# Date 2008-01-16 Time 01:15:28 PST -0800 (1200474928.21 s)
#phil __OFF__

Command line arguments: "../342.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 24688
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 342

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 47.8686, 84.6622, 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: 3.24, 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: (69.1963, 47.8686, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9307 1.96147
Completeness in resolution range: 0.945461
Completeness with d_max=infinity: 0.942595

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9307
                             d_min =   1.9615

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.8686, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9307 1.96147
Completeness in resolution range: 0.945461
Completeness with d_max=infinity: 0.942595

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9311 -  4.1975 [2178/2207]  1958   220  10.1%
  bin  2:  4.1975 -  3.3440 [2090/2113]  1882   208  10.0%
  bin  3:  3.3440 -  2.9249 [2056/2081]  1849   207  10.1%
  bin  4:  2.9249 -  2.6591 [2036/2053]  1840   196   9.6%
  bin  5:  2.6591 -  2.4694 [2029/2072]  1819   210  10.3%
  bin  6:  2.4694 -  2.3244 [2017/2045]  1827   190   9.4%
  bin  7:  2.3244 -  2.2084 [2009/2045]  1803   206  10.3%
  bin  8:  2.2084 -  2.1125 [1991/2033]  1790   201  10.1%
  bin  9:  2.1125 -  2.0314 [1979/2034]  1783   196   9.9%
  bin 10:  2.0314 -  1.9615 [1204/2036]  1079   125  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_342/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:
        1.45 -     2.14: 25
        2.14 -     2.83: 991
        2.83 -     3.52: 4445
        3.52 -     4.21: 9386
        4.21 -     4.90: 13750
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.451 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.538 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.556 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.594 3.040 -x+1,y+1/2,-z+1/2
  " OG  SER A  95 " - " O   SER A 271 "  1.643 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28592 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_342/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_342/model_refine_001.geo

CPU time processing inputs: 9.06


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 47.8686 84.6622 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: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5096   r_free= 0.5023   ksol= 0.00   Bsol= 0.00   scale= 0.778    |
|                                                                             |
| 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:   0.90 A                  |
| x-ray target function (ml) for work reflections: 6.304470                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9311 -  4.6819 0.99   1408  158 0.4225 0.4256      6.6372      6.6595|
|  2:  4.6819 -  3.7353 0.99   1363  150 0.4489 0.4333      6.8549      6.8698|
|  3:  3.7353 -  3.2688 0.99   1329  149 0.4769 0.4509      6.7188      6.7481|
|  4:  3.2688 -  2.9725 0.99   1333  142 0.4885 0.4674      6.5419      6.5229|
|  5:  2.9725 -  2.7609 0.99   1307  147 0.5446 0.5446      6.3979      6.3866|
|  6:  2.7609 -  2.5990 0.99   1308  147 0.5338 0.5522      6.2938         6.2|
|  7:  2.5990 -  2.4694 0.98   1300  148 0.5436 0.4894      6.2676      6.1969|
|  8:  2.4694 -  2.3624 0.98   1302  136 0.5429 0.5337      6.1878      6.2063|
|  9:  2.3624 -  2.2718 0.99   1294  147 0.5596 0.5772      6.1356      6.1747|
| 10:  2.2718 -  2.1936 0.98   1289  141 0.5532 0.5781      6.1211      6.1393|
| 11:  2.1936 -  2.1252 0.97   1272  148 0.5540 0.5407       6.043      6.0145|
| 12:  2.1252 -  2.0646 0.98   1276  142 0.5428 0.5475        5.97       6.002|
| 13:  2.0646 -  2.0104 0.93   1224  133 0.5534 0.5680      5.8841      5.8787|
| 14:  2.0104 -  1.9615 0.48    625   71 0.5749 0.4479      5.8797      5.7197|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9311 -  4.6819  1408   158  0.62  41.12   0.79     0.65      95413.08|
|  2:  4.6819 -  3.7353  1363   150  0.63  41.08   0.86     0.70     133620.83|
|  3:  3.7353 -  3.2688  1329   149  0.52  49.94   0.82     0.65     139259.83|
|  4:  3.2688 -  2.9725  1333   142  0.44  56.56   0.79     0.54     116746.31|
|  5:  2.9725 -  2.7609  1307   147  0.33  65.12   0.71     0.42      95753.79|
|  6:  2.7609 -  2.5990  1308   147  0.31  66.83   0.71     0.36      78872.15|
|  7:  2.5990 -  2.4694  1300   148  0.29  68.30   0.71     0.33      71402.94|
|  8:  2.4694 -  2.3624  1302   136  0.28  68.72   0.72     0.34      64594.01|
|  9:  2.3624 -  2.2718  1294   147  0.23  72.61   0.71     0.30      63045.38|
| 10:  2.2718 -  2.1936  1289   141  0.19  75.48   0.74     0.24      58792.72|
| 11:  2.1936 -  2.1252  1272   148  0.14  79.92   0.75     0.18      56023.62|
| 12:  2.1252 -  2.0646  1276   142  0.15  78.75   0.73     0.20      50899.86|
| 13:  2.0646 -  2.0104  1224   133  0.21  74.70   0.74     0.27      41010.03|
| 14:  2.0104 -  1.9615   625    71  0.36  62.82   0.69     0.41      28296.47|
|alpha:            min =        0.18 max =            0.70 mean =         0.40|
|beta:             min =    28296.47 max =       139259.83 mean =     80763.61|
|figures of merit: min =        0.00 max =            1.00 mean =         0.34|
|phase err.(work): min =        0.00 max =           90.00 mean =        64.13|
|phase err.(test): min =        0.00 max =           89.92 mean =        64.34|
|-----------------------------------------------------------------------------|

============================== 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 = 21.478196             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.007   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.047304              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 84.617   (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 |  0.869 -  1.272:        6 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.272 -  1.675:        4 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.675 -  2.078:       62 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.078 -  2.481:      408 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.481 -  2.884:     1176 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.884 -  3.287:     2387 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.287 -  3.691:     3901 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.691 -  4.094:     5279 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.094 -  4.497:     6982 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.497 -  4.900:     8434 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.301 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.088    4.900  0.869 |       2.505 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.645)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

                ----------Modify initial isotropic ADP----------               

Randomizing
|-ADP statistics (Wilson B = 11.645)------------------------------------------|
|    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: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5138   r_free= 0.5055   ksol= 0.00   Bsol= 0.00   scale= 0.749    |
|                                                                             |
| 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:   0.91 A                  |
| x-ray target function (ml) for work reflections: 6.304456                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5030   r_free= 0.4932   ksol= 0.36   Bsol= 20.00   scale= 0.964   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.42,10.47,7.64,0.00,0.00,0.00); trace/3= 8.18                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.90 A                  |
| x-ray target function (ml) for work reflections: 6.300117                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 18.499577             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.629   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.813237              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 82.032   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5030      final r-factor (work) = 0.4446          |
| start r-factor (free) = 0.4932      final r-factor (free) = 0.4594          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 111.5964 = 18.50 * 0.50 * 6.3024 + 1.00 * 53.3006                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 57.9653 = 18.50 * 0.50 * 6.2492 + 1.00 * 0.1615                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4446      final r-factor (work) = 0.4072          |
| start r-factor (free) = 0.4594      final r-factor (free) = 0.4539          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.3460 = 1.81 * 1.00 * 6.2492 + 1.00 * 0.0147                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.2763 = 1.81 * 1.00 * 6.2069 + 1.00 * 0.0218                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 36     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.645)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.56   16.24    None  None   None       |
|    all(noH): 2823   0      0.00    99.56   16.24    None  None   None       |
|    Sol.    : 438    0      0.00    99.56   25.60    None  None   None       |
|    Mac.    : 2385   0      0.00    82.79   14.52    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 -   9.956: 1090   |   5:    49.781 -  59.737:   48        |
|      1:     9.956 -  19.912:  871   |   6:    59.737 -  69.693:   14        |
|      2:    19.912 -  29.868:  443   |   7:    69.693 -  79.649:   11        |
|      3:    29.868 -  39.825:  249   |   8:    79.649 -  89.605:    5        |
|      4:    39.825 -  49.781:   91   |   9:    89.605 -  99.561:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4072 r_free = 0.4539             target_work(ml) = 6.197         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4064 r_free = 0.4523             target_work(ml) = 6.196         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4064   r_free= 0.4523   ksol= 0.36   Bsol= 20.00   scale= 1.112   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.42,10.47,7.64,0.00,0.00,0.00); trace/3= 8.18                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.195611                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4052   r_free= 0.4476   ksol= 0.30   Bsol= 20.00   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.08,6.47,4.86,0.00,0.00,0.00); trace/3= 4.80                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.196656                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.002115             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.337  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.772582              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.064  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4052      final r-factor (work) = 0.3398          |
| start r-factor (free) = 0.4476      final r-factor (free) = 0.3975          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.3864 = 12.00 * 0.50 * 6.2032 + 1.00 * 0.1605                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.8894 = 12.00 * 0.50 * 6.1300 + 1.00 * 0.1032                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3398      final r-factor (work) = 0.3187          |
| start r-factor (free) = 0.3975      final r-factor (free) = 0.3846          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7573 = 0.77 * 1.00 * 6.1300 + 1.00 * 0.0214                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6929 = 0.77 * 1.00 * 6.0489 + 1.00 * 0.0196                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.645)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.53  16.11    None  None   None       |
|    all(noH): 2823   0      0.00    104.53  16.11    None  None   None       |
|    Sol.    : 438    0      0.00    104.53  29.70    None  None   None       |
|    Mac.    : 2385   0      0.00    91.63   13.61    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 -  10.453: 1200   |   5:    52.265 -  62.718:   32        |
|      1:    10.453 -  20.906:  825   |   6:    62.718 -  73.171:   14        |
|      2:    20.906 -  31.359:  453   |   7:    73.171 -  83.624:    5        |
|      3:    31.359 -  41.812:  204   |   8:    83.624 -  94.078:    3        |
|      4:    41.812 -  52.265:   86   |   9:    94.078 - 104.531:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3187 r_free = 0.3846             target_work(ml) = 6.032         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3186 r_free = 0.3844             target_work(ml) = 6.031         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3186   r_free= 0.3844   ksol= 0.30   Bsol= 20.00   scale= 1.079   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.08,6.47,4.86,0.00,0.00,0.00); trace/3= 4.80                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.031491                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3164   r_free= 0.3811   ksol= 0.32   Bsol= 43.21   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.12,3.68,2.57,0.00,0.00,0.00); trace/3= 2.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.029629                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.184796              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.346  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.399338              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 112.026  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3164      final r-factor (work) = 0.2490          |
| start r-factor (free) = 0.3811      final r-factor (free) = 0.3109          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.8342 = 7.18 * 0.50 * 6.0492 + 1.00 * 0.1032                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.4294 = 7.18 * 0.50 * 5.9402 + 1.00 * 0.0897                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2490      final r-factor (work) = 0.2252          |
| start r-factor (free) = 0.3109      final r-factor (free) = 0.2837          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3910 = 0.40 * 1.00 * 5.9402 + 1.00 * 0.0188                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3236 = 0.40 * 1.00 * 5.7938 + 1.00 * 0.0099                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.645)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.14   15.26    None  None   None       |
|    all(noH): 2823   0      0.00    98.14   15.26    None  None   None       |
|    Sol.    : 438    0      3.58    98.14   34.76    None  None   None       |
|    Mac.    : 2385   0      0.00    76.45   11.68    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 -   9.814: 1326   |   5:    49.068 -  58.881:   72        |
|      1:     9.814 -  19.627:  802   |   6:    58.881 -  68.695:   19        |
|      2:    19.627 -  29.441:  299   |   7:    68.695 -  78.508:    5        |
|      3:    29.441 -  39.254:  184   |   8:    78.508 -  88.322:    4        |
|      4:    39.254 -  49.068:  111   |   9:    88.322 -  98.135:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2252 r_free = 0.2837             target_work(ml) = 5.754         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2247 r_free = 0.2830             target_work(ml) = 5.753         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2247   r_free= 0.2830   ksol= 0.32   Bsol= 43.21   scale= 1.045   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.12,3.68,2.57,0.00,0.00,0.00); trace/3= 2.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.752707                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2239   r_free= 0.2812   ksol= 0.32   Bsol= 40.06   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.10,2.23,1.28,0.00,0.00,0.00); trace/3= 1.14                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.750604                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.545147              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.720   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.460442              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.739  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2239      final r-factor (work) = 0.1667          |
| start r-factor (free) = 0.2812      final r-factor (free) = 0.2132          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.2604 = 4.55 * 0.50 * 5.7955 + 1.00 * 0.0897                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.8799 = 4.55 * 0.50 * 5.6346 + 1.00 * 0.0749                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1667      final r-factor (work) = 0.1514          |
| start r-factor (free) = 0.2132      final r-factor (free) = 0.1988          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6044 = 0.46 * 1.00 * 5.6346 + 1.00 * 0.0100                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5119 = 0.46 * 1.00 * 5.4320 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.645)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.64   15.57    None  None   None       |
|    all(noH): 2823   0      0.00    86.64   15.57    None  None   None       |
|    Sol.    : 438    0      3.77    86.21   39.88    None  None   None       |
|    Mac.    : 2385   0      0.00    86.64   11.10    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 -   8.664: 1202   |   5:    43.319 -  51.982:   88        |
|      1:     8.664 -  17.328:  912   |   6:    51.982 -  60.646:   88        |
|      2:    17.328 -  25.991:  250   |   7:    60.646 -  69.310:   28        |
|      3:    25.991 -  34.655:  108   |   8:    69.310 -  77.974:   18        |
|      4:    34.655 -  43.319:  121   |   9:    77.974 -  86.637:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1514 r_free = 0.1988             target_work(ml) = 5.395         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1512 r_free = 0.1987             target_work(ml) = 5.394         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1512   r_free= 0.1987   ksol= 0.32   Bsol= 40.06   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.10,2.23,1.28,0.00,0.00,0.00); trace/3= 1.14                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.394459                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1512   r_free= 0.1989   ksol= 0.32   Bsol= 46.19   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.70,1.15,0.64,0.00,0.00,0.00); trace/3= 0.36                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.396929                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.924674              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.308   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.650815              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.583  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1512      final r-factor (work) = 0.1274          |
| start r-factor (free) = 0.1989      final r-factor (free) = 0.1756          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.7448 = 3.92 * 0.50 * 5.4374 + 1.00 * 0.0749                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.5258 = 3.92 * 0.50 * 5.3259 + 1.00 * 0.0746                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1274      final r-factor (work) = 0.1229          |
| start r-factor (free) = 0.1756      final r-factor (free) = 0.1717          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4770 = 0.65 * 1.00 * 5.3259 + 1.00 * 0.0108                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4228 = 0.65 * 1.00 * 5.2417 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.645)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.60   15.57    None  None   None       |
|    all(noH): 2823   0      0.00    94.60   15.57    None  None   None       |
|    Sol.    : 438    0      3.80    84.42   41.13    None  None   None       |
|    Mac.    : 2385   0      0.00    94.60   10.88    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 -   9.460: 1386   |   5:    47.299 -  56.758:   89        |
|      1:     9.460 -  18.920:  828   |   6:    56.758 -  66.218:   66        |
|      2:    18.920 -  28.379:  190   |   7:    66.218 -  75.678:   35        |
|      3:    28.379 -  37.839:  109   |   8:    75.678 -  85.138:   11        |
|      4:    37.839 -  47.299:  104   |   9:    85.138 -  94.597:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1229 r_free = 0.1717             target_work(ml) = 5.230         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1228 r_free = 0.1717             target_work(ml) = 5.229         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1228   r_free= 0.1717   ksol= 0.32   Bsol= 46.19   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.70,1.15,0.64,0.00,0.00,0.00); trace/3= 0.36                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.229324                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9311 -  4.6819 0.99   1408  158 0.0975 0.1292        5.39      5.5477|
|  2:  4.6819 -  3.7353 0.99   1363  150 0.0893 0.1130      5.4812      5.7013|
|  3:  3.7353 -  3.2688 0.99   1329  149 0.1137 0.1724      5.5527      5.9251|
|  4:  3.2688 -  2.9725 0.99   1333  142 0.1375 0.1714      5.5306      5.7441|
|  5:  2.9725 -  2.7609 0.99   1307  147 0.1467 0.1722      5.4131      5.5291|
|  6:  2.7609 -  2.5990 0.99   1308  147 0.1420 0.2319       5.326      5.6228|
|  7:  2.5990 -  2.4694 0.98   1300  148 0.1377 0.1726      5.2549        5.43|
|  8:  2.4694 -  2.3624 0.98   1302  136 0.1292 0.1723      5.1492      5.3549|
|  9:  2.3624 -  2.2718 0.99   1294  147 0.1318 0.1887      5.1053      5.3751|
| 10:  2.2718 -  2.1936 0.98   1289  141 0.1289 0.2088      5.0785      5.3845|
| 11:  2.1936 -  2.1252 0.97   1272  148 0.1285 0.1949      5.0249      5.2703|
| 12:  2.1252 -  2.0646 0.98   1276  142 0.1251 0.1884      4.9545      5.2108|
| 13:  2.0646 -  2.0104 0.93   1224  133 0.1272 0.1943      4.8697      5.1417|
| 14:  2.0104 -  1.9615 0.48    625   71 0.1152 0.1994      4.7646      5.0439|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9311 -  4.6819  1408   158  0.94   9.69   0.98     0.96       7846.90|
|  2:  4.6819 -  3.7353  1363   150  0.95   8.89   1.03     1.01      10264.15|
|  3:  3.7353 -  3.2688  1329   149  0.92  12.85   1.04     1.03      12566.26|
|  4:  3.2688 -  2.9725  1333   142  0.90  15.58   1.02     1.01      11928.51|
|  5:  2.9725 -  2.7609  1307   147  0.88  17.99   1.01     0.98      10016.01|
|  6:  2.7609 -  2.5990  1308   147  0.88  18.30   0.99     0.95       8726.50|
|  7:  2.5990 -  2.4694  1300   148  0.89  17.57   0.99     0.95       7424.41|
|  8:  2.4694 -  2.3624  1302   136  0.89  17.08   1.01     0.99       6451.51|
|  9:  2.3624 -  2.2718  1294   147  0.89  17.82   1.01     0.99       5949.80|
| 10:  2.2718 -  2.1936  1289   141  0.89  17.61   1.00     0.97       5642.76|
| 11:  2.1936 -  2.1252  1272   148  0.88  18.65   1.01     0.96       5286.16|
| 12:  2.1252 -  2.0646  1276   142  0.90  17.18   1.01     0.99       4623.76|
| 13:  2.0646 -  2.0104  1224   133  0.88  18.05   1.01     1.00       3957.60|
| 14:  2.0104 -  1.9615   625    71  0.89  17.39   0.99     0.95       3213.42|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     3213.42 max =        12566.26 mean =      7637.29|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.90 mean =        15.91|
|phase err.(test): min =        0.00 max =           88.43 mean =        15.33|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1232   r_free= 0.1720   ksol= 0.32   Bsol= 46.44   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.95,0.65,0.30,0.00,0.00,0.00); trace/3= -0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.232494                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1232   r_free= 0.1720   ksol= 0.32   Bsol= 46.44   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.95,0.65,0.30,0.00,0.00,0.00); trace/3= -0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.232494                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9311 -  4.6819 0.99   1408  158 0.0987 0.1315      5.4067      5.5709|
|  2:  4.6819 -  3.7353 0.99   1363  150 0.0906 0.1141      5.4966      5.7202|
|  3:  3.7353 -  3.2688 0.99   1329  149 0.1144 0.1738      5.5607      5.9269|
|  4:  3.2688 -  2.9725 0.99   1333  142 0.1381 0.1710      5.5325      5.7434|
|  5:  2.9725 -  2.7609 0.99   1307  147 0.1470 0.1722      5.4145      5.5297|
|  6:  2.7609 -  2.5990 0.99   1308  147 0.1416 0.2324       5.326      5.6241|
|  7:  2.5990 -  2.4694 0.98   1300  148 0.1377 0.1732      5.2549      5.4312|
|  8:  2.4694 -  2.3624 0.98   1302  136 0.1288 0.1721       5.149      5.3563|
|  9:  2.3624 -  2.2718 0.99   1294  147 0.1313 0.1891      5.1044       5.376|
| 10:  2.2718 -  2.1936 0.98   1289  141 0.1287 0.2091      5.0775      5.3853|
| 11:  2.1936 -  2.1252 0.97   1272  148 0.1284 0.1948      5.0243       5.269|
| 12:  2.1252 -  2.0646 0.98   1276  142 0.1251 0.1884      4.9544      5.2113|
| 13:  2.0646 -  2.0104 0.93   1224  133 0.1271 0.1939      4.8698       5.141|
| 14:  2.0104 -  1.9615 0.48    625   71 0.1151 0.1988      4.7638      5.0429|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9311 -  4.6819  1408   158  0.93  10.01   0.97     0.96       8236.23|
|  2:  4.6819 -  3.7353  1363   150  0.95   9.13   1.02     1.00      10652.44|
|  3:  3.7353 -  3.2688  1329   149  0.92  13.03   1.04     1.03      12862.05|
|  4:  3.2688 -  2.9725  1333   142  0.90  15.62   1.02     1.01      11958.89|
|  5:  2.9725 -  2.7609  1307   147  0.88  18.00   1.00     0.98      10029.78|
|  6:  2.7609 -  2.5990  1308   147  0.88  18.34   0.99     0.95       8758.29|
|  7:  2.5990 -  2.4694  1300   148  0.89  17.61   0.99     0.94       7451.75|
|  8:  2.4694 -  2.3624  1302   136  0.89  17.09   1.01     0.98       6459.40|
|  9:  2.3624 -  2.2718  1294   147  0.89  17.82   1.01     0.99       5952.74|
| 10:  2.2718 -  2.1936  1289   141  0.89  17.60   1.00     0.96       5632.15|
| 11:  2.1936 -  2.1252  1272   148  0.88  18.65   1.00     0.96       5287.32|
| 12:  2.1252 -  2.0646  1276   142  0.90  17.17   1.00     0.98       4624.97|
| 13:  2.0646 -  2.0104  1224   133  0.88  18.04   1.00     0.99       3955.21|
| 14:  2.0104 -  1.9615   625    71  0.89  17.36   0.99     0.94       3199.03|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     3199.03 max =        12862.05 mean =      7727.91|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.99 mean =        15.98|
|phase err.(test): min =        0.00 max =           89.81 mean =        15.38|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.645)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.25    94.84   15.82    None  None   None       |
|    all(noH): 2823   0      0.25    94.84   15.82    None  None   None       |
|    Sol.    : 438    0      4.04    84.67   41.37    None  None   None       |
|    Mac.    : 2385   0      0.25    94.84   11.13    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:     0.246 -   9.706: 1386   |   5:    47.544 -  57.004:   89        |
|      1:     9.706 -  19.165:  828   |   6:    57.004 -  66.464:   66        |
|      2:    19.165 -  28.625:  190   |   7:    66.464 -  75.924:   35        |
|      3:    28.625 -  38.085:  109   |   8:    75.924 -  85.383:   11        |
|      4:    38.085 -  47.544:  104   |   9:    85.383 -  94.843:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 337         
Filter by distance & map next to the model:
   mapped sites are within: 0.667 - 5.030
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 333 from: 337
   mapped sites are within: 0.749 - 5.030

peak=    8.963 closest distance to " CG2 VAL A 230 " =    1.381
peak=    8.415 closest distance to " O   HOH Z 135 " =    1.898
peak=    6.863 closest distance to " O   HOH Z 138 " =    1.086
peak=    6.837 closest distance to " CG2 VAL A 296 " =    1.175
peak=    6.808 closest distance to " CD1AILE A 234 " =    1.327
peak=    6.099 closest distance to " CG  LEU A   5 " =    1.371
peak=    5.968 closest distance to " O   HOH Z 247 " =    1.529
peak=    5.679 closest distance to " O   HOH Z 278 " =    1.795
peak=    5.593 closest distance to " O   HOH Z  46 " =    1.115
peak=    5.527 closest distance to " O   HOH Z 402 " =    1.657
peak=    5.524 closest distance to " O   HOH Z 316 " =    1.160
peak=    5.459 closest distance to " O   HOH Z 279 " =    1.273
peak=    5.341 closest distance to " O   HOH Z 210 " =    1.256
peak=    5.295 closest distance to " O   HOH Z 193 " =    1.769
peak=    5.118 closest distance to " O   HOH Z 403 " =    2.095
peak=    5.087 closest distance to " NH2 ARG A  56 " =    2.233
peak=    5.060 closest distance to " O   HOH Z 272 " =    2.018
peak=    5.033 closest distance to " O   HOH Z 124 " =    1.767
peak=    5.029 closest distance to " O   HOH Z 389 " =    2.056
peak=    4.997 closest distance to " O   HOH Z  49 " =    1.325
peak=    4.905 closest distance to " O   HOH Z 236 " =    1.515
peak=    4.897 closest distance to " O   HOH Z 199 " =    1.171
peak=    4.844 closest distance to " O   HOH Z 411 " =    3.439
peak=    4.803 closest distance to " O   HOH Z 142 " =    1.617
peak=    4.792 closest distance to " O   HOH Z  48 " =    1.589
peak=    4.736 closest distance to " O   HOH Z  80 " =    2.133
peak=    4.734 closest distance to " O   HOH Z  69 " =    1.233
peak=    4.697 closest distance to " O   HOH Z  11 " =    1.270
peak=    4.691 closest distance to " CG  PRO A  54 " =    1.142
peak=    4.668 closest distance to " O   HOH Z  40 " =    1.995
peak=    4.596 closest distance to " O   HOH Z 128 " =    1.567
peak=    4.591 closest distance to " CB  VAL A 296 " =    1.049
peak=    4.558 closest distance to " O   GLY A  91 " =    1.346
peak=    4.547 closest distance to " CA  TYR A  30 " =    0.993
peak=    4.495 closest distance to " CB  GLN A 223 " =    1.383
peak=    4.492 closest distance to " O   HOH Z  43 " =    1.668
peak=    4.475 closest distance to " O   HOH Z  68 " =    2.014
peak=    4.424 closest distance to " O   HOH Z  47 " =    1.566
peak=    4.423 closest distance to " O   HOH Z 156 " =    3.045
peak=    4.422 closest distance to " O   SER A  87 " =    2.310
peak=    4.413 closest distance to " O   HOH Z 316 " =    2.093
peak=    4.407 closest distance to " O   HOH Z 234 " =    3.581
peak=    4.393 closest distance to " O   PRO A 198 " =    1.496
peak=    4.382 closest distance to " O   HOH Z 155 " =    1.804
peak=    4.375 closest distance to " O   HOH Z 134 " =    2.268
peak=    4.371 closest distance to " CG  ARG A  66 " =    1.160
peak=    4.364 closest distance to " O   HOH Z 357 " =    2.236
peak=    4.355 closest distance to " CG  PRO A 213 " =    1.239
peak=    4.345 closest distance to " CG AARG A 275 " =    1.302
peak=    4.339 closest distance to " CB  VAL A 230 " =    1.212
peak=    4.337 closest distance to " O   HOH Z 433 " =    1.580
peak=    4.334 closest distance to " O   HOH Z 154 " =    1.696
peak=    4.329 closest distance to " O   HOH Z 108 " =    1.058
peak=    4.311 closest distance to " OE1 GLU A   2 " =    1.907
peak=    4.279 closest distance to " O   HOH Z 232 " =    2.281
peak=    4.265 closest distance to " CB  ARG A 275 " =    0.917
peak=    4.259 closest distance to " O   HOH Z  48 " =    1.737
peak=    4.226 closest distance to " CB  SER A  63 " =    1.150
peak=    4.223 closest distance to " O   HOH Z 261 " =    2.076
peak=    4.223 closest distance to " O   HOH Z 263 " =    1.555
peak=    4.221 closest distance to " O   HOH Z 403 " =    1.492
peak=    4.220 closest distance to " O   HOH Z 334 " =    1.745
peak=    4.213 closest distance to " CB  ALA A 100 " =    1.271
peak=    4.211 closest distance to " CD  ARG A 269 " =    1.123
peak=    4.210 closest distance to " CD2 LEU A 228 " =    1.234
peak=    4.170 closest distance to " OE1 GLN A  11 " =    1.895
peak=    4.155 closest distance to " O   HOH Z 249 " =    1.114
peak=    4.146 closest distance to " CA  VAL A  41 " =    0.908
peak=    4.110 closest distance to " CD2 LEU A   5 " =    1.161
peak=    4.089 closest distance to " O   HOH Z 346 " =    1.489
peak=    4.085 closest distance to " CG  GLN A  77 " =    0.846
peak=    4.066 closest distance to " O   HOH Z 126 " =    1.475
peak=    4.066 closest distance to " O   HOH Z 146 " =    1.286
peak=    4.063 closest distance to " CB  ASN A 187 " =    1.655
peak=    4.044 closest distance to " O   HOH Z  15 " =    2.405
peak=    4.035 closest distance to " O   HOH Z 126 " =    2.505
peak=    4.030 closest distance to " O   HOH Z 394 " =    1.711
peak=    4.014 closest distance to " O   HOH Z 265 " =    2.370
peak=    4.012 closest distance to " O   HOH Z 414 " =    2.416
peak=    4.002 closest distance to " CA  ALA A  21 " =    1.322
peak=    3.992 closest distance to " CB  TRP A 179 " =    1.149
peak=    3.985 closest distance to " O   HOH Z 136 " =    1.257
peak=    3.972 closest distance to " CG  LEU A 228 " =    1.276
peak=    3.971 closest distance to " O   HOH Z 423 " =    1.965
peak=    3.971 closest distance to " O   HOH Z 163 " =    1.529
peak=    3.936 closest distance to " O   HOH Z 132 " =    1.211
peak=    3.929 closest distance to " CG  PRO A 198 " =    1.246
peak=    3.925 closest distance to " O   HOH Z 189 " =    2.629
peak=    3.923 closest distance to " CB  ALA A 256 " =    1.004
peak=    3.914 closest distance to " CE  LYS A 119 " =    1.169
peak=    3.908 closest distance to " O   HOH Z   4 " =    1.453
peak=    3.901 closest distance to " O   HOH Z 130 " =    2.596
peak=    3.900 closest distance to " O   HOH Z 209 " =    1.100
peak=    3.897 closest distance to " CG1 ILE A  33 " =    1.283
peak=    3.893 closest distance to " O   HOH Z 209 " =    2.391
peak=    3.882 closest distance to " CG1BVAL A  72 " =    1.693
peak=    3.850 closest distance to " CD2 TRP A 179 " =    1.428
peak=    3.848 closest distance to " O   HOH Z 431 " =    1.433
peak=    3.836 closest distance to " CD  PRO A  54 " =    1.029
peak=    3.826 closest distance to " O   HOH Z 154 " =    2.235
peak=    3.819 closest distance to " CE1 HIS A 108 " =    1.128
peak=    3.810 closest distance to " O   HOH Z 214 " =    1.238
peak=    3.807 closest distance to " CB  GLN A 183 " =    1.289
peak=    3.805 closest distance to " O   HOH Z 303 " =    2.284
peak=    3.804 closest distance to " O   HOH Z 406 " =    1.612
peak=    3.801 closest distance to " O   HOH Z 245 " =    1.327
peak=    3.799 closest distance to " O   HOH Z 273 " =    2.671
peak=    3.794 closest distance to " CG2 VAL A 296 " =    1.691
peak=    3.788 closest distance to " O   HOH Z  85 " =    1.706
peak=    3.787 closest distance to " O   HOH Z 112 " =    1.654
peak=    3.782 closest distance to " CB  PRO A  54 " =    0.763
peak=    3.777 closest distance to " O   HOH Z 344 " =    1.800
peak=    3.774 closest distance to " NZ  LYS A 117 " =    2.980
peak=    3.773 closest distance to " ND1 HIS A  81 " =    1.320
peak=    3.767 closest distance to " O   HOH Z 248 " =    1.787
peak=    3.753 closest distance to " O   HOH Z 408 " =    1.650
peak=    3.748 closest distance to " O   HOH Z 425 " =    1.442
peak=    3.739 closest distance to " O   HOH Z 188 " =    0.977
peak=    3.732 closest distance to " O   HOH Z 102 " =    1.405
peak=    3.725 closest distance to " CD  LYS A 166 " =    1.533
peak=    3.723 closest distance to " NE2 GLN A  11 " =    0.982
peak=    3.723 closest distance to " O   HOH Z 128 " =    1.731
peak=    3.720 closest distance to " CG  PRO A 243 " =    1.111
peak=    3.719 closest distance to " CG2 THR A 220 " =    0.832
peak=    3.704 closest distance to " O   HOH Z 361 " =    2.894
peak=    3.699 closest distance to " CB  VAL A 202 " =    1.519
peak=    3.692 closest distance to " O   HOH Z 409 " =    3.385
peak=    3.692 closest distance to " O   HOH Z 426 " =    1.377
peak=    3.691 closest distance to " O   HOH Z 130 " =    1.225
peak=    3.684 closest distance to " CZ3 TRP A  92 " =    1.026
peak=    3.680 closest distance to " CB  VAL A 265 " =    1.243
peak=    3.674 closest distance to " O   HOH Z  66 " =    2.142
peak=    3.671 closest distance to " CB  GLU A 152 " =    1.061
peak=    3.660 closest distance to " CG2 THR A 221 " =    1.261
peak=    3.660 closest distance to " O   HOH Z 116 " =    2.394
peak=    3.659 closest distance to " OG BSER A 210 " =    1.299
peak=    3.656 closest distance to " CB  SER A   3 " =    1.375
peak=    3.656 closest distance to " NE  ARG A  14 " =    1.232
peak=    3.650 closest distance to " O   HOH Z 345 " =    2.451
peak=    3.629 closest distance to " CB  THR A  31 " =    1.478
peak=    3.629 closest distance to " O   HOH Z  78 " =    1.699
peak=    3.624 closest distance to " O   HOH Z  97 " =    1.632
peak=    3.619 closest distance to " O   HOH Z 196 " =    1.156
peak=    3.614 closest distance to " CA  ASP A 191 " =    1.064
peak=    3.613 closest distance to " CG  LYS A 166 " =    1.552
peak=    3.612 closest distance to " O   HOH Z 214 " =    2.492
peak=    3.610 closest distance to " O   HOH Z 225 " =    1.902
peak=    3.610 closest distance to " O   HOH Z 326 " =    1.421
peak=    3.608 closest distance to " O   HOH Z 162 " =    1.722
peak=    3.607 closest distance to " O   HOH Z 422 " =    0.912
peak=    3.607 closest distance to " CB  PRO A 198 " =    1.231
peak=    3.601 closest distance to " O   HOH Z 250 " =    1.399
peak=    3.599 closest distance to " CD  ARG A 159 " =    0.824
peak=    3.599 closest distance to " OD1 ASN A  60 " =    1.229
peak=    3.596 closest distance to " CA  ARG A 195 " =    1.195
peak=    3.590 closest distance to " O   HOH Z 327 " =    1.706
peak=    3.586 closest distance to " O   HOH Z  54 " =    1.535
peak=    3.586 closest distance to " O   HOH Z 197 " =    2.191
peak=    3.579 closest distance to " O   HOH Z  35 " =    2.116
peak=    3.576 closest distance to " O   HOH Z 395 " =    1.322
peak=    3.570 closest distance to " O   HOH Z 118 " =    1.154
peak=    3.570 closest distance to " CD  LYS A 119 " =    1.429
peak=    3.567 closest distance to " O   HOH Z  38 " =    1.731
peak=    3.566 closest distance to " CB  SER A  26 " =    1.769
peak=    3.561 closest distance to " CB  ASN A 148 " =    1.299
peak=    3.556 closest distance to " N   ASN A  39 " =    1.304
peak=    3.555 closest distance to " CE BMET A  47 " =    1.194
peak=    3.548 closest distance to " CB  GLN A  58 " =    1.070
peak=    3.547 closest distance to " O   HOH Z 404 " =    1.289
peak=    3.540 closest distance to " CB  SER A  62 " =    0.884
peak=    3.539 closest distance to " CD2 LEU A 255 " =    1.236
peak=    3.536 closest distance to " O   HOH Z 156 " =    2.074
peak=    3.533 closest distance to " O   HOH Z 345 " =    1.855
peak=    3.533 closest distance to " NH2BARG A 145 " =    2.116
peak=    3.529 closest distance to " O   HOH Z 191 " =    1.343
peak=    3.522 closest distance to " CB  ALA A  71 " =    1.159
peak=    3.521 closest distance to " O   HOH Z  48 " =    2.034
peak=    3.517 closest distance to " CB  SER A 141 " =    1.035
peak=    3.513 closest distance to " CB  SER A  62 " =    0.820
peak=    3.512 closest distance to " O   HOH Z 374 " =    2.490
peak=    3.509 closest distance to " O   HOH Z 301 " =    1.703
peak=    3.506 closest distance to " O   HOH Z 421 " =    1.923
peak=    3.502 closest distance to " CB BVAL A  41 " =    1.065
peak=    3.502 closest distance to " CG2 ILE A 120 " =    1.424
peak=    3.491 closest distance to " O   HOH Z 166 " =    1.582
peak=    3.490 closest distance to " CA  TYR A 214 " =    1.110
peak=    3.488 closest distance to " O   HOH Z  39 " =    1.242
peak=    3.485 closest distance to " O   HOH Z 203 " =    1.606
peak=    3.484 closest distance to " O   HOH Z 132 " =    2.371
peak=    3.484 closest distance to " O   HOH Z 227 " =    1.571
peak=    3.483 closest distance to " CB  GLU A 128 " =    1.202
peak=    3.470 closest distance to " CD2 TYR A 186 " =    1.061
peak=    3.468 closest distance to " O   HOH Z 368 " =    2.224
peak=    3.466 closest distance to " CG  MET A 185 " =    1.229
peak=    3.466 closest distance to " O   HOH Z 365 " =    2.948
peak=    3.464 closest distance to " O   HOH Z 412 " =    3.803
peak=    3.460 closest distance to " CB  ASN A 285 " =    0.956
peak=    3.454 closest distance to " O   HOH Z  85 " =    1.720
peak=    3.451 closest distance to " O   HOH Z  88 " =    3.963
peak=    3.444 closest distance to " CB  ASN A 187 " =    1.095
peak=    3.441 closest distance to " C   ILE A 106 " =    1.890
peak=    3.435 closest distance to " O   GLY A  23 " =    2.303
peak=    3.433 closest distance to " O   HOH Z  44 " =    2.142
peak=    3.430 closest distance to " CB  LEU A 228 " =    1.459
peak=    3.429 closest distance to " OH  TYR A  30 " =    1.158
peak=    3.422 closest distance to " O   HOH Z 284 " =    2.898
peak=    3.420 closest distance to " CD2 LEU A 297 " =    0.975
peak=    3.419 closest distance to " O   HOH Z 271 " =    1.192
peak=    3.419 closest distance to " O   HOH Z 114 " =    1.297
peak=    3.418 closest distance to " CB  ARG A 259 " =    1.902
peak=    3.417 closest distance to " CB  GLN A  73 " =    1.143
peak=    3.413 closest distance to " CG1BVAL A 121 " =    1.248
peak=    3.412 closest distance to " O   HOH Z 427 " =    3.011
peak=    3.410 closest distance to " CD  ARG A 195 " =    1.042
peak=    3.410 closest distance to " CG2 ILE A  20 " =    1.273
peak=    3.407 closest distance to " NH1 ARG A  14 " =    1.131
peak=    3.405 closest distance to " CB  ARG A  79 " =    0.997
peak=    3.401 closest distance to " O   HOH Z 291 " =    1.338
peak=    3.399 closest distance to " O   ALA A 158 " =    1.213
peak=    3.396 closest distance to " O   ASP A 124 " =    1.602
peak=    3.393 closest distance to " CA  ALA A 295 " =    1.105
peak=    3.389 closest distance to " OG BSER A 258 " =    3.020
peak=    3.387 closest distance to " O   HOH Z 241 " =    2.143
peak=    3.380 closest distance to " O   HOH Z 344 " =    2.700
peak=    3.373 closest distance to " OG1 THR A 294 " =    2.271
peak=    3.369 closest distance to " O   HOH Z 313 " =    1.666
peak=    3.357 closest distance to " CA  ARG A  66 " =    1.016
peak=    3.357 closest distance to " O   HOH Z 253 " =    1.778
peak=    3.350 closest distance to " O   HOH Z 369 " =    2.071
peak=    3.347 closest distance to " O   HOH Z 423 " =    2.843
peak=    3.347 closest distance to " CG  ARG A 269 " =    1.014
peak=    3.343 closest distance to " O   HOH Z 315 " =    1.934
peak=    3.339 closest distance to " O   HOH Z 364 " =    2.243
peak=    3.337 closest distance to " O   HOH Z  61 " =    1.416
peak=    3.336 closest distance to " CB  LEU A   5 " =    1.160
peak=    3.335 closest distance to " O   ASN A 301 " =    2.499
peak=    3.332 closest distance to " CB  GLU A 277 " =    1.107
peak=    3.329 closest distance to " CG2 VAL A 257 " =    1.956
peak=    3.327 closest distance to " CA  GLY A 196 " =    1.158
peak=    3.327 closest distance to " O   HOH Z  59 " =    2.103
peak=    3.325 closest distance to " C   SER A  32 " =    1.150
peak=    3.321 closest distance to " O   HOH Z 155 " =    2.373
peak=    3.315 closest distance to " O   HOH Z 183 " =    1.759
peak=    3.314 closest distance to " CG2 THR A 251 " =    1.126
peak=    3.312 closest distance to " O   HOH Z 189 " =    2.758
peak=    3.308 closest distance to " O   HOH Z 386 " =    2.213
peak=    3.307 closest distance to " CA  THR A 294 " =    1.899
peak=    3.303 closest distance to " O   HOH Z 146 " =    1.332
peak=    3.300 closest distance to " CB  GLN A 194 " =    0.749
peak=    3.297 closest distance to " O   HOH Z 367 " =    3.205
peak=    3.295 closest distance to " O   HOH Z 271 " =    2.334
peak=    3.294 closest distance to " CB  ALA A 114 " =    1.191
peak=    3.288 closest distance to " O   HOH Z 368 " =    3.989
peak=    3.287 closest distance to " O   HOH Z 322 " =    2.245
peak=    3.281 closest distance to " O   HOH Z 435 " =    1.993
peak=    3.280 closest distance to " O   HOH Z 267 " =    2.082
peak=    3.278 closest distance to " O   HOH Z  97 " =    2.240
peak=    3.278 closest distance to " O   HOH Z 380 " =    1.873
peak=    3.274 closest distance to " O   HOH Z 132 " =    2.373
peak=    3.272 closest distance to " O   HOH Z 192 " =    1.624
peak=    3.271 closest distance to " O   HOH Z 144 " =    2.245
peak=    3.271 closest distance to " O   HOH Z 221 " =    1.124
peak=    3.269 closest distance to " CD2 PHE A 218 " =    1.000
peak=    3.263 closest distance to " CA  VAL A 126 " =    0.975
peak=    3.262 closest distance to " O   ALA A 165 " =    1.157
peak=    3.252 closest distance to " CD  LYS A  76 " =    1.806
peak=    3.251 closest distance to " CB  ARG A 190 " =    1.704
peak=    3.250 closest distance to " OD2 ASP A 286 " =    2.628
peak=    3.239 closest distance to " O   HOH Z 252 " =    1.734
peak=    3.236 closest distance to " CA  LEU A  83 " =    1.403
peak=    3.235 closest distance to " NE BARG A 190 " =    1.561
peak=    3.231 closest distance to " CA  ALA A  51 " =    1.144
peak=    3.226 closest distance to " O   HOH Z 438 " =    2.861
peak=    3.226 closest distance to " OD1 ASN A  69 " =    2.410
peak=    3.225 closest distance to " CA  ILE A 263 " =    1.000
peak=    3.223 closest distance to " O   HOH Z 359 " =    1.848
peak=    3.221 closest distance to " CB  ALA A 248 " =    1.337
peak=    3.220 closest distance to " O   HOH Z 170 " =    1.689
peak=    3.220 closest distance to " N   TYR A 247 " =    1.312
peak=    3.218 closest distance to " CA  SER A  12 " =    1.379
peak=    3.212 closest distance to " O   GLY A 211 " =    1.238
peak=    3.210 closest distance to " CA  ASN A 176 " =    1.721
peak=    3.210 closest distance to " O   HOH Z 373 " =    1.645
peak=    3.209 closest distance to " OG  SER A  62 " =    3.113
peak=    3.208 closest distance to " CG1 VAL A 153 " =    1.131
peak=    3.207 closest distance to " O   HOH Z 170 " =    1.935
peak=    3.207 closest distance to " NH2BARG A 190 " =    1.617
peak=    3.202 closest distance to " CB  TRP A 266 " =    1.235
peak=    3.202 closest distance to " NH2 ARG A 156 " =    1.111
peak=    3.198 closest distance to " CB  GLU A 175 " =    1.236
peak=    3.197 closest distance to " O   HOH Z 402 " =    2.659
peak=    3.195 closest distance to " ND1 HIS A  81 " =    1.203
peak=    3.189 closest distance to " CB  ARG A 139 " =    0.959
peak=    3.188 closest distance to " O   HOH Z 279 " =    2.004
peak=    3.187 closest distance to " CD  GLN A 194 " =    1.615
peak=    3.183 closest distance to " CA  PHE A  59 " =    1.107
peak=    3.181 closest distance to " O   HOH Z 427 " =    2.681
peak=    3.179 closest distance to " CB  PRO A 163 " =    3.866
peak=    3.179 closest distance to " O   HOH Z  32 " =    1.932
peak=    3.176 closest distance to " O   HOH Z 383 " =    1.862
peak=    3.176 closest distance to " C   GLY A  80 " =    1.107
peak=    3.174 closest distance to " CD2 HIS A  81 " =    1.325
peak=    3.173 closest distance to " O   HOH Z 116 " =    1.080
peak=    3.173 closest distance to " O   HOH Z  66 " =    1.538
peak=    3.171 closest distance to " O   HOH Z  30 " =    1.170
peak=    3.162 closest distance to " CA  GLU A 152 " =    0.976
peak=    3.158 closest distance to " O   HOH Z 194 " =    1.824
peak=    3.158 closest distance to " O   HOH Z  71 " =    1.684
peak=    3.154 closest distance to " CG2 VAL A 197 " =    1.146
peak=    3.151 closest distance to " O   HOH Z 260 " =    1.499
peak=    3.143 closest distance to " O   HOH Z 298 " =    5.030
peak=    3.139 closest distance to " CB  ALA A  34 " =    0.997
peak=    3.132 closest distance to " O   THR A  31 " =    1.592
peak=    3.129 closest distance to " O   HOH Z 343 " =    2.502
peak=    3.123 closest distance to " CB  ASN A 110 " =    1.099
peak=    3.119 closest distance to " O   HOH Z  63 " =    1.516
peak=    3.119 closest distance to " NH2AARG A 275 " =    3.569
peak=    3.117 closest distance to " CA  MET A  40 " =    1.037
peak=    3.110 closest distance to " O   HOH Z 173 " =    2.264
peak=    3.108 closest distance to " OG BSER A 164 " =    2.145
peak=    3.101 closest distance to " NH2 ARG A  79 " =    1.378
peak=    3.099 closest distance to " O   HOH Z 393 " =    1.966
peak=    3.090 closest distance to " O   HOH Z 255 " =    1.481
peak=    3.083 closest distance to " O   HOH Z 152 " =    1.583
peak=    3.075 closest distance to " CA  LEU A 282 " =    1.084
peak=    3.072 closest distance to " O   HOH Z  83 " =    1.577
peak=    3.072 closest distance to " O   HOH Z  94 " =    1.952
peak=    3.069 closest distance to " ND2 ASN A 187 " =    1.597
peak=    3.052 closest distance to " CA  ALA A 160 " =    0.921
peak=    3.047 closest distance to " O   HOH Z 271 " =    1.685
peak=    3.041 closest distance to " CD  GLU A 236 " =    1.048
peak=    3.032 closest distance to " O   HOH Z 128 " =    2.656
peak=    3.021 closest distance to " CB  TRP A 179 " =    1.894

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 215         
Filter by distance & map next to the model:
   mapped sites are within: 0.711 - 5.358
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 214 from: 215
   mapped sites are within: 0.711 - 5.358

peak=   -5.060 closest distance to " CA  SER A 164 " =    1.981
peak=   -5.003 closest distance to " CG2 VAL A 230 " =    0.872
peak=   -4.733 closest distance to " O   HOH Z  13 " =    1.432
peak=   -4.466 closest distance to " CG2BVAL A  41 " =    2.708
peak=   -4.276 closest distance to " O   HOH Z 210 " =    0.785
peak=   -4.184 closest distance to " CD  ARG A 156 " =    1.986
peak=   -4.171 closest distance to " O   VAL A  67 " =    2.822
peak=   -4.125 closest distance to " SG  CYS A 254 " =    3.115
peak=   -4.101 closest distance to " CD1 PHE A  59 " =    1.901
peak=   -4.088 closest distance to " O   HOH Z 423 " =    2.327
peak=   -4.076 closest distance to " O   HOH Z 196 " =    1.905
peak=   -4.009 closest distance to " O   HOH Z 266 " =    4.323
peak=   -3.955 closest distance to " OXT GLY A 302 " =    2.759
peak=   -3.889 closest distance to " CA  GLY A 203 " =    2.261
peak=   -3.884 closest distance to " CA  SER A 276 " =    1.362
peak=   -3.839 closest distance to " O   HOH Z 166 " =    1.833
peak=   -3.823 closest distance to " CG2 THR A 182 " =    2.240
peak=   -3.816 closest distance to " O  BHOH Z 338 " =    1.436
peak=   -3.798 closest distance to " O   HOH Z 407 " =    3.297
peak=   -3.796 closest distance to " O   LEU A 228 " =    2.344
peak=   -3.794 closest distance to " CB  ALA A 100 " =    1.749
peak=   -3.791 closest distance to " CB  ALA A 161 " =    2.446
peak=   -3.785 closest distance to " OG ASER A 134 " =    1.257
peak=   -3.772 closest distance to " NH2 ARG A  66 " =    1.281
peak=   -3.767 closest distance to " O   HOH Z 377 " =    1.062
peak=   -3.763 closest distance to " O   HOH Z 150 " =    1.220
peak=   -3.743 closest distance to " O   ASN A 187 " =    1.476
peak=   -3.732 closest distance to " CB  ALA A 248 " =    1.972
peak=   -3.728 closest distance to " O   HOH Z  46 " =    0.782
peak=   -3.717 closest distance to " CB  ALA A 248 " =    2.079
peak=   -3.717 closest distance to " C   HIS A 108 " =    1.223
peak=   -3.709 closest distance to " N   ALA A 226 " =    1.973
peak=   -3.709 closest distance to " O   HOH Z 221 " =    1.381
peak=   -3.694 closest distance to " CZ  TYR A 169 " =    1.813
peak=   -3.689 closest distance to " C   THR A 279 " =    1.084
peak=   -3.686 closest distance to " OG  SER A  26 " =    1.464
peak=   -3.681 closest distance to " CD2 LEU A 237 " =    2.550
peak=   -3.676 closest distance to " O   HOH Z 166 " =    1.473
peak=   -3.666 closest distance to " O   HOH Z 138 " =    0.971
peak=   -3.661 closest distance to " O   SER A 273 " =    1.228
peak=   -3.655 closest distance to " O   HOH Z  11 " =    1.581
peak=   -3.655 closest distance to " CD2 TYR A  30 " =    2.711
peak=   -3.650 closest distance to " OG  SER A  97 " =    2.175
peak=   -3.648 closest distance to " O   HOH Z  52 " =    2.317
peak=   -3.641 closest distance to " O   HOH Z 426 " =    1.736
peak=   -3.638 closest distance to " O   HOH Z 208 " =    1.266
peak=   -3.634 closest distance to " O   HOH Z 151 " =    1.204
peak=   -3.634 closest distance to " CD2 PHE A  59 " =    2.448
peak=   -3.633 closest distance to " O   ALA A 161 " =    1.333
peak=   -3.632 closest distance to " O   HOH Z 119 " =    1.880
peak=   -3.621 closest distance to " CG1 VAL A 112 " =    2.335
peak=   -3.610 closest distance to " O   HOH Z 234 " =    4.146
peak=   -3.608 closest distance to " O   HOH Z 126 " =    1.894
peak=   -3.606 closest distance to " O   HOH Z 120 " =    1.072
peak=   -3.600 closest distance to " CE1 HIS A  81 " =    1.315
peak=   -3.598 closest distance to " OG1 THR A   4 " =    1.718
peak=   -3.596 closest distance to " C   ASN A 285 " =    2.288
peak=   -3.595 closest distance to " CG  ARG A 219 " =    2.398
peak=   -3.585 closest distance to " O   MET A  40 " =    2.822
peak=   -3.584 closest distance to " O   HOH Z  71 " =    1.271
peak=   -3.582 closest distance to " CB  CYS A 254 " =    2.633
peak=   -3.578 closest distance to " OG1 THR A  82 " =    1.211
peak=   -3.575 closest distance to " O   GLN A  11 " =    1.233
peak=   -3.571 closest distance to " O   HOH Z 385 " =    3.631
peak=   -3.566 closest distance to " CD1 LEU A 101 " =    2.513
peak=   -3.563 closest distance to " O   HOH Z 426 " =    2.327
peak=   -3.546 closest distance to " CD  ARG A 195 " =    5.040
peak=   -3.545 closest distance to " CD1 TYR A 247 " =    2.251
peak=   -3.541 closest distance to " O   HOH Z 435 " =    1.985
peak=   -3.540 closest distance to " O   HOH Z  60 " =    1.783
peak=   -3.531 closest distance to " N   SER A 210 " =    1.317
peak=   -3.519 closest distance to " O   HOH Z  48 " =    1.289
peak=   -3.518 closest distance to " OD1 ASP A 200 " =    1.194
peak=   -3.516 closest distance to " C   GLY A 133 " =    1.314
peak=   -3.513 closest distance to " N   GLN A  58 " =    1.925
peak=   -3.512 closest distance to " CB  LEU A 167 " =    2.130
peak=   -3.505 closest distance to " C   ALA A 158 " =    1.195
peak=   -3.497 closest distance to " CZ2 TRP A 179 " =    1.338
peak=   -3.496 closest distance to " CD  GLN A  88 " =    0.908
peak=   -3.486 closest distance to " C   GLY A  91 " =    1.467
peak=   -3.480 closest distance to " O   HOH Z 132 " =    0.960
peak=   -3.475 closest distance to " CD1 LEU A 228 " =    2.228
peak=   -3.474 closest distance to " O   SER A 146 " =    0.960
peak=   -3.465 closest distance to " CG1 VAL A  78 " =    2.475
peak=   -3.465 closest distance to " OG  SER A 206 " =    1.577
peak=   -3.462 closest distance to " O   HOH Z 351 " =    1.439
peak=   -3.459 closest distance to " ND2 ASN A 252 " =    1.725
peak=   -3.458 closest distance to " CD1 TRP A 179 " =    1.166
peak=   -3.455 closest distance to " CD2 LEU A 300 " =    2.773
peak=   -3.448 closest distance to " ND2 ASN A  39 " =    1.150
peak=   -3.431 closest distance to " O   HOH Z 191 " =    5.358
peak=   -3.428 closest distance to " O   PHE A 218 " =    1.302
peak=   -3.428 closest distance to " O   HOH Z 424 " =    2.897
peak=   -3.421 closest distance to " CG2 VAL A 189 " =    1.934
peak=   -3.420 closest distance to " CA  ASP A 298 " =    1.036
peak=   -3.414 closest distance to " O   VAL A 197 " =    1.281
peak=   -3.411 closest distance to " OD1 ASP A 191 " =    1.715
peak=   -3.407 closest distance to " O   HOH Z 176 " =    1.806
peak=   -3.407 closest distance to " CA  ASP A  27 " =    2.407
peak=   -3.405 closest distance to " O   HOH Z  39 " =    1.343
peak=   -3.399 closest distance to " CG  ASP A 231 " =    0.813
peak=   -3.396 closest distance to " O   HOH Z 171 " =    2.211
peak=   -3.393 closest distance to " O   VAL A 174 " =    2.064
peak=   -3.393 closest distance to " O   HOH Z 422 " =    1.375
peak=   -3.383 closest distance to " CE1 PHE A 204 " =    2.508
peak=   -3.380 closest distance to " O   HOH Z 427 " =    1.304
peak=   -3.377 closest distance to " O   HOH Z 313 " =    2.250
peak=   -3.375 closest distance to " CG1 VAL A 197 " =    2.165
peak=   -3.363 closest distance to " O   HOH Z 407 " =    1.314
peak=   -3.362 closest distance to " CB  PRO A 280 " =    2.300
peak=   -3.362 closest distance to " O   HOH Z 210 " =    2.473
peak=   -3.356 closest distance to " N   THR A 235 " =    1.241
peak=   -3.346 closest distance to " CG2 VAL A 296 " =    1.134
peak=   -3.345 closest distance to " O   ALA A   1 " =    1.890
peak=   -3.342 closest distance to " CB  PRO A 163 " =    2.896
peak=   -3.341 closest distance to " OD2 ASP A  50 " =    1.486
peak=   -3.339 closest distance to " O   HOH Z 290 " =    0.961
peak=   -3.337 closest distance to " O   HOH Z 297 " =    2.828
peak=   -3.334 closest distance to " O   HOH Z 340 " =    1.165
peak=   -3.332 closest distance to " O   HOH Z 138 " =    1.502
peak=   -3.332 closest distance to " O   HOH Z 263 " =    0.812
peak=   -3.331 closest distance to " O   HOH Z 380 " =    4.603
peak=   -3.328 closest distance to " CG  GLN A  11 " =    1.853
peak=   -3.327 closest distance to " O   HOH Z  92 " =    1.393
peak=   -3.323 closest distance to " CE  MET A 105 " =    2.043
peak=   -3.320 closest distance to " O   PRO A 198 " =    1.307
peak=   -3.318 closest distance to " CE  LYS A 166 " =    3.053
peak=   -3.316 closest distance to " O   HOH Z 313 " =    1.424
peak=   -3.311 closest distance to " OG BSER A 134 " =    1.477
peak=   -3.305 closest distance to " CG  LYS A 193 " =    2.301
peak=   -3.305 closest distance to " O   HOH Z 250 " =    1.381
peak=   -3.304 closest distance to " O   HOH Z  88 " =    4.487
peak=   -3.300 closest distance to " CB  GLN A 223 " =    1.836
peak=   -3.300 closest distance to " O   ASN A  45 " =    1.820
peak=   -3.297 closest distance to " N   GLY A  17 " =    1.497
peak=   -3.295 closest distance to " O   HOH Z 124 " =    1.433
peak=   -3.294 closest distance to " NH1 ARG A 195 " =    2.630
peak=   -3.291 closest distance to " SG  CYS A 260 " =    2.445
peak=   -3.290 closest distance to " NH1BARG A 190 " =    2.212
peak=   -3.283 closest distance to " O   HOH Z 311 " =    3.225
peak=   -3.283 closest distance to " O   TRP A  92 " =    1.961
peak=   -3.277 closest distance to " CD2 TYR A 293 " =    1.992
peak=   -3.276 closest distance to " CD1 TRP A  70 " =    1.869
peak=   -3.275 closest distance to " N   ALA A 248 " =    1.806
peak=   -3.272 closest distance to " CG  MET A 105 " =    0.851
peak=   -3.264 closest distance to " O   HOH Z 345 " =    2.365
peak=   -3.260 closest distance to " CG  PRO A 243 " =    1.531
peak=   -3.259 closest distance to " O   HOH Z 139 " =    3.239
peak=   -3.255 closest distance to " O   HOH Z 165 " =    2.029
peak=   -3.254 closest distance to " O   ALA A  34 " =    2.085
peak=   -3.252 closest distance to " O   HOH Z 136 " =    1.847
peak=   -3.249 closest distance to " NE1 TRP A 266 " =    2.203
peak=   -3.249 closest distance to " OE2 GLU A   2 " =    1.575
peak=   -3.248 closest distance to " O   HOH Z 130 " =    2.442
peak=   -3.246 closest distance to " O   HOH Z 422 " =    1.031
peak=   -3.246 closest distance to " CB  PHE A 208 " =    2.313
peak=   -3.245 closest distance to " NH2 ARG A  79 " =    1.932
peak=   -3.244 closest distance to " CA  GLY A 133 " =    1.957
peak=   -3.236 closest distance to " ND2 ASN A  69 " =    1.664
peak=   -3.229 closest distance to " OD1 ASN A  39 " =    2.210
peak=   -3.229 closest distance to " O   HOH Z  15 " =    1.498
peak=   -3.220 closest distance to " OD2 ASP A 171 " =    1.582
peak=   -3.215 closest distance to " CG  ARG A 269 " =    2.172
peak=   -3.212 closest distance to " OD1 ASN A 148 " =    1.660
peak=   -3.206 closest distance to " CA  GLY A  98 " =    2.138
peak=   -3.194 closest distance to " O   HOH Z 193 " =    1.498
peak=   -3.194 closest distance to " OD1 ASP A 171 " =    1.665
peak=   -3.189 closest distance to " CG  GLN A  58 " =    1.220
peak=   -3.189 closest distance to " CD1 LEU A  96 " =    2.125
peak=   -3.187 closest distance to " O   HOH Z 126 " =    1.455
peak=   -3.183 closest distance to " CB  ASP A 132 " =    2.287
peak=   -3.181 closest distance to " CD2 LEU A 237 " =    2.916
peak=   -3.180 closest distance to " O   HOH Z 200 " =    1.097
peak=   -3.179 closest distance to " O   HOH Z   6 " =    2.150
peak=   -3.178 closest distance to " O   HOH Z 198 " =    2.252
peak=   -3.175 closest distance to " O   HOH Z 219 " =    3.065
peak=   -3.173 closest distance to " CZ3 TRP A 266 " =    1.666
peak=   -3.167 closest distance to " CE  MET A 105 " =    2.174
peak=   -3.151 closest distance to " CE3 TRP A 150 " =    2.359
peak=   -3.148 closest distance to " O   ALA A  34 " =    2.376
peak=   -3.148 closest distance to " O   HOH Z 368 " =    1.985
peak=   -3.147 closest distance to " CG AARG A 102 " =    1.966
peak=   -3.146 closest distance to " O   HOH Z 115 " =    4.722
peak=   -3.143 closest distance to " CE BMET A  47 " =    1.341
peak=   -3.140 closest distance to " O   ALA A  51 " =    1.466
peak=   -3.131 closest distance to " CG1AVAL A  72 " =    1.969
peak=   -3.130 closest distance to " O   HOH Z 135 " =    1.315
peak=   -3.128 closest distance to " O   HOH Z 146 " =    0.711
peak=   -3.128 closest distance to " NE2 GLN A  58 " =    2.349
peak=   -3.127 closest distance to " ND2 ASN A 173 " =    1.625
peak=   -3.126 closest distance to " CE3 TRP A  70 " =    1.856
peak=   -3.120 closest distance to " O   CYS A 260 " =    0.934
peak=   -3.113 closest distance to " CA  VAL A 197 " =    0.925
peak=   -3.112 closest distance to " O   HOH Z 420 " =    5.134
peak=   -3.111 closest distance to " O   THR A  52 " =    1.780
peak=   -3.109 closest distance to " C   LEU A 101 " =    1.055
peak=   -3.108 closest distance to " O   HOH Z 361 " =    3.485
peak=   -3.107 closest distance to " CA  ARG A  66 " =    1.741
peak=   -3.100 closest distance to " CD2 HIS A 115 " =    1.004
peak=   -3.095 closest distance to " NH2BARG A 145 " =    2.331
peak=   -3.090 closest distance to " O   HOH Z 389 " =    1.318
peak=   -3.089 closest distance to " CA  ALA A 137 " =    2.470
peak=   -3.084 closest distance to " CA  LYS A 166 " =    2.203
peak=   -3.083 closest distance to " O   HOH Z 222 " =    1.246
peak=   -3.077 closest distance to " O   HOH Z 184 " =    1.241
peak=   -3.073 closest distance to " O   HOH Z 384 " =    2.415
peak=   -3.072 closest distance to " O   HOH Z 412 " =    5.051
peak=   -3.056 closest distance to " O   HOH Z 166 " =    1.050
peak=   -3.055 closest distance to " O   HOH Z 396 " =    1.527
peak=   -3.049 closest distance to " O   HOH Z 145 " =    1.657
peak=   -3.043 closest distance to " O   HOH Z 233 " =    2.243
peak=   -3.037 closest distance to " NH2 ARG A 159 " =    2.396
peak=   -3.030 closest distance to " OG BSER A 134 " =    1.755
peak=   -3.007 closest distance to " CB  PRO A 163 " =    2.288

================= 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    :  0.5096 0.5023   6.304470e+00   6.293795e+00
   1_bss:  0.5030 0.4932   6.300117e+00   6.288400e+00
   1_xyz:  0.4446 0.4594   6.240098e+00   6.259080e+00
   1_adp:  0.4072 0.4539   6.196602e+00   6.249894e+00
   1_occ:  0.4064 0.4523   6.195611e+00   6.249799e+00
   2_bss:  0.4052 0.4476   6.196656e+00   6.248278e+00
   2_xyz:  0.3398 0.3975   6.070529e+00   6.174325e+00
   2_adp:  0.3187 0.3846   6.031829e+00   6.151640e+00
   2_occ:  0.3186 0.3844   6.031491e+00   6.151537e+00
   3_bss:  0.3164 0.3811   6.029629e+00   6.150825e+00
   3_xyz:  0.2490 0.3109   5.833197e+00   5.995293e+00
   3_adp:  0.2252 0.2837   5.753580e+00   5.920894e+00
   3_occ:  0.2247 0.2830   5.752707e+00   5.920304e+00
   4_bss:  0.2239 0.2812   5.750604e+00   5.915933e+00
   4_xyz:  0.1667 0.2132   5.476637e+00   5.675231e+00
   4_adp:  0.1514 0.1988   5.394654e+00   5.603945e+00
   4_occ:  0.1512 0.1987   5.394459e+00   5.604314e+00
   5_bss:  0.1512 0.1989   5.396929e+00   5.607089e+00
   5_xyz:  0.1274 0.1756   5.256867e+00   5.489820e+00
   5_adp:  0.1229 0.1717   5.229684e+00   5.468415e+00
   5_occ:  0.1228 0.1717   5.229324e+00   5.468462e+00
   5_bss:  0.1232 0.1720   5.232494e+00   5.472180e+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:  0.357  20.000   6.416  10.470   7.643   0.000   0.000   0.000
   1_xyz:  0.357  20.000   6.416  10.470   7.643   0.000   0.000   0.000
   1_adp:  0.357  20.000   6.416  10.470   7.643   0.000   0.000   0.000
   1_occ:  0.357  20.000   6.416  10.470   7.643   0.000   0.000   0.000
   2_bss:  0.300  20.000   3.075   6.468   4.861   0.000   0.000   0.000
   2_xyz:  0.300  20.000   3.075   6.468   4.861   0.000   0.000   0.000
   2_adp:  0.300  20.000   3.075   6.468   4.861   0.000   0.000   0.000
   2_occ:  0.300  20.000   3.075   6.468   4.861   0.000   0.000   0.000
   3_bss:  0.318  43.208   1.118   3.681   2.572   0.000   0.000   0.000
   3_xyz:  0.318  43.208   1.118   3.681   2.572   0.000   0.000   0.000
   3_adp:  0.318  43.208   1.118   3.681   2.572   0.000   0.000   0.000
   3_occ:  0.318  43.208   1.118   3.681   2.572   0.000   0.000   0.000
   4_bss:  0.324  40.059  -0.097   2.232   1.277   0.000   0.000   0.000
   4_xyz:  0.324  40.059  -0.097   2.232   1.277   0.000   0.000   0.000
   4_adp:  0.324  40.059  -0.097   2.232   1.277   0.000   0.000   0.000
   4_occ:  0.324  40.059  -0.097   2.232   1.277   0.000   0.000   0.000
   5_bss:  0.325  46.192  -0.701   1.152   0.641   0.000   0.000   0.000
   5_xyz:  0.325  46.192  -0.701   1.152   0.641   0.000   0.000   0.000
   5_adp:  0.325  46.192  -0.701   1.152   0.641   0.000   0.000   0.000
   5_occ:  0.325  46.192  -0.701   1.152   0.641   0.000   0.000   0.000
   5_bss:  0.325  46.438  -0.949   0.645   0.304   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  64.147 0.3401  0.4024    80753.031
   1_bss:  64.460 0.3342  0.4950    78582.862
   1_xyz:  60.206 0.3876  0.5592    67523.033
   1_adp:  56.648 0.4342  0.7106    64027.336
   1_occ:  56.489 0.4362  0.7126    63741.633
   2_bss:  56.268 0.4389  0.6423    63186.939
   2_xyz:  45.853 0.5703  0.8382    46273.790
   2_adp:  42.966 0.6060  0.8902    42065.158
   2_occ:  42.956 0.6061  0.8898    42018.825
   3_bss:  42.584 0.6105  0.8267    41423.224
   3_xyz:  33.020 0.7227  0.9491    26329.300
   3_adp:  29.245 0.7658  0.9740    21898.986
   3_occ:  29.221 0.7661  0.9742    21873.372
   4_bss:  29.084 0.7674  0.9294    21613.016
   4_xyz:  20.985 0.8513  0.9949    11812.746
   4_adp:  18.940 0.8716  1.0031    10089.546
   4_occ:  18.944 0.8716  1.0031    10100.292
   5_bss:  18.966 0.8715  0.9758    10183.519
   5_xyz:  16.413 0.8943  0.9853     7933.275
   5_adp:  15.857 0.8995  0.9827     7634.803
   5_occ:  15.852 0.8996  0.9827     7636.235
   5_bss:  15.916 0.8991  0.9785     7726.873
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.3301e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.3301e+01
   1_xyz:   1.806  0.014  0.110 18.449  0.007  4.118   1.6147e-01
   1_adp:   1.806  0.014  0.110 18.449  0.007  4.118   1.6147e-01
   1_occ:   1.806  0.014  0.110 18.449  0.007  4.118   1.6147e-01
   2_bss:   1.806  0.014  0.110 18.449  0.007  4.118   1.6147e-01
   2_xyz:   1.304  0.009  0.085 16.762  0.006  4.108   1.0317e-01
   2_adp:   1.304  0.009  0.085 16.762  0.006  4.108   1.0317e-01
   2_occ:   1.304  0.009  0.085 16.762  0.006  4.108   1.0317e-01
   3_bss:   1.304  0.009  0.085 16.762  0.006  4.108   1.0317e-01
   3_xyz:   1.267  0.008  0.091 16.097  0.005  4.108   8.9666e-02
   3_adp:   1.267  0.008  0.091 16.097  0.005  4.108   8.9666e-02
   3_occ:   1.267  0.008  0.091 16.097  0.005  4.108   8.9666e-02
   4_bss:   1.267  0.008  0.091 16.097  0.005  4.108   8.9666e-02
   4_xyz:   1.085  0.008  0.076 15.509  0.004  4.120   7.4885e-02
   4_adp:   1.085  0.008  0.076 15.509  0.004  4.120   7.4885e-02
   4_occ:   1.085  0.008  0.076 15.509  0.004  4.120   7.4885e-02
   5_bss:   1.085  0.008  0.076 15.509  0.004  4.120   7.4885e-02
   5_xyz:   1.141  0.008  0.086 15.632  0.004  4.116   7.4588e-02
   5_adp:   1.141  0.008  0.086 15.632  0.004  4.116   7.4588e-02
   5_occ:   1.141  0.008  0.086 15.632  0.004  4.116   7.4588e-02
   5_bss:   1.141  0.008  0.086 15.632  0.004  4.116   7.4588e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.869   6.9047e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.869   6.9047e+00
   1_xyz:  15.899  0.175  0.518 87.154  0.054  2.122   1.0687e-01
   1_adp:  15.899  0.175  0.518 87.154  0.054  2.122   1.0687e-01
   1_occ:  15.899  0.175  0.518 87.154  0.054  2.122   1.0687e-01
   2_bss:  15.899  0.175  0.518 87.154  0.054  2.122   1.0687e-01
   2_xyz:   9.662  0.112  0.276 85.782  0.056  1.955   7.8251e-02
   2_adp:   9.662  0.112  0.276 85.782  0.056  1.955   7.8251e-02
   2_occ:   9.662  0.112  0.276 85.782  0.056  1.955   7.8251e-02
   3_bss:   9.662  0.112  0.276 85.782  0.056  1.955   7.8251e-02
   3_xyz:   7.510  0.054  0.361 84.764  0.047  2.145   1.1008e-01
   3_adp:   7.510  0.054  0.361 84.764  0.047  2.145   1.1008e-01
   3_occ:   7.510  0.054  0.361 84.764  0.047  2.145   1.1008e-01
   4_bss:   7.510  0.054  0.361 84.764  0.047  2.145   1.1008e-01
   4_xyz:   7.940  0.068  0.380 81.877  0.031  2.249   1.3771e-01
   4_adp:   7.940  0.068  0.380 81.877  0.031  2.249   1.3771e-01
   4_occ:   7.940  0.068  0.380 81.877  0.031  2.249   1.3771e-01
   5_bss:   7.940  0.068  0.380 81.877  0.031  2.249   1.3771e-01
   5_xyz:   7.202  0.049  0.638 82.830  0.035  2.270   5.5106e-02
   5_adp:   7.202  0.049  0.638 82.830  0.035  2.270   5.5106e-02
   5_occ:   7.202  0.049  0.638 82.830  0.035  2.270   5.5106e-02
   5_bss:   7.202  0.049  0.638 82.830  0.035  2.270   5.5106e-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:  99.56   0.00  16.24  82.79   0.00  14.52  99.56   0.00  25.60
   1_occ:  99.56   0.00  16.24  82.79   0.00  14.52  99.56   0.00  25.60
   2_bss:  99.56   0.00  16.24  82.79   0.00  14.52  99.56   0.00  25.60
   2_xyz:  99.56   0.00  16.24  82.79   0.00  14.52  99.56   0.00  25.60
   2_adp: 104.53   0.00  16.11  91.63   0.00  13.61 104.53   0.00  29.70
   2_occ: 104.53   0.00  16.11  91.63   0.00  13.61 104.53   0.00  29.70
   3_bss: 104.53   0.00  16.11  91.63   0.00  13.61 104.53   0.00  29.70
   3_xyz: 104.53   0.00  16.11  91.63   0.00  13.61 104.53   0.00  29.70
   3_adp:  98.14   0.00  15.26  76.45   0.00  11.68  98.14   3.58  34.76
   3_occ:  98.14   0.00  15.26  76.45   0.00  11.68  98.14   3.58  34.76
   4_bss:  98.14   0.00  15.26  76.45   0.00  11.68  98.14   3.58  34.76
   4_xyz:  98.14   0.00  15.26  76.45   0.00  11.68  98.14   3.58  34.76
   4_adp:  86.64   0.00  15.57  86.64   0.00  11.10  86.21   3.77  39.88
   4_occ:  86.64   0.00  15.57  86.64   0.00  11.10  86.21   3.77  39.88
   5_bss:  86.64   0.00  15.57  86.64   0.00  11.10  86.21   3.77  39.88
   5_xyz:  86.64   0.00  15.57  86.64   0.00  11.10  86.21   3.77  39.88
   5_adp:  94.60   0.00  15.57  94.60   0.00  10.88  84.42   3.80  41.13
   5_occ:  94.60   0.00  15.57  94.60   0.00  10.88  84.42   3.80  41.13
   5_bss:  94.84   0.25  15.82  94.84   0.25  11.13  84.67   4.04  41.37
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.175    0.023    0.417
   1_adp:    1.175    0.023    0.417
   1_occ:    1.175    0.023    0.417
   2_bss:    1.175    0.023    0.417
   2_xyz:    2.100    0.066    0.602
   2_adp:    2.100    0.066    0.602
   2_occ:    2.100    0.066    0.602
   3_bss:    2.100    0.066    0.602
   3_xyz:    1.684    0.043    0.740
   3_adp:    1.684    0.043    0.740
   3_occ:    1.684    0.043    0.740
   4_bss:    1.684    0.043    0.740
   4_xyz:    1.846    0.067    0.849
   4_adp:    1.846    0.067    0.849
   4_occ:    1.846    0.067    0.849
   5_bss:    1.846    0.067    0.849
   5_xyz:    1.867    0.072    0.892
   5_adp:    1.867    0.072    0.892
   5_occ:    1.867    0.072    0.892
   5_bss:    1.867    0.072    0.892
------------------------------------------------------------------------

CPU time actual refinement: 349.98


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_342/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_342/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_342/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_342/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_342/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 349.83 
  Macro-tasks:
    bulk solvent and scale       = 44.58  
    individual site refinement   = 148.01 
    weights calculation          = 32.42  
    collect and process          = 6.27   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 231.40 
  Micro-tasks:
    mask                            = 2.99   
    f_calc                          = 109.27 
    alpha_beta                      = 8.09   
    target                          = 1.12   
    gradients_wrt_atomic_parameters = 120.12 
    fmodel                         = 7.84   
    r_factors                      = 0.30   
    phase_errors                   = 10.08  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 260.04 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.893 micro seconds
Total CPU time: 6.06 minutes
from_scatterers_fft:    642 calls, 108.91 s
gradients_fft:          586 calls, 106.62 s

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

# Date 2008-01-16 Time 01:21:31 PST -0800 (1200475291.12 s)
Start R-work = 0.5096, R-free = 0.5023 (no bulk solvent and anisotropic scale)
Final R-work = 0.1400, R-free = 0.1885 (no bulk solvent and anisotropic scale)

Start R-work = 0.5030, R-free = 0.4932
Final R-work = 0.1232, R-free = 0.1720