# Date 2008-01-16 Time 02:50:44 PST -0800 (1200480644.15 s)
#phil __OFF__

Command line arguments: "../997.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 = 11807
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 997

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.3037, 46.2261, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 46.2261, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1984 1.97356
Completeness in resolution range: 0.93889
Completeness with d_max=infinity: 0.936198

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1984
                             d_min =   1.9736

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 46.2261, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1984 1.97356
Completeness in resolution range: 0.93889
Completeness with d_max=infinity: 0.936198

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1989 -  4.2243 [2196/2223]  1975   221  10.1%
  bin  2:  4.2243 -  3.3649 [2110/2130]  1900   210  10.0%
  bin  3:  3.3649 -  2.9431 [2074/2093]  1868   206   9.9%
  bin  4:  2.9431 -  2.6756 [2056/2086]  1847   209  10.2%
  bin  5:  2.6756 -  2.4847 [2044/2063]  1848   196   9.6%
  bin  6:  2.4847 -  2.3388 [2046/2071]  1832   214  10.5%
  bin  7:  2.3388 -  2.2220 [2023/2051]  1819   204  10.1%
  bin  8:  2.2220 -  2.1256 [2009/2045]  1809   200  10.0%
  bin  9:  2.1256 -  2.0439 [2016/2058]  1820   196   9.7%
  bin 10:  2.0439 -  1.9736 [1015/2044]   912   103  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_997/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 26
        2.42 -     3.04: 2176
        3.04 -     3.66: 4693
        3.66 -     4.28: 8984
        4.28 -     4.90: 12289
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 201 " - " O   HOH Z 349 "  2.068 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.091 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  2.148 3.040 x,y+1,z
  " O   HOH Z 324 " - " O   HOH Z 374 "  2.193 3.040 -x,y-1/2,-z+1/2
  ... (remaining 28163 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_997/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_997/model_refine_001.geo

CPU time processing inputs: 9.03


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 46.22605 87.2539 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: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4796   r_free= 0.4683   ksol= 0.00   Bsol= 0.00   scale= 0.789    |
|                                                                             |
| 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:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.282090                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1989 -  4.7123 0.99   1420  158 0.4029 0.3812      6.6015      6.5707|
|  2:  4.7123 -  3.7589 0.99   1374  155 0.3934 0.3858      6.7896       6.767|
|  3:  3.7589 -  3.2892 0.99   1341  142 0.4249 0.4026      6.6467      6.6198|
|  4:  3.2892 -  2.9910 0.99   1332  155 0.4685 0.4364      6.5259      6.4955|
|  5:  2.9910 -  2.7780 0.99   1338  149 0.5130 0.5015      6.3734      6.3657|
|  6:  2.7780 -  2.6151 0.99   1324  146 0.5071 0.5143      6.2667      6.2176|
|  7:  2.6151 -  2.4847 0.99   1309  137 0.5350 0.4895       6.248      6.1785|
|  8:  2.4847 -  2.3770 0.98   1299  152 0.5272 0.4809       6.171      6.1824|
|  9:  2.3770 -  2.2858 0.98   1305  148 0.5191 0.5344       6.121      6.1832|
| 10:  2.2858 -  2.2072 1.00   1300  147 0.5297 0.4986      6.0984      6.0687|
| 11:  2.2072 -  2.1383 0.98   1312  136 0.5186 0.5210      6.0382      6.0295|
| 12:  2.1383 -  2.0774 0.98   1292  145 0.5321 0.5607      5.9471      5.9904|
| 13:  2.0774 -  2.0228 0.98   1265  141 0.5362 0.5235      5.8799      5.7978|
| 14:  2.0228 -  1.9736 0.32    419   48 0.5541 0.4955      5.8837      5.8409|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1989 -  4.7123  1420   158  0.69  34.79   0.79     0.74      73912.19|
|  2:  4.7123 -  3.7589  1374   155  0.73  32.97   0.87     0.79      98504.02|
|  3:  3.7589 -  3.2892  1341   142  0.62  41.81   0.85     0.74     105330.65|
|  4:  3.2892 -  2.9910  1332   155  0.54  48.73   0.78     0.64      94708.50|
|  5:  2.9910 -  2.7780  1338   149  0.45  56.02   0.73     0.55      79572.05|
|  6:  2.7780 -  2.6151  1324   146  0.42  58.63   0.72     0.48      69730.64|
|  7:  2.6151 -  2.4847  1309   137  0.36  63.26   0.73     0.41      65610.42|
|  8:  2.4847 -  2.3770  1299   152  0.32  66.01   0.71     0.38      61142.33|
|  9:  2.3770 -  2.2858  1305   148  0.32  66.26   0.73     0.37      56326.34|
| 10:  2.2858 -  2.2072  1300   147  0.33  65.70   0.74     0.39      50791.59|
| 11:  2.2072 -  2.1383  1312   136  0.30  67.62   0.78     0.38      49551.46|
| 12:  2.1383 -  2.0774  1292   145  0.29  68.65   0.72     0.37      45139.27|
| 13:  2.0774 -  2.0228  1265   141  0.30  67.77   0.71     0.39      38295.99|
| 14:  2.0228 -  1.9736   419    48  0.43  57.77   0.71     0.46      26724.16|
|alpha:            min =        0.37 max =            0.79 mean =         0.51|
|beta:             min =    26724.16 max =       105330.65 mean =     67742.88|
|figures of merit: min =        0.00 max =            1.00 mean =         0.44|
|phase err.(work): min =        0.00 max =           89.99 mean =        56.50|
|phase err.(test): min =        0.00 max =           89.94 mean =        56.62|
|-----------------------------------------------------------------------------|

============================== 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 = 13.968903             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.347   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.214328              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.938   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       28 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      170 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      681 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1501 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2610 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3934 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5041 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6529 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7672 |
|-----------------------------------------------------------------------------|
|-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 |       53.958 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.795 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.999)------------------------------------------|
|    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 = 11.999)------------------------------------------|
|    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: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4853   r_free= 0.4710   ksol= 0.00   Bsol= 0.00   scale= 0.760    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.283749                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4725   r_free= 0.4542   ksol= 0.34   Bsol= 20.00   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.98,8.94,8.69,0.00,0.00,0.00); trace/3= 8.54                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.276011                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.069144             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.630   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.164859              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.793   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4725      final r-factor (work) = 0.3872          |
| start r-factor (free) = 0.4542      final r-factor (free) = 0.4035          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 91.8414 = 12.07 * 0.50 * 6.2777 + 1.00 * 53.9579                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.4947 = 12.07 * 0.50 * 6.1900 + 1.00 * 0.1408                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3872      final r-factor (work) = 0.3403          |
| start r-factor (free) = 0.4035      final r-factor (free) = 0.3960          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.2249 = 1.16 * 1.00 * 6.1900 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1212 = 1.16 * 1.00 * 6.0987 + 1.00 * 0.0171                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.999)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.16   13.79    None  None   None       |
|    all(noH): 2823   0      0.00    80.16   13.79    None  None   None       |
|    Sol.    : 438    0      0.00    80.16   27.40    None  None   None       |
|    Mac.    : 2385   0      0.00    68.00   11.30    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.016: 1108   |   5:    40.081 -  48.097:   68        |
|      1:     8.016 -  16.033:  788   |   6:    48.097 -  56.114:   40        |
|      2:    16.033 -  24.049:  448   |   7:    56.114 -  64.130:   13        |
|      3:    24.049 -  32.065:  240   |   8:    64.130 -  72.146:   10        |
|      4:    32.065 -  40.081:  106   |   9:    72.146 -  80.162:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3403 r_free = 0.3960             target_work(ml) = 6.082         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3397 r_free = 0.3965             target_work(ml) = 6.081         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3397   r_free= 0.3965   ksol= 0.34   Bsol= 20.00   scale= 1.110   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.98,8.94,8.69,0.00,0.00,0.00); trace/3= 8.54                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.081411                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3365   r_free= 0.3913   ksol= 0.35   Bsol= 50.00   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.71,4.91,5.29,0.00,0.00,0.00); trace/3= 4.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.081448                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.278635              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.433   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.512198              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.583  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3365      final r-factor (work) = 0.2394          |
| start r-factor (free) = 0.3913      final r-factor (free) = 0.2928          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.4144 = 9.28 * 0.50 * 6.0943 + 1.00 * 0.1408                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.7020 = 9.28 * 0.50 * 5.9518 + 1.00 * 0.0897                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2394      final r-factor (work) = 0.2090          |
| start r-factor (free) = 0.2928      final r-factor (free) = 0.2679          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0657 = 0.51 * 1.00 * 5.9518 + 1.00 * 0.0172                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9479 = 0.51 * 1.00 * 5.7313 + 1.00 * 0.0124                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.999)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.02   13.24    None  None   None       |
|    all(noH): 2823   0      0.00    86.02   13.24    None  None   None       |
|    Sol.    : 438    0      0.00    86.02   34.20    None  None   None       |
|    Mac.    : 2385   0      0.00    74.60   9.39     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.602: 1407   |   5:    43.009 -  51.611:   74        |
|      1:     8.602 -  17.204:  738   |   6:    51.611 -  60.213:   45        |
|      2:    17.204 -  25.806:  252   |   7:    60.213 -  68.815:   14        |
|      3:    25.806 -  34.407:  151   |   8:    68.815 -  77.416:    3        |
|      4:    34.407 -  43.009:  137   |   9:    77.416 -  86.018:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2090 r_free = 0.2679             target_work(ml) = 5.685         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2089 r_free = 0.2678             target_work(ml) = 5.685         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2089   r_free= 0.2678   ksol= 0.35   Bsol= 50.00   scale= 1.058   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.71,4.91,5.29,0.00,0.00,0.00); trace/3= 4.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.684879                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2068   r_free= 0.2651   ksol= 0.32   Bsol= 54.29   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.66,2.41,3.68,0.00,0.00,0.00); trace/3= 2.92                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.683942                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.094869              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.596  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.810133              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.046  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2068      final r-factor (work) = 0.1508          |
| start r-factor (free) = 0.2651      final r-factor (free) = 0.2015          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.7117 = 5.09 * 0.50 * 5.7399 + 1.00 * 0.0897                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.2431 = 5.09 * 0.50 * 5.5622 + 1.00 * 0.0739                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1508      final r-factor (work) = 0.1367          |
| start r-factor (free) = 0.2015      final r-factor (free) = 0.1880          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5184 = 0.81 * 1.00 * 5.5622 + 1.00 * 0.0124                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3556 = 0.81 * 1.00 * 5.3598 + 1.00 * 0.0134                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.999)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.32   13.88    None  None   None       |
|    all(noH): 2823   0      0.00    87.32   13.88    None  None   None       |
|    Sol.    : 438    0      1.84    87.32   39.26    None  None   None       |
|    Mac.    : 2385   0      0.00    81.01   9.21     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 -   8.732: 1538   |   5:    43.662 -  52.394:   94        |
|      1:     8.732 -  17.465:  658   |   6:    52.394 -  61.126:   71        |
|      2:    17.465 -  26.197:  188   |   7:    61.126 -  69.859:   41        |
|      3:    26.197 -  34.929:  118   |   8:    69.859 -  78.591:   10        |
|      4:    34.929 -  43.662:  100   |   9:    78.591 -  87.323:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1367 r_free = 0.1880             target_work(ml) = 5.325         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1366 r_free = 0.1879             target_work(ml) = 5.325         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1366   r_free= 0.1879   ksol= 0.32   Bsol= 54.29   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.66,2.41,3.68,0.00,0.00,0.00); trace/3= 2.92                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.324594                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1366   r_free= 0.1871   ksol= 0.32   Bsol= 54.29   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.99,1.60,3.15,0.00,0.00,0.00); trace/3= 2.25                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.322934                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.798447              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 116.719  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.161477              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.407  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1366      final r-factor (work) = 0.1232          |
| start r-factor (free) = 0.1871      final r-factor (free) = 0.1730          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5783 = 2.80 * 0.50 * 5.3633 + 1.00 * 0.0739                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4606 = 2.80 * 0.50 * 5.2839 + 1.00 * 0.0673                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1232      final r-factor (work) = 0.1227          |
| start r-factor (free) = 0.1730      final r-factor (free) = 0.1678          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8665 = 0.16 * 1.00 * 5.2839 + 1.00 * 0.0132                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8599 = 0.16 * 1.00 * 5.2416 + 1.00 * 0.0135                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.999)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.23   13.20    None  None   None       |
|    all(noH): 2823   0      0.00    83.23   13.20    None  None   None       |
|    Sol.    : 438    0      2.97    83.23   36.60    None  None   None       |
|    Mac.    : 2385   0      0.00    79.69   8.90     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 -   8.324: 1516   |   5:    41.617 -  49.941:   89        |
|      1:     8.324 -  16.647:  711   |   6:    49.941 -  58.264:   62        |
|      2:    16.647 -  24.970:  173   |   7:    58.264 -  66.588:   35        |
|      3:    24.970 -  33.294:  112   |   8:    66.588 -  74.911:   16        |
|      4:    33.294 -  41.617:  104   |   9:    74.911 -  83.234:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1227 r_free = 0.1678             target_work(ml) = 5.224         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1226 r_free = 0.1675             target_work(ml) = 5.223         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1226   r_free= 0.1675   ksol= 0.32   Bsol= 54.29   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.99,1.60,3.15,0.00,0.00,0.00); trace/3= 2.25                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.222942                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1226   r_free= 0.1674   ksol= 0.32   Bsol= 51.69   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.80,1.40,3.08,0.00,0.00,0.00); trace/3= 2.09                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.222851                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.741374              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 145.057  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.203033              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.114   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1226      final r-factor (work) = 0.1207          |
| start r-factor (free) = 0.1674      final r-factor (free) = 0.1631          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6304 = 1.74 * 0.50 * 5.2408 + 1.00 * 0.0673                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5989 = 1.74 * 0.50 * 5.2164 + 1.00 * 0.0570                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1207      final r-factor (work) = 0.1202          |
| start r-factor (free) = 0.1631      final r-factor (free) = 0.1630          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0714 = 0.20 * 1.00 * 5.2164 + 1.00 * 0.0123                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0750 = 0.20 * 1.00 * 5.2042 + 1.00 * 0.0184                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.999)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.88   12.90    None  None   None       |
|    all(noH): 2823   0      0.00    79.88   12.90    None  None   None       |
|    Sol.    : 438    0      2.80    77.46   35.16    None  None   None       |
|    Mac.    : 2385   0      0.00    79.88   8.81     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.988: 1459   |   5:    39.938 -  47.926:   86        |
|      1:     7.988 -  15.975:  736   |   6:    47.926 -  55.913:   71        |
|      2:    15.975 -  23.963:  195   |   7:    55.913 -  63.901:   24        |
|      3:    23.963 -  31.950:  116   |   8:    63.901 -  71.888:   18        |
|      4:    31.950 -  39.938:  113   |   9:    71.888 -  79.876:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1202 r_free = 0.1630             target_work(ml) = 5.205         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1200 r_free = 0.1629             target_work(ml) = 5.204         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1200   r_free= 0.1629   ksol= 0.32   Bsol= 51.69   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.80,1.40,3.08,0.00,0.00,0.00); trace/3= 2.09                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.204010                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1989 -  4.7123 0.99   1420  158 0.0996 0.1335      5.3873      5.5784|
|  2:  4.7123 -  3.7589 0.99   1374  155 0.0907 0.1113      5.4753      5.6305|
|  3:  3.7589 -  3.2892 0.99   1341  142 0.1125 0.1620      5.5167      5.8578|
|  4:  3.2892 -  2.9910 0.99   1332  155 0.1307 0.1733      5.4937      5.6512|
|  5:  2.9910 -  2.7780 0.99   1338  149 0.1447 0.1753      5.3859      5.5824|
|  6:  2.7780 -  2.6151 0.99   1324  146 0.1327 0.2004      5.2498      5.5192|
|  7:  2.6151 -  2.4847 0.99   1309  137 0.1391 0.1628       5.238      5.3439|
|  8:  2.4847 -  2.3770 0.98   1299  152 0.1280 0.1822       5.131      5.3938|
|  9:  2.3770 -  2.2858 0.98   1305  148 0.1328 0.1988      5.1261      5.3996|
| 10:  2.2858 -  2.2072 1.00   1300  147 0.1220 0.1670      5.0087      5.2023|
| 11:  2.2072 -  2.1383 0.98   1312  136 0.1197 0.1974      4.9968      5.3925|
| 12:  2.1383 -  2.0774 0.98   1292  145 0.1232 0.1697      4.9096      5.1291|
| 13:  2.0774 -  2.0228 0.98   1265  141 0.1216 0.1673       4.821      5.0306|
| 14:  2.0228 -  1.9736 0.32    419   48 0.1155 0.1489      4.7281      4.8453|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1989 -  4.7123  1420   158  0.94   9.00   0.97     0.95       7056.29|
|  2:  4.7123 -  3.7589  1374   155  0.95   8.10   1.01     0.99       9405.04|
|  3:  3.7589 -  3.2892  1341   142  0.93  11.84   1.02     1.02      11084.60|
|  4:  3.2892 -  2.9910  1332   155  0.91  14.45   1.00     0.98      10885.01|
|  5:  2.9910 -  2.7780  1338   149  0.89  16.81   0.99     0.97       9054.90|
|  6:  2.7780 -  2.6151  1324   146  0.89  16.72   0.98     0.96       7443.48|
|  7:  2.6151 -  2.4847  1309   137  0.90  16.41   0.99     0.96       6835.85|
|  8:  2.4847 -  2.3770  1299   152  0.90  16.60   0.98     0.96       5933.97|
|  9:  2.3770 -  2.2858  1305   148  0.89  17.11   1.00     0.95       5907.73|
| 10:  2.2858 -  2.2072  1300   147  0.89  16.92   1.00     0.96       4871.38|
| 11:  2.2072 -  2.1383  1312   136  0.90  16.60   0.99     0.94       4742.41|
| 12:  2.1383 -  2.0774  1292   145  0.90  16.68   1.01     1.01       4182.43|
| 13:  2.0774 -  2.0228  1265   141  0.90  17.03   0.99     0.97       3530.32|
| 14:  2.0228 -  1.9736   419    48  0.91  15.04   0.98     0.96       2803.42|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2803.42 max =        11084.60 mean =      6933.71|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.83 mean =        14.87|
|phase err.(test): min =        0.00 max =           89.46 mean =        14.27|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1200   r_free= 0.1629   ksol= 0.32   Bsol= 53.76   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.30,-0.71,1.01,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.203992                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1200   r_free= 0.1629   ksol= 0.32   Bsol= 53.76   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.30,-0.71,1.01,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.203992                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1989 -  4.7123 0.99   1420  158 0.0996 0.1335      5.3873      5.5783|
|  2:  4.7123 -  3.7589 0.99   1374  155 0.0907 0.1113      5.4753      5.6305|
|  3:  3.7589 -  3.2892 0.99   1341  142 0.1125 0.1620      5.5166      5.8575|
|  4:  3.2892 -  2.9910 0.99   1332  155 0.1306 0.1733      5.4936      5.6512|
|  5:  2.9910 -  2.7780 0.99   1338  149 0.1447 0.1754      5.3859      5.5826|
|  6:  2.7780 -  2.6151 0.99   1324  146 0.1326 0.2002      5.2498      5.5187|
|  7:  2.6151 -  2.4847 0.99   1309  137 0.1391 0.1629      5.2379      5.3438|
|  8:  2.4847 -  2.3770 0.98   1299  152 0.1280 0.1821      5.1309      5.3938|
|  9:  2.3770 -  2.2858 0.98   1305  148 0.1328 0.1987      5.1261      5.3993|
| 10:  2.2858 -  2.2072 1.00   1300  147 0.1219 0.1670      5.0088      5.2028|
| 11:  2.2072 -  2.1383 0.98   1312  136 0.1197 0.1975      4.9969      5.3928|
| 12:  2.1383 -  2.0774 0.98   1292  145 0.1232 0.1698      4.9098      5.1294|
| 13:  2.0774 -  2.0228 0.98   1265  141 0.1216 0.1671      4.8209      5.0301|
| 14:  2.0228 -  1.9736 0.32    419   48 0.1155 0.1489      4.7276      4.8449|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1989 -  4.7123  1420   158  0.94   8.99   0.97     0.95       7053.96|
|  2:  4.7123 -  3.7589  1374   155  0.95   8.10   1.01     0.99       9402.59|
|  3:  3.7589 -  3.2892  1341   142  0.93  11.83   1.02     1.02      11082.62|
|  4:  3.2892 -  2.9910  1332   155  0.91  14.45   1.00     0.98      10884.39|
|  5:  2.9910 -  2.7780  1338   149  0.89  16.81   0.99     0.97       9052.56|
|  6:  2.7780 -  2.6151  1324   146  0.89  16.71   0.98     0.95       7442.61|
|  7:  2.6151 -  2.4847  1309   137  0.90  16.41   0.99     0.96       6834.02|
|  8:  2.4847 -  2.3770  1299   152  0.90  16.60   0.98     0.96       5932.88|
|  9:  2.3770 -  2.2858  1305   148  0.89  17.11   0.99     0.95       5906.32|
| 10:  2.2858 -  2.2072  1300   147  0.89  16.93   1.00     0.96       4874.16|
| 11:  2.2072 -  2.1383  1312   136  0.90  16.61   0.99     0.94       4746.14|
| 12:  2.1383 -  2.0774  1292   145  0.90  16.68   1.01     1.01       4185.34|
| 13:  2.0774 -  2.0228  1265   141  0.90  17.02   0.99     0.96       3529.69|
| 14:  2.0228 -  1.9736   419    48  0.91  15.03   0.98     0.96       2800.95|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2800.95 max =        11082.62 mean =      6933.16|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.83 mean =        14.87|
|phase err.(test): min =        0.00 max =           89.46 mean =        14.26|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.999)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.07    81.95   14.97    None  None   None       |
|    all(noH): 2823   0      2.07    81.95   14.97    None  None   None       |
|    Sol.    : 438    0      4.87    79.53   37.23    None  None   None       |
|    Mac.    : 2385   0      2.07    81.95   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:     2.071 -  10.059: 1459   |   5:    42.009 -  49.997:   86        |
|      1:    10.059 -  18.047:  736   |   6:    49.997 -  57.985:   71        |
|      2:    18.047 -  26.034:  195   |   7:    57.985 -  65.972:   24        |
|      3:    26.034 -  34.022:  116   |   8:    65.972 -  73.960:   18        |
|      4:    34.022 -  42.009:  113   |   9:    73.960 -  81.947:    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)= 324         
Filter by distance & map next to the model:
   mapped sites are within: 0.374 - 4.790
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 321 from: 324
   mapped sites are within: 0.700 - 4.790

peak=   10.765 closest distance to " CB  VAL A 230 " =    1.484
peak=    7.565 closest distance to " CG2 VAL A 296 " =    1.184
peak=    6.528 closest distance to " CD2 LEU A   5 " =    1.307
peak=    5.668 closest distance to " CG  PRO A  54 " =    1.471
peak=    5.543 closest distance to " O   HOH Z 111 " =    1.882
peak=    5.519 closest distance to " O   HOH Z 232 " =    2.264
peak=    5.508 closest distance to " NE2 GLN A  11 " =    1.178
peak=    5.396 closest distance to " CG  LEU A   5 " =    1.223
peak=    5.126 closest distance to " CG  LEU A 228 " =    1.185
peak=    5.122 closest distance to " CB  GLN A 223 " =    1.454
peak=    5.116 closest distance to " O   HOH Z   9 " =    1.908
peak=    5.099 closest distance to " CG  PRO A 198 " =    1.341
peak=    4.996 closest distance to " O   HOH Z 142 " =    2.110
peak=    4.982 closest distance to " O   HOH Z   7 " =    1.503
peak=    4.940 closest distance to " O   HOH Z 222 " =    1.317
peak=    4.835 closest distance to " CB  PRO A  54 " =    1.044
peak=    4.814 closest distance to " O   HOH Z 287 " =    2.003
peak=    4.767 closest distance to " CB  SER A  63 " =    1.318
peak=    4.653 closest distance to " CG  PRO A 280 " =    0.890
peak=    4.647 closest distance to " CB  GLN A 183 " =    1.210
peak=    4.632 closest distance to " O   HOH Z 427 " =    2.676
peak=    4.581 closest distance to " CB  ASN A 148 " =    1.371
peak=    4.567 closest distance to " O   HOH Z 130 " =    1.116
peak=    4.536 closest distance to " ND2 ASN A 187 " =    1.579
peak=    4.503 closest distance to " CB  ASP A 124 " =    0.793
peak=    4.489 closest distance to " CD2 LEU A 228 " =    1.218
peak=    4.452 closest distance to " O   HOH Z 126 " =    2.057
peak=    4.441 closest distance to " O   PRO A 198 " =    1.599
peak=    4.415 closest distance to " O   HOH Z 425 " =    1.566
peak=    4.398 closest distance to " O   HOH Z 369 " =    2.033
peak=    4.393 closest distance to " CG  PRO A 213 " =    1.285
peak=    4.390 closest distance to " CB  VAL A 230 " =    1.184
peak=    4.366 closest distance to " O   HOH Z 298 " =    1.930
peak=    4.360 closest distance to " CA  VAL A 296 " =    1.135
peak=    4.349 closest distance to " O   HOH Z 265 " =    2.139
peak=    4.312 closest distance to " CB  ASN A  39 " =    0.939
peak=    4.311 closest distance to " O   HOH Z   2 " =    1.765
peak=    4.298 closest distance to " CG  LEU A 167 " =    1.262
peak=    4.297 closest distance to " O   HOH Z 303 " =    2.247
peak=    4.296 closest distance to " O   HOH Z  44 " =    2.359
peak=    4.295 closest distance to " CB  SER A   3 " =    1.483
peak=    4.292 closest distance to " CB  TRP A 266 " =    0.993
peak=    4.256 closest distance to " CB  SER A 216 " =    0.917
peak=    4.252 closest distance to " CD  ARG A  66 " =    2.232
peak=    4.241 closest distance to " CG  PRO A 243 " =    1.131
peak=    4.182 closest distance to " CB  ASN A 142 " =    0.965
peak=    4.164 closest distance to " CA  SER A  87 " =    0.917
peak=    4.117 closest distance to " O   HOH Z 423 " =    1.617
peak=    4.115 closest distance to " CB  ARG A 275 " =    0.948
peak=    4.107 closest distance to " CD  ARG A 159 " =    0.770
peak=    4.037 closest distance to " O   HOH Z  30 " =    1.755
peak=    4.028 closest distance to " NH1AARG A 145 " =    1.137
peak=    4.017 closest distance to " N   PHE A 130 " =    1.293
peak=    4.007 closest distance to " CB  ARG A  79 " =    1.394
peak=    4.002 closest distance to " CB  SER A 210 " =    0.822
peak=    3.998 closest distance to " O   HOH Z   1 " =    1.954
peak=    3.991 closest distance to " O   HOH Z  78 " =    1.607
peak=    3.989 closest distance to " CG  ARG A 138 " =    1.217
peak=    3.983 closest distance to " O   HOH Z 234 " =    3.924
peak=    3.959 closest distance to " O   HOH Z 126 " =    1.471
peak=    3.956 closest distance to " CB  GLU A 128 " =    1.038
peak=    3.955 closest distance to " O   HOH Z  88 " =    3.063
peak=    3.950 closest distance to " CB  ASN A 187 " =    1.035
peak=    3.941 closest distance to " CB  VAL A 202 " =    1.617
peak=    3.937 closest distance to " O   HOH Z 316 " =    3.048
peak=    3.932 closest distance to " CZ  PHE A 218 " =    1.042
peak=    3.930 closest distance to " CB  GLU A 152 " =    1.255
peak=    3.900 closest distance to " CA  ALA A  51 " =    1.028
peak=    3.896 closest distance to " NH2AARG A 190 " =    1.703
peak=    3.889 closest distance to " O   HOH Z 411 " =    3.434
peak=    3.884 closest distance to " O   HOH Z  63 " =    1.307
peak=    3.883 closest distance to " O   HOH Z 362 " =    2.495
peak=    3.879 closest distance to " ND1 HIS A  86 " =    1.769
peak=    3.871 closest distance to " O   HOH Z 389 " =    1.875
peak=    3.865 closest distance to " CB  VAL A 265 " =    1.370
peak=    3.851 closest distance to " O   HOH Z 272 " =    1.844
peak=    3.839 closest distance to " O   SER A  87 " =    2.389
peak=    3.829 closest distance to " O   HOH Z  78 " =    2.346
peak=    3.794 closest distance to " O   HOH Z 410 " =    1.549
peak=    3.787 closest distance to " O   HOH Z 437 " =    2.026
peak=    3.774 closest distance to " O   HOH Z 184 " =    1.486
peak=    3.767 closest distance to " CG2 THR A 221 " =    1.010
peak=    3.763 closest distance to " CB  MET A  40 " =    0.841
peak=    3.762 closest distance to " OD1 ASN A  69 " =    2.575
peak=    3.760 closest distance to " O   HOH Z 222 " =    2.226
peak=    3.758 closest distance to " O   HOH Z 261 " =    2.245
peak=    3.744 closest distance to " O   HOH Z  10 " =    1.834
peak=    3.742 closest distance to " O   HOH Z 346 " =    1.618
peak=    3.737 closest distance to " O   TYR A 116 " =    1.293
peak=    3.736 closest distance to " CD  ARG A  66 " =    2.507
peak=    3.728 closest distance to " CB  VAL A 250 " =    1.101
peak=    3.728 closest distance to " CB  SER A 212 " =    1.321
peak=    3.719 closest distance to " O   HOH Z 132 " =    2.599
peak=    3.718 closest distance to " CA  TYR A  30 " =    0.972
peak=    3.716 closest distance to " O   HOH Z 193 " =    1.919
peak=    3.716 closest distance to " NH1 ARG A  14 " =    0.931
peak=    3.699 closest distance to " O   HOH Z 214 " =    2.105
peak=    3.698 closest distance to " CG2 VAL A 257 " =    0.940
peak=    3.691 closest distance to " O   HOH Z 158 " =    3.047
peak=    3.671 closest distance to " NE AARG A 275 " =    1.411
peak=    3.668 closest distance to " CA  TYR A 116 " =    1.425
peak=    3.654 closest distance to " CB  ARG A 190 " =    1.616
peak=    3.651 closest distance to " CG  GLN A  88 " =    1.080
peak=    3.648 closest distance to " CB BVAL A  41 " =    1.330
peak=    3.646 closest distance to " CB  ASN A 110 " =    1.072
peak=    3.640 closest distance to " CB  LEU A 228 " =    1.200
peak=    3.638 closest distance to " O   HOH Z 403 " =    1.568
peak=    3.637 closest distance to " O   HOH Z 193 " =    2.031
peak=    3.629 closest distance to " O   HOH Z   1 " =    1.847
peak=    3.619 closest distance to " CA  THR A 264 " =    0.761
peak=    3.615 closest distance to " CB  ALA A 104 " =    0.728
peak=    3.613 closest distance to " CB  LEU A 143 " =    1.175
peak=    3.610 closest distance to " O   HOH Z 193 " =    1.701
peak=    3.609 closest distance to " CD  LYS A 166 " =    1.307
peak=    3.607 closest distance to " CZ  PHE A 192 " =    0.977
peak=    3.600 closest distance to " OG  SER A  97 " =    2.924
peak=    3.593 closest distance to " CB  GLU A  46 " =    0.970
peak=    3.584 closest distance to " O   HOH Z 217 " =    3.088
peak=    3.582 closest distance to " CB  THR A 157 " =    1.180
peak=    3.579 closest distance to " CD  ARG A 269 " =    0.929
peak=    3.577 closest distance to " O   HOH Z 380 " =    1.745
peak=    3.576 closest distance to " CA  ILE A 106 " =    0.773
peak=    3.574 closest distance to " CD1 LEU A 300 " =    1.212
peak=    3.567 closest distance to " CA  ASN A 215 " =    1.218
peak=    3.566 closest distance to " O   PRO A 198 " =    1.325
peak=    3.565 closest distance to " O   HOH Z 273 " =    2.667
peak=    3.559 closest distance to " OG  SER A  62 " =    2.816
peak=    3.555 closest distance to " O   HOH Z 148 " =    3.546
peak=    3.552 closest distance to " CG1 ILE A 151 " =    1.209
peak=    3.550 closest distance to " O   HOH Z 368 " =    2.014
peak=    3.548 closest distance to " O   HOH Z 153 " =    3.709
peak=    3.546 closest distance to " O   HOH Z   3 " =    1.901
peak=    3.545 closest distance to " O   HOH Z 263 " =    1.698
peak=    3.536 closest distance to " O   HOH Z  59 " =    1.957
peak=    3.533 closest distance to " O   ASN A 209 " =    1.424
peak=    3.517 closest distance to " CB  HIS A 108 " =    0.785
peak=    3.513 closest distance to " NE2 HIS A 207 " =    1.091
peak=    3.512 closest distance to " CG BARG A 102 " =    1.909
peak=    3.511 closest distance to " CE  LYS A  76 " =    0.873
peak=    3.508 closest distance to " N   SER A 271 " =    0.981
peak=    3.504 closest distance to " CD2 TYR A 186 " =    1.126
peak=    3.495 closest distance to " NH2AARG A 145 " =    1.149
peak=    3.490 closest distance to " CD1 LEU A   5 " =    1.356
peak=    3.483 closest distance to " CB  GLN A  88 " =    1.301
peak=    3.483 closest distance to " OE2 GLU A   2 " =    1.926
peak=    3.482 closest distance to " O   HOH Z 109 " =    2.475
peak=    3.482 closest distance to " OG BSER A 164 " =    2.301
peak=    3.482 closest distance to " CA  ALA A 154 " =    1.027
peak=    3.480 closest distance to " O   HOH Z  21 " =    1.753
peak=    3.478 closest distance to " CA  ALA A 299 " =    0.972
peak=    3.472 closest distance to " O   HOH Z 392 " =    1.262
peak=    3.472 closest distance to " O   HOH Z  40 " =    1.963
peak=    3.458 closest distance to " CD BLYS A 290 " =    1.047
peak=    3.458 closest distance to " O   HOH Z 332 " =    1.560
peak=    3.456 closest distance to " CA  ILE A 234 " =    1.010
peak=    3.455 closest distance to " CA  ARG A  36 " =    1.167
peak=    3.452 closest distance to " CB  GLU A 277 " =    3.577
peak=    3.448 closest distance to " CG1 ILE A  49 " =    1.533
peak=    3.444 closest distance to " CB  LYS A 117 " =    1.250
peak=    3.442 closest distance to " O   HOH Z 171 " =    4.166
peak=    3.438 closest distance to " CB  LEU A  83 " =    0.782
peak=    3.434 closest distance to " O   HOH Z 419 " =    1.837
peak=    3.432 closest distance to " O   HOH Z 130 " =    1.898
peak=    3.428 closest distance to " O   HOH Z 147 " =    1.726
peak=    3.427 closest distance to " CA  ARG A 195 " =    1.237
peak=    3.424 closest distance to " CE3 TRP A 150 " =    0.960
peak=    3.423 closest distance to " CB  LEU A 237 " =    0.839
peak=    3.422 closest distance to " CA  ALA A 295 " =    0.991
peak=    3.416 closest distance to " O   HOH Z 156 " =    3.006
peak=    3.414 closest distance to " O   HOH Z  61 " =    1.610
peak=    3.414 closest distance to " O   HOH Z 359 " =    1.369
peak=    3.410 closest distance to " O   HOH Z 180 " =    2.054
peak=    3.408 closest distance to " N   SER A 135 " =    1.222
peak=    3.405 closest distance to " CD1AILE A 234 " =    0.976
peak=    3.405 closest distance to " O   HOH Z  61 " =    1.601
peak=    3.403 closest distance to " CE3 TRP A  85 " =    1.125
peak=    3.401 closest distance to " CA  GLY A 136 " =    0.906
peak=    3.394 closest distance to " CB  ALA A 248 " =    1.053
peak=    3.393 closest distance to " N   GLN A 278 " =    1.085
peak=    3.386 closest distance to " CZ3 TRP A 266 " =    1.095
peak=    3.379 closest distance to " O   HOH Z 284 " =    3.086
peak=    3.378 closest distance to " CD  ARG A  24 " =    1.113
peak=    3.378 closest distance to " NH2BARG A 190 " =    1.471
peak=    3.375 closest distance to " CA  ARG A 102 " =    1.155
peak=    3.375 closest distance to " O   HOH Z  68 " =    1.985
peak=    3.374 closest distance to " CA  LEU A 282 " =    1.090
peak=    3.367 closest distance to " O   HOH Z 368 " =    3.579
peak=    3.367 closest distance to " O   HOH Z 128 " =    1.768
peak=    3.363 closest distance to " O   HOH Z 305 " =    3.578
peak=    3.362 closest distance to " CB  ASP A 140 " =    0.870
peak=    3.357 closest distance to " CG1 VAL A 296 " =    1.243
peak=    3.354 closest distance to " O   HOH Z 424 " =    3.001
peak=    3.352 closest distance to " CG1 VAL A 153 " =    0.902
peak=    3.352 closest distance to " O   HOH Z 310 " =    2.211
peak=    3.351 closest distance to " O   HOH Z  57 " =    1.145
peak=    3.350 closest distance to " O   HOH Z 248 " =    1.729
peak=    3.340 closest distance to " ND1 HIS A  81 " =    1.837
peak=    3.340 closest distance to " OH  TYR A 186 " =    0.989
peak=    3.338 closest distance to " CB  THR A  82 " =    1.316
peak=    3.337 closest distance to " CZ3 TRP A 123 " =    1.407
peak=    3.333 closest distance to " CB  ILE A 120 " =    1.348
peak=    3.325 closest distance to " CE1 TYR A 186 " =    1.310
peak=    3.324 closest distance to " O   HOH Z 183 " =    1.335
peak=    3.322 closest distance to " O   HOH Z 133 " =    1.725
peak=    3.322 closest distance to " O   HOH Z 128 " =    2.052
peak=    3.322 closest distance to " O   HOH Z 188 " =    1.989
peak=    3.321 closest distance to " O   HOH Z 116 " =    3.230
peak=    3.316 closest distance to " O   HOH Z  22 " =    1.975
peak=    3.313 closest distance to " O   HOH Z 409 " =    2.580
peak=    3.311 closest distance to " CB  ALA A 114 " =    1.070
peak=    3.310 closest distance to " O   HOH Z 350 " =    1.594
peak=    3.309 closest distance to " O   HOH Z 352 " =    1.804
peak=    3.308 closest distance to " CB  TRP A 179 " =    1.454
peak=    3.305 closest distance to " CA  ALA A 291 " =    0.928
peak=    3.304 closest distance to " O   HOH Z  20 " =    1.775
peak=    3.302 closest distance to " CB  ALA A  34 " =    1.119
peak=    3.302 closest distance to " OG ASER A 212 " =    1.731
peak=    3.302 closest distance to " CA  LYS A 290 " =    1.322
peak=    3.302 closest distance to " O   HOH Z 326 " =    2.161
peak=    3.301 closest distance to " O   HOH Z  58 " =    1.838
peak=    3.298 closest distance to " OG BSER A 210 " =    1.135
peak=    3.294 closest distance to " O   HOH Z 258 " =    2.231
peak=    3.292 closest distance to " O   HOH Z 196 " =    1.400
peak=    3.289 closest distance to " CB  ALA A   1 " =    4.790
peak=    3.285 closest distance to " O   HOH Z 185 " =    1.898
peak=    3.284 closest distance to " CD1 ILE A  33 " =    1.793
peak=    3.284 closest distance to " CB  SER A  62 " =    1.162
peak=    3.277 closest distance to " N   ARG A 156 " =    1.290
peak=    3.276 closest distance to " OG BSER A 212 " =    2.710
peak=    3.275 closest distance to " CB  GLN A 103 " =    1.062
peak=    3.273 closest distance to " CB  MET A  47 " =    1.014
peak=    3.270 closest distance to " CA  TYR A  30 " =    1.087
peak=    3.269 closest distance to " OG  SER A  62 " =    3.062
peak=    3.267 closest distance to " CB  PRO A 243 " =    1.216
peak=    3.267 closest distance to " CD2 TRP A 179 " =    1.268
peak=    3.266 closest distance to " CA  ARG A 159 " =    1.234
peak=    3.266 closest distance to " O   HOH Z 406 " =    1.546
peak=    3.265 closest distance to " CG BARG A 275 " =    1.245
peak=    3.261 closest distance to " N   TYR A  15 " =    0.881
peak=    3.259 closest distance to " CG  ARG A 159 " =    0.974
peak=    3.258 closest distance to " CA  GLU A 152 " =    1.015
peak=    3.257 closest distance to " CB  GLN A  89 " =    1.203
peak=    3.255 closest distance to " N   ASN A 127 " =    1.262
peak=    3.247 closest distance to " O   THR A 294 " =    1.119
peak=    3.246 closest distance to " O   HOH Z 345 " =    3.367
peak=    3.246 closest distance to " CG1 ILE A  33 " =    1.283
peak=    3.244 closest distance to " OD2 ASP A 286 " =    2.761
peak=    3.243 closest distance to " CB  GLU A 175 " =    1.024
peak=    3.240 closest distance to " O   HOH Z 371 " =    2.727
peak=    3.232 closest distance to " N   CYS A 260 " =    0.700
peak=    3.232 closest distance to " CD  GLN A 240 " =    1.645
peak=    3.232 closest distance to " CB  TRP A 150 " =    1.358
peak=    3.231 closest distance to " O   HOH Z 422 " =    2.676
peak=    3.231 closest distance to " CB  SER A 276 " =    1.262
peak=    3.230 closest distance to " CA  ALA A 233 " =    1.146
peak=    3.225 closest distance to " CG2 ILE A  20 " =    1.603
peak=    3.224 closest distance to " CB  ALA A  10 " =    0.911
peak=    3.224 closest distance to " CG  GLN A  89 " =    1.542
peak=    3.223 closest distance to " OG  SER A 276 " =    1.165
peak=    3.223 closest distance to " CB  ALA A 291 " =    1.251
peak=    3.222 closest distance to " CA  ALA A  21 " =    1.215
peak=    3.220 closest distance to " NH1 ARG A 138 " =    1.182
peak=    3.219 closest distance to " OG  SER A 135 " =    1.298
peak=    3.216 closest distance to " CZ  PHE A  38 " =    1.248
peak=    3.212 closest distance to " CZ3 TRP A  92 " =    1.404
peak=    3.211 closest distance to " O   MET A 105 " =    1.738
peak=    3.211 closest distance to " CA  LYS A 117 " =    1.132
peak=    3.210 closest distance to " CD  ARG A 219 " =    1.098
peak=    3.205 closest distance to " O   HOH Z 329 " =    2.990
peak=    3.204 closest distance to " CE3 TRP A 274 " =    1.234
peak=    3.202 closest distance to " ND2 ASN A 249 " =    0.832
peak=    3.198 closest distance to " CA  TYR A 186 " =    1.578
peak=    3.196 closest distance to " O   HOH Z 327 " =    1.662
peak=    3.191 closest distance to " CB  ALA A   9 " =    1.526
peak=    3.190 closest distance to " CB  ALA A 180 " =    1.413
peak=    3.189 closest distance to " CD  ARG A 195 " =    3.454
peak=    3.188 closest distance to " O   HOH Z 361 " =    1.337
peak=    3.186 closest distance to " O   HOH Z  59 " =    1.801
peak=    3.184 closest distance to " CB  ALA A 248 " =    1.297
peak=    3.182 closest distance to " CB  ALA A 242 " =    0.787
peak=    3.179 closest distance to " O   HOH Z 122 " =    1.885
peak=    3.178 closest distance to " O   HOH Z  65 " =    1.161
peak=    3.178 closest distance to " CA  MET A 105 " =    0.883
peak=    3.177 closest distance to " CG2 ILE A 234 " =    0.974
peak=    3.166 closest distance to " CG  MET A 113 " =    1.373
peak=    3.165 closest distance to " CD2 LEU A 255 " =    1.678
peak=    3.164 closest distance to " CG  LYS A 119 " =    1.216
peak=    3.163 closest distance to " O   HOH Z 154 " =    1.895
peak=    3.162 closest distance to " O   HOH Z 148 " =    2.257
peak=    3.157 closest distance to " CG  GLN A 278 " =    1.334
peak=    3.156 closest distance to " OG BSER A 134 " =    2.880
peak=    3.155 closest distance to " CA  THR A 221 " =    0.892
peak=    3.155 closest distance to " O   HOH Z 385 " =    3.883
peak=    3.155 closest distance to " CG2 ILE A 239 " =    0.722
peak=    3.150 closest distance to " O   HOH Z 290 " =    1.165
peak=    3.147 closest distance to " CB  ASN A 173 " =    0.999
peak=    3.144 closest distance to " O   HOH Z 334 " =    1.529
peak=    3.142 closest distance to " CD  ARG A  14 " =    1.238
peak=    3.139 closest distance to " CA  ALA A 160 " =    1.010
peak=    3.138 closest distance to " CA  CYS A 201 " =    1.630
peak=    3.136 closest distance to " CB  TYR A 116 " =    0.969
peak=    3.134 closest distance to " O   HOH Z  85 " =    2.004
peak=    3.130 closest distance to " O   HOH Z 425 " =    1.960
peak=    3.130 closest distance to " O   HOH Z 173 " =    1.735
peak=    3.130 closest distance to " O   PHE A 192 " =    1.368
peak=    3.129 closest distance to " O   CYS A 168 " =    1.321
peak=    3.126 closest distance to " O   HOH Z 172 " =    2.791
peak=    3.121 closest distance to " CA  GLY A 267 " =    0.991
peak=    3.120 closest distance to " CA  MET A  40 " =    1.094
peak=    3.116 closest distance to " N   SER A 146 " =    1.613
peak=    3.110 closest distance to " O   HOH Z 291 " =    1.563
peak=    3.102 closest distance to " O   HOH Z  97 " =    1.974
peak=    3.100 closest distance to " OG1 THR A 294 " =    3.638
peak=    3.091 closest distance to " CD1 LEU A 281 " =    1.076
peak=    3.078 closest distance to " NZ BLYS A 290 " =    0.967
peak=    3.072 closest distance to " CB  TYR A  30 " =    1.417
peak=    3.065 closest distance to " O   HOH Z 344 " =    3.028
peak=    3.064 closest distance to " CB  ASN A 224 " =    0.985
peak=    3.063 closest distance to " CB  ALA A 114 " =    1.450
peak=    3.051 closest distance to " O   HOH Z 294 " =    1.541
peak=    3.032 closest distance to " O   HOH Z 260 " =    1.413

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.428 - 5.425
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 198 from: 204
   mapped sites are within: 0.725 - 5.425

peak=   -5.719 closest distance to " CG2 VAL A 230 " =    0.744
peak=   -4.615 closest distance to " O   HOH Z 290 " =    1.110
peak=   -4.579 closest distance to " CB  PRO A 243 " =    2.616
peak=   -4.307 closest distance to " CD  ARG A  14 " =    3.188
peak=   -4.215 closest distance to " O   HOH Z 231 " =    1.725
peak=   -4.145 closest distance to " O   PRO A 198 " =    1.157
peak=   -4.106 closest distance to " N   ALA A  43 " =    2.579
peak=   -4.082 closest distance to " CG1 VAL A 112 " =    2.632
peak=   -4.058 closest distance to " O   HOH Z 351 " =    1.458
peak=   -4.054 closest distance to " CD1 TYR A 247 " =    2.835
peak=   -4.036 closest distance to " NH2 ARG A  79 " =    1.971
peak=   -4.000 closest distance to " CD1 LEU A 255 " =    2.992
peak=   -3.998 closest distance to " CG2 VAL A 296 " =    1.101
peak=   -3.987 closest distance to " N   THR A 157 " =    1.535
peak=   -3.967 closest distance to " O   GLY A 203 " =    2.538
peak=   -3.961 closest distance to " CD  ARG A 156 " =    2.044
peak=   -3.929 closest distance to " O   HOH Z 211 " =    1.202
peak=   -3.878 closest distance to " O   HOH Z  65 " =    1.110
peak=   -3.870 closest distance to " OG BSER A 134 " =    1.506
peak=   -3.820 closest distance to " CB  ALA A 161 " =    2.626
peak=   -3.817 closest distance to " CA  GLY A 241 " =    2.419
peak=   -3.810 closest distance to " O   HOH Z  52 " =    1.575
peak=   -3.801 closest distance to " O   HOH Z 389 " =    2.098
peak=   -3.796 closest distance to " O   HOH Z 411 " =    5.240
peak=   -3.789 closest distance to " CD  GLN A 223 " =    2.394
peak=   -3.786 closest distance to " O   HOH Z 394 " =    1.485
peak=   -3.766 closest distance to " CZ3 TRP A 179 " =    1.193
peak=   -3.744 closest distance to " CB  ALA A  43 " =    2.546
peak=   -3.720 closest distance to " OE1 GLN A  88 " =    0.962
peak=   -3.711 closest distance to " O   ILE A  49 " =    1.718
peak=   -3.707 closest distance to " O   VAL A  67 " =    2.469
peak=   -3.696 closest distance to " O   HOH Z 359 " =    1.562
peak=   -3.694 closest distance to " CD2 LEU A   5 " =    0.943
peak=   -3.688 closest distance to " C   ALA A 158 " =    1.436
peak=   -3.682 closest distance to " CB  PRO A 163 " =    2.397
peak=   -3.676 closest distance to " CZ2 TRP A 274 " =    0.860
peak=   -3.674 closest distance to " ND2 ASN A 187 " =    1.487
peak=   -3.667 closest distance to " CB  ALA A 248 " =    2.104
peak=   -3.666 closest distance to " CD1 LEU A 101 " =    2.351
peak=   -3.654 closest distance to " NH2AARG A 275 " =    5.425
peak=   -3.654 closest distance to " CG  MET A 105 " =    0.983
peak=   -3.653 closest distance to " O   HOH Z  51 " =    0.931
peak=   -3.648 closest distance to " CD  GLU A 277 " =    1.021
peak=   -3.636 closest distance to " CE2 TYR A  30 " =    2.760
peak=   -3.628 closest distance to " O   ARG A 145 " =    1.442
peak=   -3.627 closest distance to " CB  ALA A 248 " =    2.471
peak=   -3.623 closest distance to " O   PRO A 163 " =    1.960
peak=   -3.603 closest distance to " OG  SER A  87 " =    1.443
peak=   -3.600 closest distance to " CB  ALA A   9 " =    2.502
peak=   -3.599 closest distance to " O   HOH Z  60 " =    2.650
peak=   -3.582 closest distance to " O   HOH Z 185 " =    2.206
peak=   -3.577 closest distance to " CA  GLY A  98 " =    1.957
peak=   -3.572 closest distance to " CG  LEU A   5 " =    0.918
peak=   -3.563 closest distance to " O   HOH Z  43 " =    1.758
peak=   -3.557 closest distance to " OG  SER A  97 " =    2.237
peak=   -3.551 closest distance to " O   HOH Z 111 " =    1.824
peak=   -3.541 closest distance to " CD  GLN A  58 " =    0.827
peak=   -3.541 closest distance to " CB  TRP A  85 " =    2.513
peak=   -3.540 closest distance to " CA  ASP A  27 " =    2.425
peak=   -3.534 closest distance to " O   VAL A 189 " =    2.506
peak=   -3.520 closest distance to " O   HOH Z 166 " =    1.991
peak=   -3.519 closest distance to " CD1 LEU A 228 " =    2.381
peak=   -3.516 closest distance to " CD  PRO A 213 " =    2.067
peak=   -3.508 closest distance to " CB  VAL A 230 " =    0.997
peak=   -3.500 closest distance to " O   HOH Z  39 " =    0.900
peak=   -3.495 closest distance to " O   HOH Z 139 " =    0.966
peak=   -3.494 closest distance to " CA  GLY A 203 " =    2.425
peak=   -3.492 closest distance to " O   HOH Z 193 " =    1.897
peak=   -3.488 closest distance to " C   LYS A  76 " =    1.285
peak=   -3.486 closest distance to " O   HOH Z 103 " =    1.862
peak=   -3.484 closest distance to " O   HOH Z 275 " =    1.886
peak=   -3.482 closest distance to " O   HOH Z 140 " =    1.294
peak=   -3.479 closest distance to " CG  TRP A 266 " =    1.781
peak=   -3.476 closest distance to " CD2 TYR A 293 " =    1.881
peak=   -3.476 closest distance to " O   GLY A  17 " =    1.285
peak=   -3.474 closest distance to " C   LEU A 222 " =    0.845
peak=   -3.470 closest distance to " O   GLY A  80 " =    2.571
peak=   -3.467 closest distance to " CE  LYS A  76 " =    2.662
peak=   -3.467 closest distance to " CB  PHE A 130 " =    1.324
peak=   -3.466 closest distance to " C   MET A 188 " =    1.445
peak=   -3.462 closest distance to " O   GLY A 211 " =    1.252
peak=   -3.439 closest distance to " O   HOH Z 359 " =    3.237
peak=   -3.417 closest distance to " O   HOH Z 166 " =    1.306
peak=   -3.405 closest distance to " O   HOH Z   2 " =    1.832
peak=   -3.399 closest distance to " O   HOH Z 281 " =    2.613
peak=   -3.397 closest distance to " CA  GLY A 241 " =    3.117
peak=   -3.392 closest distance to " CD  LYS A 289 " =    2.447
peak=   -3.391 closest distance to " N   ALA A 226 " =    2.096
peak=   -3.389 closest distance to " CG  GLN A  88 " =    0.863
peak=   -3.385 closest distance to " O   HOH Z 131 " =    4.083
peak=   -3.381 closest distance to " CB  ASP A 132 " =    2.336
peak=   -3.374 closest distance to " ND2 ASN A  45 " =    1.223
peak=   -3.368 closest distance to " O   HOH Z 407 " =    3.296
peak=   -3.368 closest distance to " O   HOH Z  44 " =    2.307
peak=   -3.355 closest distance to " O   HOH Z 238 " =    0.880
peak=   -3.355 closest distance to " CE BMET A  47 " =    1.606
peak=   -3.354 closest distance to " CG2 ILE A 151 " =    2.619
peak=   -3.350 closest distance to " O   HOH Z 191 " =    5.372
peak=   -3.349 closest distance to " CB  CYS A 201 " =    2.282
peak=   -3.344 closest distance to " ND2 ASN A  60 " =    1.456
peak=   -3.343 closest distance to " CE2 PHE A 218 " =    2.519
peak=   -3.336 closest distance to " O   HOH Z 198 " =    2.405
peak=   -3.335 closest distance to " CB  PHE A 192 " =    1.659
peak=   -3.330 closest distance to " O   HOH Z  73 " =    2.023
peak=   -3.325 closest distance to " C   ASN A 285 " =    2.314
peak=   -3.325 closest distance to " CE3 TRP A 150 " =    2.051
peak=   -3.324 closest distance to " CG1 VAL A 296 " =    1.374
peak=   -3.324 closest distance to " O   SER A  87 " =    2.012
peak=   -3.320 closest distance to " O   HOH Z 389 " =    1.401
peak=   -3.312 closest distance to " CG1 VAL A 112 " =    3.181
peak=   -3.308 closest distance to " O   ASP A  27 " =    1.805
peak=   -3.305 closest distance to " CG  ASP A 231 " =    0.725
peak=   -3.297 closest distance to " O   HOH Z 292 " =    1.569
peak=   -3.292 closest distance to " N   SER A 212 " =    1.896
peak=   -3.291 closest distance to " CD1 ILE A 199 " =    2.587
peak=   -3.291 closest distance to " CA  SER A 135 " =    1.371
peak=   -3.290 closest distance to " O   LEU A 101 " =    2.820
peak=   -3.290 closest distance to " ND2 ASN A 285 " =    2.093
peak=   -3.288 closest distance to " CG2 VAL A 202 " =    2.761
peak=   -3.287 closest distance to " CB  VAL A 296 " =    1.059
peak=   -3.284 closest distance to " C   GLU A 236 " =    0.839
peak=   -3.282 closest distance to " CD2 LEU A 300 " =    2.516
peak=   -3.281 closest distance to " CD1 ILE A  33 " =    2.428
peak=   -3.281 closest distance to " O   SER A  22 " =    2.395
peak=   -3.277 closest distance to " CB  ALA A 227 " =    2.443
peak=   -3.275 closest distance to " N   GLY A  23 " =    2.327
peak=   -3.270 closest distance to " O   HOH Z 389 " =    4.735
peak=   -3.263 closest distance to " CB  ALA A 114 " =    2.447
peak=   -3.261 closest distance to " O   HOH Z 128 " =    2.581
peak=   -3.258 closest distance to " OG  SER A 206 " =    1.777
peak=   -3.257 closest distance to " O   HOH Z 143 " =    1.518
peak=   -3.253 closest distance to " O   HOH Z 108 " =    1.460
peak=   -3.251 closest distance to " CB  ALA A 291 " =    2.194
peak=   -3.250 closest distance to " O   HOH Z 100 " =    1.116
peak=   -3.250 closest distance to " O   HOH Z 118 " =    1.924
peak=   -3.247 closest distance to " NZ  LYS A 166 " =    1.179
peak=   -3.243 closest distance to " O   HOH Z 353 " =    1.901
peak=   -3.242 closest distance to " CB  CYS A 201 " =    2.448
peak=   -3.240 closest distance to " O   PRO A 198 " =    1.328
peak=   -3.235 closest distance to " CG1BVAL A  72 " =    2.228
peak=   -3.233 closest distance to " OH  TYR A 172 " =    1.772
peak=   -3.233 closest distance to " O   HOH Z  86 " =    2.704
peak=   -3.230 closest distance to " ND2 ASN A  45 " =    1.649
peak=   -3.224 closest distance to " O   HOH Z  11 " =    1.970
peak=   -3.219 closest distance to " CD2 PHE A  61 " =    1.951
peak=   -3.215 closest distance to " O   HOH Z 136 " =    0.990
peak=   -3.214 closest distance to " C   GLN A 240 " =    2.447
peak=   -3.211 closest distance to " O   HOH Z 371 " =    1.190
peak=   -3.211 closest distance to " CB  TYR A  15 " =    2.159
peak=   -3.210 closest distance to " O   VAL A  67 " =    2.794
peak=   -3.208 closest distance to " CA  ASP A 298 " =    1.075
peak=   -3.208 closest distance to " CE3 TRP A  70 " =    1.638
peak=   -3.204 closest distance to " OG BSER A 134 " =    1.885
peak=   -3.203 closest distance to " CG  PRO A 163 " =    2.561
peak=   -3.200 closest distance to " N   ASP A 270 " =    1.488
peak=   -3.199 closest distance to " CD1 PHE A  59 " =    2.030
peak=   -3.199 closest distance to " O   HOH Z  38 " =    1.570
peak=   -3.196 closest distance to " O   HOH Z  60 " =    1.697
peak=   -3.193 closest distance to " CD1 LEU A   5 " =    2.546
peak=   -3.191 closest distance to " O   HOH Z 282 " =    4.934
peak=   -3.187 closest distance to " C   HIS A 108 " =    1.170
peak=   -3.186 closest distance to " CD2 HIS A 207 " =    2.449
peak=   -3.184 closest distance to " OD1 ASN A 148 " =    1.398
peak=   -3.183 closest distance to " O   HOH Z 102 " =    1.506
peak=   -3.183 closest distance to " ND2BASN A 224 " =    1.507
peak=   -3.181 closest distance to " O   HOH Z 144 " =    1.183
peak=   -3.181 closest distance to " CB  SER A  63 " =    3.350
peak=   -3.178 closest distance to " CB  PHE A 283 " =    2.843
peak=   -3.175 closest distance to " O   HOH Z 417 " =    2.955
peak=   -3.167 closest distance to " O   HOH Z 179 " =    2.257
peak=   -3.167 closest distance to " N   LYS A 166 " =    1.838
peak=   -3.167 closest distance to " CG2 THR A  42 " =    1.893
peak=   -3.166 closest distance to " CB  CYS A 254 " =    2.020
peak=   -3.164 closest distance to " O   HOH Z 350 " =    1.853
peak=   -3.160 closest distance to " CD  PRO A 243 " =    1.994
peak=   -3.158 closest distance to " OG1 THR A 178 " =    1.303
peak=   -3.158 closest distance to " O   HOH Z 357 " =    1.884
peak=   -3.155 closest distance to " CB  PRO A  54 " =    2.548
peak=   -3.144 closest distance to " CB  ALA A 244 " =    2.118
peak=   -3.136 closest distance to " N   GLN A  58 " =    1.888
peak=   -3.133 closest distance to " O   HOH Z  63 " =    1.962
peak=   -3.131 closest distance to " OD1 ASN A 187 " =    1.519
peak=   -3.130 closest distance to " O   PHE A 218 " =    1.583
peak=   -3.126 closest distance to " CG1 VAL A 197 " =    2.392
peak=   -3.123 closest distance to " CB  ALA A 291 " =    2.287
peak=   -3.122 closest distance to " CE2 TRP A  70 " =    2.319
peak=   -3.113 closest distance to " O   HOH Z 184 " =    1.945
peak=   -3.110 closest distance to " O   HOH Z 216 " =    1.493
peak=   -3.089 closest distance to " O   ASP A 272 " =    2.288
peak=   -3.075 closest distance to " O   HOH Z 390 " =    2.387
peak=   -3.068 closest distance to " CB  LYS A 289 " =    3.103
peak=   -3.064 closest distance to " O   HOH Z 200 " =    3.441
peak=   -3.057 closest distance to " CD  LYS A 166 " =    2.583
peak=   -3.055 closest distance to " OG BSER A 164 " =    0.997
peak=   -3.052 closest distance to " O   HOH Z 406 " =    2.199
peak=   -3.051 closest distance to " O   HOH Z 134 " =    3.386
peak=   -3.036 closest distance to " CD1 PHE A  61 " =    2.972
peak=   -3.007 closest distance to " O   HOH Z 380 " =    1.093

================= 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    :  0.4796 0.4683   6.282090e+00   6.263390e+00
   1_bss:  0.4725 0.4542   6.276011e+00   6.256189e+00
   1_xyz:  0.3872 0.4035   6.160586e+00   6.186515e+00
   1_adp:  0.3403 0.3960   6.082056e+00   6.169075e+00
   1_occ:  0.3397 0.3965   6.081411e+00   6.169280e+00
   2_bss:  0.3365 0.3913   6.081448e+00   6.167111e+00
   2_xyz:  0.2394 0.2928   5.792910e+00   5.947629e+00
   2_adp:  0.2090 0.2679   5.685482e+00   5.865828e+00
   2_occ:  0.2089 0.2678   5.684879e+00   5.865313e+00
   3_bss:  0.2068 0.2651   5.683942e+00   5.862976e+00
   3_xyz:  0.1508 0.2015   5.402088e+00   5.619209e+00
   3_adp:  0.1367 0.1880   5.325138e+00   5.554478e+00
   3_occ:  0.1366 0.1879   5.324594e+00   5.553920e+00
   4_bss:  0.1366 0.1871   5.322934e+00   5.550359e+00
   4_xyz:  0.1232 0.1730   5.239327e+00   5.476342e+00
   4_adp:  0.1227 0.1678   5.223823e+00   5.446901e+00
   4_occ:  0.1226 0.1675   5.222942e+00   5.445923e+00
   5_bss:  0.1226 0.1674   5.222851e+00   5.445650e+00
   5_xyz:  0.1207 0.1631   5.206179e+00   5.427541e+00
   5_adp:  0.1202 0.1630   5.204768e+00   5.429260e+00
   5_occ:  0.1200 0.1629   5.204010e+00   5.428414e+00
   5_bss:  0.1200 0.1629   5.203992e+00   5.428374e+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:  0.344  20.001   7.976   8.944   8.689   0.000   0.000   0.000
   1_xyz:  0.344  20.001   7.976   8.944   8.689   0.000   0.000   0.000
   1_adp:  0.344  20.001   7.976   8.944   8.689   0.000   0.000   0.000
   1_occ:  0.344  20.001   7.976   8.944   8.689   0.000   0.000   0.000
   2_bss:  0.347  50.001   4.706   4.912   5.288   0.000   0.000   0.000
   2_xyz:  0.347  50.001   4.706   4.912   5.288   0.000   0.000   0.000
   2_adp:  0.347  50.001   4.706   4.912   5.288   0.000   0.000   0.000
   2_occ:  0.347  50.001   4.706   4.912   5.288   0.000   0.000   0.000
   3_bss:  0.322  54.292   2.659   2.407   3.680   0.000   0.000   0.000
   3_xyz:  0.322  54.292   2.659   2.407   3.680   0.000   0.000   0.000
   3_adp:  0.322  54.292   2.659   2.407   3.680   0.000   0.000   0.000
   3_occ:  0.322  54.292   2.659   2.407   3.680   0.000   0.000   0.000
   4_bss:  0.320  54.292   1.992   1.603   3.148   0.000   0.000   0.000
   4_xyz:  0.320  54.292   1.992   1.603   3.148   0.000   0.000   0.000
   4_adp:  0.320  54.292   1.992   1.603   3.148   0.000   0.000   0.000
   4_occ:  0.320  54.292   1.992   1.603   3.148   0.000   0.000   0.000
   5_bss:  0.321  51.687   1.805   1.401   3.075   0.000   0.000   0.000
   5_xyz:  0.321  51.687   1.805   1.401   3.075   0.000   0.000   0.000
   5_adp:  0.321  51.687   1.805   1.401   3.075   0.000   0.000   0.000
   5_occ:  0.321  51.687   1.805   1.401   3.075   0.000   0.000   0.000
   5_bss:  0.321  53.759  -0.301  -0.711   1.012   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  56.508 0.4383  0.5128    67741.000
   1_bss:  56.731 0.4343  0.6518    66503.677
   1_xyz:  47.522 0.5496  0.8012    49137.660
   1_adp:  44.420 0.5884  0.9091    45709.531
   1_occ:  44.474 0.5877  0.9069    45753.415
   2_bss:  44.116 0.5920  0.8083    45195.077
   2_xyz:  30.813 0.7473  0.9775    23119.928
   2_adp:  27.060 0.7892  1.0037    18734.223
   2_occ:  27.045 0.7894  1.0034    18698.948
   3_bss:  26.953 0.7903  0.9336    18619.015
   3_xyz:  19.444 0.8664  0.9904    10385.090
   3_adp:  17.833 0.8819  0.9950     9146.070
   3_occ:  17.827 0.8819  0.9948     9129.024
   4_bss:  17.759 0.8824  0.9711     9033.293
   4_xyz:  16.026 0.8978  0.9758     7618.424
   4_adp:  15.300 0.9044  0.9760     7222.578
   4_occ:  15.287 0.9045  0.9759     7197.177
   5_bss:  15.283 0.9045  0.9706     7192.629
   5_xyz:  14.829 0.9085  0.9727     6908.791
   5_adp:  14.819 0.9087  0.9707     6945.411
   5_occ:  14.811 0.9087  0.9706     6933.675
   5_bss:  14.811 0.9087  0.9698     6933.128
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3958e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3958e+01
   1_xyz:   1.684  0.013  0.108 18.312  0.006  4.109   1.4078e-01
   1_adp:   1.684  0.013  0.108 18.312  0.006  4.109   1.4078e-01
   1_occ:   1.684  0.013  0.108 18.312  0.006  4.109   1.4078e-01
   2_bss:   1.684  0.013  0.108 18.312  0.006  4.109   1.4078e-01
   2_xyz:   1.214  0.009  0.088 16.612  0.005  4.108   8.9686e-02
   2_adp:   1.214  0.009  0.088 16.612  0.005  4.108   8.9686e-02
   2_occ:   1.214  0.009  0.088 16.612  0.005  4.108   8.9686e-02
   3_bss:   1.214  0.009  0.088 16.612  0.005  4.108   8.9686e-02
   3_xyz:   1.119  0.008  0.086 15.847  0.004  4.125   7.3884e-02
   3_adp:   1.119  0.008  0.086 15.847  0.004  4.125   7.3884e-02
   3_occ:   1.119  0.008  0.086 15.847  0.004  4.125   7.3884e-02
   4_bss:   1.119  0.008  0.086 15.847  0.004  4.125   7.3884e-02
   4_xyz:   1.047  0.008  0.081 15.709  0.003  4.112   6.7323e-02
   4_adp:   1.047  0.008  0.081 15.709  0.003  4.112   6.7323e-02
   4_occ:   1.047  0.008  0.081 15.709  0.003  4.112   6.7323e-02
   5_bss:   1.047  0.008  0.081 15.709  0.003  4.112   6.7323e-02
   5_xyz:   0.953  0.007  0.075 15.114  0.003  4.113   5.7049e-02
   5_adp:   0.953  0.007  0.075 15.114  0.003  4.113   5.7049e-02
   5_occ:   0.953  0.007  0.075 15.114  0.003  4.113   5.7049e-02
   5_bss:   0.953  0.007  0.075 15.114  0.003  4.113   5.7049e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9953e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9953e+00
   1_xyz:  13.595  0.172  0.420 86.325  0.035  2.233   1.0099e-01
   1_adp:  13.595  0.172  0.420 86.325  0.035  2.233   1.0099e-01
   1_occ:  13.595  0.172  0.420 86.325  0.035  2.233   1.0099e-01
   2_bss:  13.595  0.172  0.420 86.325  0.035  2.233   1.0099e-01
   2_xyz:   6.708  0.077  0.302 87.780  0.043  2.199   6.9738e-02
   2_adp:   6.708  0.077  0.302 87.780  0.043  2.199   6.9738e-02
   2_occ:   6.708  0.077  0.302 87.780  0.043  2.199   6.9738e-02
   3_bss:   6.708  0.077  0.302 87.780  0.043  2.199   6.9738e-02
   3_xyz:   8.363  0.066  0.463 83.288  0.018  2.253   6.1663e-02
   3_adp:   8.363  0.066  0.463 83.288  0.018  2.253   6.1663e-02
   3_occ:   8.363  0.066  0.463 83.288  0.018  2.253   6.1663e-02
   4_bss:   8.363  0.066  0.463 83.288  0.018  2.253   6.1663e-02
   4_xyz:   9.155  0.056  0.475 82.795  0.032  2.314   4.4403e-02
   4_adp:   9.155  0.056  0.475 82.795  0.032  2.314   4.4403e-02
   4_occ:   9.155  0.056  0.475 82.795  0.032  2.314   4.4403e-02
   5_bss:   9.155  0.056  0.475 82.795  0.032  2.314   4.4403e-02
   5_xyz:   7.778  0.049  0.425 83.355  0.031  2.363   3.6767e-02
   5_adp:   7.778  0.049  0.425 83.355  0.031  2.363   3.6767e-02
   5_occ:   7.778  0.049  0.425 83.355  0.031  2.363   3.6767e-02
   5_bss:   7.778  0.049  0.425 83.355  0.031  2.363   3.6767e-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:  80.16   0.00  13.79  68.00   0.00  11.30  80.16   0.00  27.40
   1_occ:  80.16   0.00  13.79  68.00   0.00  11.30  80.16   0.00  27.40
   2_bss:  80.16   0.00  13.79  68.00   0.00  11.30  80.16   0.00  27.40
   2_xyz:  80.16   0.00  13.79  68.00   0.00  11.30  80.16   0.00  27.40
   2_adp:  86.02   0.00  13.24  74.60   0.00   9.39  86.02   0.00  34.20
   2_occ:  86.02   0.00  13.24  74.60   0.00   9.39  86.02   0.00  34.20
   3_bss:  86.02   0.00  13.24  74.60   0.00   9.39  86.02   0.00  34.20
   3_xyz:  86.02   0.00  13.24  74.60   0.00   9.39  86.02   0.00  34.20
   3_adp:  87.32   0.00  13.88  81.01   0.00   9.21  87.32   1.84  39.26
   3_occ:  87.32   0.00  13.88  81.01   0.00   9.21  87.32   1.84  39.26
   4_bss:  87.32   0.00  13.88  81.01   0.00   9.21  87.32   1.84  39.26
   4_xyz:  87.32   0.00  13.88  81.01   0.00   9.21  87.32   1.84  39.26
   4_adp:  83.23   0.00  13.20  79.69   0.00   8.90  83.23   2.97  36.60
   4_occ:  83.23   0.00  13.20  79.69   0.00   8.90  83.23   2.97  36.60
   5_bss:  83.23   0.00  13.20  79.69   0.00   8.90  83.23   2.97  36.60
   5_xyz:  83.23   0.00  13.20  79.69   0.00   8.90  83.23   2.97  36.60
   5_adp:  79.88   0.00  12.90  79.88   0.00   8.81  77.46   2.80  35.16
   5_occ:  79.88   0.00  12.90  79.88   0.00   8.81  77.46   2.80  35.16
   5_bss:  81.95   2.07  14.97  81.95   2.07  10.88  79.53   4.87  37.23
------------------------------------------------------------------------
 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:    1.239    0.021    0.410
   1_adp:    1.239    0.021    0.410
   1_occ:    1.239    0.021    0.410
   2_bss:    1.239    0.021    0.410
   2_xyz:    1.431    0.038    0.603
   2_adp:    1.431    0.038    0.603
   2_occ:    1.431    0.038    0.603
   3_bss:    1.431    0.038    0.603
   3_xyz:    1.640    0.048    0.682
   3_adp:    1.640    0.048    0.682
   3_occ:    1.640    0.048    0.682
   4_bss:    1.640    0.048    0.682
   4_xyz:    1.823    0.032    0.707
   4_adp:    1.823    0.032    0.707
   4_occ:    1.823    0.032    0.707
   5_bss:    1.823    0.032    0.707
   5_xyz:    1.872    0.057    0.717
   5_adp:    1.872    0.057    0.717
   5_occ:    1.872    0.057    0.717
   5_bss:    1.872    0.057    0.717
------------------------------------------------------------------------

CPU time actual refinement: 339.87


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_997/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_997/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_997/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_997/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_997/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 339.72 
  Macro-tasks:
    bulk solvent and scale       = 38.94  
    individual site refinement   = 145.21 
    weights calculation          = 31.26  
    collect and process          = 6.36   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 221.88 
  Micro-tasks:
    mask                            = 1.78   
    f_calc                          = 107.81 
    alpha_beta                      = 8.32   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 118.31 
    fmodel                         = 7.10   
    r_factors                      = 0.20   
    phase_errors                   = 10.50  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 255.45 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.770 micro seconds
Total CPU time: 5.89 minutes
from_scatterers_fft:    644 calls, 107.52 s
gradients_fft:          589 calls, 104.87 s

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

# Date 2008-01-16 Time 02:56:36 PST -0800 (1200480996.89 s)
Start R-work = 0.4796, R-free = 0.4683 (no bulk solvent and anisotropic scale)
Final R-work = 0.1372, R-free = 0.1803 (no bulk solvent and anisotropic scale)

Start R-work = 0.4725, R-free = 0.4542
Final R-work = 0.1200, R-free = 0.1629