# Date 2008-01-16 Time 03:09:50 PST -0800 (1200481790.28 s)
#phil __OFF__

Command line arguments: "../1131.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 28387
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1131

-------------------------------------------------------------------------------
  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: (71.655, 46.4607, 88.1178, 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: 3.25, per 1000 atoms: 1.15


================================== 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: (71.655, 46.4607, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2939 1.98365
Completeness in resolution range: 0.935036
Completeness with d_max=infinity: 0.932366

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2939
                             d_min =   1.9836

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: (71.655, 46.4607, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2939 1.98365
Completeness in resolution range: 0.935036
Completeness with d_max=infinity: 0.932366

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2943 -  4.2460 [2202/2229]  1981   221  10.0%
  bin  2:  4.2460 -  3.3822 [2121/2141]  1909   212  10.0%
  bin  3:  3.3822 -  2.9582 [2082/2101]  1876   206   9.9%
  bin  4:  2.9582 -  2.6893 [2070/2100]  1859   211  10.2%
  bin  5:  2.6893 -  2.4974 [2057/2076]  1860   197   9.6%
  bin  6:  2.4974 -  2.3507 [2057/2082]  1844   213  10.4%
  bin  7:  2.3507 -  2.2334 [2030/2058]  1824   206  10.1%
  bin  8:  2.2334 -  2.1364 [2015/2051]  1813   202  10.0%
  bin  9:  2.1364 -  2.0544 [2032/2074]  1835   197   9.7%
  bin 10:  2.0544 -  1.9836 [ 923/2038]   829    94  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1131/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 21
        2.42 -     3.04: 2168
        3.04 -     3.66: 4634
        3.66 -     4.28: 8905
        4.28 -     4.90: 12207
  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
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 324 " - " O   HOH Z 374 "  2.219 3.040 -x,y-1/2,-z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.305 3.040 x,y+1,z
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  ... (remaining 27930 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_1131/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1131/model_refine_001.geo

CPU time processing inputs: 9.10


============================ 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 = 71.655 46.4607 88.1178 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 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4934   r_free= 0.4804   ksol= 0.00   Bsol= 0.00   scale= 0.774    |
|                                                                             |
| 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:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.293083                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2943 -  4.7365 0.99   1426  158 0.4099 0.3856      6.6211      6.5687|
|  2:  4.7365 -  3.7782 0.99   1382  155 0.4127 0.4259      6.8163      6.8587|
|  3:  3.7782 -  3.3061 0.99   1343  144 0.4568 0.4298      6.6812      6.6441|
|  4:  3.3061 -  3.0063 0.99   1344  156 0.4917 0.4545      6.5453      6.4904|
|  5:  3.0063 -  2.7922 0.99   1335  149 0.5243 0.4978      6.3774      6.3728|
|  6:  2.7922 -  2.6285 0.99   1331  147 0.5158 0.5331      6.2689      6.2165|
|  7:  2.6285 -  2.4974 0.99   1324  138 0.5454 0.4933      6.2495      6.1909|
|  8:  2.4974 -  2.3891 0.98   1300  153 0.5453 0.5269      6.1812      6.1946|
|  9:  2.3891 -  2.2975 0.98   1303  144 0.5327 0.5886      6.1248      6.1952|
| 10:  2.2975 -  2.2184 1.00   1323  152 0.5347 0.5147      6.0994      6.0748|
| 11:  2.2184 -  2.1493 0.98   1307  138 0.5233 0.4976      6.0348      6.0353|
| 12:  2.1493 -  2.0880 0.98   1297  145 0.5428 0.5223      5.9505      5.9747|
| 13:  2.0880 -  2.0331 0.96   1258  138 0.5337 0.4823      5.8824      5.7872|
| 14:  2.0331 -  1.9836 0.27    357   42 0.5365 0.5329      5.8618      5.8623|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2943 -  4.7365  1426   158  0.69  35.42   0.78     0.73      76321.64|
|  2:  4.7365 -  3.7782  1382   155  0.70  35.36   0.86     0.77     110364.32|
|  3:  3.7782 -  3.3061  1343   144  0.59  44.81   0.82     0.71     116607.24|
|  4:  3.3061 -  3.0063  1344   156  0.50  51.55   0.76     0.61     103034.42|
|  5:  3.0063 -  2.7922  1335   149  0.42  58.15   0.72     0.51      82688.26|
|  6:  2.7922 -  2.6285  1331   147  0.37  61.88   0.71     0.43      72782.54|
|  7:  2.6285 -  2.4974  1324   138  0.32  65.87   0.71     0.37      68878.17|
|  8:  2.4974 -  2.3891  1300   153  0.28  69.20   0.70     0.33      64111.53|
|  9:  2.3891 -  2.2975  1303   144  0.28  69.22   0.70     0.33      59966.39|
| 10:  2.2975 -  2.2184  1323   152  0.29  68.53   0.73     0.34      53042.72|
| 11:  2.2184 -  2.1493  1307   138  0.29  68.61   0.77     0.36      49741.71|
| 12:  2.1493 -  2.0880  1297   145  0.31  67.13   0.71     0.39      44067.70|
| 13:  2.0880 -  2.0331  1258   138  0.32  65.95   0.70     0.42      37044.92|
| 14:  2.0331 -  1.9836   357    42  0.41  59.09   0.71     0.44      27755.04|
|alpha:            min =        0.33 max =            0.77 mean =         0.49|
|beta:             min =    27755.04 max =       116607.24 mean =     71765.91|
|figures of merit: min =        0.00 max =            1.00 mean =         0.42|
|phase err.(work): min =        0.00 max =           90.00 mean =        58.29|
|phase err.(test): min =        0.00 max =           89.99 mean =        58.24|
|-----------------------------------------------------------------------------|

============================== 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 = 16.379937             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.672   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.404789              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.842   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      170 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      682 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1479 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2599 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3866 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5018 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6482 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7582 |
|-----------------------------------------------------------------------------|
|-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 |       54.359 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.696 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.207)------------------------------------------|
|    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 = 12.207)------------------------------------------|
|    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 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4978   r_free= 0.4862   ksol= 0.00   Bsol= 0.00   scale= 0.746    |
|                                                                             |
| 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:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.294392                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4855   r_free= 0.4724   ksol= 0.34   Bsol= 50.00   scale= 0.963   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.06,6.98,10.00,0.00,0.00,0.00); trace/3= 8.35                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.289265                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.324296             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.589   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.329093              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.796   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4855      final r-factor (work) = 0.4079          |
| start r-factor (free) = 0.4724      final r-factor (free) = 0.4247          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 99.3902 = 14.32 * 0.50 * 6.2874 + 1.00 * 54.3592                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 44.6508 = 14.32 * 0.50 * 6.2131 + 1.00 * 0.1516                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4079      final r-factor (work) = 0.3596          |
| start r-factor (free) = 0.4247      final r-factor (free) = 0.4148          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.2722 = 1.33 * 1.00 * 6.2131 + 1.00 * 0.0145                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.1692 = 1.33 * 1.00 * 6.1316 + 1.00 * 0.0198                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.207)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.27   15.22    None  None   None       |
|    all(noH): 2823   0      0.00    88.27   15.22    None  None   None       |
|    Sol.    : 438    0      0.00    88.27   29.58    None  None   None       |
|    Mac.    : 2385   0      0.00    75.41   12.58    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 -   8.827: 1157   |   5:    44.133 -  52.960:   70        |
|      1:     8.827 -  17.653:  758   |   6:    52.960 -  61.787:   51        |
|      2:    17.653 -  26.480:  442   |   7:    61.787 -  70.613:   23        |
|      3:    26.480 -  35.307:  202   |   8:    70.613 -  79.440:    7        |
|      4:    35.307 -  44.133:  110   |   9:    79.440 -  88.267:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3596 r_free = 0.4148             target_work(ml) = 6.116         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3590 r_free = 0.4152             target_work(ml) = 6.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3590   r_free= 0.4152   ksol= 0.34   Bsol= 50.00   scale= 1.098   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.06,6.98,10.00,0.00,0.00,0.00); trace/3= 8.35                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.115183                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3571   r_free= 0.4124   ksol= 0.33   Bsol= 50.00   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.82,3.65,6.52,0.00,0.00,0.00); trace/3= 5.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.115797                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.625164              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.567   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.486136              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.567  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3571      final r-factor (work) = 0.2707          |
| start r-factor (free) = 0.4124      final r-factor (free) = 0.3283          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.5060 = 7.63 * 0.50 * 6.1256 + 1.00 * 0.1516                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.0076 = 7.63 * 0.50 * 6.0080 + 1.00 * 0.1016                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2707      final r-factor (work) = 0.2449          |
| start r-factor (free) = 0.3283      final r-factor (free) = 0.2992          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9407 = 0.49 * 1.00 * 6.0080 + 1.00 * 0.0200                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8559 = 0.49 * 1.00 * 5.8495 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.207)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.19   13.96    None  None   None       |
|    all(noH): 2823   0      0.00    87.19   13.96    None  None   None       |
|    Sol.    : 438    0      0.00    87.19   34.34    None  None   None       |
|    Mac.    : 2385   0      0.00    75.12   10.22    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.719: 1319   |   5:    43.594 -  52.312:   73        |
|      1:     8.719 -  17.438:  787   |   6:    52.312 -  61.031:   38        |
|      2:    17.438 -  26.156:  290   |   7:    61.031 -  69.750:   22        |
|      3:    26.156 -  34.875:  161   |   8:    69.750 -  78.469:    7        |
|      4:    34.875 -  43.594:  124   |   9:    78.469 -  87.187:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2449 r_free = 0.2992             target_work(ml) = 5.811         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2447 r_free = 0.2988             target_work(ml) = 5.811         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2447   r_free= 0.2988   ksol= 0.33   Bsol= 50.00   scale= 1.053   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.82,3.65,6.52,0.00,0.00,0.00); trace/3= 5.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.810724                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2428   r_free= 0.2991   ksol= 0.31   Bsol= 57.68   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.57,1.79,4.13,0.00,0.00,0.00); trace/3= 2.83                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.811898                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.441923              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.058   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.779465              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.922  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2428      final r-factor (work) = 0.1779          |
| start r-factor (free) = 0.2991      final r-factor (free) = 0.2316          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.1014 = 4.44 * 0.50 * 5.8532 + 1.00 * 0.1016                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.7216 = 4.44 * 0.50 * 5.6953 + 1.00 * 0.0725                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1779      final r-factor (work) = 0.1612          |
| start r-factor (free) = 0.2316      final r-factor (free) = 0.2156          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4515 = 0.78 * 1.00 * 5.6953 + 1.00 * 0.0123                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3013 = 0.78 * 1.00 * 5.4994 + 1.00 * 0.0147                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.207)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.69   14.76    None  None   None       |
|    all(noH): 2823   0      0.00    91.69   14.76    None  None   None       |
|    Sol.    : 438    0      1.62    91.69   40.72    None  None   None       |
|    Mac.    : 2385   0      0.00    77.64   9.99     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.169: 1488   |   5:    45.844 -  55.013:   94        |
|      1:     9.169 -  18.338:  689   |   6:    55.013 -  64.182:   64        |
|      2:    18.338 -  27.507:  213   |   7:    64.182 -  73.351:   42        |
|      3:    27.507 -  36.675:  120   |   8:    73.351 -  82.520:   17        |
|      4:    36.675 -  45.844:   92   |   9:    82.520 -  91.688:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1612 r_free = 0.2156             target_work(ml) = 5.469         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1611 r_free = 0.2155             target_work(ml) = 5.468         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1611   r_free= 0.2155   ksol= 0.31   Bsol= 57.68   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.57,1.79,4.13,0.00,0.00,0.00); trace/3= 2.83                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.468305                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1609   r_free= 0.2155   ksol= 0.33   Bsol= 73.37   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.68,1.13,3.27,0.00,0.00,0.00); trace/3= 2.03                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.468075                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.482967              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.484  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.204519              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.552  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1609      final r-factor (work) = 0.1358          |
| start r-factor (free) = 0.2155      final r-factor (free) = 0.1890          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6550 = 3.48 * 0.50 * 5.5025 + 1.00 * 0.0725                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4811 = 3.48 * 0.50 * 5.4016 + 1.00 * 0.0742                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1358      final r-factor (work) = 0.1336          |
| start r-factor (free) = 0.1890      final r-factor (free) = 0.1820          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1193 = 0.20 * 1.00 * 5.4016 + 1.00 * 0.0145                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0994 = 0.20 * 1.00 * 5.3240 + 1.00 * 0.0105                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.207)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.56   14.05    None  None   None       |
|    all(noH): 2823   0      0.00    88.56   14.05    None  None   None       |
|    Sol.    : 438    0      2.73    88.56   38.33    None  None   None       |
|    Mac.    : 2385   0      0.00    76.22   9.59     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.857: 1493   |   5:    44.282 -  53.139:   88        |
|      1:     8.857 -  17.713:  732   |   6:    53.139 -  61.995:   54        |
|      2:    17.713 -  26.569:  185   |   7:    61.995 -  70.852:   33        |
|      3:    26.569 -  35.426:  112   |   8:    70.852 -  79.708:   16        |
|      4:    35.426 -  44.282:  106   |   9:    79.708 -  88.565:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1336 r_free = 0.1820             target_work(ml) = 5.301         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1335 r_free = 0.1819             target_work(ml) = 5.300         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1335   r_free= 0.1819   ksol= 0.33   Bsol= 73.37   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.68,1.13,3.27,0.00,0.00,0.00); trace/3= 2.03                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.299844                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1336   r_free= 0.1816   ksol= 0.33   Bsol= 65.56   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.30,0.83,2.82,0.00,0.00,0.00); trace/3= 1.65                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.299954                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.182902              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 118.864  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.302658              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.226  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1336      final r-factor (work) = 0.1230          |
| start r-factor (free) = 0.1816      final r-factor (free) = 0.1704          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5479 = 3.18 * 0.50 * 5.3245 + 1.00 * 0.0742                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4613 = 3.18 * 0.50 * 5.2650 + 1.00 * 0.0824                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1230      final r-factor (work) = 0.1209          |
| start r-factor (free) = 0.1704      final r-factor (free) = 0.1681          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6038 = 0.30 * 1.00 * 5.2650 + 1.00 * 0.0103                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5938 = 0.30 * 1.00 * 5.2240 + 1.00 * 0.0127                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.207)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.82   13.82    None  None   None       |
|    all(noH): 2823   0      0.00    90.82   13.82    None  None   None       |
|    Sol.    : 438    0      2.89    90.82   37.55    None  None   None       |
|    Mac.    : 2385   0      0.00    78.14   9.47     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 -   9.082: 1530   |   5:    45.410 -  54.492:   91        |
|      1:     9.082 -  18.164:  721   |   6:    54.492 -  63.574:   48        |
|      2:    18.164 -  27.246:  172   |   7:    63.574 -  72.657:   25        |
|      3:    27.246 -  36.328:  118   |   8:    72.657 -  81.739:   11        |
|      4:    36.328 -  45.410:  106   |   9:    81.739 -  90.821:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1209 r_free = 0.1681             target_work(ml) = 5.217         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1208 r_free = 0.1679             target_work(ml) = 5.217         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1208   r_free= 0.1679   ksol= 0.33   Bsol= 65.56   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.30,0.83,2.82,0.00,0.00,0.00); trace/3= 1.65                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.216882                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2943 -  4.7365 0.99   1426  158 0.0988 0.1365      5.3889      5.6009|
|  2:  4.7365 -  3.7782 0.99   1382  155 0.0878 0.1160      5.4687       5.676|
|  3:  3.7782 -  3.3061 0.99   1343  144 0.1146 0.1631       5.532      5.8523|
|  4:  3.3061 -  3.0063 0.99   1344  156 0.1335 0.1792        5.51      5.6893|
|  5:  3.0063 -  2.7922 0.99   1335  149 0.1475 0.1800       5.412      5.6112|
|  6:  2.7922 -  2.6285 0.99   1331  147 0.1383 0.2088      5.2809      5.5411|
|  7:  2.6285 -  2.4974 0.99   1324  138 0.1396 0.1689      5.2551       5.383|
|  8:  2.4974 -  2.3891 0.98   1300  153 0.1281 0.1850      5.1473      5.4096|
|  9:  2.3891 -  2.2975 0.98   1303  144 0.1346 0.2050      5.1311      5.4124|
| 10:  2.2975 -  2.2184 1.00   1323  152 0.1217 0.1655      5.0081      5.1825|
| 11:  2.2184 -  2.1493 0.98   1307  138 0.1215 0.1982      4.9992      5.4054|
| 12:  2.1493 -  2.0880 0.98   1297  145 0.1239 0.1845       4.923      5.1642|
| 13:  2.0880 -  2.0331 0.96   1258  138 0.1195 0.1671      4.8313      5.0435|
| 14:  2.0331 -  1.9836 0.27    357   42 0.1097 0.1591      4.7191      4.9181|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2943 -  4.7365  1426   158  0.94   9.19   0.97     0.95       7417.19|
|  2:  4.7365 -  3.7782  1382   155  0.95   8.37   1.00     0.99       9812.02|
|  3:  3.7782 -  3.3061  1343   144  0.93  12.44   1.02     1.02      11687.48|
|  4:  3.3061 -  3.0063  1344   156  0.91  15.00   1.00     0.98      11493.00|
|  5:  3.0063 -  2.7922  1335   149  0.89  17.44   0.99     0.98       9731.47|
|  6:  2.7922 -  2.6285  1331   147  0.88  17.76   0.97     0.95       8108.04|
|  7:  2.6285 -  2.4974  1324   138  0.89  17.11   0.99     0.94       7323.55|
|  8:  2.4974 -  2.3891  1300   153  0.89  17.28   0.98     0.95       6286.61|
|  9:  2.3891 -  2.2975  1303   144  0.89  17.62   0.99     0.95       6028.72|
| 10:  2.2975 -  2.2184  1323   152  0.90  16.64   1.00     0.97       4872.62|
| 11:  2.2184 -  2.1493  1307   138  0.89  17.03   0.99     0.93       4779.19|
| 12:  2.1493 -  2.0880  1297   145  0.90  16.92   1.00     1.00       4335.97|
| 13:  2.0880 -  2.0331  1258   138  0.89  18.05   0.99     0.97       3796.82|
| 14:  2.0331 -  1.9836   357    42  0.91  14.92   0.97     0.94       2847.43|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2847.43 max =        11687.48 mean =      7311.25|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.98 mean =        15.36|
|phase err.(test): min =        0.00 max =           88.99 mean =        14.73|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1208   r_free= 0.1679   ksol= 0.32   Bsol= 61.38   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.33,-0.80,1.13,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.216860                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.29 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1208   r_free= 0.1679   ksol= 0.32   Bsol= 61.38   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.33,-0.80,1.13,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.216860                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2943 -  4.7365 0.99   1426  158 0.0985 0.1360      5.3857      5.5989|
|  2:  4.7365 -  3.7782 0.99   1382  155 0.0874 0.1158      5.4663      5.6734|
|  3:  3.7782 -  3.3061 0.99   1343  144 0.1145 0.1629      5.5309      5.8512|
|  4:  3.3061 -  3.0063 0.99   1344  156 0.1336 0.1795      5.5109      5.6907|
|  5:  3.0063 -  2.7922 0.99   1335  149 0.1476 0.1800      5.4132      5.6125|
|  6:  2.7922 -  2.6285 0.99   1331  147 0.1386 0.2092      5.2823       5.543|
|  7:  2.6285 -  2.4974 0.99   1324  138 0.1397 0.1690      5.2562      5.3841|
|  8:  2.4974 -  2.3891 0.98   1300  153 0.1282 0.1851      5.1481      5.4103|
|  9:  2.3891 -  2.2975 0.98   1303  144 0.1346 0.2050      5.1316      5.4128|
| 10:  2.2975 -  2.2184 1.00   1323  152 0.1219 0.1656      5.0086      5.1824|
| 11:  2.2184 -  2.1493 0.98   1307  138 0.1215 0.1982      4.9992      5.4049|
| 12:  2.1493 -  2.0880 0.98   1297  145 0.1239 0.1844      4.9229      5.1643|
| 13:  2.0880 -  2.0331 0.96   1258  138 0.1196 0.1672      4.8316      5.0438|
| 14:  2.0331 -  1.9836 0.27    357   42 0.1097 0.1591      4.7196      4.9188|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2943 -  4.7365  1426   158  0.94   9.14   0.97     0.95       7381.05|
|  2:  4.7365 -  3.7782  1382   155  0.95   8.35   1.00     0.99       9774.44|
|  3:  3.7782 -  3.3061  1343   144  0.93  12.41   1.02     1.02      11657.55|
|  4:  3.3061 -  3.0063  1344   156  0.91  15.00   1.00     0.98      11498.34|
|  5:  3.0063 -  2.7922  1335   149  0.89  17.46   0.99     0.98       9758.98|
|  6:  2.7922 -  2.6285  1331   147  0.88  17.79   0.97     0.95       8132.47|
|  7:  2.6285 -  2.4974  1324   138  0.89  17.14   0.98     0.94       7344.39|
|  8:  2.4974 -  2.3891  1300   153  0.89  17.30   0.98     0.95       6299.31|
|  9:  2.3891 -  2.2975  1303   144  0.89  17.63   0.99     0.95       6040.39|
| 10:  2.2975 -  2.2184  1323   152  0.90  16.65   1.00     0.97       4874.72|
| 11:  2.2184 -  2.1493  1307   138  0.89  17.03   0.99     0.93       4779.11|
| 12:  2.1493 -  2.0880  1297   145  0.90  16.91   1.00     1.00       4333.89|
| 13:  2.0880 -  2.0331  1258   138  0.89  18.05   0.99     0.97       3798.70|
| 14:  2.0331 -  1.9836   357    42  0.91  14.93   0.97     0.94       2850.99|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2850.99 max =        11657.55 mean =      7311.00|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.92 mean =        15.36|
|phase err.(test): min =        0.00 max =           88.93 mean =        14.74|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.207)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.63    92.45   15.45    None  None   None       |
|    all(noH): 2823   0      1.63    92.45   15.45    None  None   None       |
|    Sol.    : 438    0      4.52    92.45   39.18    None  None   None       |
|    Mac.    : 2385   0      1.63    79.76   11.09    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.627 -  10.709: 1530   |   5:    47.037 -  56.119:   91        |
|      1:    10.709 -  19.791:  721   |   6:    56.119 -  65.201:   48        |
|      2:    19.791 -  28.873:  172   |   7:    65.201 -  74.283:   25        |
|      3:    28.873 -  37.955:  118   |   8:    74.283 -  83.365:   11        |
|      4:    37.955 -  47.037:  106   |   9:    83.365 -  92.448:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 337         
Filter by distance & map next to the model:
   mapped sites are within: 0.422 - 4.879
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 332 from: 337
   mapped sites are within: 0.712 - 4.879

peak=   10.641 closest distance to " CB  VAL A 230 " =    1.474
peak=    7.070 closest distance to " CG2 VAL A 296 " =    1.176
peak=    6.280 closest distance to " CG  ARG A 138 " =    1.089
peak=    6.137 closest distance to " CD2 LEU A   5 " =    1.241
peak=    5.621 closest distance to " NE2 GLN A  11 " =    1.176
peak=    5.542 closest distance to " O   HOH Z 232 " =    2.267
peak=    5.506 closest distance to " O   HOH Z 142 " =    2.239
peak=    5.477 closest distance to " CG  PRO A  54 " =    1.384
peak=    5.345 closest distance to " O   HOH Z 222 " =    1.398
peak=    5.307 closest distance to " CG  LEU A   5 " =    1.225
peak=    5.276 closest distance to " CB  GLN A 223 " =    1.551
peak=    5.039 closest distance to " O   HOH Z   7 " =    1.433
peak=    4.934 closest distance to " NH1 ARG A 138 " =    1.082
peak=    4.837 closest distance to " O   HOH Z 111 " =    1.828
peak=    4.828 closest distance to " CG  LEU A 228 " =    1.146
peak=    4.747 closest distance to " CB  ASP A 124 " =    0.797
peak=    4.725 closest distance to " CB  SER A  63 " =    1.265
peak=    4.707 closest distance to " O   HOH Z   9 " =    1.948
peak=    4.706 closest distance to " CB  ASN A 148 " =    1.398
peak=    4.674 closest distance to " O   HOH Z 298 " =    2.140
peak=    4.669 closest distance to " O   HOH Z 369 " =    2.049
peak=    4.580 closest distance to " CB  GLN A 183 " =    1.235
peak=    4.466 closest distance to " O   HOH Z 287 " =    2.193
peak=    4.445 closest distance to " CZ  PHE A 218 " =    1.100
peak=    4.357 closest distance to " CG  LEU A 167 " =    1.259
peak=    4.355 closest distance to " O   HOH Z 427 " =    2.873
peak=    4.352 closest distance to " O   HOH Z 265 " =    1.968
peak=    4.319 closest distance to " CG  PRO A 243 " =    1.128
peak=    4.317 closest distance to " ND2 ASN A 187 " =    1.584
peak=    4.300 closest distance to " O   HOH Z 303 " =    2.228
peak=    4.280 closest distance to " CG  PRO A 198 " =    1.259
peak=    4.255 closest distance to " O   HOH Z 183 " =    1.382
peak=    4.240 closest distance to " CD  ARG A 159 " =    0.776
peak=    4.200 closest distance to " CB  VAL A 265 " =    1.348
peak=    4.189 closest distance to " CG  PRO A 213 " =    1.324
peak=    4.174 closest distance to " O   HOH Z 102 " =    1.248
peak=    4.169 closest distance to " CD  ARG A  66 " =    2.256
peak=    4.158 closest distance to " O   HOH Z 126 " =    1.533
peak=    4.152 closest distance to " CB  ASN A 142 " =    0.920
peak=    4.142 closest distance to " O   PRO A 198 " =    1.600
peak=    4.129 closest distance to " O   SER A  87 " =    2.368
peak=    4.110 closest distance to " CB  TRP A 266 " =    1.028
peak=    4.069 closest distance to " NH2AARG A 190 " =    1.834
peak=    4.062 closest distance to " CD2 LEU A 228 " =    1.223
peak=    4.060 closest distance to " O   HOH Z 423 " =    1.732
peak=    4.053 closest distance to " CB  GLU A 152 " =    1.202
peak=    4.049 closest distance to " CA  ALA A  51 " =    1.007
peak=    4.041 closest distance to " CB  PRO A  54 " =    1.003
peak=    4.034 closest distance to " O   HOH Z 425 " =    1.483
peak=    4.015 closest distance to " CB  VAL A 230 " =    1.277
peak=    4.009 closest distance to " NH1AARG A 145 " =    1.239
peak=    3.996 closest distance to " CE  LYS A  76 " =    0.912
peak=    3.978 closest distance to " O   HOH Z 145 " =    1.895
peak=    3.968 closest distance to " O   HOH Z 353 " =    2.545
peak=    3.961 closest distance to " O   HOH Z  88 " =    3.130
peak=    3.909 closest distance to " O   HOH Z 411 " =    3.102
peak=    3.908 closest distance to " O   HOH Z 126 " =    2.120
peak=    3.908 closest distance to " O   HOH Z 346 " =    1.640
peak=    3.907 closest distance to " O   HOH Z 272 " =    1.827
peak=    3.895 closest distance to " O   HOH Z 406 " =    1.567
peak=    3.880 closest distance to " CB  ARG A 275 " =    0.955
peak=    3.875 closest distance to " CB  ASN A  39 " =    0.912
peak=    3.862 closest distance to " NH1 ARG A  56 " =    1.057
peak=    3.859 closest distance to " O   HOH Z 188 " =    2.972
peak=    3.859 closest distance to " O   HOH Z 193 " =    1.994
peak=    3.854 closest distance to " CD1AILE A 234 " =    1.018
peak=    3.844 closest distance to " CD  ARG A 138 " =    1.349
peak=    3.836 closest distance to " CB  SER A 212 " =    1.277
peak=    3.832 closest distance to " CB  GLN A  88 " =    1.275
peak=    3.818 closest distance to " CZ3 TRP A 266 " =    1.100
peak=    3.816 closest distance to " O   HOH Z 410 " =    1.530
peak=    3.815 closest distance to " CB  VAL A 296 " =    1.158
peak=    3.814 closest distance to " O   HOH Z 158 " =    3.089
peak=    3.797 closest distance to " CB  ARG A 190 " =    1.478
peak=    3.783 closest distance to " CB  ARG A  79 " =    1.407
peak=    3.775 closest distance to " CG1 VAL A 153 " =    0.926
peak=    3.769 closest distance to " CD1 LEU A 300 " =    1.151
peak=    3.764 closest distance to " CB  SER A 210 " =    0.841
peak=    3.763 closest distance to " CB  LEU A 228 " =    1.222
peak=    3.753 closest distance to " CD  ARG A 269 " =    0.901
peak=    3.753 closest distance to " O   HOH Z 148 " =    3.605
peak=    3.750 closest distance to " O   HOH Z 368 " =    2.079
peak=    3.747 closest distance to " CG2 THR A 221 " =    1.126
peak=    3.745 closest distance to " O   HOH Z 316 " =    3.104
peak=    3.731 closest distance to " CD  GLN A 240 " =    1.556
peak=    3.729 closest distance to " O   HOH Z 180 " =    2.127
peak=    3.726 closest distance to " CB  GLU A  46 " =    0.952
peak=    3.723 closest distance to " O   HOH Z 207 " =    1.225
peak=    3.722 closest distance to " CA  SER A  87 " =    0.914
peak=    3.722 closest distance to " O   HOH Z 437 " =    1.684
peak=    3.721 closest distance to " O   HOH Z 167 " =    1.721
peak=    3.718 closest distance to " CB  VAL A 202 " =    1.527
peak=    3.718 closest distance to " CD2 TRP A 179 " =    1.266
peak=    3.716 closest distance to " O   HOH Z 156 " =    2.846
peak=    3.709 closest distance to " O   HOH Z 290 " =    1.168
peak=    3.709 closest distance to " O   HOH Z 185 " =    1.955
peak=    3.693 closest distance to " O   HOH Z 234 " =    3.915
peak=    3.691 closest distance to " O   HOH Z   2 " =    1.745
peak=    3.691 closest distance to " CD1 ILE A  33 " =    1.932
peak=    3.687 closest distance to " CD  LYS A 166 " =    1.231
peak=    3.685 closest distance to " CG BARG A 102 " =    1.945
peak=    3.683 closest distance to " O   HOH Z 380 " =    1.808
peak=    3.681 closest distance to " CA  ASP A 162 " =    0.914
peak=    3.677 closest distance to " N   PHE A 130 " =    1.276
peak=    3.666 closest distance to " O   HOH Z 273 " =    2.761
peak=    3.662 closest distance to " O   HOH Z  10 " =    1.839
peak=    3.657 closest distance to " CB  SER A   3 " =    1.559
peak=    3.651 closest distance to " O   HOH Z  57 " =    1.383
peak=    3.651 closest distance to " CB  SER A 216 " =    0.937
peak=    3.649 closest distance to " CA  TYR A  30 " =    1.027
peak=    3.638 closest distance to " N   SER A 271 " =    0.964
peak=    3.636 closest distance to " O   HOH Z 359 " =    1.487
peak=    3.634 closest distance to " CB  GLU A 277 " =    3.644
peak=    3.620 closest distance to " CG1 ILE A 151 " =    1.303
peak=    3.614 closest distance to " CA  ARG A 102 " =    1.135
peak=    3.610 closest distance to " O   HOH Z  44 " =    2.073
peak=    3.607 closest distance to " O   HOH Z 285 " =    2.152
peak=    3.606 closest distance to " CA  ALA A 160 " =    1.096
peak=    3.591 closest distance to " CB  ARG A 138 " =    1.346
peak=    3.580 closest distance to " O   ASP A 200 " =    1.540
peak=    3.579 closest distance to " O   HOH Z 214 " =    2.254
peak=    3.578 closest distance to " CA  TYR A 186 " =    1.589
peak=    3.577 closest distance to " O   HOH Z 332 " =    1.612
peak=    3.572 closest distance to " O   HOH Z 345 " =    3.455
peak=    3.569 closest distance to " CG  GLN A  88 " =    1.118
peak=    3.564 closest distance to " CA  TYR A 116 " =    1.448
peak=    3.551 closest distance to " CB  ALA A   9 " =    1.608
peak=    3.550 closest distance to " CB  LEU A 237 " =    0.815
peak=    3.548 closest distance to " O   HOH Z  30 " =    1.807
peak=    3.547 closest distance to " OE2 GLU A   2 " =    2.004
peak=    3.546 closest distance to " CA  ILE A 234 " =    1.060
peak=    3.545 closest distance to " O   HOH Z  78 " =    1.569
peak=    3.545 closest distance to " CA  ARG A 159 " =    1.214
peak=    3.543 closest distance to " CB  PRO A 243 " =    1.323
peak=    3.537 closest distance to " NE AARG A 275 " =    1.535
peak=    3.536 closest distance to " O   TYR A 116 " =    1.235
peak=    3.534 closest distance to " CE3 TRP A  85 " =    1.143
peak=    3.533 closest distance to " OG  SER A 135 " =    1.282
peak=    3.527 closest distance to " CD BLYS A 290 " =    1.075
peak=    3.527 closest distance to " O   HOH Z 184 " =    1.485
peak=    3.526 closest distance to " CB  ALA A 248 " =    1.040
peak=    3.525 closest distance to " CA  ARG A 195 " =    1.247
peak=    3.525 closest distance to " CA  ALA A 291 " =    0.932
peak=    3.522 closest distance to " O   HOH Z   1 " =    1.793
peak=    3.520 closest distance to " CB  ILE A 120 " =    1.297
peak=    3.516 closest distance to " ND1 HIS A  81 " =    1.959
peak=    3.515 closest distance to " CB  TRP A 150 " =    1.313
peak=    3.513 closest distance to " O   HOH Z  61 " =    1.614
peak=    3.513 closest distance to " CG2 ILE A 234 " =    0.985
peak=    3.511 closest distance to " CD  ARG A  66 " =    2.533
peak=    3.503 closest distance to " CB AVAL A  41 " =    1.334
peak=    3.500 closest distance to " O   HOH Z  80 " =    1.614
peak=    3.495 closest distance to " N   ALA A 256 " =    1.058
peak=    3.485 closest distance to " CD1 LEU A   5 " =    1.365
peak=    3.482 closest distance to " O   HOH Z   1 " =    1.863
peak=    3.482 closest distance to " CB  ASP A 140 " =    0.888
peak=    3.481 closest distance to " CA  VAL A 125 " =    1.165
peak=    3.479 closest distance to " CA  ASN A 127 " =    1.085
peak=    3.471 closest distance to " O   HOH Z  59 " =    1.935
peak=    3.467 closest distance to " O   HOH Z 211 " =    1.269
peak=    3.461 closest distance to " CA  LYS A 117 " =    1.125
peak=    3.455 closest distance to " N   CYS A 260 " =    0.805
peak=    3.447 closest distance to " O   HOH Z 389 " =    1.870
peak=    3.444 closest distance to " CE1 TYR A 186 " =    1.347
peak=    3.440 closest distance to " CB  MET A  40 " =    0.814
peak=    3.435 closest distance to " CE3 TRP A 150 " =    1.030
peak=    3.434 closest distance to " O   HOH Z 302 " =    1.798
peak=    3.432 closest distance to " OG  SER A  62 " =    2.799
peak=    3.432 closest distance to " CB  THR A  82 " =    1.266
peak=    3.425 closest distance to " CG  GLN A  89 " =    1.555
peak=    3.424 closest distance to " CB  ASN A 110 " =    1.149
peak=    3.423 closest distance to " CA  ALA A 295 " =    1.096
peak=    3.420 closest distance to " CB  ALA A   1 " =    4.879
peak=    3.420 closest distance to " O   HOH Z 171 " =    4.205
peak=    3.418 closest distance to " O   HOH Z 132 " =    2.533
peak=    3.414 closest distance to " CA  GLY A 267 " =    1.071
peak=    3.407 closest distance to " O   HOH Z 238 " =    2.274
peak=    3.406 closest distance to " CB  ALA A 104 " =    0.780
peak=    3.406 closest distance to " O   HOH Z 258 " =    2.069
peak=    3.406 closest distance to " NE2 HIS A 207 " =    1.184
peak=    3.403 closest distance to " CG2 VAL A 257 " =    0.900
peak=    3.402 closest distance to " O   HOH Z 251 " =    1.564
peak=    3.394 closest distance to " CA  GLN A  94 " =    0.736
peak=    3.390 closest distance to " CD2 LEU A 255 " =    1.679
peak=    3.389 closest distance to " CG BARG A 275 " =    1.296
peak=    3.386 closest distance to " O   HOH Z 305 " =    1.941
peak=    3.376 closest distance to " CB  LEU A 143 " =    1.237
peak=    3.376 closest distance to " O   MET A 105 " =    1.894
peak=    3.375 closest distance to " O   HOH Z 392 " =    1.331
peak=    3.371 closest distance to " O   HOH Z  53 " =    2.461
peak=    3.363 closest distance to " O   PHE A 192 " =    1.399
peak=    3.362 closest distance to " O   HOH Z  61 " =    1.550
peak=    3.361 closest distance to " N   SER A 135 " =    1.327
peak=    3.356 closest distance to " CB  ASN A 187 " =    1.055
peak=    3.352 closest distance to " O   HOH Z  21 " =    1.793
peak=    3.347 closest distance to " CA  ARG A 139 " =    1.011
peak=    3.345 closest distance to " O   HOH Z 403 " =    1.603
peak=    3.343 closest distance to " O   HOH Z 148 " =    2.236
peak=    3.343 closest distance to " CG1 ILE A  49 " =    1.605
peak=    3.342 closest distance to " O   HOH Z 218 " =    4.774
peak=    3.339 closest distance to " CE3 TRP A 274 " =    1.317
peak=    3.338 closest distance to " N   ASN A 127 " =    1.302
peak=    3.337 closest distance to " O   HOH Z 109 " =    2.698
peak=    3.335 closest distance to " CB  SER A  62 " =    1.066
peak=    3.333 closest distance to " CA  ALA A 158 " =    1.194
peak=    3.332 closest distance to " OG  SER A  62 " =    3.102
peak=    3.328 closest distance to " O   HOH Z 329 " =    4.093
peak=    3.326 closest distance to " CD  ARG A  14 " =    1.271
peak=    3.326 closest distance to " OG  SER A 276 " =    1.248
peak=    3.325 closest distance to " CA  ASP A 124 " =    0.712
peak=    3.325 closest distance to " CB  TRP A 179 " =    1.371
peak=    3.322 closest distance to " CA  LEU A 282 " =    0.983
peak=    3.318 closest distance to " O   THR A 182 " =    1.400
peak=    3.311 closest distance to " CB  ALA A  34 " =    1.053
peak=    3.307 closest distance to " O   HOH Z 280 " =    3.102
peak=    3.307 closest distance to " O   HOH Z 411 " =    1.464
peak=    3.305 closest distance to " O   HOH Z  64 " =    2.249
peak=    3.303 closest distance to " CZ  PHE A  38 " =    1.265
peak=    3.302 closest distance to " NZ  LYS A 117 " =    3.160
peak=    3.301 closest distance to " O   ASP A 124 " =    1.206
peak=    3.299 closest distance to " CZ3 TRP A  92 " =    1.325
peak=    3.297 closest distance to " O   HOH Z 147 " =    1.714
peak=    3.296 closest distance to " CA  MET A  40 " =    1.371
peak=    3.293 closest distance to " O   HOH Z 422 " =    2.750
peak=    3.293 closest distance to " O   HOH Z 409 " =    2.567
peak=    3.292 closest distance to " CD1 LEU A 101 " =    1.180
peak=    3.289 closest distance to " CB  SER A 273 " =    0.935
peak=    3.289 closest distance to " CG2 ILE A 151 " =    0.834
peak=    3.288 closest distance to " O   HOH Z 128 " =    2.240
peak=    3.286 closest distance to " O   HOH Z 172 " =    3.095
peak=    3.286 closest distance to " O   HOH Z 352 " =    1.807
peak=    3.282 closest distance to " CB  ALA A 242 " =    0.878
peak=    3.280 closest distance to " CG2 ILE A  20 " =    1.556
peak=    3.277 closest distance to " O   HOH Z 409 " =    3.149
peak=    3.274 closest distance to " O   ASN A 209 " =    1.399
peak=    3.273 closest distance to " CD2 TYR A 186 " =    1.145
peak=    3.271 closest distance to " O   HOH Z 329 " =    3.003
peak=    3.270 closest distance to " CA  THR A 264 " =    0.832
peak=    3.268 closest distance to " OD1 ASN A  60 " =    1.116
peak=    3.267 closest distance to " CD1 ILE A 199 " =    1.041
peak=    3.267 closest distance to " CB  GLN A 103 " =    1.063
peak=    3.267 closest distance to " CA  PRO A  54 " =    1.384
peak=    3.266 closest distance to " OG1 THR A 279 " =    1.516
peak=    3.264 closest distance to " O   HOH Z 145 " =    1.844
peak=    3.264 closest distance to " O   HOH Z 368 " =    4.159
peak=    3.262 closest distance to " NH1 ARG A  14 " =    0.900
peak=    3.261 closest distance to " O   HOH Z  20 " =    1.817
peak=    3.259 closest distance to " CB  TYR A  30 " =    1.210
peak=    3.257 closest distance to " O   HOH Z 281 " =    2.533
peak=    3.250 closest distance to " O   HOH Z 196 " =    1.259
peak=    3.248 closest distance to " CG  GLU A  37 " =    0.931
peak=    3.248 closest distance to " O   HOH Z 175 " =    3.732
peak=    3.245 closest distance to " CB  GLN A  89 " =    1.259
peak=    3.245 closest distance to " O   HOH Z  89 " =    1.730
peak=    3.245 closest distance to " O   HOH Z 193 " =    1.644
peak=    3.243 closest distance to " OD1 ASN A  69 " =    2.521
peak=    3.241 closest distance to " CB  MET A  47 " =    0.975
peak=    3.240 closest distance to " CA  ALA A 184 " =    1.094
peak=    3.234 closest distance to " O   HOH Z 130 " =    2.046
peak=    3.234 closest distance to " CB  HIS A 108 " =    0.809
peak=    3.231 closest distance to " O   HOH Z 188 " =    2.008
peak=    3.226 closest distance to " CG  MET A 185 " =    1.265
peak=    3.224 closest distance to " CB  LYS A 117 " =    1.193
peak=    3.221 closest distance to " O   HOH Z  68 " =    2.050
peak=    3.221 closest distance to " O   PRO A 198 " =    1.339
peak=    3.220 closest distance to " O   HOH Z 200 " =    3.070
peak=    3.220 closest distance to " CB  TYR A 116 " =    0.898
peak=    3.216 closest distance to " CD  ARG A 195 " =    3.558
peak=    3.215 closest distance to " O   HOH Z 235 " =    1.734
peak=    3.213 closest distance to " CD  LYS A  76 " =    1.941
peak=    3.212 closest distance to " O   HOH Z   3 " =    2.079
peak=    3.210 closest distance to " CA  GLU A  46 " =    1.105
peak=    3.209 closest distance to " CG  LYS A 119 " =    1.123
peak=    3.207 closest distance to " C   ALA A 299 " =    0.981
peak=    3.205 closest distance to " O   HOH Z 421 " =    2.234
peak=    3.204 closest distance to " CB  ALA A  43 " =    0.873
peak=    3.203 closest distance to " O   HOH Z 170 " =    1.120
peak=    3.203 closest distance to " O   HOH Z 371 " =    2.858
peak=    3.201 closest distance to " O   HOH Z 128 " =    1.623
peak=    3.197 closest distance to " O   HOH Z 213 " =    2.097
peak=    3.196 closest distance to " O   HOH Z 303 " =    2.940
peak=    3.194 closest distance to " O   HOH Z 124 " =    1.879
peak=    3.193 closest distance to " O   HOH Z 166 " =    3.703
peak=    3.193 closest distance to " CB  ASN A 285 " =    0.930
peak=    3.191 closest distance to " CB  VAL A 268 " =    0.835
peak=    3.187 closest distance to " CG  ARG A 269 " =    1.763
peak=    3.186 closest distance to " CD  ARG A 195 " =    1.138
peak=    3.182 closest distance to " O   HOH Z 148 " =    1.455
peak=    3.180 closest distance to " CA  MET A 105 " =    0.886
peak=    3.177 closest distance to " CA  ASN A  74 " =    1.382
peak=    3.176 closest distance to " CB  TYR A 247 " =    0.981
peak=    3.174 closest distance to " O   PHE A  61 " =    1.470
peak=    3.172 closest distance to " O   ASN A  74 " =    1.491
peak=    3.170 closest distance to " CG  ARG A 159 " =    1.004
peak=    3.167 closest distance to " O   HOH Z 176 " =    1.729
peak=    3.164 closest distance to " N   SER A  12 " =    1.568
peak=    3.158 closest distance to " O   HOH Z 408 " =    3.112
peak=    3.153 closest distance to " O   HOH Z 116 " =    1.838
peak=    3.150 closest distance to " O   HOH Z 215 " =    2.737
peak=    3.148 closest distance to " O   HOH Z 394 " =    3.790
peak=    3.142 closest distance to " O   HOH Z 153 " =    3.778
peak=    3.142 closest distance to " CA  ALA A 154 " =    1.114
peak=    3.138 closest distance to " CA  GLY A 241 " =    0.822
peak=    3.135 closest distance to " O   HOH Z 417 " =    3.508
peak=    3.133 closest distance to " CA  ARG A  36 " =    1.182
peak=    3.133 closest distance to " O   HOH Z 294 " =    1.550
peak=    3.133 closest distance to " CB  LEU A  83 " =    0.732
peak=    3.131 closest distance to " CB  LEU A 300 " =    0.876
peak=    3.129 closest distance to " CB  SER A  26 " =    1.809
peak=    3.125 closest distance to " CG1 VAL A 296 " =    1.256
peak=    3.119 closest distance to " CA  ALA A  21 " =    1.223
peak=    3.112 closest distance to " N   TYR A  15 " =    0.930
peak=    3.112 closest distance to " CE  MET A  93 " =    1.559
peak=    3.108 closest distance to " NH2AARG A 145 " =    1.230
peak=    3.104 closest distance to " O   HOH Z 173 " =    1.762
peak=    3.102 closest distance to " CA  VAL A 112 " =    1.134
peak=    3.101 closest distance to " O   HOH Z 238 " =    3.188
peak=    3.099 closest distance to " O   HOH Z  58 " =    1.756
peak=    3.092 closest distance to " O   HOH Z  35 " =    4.751
peak=    3.083 closest distance to " O   HOH Z 222 " =    2.292
peak=    3.080 closest distance to " CA  ILE A 106 " =    0.795
peak=    3.076 closest distance to " CB  GLU A 175 " =    0.896
peak=    3.073 closest distance to " OG BSER A 164 " =    2.365
peak=    3.073 closest distance to " CB  ALA A 100 " =    1.372
peak=    3.068 closest distance to " N   ALA A   7 " =    1.330
peak=    3.067 closest distance to " O   HOH Z 128 " =    1.417
peak=    3.059 closest distance to " O   HOH Z 368 " =    3.621
peak=    3.059 closest distance to " O   HOH Z 425 " =    2.258
peak=    3.056 closest distance to " CB  ASP A 171 " =    1.308
peak=    3.053 closest distance to " CZ  PHE A 192 " =    1.072
peak=    3.049 closest distance to " O   HOH Z  85 " =    2.002
peak=    3.043 closest distance to " O   HOH Z 248 " =    1.759

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 209         
Filter by distance & map next to the model:
   mapped sites are within: 0.261 - 5.578
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 205 from: 209
   mapped sites are within: 0.763 - 5.578

peak=   -5.447 closest distance to " CG2 VAL A 230 " =    0.763
peak=   -4.275 closest distance to " O   PRO A 198 " =    1.259
peak=   -4.221 closest distance to " O   HOH Z 162 " =    2.604
peak=   -4.218 closest distance to " O   HOH Z  52 " =    1.420
peak=   -4.193 closest distance to " O   HOH Z 231 " =    1.873
peak=   -4.130 closest distance to " OG BSER A 134 " =    1.502
peak=   -4.112 closest distance to " CD  ARG A  14 " =    3.209
peak=   -4.104 closest distance to " CG2 VAL A 296 " =    0.941
peak=   -4.077 closest distance to " OE1 GLN A  88 " =    1.002
peak=   -4.073 closest distance to " CG  GLN A 223 " =    2.531
peak=   -4.048 closest distance to " CZ2 TRP A  92 " =    2.883
peak=   -3.961 closest distance to " CA  ASP A  27 " =    2.515
peak=   -3.944 closest distance to " CB  ALA A  43 " =    2.624
peak=   -3.933 closest distance to " CG1 VAL A 112 " =    2.670
peak=   -3.932 closest distance to " O   HOH Z 275 " =    1.918
peak=   -3.925 closest distance to " O   HOH Z 102 " =    1.268
peak=   -3.910 closest distance to " CD  ARG A 156 " =    2.130
peak=   -3.893 closest distance to " CB  PRO A 163 " =    2.436
peak=   -3.887 closest distance to " O   HOH Z  44 " =    2.385
peak=   -3.878 closest distance to " CG  TRP A 266 " =    1.804
peak=   -3.872 closest distance to " O   HOH Z 290 " =    1.274
peak=   -3.864 closest distance to " O   HOH Z 216 " =    1.129
peak=   -3.852 closest distance to " O   HOH Z 394 " =    1.538
peak=   -3.850 closest distance to " O   PRO A 163 " =    1.961
peak=   -3.827 closest distance to " CG  ARG A 138 " =    0.943
peak=   -3.807 closest distance to " OG  SER A  97 " =    2.367
peak=   -3.801 closest distance to " CG2BVAL A  41 " =    2.341
peak=   -3.784 closest distance to " O   HOH Z 183 " =    1.256
peak=   -3.769 closest distance to " CD1 TYR A 247 " =    2.795
peak=   -3.761 closest distance to " CB  VAL A 230 " =    1.078
peak=   -3.759 closest distance to " CG1 VAL A 250 " =    2.678
peak=   -3.755 closest distance to " CA  GLY A 241 " =    3.143
peak=   -3.740 closest distance to " O   HOH Z 108 " =    1.268
peak=   -3.736 closest distance to " CD1 LEU A 101 " =    2.451
peak=   -3.722 closest distance to " O   MET A  40 " =    2.923
peak=   -3.720 closest distance to " CB  TRP A  85 " =    2.546
peak=   -3.714 closest distance to " C   LEU A 222 " =    0.975
peak=   -3.700 closest distance to " CD  ARG A 138 " =    1.275
peak=   -3.700 closest distance to " O   HOH Z  65 " =    1.219
peak=   -3.696 closest distance to " OG  SER A  87 " =    1.354
peak=   -3.681 closest distance to " CA  GLY A 241 " =    2.413
peak=   -3.673 closest distance to " CA  GLY A  98 " =    2.003
peak=   -3.661 closest distance to " C   ALA A 158 " =    1.403
peak=   -3.659 closest distance to " NH2AARG A 275 " =    5.578
peak=   -3.651 closest distance to " O   VAL A 189 " =    2.544
peak=   -3.641 closest distance to " O   HOH Z 359 " =    3.092
peak=   -3.640 closest distance to " O   HOH Z  38 " =    1.447
peak=   -3.634 closest distance to " O   HOH Z 389 " =    2.145
peak=   -3.629 closest distance to " O   GLY A 203 " =    2.483
peak=   -3.627 closest distance to " CG1 VAL A 112 " =    3.128
peak=   -3.627 closest distance to " CD  GLN A  58 " =    0.779
peak=   -3.625 closest distance to " CE3 TRP A 150 " =    2.458
peak=   -3.621 closest distance to " ND2 ASN A  60 " =    1.625
peak=   -3.619 closest distance to " CE2 TYR A  30 " =    2.677
peak=   -3.617 closest distance to " O   HOH Z 166 " =    2.421
peak=   -3.598 closest distance to " CG1 VAL A 265 " =    2.440
peak=   -3.594 closest distance to " N   ALA A  43 " =    2.702
peak=   -3.576 closest distance to " O   HOH Z 435 " =    2.969
peak=   -3.569 closest distance to " O   HOH Z 118 " =    1.171
peak=   -3.565 closest distance to " O   HOH Z  60 " =    2.597
peak=   -3.562 closest distance to " N   THR A 157 " =    1.570
peak=   -3.545 closest distance to " O   HOH Z  73 " =    2.094
peak=   -3.534 closest distance to " O   HOH Z 144 " =    1.460
peak=   -3.534 closest distance to " ND2 ASN A 187 " =    1.402
peak=   -3.517 closest distance to " O   HOH Z 351 " =    1.600
peak=   -3.499 closest distance to " O   HOH Z 111 " =    1.831
peak=   -3.499 closest distance to " CA  GLY A 133 " =    2.229
peak=   -3.495 closest distance to " O   HOH Z 429 " =    2.032
peak=   -3.492 closest distance to " OD1 ASN A  60 " =    0.840
peak=   -3.491 closest distance to " O   HOH Z 377 " =    1.806
peak=   -3.490 closest distance to " O   ASP A  27 " =    1.827
peak=   -3.486 closest distance to " O   GLY A  17 " =    1.285
peak=   -3.485 closest distance to " CB  PHE A 130 " =    1.296
peak=   -3.483 closest distance to " CD  LYS A 289 " =    2.369
peak=   -3.483 closest distance to " C   LYS A  76 " =    1.522
peak=   -3.482 closest distance to " CE1 TYR A 169 " =    2.614
peak=   -3.477 closest distance to " CB  ALA A 161 " =    2.614
peak=   -3.471 closest distance to " CZ  PHE A 130 " =    1.061
peak=   -3.467 closest distance to " OD1 ASP A 171 " =    1.673
peak=   -3.464 closest distance to " O   HOH Z 426 " =    1.717
peak=   -3.458 closest distance to " CZ3 TRP A 179 " =    1.170
peak=   -3.449 closest distance to " O   HOH Z 131 " =    4.116
peak=   -3.448 closest distance to " CD1 LEU A 228 " =    2.420
peak=   -3.445 closest distance to " OG BSER A 134 " =    1.857
peak=   -3.441 closest distance to " O   HOH Z  63 " =    1.750
peak=   -3.440 closest distance to " O   HOH Z 140 " =    1.479
peak=   -3.438 closest distance to " CZ  PHE A  38 " =    2.603
peak=   -3.438 closest distance to " CG  GLN A  88 " =    0.866
peak=   -3.436 closest distance to " O   HOH Z 112 " =    1.168
peak=   -3.435 closest distance to " O   HOH Z 145 " =    1.426
peak=   -3.434 closest distance to " O   HOH Z 207 " =    1.206
peak=   -3.432 closest distance to " CG1 VAL A 296 " =    1.445
peak=   -3.426 closest distance to " O   HOH Z   9 " =    1.661
peak=   -3.414 closest distance to " CG2 VAL A 202 " =    2.835
peak=   -3.413 closest distance to " O   PRO A 243 " =    2.463
peak=   -3.402 closest distance to " O   GLN A 240 " =    2.530
peak=   -3.399 closest distance to " CD1 ILE A  33 " =    2.544
peak=   -3.397 closest distance to " O   HOH Z  11 " =    1.966
peak=   -3.396 closest distance to " NH2 ARG A  79 " =    2.072
peak=   -3.393 closest distance to " CB  ASP A 132 " =    2.378
peak=   -3.392 closest distance to " C   ASN A 285 " =    2.507
peak=   -3.380 closest distance to " O   HOH Z 412 " =    4.515
peak=   -3.379 closest distance to " O   ILE A  49 " =    1.726
peak=   -3.377 closest distance to " O   HOH Z 198 " =    2.589
peak=   -3.377 closest distance to " O   SER A  22 " =    2.592
peak=   -3.375 closest distance to " CA  GLY A 203 " =    2.591
peak=   -3.375 closest distance to " O   HOH Z 166 " =    1.282
peak=   -3.374 closest distance to " CD2 HIS A 207 " =    2.396
peak=   -3.367 closest distance to " N   ALA A 226 " =    2.037
peak=   -3.363 closest distance to " O   HOH Z  43 " =    1.665
peak=   -3.360 closest distance to " CG  LEU A 228 " =    0.947
peak=   -3.358 closest distance to " CE BMET A  47 " =    1.474
peak=   -3.356 closest distance to " CG  LEU A   5 " =    0.952
peak=   -3.347 closest distance to " O   HOH Z 411 " =    5.104
peak=   -3.345 closest distance to " O   GLY A  80 " =    2.556
peak=   -3.339 closest distance to " NH2 ARG A 219 " =    1.664
peak=   -3.334 closest distance to " CD  LYS A 166 " =    2.719
peak=   -3.332 closest distance to " CD  GLU A 277 " =    1.188
peak=   -3.331 closest distance to " C   ARG A 269 " =    1.485
peak=   -3.329 closest distance to " CG2 ILE A  20 " =    2.951
peak=   -3.321 closest distance to " O   HOH Z 295 " =    1.534
peak=   -3.319 closest distance to " O   HOH Z  51 " =    0.973
peak=   -3.315 closest distance to " O   GLU A  53 " =    1.609
peak=   -3.310 closest distance to " O   HOH Z 281 " =    2.759
peak=   -3.296 closest distance to " O   HOH Z 368 " =    1.619
peak=   -3.295 closest distance to " CD  PRO A 243 " =    1.949
peak=   -3.295 closest distance to " OE1 GLN A  77 " =    0.994
peak=   -3.294 closest distance to " CB  ALA A 248 " =    2.364
peak=   -3.292 closest distance to " C   LEU A 143 " =    1.162
peak=   -3.289 closest distance to " CD  GLN A  55 " =    1.099
peak=   -3.289 closest distance to " OE1 GLN A 278 " =    1.132
peak=   -3.282 closest distance to " CA  ASP A 298 " =    1.103
peak=   -3.278 closest distance to " CG1 VAL A  78 " =    2.388
peak=   -3.277 closest distance to " CD2 LEU A   5 " =    1.068
peak=   -3.274 closest distance to " O   ARG A 145 " =    1.479
peak=   -3.274 closest distance to " O   HOH Z 377 " =    0.879
peak=   -3.272 closest distance to " OG  SER A 141 " =    1.802
peak=   -3.265 closest distance to " CG  PRO A 163 " =    2.589
peak=   -3.265 closest distance to " C   MET A 188 " =    1.444
peak=   -3.264 closest distance to " O   HOH Z 357 " =    1.969
peak=   -3.262 closest distance to " CG  MET A 105 " =    0.996
peak=   -3.261 closest distance to " O   HOH Z  70 " =    2.045
peak=   -3.259 closest distance to " O   HOH Z 251 " =    4.853
peak=   -3.256 closest distance to " O   HOH Z 389 " =    1.603
peak=   -3.251 closest distance to " CE2 TRP A  70 " =    2.428
peak=   -3.249 closest distance to " CG1 VAL A 112 " =    2.591
peak=   -3.245 closest distance to " CA  SER A  62 " =    2.626
peak=   -3.242 closest distance to " O   HOH Z 147 " =    1.965
peak=   -3.241 closest distance to " CE  LYS A  76 " =    2.853
peak=   -3.234 closest distance to " O   SER A 210 " =    1.904
peak=   -3.231 closest distance to " C   ASN A 148 " =    1.807
peak=   -3.228 closest distance to " O   HOH Z 185 " =    2.284
peak=   -3.227 closest distance to " CB  ALA A 227 " =    2.461
peak=   -3.227 closest distance to " NE2 GLN A  58 " =    5.033
peak=   -3.210 closest distance to " O   HOH Z  60 " =    1.487
peak=   -3.209 closest distance to " O   HOH Z   2 " =    2.079
peak=   -3.209 closest distance to " CB  PHE A 192 " =    1.712
peak=   -3.209 closest distance to " O   HOH Z 313 " =    1.489
peak=   -3.208 closest distance to " CZ2 TRP A 274 " =    0.903
peak=   -3.206 closest distance to " OG  SER A  28 " =    2.176
peak=   -3.205 closest distance to " O   HOH Z 275 " =    1.479
peak=   -3.203 closest distance to " OG1 THR A 246 " =    1.397
peak=   -3.200 closest distance to " O   SER A  62 " =    1.722
peak=   -3.196 closest distance to " CE3 TRP A  70 " =    1.771
peak=   -3.195 closest distance to " ND2 ASN A  45 " =    2.322
peak=   -3.194 closest distance to " N   ASP A 132 " =    2.031
peak=   -3.191 closest distance to " O   SER A 271 " =    2.266
peak=   -3.188 closest distance to " O   HOH Z  44 " =    1.067
peak=   -3.188 closest distance to " CG  HIS A  86 " =    1.092
peak=   -3.185 closest distance to " CD2 TYR A 293 " =    2.032
peak=   -3.184 closest distance to " OE1 GLN A  89 " =    1.907
peak=   -3.181 closest distance to " OG  SER A  62 " =    4.449
peak=   -3.181 closest distance to " CB  ALA A 291 " =    2.051
peak=   -3.177 closest distance to " CZ  PHE A 192 " =    2.497
peak=   -3.174 closest distance to " CG  PHE A 283 " =    2.741
peak=   -3.171 closest distance to " OE1 GLU A  44 " =    0.997
peak=   -3.168 closest distance to " O   PHE A 218 " =    1.551
peak=   -3.167 closest distance to " C   GLU A 236 " =    0.937
peak=   -3.165 closest distance to " O   HOH Z 359 " =    1.632
peak=   -3.160 closest distance to " O   HOH Z 374 " =    1.932
peak=   -3.158 closest distance to " N   ALA A 244 " =    1.374
peak=   -3.155 closest distance to " O   HOH Z 407 " =    3.161
peak=   -3.149 closest distance to " O   HOH Z 165 " =    1.953
peak=   -3.149 closest distance to " N   LYS A 166 " =    1.849
peak=   -3.145 closest distance to " OE1 GLN A 183 " =    1.666
peak=   -3.140 closest distance to " O   HOH Z 193 " =    2.051
peak=   -3.131 closest distance to " O   HOH Z  10 " =    1.575
peak=   -3.119 closest distance to " CG  GLN A 278 " =    2.260
peak=   -3.118 closest distance to " O   HOH Z   9 " =    3.241
peak=   -3.112 closest distance to " O   HOH Z 136 " =    0.881
peak=   -3.107 closest distance to " O   HOH Z 109 " =    1.083
peak=   -3.101 closest distance to " N   ASP A 191 " =    1.175
peak=   -3.099 closest distance to " CA  SER A 135 " =    1.309
peak=   -3.097 closest distance to " CB  PRO A  54 " =    2.545
peak=   -3.097 closest distance to " OG  SER A 206 " =    1.831
peak=   -3.092 closest distance to " O   HOH Z 389 " =    4.818
peak=   -3.084 closest distance to " CD1 PHE A  61 " =    3.015
peak=   -3.072 closest distance to " CD1 ILE A 199 " =    2.630
peak=   -3.070 closest distance to " O   HOH Z 174 " =    2.672
peak=   -3.062 closest distance to " O   HOH Z  52 " =    1.800
peak=   -3.050 closest distance to " CB  TYR A  15 " =    2.221
peak=   -3.049 closest distance to " O   HOH Z 252 " =    3.633
peak=   -3.046 closest distance to " NZ  LYS A 166 " =    1.132
peak=   -3.024 closest distance to " CD1 LEU A 297 " =    2.651
peak=   -3.021 closest distance to " O   HOH Z 380 " =    1.066

================= 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    :  0.4934 0.4804   6.293083e+00   6.276291e+00
   1_bss:  0.4855 0.4724   6.289265e+00   6.271486e+00
   1_xyz:  0.4079 0.4247   6.189754e+00   6.211645e+00
   1_adp:  0.3596 0.4148   6.115676e+00   6.194711e+00
   1_occ:  0.3590 0.4152   6.115183e+00   6.195519e+00
   2_bss:  0.3571 0.4124   6.115797e+00   6.194164e+00
   2_xyz:  0.2707 0.3283   5.892516e+00   6.035121e+00
   2_adp:  0.2449 0.2992   5.811382e+00   5.962711e+00
   2_occ:  0.2447 0.2988   5.810724e+00   5.961984e+00
   3_bss:  0.2428 0.2991   5.811898e+00   5.963178e+00
   3_xyz:  0.1779 0.2316   5.544319e+00   5.741836e+00
   3_adp:  0.1612 0.2156   5.468903e+00   5.683754e+00
   3_occ:  0.1611 0.2155   5.468305e+00   5.683307e+00
   4_bss:  0.1609 0.2155   5.468075e+00   5.682438e+00
   4_xyz:  0.1358 0.1890   5.327773e+00   5.560138e+00
   4_adp:  0.1336 0.1820   5.300652e+00   5.518912e+00
   4_occ:  0.1335 0.1819   5.299844e+00   5.517922e+00
   5_bss:  0.1336 0.1816   5.299954e+00   5.516723e+00
   5_xyz:  0.1230 0.1704   5.232496e+00   5.462968e+00
   5_adp:  0.1209 0.1681   5.217390e+00   5.452326e+00
   5_occ:  0.1208 0.1679   5.216882e+00   5.452047e+00
   5_bss:  0.1208 0.1679   5.216860e+00   5.452098e+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:  0.341  50.000   8.058   6.980  10.005   0.000   0.000   0.000
   1_xyz:  0.341  50.000   8.058   6.980  10.005   0.000   0.000   0.000
   1_adp:  0.341  50.000   8.058   6.980  10.005   0.000   0.000   0.000
   1_occ:  0.341  50.000   8.058   6.980  10.005   0.000   0.000   0.000
   2_bss:  0.327  50.000   4.822   3.655   6.522   0.000   0.000   0.000
   2_xyz:  0.327  50.000   4.822   3.655   6.522   0.000   0.000   0.000
   2_adp:  0.327  50.000   4.822   3.655   6.522   0.000   0.000   0.000
   2_occ:  0.327  50.000   4.822   3.655   6.522   0.000   0.000   0.000
   3_bss:  0.315  57.684   2.568   1.795   4.133   0.000   0.000   0.000
   3_xyz:  0.315  57.684   2.568   1.795   4.133   0.000   0.000   0.000
   3_adp:  0.315  57.684   2.568   1.795   4.133   0.000   0.000   0.000
   3_occ:  0.315  57.684   2.568   1.795   4.133   0.000   0.000   0.000
   4_bss:  0.334  73.369   1.683   1.126   3.266   0.000   0.000   0.000
   4_xyz:  0.334  73.369   1.683   1.126   3.266   0.000   0.000   0.000
   4_adp:  0.334  73.369   1.683   1.126   3.266   0.000   0.000   0.000
   4_occ:  0.334  73.369   1.683   1.126   3.266   0.000   0.000   0.000
   5_bss:  0.327  65.563   1.299   0.826   2.818   0.000   0.000   0.000
   5_xyz:  0.327  65.563   1.299   0.826   2.818   0.000   0.000   0.000
   5_adp:  0.327  65.563   1.299   0.826   2.818   0.000   0.000   0.000
   5_occ:  0.327  65.563   1.299   0.826   2.818   0.000   0.000   0.000
   5_bss:  0.318  61.376  -0.326  -0.802   1.129   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  58.286 0.4157  0.4864    71766.128
   1_bss:  58.266 0.4153  0.6206    70973.903
   1_xyz:  49.716 0.5228  0.7562    53531.754
   1_adp:  46.858 0.5588  0.8699    50106.818
   1_occ:  46.962 0.5574  0.8665    50266.152
   2_bss:  46.749 0.5599  0.7762    49860.092
   2_xyz:  35.211 0.6975  0.9347    29538.712
   2_adp:  31.322 0.7428  0.9655    24400.748
   2_occ:  31.328 0.7427  0.9646    24337.862
   3_bss:  31.319 0.7429  0.8948    24441.148
   3_xyz:  22.733 0.8342  0.9770    13783.272
   3_adp:  21.011 0.8517  0.9850    12118.825
   3_occ:  21.001 0.8518  0.9848    12097.284
   4_bss:  20.960 0.8522  0.9575    12066.175
   4_xyz:  17.956 0.8805  0.9717     9184.349
   4_adp:  16.913 0.8905  0.9747     8521.610
   4_occ:  16.893 0.8907  0.9745     8492.101
   5_bss:  16.880 0.8907  0.9617     8465.508
   5_xyz:  15.585 0.9021  0.9681     7494.143
   5_adp:  15.304 0.9046  0.9663     7320.430
   5_occ:  15.296 0.9047  0.9663     7311.292
   5_bss:  15.298 0.9047  0.9655     7311.050
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.4359e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.4359e+01
   1_xyz:   1.761  0.014  0.112 18.340  0.007  4.110   1.5164e-01
   1_adp:   1.761  0.014  0.112 18.340  0.007  4.110   1.5164e-01
   1_occ:   1.761  0.014  0.112 18.340  0.007  4.110   1.5164e-01
   2_bss:   1.761  0.014  0.112 18.340  0.007  4.110   1.5164e-01
   2_xyz:   1.265  0.010  0.087 16.646  0.005  4.110   1.0165e-01
   2_adp:   1.265  0.010  0.087 16.646  0.005  4.110   1.0165e-01
   2_occ:   1.265  0.010  0.087 16.646  0.005  4.110   1.0165e-01
   3_bss:   1.265  0.010  0.087 16.646  0.005  4.110   1.0165e-01
   3_xyz:   1.116  0.008  0.083 16.005  0.004  4.132   7.2539e-02
   3_adp:   1.116  0.008  0.083 16.005  0.004  4.132   7.2539e-02
   3_occ:   1.116  0.008  0.083 16.005  0.004  4.132   7.2539e-02
   4_bss:   1.116  0.008  0.083 16.005  0.004  4.132   7.2539e-02
   4_xyz:   1.090  0.009  0.083 15.716  0.004  4.117   7.4233e-02
   4_adp:   1.090  0.009  0.083 15.716  0.004  4.117   7.4233e-02
   4_occ:   1.090  0.009  0.083 15.716  0.004  4.117   7.4233e-02
   5_bss:   1.090  0.009  0.083 15.716  0.004  4.117   7.4233e-02
   5_xyz:   1.172  0.011  0.090 15.697  0.004  4.125   8.2353e-02
   5_adp:   1.172  0.011  0.090 15.697  0.004  4.125   8.2353e-02
   5_occ:   1.172  0.011  0.090 15.697  0.004  4.125   8.2353e-02
   5_bss:   1.172  0.011  0.090 15.697  0.004  4.125   8.2353e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0481e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0481e+00
   1_xyz:  14.748  0.179  0.454 85.623  0.040  2.234   1.1003e-01
   1_adp:  14.748  0.179  0.454 85.623  0.040  2.234   1.1003e-01
   1_occ:  14.748  0.179  0.454 85.623  0.040  2.234   1.1003e-01
   2_bss:  14.748  0.179  0.454 85.623  0.040  2.234   1.1003e-01
   2_xyz:   6.718  0.093  0.300 84.471  0.045  2.142   1.9626e-01
   2_adp:   6.718  0.093  0.300 84.471  0.045  2.142   1.9626e-01
   2_occ:   6.718  0.093  0.300 84.471  0.045  2.142   1.9626e-01
   3_bss:   6.718  0.093  0.300 84.471  0.045  2.142   1.9626e-01
   3_xyz:   8.589  0.064  0.377 84.535  0.032  2.333   5.8529e-02
   3_adp:   8.589  0.064  0.377 84.535  0.032  2.333   5.8529e-02
   3_occ:   8.589  0.064  0.377 84.535  0.032  2.333   5.8529e-02
   4_bss:   8.589  0.064  0.377 84.535  0.032  2.333   5.8529e-02
   4_xyz:   8.474  0.070  0.425 82.044  0.039  2.354   7.6083e-02
   4_adp:   8.474  0.070  0.425 82.044  0.039  2.354   7.6083e-02
   4_occ:   8.474  0.070  0.425 82.044  0.039  2.354   7.6083e-02
   5_bss:   8.474  0.070  0.425 82.044  0.039  2.354   7.6083e-02
   5_xyz:  10.267  0.075  0.561 84.277  0.039  2.303   5.3278e-02
   5_adp:  10.267  0.075  0.561 84.277  0.039  2.303   5.3278e-02
   5_occ:  10.267  0.075  0.561 84.277  0.039  2.303   5.3278e-02
   5_bss:  10.267  0.075  0.561 84.277  0.039  2.303   5.3278e-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:  88.27   0.00  15.22  75.41   0.00  12.58  88.27   0.00  29.58
   1_occ:  88.27   0.00  15.22  75.41   0.00  12.58  88.27   0.00  29.58
   2_bss:  88.27   0.00  15.22  75.41   0.00  12.58  88.27   0.00  29.58
   2_xyz:  88.27   0.00  15.22  75.41   0.00  12.58  88.27   0.00  29.58
   2_adp:  87.19   0.00  13.96  75.12   0.00  10.22  87.19   0.00  34.34
   2_occ:  87.19   0.00  13.96  75.12   0.00  10.22  87.19   0.00  34.34
   3_bss:  87.19   0.00  13.96  75.12   0.00  10.22  87.19   0.00  34.34
   3_xyz:  87.19   0.00  13.96  75.12   0.00  10.22  87.19   0.00  34.34
   3_adp:  91.69   0.00  14.76  77.64   0.00   9.99  91.69   1.62  40.72
   3_occ:  91.69   0.00  14.76  77.64   0.00   9.99  91.69   1.62  40.72
   4_bss:  91.69   0.00  14.76  77.64   0.00   9.99  91.69   1.62  40.72
   4_xyz:  91.69   0.00  14.76  77.64   0.00   9.99  91.69   1.62  40.72
   4_adp:  88.56   0.00  14.05  76.22   0.00   9.59  88.56   2.73  38.33
   4_occ:  88.56   0.00  14.05  76.22   0.00   9.59  88.56   2.73  38.33
   5_bss:  88.56   0.00  14.05  76.22   0.00   9.59  88.56   2.73  38.33
   5_xyz:  88.56   0.00  14.05  76.22   0.00   9.59  88.56   2.73  38.33
   5_adp:  90.82   0.00  13.82  78.14   0.00   9.47  90.82   2.89  37.55
   5_occ:  90.82   0.00  13.82  78.14   0.00   9.47  90.82   2.89  37.55
   5_bss:  92.45   1.63  15.45  79.76   1.63  11.09  92.45   4.52  39.18
------------------------------------------------------------------------
 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:    1.253    0.014    0.415
   1_adp:    1.253    0.014    0.415
   1_occ:    1.253    0.014    0.415
   2_bss:    1.253    0.014    0.415
   2_xyz:    1.707    0.069    0.609
   2_adp:    1.707    0.069    0.609
   2_occ:    1.707    0.069    0.609
   3_bss:    1.707    0.069    0.609
   3_xyz:    1.599    0.026    0.685
   3_adp:    1.599    0.026    0.685
   3_occ:    1.599    0.026    0.685
   4_bss:    1.599    0.026    0.685
   4_xyz:    1.713    0.025    0.734
   4_adp:    1.713    0.025    0.734
   4_occ:    1.713    0.025    0.734
   5_bss:    1.713    0.025    0.734
   5_xyz:    1.831    0.041    0.758
   5_adp:    1.831    0.041    0.758
   5_occ:    1.831    0.041    0.758
   5_bss:    1.831    0.041    0.758
------------------------------------------------------------------------

CPU time actual refinement: 344.65


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1131/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_1131/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1131/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1131/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1131/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 344.50 
  Macro-tasks:
    bulk solvent and scale       = 34.64  
    individual site refinement   = 147.21 
    weights calculation          = 31.86  
    collect and process          = 6.42   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 220.24 
  Micro-tasks:
    mask                            = 2.47   
    f_calc                          = 111.86 
    alpha_beta                      = 8.26   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 121.67 
    fmodel                         = 6.16   
    r_factors                      = 0.16   
    phase_errors                   = 10.47  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 262.47 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.839 micro seconds
Total CPU time: 5.97 minutes
from_scatterers_fft:    653 calls, 111.45 s
gradients_fft:          598 calls, 108.11 s

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

# Date 2008-01-16 Time 03:15:48 PST -0800 (1200482148.02 s)
Start R-work = 0.4934, R-free = 0.4804 (no bulk solvent and anisotropic scale)
Final R-work = 0.1378, R-free = 0.1855 (no bulk solvent and anisotropic scale)

Start R-work = 0.4855, R-free = 0.4724
Final R-work = 0.1208, R-free = 0.1679