.63     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 -   6.599: 1397   |   5:    32.994 -  39.593:   91        |
|      1:     6.599 -  13.198:  747   |   6:    39.593 -  46.192:   95        |
|      2:    13.198 -  19.796:  189   |   7:    46.192 -  52.790:   49        |
|      3:    19.796 -  26.395:  126   |   8:    52.790 -  59.389:   18        |
|      4:    26.395 -  32.994:  104   |   9:    59.389 -  65.988:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1639 r_free = 0.2010             target_work(ml) = 5.450         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1638 r_free = 0.2010             target_work(ml) = 5.450         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1638   r_free= 0.2010   ksol= 0.33   Bsol= 40.74   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.65,5.56,5.11,0.00,0.00,0.00); trace/3= 4.77                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.449880                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1630   r_free= 0.2014   ksol= 0.32   Bsol= 47.28   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.55,3.95,4.31,0.00,0.00,0.00); trace/3= 3.60                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.449541                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.269010              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.713  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.326258              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 97.712   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1630      final r-factor (work) = 0.1303          |
| start r-factor (free) = 0.2014      final r-factor (free) = 0.1651          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2892 = 2.27 * 0.50 * 5.4871 + 1.00 * 0.0641                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1275 = 2.27 * 0.50 * 5.3483 + 1.00 * 0.0598                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1303      final r-factor (work) = 0.1244          |
| start r-factor (free) = 0.1651      final r-factor (free) = 0.1605          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7621 = 0.33 * 1.00 * 5.3483 + 1.00 * 0.0172                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7168 = 0.33 * 1.00 * 5.2267 + 1.00 * 0.0116                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.926)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.03   11.62    None  None   None       |
|    all(noH): 2823   0      0.00    72.03   11.62    None  None   None       |
|    Sol.    : 438    0      0.78    65.00   33.61    None  None   None       |
|    Mac.    : 2385   0      0.00    72.03   7.58     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 -   7.203: 1554   |   5:    36.014 -  43.216:  104        |
|      1:     7.203 -  14.405:  639   |   6:    43.216 -  50.419:   78        |
|      2:    14.405 -  21.608:  166   |   7:    50.419 -  57.622:   44        |
|      3:    21.608 -  28.811:  110   |   8:    57.622 -  64.824:   22        |
|      4:    28.811 -  36.014:  103   |   9:    64.824 -  72.027:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1244 r_free = 0.1605             target_work(ml) = 5.212         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1243 r_free = 0.1604             target_work(ml) = 5.212         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1243   r_free= 0.1604   ksol= 0.32   Bsol= 47.28   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.55,3.95,4.31,0.00,0.00,0.00); trace/3= 3.60                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.211737                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1245   r_free= 0.1606   ksol= 0.33   Bsol= 47.28   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.39,3.45,4.17,0.00,0.00,0.00); trace/3= 3.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.213119                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.206049              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 128.935  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.245806              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 109.329  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1245      final r-factor (work) = 0.1156          |
| start r-factor (free) = 0.1606      final r-factor (free) = 0.1567          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8258 = 2.21 * 0.50 * 5.2274 + 1.00 * 0.0598                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7784 = 2.21 * 0.50 * 5.1805 + 1.00 * 0.0643                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1156      final r-factor (work) = 0.1154          |
| start r-factor (free) = 0.1567      final r-factor (free) = 0.1561          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2860 = 0.25 * 1.00 * 5.1805 + 1.00 * 0.0126                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2915 = 0.25 * 1.00 * 5.1654 + 1.00 * 0.0218                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.926)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    73.45   11.41    None  None   None       |
|    all(noH): 2823   0      0.00    73.45   11.41    None  None   None       |
|    Sol.    : 438    0      1.00    65.23   32.86    None  None   None       |
|    Mac.    : 2385   0      0.00    73.45   7.47     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 -   7.345: 1610   |   5:    36.726 -  44.071:   95        |
|      1:     7.345 -  14.690:  598   |   6:    44.071 -  51.416:   72        |
|      2:    14.690 -  22.036:  176   |   7:    51.416 -  58.762:   37        |
|      3:    22.036 -  29.381:  112   |   8:    58.762 -  66.107:   16        |
|      4:    29.381 -  36.726:  105   |   9:    66.107 -  73.452:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1154 r_free = 0.1561             target_work(ml) = 5.164         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1152 r_free = 0.1561             target_work(ml) = 5.164         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1152   r_free= 0.1561   ksol= 0.33   Bsol= 47.28   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.39,3.45,4.17,0.00,0.00,0.00); trace/3= 3.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.163736                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1152   r_free= 0.1561   ksol= 0.33   Bsol= 47.28   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.41,3.35,4.20,0.00,0.00,0.00); trace/3= 3.32                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.163690                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.463893              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 149.149  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.299264              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.373   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1152      final r-factor (work) = 0.1164          |
| start r-factor (free) = 0.1561      final r-factor (free) = 0.1569          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8449 = 1.46 * 0.50 * 5.1647 + 1.00 * 0.0646                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8383 = 1.46 * 0.50 * 5.1691 + 1.00 * 0.0548                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1164      final r-factor (work) = 0.1164          |
| start r-factor (free) = 0.1569      final r-factor (free) = 0.1572          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5765 = 0.30 * 1.00 * 5.1691 + 1.00 * 0.0295                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5936 = 0.30 * 1.00 * 5.1701 + 1.00 * 0.0464                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.926)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.06   11.36    None  None   None       |
|    all(noH): 2823   0      0.00    74.06   11.36    None  None   None       |
|    Sol.    : 438    0      0.72    65.53   32.80    None  None   None       |
|    Mac.    : 2385   0      0.00    74.06   7.42     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 -   7.406: 1630   |   5:    37.032 -  44.438:   95        |
|      1:     7.406 -  14.813:  575   |   6:    44.438 -  51.844:   70        |
|      2:    14.813 -  22.219:  176   |   7:    51.844 -  59.251:   37        |
|      3:    22.219 -  29.625:  112   |   8:    59.251 -  66.657:   13        |
|      4:    29.625 -  37.032:  113   |   9:    66.657 -  74.063:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1164 r_free = 0.1572             target_work(ml) = 5.172         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1164 r_free = 0.1572             target_work(ml) = 5.172         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1164   r_free= 0.1572   ksol= 0.33   Bsol= 47.28   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.41,3.35,4.20,0.00,0.00,0.00); trace/3= 3.32                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.171675                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9044 -  4.7261 0.99   1401  157 0.1036 0.1315      5.4117      5.5496|
|  2:  4.7261 -  3.7713 0.99   1346  151 0.0900 0.1077      5.4665      5.6477|
|  3:  3.7713 -  3.3005 0.99   1324  148 0.1097 0.1509        5.49       5.852|
|  4:  3.3005 -  3.0014 0.99   1310  135 0.1235 0.1532      5.4619      5.5921|
|  5:  3.0014 -  2.7878 0.99   1306  150 0.1392 0.1645      5.3591      5.5013|
|  6:  2.7878 -  2.6243 0.98   1298  143 0.1301 0.2074      5.2427      5.5251|
|  7:  2.6243 -  2.4935 0.99   1289  152 0.1287 0.1610       5.189      5.3393|
|  8:  2.4935 -  2.3855 0.98   1308  136 0.1196 0.1727       5.104      5.3709|
|  9:  2.3855 -  2.2940 0.98   1282  146 0.1245 0.1965      5.0555      5.3619|
| 10:  2.2940 -  2.2151 0.97   1257  139 0.1186 0.1502      4.9962      5.1412|
| 11:  2.2151 -  2.1460 0.99   1287  146 0.1189 0.1787      4.9439      5.2545|
| 12:  2.1460 -  2.0848 0.98   1279  140 0.1147 0.1674      4.8705      5.1638|
| 13:  2.0848 -  2.0301 0.97   1252  135 0.1162 0.1786       4.803      5.0579|
| 14:  2.0301 -  1.9807 0.54    691   81 0.1153 0.1708      4.7433      4.9341|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9044 -  4.7261  1401   157  0.94   9.24   0.97     0.95       7365.81|
|  2:  4.7261 -  3.7713  1346   151  0.95   8.03   1.01     0.99       9026.54|
|  3:  3.7713 -  3.3005  1324   148  0.94  11.17   1.02     1.01      10435.76|
|  4:  3.3005 -  3.0014  1310   135  0.92  13.44   1.00     0.99      10263.54|
|  5:  3.0014 -  2.7878  1306   150  0.90  16.24   0.99     0.96       8532.73|
|  6:  2.7878 -  2.6243  1298   143  0.90  16.58   0.97     0.94       7249.66|
|  7:  2.6243 -  2.4935  1289   152  0.90  15.71   0.98     0.95       6314.63|
|  8:  2.4935 -  2.3855  1308   136  0.91  15.26   0.99     0.96       5656.19|
|  9:  2.3855 -  2.2940  1282   146  0.90  16.39   1.00     0.97       5223.60|
| 10:  2.2940 -  2.2151  1257   139  0.90  16.24   0.99     0.96       4638.77|
| 11:  2.2151 -  2.1460  1287   146  0.90  15.95   0.99     0.95       4301.15|
| 12:  2.1460 -  2.0848  1279   140  0.91  15.11   1.00     0.99       3778.69|
| 13:  2.0848 -  2.0301  1252   135  0.90  15.96   0.99     0.98       3387.84|
| 14:  2.0301 -  1.9807   691    81  0.90  15.78   0.97     0.92       2858.59|
|alpha:            min =        0.92 max =            1.01 mean =         0.97|
|beta:             min =     2858.59 max =        10435.76 mean =      6519.34|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.25|
|phase err.(test): min =        0.00 max =           89.72 mean =        13.79|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1164   r_free= 0.1572   ksol= 0.32   Bsol= 50.35   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.90,0.01,0.90,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.171681                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1164   r_free= 0.1572   ksol= 0.32   Bsol= 50.35   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.90,0.01,0.90,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.171681                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9044 -  4.7261 0.99   1401  157 0.1036 0.1315      5.4113      5.5496|
|  2:  4.7261 -  3.7713 0.99   1346  151 0.0901 0.1077      5.4666      5.6477|
|  3:  3.7713 -  3.3005 0.99   1324  148 0.1097 0.1510      5.4901      5.8521|
|  4:  3.3005 -  3.0014 0.99   1310  135 0.1235 0.1531      5.4619       5.592|
|  5:  3.0014 -  2.7878 0.99   1306  150 0.1392 0.1646      5.3591      5.5013|
|  6:  2.7878 -  2.6243 0.98   1298  143 0.1301 0.2074      5.2427      5.5248|
|  7:  2.6243 -  2.4935 0.99   1289  152 0.1287 0.1610       5.189      5.3395|
|  8:  2.4935 -  2.3855 0.98   1308  136 0.1196 0.1726       5.104      5.3709|
|  9:  2.3855 -  2.2940 0.98   1282  146 0.1245 0.1965      5.0555      5.3618|
| 10:  2.2940 -  2.2151 0.97   1257  139 0.1186 0.1503      4.9964      5.1417|
| 11:  2.2151 -  2.1460 0.99   1287  146 0.1189 0.1787      4.9441      5.2546|
| 12:  2.1460 -  2.0848 0.98   1279  140 0.1147 0.1676      4.8705      5.1642|
| 13:  2.0848 -  2.0301 0.97   1252  135 0.1162 0.1785       4.803      5.0574|
| 14:  2.0301 -  1.9807 0.54    691   81 0.1153 0.1707      4.7433       4.934|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9044 -  4.7261  1401   157  0.94   9.23   0.97     0.95       7357.62|
|  2:  4.7261 -  3.7713  1346   151  0.95   8.03   1.01     0.99       9025.03|
|  3:  3.7713 -  3.3005  1324   148  0.94  11.17   1.02     1.01      10438.34|
|  4:  3.3005 -  3.0014  1310   135  0.92  13.44   1.00     0.99      10263.88|
|  5:  3.0014 -  2.7878  1306   150  0.90  16.24   0.99     0.96       8531.57|
|  6:  2.7878 -  2.6243  1298   143  0.90  16.58   0.97     0.94       7248.74|
|  7:  2.6243 -  2.4935  1289   152  0.90  15.71   0.98     0.95       6314.20|
|  8:  2.4935 -  2.3855  1308   136  0.91  15.26   0.99     0.97       5656.33|
|  9:  2.3855 -  2.2940  1282   146  0.90  16.39   1.00     0.97       5224.60|
| 10:  2.2940 -  2.2151  1257   139  0.90  16.24   1.00     0.96       4640.37|
| 11:  2.2151 -  2.1460  1287   146  0.90  15.96   0.99     0.95       4303.21|
| 12:  2.1460 -  2.0848  1279   140  0.91  15.11   1.01     1.00       3779.09|
| 13:  2.0848 -  2.0301  1252   135  0.90  15.96   1.00     0.98       3387.41|
| 14:  2.0301 -  1.9807   691    81  0.90  15.78   0.97     0.92       2858.03|
|alpha:            min =        0.92 max =            1.01 mean =         0.97|
|beta:             min =     2858.03 max =        10438.34 mean =      6518.94|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.25|
|phase err.(test): min =        0.00 max =           89.72 mean =        13.79|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.926)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.39    77.46   14.75    None  None   None       |
|    all(noH): 2823   0      3.39    77.46   14.75    None  None   None       |
|    Sol.    : 438    0      4.12    68.93   36.20    None  None   None       |
|    Mac.    : 2385   0      3.39    77.46   10.81    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:     3.394 -  10.800: 1630   |   5:    40.426 -  47.832:   95        |
|      1:    10.800 -  18.207:  575   |   6:    47.832 -  55.238:   70        |
|      2:    18.207 -  25.613:  176   |   7:    55.238 -  62.645:   37        |
|      3:    25.613 -  33.019:  112   |   8:    62.645 -  70.051:   13        |
|      4:    33.019 -  40.426:  113   |   9:    70.051 -  77.457:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 305         
Filter by distance & map next to the model:
   mapped sites are within: 0.246 - 4.001
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 297 from: 305
   mapped sites are within: 0.709 - 4.001

peak=   11.105 closest distance to " CB  VAL A 230 " =    1.470
peak=    6.157 closest distance to " CG  LEU A   5 " =    1.253
peak=    5.728 closest distance to " CG2 VAL A 296 " =    1.029
peak=    5.691 closest distance to " CG1 VAL A 296 " =    1.149
peak=    5.618 closest distance to " CB  GLN A 223 " =    1.415
peak=    5.538 closest distance to " CG  PRO A  54 " =    1.328
peak=    5.445 closest distance to " CB  VAL A 296 " =    1.082
peak=    5.381 closest distance to " CD2 LEU A   5 " =    1.203
peak=    5.327 closest distance to " NH2 ARG A  56 " =    2.220
peak=    5.254 closest distance to " CB  ARG A 275 " =    0.928
peak=    5.181 closest distance to " CG  LEU A 228 " =    1.213
peak=    5.013 closest distance to " CB  PRO A  54 " =    0.990
peak=    4.927 closest distance to " CG  PRO A 198 " =    1.243
peak=    4.828 closest distance to " O   HOH Z 209 " =    2.285
peak=    4.748 closest distance to " CG  PRO A 243 " =    1.118
peak=    4.691 closest distance to " CB  SER A  63 " =    1.168
peak=    4.677 closest distance to " O   HOH Z 232 " =    2.335
peak=    4.675 closest distance to " O   HOH Z 402 " =    1.510
peak=    4.651 closest distance to " CZ  PHE A 218 " =    1.152
peak=    4.630 closest distance to " O   HOH Z 265 " =    2.243
peak=    4.573 closest distance to " CG  PRO A 213 " =    1.294
peak=    4.552 closest distance to " O   HOH Z 142 " =    1.663
peak=    4.536 closest distance to " CB  GLN A 183 " =    1.294
peak=    4.507 closest distance to " CB  VAL A 230 " =    1.206
peak=    4.484 closest distance to " CB  GLU A 152 " =    1.170
peak=    4.450 closest distance to " C   PRO A 198 " =    1.492
peak=    4.435 closest distance to " CD2 LEU A 228 " =    1.219
peak=    4.420 closest distance to " O   HOH Z 126 " =    1.872
peak=    4.398 closest distance to " O   SER A  87 " =    2.194
peak=    4.397 closest distance to " O   HOH Z 272 " =    1.906
peak=    4.369 closest distance to " CA  TYR A  30 " =    0.910
peak=    4.288 closest distance to " O   HOH Z 234 " =    3.689
peak=    4.279 closest distance to " O   HOH Z 287 " =    1.909
peak=    4.267 closest distance to " O   HOH Z 403 " =    1.720
peak=    4.250 closest distance to " O   HOH Z 248 " =    1.586
peak=    4.245 closest distance to " O   HOH Z  43 " =    2.134
peak=    4.243 closest distance to " O   HOH Z 346 " =    1.564
peak=    4.212 closest distance to " NE2 GLN A  11 " =    1.062
peak=    4.212 closest distance to " CB  ASN A 148 " =    1.401
peak=    4.204 closest distance to " O   HOH Z  61 " =    1.640
peak=    4.155 closest distance to " O   HOH Z 193 " =    1.782
peak=    4.154 closest distance to " O   HOH Z 423 " =    1.787
peak=    4.111 closest distance to " ND2 ASN A 187 " =    1.559
peak=    4.076 closest distance to " CB  ASN A  39 " =    0.852
peak=    4.063 closest distance to " O   HOH Z 369 " =    2.220
peak=    4.056 closest distance to " CB  ARG A  79 " =    1.356
peak=    4.043 closest distance to " CB  SER A   3 " =    1.242
peak=    4.033 closest distance to " O   HOH Z  85 " =    1.399
peak=    4.031 closest distance to " O   HOH Z 298 " =    1.778
peak=    4.015 closest distance to " CB  GLU A 277 " =    3.619
peak=    4.011 closest distance to " O   HOH Z 368 " =    2.259
peak=    4.005 closest distance to " O   HOH Z 189 " =    2.758
peak=    4.002 closest distance to " O   HOH Z 280 " =    2.914
peak=    3.991 closest distance to " CA  ALA A  51 " =    0.957
peak=    3.974 closest distance to " O   HOH Z 126 " =    2.209
peak=    3.971 closest distance to " N   ASN A  39 " =    1.153
peak=    3.959 closest distance to " O   HOH Z  97 " =    2.016
peak=    3.901 closest distance to " O   HOH Z  97 " =    2.342
peak=    3.888 closest distance to " CB  ARG A 190 " =    1.703
peak=    3.876 closest distance to " CA  ARG A  36 " =    1.042
peak=    3.862 closest distance to " O   HOH Z 316 " =    3.027
peak=    3.852 closest distance to " O   HOH Z 303 " =    2.134
peak=    3.845 closest distance to " O   TRP A 274 " =    1.869
peak=    3.841 closest distance to " CA  ALA A  21 " =    1.174
peak=    3.839 closest distance to " O   HOH Z 102 " =    1.312
peak=    3.831 closest distance to " CB  GLU A 128 " =    1.119
peak=    3.830 closest distance to " O   HOH Z 250 " =    1.388
peak=    3.830 closest distance to " O   HOH Z 251 " =    1.431
peak=    3.829 closest distance to " CD1 LEU A  96 " =    0.727
peak=    3.821 closest distance to " CB  TRP A 266 " =    0.987
peak=    3.815 closest distance to " CD2 TRP A 179 " =    1.338
peak=    3.799 closest distance to " CB  VAL A 265 " =    1.261
peak=    3.795 closest distance to " O   HOH Z 371 " =    3.189
peak=    3.790 closest distance to " O   HOH Z  48 " =    1.640
peak=    3.789 closest distance to " CB  VAL A 202 " =    1.449
peak=    3.785 closest distance to " O   HOH Z  68 " =    2.018
peak=    3.780 closest distance to " O   HOH Z 158 " =    3.112
peak=    3.774 closest distance to " O   HOH Z 427 " =    2.890
peak=    3.768 closest distance to " O   HOH Z 389 " =    1.901
peak=    3.766 closest distance to " NH2 ARG A 156 " =    1.063
peak=    3.756 closest distance to " CD  LYS A 166 " =    1.312
peak=    3.744 closest distance to " O   HOH Z 273 " =    2.883
peak=    3.737 closest distance to " O   HOH Z 261 " =    1.956
peak=    3.735 closest distance to " CB  GLU A  46 " =    1.042
peak=    3.735 closest distance to " CE1 TYR A 186 " =    1.273
peak=    3.729 closest distance to " CD  ARG A 269 " =    1.010
peak=    3.727 closest distance to " O   HOH Z  59 " =    2.258
peak=    3.725 closest distance to " CB  ARG A 139 " =    0.884
peak=    3.724 closest distance to " CG2AVAL A  72 " =    1.748
peak=    3.724 closest distance to " O   HOH Z 411 " =    3.858
peak=    3.723 closest distance to " O   HOH Z 214 " =    2.470
peak=    3.714 closest distance to " O   HOH Z 422 " =    2.644
peak=    3.713 closest distance to " OD1 ASN A  69 " =    2.512
peak=    3.700 closest distance to " CG1 ILE A  49 " =    1.574
peak=    3.698 closest distance to " O   HOH Z 344 " =    2.912
peak=    3.696 closest distance to " CB  SER A  26 " =    1.777
peak=    3.692 closest distance to " O   HOH Z  54 " =    1.559
peak=    3.690 closest distance to " O   HOH Z 407 " =    2.677
peak=    3.678 closest distance to " CB  TRP A 179 " =    1.350
peak=    3.669 closest distance to " CB  ARG A  79 " =    0.906
peak=    3.667 closest distance to " O   HOH Z 124 " =    1.265
peak=    3.666 closest distance to " O   HOH Z 247 " =    1.369
peak=    3.661 closest distance to " CA  ASN A 215 " =    1.070
peak=    3.661 closest distance to " CG AARG A 275 " =    1.264
peak=    3.655 closest distance to " CG  ARG A  66 " =    2.740
peak=    3.654 closest distance to " CA  ARG A 195 " =    1.196
peak=    3.653 closest distance to " O   HOH Z  40 " =    1.780
peak=    3.652 closest distance to " O   HOH Z  80 " =    1.816
peak=    3.637 closest distance to " CB  PRO A 198 " =    1.024
peak=    3.631 closest distance to " CG2 ILE A  20 " =    1.403
peak=    3.628 closest distance to " CB  ALA A   9 " =    1.647
peak=    3.612 closest distance to " CE1 HIS A 108 " =    1.177
peak=    3.610 closest distance to " O   HOH Z 417 " =    3.143
peak=    3.610 closest distance to " O   HOH Z 193 " =    2.015
peak=    3.604 closest distance to " OG  SER A 276 " =    1.336
peak=    3.603 closest distance to " CB  THR A  31 " =    1.428
peak=    3.602 closest distance to " CB  ALA A 295 " =    1.156
peak=    3.599 closest distance to " CG2 ILE A 120 " =    1.176
peak=    3.598 closest distance to " NZ  LYS A 117 " =    3.142
peak=    3.596 closest distance to " O   HOH Z 145 " =    2.304
peak=    3.591 closest distance to " CB  ALA A 248 " =    1.328
peak=    3.589 closest distance to " CD2 LEU A 297 " =    0.852
peak=    3.587 closest distance to " O   HOH Z 313 " =    1.753
peak=    3.579 closest distance to " O   HOH Z  78 " =    1.664
peak=    3.578 closest distance to " O   HOH Z 154 " =    1.416
peak=    3.568 closest distance to " CB  ASP A 140 " =    0.987
peak=    3.568 closest distance to " OD2 ASP A 298 " =    3.813
peak=    3.565 closest distance to " CG  GLN A  58 " =    2.834
peak=    3.564 closest distance to " CB  ASN A 187 " =    1.060
peak=    3.555 closest distance to " OG BSER A 164 " =    2.234
peak=    3.551 closest distance to " O   HOH Z 245 " =    1.387
peak=    3.549 closest distance to " CA  ILE A 106 " =    0.741
peak=    3.548 closest distance to " CD  ARG A 159 " =    0.724
peak=    3.546 closest distance to " O   HOH Z 435 " =    1.984
peak=    3.544 closest distance to " O   HOH Z  15 " =    2.146
peak=    3.533 closest distance to " O   HOH Z 383 " =    1.960
peak=    3.519 closest distance to " O   HOH Z 227 " =    1.495
peak=    3.516 closest distance to " O   HOH Z 357 " =    2.014
peak=    3.513 closest distance to " CG  MET A 185 " =    1.121
peak=    3.502 closest distance to " O   HOH Z 365 " =    2.868
peak=    3.488 closest distance to " CA  ASP A 191 " =    1.120
peak=    3.482 closest distance to " O   HOH Z  21 " =    1.806
peak=    3.480 closest distance to " O   HOH Z 130 " =    2.282
peak=    3.479 closest distance to " CB  GLN A  88 " =    1.159
peak=    3.477 closest distance to " CG2 VAL A 257 " =    0.831
peak=    3.475 closest distance to " CB  ALA A 104 " =    0.735
peak=    3.472 closest distance to " CD  LYS A  76 " =    1.978
peak=    3.470 closest distance to " CZ  PHE A  38 " =    1.170
peak=    3.469 closest distance to " N   SER A 135 " =    1.372
peak=    3.469 closest distance to " CE  LYS A  76 " =    0.883
peak=    3.468 closest distance to " O   HOH Z 426 " =    1.504
peak=    3.464 closest distance to " CG1 ILE A  33 " =    1.291
peak=    3.462 closest distance to " O   HOH Z 258 " =    2.294
peak=    3.462 closest distance to " O   HOH Z 404 " =    2.271
peak=    3.454 closest distance to " CZ3 TRP A  85 " =    0.978
peak=    3.452 closest distance to " O   HOH Z 345 " =    3.136
peak=    3.452 closest distance to " O   ASP A 124 " =    1.182
peak=    3.444 closest distance to " O   HOH Z  88 " =    2.667
peak=    3.441 closest distance to " CB  GLN A 278 " =    0.872
peak=    3.438 closest distance to " CB  ASN A 142 " =    1.106
peak=    3.419 closest distance to " O   HOH Z 294 " =    1.584
peak=    3.418 closest distance to " O   HOH Z 128 " =    1.942
peak=    3.418 closest distance to " O   HOH Z 421 " =    1.559
peak=    3.415 closest distance to " CA  LYS A 117 " =    1.290
peak=    3.415 closest distance to " CB  ALA A 291 " =    1.224
peak=    3.415 closest distance to " NE2 GLN A  77 " =    3.315
peak=    3.408 closest distance to " CA  TYR A 116 " =    1.465
peak=    3.408 closest distance to " NH1BARG A 190 " =    2.127
peak=    3.408 closest distance to " CG  LEU A 167 " =    1.164
peak=    3.407 closest distance to " O   HOH Z 147 " =    1.814
peak=    3.402 closest distance to " O   ALA A 165 " =    1.485
peak=    3.396 closest distance to " O   HOH Z 285 " =    2.875
peak=    3.395 closest distance to " O   HOH Z 197 " =    2.859
peak=    3.392 closest distance to " CB  ALA A 114 " =    1.105
peak=    3.377 closest distance to " CB  PRO A 243 " =    1.263
peak=    3.375 closest distance to " CA  ALA A 295 " =    1.046
peak=    3.375 closest distance to " CB  GLN A  89 " =    1.214
peak=    3.375 closest distance to " O   HOH Z 203 " =    1.727
peak=    3.370 closest distance to " CG1 VAL A 153 " =    0.932
peak=    3.370 closest distance to " O   HOH Z  66 " =    2.335
peak=    3.368 closest distance to " O   HOH Z 109 " =    2.511
peak=    3.367 closest distance to " CB  ASN A 110 " =    1.099
peak=    3.367 closest distance to " N   PHE A 130 " =    1.280
peak=    3.366 closest distance to " O   HOH Z 128 " =    2.095
peak=    3.364 closest distance to " CB  PRO A  90 " =    1.050
peak=    3.364 closest distance to " CD1 LEU A 300 " =    1.244
peak=    3.363 closest distance to " N   SER A 288 " =    1.732
peak=    3.360 closest distance to " CG2 ILE A  49 " =    1.431
peak=    3.358 closest distance to " CB  HIS A 108 " =    0.789
peak=    3.346 closest distance to " O   HOH Z 368 " =    3.529
peak=    3.346 closest distance to " CB  SER A 273 " =    0.870
peak=    3.340 closest distance to " CA  ASN A 217 " =    1.281
peak=    3.340 closest distance to " O   HOH Z 380 " =    1.843
peak=    3.339 closest distance to " N   ARG A 190 " =    1.002
peak=    3.335 closest distance to " OH  TYR A 116 " =    1.105
peak=    3.330 closest distance to " O   HOH Z 112 " =    1.679
peak=    3.324 closest distance to " O   HOH Z 214 " =    2.553
peak=    3.321 closest distance to " O   HOH Z 128 " =    1.558
peak=    3.319 closest distance to " O   HOH Z 367 " =    3.490
peak=    3.311 closest distance to " OE1 GLN A  11 " =    1.793
peak=    3.309 closest distance to " O   HOH Z 185 " =    1.686
peak=    3.308 closest distance to " CD  LYS A 119 " =    1.920
peak=    3.308 closest distance to " CA  THR A 264 " =    0.774
peak=    3.307 closest distance to " CA  ASP A 162 " =    1.020
peak=    3.303 closest distance to " CB  ALA A 242 " =    0.843
peak=    3.302 closest distance to " O   MET A 105 " =    1.829
peak=    3.301 closest distance to " O   HOH Z 251 " =    1.753
peak=    3.300 closest distance to " O   HOH Z 263 " =    1.640
peak=    3.298 closest distance to " OD2 ASP A 286 " =    2.819
peak=    3.298 closest distance to " O   HOH Z 291 " =    1.478
peak=    3.297 closest distance to " NH1AARG A 145 " =    1.219
peak=    3.287 closest distance to " NH2BARG A 145 " =    2.107
peak=    3.285 closest distance to " O   HOH Z 437 " =    1.961
peak=    3.284 closest distance to " O   HOH Z 148 " =    3.282
peak=    3.277 closest distance to " O   HOH Z 414 " =    1.571
peak=    3.277 closest distance to " OG BSER A 134 " =    2.797
peak=    3.275 closest distance to " O   ASN A  74 " =    1.646
peak=    3.274 closest distance to " O   HOH Z 423 " =    3.288
peak=    3.271 closest distance to " CB  ARG A 219 " =    1.187
peak=    3.271 closest distance to " CB  SER A  62 " =    0.921
peak=    3.271 closest distance to " O   HOH Z   4 " =    1.686
peak=    3.269 closest distance to " O   HOH Z 250 " =    1.397
peak=    3.269 closest distance to " CG2 ILE A 106 " =    0.843
peak=    3.264 closest distance to " O   HOH Z 359 " =    1.461
peak=    3.264 closest distance to " CA  ILE A 234 " =    0.736
peak=    3.264 closest distance to " CA  LEU A 282 " =    1.125
peak=    3.261 closest distance to " N   ASP A 162 " =    1.316
peak=    3.259 closest distance to " O   HOH Z  44 " =    1.857
peak=    3.252 closest distance to " CZ2 TRP A 274 " =    1.535
peak=    3.246 closest distance to " O   HOH Z  19 " =    1.826
peak=    3.242 closest distance to " CB  PHE A 204 " =    0.831
peak=    3.236 closest distance to " N   GLU A  44 " =    2.170
peak=    3.236 closest distance to " O   HOH Z 438 " =    2.590
peak=    3.233 closest distance to " O   HOH Z 180 " =    2.164
peak=    3.233 closest distance to " CA  ASP A 140 " =    1.256
peak=    3.229 closest distance to " CA  ALA A 154 " =    0.971
peak=    3.229 closest distance to " CB  ASN A 215 " =    1.161
peak=    3.228 closest distance to " CG2 ILE A 234 " =    2.073
peak=    3.228 closest distance to " CA  SER A  32 " =    1.619
peak=    3.226 closest distance to " O   HOH Z 141 " =    1.536
peak=    3.224 closest distance to " CA  ASP A 191 " =    0.755
peak=    3.224 closest distance to " CB  TRP A 150 " =    1.453
peak=    3.222 closest distance to " CB  MET A  47 " =    1.045
peak=    3.221 closest distance to " O   HOH Z 419 " =    1.663
peak=    3.220 closest distance to " O   HOH Z 305 " =    3.644
peak=    3.218 closest distance to " CA  ALA A 160 " =    0.927
peak=    3.216 closest distance to " CG  GLN A 205 " =    0.976
peak=    3.212 closest distance to " CA  ASN A 176 " =    1.083
peak=    3.212 closest distance to " CB  ILE A 120 " =    1.375
peak=    3.212 closest distance to " O   GLY A  91 " =    1.359
peak=    3.210 closest distance to " CA  ALA A 291 " =    0.850
peak=    3.202 closest distance to " C   ALA A 299 " =    0.922
peak=    3.200 closest distance to " CA  PHE A 283 " =    1.027
peak=    3.200 closest distance to " O   HOH Z 234 " =    1.837
peak=    3.197 closest distance to " CG  LEU A 281 " =    1.132
peak=    3.195 closest distance to " O   HOH Z 353 " =    2.672
peak=    3.195 closest distance to " CA  LYS A 290 " =    1.095
peak=    3.190 closest distance to " CG  MET A 185 " =    1.032
peak=    3.189 closest distance to " CG2 THR A 221 " =    1.227
peak=    3.186 closest distance to " CB  LEU A 143 " =    1.137
peak=    3.177 closest distance to " CE  LYS A 119 " =    1.012
peak=    3.164 closest distance to " ND2 ASN A 249 " =    0.912
peak=    3.162 closest distance to " CB  GLN A 103 " =    0.911
peak=    3.160 closest distance to " N   VAL A 126 " =    1.521
peak=    3.160 closest distance to " O   HOH Z 134 " =    1.352
peak=    3.151 closest distance to " O   HOH Z 406 " =    1.443
peak=    3.151 closest distance to " CA  ALA A  84 " =    1.208
peak=    3.141 closest distance to " CG  GLN A  77 " =    2.156
peak=    3.140 closest distance to " O   HOH Z 293 " =    1.806
peak=    3.140 closest distance to " N   ARG A 156 " =    1.424
peak=    3.138 closest distance to " CG1 ILE A 120 " =    1.035
peak=    3.136 closest distance to " CA  SER A  87 " =    0.977
peak=    3.136 closest distance to " CA  ALA A 158 " =    1.265
peak=    3.134 closest distance to " CA  THR A 221 " =    0.880
peak=    3.131 closest distance to " O   SER A 164 " =    1.187
peak=    3.129 closest distance to " CD1 ILE A  33 " =    1.684
peak=    3.128 closest distance to " CZ2 TRP A 150 " =    1.079
peak=    3.127 closest distance to " O   HOH Z  48 " =    1.544
peak=    3.125 closest distance to " O   HOH Z 329 " =    4.001
peak=    3.122 closest distance to " O   HOH Z 163 " =    1.515
peak=    3.120 closest distance to " CD1 ILE A 199 " =    0.898
peak=    3.120 closest distance to " CG2 THR A 220 " =    0.718
peak=    3.116 closest distance to " CD1 LEU A 222 " =    0.803
peak=    3.115 closest distance to " O   HOH Z  88 " =    2.907
peak=    3.114 closest distance to " O   HOH Z   9 " =    2.174
peak=    3.112 closest distance to " O   HOH Z  47 " =    1.711
peak=    3.110 closest distance to " CG2 THR A  18 " =    1.250
peak=    3.109 closest distance to " O   HOH Z 355 " =    1.861
peak=    3.081 closest distance to " CG2AVAL A 121 " =    2.148
peak=    3.077 closest distance to " O   HOH Z 302 " =    1.936
peak=    3.065 closest distance to " CB  ALA A 100 " =    1.199
peak=    3.060 closest distance to " OG  SER A 245 " =    1.571
peak=    3.059 closest distance to " CD2 LEU A   5 " =    0.709
peak=    3.058 closest distance to " O   HOH Z  90 " =    3.350
peak=    3.045 closest distance to " CG  ARG A  66 " =    0.936
peak=    3.041 closest distance to " O  BHOH Z  74 " =    1.385
peak=    3.039 closest distance to " CA  MET A 105 " =    0.978

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 190         
Filter by distance & map next to the model:
   mapped sites are within: 0.646 - 5.562
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 187 from: 190
   mapped sites are within: 0.774 - 5.562

peak=   -4.757 closest distance to " CD  GLN A  58 " =    1.062
peak=   -4.524 closest distance to " SG  CYS A 254 " =    3.309
peak=   -4.317 closest distance to " CD  ARG A 156 " =    2.035
peak=   -4.252 closest distance to " CG1 VAL A 296 " =    1.075
peak=   -4.224 closest distance to " O   HOH Z 266 " =    5.243
peak=   -4.189 closest distance to " O   VAL A  67 " =    2.662
peak=   -4.159 closest distance to " O   HOH Z 290 " =    1.007
peak=   -4.158 closest distance to " ND2 ASN A 187 " =    1.559
peak=   -4.146 closest distance to " O   HOH Z 196 " =    2.110
peak=   -4.143 closest distance to " CD2 PHE A 192 " =    2.085
peak=   -4.141 closest distance to " C   HIS A 108 " =    1.217
peak=   -4.127 closest distance to " O   HOH Z 166 " =    1.733
peak=   -4.072 closest distance to " O   HOH Z 351 " =    1.537
peak=   -4.019 closest distance to " CG  ASP A 231 " =    0.813
peak=   -3.950 closest distance to " CZ3 TRP A 179 " =    1.298
peak=   -3.931 closest distance to " O   PRO A 163 " =    2.222
peak=   -3.931 closest distance to " CE2 TYR A  30 " =    2.798
peak=   -3.927 closest distance to " CD1 LEU A 101 " =    2.408
peak=   -3.898 closest distance to " CB  PRO A 243 " =    2.682
peak=   -3.897 closest distance to " OG BSER A 134 " =    1.258
peak=   -3.894 closest distance to " CB  ALA A 248 " =    2.337
peak=   -3.883 closest distance to " OXT GLY A 302 " =    2.786
peak=   -3.875 closest distance to " CG  GLN A 223 " =    2.099
peak=   -3.845 closest distance to " N   ALA A 226 " =    1.986
peak=   -3.845 closest distance to " O   HOH Z 394 " =    1.595
peak=   -3.825 closest distance to " OG  SER A  97 " =    2.335
peak=   -3.824 closest distance to " NE2 GLN A  88 " =    0.959
peak=   -3.817 closest distance to " CG1 VAL A 112 " =    2.742
peak=   -3.813 closest distance to " O   HOH Z 231 " =    2.114
peak=   -3.779 closest distance to " C   THR A 279 " =    1.173
peak=   -3.775 closest distance to " O   PRO A 198 " =    1.191
peak=   -3.759 closest distance to " O   HOH Z 114 " =    3.212
peak=   -3.729 closest distance to " ND2 ASN A  45 " =    1.047
peak=   -3.728 closest distance to " CB  ALA A 248 " =    2.053
peak=   -3.727 closest distance to " CB  ALA A 161 " =    2.584
peak=   -3.717 closest distance to " CG2 ILE A 263 " =    2.352
peak=   -3.675 closest distance to " CA  ASP A 298 " =    1.095
peak=   -3.667 closest distance to " O   SER A 210 " =    1.958
peak=   -3.654 closest distance to " O   HOH Z  37 " =    1.842
peak=   -3.651 closest distance to " CA  VAL A  67 " =    2.923
peak=   -3.648 closest distance to " CE3 TRP A 150 " =    2.147
peak=   -3.648 closest distance to " CD2 TYR A 293 " =    1.962
peak=   -3.647 closest distance to " CD2 LEU A 237 " =    2.586
peak=   -3.638 closest distance to " O   SER A 271 " =    2.148
peak=   -3.605 closest distance to " CG2 VAL A 296 " =    1.275
peak=   -3.592 closest distance to " O   ASN A  45 " =    1.879
peak=   -3.578 closest distance to " O   HOH Z 165 " =    1.938
peak=   -3.574 closest distance to " OD2 ASP A 171 " =    2.361
peak=   -3.565 closest distance to " O   HOH Z 423 " =    2.192
peak=   -3.563 closest distance to " CB  PRO A 163 " =    2.554
peak=   -3.559 closest distance to " CE  MET A 105 " =    2.097
peak=   -3.551 closest distance to " OD1 ASN A 148 " =    1.426
peak=   -3.534 closest distance to " O   HOH Z  44 " =    2.228
peak=   -3.528 closest distance to " C   MET A 188 " =    1.431
peak=   -3.516 closest distance to " CD1 PHE A  59 " =    2.259
peak=   -3.514 closest distance to " CD  LYS A 289 " =    2.532
peak=   -3.513 closest distance to " CD1 PHE A  59 " =    1.940
peak=   -3.511 closest distance to " CZ  TYR A 169 " =    1.780
peak=   -3.502 closest distance to " C   ASP A 231 " =    2.539
peak=   -3.487 closest distance to " N   THR A 235 " =    1.278
peak=   -3.487 closest distance to " O   HOH Z  13 " =    1.593
peak=   -3.468 closest distance to " O   HOH Z 407 " =    2.890
peak=   -3.459 closest distance to " CD1 LEU A 255 " =    2.777
peak=   -3.447 closest distance to " O   HOH Z 185 " =    2.500
peak=   -3.446 closest distance to " N   THR A  52 " =    1.642
peak=   -3.445 closest distance to " NH2AARG A 275 " =    4.929
peak=   -3.445 closest distance to " O   HOH Z 150 " =    2.193
peak=   -3.440 closest distance to " O   HOH Z 301 " =    2.489
peak=   -3.436 closest distance to " CD  ARG A 139 " =    1.640
peak=   -3.430 closest distance to " CG  ARG A 269 " =    2.282
peak=   -3.430 closest distance to " O   HOH Z  11 " =    1.924
peak=   -3.426 closest distance to " O   VAL A 189 " =    2.665
peak=   -3.422 closest distance to " CD1 LEU A  25 " =    2.501
peak=   -3.419 closest distance to " O   HOH Z 131 " =    4.092
peak=   -3.416 closest distance to " CD1 LEU A 101 " =    2.962
peak=   -3.415 closest distance to " O   HOH Z  52 " =    1.755
peak=   -3.407 closest distance to " C   ALA A 158 " =    1.285
peak=   -3.407 closest distance to " O   HOH Z 389 " =    1.888
peak=   -3.401 closest distance to " O   HOH Z 222 " =    1.555
peak=   -3.395 closest distance to " N   GLN A  58 " =    1.954
peak=   -3.392 closest distance to " OG  SER A   3 " =    1.534
peak=   -3.390 closest distance to " O   HOH Z 353 " =    2.129
peak=   -3.389 closest distance to " CB  ALA A 291 " =    2.259
peak=   -3.381 closest distance to " CB  ASP A 132 " =    2.304
peak=   -3.381 closest distance to " O   HOH Z 136 " =    2.418
peak=   -3.379 closest distance to " CG  GLU A 277 " =    1.153
peak=   -3.374 closest distance to " C   ILE A 239 " =    2.121
peak=   -3.371 closest distance to " N   ALA A 248 " =    1.768
peak=   -3.368 closest distance to " O   HOH Z 193 " =    1.717
peak=   -3.368 closest distance to " CD2 LEU A 167 " =    1.843
peak=   -3.365 closest distance to " O   ARG A  24 " =    2.046
peak=   -3.359 closest distance to " NE1 TRP A 266 " =    2.394
peak=   -3.356 closest distance to " CG  TRP A 266 " =    1.938
peak=   -3.351 closest distance to " OG  SER A  63 " =    1.110
peak=   -3.342 closest distance to " O   HOH Z  60 " =    2.222
peak=   -3.339 closest distance to " O   HOH Z 369 " =    2.254
peak=   -3.338 closest distance to " O   GLY A 196 " =    1.187
peak=   -3.333 closest distance to " CA  GLY A 241 " =    2.448
peak=   -3.333 closest distance to " CD  GLN A  88 " =    0.774
peak=   -3.325 closest distance to " OG  SER A 206 " =    1.623
peak=   -3.324 closest distance to " N   VAL A 230 " =    1.063
peak=   -3.323 closest distance to " CB  ASN A  69 " =    1.149
peak=   -3.321 closest distance to " ND2 ASN A  69 " =    1.810
peak=   -3.321 closest distance to " O   HOH Z 177 " =    1.716
peak=   -3.321 closest distance to " CD1 ILE A 199 " =    2.495
peak=   -3.321 closest distance to " O   GLY A  75 " =    1.821
peak=   -3.319 closest distance to " CG  GLU A  53 " =    1.482
peak=   -3.316 closest distance to " NE2 GLN A  88 " =    1.898
peak=   -3.314 closest distance to " O   HOH Z 174 " =    4.158
peak=   -3.303 closest distance to " OD1 ASN A 249 " =    2.265
peak=   -3.302 closest distance to " OG ASER A 134 " =    1.361
peak=   -3.301 closest distance to " CG  ASP A  50 " =    2.349
peak=   -3.299 closest distance to " N   THR A 157 " =    1.548
peak=   -3.298 closest distance to " O   HOH Z 283 " =    1.974
peak=   -3.297 closest distance to " CE BMET A  47 " =    1.652
peak=   -3.291 closest distance to " NE2 GLN A 103 " =    1.801
peak=   -3.291 closest distance to " O   ALA A 161 " =    1.728
peak=   -3.290 closest distance to " CB  ALA A  43 " =    2.437
peak=   -3.285 closest distance to " ND2 ASN A  39 " =    1.193
peak=   -3.280 closest distance to " O   HOH Z 102 " =    1.629
peak=   -3.277 closest distance to " O   HOH Z  10 " =    1.527
peak=   -3.275 closest distance to " O   HOH Z 191 " =    5.562
peak=   -3.274 closest distance to " CD2 LEU A 300 " =    2.550
peak=   -3.273 closest distance to " ND2 ASN A  45 " =    1.642
peak=   -3.272 closest distance to " O   HOH Z  88 " =    4.336
peak=   -3.271 closest distance to " CB  SER A 210 " =    1.128
peak=   -3.269 closest distance to " CG  MET A 105 " =    0.880
peak=   -3.259 closest distance to " N   ALA A  43 " =    2.549
peak=   -3.258 closest distance to " NH2 ARG A  79 " =    2.032
peak=   -3.249 closest distance to " O   HOH Z 166 " =    1.778
peak=   -3.245 closest distance to " O   HOH Z 234 " =    4.130
peak=   -3.244 closest distance to " O   HOH Z 392 " =    1.847
peak=   -3.236 closest distance to " CG1 VAL A 112 " =    2.633
peak=   -3.234 closest distance to " CA  GLY A 133 " =    1.943
peak=   -3.231 closest distance to " CA  VAL A 296 " =    0.931
peak=   -3.230 closest distance to " O   HOH Z 210 " =    1.028
peak=   -3.226 closest distance to " C   LEU A 143 " =    0.989
peak=   -3.225 closest distance to " CG1 VAL A 112 " =    2.813
peak=   -3.224 closest distance to " O   GLU A 152 " =    1.612
peak=   -3.222 closest distance to " CG  LEU A   5 " =    1.554
peak=   -3.213 closest distance to " O   HOH Z 252 " =    4.022
peak=   -3.213 closest distance to " O   HOH Z   6 " =    1.727
peak=   -3.210 closest distance to " O   HOH Z 174 " =    2.269
peak=   -3.210 closest distance to " O   ALA A  34 " =    2.538
peak=   -3.209 closest distance to " OXT GLY A 302 " =    3.435
peak=   -3.206 closest distance to " O   HOH Z 211 " =    1.714
peak=   -3.202 closest distance to " C   SER A 206 " =    1.565
peak=   -3.201 closest distance to " N   SER A   3 " =    2.096
peak=   -3.201 closest distance to " O   HOH Z 154 " =    1.660
peak=   -3.195 closest distance to " O   SER A  95 " =    1.661
peak=   -3.195 closest distance to " CD  ARG A 195 " =    5.122
peak=   -3.191 closest distance to " CD  PRO A 243 " =    2.097
peak=   -3.190 closest distance to " O   HOH Z 313 " =    1.246
peak=   -3.188 closest distance to " O   LEU A 167 " =    1.514
peak=   -3.188 closest distance to " O   ALA A  10 " =    1.832
peak=   -3.187 closest distance to " O   HOH Z 128 " =    2.552
peak=   -3.177 closest distance to " C   ASP A 270 " =    1.205
peak=   -3.176 closest distance to " NE2 GLN A 194 " =    1.825
peak=   -3.176 closest distance to " N   VAL A  41 " =    1.864
peak=   -3.175 closest distance to " OG1 THR A  82 " =    1.329
peak=   -3.171 closest distance to " O   HOH Z 171 " =    2.017
peak=   -3.170 closest distance to " CA  GLY A 241 " =    3.090
peak=   -3.160 closest distance to " O   HOH Z 377 " =    1.506
peak=   -3.154 closest distance to " CG  GLN A  11 " =    1.801
peak=   -3.147 closest distance to " O   ALA A   1 " =    1.686
peak=   -3.144 closest distance to " ND2 ASN A 249 " =    2.398
peak=   -3.140 closest distance to " O   HOH Z 426 " =    1.809
peak=   -3.139 closest distance to " N   HIS A 115 " =    2.207
peak=   -3.139 closest distance to " N   SER A 276 " =    1.375
peak=   -3.137 closest distance to " O   HOH Z 297 " =    2.798
peak=   -3.136 closest distance to " CZ  PHE A  38 " =    2.113
peak=   -3.135 closest distance to " CD2 LEU A 237 " =    2.805
peak=   -3.134 closest distance to " O   GLY A  80 " =    2.384
peak=   -3.130 closest distance to " O   HOH Z 285 " =    1.684
peak=   -3.128 closest distance to " OG1 THR A 246 " =    1.384
peak=   -3.121 closest distance to " O   HOH Z 397 " =    1.206
peak=   -3.116 closest distance to " O   GLY A 203 " =    2.320
peak=   -3.114 closest distance to " O   HOH Z 313 " =    1.822
peak=   -3.111 closest distance to " O   ALA A  51 " =    1.433
peak=   -3.103 closest distance to " CG1 VAL A  78 " =    2.566
peak=   -3.101 closest distance to " NH2 ARG A  66 " =    1.701
peak=   -3.090 closest distance to " CE  LYS A 166 " =    3.052
peak=   -3.088 closest distance to " N   ALA A 248 " =    2.380
peak=   -3.077 closest distance to " O   PRO A 198 " =    1.270
peak=   -3.060 closest distance to " O   HOH Z 377 " =    1.628
peak=   -3.056 closest distance to " O   VAL A 174 " =    2.100
peak=   -3.056 closest distance to " CG  PHE A 283 " =    2.728

================= 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    :  0.4453 0.4295   6.242070e+00   6.217547e+00
   1_bss:  0.4369 0.4208   6.234043e+00   6.208367e+00
   1_xyz:  0.3278 0.3468   6.034971e+00   6.071102e+00
   1_adp:  0.2669 0.3033   5.868425e+00   5.966108e+00
   1_occ:  0.2664 0.3038   5.867395e+00   5.966900e+00
   2_bss:  0.2627 0.2994   5.867873e+00   5.965167e+00
   2_xyz:  0.1797 0.2164   5.528904e+00   5.691493e+00
   2_adp:  0.1639 0.2010   5.450151e+00   5.620491e+00
   2_occ:  0.1638 0.2010   5.449880e+00   5.621209e+00
   3_bss:  0.1630 0.2014   5.449541e+00   5.619610e+00
   3_xyz:  0.1303 0.1651   5.249023e+00   5.447025e+00
   3_adp:  0.1244 0.1605   5.212166e+00   5.417808e+00
   3_occ:  0.1243 0.1604   5.211737e+00   5.417377e+00
   4_bss:  0.1245 0.1606   5.213119e+00   5.417351e+00
   4_xyz:  0.1156 0.1567   5.166888e+00   5.393037e+00
   4_adp:  0.1154 0.1561   5.164361e+00   5.391011e+00
   4_occ:  0.1152 0.1561   5.163736e+00   5.390946e+00
   5_bss:  0.1152 0.1561   5.163690e+00   5.390899e+00
   5_xyz:  0.1164 0.1569   5.171006e+00   5.394743e+00
   5_adp:  0.1164 0.1572   5.171782e+00   5.396868e+00
   5_occ:  0.1164 0.1572   5.171675e+00   5.396869e+00
   5_bss:  0.1164 0.1572   5.171681e+00   5.396891e+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:  0.342  20.000   6.910   9.335   8.223   0.000   0.000   0.000
   1_xyz:  0.342  20.000   6.910   9.335   8.223   0.000   0.000   0.000
   1_adp:  0.342  20.000   6.910   9.335   8.223   0.000   0.000   0.000
   1_occ:  0.342  20.000   6.910   9.335   8.223   0.000   0.000   0.000
   2_bss:  0.329  40.736   3.653   5.556   5.108   0.000   0.000   0.000
   2_xyz:  0.329  40.736   3.653   5.556   5.108   0.000   0.000   0.000
   2_adp:  0.329  40.736   3.653   5.556   5.108   0.000   0.000   0.000
   2_occ:  0.329  40.736   3.653   5.556   5.108   0.000   0.000   0.000
   3_bss:  0.319  47.277   2.552   3.947   4.306   0.000   0.000   0.000
   3_xyz:  0.319  47.277   2.552   3.947   4.306   0.000   0.000   0.000
   3_adp:  0.319  47.277   2.552   3.947   4.306   0.000   0.000   0.000
   3_occ:  0.319  47.277   2.552   3.947   4.306   0.000   0.000   0.000
   4_bss:  0.327  47.277   2.392   3.447   4.166   0.000   0.000   0.000
   4_xyz:  0.327  47.277   2.392   3.447   4.166   0.000   0.000   0.000
   4_adp:  0.327  47.277   2.392   3.447   4.166   0.000   0.000   0.000
   4_occ:  0.327  47.277   2.392   3.447   4.166   0.000   0.000   0.000
   5_bss:  0.327  47.277   2.414   3.349   4.202   0.000   0.000   0.000
   5_xyz:  0.327  47.277   2.414   3.349   4.202   0.000   0.000   0.000
   5_adp:  0.327  47.277   2.414   3.349   4.202   0.000   0.000   0.000
   5_occ:  0.327  47.277   2.414   3.349   4.202   0.000   0.000   0.000
   5_bss:  0.325  50.348  -0.903   0.006   0.897   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  47.887 0.5486  0.6142    53247.139
   1_bss:  47.514 0.5516  0.7911    51198.828
   1_xyz:  37.487 0.6715  0.9332    32741.915
   1_adp:  30.926 0.7480  1.0246    24188.762
   1_occ:  30.962 0.7476  1.0232    24225.492
   2_bss:  30.784 0.7496  0.9092    24010.286
   2_xyz:  21.540 0.8461  0.9886    12232.610
   2_adp:  19.578 0.8657  1.0025    10565.460
   2_occ:  19.597 0.8655  1.0022    10573.692
   3_bss:  19.534 0.8661  0.9609    10526.469
   3_xyz:  15.481 0.9024  0.9805     7179.024
   3_adp:  14.774 0.9087  0.9820     6799.480
   3_occ:  14.767 0.9087  0.9820     6796.420
   4_bss:  14.768 0.9088  0.9725     6813.161
   4_xyz:  14.188 0.9137  0.9741     6484.113
   4_adp:  14.114 0.9144  0.9713     6466.497
   4_occ:  14.105 0.9146  0.9711     6467.031
   5_bss:  14.103 0.9146  0.9707     6466.988
   5_xyz:  14.154 0.9142  0.9703     6497.017
   5_adp:  14.207 0.9137  0.9670     6517.758
   5_occ:  14.206 0.9137  0.9670     6518.176
   5_bss:  14.207 0.9137  0.9695     6517.768
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.3840e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.3840e+01
   1_xyz:   1.583  0.012  0.105 17.768  0.006  4.112   1.2463e-01
   1_adp:   1.583  0.012  0.105 17.768  0.006  4.112   1.2463e-01
   1_occ:   1.583  0.012  0.105 17.768  0.006  4.112   1.2463e-01
   2_bss:   1.583  0.012  0.105 17.768  0.006  4.112   1.2463e-01
   2_xyz:   1.025  0.007  0.073 15.926  0.004  4.125   6.4004e-02
   2_adp:   1.025  0.007  0.073 15.926  0.004  4.125   6.4004e-02
   2_occ:   1.025  0.007  0.073 15.926  0.004  4.125   6.4004e-02
   3_bss:   1.025  0.007  0.073 15.926  0.004  4.125   6.4004e-02
   3_xyz:   0.994  0.006  0.078 15.601  0.004  4.125   5.9812e-02
   3_adp:   0.994  0.006  0.078 15.601  0.004  4.125   5.9812e-02
   3_occ:   0.994  0.006  0.078 15.601  0.004  4.125   5.9812e-02
   4_bss:   0.994  0.006  0.078 15.601  0.004  4.125   5.9812e-02
   4_xyz:   1.038  0.008  0.083 15.539  0.004  4.131   6.4267e-02
   4_adp:   1.038  0.008  0.083 15.539  0.004  4.131   6.4267e-02
   4_occ:   1.038  0.008  0.083 15.539  0.004  4.131   6.4267e-02
   5_bss:   1.038  0.008  0.083 15.539  0.004  4.131   6.4267e-02
   5_xyz:   0.936  0.006  0.075 15.176  0.003  4.116   5.4781e-02
   5_adp:   0.936  0.006  0.075 15.176  0.003  4.116   5.4781e-02
   5_occ:   0.936  0.006  0.075 15.176  0.003  4.116   5.4781e-02
   5_bss:   0.936  0.006  0.075 15.176  0.003  4.116   5.4781e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9799e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9799e+00
   1_xyz:  14.347  0.147  0.478 85.538  0.037  2.319   9.4257e-02
   1_adp:  14.347  0.147  0.478 85.538  0.037  2.319   9.4257e-02
   1_occ:  14.347  0.147  0.478 85.538  0.037  2.319   9.4257e-02
   2_bss:  14.347  0.147  0.478 85.538  0.037  2.319   9.4257e-02
   2_xyz:   7.026  0.091  0.253 82.813  0.034  2.199   5.5082e-02
   2_adp:   7.026  0.091  0.253 82.813  0.034  2.199   5.5082e-02
   2_occ:   7.026  0.091  0.253 82.813  0.034  2.199   5.5082e-02
   3_bss:   7.026  0.091  0.253 82.813  0.034  2.199   5.5082e-02
   3_xyz:   6.616  0.043  0.418 81.485  0.040  2.312   3.9090e-02
   3_adp:   6.616  0.043  0.418 81.485  0.040  2.312   3.9090e-02
   3_occ:   6.616  0.043  0.418 81.485  0.040  2.312   3.9090e-02
   4_bss:   6.616  0.043  0.418 81.485  0.040  2.312   3.9090e-02
   4_xyz:   7.387  0.048  0.493 82.602  0.037  2.295   4.3231e-02
   4_adp:   7.387  0.048  0.493 82.602  0.037  2.295   4.3231e-02
   4_occ:   7.387  0.048  0.493 82.602  0.037  2.295   4.3231e-02
   5_bss:   7.387  0.048  0.493 82.602  0.037  2.295   4.3231e-02
   5_xyz:   6.669  0.044  0.372 81.914  0.034  2.357   2.9675e-02
   5_adp:   6.669  0.044  0.372 81.914  0.034  2.357   2.9675e-02
   5_occ:   6.669  0.044  0.372 81.914  0.034  2.357   2.9675e-02
   5_bss:   6.669  0.044  0.372 81.914  0.034  2.357   2.9675e-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:  63.12   0.00  11.06  59.52   0.00   8.12  63.12   0.00  27.04
   1_occ:  63.12   0.00  11.06  59.52   0.00   8.12  63.12   0.00  27.04
   2_bss:  63.12   0.00  11.06  59.52   0.00   8.12  63.12   0.00  27.04
   2_xyz:  63.12   0.00  11.06  59.52   0.00   8.12  63.12   0.00  27.04
   2_adp:  65.99   0.00  11.30  65.99   0.00   7.63  64.10   0.93  31.29
   2_occ:  65.99   0.00  11.30  65.99   0.00   7.63  64.10   0.93  31.29
   3_bss:  65.99   0.00  11.30  65.99   0.00   7.63  64.10   0.93  31.29
   3_xyz:  65.99   0.00  11.30  65.99   0.00   7.63  64.10   0.93  31.29
   3_adp:  72.03   0.00  11.62  72.03   0.00   7.58  65.00   0.78  33.61
   3_occ:  72.03   0.00  11.62  72.03   0.00   7.58  65.00   0.78  33.61
   4_bss:  72.03   0.00  11.62  72.03   0.00   7.58  65.00   0.78  33.61
   4_xyz:  72.03   0.00  11.62  72.03   0.00   7.58  65.00   0.78  33.61
   4_adp:  73.45   0.00  11.41  73.45   0.00   7.47  65.23   1.00  32.86
   4_occ:  73.45   0.00  11.41  73.45   0.00   7.47  65.23   1.00  32.86
   5_bss:  73.45   0.00  11.41  73.45   0.00   7.47  65.23   1.00  32.86
   5_xyz:  73.45   0.00  11.41  73.45   0.00   7.47  65.23   1.00  32.86
   5_adp:  74.06   0.00  11.36  74.06   0.00   7.42  65.53   0.72  32.80
   5_occ:  74.06   0.00  11.36  74.06   0.00   7.42  65.53   0.72  32.80
   5_bss:  77.46   3.39  14.75  77.46   3.39  10.81  68.93   4.12  36.20
------------------------------------------------------------------------
 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:    1.220    0.012    0.408
   1_adp:    1.220    0.012    0.408
   1_occ:    1.220    0.012    0.408
   2_bss:    1.220    0.012    0.408
   2_xyz:    1.649    0.031    0.525
   2_adp:    1.649    0.031    0.525
   2_occ:    1.649    0.031    0.525
   3_bss:    1.649    0.031    0.525
   3_xyz:    1.621    0.025    0.565
   3_adp:    1.621    0.025    0.565
   3_occ:    1.621    0.025    0.565
   4_bss:    1.621    0.025    0.565
   4_xyz:    1.747    0.010    0.589
   4_adp:    1.747    0.010    0.589
   4_occ:    1.747    0.010    0.589
   5_bss:    1.747    0.010    0.589
   5_xyz:    1.839    0.008    0.594
   5_adp:    1.839    0.008    0.594
   5_occ:    1.839    0.008    0.594
   5_bss:    1.839    0.008    0.594
------------------------------------------------------------------------

CPU time actual refinement: 333.14


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_446/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_446/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_446/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_446/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_446/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 332.99 
  Macro-tasks:
    bulk solvent and scale       = 43.95  
    individual site refinement   = 131.29 
    weights calculation          = 32.79  
    collect and process          = 6.70   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 214.83 
  Micro-tasks:
    mask                            = 1.65   
    f_calc                          = 102.05 
    alpha_beta                      = 8.35   
    target                          = 1.21   
    gradients_wrt_atomic_parameters = 107.89 
    fmodel                         = 7.63   
    r_factors                      = 0.29   
    phase_errors                   = 11.71  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 241.02 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.703 micro seconds
Total CPU time: 5.77 minutes
from_scatterers_fft:    656 calls, 101.59 s
gradients_fft:          600 calls,  96.42 s

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

# Date 2008-01-16 Time 01:34:28 PST -0800 (1200476068.52 s)
Start R-work = 0.4453, R-free = 0.4295 (no bulk solvent and anisotropic scale)
Final R-work = 0.1339, R-free = 0.1730 (no bulk solvent and anisotropic scale)

Start R-work = 0.4369, R-free = 0.4208
Final R-work = 0.1164, R-free = 0.1572