# Date 2008-01-16 Time 01:03:41 PST -0800 (1200474221.41 s)
#phil __OFF__

Command line arguments: "../264.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 = 18690
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 264

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 46.2261, 84.2302, 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: (69.1963, 46.2261, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.728 1.95107
Completeness in resolution range: 0.967645
Completeness with d_max=infinity: 0.964595

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7280
                             d_min =   1.9511

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 46.2261, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.728 1.95107
Completeness in resolution range: 0.967645
Completeness with d_max=infinity: 0.964595

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7284 -  4.1745 [2117/2144]  1906   211  10.0%
  bin  2:  4.1745 -  3.3260 [2042/2058]  1837   205  10.0%
  bin  3:  3.3260 -  2.9093 [2019/2038]  1815   204  10.1%
  bin  4:  2.9093 -  2.6449 [2005/2035]  1810   195   9.7%
  bin  5:  2.6449 -  2.4563 [1982/2001]  1782   200  10.1%
  bin  6:  2.4563 -  2.3121 [1957/1982]  1763   194   9.9%
  bin  7:  2.3121 -  2.1967 [1970/2004]  1771   199  10.1%
  bin  8:  2.1967 -  2.1013 [1956/1986]  1760   196  10.0%
  bin  9:  2.1013 -  2.0206 [1961/2003]  1765   196  10.0%
  bin 10:  2.0206 -  1.9511 [1580/1993]  1421   159  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_264/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:
        1.08 -     1.84: 12
        1.84 -     2.61: 109
        2.61 -     3.37: 4334
        3.37 -     4.14: 9644
        4.14 -     4.90: 15046
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.076 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.380 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.391 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.482 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.575 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 29140 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_264/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_264/model_refine_001.geo

CPU time processing inputs: 9.25


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 46.22605 84.23025 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: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5093   r_free= 0.5028   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:   0.89 A                  |
| x-ray target function (ml) for work reflections: 6.301545                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7284 -  4.6559 0.99   1378  154 0.4232 0.4322      6.6329       6.664|
|  2:  4.6559 -  3.7151 0.99   1336  145 0.4579 0.4331      6.8541      6.8488|
|  3:  3.7151 -  3.2512 0.99   1300  147 0.4773 0.4614      6.7291      6.8062|
|  4:  3.2512 -  2.9566 0.99   1294  144 0.4907 0.4787      6.5703      6.5163|
|  5:  2.9566 -  2.7461 0.99   1281  141 0.5431 0.5213      6.4048      6.3765|
|  6:  2.7461 -  2.5851 0.99   1282  145 0.5366 0.5741       6.303      6.2828|
|  7:  2.5851 -  2.4563 0.99   1279  139 0.5309 0.4871      6.2641      6.2157|
|  8:  2.4563 -  2.3498 0.98   1264  145 0.5499 0.5690      6.1997      6.1811|
|  9:  2.3498 -  2.2597 0.98   1273  139 0.5445 0.5453      6.1317      6.1675|
| 10:  2.2597 -  2.1820 0.99   1249  141 0.5593 0.5146      6.1217      6.1327|
| 11:  2.1820 -  2.1139 0.99   1274  139 0.5400 0.5668      6.0595      6.0824|
| 12:  2.1139 -  2.0537 0.97   1239  137 0.5413 0.5164      5.9953      6.0142|
| 13:  2.0537 -  1.9997 0.99   1255  142 0.5547 0.4930      5.8944      5.8643|
| 14:  1.9997 -  1.9511 0.72    926  101 0.5507 0.5521      5.8521      5.7676|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7284 -  4.6559  1378   154  0.60  42.64   0.79     0.65     100762.68|
|  2:  4.6559 -  3.7151  1336   145  0.61  42.55   0.85     0.71     144083.18|
|  3:  3.7151 -  3.2512  1300   147  0.51  50.99   0.84     0.66     148546.20|
|  4:  3.2512 -  2.9566  1294   144  0.44  56.87   0.81     0.56     124620.94|
|  5:  2.9566 -  2.7461  1281   141  0.35  63.45   0.72     0.45      94051.96|
|  6:  2.7461 -  2.5851  1282   145  0.32  66.21   0.72     0.37      80039.36|
|  7:  2.5851 -  2.4563  1279   139  0.25  71.37   0.74     0.29      74501.44|
|  8:  2.4563 -  2.3498  1264   145  0.22  73.34   0.73     0.28      69381.46|
|  9:  2.3498 -  2.2597  1273   139  0.22  73.77   0.73     0.26      63192.89|
| 10:  2.2597 -  2.1820  1249   141  0.23  72.87   0.75     0.29      56940.66|
| 11:  2.1820 -  2.1139  1274   139  0.20  74.99   0.78     0.26      53296.22|
| 12:  2.1139 -  2.0537  1239   137  0.21  74.25   0.76     0.28      49571.17|
| 13:  2.0537 -  1.9997  1255   142  0.20  74.82   0.74     0.27      41774.58|
| 14:  1.9997 -  1.9511   926   101  0.22  73.34   0.73     0.26      32872.29|
|alpha:            min =        0.26 max =            0.71 mean =         0.41|
|beta:             min =    32872.29 max =       148546.20 mean =     82560.44|
|figures of merit: min =        0.00 max =            1.00 mean =         0.33|
|phase err.(work): min =        0.00 max =           89.99 mean =        64.66|
|phase err.(test): min =        0.00 max =           89.96 mean =        65.02|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 21.886203             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.533   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.524722              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 83.888   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  0.529 -  0.966:        1 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  0.966 -  1.403:        3 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.403 -  1.840:       17 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  1.840 -  2.277:      206 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.277 -  2.714:      842 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.714 -  3.151:     2156 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.151 -  3.589:     3729 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.589 -  4.026:     5570 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.026 -  4.463:     7486 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.463 -  4.900:     9158 |
|-----------------------------------------------------------------------------|
|-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 |       52.556 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.085    4.900  0.529 |       2.909 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.244)------------------------------------------|
|    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 = 11.244)------------------------------------------|
|    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: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5133   r_free= 0.5057   ksol= 0.00   Bsol= 0.00   scale= 0.758    |
|                                                                             |
| 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:   0.89 A                  |
| x-ray target function (ml) for work reflections: 6.302337                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5010   r_free= 0.4927   ksol= 0.38   Bsol= 0.00   scale= 0.980    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.63,8.83,9.08,0.00,0.00,0.00); trace/3= 8.18                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.89 A                  |
| x-ray target function (ml) for work reflections: 6.296295                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.430102             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.438   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.969740              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.136   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5010      final r-factor (work) = 0.4454          |
| start r-factor (free) = 0.4927      final r-factor (free) = 0.4584          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 104.2982 = 16.43 * 0.50 * 6.2984 + 1.00 * 52.5564                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 51.4926 = 16.43 * 0.50 * 6.2502 + 1.00 * 0.1468                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4454      final r-factor (work) = 0.4054          |
| start r-factor (free) = 0.4584      final r-factor (free) = 0.4565          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.3256 = 1.97 * 1.00 * 6.2502 + 1.00 * 0.0143                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.2393 = 1.97 * 1.00 * 6.2016 + 1.00 * 0.0237                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.244)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.07   15.89    None  None   None       |
|    all(noH): 2823   0      0.00    81.07   15.89    None  None   None       |
|    Sol.    : 438    0      0.00    81.07   23.93    None  None   None       |
|    Mac.    : 2385   0      0.00    73.19   14.41    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 -   8.107:  903   |   5:    40.536 -  48.643:   82        |
|      1:     8.107 -  16.215:  766   |   6:    48.643 -  56.751:   38        |
|      2:    16.215 -  24.322:  550   |   7:    56.751 -  64.858:   17        |
|      3:    24.322 -  32.429:  273   |   8:    64.858 -  72.965:    4        |
|      4:    32.429 -  40.536:  187   |   9:    72.965 -  81.072:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4054 r_free = 0.4565             target_work(ml) = 6.193         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4050 r_free = 0.4570             target_work(ml) = 6.193         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4050   r_free= 0.4570   ksol= 0.38   Bsol= 0.00   scale= 1.122    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.63,8.83,9.08,0.00,0.00,0.00); trace/3= 8.18                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.192582                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4021   r_free= 0.4552   ksol= 0.40   Bsol= 50.00   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.01,4.43,5.56,0.00,0.00,0.00); trace/3= 4.33                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.193604                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.580057             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.343  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.776549              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.252  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4021      final r-factor (work) = 0.3305          |
| start r-factor (free) = 0.4552      final r-factor (free) = 0.3953          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 39.1215 = 12.58 * 0.50 * 6.1963 + 1.00 * 0.1468                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.6153 = 12.58 * 0.50 * 6.1231 + 1.00 * 0.1011                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3305      final r-factor (work) = 0.3069          |
| start r-factor (free) = 0.3953      final r-factor (free) = 0.3752          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7837 = 0.78 * 1.00 * 6.1231 + 1.00 * 0.0289                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7164 = 0.78 * 1.00 * 6.0236 + 1.00 * 0.0387                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.244)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.27   15.31    None  None   None       |
|    all(noH): 2823   0      0.00    84.27   15.31    None  None   None       |
|    Sol.    : 438    0      0.00    80.29   29.81    None  None   None       |
|    Mac.    : 2385   0      0.00    84.27   12.64    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.427:  977   |   5:    42.137 -  50.564:   67        |
|      1:     8.427 -  16.855:  907   |   6:    50.564 -  58.991:   31        |
|      2:    16.855 -  25.282:  443   |   7:    58.991 -  67.419:   11        |
|      3:    25.282 -  33.709:  224   |   8:    67.419 -  75.846:    4        |
|      4:    33.709 -  42.137:  154   |   9:    75.846 -  84.273:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3069 r_free = 0.3752             target_work(ml) = 6.001         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3065 r_free = 0.3753             target_work(ml) = 6.001         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3065   r_free= 0.3753   ksol= 0.40   Bsol= 50.00   scale= 1.082   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.01,4.43,5.56,0.00,0.00,0.00); trace/3= 4.33                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 6.001365                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3046   r_free= 0.3731   ksol= 0.34   Bsol= 39.91   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.37,2.06,3.03,0.00,0.00,0.00); trace/3= 2.15                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 5.999675                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.323521              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.602  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.951606              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.291   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3046      final r-factor (work) = 0.2451          |
| start r-factor (free) = 0.3731      final r-factor (free) = 0.3089          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.1190 = 4.32 * 0.50 * 6.0219 + 1.00 * 0.1011                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.8563 = 4.32 * 0.50 * 5.9141 + 1.00 * 0.0715                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2451      final r-factor (work) = 0.2225          |
| start r-factor (free) = 0.3089      final r-factor (free) = 0.2929          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6465 = 0.95 * 1.00 * 5.9141 + 1.00 * 0.0187                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5137 = 0.95 * 1.00 * 5.7777 + 1.00 * 0.0157                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.244)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.49  15.79    None  None   None       |
|    all(noH): 2823   0      0.00    100.49  15.79    None  None   None       |
|    Sol.    : 438    0      1.20    81.27   38.33    None  None   None       |
|    Mac.    : 2385   0      0.00    100.49  11.65    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.049: 1374   |   5:    50.245 -  60.294:   71        |
|      1:    10.049 -  20.098:  756   |   6:    60.294 -  70.343:   45        |
|      2:    20.098 -  30.147:  265   |   7:    70.343 -  80.392:   15        |
|      3:    30.147 -  40.196:  167   |   8:    80.392 -  90.442:    1        |
|      4:    40.196 -  50.245:  125   |   9:    90.442 - 100.491:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2225 r_free = 0.2929             target_work(ml) = 5.752         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2222 r_free = 0.2924             target_work(ml) = 5.751         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2222   r_free= 0.2924   ksol= 0.34   Bsol= 39.91   scale= 1.049   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.37,2.06,3.03,0.00,0.00,0.00); trace/3= 2.15                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.750750                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2220   r_free= 0.2921   ksol= 0.32   Bsol= 35.75   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.67,1.14,2.03,0.00,0.00,0.00); trace/3= 1.28                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.748727                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.827525              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.742  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.175797              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.311  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2220      final r-factor (work) = 0.1774          |
| start r-factor (free) = 0.2921      final r-factor (free) = 0.2394          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2397 = 2.83 * 0.50 * 5.7776 + 1.00 * 0.0715                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0580 = 2.83 * 0.50 * 5.6583 + 1.00 * 0.0584                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1774      final r-factor (work) = 0.1701          |
| start r-factor (free) = 0.2394      final r-factor (free) = 0.2219          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0103 = 0.18 * 1.00 * 5.6583 + 1.00 * 0.0156                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0032 = 0.18 * 1.00 * 5.5342 + 1.00 * 0.0303                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.244)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.60   15.19    None  None   None       |
|    all(noH): 2823   0      0.00    97.60   15.19    None  None   None       |
|    Sol.    : 438    0      2.69    82.06   37.72    None  None   None       |
|    Mac.    : 2385   0      0.00    97.60   11.05    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.760: 1469   |   5:    48.801 -  58.561:   68        |
|      1:     9.760 -  19.520:  726   |   6:    58.561 -  68.321:   44        |
|      2:    19.520 -  29.280:  216   |   7:    68.321 -  78.081:   13        |
|      3:    29.280 -  39.041:  162   |   8:    78.081 -  87.841:    2        |
|      4:    39.041 -  48.801:  119   |   9:    87.841 -  97.601:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1701 r_free = 0.2219             target_work(ml) = 5.497         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1697 r_free = 0.2211             target_work(ml) = 5.495         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1697   r_free= 0.2211   ksol= 0.32   Bsol= 35.75   scale= 1.041   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.67,1.14,2.03,0.00,0.00,0.00); trace/3= 1.28                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.494823                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1696   r_free= 0.2206   ksol= 0.32   Bsol= 30.56   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.03,0.36,1.17,0.00,0.00,0.00); trace/3= 0.50                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.494960                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.074326              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.555  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.650739              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.778   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1696      final r-factor (work) = 0.1419          |
| start r-factor (free) = 0.2206      final r-factor (free) = 0.1859          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7984 = 2.07 * 0.50 * 5.5343 + 1.00 * 0.0584                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6754 = 2.07 * 0.50 * 5.4161 + 1.00 * 0.0580                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1419      final r-factor (work) = 0.1331          |
| start r-factor (free) = 0.1859      final r-factor (free) = 0.1793          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5419 = 0.65 * 1.00 * 5.4161 + 1.00 * 0.0174                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4571 = 0.65 * 1.00 * 5.2959 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.244)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.86   15.42    None  None   None       |
|    all(noH): 2823   0      0.00    98.86   15.42    None  None   None       |
|    Sol.    : 438    0      4.19    84.97   41.17    None  None   None       |
|    Mac.    : 2385   0      0.00    98.86   10.69    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.886: 1537   |   5:    49.430 -  59.316:   84        |
|      1:     9.886 -  19.772:  703   |   6:    59.316 -  69.202:   63        |
|      2:    19.772 -  29.658:  169   |   7:    69.202 -  79.088:   21        |
|      3:    29.658 -  39.544:  124   |   8:    79.088 -  88.974:    6        |
|      4:    39.544 -  49.430:  112   |   9:    88.974 -  98.860:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1331 r_free = 0.1793             target_work(ml) = 5.279         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1330 r_free = 0.1790             target_work(ml) = 5.279         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1330   r_free= 0.1790   ksol= 0.32   Bsol= 30.56   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.03,0.36,1.17,0.00,0.00,0.00); trace/3= 0.50                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.278632                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7284 -  4.6559 0.99   1378  154 0.1139 0.1390      5.5024      5.6248|
|  2:  4.6559 -  3.7151 0.99   1336  145 0.1028 0.1347      5.5842      5.8169|
|  3:  3.7151 -  3.2512 0.99   1300  147 0.1292 0.1531      5.6362      5.8643|
|  4:  3.2512 -  2.9566 0.99   1294  144 0.1469 0.1971      5.6174      5.8072|
|  5:  2.9566 -  2.7461 0.99   1281  141 0.1516 0.1875      5.4348       5.585|
|  6:  2.7461 -  2.5851 0.99   1282  145 0.1416 0.2053      5.3291      5.5398|
|  7:  2.5851 -  2.4563 0.99   1279  139 0.1457 0.1909       5.289      5.5056|
|  8:  2.4563 -  2.3498 0.98   1264  145 0.1427 0.2021      5.2273      5.4755|
|  9:  2.3498 -  2.2597 0.98   1273  139 0.1413 0.1984      5.1722      5.4015|
| 10:  2.2597 -  2.1820 0.99   1249  141 0.1327 0.1914      5.0932      5.2968|
| 11:  2.1820 -  2.1139 0.99   1274  139 0.1350 0.2079      5.0586      5.4305|
| 12:  2.1139 -  2.0537 0.97   1239  137 0.1305 0.1759      5.0065      5.2541|
| 13:  2.0537 -  1.9997 0.99   1255  142 0.1344 0.2104      4.9346        5.21|
| 14:  1.9997 -  1.9511 0.72    926  101 0.1287 0.1870      4.8288      5.0472|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7284 -  4.6559  1378   154  0.93  10.58   0.99     0.97       9040.80|
|  2:  4.6559 -  3.7151  1336   145  0.94   9.47   1.05     1.03      11252.67|
|  3:  3.7151 -  3.2512  1300   147  0.92  13.66   1.06     1.04      13433.97|
|  4:  3.2512 -  2.9566  1294   144  0.90  15.89   1.03     1.02      13585.01|
|  5:  2.9566 -  2.7461  1281   141  0.88  17.71   1.01     0.97       9851.35|
|  6:  2.7461 -  2.5851  1282   145  0.89  17.67   1.00     0.95       8634.25|
|  7:  2.5851 -  2.4563  1279   139  0.88  18.69   1.01     0.98       7993.04|
|  8:  2.4563 -  2.3498  1264   145  0.88  18.18   1.01     0.98       7132.24|
|  9:  2.3498 -  2.2597  1273   139  0.89  17.65   1.03     1.01       6470.41|
| 10:  2.2597 -  2.1820  1249   141  0.89  17.67   1.03     0.99       5584.03|
| 11:  2.1820 -  2.1139  1274   139  0.88  18.60   1.03     0.98       5420.77|
| 12:  2.1139 -  2.0537  1239   137  0.89  17.60   1.04     1.01       5078.29|
| 13:  2.0537 -  1.9997  1255   142  0.88  18.70   1.04     1.03       4443.54|
| 14:  1.9997 -  1.9511   926   101  0.89  17.93   1.02     0.98       3500.70|
|alpha:            min =        0.95 max =            1.04 mean =         1.00|
|beta:             min =     3500.70 max =        13585.01 mean =      8093.56|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.99 mean =        16.33|
|phase err.(test): min =        0.00 max =           89.86 mean =        15.71|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1330   r_free= 0.1791   ksol= 0.32   Bsol= 31.38   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.43,-0.14,0.57,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.278058                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1330   r_free= 0.1791   ksol= 0.32   Bsol= 31.38   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.43,-0.14,0.57,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.278058                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7284 -  4.6559 0.99   1378  154 0.1136 0.1405      5.5003      5.6221|
|  2:  4.6559 -  3.7151 0.99   1336  145 0.1032 0.1357      5.5879      5.8245|
|  3:  3.7151 -  3.2512 0.99   1300  147 0.1298 0.1540      5.6428      5.8687|
|  4:  3.2512 -  2.9566 0.99   1294  144 0.1472 0.1984      5.6187      5.8145|
|  5:  2.9566 -  2.7461 0.99   1281  141 0.1513 0.1860      5.4343      5.5815|
|  6:  2.7461 -  2.5851 0.99   1282  145 0.1416 0.2055      5.3287      5.5407|
|  7:  2.5851 -  2.4563 0.99   1279  139 0.1452 0.1907       5.288      5.5084|
|  8:  2.4563 -  2.3498 0.98   1264  145 0.1421 0.2000      5.2241      5.4688|
|  9:  2.3498 -  2.2597 0.98   1273  139 0.1411 0.1977      5.1693      5.4014|
| 10:  2.2597 -  2.1820 0.99   1249  141 0.1322 0.1909      5.0889      5.2947|
| 11:  2.1820 -  2.1139 0.99   1274  139 0.1348 0.2070      5.0573      5.4264|
| 12:  2.1139 -  2.0537 0.97   1239  137 0.1304 0.1760      5.0048      5.2535|
| 13:  2.0537 -  1.9997 0.99   1255  142 0.1341 0.2094       4.933      5.2058|
| 14:  1.9997 -  1.9511 0.72    926  101 0.1289 0.1865      4.8275      5.0452|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7284 -  4.6559  1378   154  0.93  10.53   0.98     0.96       8993.70|
|  2:  4.6559 -  3.7151  1336   145  0.94   9.58   1.04     1.02      11370.68|
|  3:  3.7151 -  3.2512  1300   147  0.92  13.75   1.05     1.04      13646.44|
|  4:  3.2512 -  2.9566  1294   144  0.90  15.86   1.03     1.02      13606.09|
|  5:  2.9566 -  2.7461  1281   141  0.88  17.73   1.01     0.97       9873.09|
|  6:  2.7461 -  2.5851  1282   145  0.89  17.67   0.99     0.95       8631.55|
|  7:  2.5851 -  2.4563  1279   139  0.88  18.66   1.00     0.97       7992.12|
|  8:  2.4563 -  2.3498  1264   145  0.88  18.13   1.01     0.97       7088.00|
|  9:  2.3498 -  2.2597  1273   139  0.89  17.58   1.02     1.00       6422.51|
| 10:  2.2597 -  2.1820  1249   141  0.89  17.61   1.02     0.98       5547.78|
| 11:  2.1820 -  2.1139  1274   139  0.88  18.55   1.02     0.97       5398.71|
| 12:  2.1139 -  2.0537  1239   137  0.89  17.53   1.03     1.00       5051.43|
| 13:  2.0537 -  1.9997  1255   142  0.88  18.66   1.02     1.02       4423.32|
| 14:  1.9997 -  1.9511   926   101  0.89  17.87   1.01     0.97       3483.10|
|alpha:            min =        0.95 max =            1.04 mean =         0.99|
|beta:             min =     3483.10 max =        13646.44 mean =      8102.31|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.70 mean =        16.31|
|phase err.(test): min =        0.00 max =           89.67 mean =        15.68|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.244)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.30    99.16   15.72    None  None   None       |
|    all(noH): 2823   0      0.30    99.16   15.72    None  None   None       |
|    Sol.    : 438    0      4.49    85.27   41.47    None  None   None       |
|    Mac.    : 2385   0      0.30    99.16   10.99    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.302 -  10.188: 1537   |   5:    49.731 -  59.617:   84        |
|      1:    10.188 -  20.074:  703   |   6:    59.617 -  69.503:   63        |
|      2:    20.074 -  29.959:  169   |   7:    69.503 -  79.389:   21        |
|      3:    29.959 -  39.845:  124   |   8:    79.389 -  89.275:    6        |
|      4:    39.845 -  49.731:  112   |   9:    89.275 -  99.161:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 360         
Filter by distance & map next to the model:
   mapped sites are within: 0.291 - 5.524
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 355 from: 360
   mapped sites are within: 0.759 - 5.524

peak=   10.191 closest distance to " CB  VAL A 296 " =    1.521
peak=   10.157 closest distance to " CB  VAL A 230 " =    1.434
peak=    7.659 closest distance to " O   HOH Z 138 " =    1.105
peak=    7.141 closest distance to " CG  ARG A 138 " =    1.220
peak=    6.481 closest distance to " O   HOH Z 130 " =    1.366
peak=    6.183 closest distance to " O   HOH Z 205 " =    1.360
peak=    6.155 closest distance to " O   HOH Z  65 " =    1.292
peak=    6.058 closest distance to " CD1AILE A 234 " =    1.127
peak=    6.001 closest distance to " O   HOH Z 381 " =    1.205
peak=    5.908 closest distance to " CD2 LEU A   5 " =    1.343
peak=    5.872 closest distance to " O   HOH Z 199 " =    1.455
peak=    5.688 closest distance to " O   HOH Z 279 " =    1.187
peak=    5.655 closest distance to " O   HOH Z 193 " =    1.845
peak=    5.612 closest distance to " CG  ASN A  60 " =    1.239
peak=    5.552 closest distance to " O   HOH Z 278 " =    2.183
peak=    5.478 closest distance to " O   HOH Z 236 " =    1.676
peak=    5.346 closest distance to " O   HOH Z 385 " =    1.055
peak=    5.298 closest distance to " O   HOH Z 120 " =    1.102
peak=    5.256 closest distance to " CB  ARG A 275 " =    1.094
peak=    5.219 closest distance to " O   HOH Z 124 " =    1.742
peak=    5.204 closest distance to " O   PRO A 198 " =    1.336
peak=    5.166 closest distance to " O   HOH Z 138 " =    1.898
peak=    5.125 closest distance to " O   HOH Z 214 " =    1.508
peak=    5.120 closest distance to " O   HOH Z 117 " =    1.465
peak=    4.952 closest distance to " CB  ASN A 187 " =    2.092
peak=    4.925 closest distance to " O   HOH Z 347 " =    1.077
peak=    4.923 closest distance to " O   HOH Z   7 " =    1.505
peak=    4.890 closest distance to " O   HOH Z 403 " =    1.448
peak=    4.868 closest distance to " NH2 ARG A  56 " =    1.990
peak=    4.863 closest distance to " O   HOH Z 326 " =    1.602
peak=    4.808 closest distance to " NE2 GLN A  11 " =    1.105
peak=    4.704 closest distance to " O   HOH Z  59 " =    1.815
peak=    4.695 closest distance to " O   HOH Z 344 " =    1.404
peak=    4.596 closest distance to " O   HOH Z 424 " =    1.325
peak=    4.572 closest distance to " O   HOH Z  78 " =    1.802
peak=    4.564 closest distance to " O   HOH Z 134 " =    1.533
peak=    4.539 closest distance to " O   HOH Z 427 " =    2.419
peak=    4.535 closest distance to " O   HOH Z 423 " =    1.582
peak=    4.506 closest distance to " CB  PRO A  54 " =    1.100
peak=    4.501 closest distance to " CG  GLN A  11 " =    2.203
peak=    4.494 closest distance to " O   HOH Z 316 " =    2.332
peak=    4.492 closest distance to " CD2 LEU A 228 " =    1.244
peak=    4.478 closest distance to " O   HOH Z 188 " =    1.243
peak=    4.411 closest distance to " CE AMET A  47 " =    1.096
peak=    4.405 closest distance to " O   HOH Z  28 " =    1.319
peak=    4.404 closest distance to " CB  ASN A  60 " =    0.935
peak=    4.398 closest distance to " CB  VAL A 230 " =    1.059
peak=    4.394 closest distance to " O   HOH Z 276 " =    1.664
peak=    4.385 closest distance to " O   HOH Z  97 " =    1.392
peak=    4.357 closest distance to " NE2 GLN A  55 " =    1.213
peak=    4.355 closest distance to " O   HOH Z 132 " =    1.470
peak=    4.334 closest distance to " CB  SER A   3 " =    1.234
peak=    4.318 closest distance to " CG  PRO A 213 " =    1.236
peak=    4.259 closest distance to " O   HOH Z 202 " =    1.376
peak=    4.237 closest distance to " O   HOH Z 146 " =    1.824
peak=    4.213 closest distance to " O   HOH Z 148 " =    1.937
peak=    4.205 closest distance to " O   HOH Z 390 " =    1.080
peak=    4.195 closest distance to " O   HOH Z 284 " =    1.652
peak=    4.183 closest distance to " CG  LEU A   5 " =    1.282
peak=    4.181 closest distance to " CG  PRO A  54 " =    1.226
peak=    4.179 closest distance to " O   HOH Z 273 " =    1.079
peak=    4.178 closest distance to " CB  ARG A 275 " =    1.305
peak=    4.167 closest distance to " CB  VAL A 265 " =    1.280
peak=    4.162 closest distance to " CD  GLN A  58 " =    5.524
peak=    4.150 closest distance to " O   HOH Z 414 " =    1.307
peak=    4.131 closest distance to " O   HOH Z 291 " =    1.468
peak=    4.126 closest distance to " CA  GLY A 241 " =    3.608
peak=    4.124 closest distance to " O   HOH Z 123 " =    1.262
peak=    4.111 closest distance to " CG  PRO A 198 " =    1.305
peak=    4.107 closest distance to " NH1 ARG A 138 " =    1.032
peak=    4.102 closest distance to " OG ASER A 134 " =    1.496
peak=    4.087 closest distance to " O   HOH Z  11 " =    1.495
peak=    4.083 closest distance to " O   HOH Z 287 " =    1.562
peak=    4.077 closest distance to " CB  PRO A 198 " =    0.998
peak=    4.072 closest distance to " O   HOH Z 426 " =    1.245
peak=    4.056 closest distance to " O   HOH Z 192 " =    1.575
peak=    4.054 closest distance to " O   HOH Z 249 " =    1.240
peak=    4.048 closest distance to " O   HOH Z 410 " =    1.360
peak=    4.043 closest distance to " O   HOH Z  51 " =    1.355
peak=    4.042 closest distance to " O   HOH Z 108 " =    1.368
peak=    4.036 closest distance to " O   HOH Z 260 " =    1.639
peak=    4.034 closest distance to " O   HOH Z 269 " =    1.159
peak=    4.010 closest distance to " NH1 ARG A  14 " =    0.975
peak=    4.007 closest distance to " CB  ALA A   1 " =    1.100
peak=    4.006 closest distance to " NE1 TRP A 274 " =    1.003
peak=    4.003 closest distance to " O   HOH Z 143 " =    1.455
peak=    4.001 closest distance to " O   HOH Z 263 " =    1.402
peak=    3.975 closest distance to " O   HOH Z  97 " =    1.905
peak=    3.967 closest distance to " OD2 ASP A 286 " =    2.464
peak=    3.957 closest distance to " O   HOH Z 227 " =    2.017
peak=    3.939 closest distance to " CB  ASN A 148 " =    1.200
peak=    3.936 closest distance to " O   HOH Z 429 " =    0.920
peak=    3.906 closest distance to " CE1 PHE A  61 " =    1.227
peak=    3.905 closest distance to " O   HOH Z 147 " =    1.475
peak=    3.904 closest distance to " O   HOH Z 280 " =    1.609
peak=    3.889 closest distance to " CB  LEU A 255 " =    0.899
peak=    3.888 closest distance to " CE  MET A  93 " =    1.406
peak=    3.886 closest distance to " O   HOH Z 220 " =    1.335
peak=    3.866 closest distance to " O   HOH Z  89 " =    1.501
peak=    3.864 closest distance to " O   HOH Z 269 " =    3.250
peak=    3.859 closest distance to " NE2 GLN A  73 " =    1.731
peak=    3.857 closest distance to " O   HOH Z 112 " =    0.931
peak=    3.849 closest distance to " NH2BARG A 190 " =    1.568
peak=    3.847 closest distance to " NH2BARG A 145 " =    1.420
peak=    3.837 closest distance to " O   HOH Z 245 " =    1.339
peak=    3.823 closest distance to " O   HOH Z 272 " =    1.811
peak=    3.822 closest distance to " CB  ARG A 102 " =    0.874
peak=    3.821 closest distance to " CG  GLN A  88 " =    1.033
peak=    3.815 closest distance to " O   HOH Z   9 " =    0.979
peak=    3.812 closest distance to " CD1 LEU A   5 " =    1.821
peak=    3.810 closest distance to " O   HOH Z 361 " =    1.663
peak=    3.786 closest distance to " CA  ILE A 234 " =    0.914
peak=    3.780 closest distance to " CA  VAL A 126 " =    1.320
peak=    3.778 closest distance to " O   HOH Z 108 " =    1.614
peak=    3.765 closest distance to " O   HOH Z  43 " =    1.563
peak=    3.756 closest distance to " O   SER A  62 " =    0.913
peak=    3.746 closest distance to " O   HOH Z 136 " =    1.078
peak=    3.746 closest distance to " CA  ASN A 284 " =    1.070
peak=    3.742 closest distance to " CA  TYR A  30 " =    1.050
peak=    3.742 closest distance to " O   HOH Z 234 " =    2.113
peak=    3.733 closest distance to " O   HOH Z  50 " =    1.633
peak=    3.730 closest distance to " O   HOH Z 100 " =    1.208
peak=    3.724 closest distance to " NE2 HIS A 115 " =    1.086
peak=    3.720 closest distance to " CA  THR A 264 " =    0.823
peak=    3.717 closest distance to " CG2 ILE A 234 " =    0.977
peak=    3.717 closest distance to " OG  SER A  62 " =    3.141
peak=    3.712 closest distance to " CB  SER A 216 " =    0.933
peak=    3.706 closest distance to " O   HOH Z  61 " =    1.471
peak=    3.703 closest distance to " O   HOH Z  63 " =    1.282
peak=    3.697 closest distance to " CG  LEU A 167 " =    1.092
peak=    3.686 closest distance to " O   HOH Z 305 " =    2.962
peak=    3.671 closest distance to " O   HOH Z 133 " =    1.402
peak=    3.669 closest distance to " C   ALA A 299 " =    0.999
peak=    3.667 closest distance to " CG2 THR A 221 " =    1.280
peak=    3.660 closest distance to " O   SER A  87 " =    2.305
peak=    3.657 closest distance to " O   HOH Z 250 " =    2.233
peak=    3.657 closest distance to " O   HOH Z 203 " =    1.397
peak=    3.651 closest distance to " CB  GLN A 183 " =    1.123
peak=    3.641 closest distance to " O   HOH Z   1 " =    1.729
peak=    3.640 closest distance to " CD  ARG A 269 " =    1.001
peak=    3.638 closest distance to " O   HOH Z   9 " =    2.167
peak=    3.630 closest distance to " CG1BVAL A 121 " =    1.098
peak=    3.623 closest distance to " O   HOH Z 189 " =    2.100
peak=    3.622 closest distance to " O   HOH Z 217 " =    1.686
peak=    3.620 closest distance to " CG  TRP A 179 " =    2.224
peak=    3.616 closest distance to " ND1 HIS A  81 " =    1.208
peak=    3.613 closest distance to " O   HOH Z 284 " =    1.400
peak=    3.610 closest distance to " CA  PHE A 283 " =    1.088
peak=    3.610 closest distance to " O   HOH Z 152 " =    2.442
peak=    3.607 closest distance to " CA  LEU A 282 " =    1.354
peak=    3.606 closest distance to " O   HOH Z 247 " =    1.277
peak=    3.600 closest distance to " O   HOH Z 250 " =    1.346
peak=    3.595 closest distance to " CB  TYR A 169 " =    0.793
peak=    3.588 closest distance to " O   HOH Z 214 " =    1.659
peak=    3.587 closest distance to " O   HOH Z  93 " =    2.114
peak=    3.586 closest distance to " CB  GLN A 223 " =    1.525
peak=    3.584 closest distance to " O   HOH Z 209 " =    1.109
peak=    3.580 closest distance to " O   HOH Z 371 " =    1.712
peak=    3.560 closest distance to " N   GLN A 278 " =    1.002
peak=    3.555 closest distance to " O   HOH Z 357 " =    1.739
peak=    3.552 closest distance to " CB  TRP A 179 " =    1.224
peak=    3.545 closest distance to " O   HOH Z 234 " =    3.349
peak=    3.544 closest distance to " O   HOH Z 145 " =    1.980
peak=    3.543 closest distance to " O   HOH Z  44 " =    1.855
peak=    3.543 closest distance to " O   HOH Z 366 " =    1.860
peak=    3.542 closest distance to " CB  ARG A 138 " =    1.391
peak=    3.541 closest distance to " CG1AVAL A 121 " =    1.054
peak=    3.529 closest distance to " CA  PRO A 163 " =    0.904
peak=    3.526 closest distance to " O   HOH Z  80 " =    1.987
peak=    3.524 closest distance to " OD1 ASN A  45 " =    1.189
peak=    3.521 closest distance to " CA  ALA A  21 " =    1.148
peak=    3.511 closest distance to " CB  GLN A  88 " =    1.406
peak=    3.507 closest distance to " O   HOH Z  66 " =    2.074
peak=    3.498 closest distance to " CD2 HIS A 115 " =    1.009
peak=    3.497 closest distance to " O   HOH Z  37 " =    1.158
peak=    3.494 closest distance to " CG2 THR A 279 " =    1.779
peak=    3.493 closest distance to " O   HOH Z 251 " =    1.745
peak=    3.492 closest distance to " O   HOH Z 129 " =    0.896
peak=    3.491 closest distance to " O   HOH Z 363 " =    1.147
peak=    3.490 closest distance to " CG  GLN A  77 " =    0.970
peak=    3.485 closest distance to " O   HOH Z 366 " =    2.757
peak=    3.484 closest distance to " CG  LEU A 281 " =    1.094
peak=    3.483 closest distance to " NE2 GLN A 223 " =    1.710
peak=    3.479 closest distance to " O   HOH Z 302 " =    1.429
peak=    3.472 closest distance to " C   SER A 164 " =    1.089
peak=    3.470 closest distance to " O   HOH Z 364 " =    1.892
peak=    3.462 closest distance to " CG2AVAL A  72 " =    2.947
peak=    3.460 closest distance to " O   HOH Z  39 " =    1.340
peak=    3.460 closest distance to " N   PHE A 130 " =    1.364
peak=    3.451 closest distance to " O   HOH Z  88 " =    2.388
peak=    3.449 closest distance to " NH2BARG A 145 " =    2.138
peak=    3.447 closest distance to " O   HOH Z 261 " =    1.619
peak=    3.445 closest distance to " N   TYR A  15 " =    1.054
peak=    3.443 closest distance to " NH1BARG A 145 " =    1.574
peak=    3.443 closest distance to " CE  MET A  40 " =    0.995
peak=    3.443 closest distance to " CG  LYS A 166 " =    1.368
peak=    3.443 closest distance to " O   HOH Z  22 " =    1.975
peak=    3.438 closest distance to " O   HOH Z 389 " =    1.396
peak=    3.438 closest distance to " O   HOH Z 389 " =    2.852
peak=    3.434 closest distance to " CB BVAL A  41 " =    1.285
peak=    3.433 closest distance to " CA  LYS A 117 " =    1.223
peak=    3.431 closest distance to " O   HOH Z 284 " =    2.549
peak=    3.430 closest distance to " O   HOH Z 402 " =    1.630
peak=    3.428 closest distance to " O   HOH Z  24 " =    1.443
peak=    3.427 closest distance to " CB  VAL A 202 " =    1.680
peak=    3.426 closest distance to " CA  ARG A  66 " =    0.938
peak=    3.422 closest distance to " O   HOH Z 303 " =    1.684
peak=    3.422 closest distance to " CG  MET A 185 " =    0.934
peak=    3.422 closest distance to " CB  PHE A 225 " =    1.278
peak=    3.417 closest distance to " OD1 ASP A 286 " =    1.259
peak=    3.416 closest distance to " CG  LYS A  76 " =    1.439
peak=    3.409 closest distance to " O   GLY A 147 " =    1.377
peak=    3.406 closest distance to " O   HOH Z  89 " =    2.289
peak=    3.404 closest distance to " O   HOH Z 344 " =    2.750
peak=    3.403 closest distance to " OE1 GLU A   2 " =    1.997
peak=    3.402 closest distance to " CG2 VAL A 257 " =    0.964
peak=    3.400 closest distance to " NH1BARG A 190 " =    1.990
peak=    3.398 closest distance to " O   HOH Z 128 " =    2.074
peak=    3.397 closest distance to " O   HOH Z 425 " =    2.094
peak=    3.390 closest distance to " CA  ASN A 127 " =    1.155
peak=    3.389 closest distance to " NZ  LYS A  48 " =    1.835
peak=    3.382 closest distance to " O   HOH Z   8 " =    1.568
peak=    3.379 closest distance to " CB  GLU A 277 " =    3.427
peak=    3.375 closest distance to " O   HOH Z 425 " =    1.411
peak=    3.374 closest distance to " CD1 ILE A  33 " =    1.611
peak=    3.372 closest distance to " O   HOH Z  53 " =    2.394
peak=    3.371 closest distance to " NE BARG A 145 " =    0.973
peak=    3.369 closest distance to " O   HOH Z 332 " =    1.425
peak=    3.367 closest distance to " O   HOH Z 130 " =    2.023
peak=    3.367 closest distance to " CB  SER A  26 " =    1.487
peak=    3.364 closest distance to " O   HOH Z  58 " =    1.664
peak=    3.361 closest distance to " O   HOH Z 400 " =    0.783
peak=    3.352 closest distance to " CB  ASP A 200 " =    0.985
peak=    3.349 closest distance to " O   HOH Z 183 " =    1.742
peak=    3.346 closest distance to " O   HOH Z 184 " =    1.299
peak=    3.345 closest distance to " O   HOH Z 193 " =    1.821
peak=    3.339 closest distance to " O   HOH Z 423 " =    1.696
peak=    3.332 closest distance to " CB  GLN A 278 " =    0.759
peak=    3.331 closest distance to " O   HOH Z 427 " =    1.184
peak=    3.328 closest distance to " O   HOH Z 137 " =    1.598
peak=    3.324 closest distance to " CG  LYS A 119 " =    1.127
peak=    3.323 closest distance to " O   HOH Z  69 " =    1.047
peak=    3.323 closest distance to " O   HOH Z 267 " =    2.060
peak=    3.322 closest distance to " O   HOH Z 213 " =    1.766
peak=    3.319 closest distance to " O   ASN A 301 " =    2.479
peak=    3.319 closest distance to " O   HOH Z 212 " =    1.519
peak=    3.318 closest distance to " O   HOH Z 395 " =    1.472
peak=    3.315 closest distance to " O   HOH Z 367 " =    3.990
peak=    3.314 closest distance to " O   HOH Z 290 " =    1.083
peak=    3.313 closest distance to " O   HOH Z 226 " =    1.105
peak=    3.311 closest distance to " CG  LEU A 228 " =    1.191
peak=    3.308 closest distance to " N   TRP A 177 " =    1.529
peak=    3.304 closest distance to " O   HOH Z 327 " =    1.554
peak=    3.301 closest distance to " O   HOH Z 428 " =    1.203
peak=    3.301 closest distance to " O   HOH Z 124 " =    2.195
peak=    3.301 closest distance to " CB  ASN A 148 " =    1.868
peak=    3.299 closest distance to " O   PHE A  38 " =    1.973
peak=    3.297 closest distance to " NE2 GLN A 278 " =    3.789
peak=    3.295 closest distance to " NZ  LYS A 117 " =    0.952
peak=    3.295 closest distance to " O   HOH Z 392 " =    1.308
peak=    3.295 closest distance to " O   HOH Z   6 " =    1.559
peak=    3.294 closest distance to " O   HOH Z  28 " =    2.389
peak=    3.293 closest distance to " OG1 THR A 294 " =    1.831
peak=    3.283 closest distance to " O   HOH Z 172 " =    3.458
peak=    3.282 closest distance to " O   HOH Z  98 " =    1.421
peak=    3.281 closest distance to " CG  GLN A  77 " =    2.188
peak=    3.278 closest distance to " N   GLY A 111 " =    1.187
peak=    3.275 closest distance to " O   HOH Z  63 " =    1.583
peak=    3.275 closest distance to " O   HOH Z 153 " =    1.582
peak=    3.274 closest distance to " NH1 ARG A 219 " =    0.906
peak=    3.271 closest distance to " NH2 ARG A 138 " =    2.320
peak=    3.270 closest distance to " OH  TYR A 116 " =    1.212
peak=    3.269 closest distance to " CA  VAL A  41 " =    0.917
peak=    3.268 closest distance to " O   HOH Z 156 " =    2.933
peak=    3.268 closest distance to " OE1 GLN A  77 " =    1.347
peak=    3.267 closest distance to " CB  ASN A  69 " =    1.595
peak=    3.266 closest distance to " ND1 HIS A  81 " =    1.171
peak=    3.266 closest distance to " O   HOH Z 419 " =    1.883
peak=    3.266 closest distance to " CG  ASP A 238 " =    0.844
peak=    3.263 closest distance to " CB  SER A  62 " =    1.212
peak=    3.263 closest distance to " CB  GLU A 128 " =    1.162
peak=    3.261 closest distance to " O   HOH Z 383 " =    2.368
peak=    3.260 closest distance to " CG  GLN A  89 " =    1.438
peak=    3.256 closest distance to " CG  PRO A 243 " =    1.287
peak=    3.253 closest distance to " O   HOH Z  33 " =    1.897
peak=    3.251 closest distance to " O   HOH Z 112 " =    1.071
peak=    3.250 closest distance to " O   HOH Z 111 " =    1.922
peak=    3.248 closest distance to " CG  PRO A 163 " =    3.468
peak=    3.248 closest distance to " CD1 LEU A 228 " =    1.663
peak=    3.244 closest distance to " CZ AARG A 102 " =    1.598
peak=    3.244 closest distance to " CD1 LEU A 228 " =    1.469
peak=    3.241 closest distance to " CA  ALA A 295 " =    1.131
peak=    3.238 closest distance to " O   HOH Z 374 " =    1.182
peak=    3.237 closest distance to " CG1 VAL A 153 " =    0.855
peak=    3.236 closest distance to " O   HOH Z 380 " =    1.912
peak=    3.232 closest distance to " C   PHE A  59 " =    1.179
peak=    3.231 closest distance to " O   HOH Z 118 " =    2.025
peak=    3.228 closest distance to " O   HOH Z 233 " =    1.551
peak=    3.227 closest distance to " CB  ALA A 291 " =    1.528
peak=    3.226 closest distance to " O   HOH Z 410 " =    1.077
peak=    3.226 closest distance to " O   HOH Z 358 " =    1.242
peak=    3.225 closest distance to " CB  ARG A  79 " =    1.572
peak=    3.223 closest distance to " O   HOH Z  88 " =    2.979
peak=    3.221 closest distance to " O   HOH Z 191 " =    1.975
peak=    3.220 closest distance to " O   HOH Z  43 " =    2.779
peak=    3.219 closest distance to " O   HOH Z 272 " =    2.169
peak=    3.217 closest distance to " O   HOH Z 418 " =    1.799
peak=    3.214 closest distance to " CB  THR A  52 " =    1.188
peak=    3.211 closest distance to " O   HOH Z 222 " =    2.150
peak=    3.200 closest distance to " O   HOH Z 392 " =    2.068
peak=    3.199 closest distance to " NZ  LYS A  76 " =    1.479
peak=    3.199 closest distance to " O   SER A  26 " =    1.723
peak=    3.198 closest distance to " CA  ALA A  43 " =    1.075
peak=    3.192 closest distance to " O   HOH Z  68 " =    1.628
peak=    3.187 closest distance to " O   HOH Z 261 " =    1.608
peak=    3.187 closest distance to " CB  ALA A   1 " =    4.214
peak=    3.185 closest distance to " O   HOH Z 134 " =    1.894
peak=    3.183 closest distance to " O   HOH Z 417 " =    2.974
peak=    3.179 closest distance to " O   HOH Z 375 " =    1.033
peak=    3.179 closest distance to " O   HOH Z 289 " =    1.432
peak=    3.178 closest distance to " O   GLY A  35 " =    0.985
peak=    3.177 closest distance to " O   HOH Z 133 " =    2.276
peak=    3.176 closest distance to " OG BSER A 134 " =    2.853
peak=    3.175 closest distance to " NH2 ARG A 219 " =    1.805
peak=    3.163 closest distance to " O   HOH Z 406 " =    1.117
peak=    3.160 closest distance to " O   HOH Z 222 " =    2.141
peak=    3.152 closest distance to " O   HOH Z 115 " =    1.781
peak=    3.151 closest distance to " O   HOH Z 293 " =    1.356
peak=    3.149 closest distance to " O   HOH Z  13 " =    1.803
peak=    3.147 closest distance to " CZ2 TRP A 274 " =    1.844
peak=    3.147 closest distance to " O   HOH Z  54 " =    0.964
peak=    3.145 closest distance to " O   HOH Z 196 " =    1.348
peak=    3.145 closest distance to " O   HOH Z 311 " =    1.581
peak=    3.140 closest distance to " CE BLYS A 290 " =    1.007
peak=    3.138 closest distance to " CA  GLN A 194 " =    0.960
peak=    3.137 closest distance to " O   SER A 164 " =    1.553
peak=    3.137 closest distance to " CE2 PHE A  16 " =    1.074
peak=    3.136 closest distance to " O   HOH Z 144 " =    2.156
peak=    3.136 closest distance to " CA  ARG A 195 " =    1.159
peak=    3.132 closest distance to " O   HOH Z  88 " =    4.498
peak=    3.131 closest distance to " CA  GLY A  80 " =    0.781
peak=    3.126 closest distance to " CE3 TRP A 274 " =    2.294
peak=    3.125 closest distance to " O   HOH Z  69 " =    2.147
peak=    3.110 closest distance to " CA  LYS A  48 " =    1.257
peak=    3.107 closest distance to " O   HOH Z  40 " =    2.437
peak=    3.102 closest distance to " O   HOH Z 389 " =    1.319
peak=    3.093 closest distance to " CZ3 TRP A 274 " =    2.255
peak=    3.093 closest distance to " O   HOH Z 112 " =    1.329
peak=    3.085 closest distance to " O   HOH Z  47 " =    1.651
peak=    3.080 closest distance to " O   HOH Z 395 " =    3.213
peak=    3.075 closest distance to " CB  MET A  40 " =    0.942
peak=    3.067 closest distance to " O   HOH Z 279 " =    3.359
peak=    3.046 closest distance to " NH1AARG A 145 " =    0.800
peak=    3.045 closest distance to " O   HOH Z 364 " =    1.454
peak=    3.040 closest distance to " O   HOH Z  10 " =    1.763

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 198         
Filter by distance & map next to the model:
   mapped sites are within: 0.650 - 5.542
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 196 from: 198
   mapped sites are within: 0.783 - 5.542

peak=   -4.826 closest distance to " N   GLN A  58 " =    1.000
peak=   -4.465 closest distance to " CD  ARG A 138 " =    1.291
peak=   -4.409 closest distance to " O   PRO A 198 " =    1.033
peak=   -4.366 closest distance to " OG ASER A 134 " =    1.071
peak=   -4.358 closest distance to " N   THR A  52 " =    1.752
peak=   -4.319 closest distance to " NH2 ARG A  79 " =    1.838
peak=   -4.292 closest distance to " O   HOH Z 385 " =    0.936
peak=   -4.285 closest distance to " O   HOH Z 347 " =    0.856
peak=   -4.262 closest distance to " N   GLN A  58 " =    2.263
peak=   -4.168 closest distance to " CA  VAL A  67 " =    2.901
peak=   -4.122 closest distance to " CD  ARG A  14 " =    3.143
peak=   -4.103 closest distance to " O   HOH Z  93 " =    1.344
peak=   -4.077 closest distance to " CG  GLN A  88 " =    0.906
peak=   -4.058 closest distance to " C   HIS A 108 " =    1.190
peak=   -4.039 closest distance to " NH1 ARG A  56 " =    2.503
peak=   -4.028 closest distance to " O   HOH Z 164 " =    5.542
peak=   -4.020 closest distance to " C   ASN A 187 " =    1.727
peak=   -4.011 closest distance to " CG  ARG A 138 " =    0.851
peak=   -3.935 closest distance to " CD  ARG A 156 " =    1.937
peak=   -3.926 closest distance to " CA  GLY A  23 " =    1.884
peak=   -3.910 closest distance to " OD1 ASN A  39 " =    2.070
peak=   -3.880 closest distance to " CE2 TYR A  30 " =    2.862
peak=   -3.877 closest distance to " OG  SER A   3 " =    1.189
peak=   -3.853 closest distance to " O   HOH Z 388 " =    1.746
peak=   -3.850 closest distance to " N   HIS A 115 " =    2.008
peak=   -3.849 closest distance to " C   ASN A 285 " =    1.995
peak=   -3.849 closest distance to " OG BSER A 134 " =    1.156
peak=   -3.821 closest distance to " CE2 TYR A 116 " =    3.068
peak=   -3.807 closest distance to " CB  ASP A  27 " =    2.409
peak=   -3.770 closest distance to " O   HOH Z  24 " =    1.383
peak=   -3.755 closest distance to " O   HOH Z 266 " =    4.444
peak=   -3.734 closest distance to " O   HOH Z 419 " =    0.980
peak=   -3.705 closest distance to " OE1 GLU A 277 " =    2.152
peak=   -3.700 closest distance to " O   PRO A 163 " =    1.838
peak=   -3.688 closest distance to " CA  GLY A 133 " =    1.869
peak=   -3.686 closest distance to " CB  ALA A 248 " =    1.947
peak=   -3.680 closest distance to " CA  GLY A  35 " =    2.071
peak=   -3.673 closest distance to " CD  GLU A 152 " =    2.441
peak=   -3.645 closest distance to " O   SER A 135 " =    1.553
peak=   -3.635 closest distance to " NE1 TRP A 274 " =    1.106
peak=   -3.632 closest distance to " CE  LYS A  76 " =    2.966
peak=   -3.624 closest distance to " O   HOH Z 188 " =    4.563
peak=   -3.608 closest distance to " CE2 PHE A 218 " =    2.721
peak=   -3.592 closest distance to " CD1 LEU A 255 " =    2.783
peak=   -3.589 closest distance to " O   HOH Z 231 " =    1.713
peak=   -3.574 closest distance to " O   HOH Z  88 " =    2.224
peak=   -3.562 closest distance to " ND1 HIS A 115 " =    0.977
peak=   -3.557 closest distance to " O   HOH Z 134 " =    1.888
peak=   -3.554 closest distance to " OD1 ASP A 200 " =    1.035
peak=   -3.552 closest distance to " OG1 THR A 246 " =    1.296
peak=   -3.544 closest distance to " OG1 THR A 178 " =    1.066
peak=   -3.541 closest distance to " O   HOH Z 298 " =    1.140
peak=   -3.535 closest distance to " O   HOH Z 166 " =    1.634
peak=   -3.519 closest distance to " O   VAL A 125 " =    2.023
peak=   -3.516 closest distance to " O   HOH Z 193 " =    1.348
peak=   -3.509 closest distance to " O   HOH Z 137 " =    1.420
peak=   -3.505 closest distance to " OD2 ASP A 191 " =    1.359
peak=   -3.488 closest distance to " O   HOH Z  98 " =    1.751
peak=   -3.485 closest distance to " O   HOH Z 407 " =    2.969
peak=   -3.485 closest distance to " CG1 ILE A 234 " =    1.839
peak=   -3.484 closest distance to " O   HOH Z 138 " =    0.824
peak=   -3.480 closest distance to " O   VAL A  67 " =    2.763
peak=   -3.474 closest distance to " O   ALA A 165 " =    1.028
peak=   -3.471 closest distance to " CB  ALA A 244 " =    2.168
peak=   -3.465 closest distance to " O   HOH Z 404 " =    1.431
peak=   -3.462 closest distance to " O   HOH Z 317 " =    3.120
peak=   -3.450 closest distance to " CD1 PHE A 225 " =    1.694
peak=   -3.440 closest distance to " O   ASN A 187 " =    1.306
peak=   -3.439 closest distance to " CD2 LEU A 237 " =    2.457
peak=   -3.435 closest distance to " O   HOH Z 217 " =    3.802
peak=   -3.435 closest distance to " O   HOH Z 377 " =    0.933
peak=   -3.429 closest distance to " N   GLN A  88 " =    1.679
peak=   -3.428 closest distance to " O   HOH Z 308 " =    1.567
peak=   -3.422 closest distance to " O   HOH Z 198 " =    1.826
peak=   -3.418 closest distance to " CG  ASP A  50 " =    2.167
peak=   -3.413 closest distance to " O   MET A 188 " =    1.663
peak=   -3.409 closest distance to " CZ  PHE A 130 " =    2.134
peak=   -3.408 closest distance to " O   MET A  40 " =    2.864
peak=   -3.405 closest distance to " O   HOH Z 350 " =    2.090
peak=   -3.402 closest distance to " O   SER A 245 " =    1.258
peak=   -3.400 closest distance to " O   HOH Z 124 " =    1.289
peak=   -3.391 closest distance to " O   HOH Z 250 " =    1.299
peak=   -3.389 closest distance to " O   GLY A  98 " =    2.154
peak=   -3.388 closest distance to " O   HOH Z 193 " =    2.006
peak=   -3.384 closest distance to " CG  PRO A 198 " =    1.552
peak=   -3.383 closest distance to " O   HOH Z 372 " =    2.405
peak=   -3.372 closest distance to " CG  PHE A 283 " =    2.473
peak=   -3.368 closest distance to " N   ALA A 248 " =    1.749
peak=   -3.361 closest distance to " CD  PRO A 198 " =    1.299
peak=   -3.351 closest distance to " O   VAL A 197 " =    1.435
peak=   -3.350 closest distance to " CB  CYS A 201 " =    2.497
peak=   -3.346 closest distance to " O   HOH Z 385 " =    1.073
peak=   -3.344 closest distance to " CG  LEU A 228 " =    1.104
peak=   -3.340 closest distance to " O   TRP A  92 " =    1.543
peak=   -3.338 closest distance to " NH2AARG A 275 " =    4.989
peak=   -3.333 closest distance to " O   HOH Z 153 " =    1.553
peak=   -3.331 closest distance to " C   ASP A 124 " =    1.139
peak=   -3.328 closest distance to " O   HOH Z 134 " =    2.436
peak=   -3.322 closest distance to " O   SER A  62 " =    1.144
peak=   -3.321 closest distance to " CZ  PHE A  16 " =    1.236
peak=   -3.314 closest distance to " CB  ALA A  43 " =    2.182
peak=   -3.310 closest distance to " O   HOH Z  63 " =    1.153
peak=   -3.309 closest distance to " OG1 THR A   4 " =    1.716
peak=   -3.301 closest distance to " N   ALA A   1 " =    1.376
peak=   -3.298 closest distance to " CG  PRO A 243 " =    1.221
peak=   -3.296 closest distance to " O   ALA A  51 " =    1.213
peak=   -3.296 closest distance to " CG  PRO A 163 " =    2.733
peak=   -3.295 closest distance to " O   HOH Z 365 " =    1.187
peak=   -3.291 closest distance to " O   HOH Z 191 " =    4.941
peak=   -3.289 closest distance to " CD  LYS A 289 " =    2.515
peak=   -3.285 closest distance to " OE2 GLU A   2 " =    1.054
peak=   -3.283 closest distance to " O   GLY A  57 " =    1.568
peak=   -3.278 closest distance to " C   ILE A 239 " =    2.033
peak=   -3.276 closest distance to " O   HOH Z 145 " =    2.434
peak=   -3.276 closest distance to " O   ALA A 161 " =    1.635
peak=   -3.274 closest distance to " O   HOH Z 359 " =    2.116
peak=   -3.267 closest distance to " O   HOH Z 117 " =    1.145
peak=   -3.262 closest distance to " CD1 LEU A 101 " =    2.183
peak=   -3.256 closest distance to " O   HOH Z 290 " =    1.058
peak=   -3.255 closest distance to " O   SER A  22 " =    2.383
peak=   -3.251 closest distance to " O   GLY A  80 " =    2.444
peak=   -3.249 closest distance to " O   PRO A 243 " =    2.520
peak=   -3.247 closest distance to " O   GLN A  89 " =    1.191
peak=   -3.245 closest distance to " ND2 ASN A 209 " =    1.727
peak=   -3.245 closest distance to " CE3 TRP A 150 " =    1.943
peak=   -3.243 closest distance to " OG  SER A 245 " =    1.432
peak=   -3.242 closest distance to " O   HOH Z 175 " =    0.979
peak=   -3.241 closest distance to " O   HOH Z 205 " =    0.944
peak=   -3.238 closest distance to " ND2 ASN A  45 " =    1.050
peak=   -3.236 closest distance to " C   PHE A 155 " =    0.802
peak=   -3.232 closest distance to " C   LEU A 143 " =    1.147
peak=   -3.232 closest distance to " O   HOH Z  28 " =    0.814
peak=   -3.230 closest distance to " CB  ALA A   7 " =    1.953
peak=   -3.228 closest distance to " CA  THR A 235 " =    1.629
peak=   -3.223 closest distance to " N   SER A 276 " =    1.028
peak=   -3.217 closest distance to " NE BARG A 275 " =    1.264
peak=   -3.217 closest distance to " O   HOH Z  56 " =    1.878
peak=   -3.216 closest distance to " O   HOH Z 424 " =    1.471
peak=   -3.213 closest distance to " CG1BVAL A  72 " =    4.267
peak=   -3.212 closest distance to " N   GLN A  77 " =    1.454
peak=   -3.210 closest distance to " O   SER A  22 " =    1.452
peak=   -3.209 closest distance to " CE3 TRP A 179 " =    1.968
peak=   -3.204 closest distance to " N   PHE A  59 " =    1.270
peak=   -3.201 closest distance to " O   HOH Z   9 " =    1.541
peak=   -3.201 closest distance to " O   HOH Z 245 " =    1.409
peak=   -3.200 closest distance to " O   HOH Z 220 " =    1.913
peak=   -3.198 closest distance to " CG  ASN A  60 " =    0.989
peak=   -3.196 closest distance to " CD  ARG A 219 " =    2.450
peak=   -3.193 closest distance to " O   ASP A 200 " =    0.940
peak=   -3.189 closest distance to " OG  SER A   3 " =    1.553
peak=   -3.188 closest distance to " O   HOH Z 131 " =    3.747
peak=   -3.187 closest distance to " O   HOH Z 139 " =    3.490
peak=   -3.186 closest distance to " CB  ALA A 248 " =    1.851
peak=   -3.184 closest distance to " O   HOH Z 414 " =    2.366
peak=   -3.183 closest distance to " O   HOH Z 387 " =    2.235
peak=   -3.181 closest distance to " N   THR A 235 " =    1.088
peak=   -3.178 closest distance to " CG1 VAL A 197 " =    1.836
peak=   -3.177 closest distance to " CD1 LEU A  96 " =    2.178
peak=   -3.173 closest distance to " O   HOH Z 231 " =    1.409
peak=   -3.171 closest distance to " O   HOH Z 256 " =    1.067
peak=   -3.169 closest distance to " O   HOH Z 234 " =    3.000
peak=   -3.166 closest distance to " CB  SER A 273 " =    1.744
peak=   -3.160 closest distance to " OG ASER A 258 " =    2.853
peak=   -3.159 closest distance to " CD  GLU A 277 " =    1.034
peak=   -3.159 closest distance to " O   SER A  26 " =    1.076
peak=   -3.159 closest distance to " NH1BARG A 145 " =    4.598
peak=   -3.157 closest distance to " O   HOH Z 426 " =    1.985
peak=   -3.151 closest distance to " C   ASN A 217 " =    1.530
peak=   -3.151 closest distance to " O   GLY A 118 " =    1.381
peak=   -3.149 closest distance to " O   HOH Z 423 " =    2.595
peak=   -3.146 closest distance to " NH1AARG A 102 " =    2.271
peak=   -3.145 closest distance to " O   THR A 220 " =    1.530
peak=   -3.144 closest distance to " O   HOH Z  89 " =    0.906
peak=   -3.135 closest distance to " O   TRP A  70 " =    1.445
peak=   -3.132 closest distance to " O   HOH Z  13 " =    1.232
peak=   -3.131 closest distance to " CG  ARG A 139 " =    1.287
peak=   -3.129 closest distance to " OH  TYR A 169 " =    0.912
peak=   -3.127 closest distance to " CG  GLN A  11 " =    1.763
peak=   -3.123 closest distance to " N   LYS A 166 " =    1.781
peak=   -3.121 closest distance to " CD2 PHE A  61 " =    1.055
peak=   -3.119 closest distance to " CD  LYS A 166 " =    1.069
peak=   -3.113 closest distance to " O   ASN A 215 " =    1.510
peak=   -3.111 closest distance to " O   HOH Z 274 " =    2.796
peak=   -3.109 closest distance to " CG  ARG A 219 " =    2.752
peak=   -3.107 closest distance to " C   SER A  63 " =    0.972
peak=   -3.107 closest distance to " OD1 ASN A 301 " =    2.077
peak=   -3.103 closest distance to " CG  ASP A 231 " =    0.783
peak=   -3.101 closest distance to " CG BMET A  47 " =    1.905
peak=   -3.099 closest distance to " NE2 GLN A  58 " =    1.967
peak=   -3.096 closest distance to " CB  ALA A 131 " =    1.820
peak=   -3.086 closest distance to " CE3 TRP A 274 " =    2.471
peak=   -3.084 closest distance to " O   THR A 251 " =    1.742
peak=   -3.074 closest distance to " O   HOH Z 385 " =    2.092
peak=   -3.061 closest distance to " OG ASER A 134 " =    0.868
peak=   -3.030 closest distance to " O   HOH Z 211 " =    1.028
peak=   -3.023 closest distance to " O   GLN A  73 " =    1.588

================= 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    :  0.5093 0.5028   6.301545e+00   6.296669e+00
   1_bss:  0.5010 0.4927   6.296295e+00   6.285938e+00
   1_xyz:  0.4454 0.4584   6.238813e+00   6.256884e+00
   1_adp:  0.4054 0.4565   6.192927e+00   6.253542e+00
   1_occ:  0.4050 0.4570   6.192582e+00   6.254246e+00
   2_bss:  0.4021 0.4552   6.193604e+00   6.254174e+00
   2_xyz:  0.3305 0.3953   6.048534e+00   6.168528e+00
   2_adp:  0.3069 0.3752   6.001231e+00   6.133913e+00
   2_occ:  0.3065 0.3753   6.001365e+00   6.134055e+00
   3_bss:  0.3046 0.3731   5.999675e+00   6.132912e+00
   3_xyz:  0.2451 0.3089   5.818770e+00   5.991224e+00
   3_adp:  0.2225 0.2929   5.751564e+00   5.949494e+00
   3_occ:  0.2222 0.2924   5.750750e+00   5.948789e+00
   4_bss:  0.2220 0.2921   5.748727e+00   5.946474e+00
   4_xyz:  0.1774 0.2394   5.549327e+00   5.768306e+00
   4_adp:  0.1701 0.2219   5.496802e+00   5.700035e+00
   4_occ:  0.1697 0.2211   5.494823e+00   5.697321e+00
   5_bss:  0.1696 0.2206   5.494960e+00   5.696582e+00
   5_xyz:  0.1419 0.1859   5.327291e+00   5.539293e+00
   5_adp:  0.1331 0.1793   5.279280e+00   5.503770e+00
   5_occ:  0.1330 0.1790   5.278632e+00   5.502715e+00
   5_bss:  0.1330 0.1791   5.278058e+00   5.502565e+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:  0.381   0.000   6.631   8.831   9.082   0.000   0.000   0.000
   1_xyz:  0.381   0.000   6.631   8.831   9.082   0.000   0.000   0.000
   1_adp:  0.381   0.000   6.631   8.831   9.082   0.000   0.000   0.000
   1_occ:  0.381   0.000   6.631   8.831   9.082   0.000   0.000   0.000
   2_bss:  0.399  50.000   3.011   4.429   5.564   0.000   0.000   0.000
   2_xyz:  0.399  50.000   3.011   4.429   5.564   0.000   0.000   0.000
   2_adp:  0.399  50.000   3.011   4.429   5.564   0.000   0.000   0.000
   2_occ:  0.399  50.000   3.011   4.429   5.564   0.000   0.000   0.000
   3_bss:  0.339  39.915   1.366   2.061   3.034   0.000   0.000   0.000
   3_xyz:  0.339  39.915   1.366   2.061   3.034   0.000   0.000   0.000
   3_adp:  0.339  39.915   1.366   2.061   3.034   0.000   0.000   0.000
   3_occ:  0.339  39.915   1.366   2.061   3.034   0.000   0.000   0.000
   4_bss:  0.323  35.755   0.673   1.139   2.033   0.000   0.000   0.000
   4_xyz:  0.323  35.755   0.673   1.139   2.033   0.000   0.000   0.000
   4_adp:  0.323  35.755   0.673   1.139   2.033   0.000   0.000   0.000
   4_occ:  0.323  35.755   0.673   1.139   2.033   0.000   0.000   0.000
   5_bss:  0.317  30.555  -0.033   0.356   1.167   0.000   0.000   0.000
   5_xyz:  0.317  30.555  -0.033   0.356   1.167   0.000   0.000   0.000
   5_adp:  0.317  30.555  -0.033   0.356   1.167   0.000   0.000   0.000
   5_occ:  0.317  30.555  -0.033   0.356   1.167   0.000   0.000   0.000
   5_bss:  0.315  31.384  -0.427  -0.139   0.566   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  64.693 0.3332  0.4054    82560.557
   1_bss:  64.011 0.3406  0.5156    78857.321
   1_xyz:  55.919 0.4450  0.6669    65842.083
   1_adp:  54.498 0.4634  0.7669    64817.614
   1_occ:  54.689 0.4609  0.7613    65038.030
   2_bss:  54.395 0.4646  0.6786    64920.284
   2_xyz:  43.845 0.5956  0.8671    44415.829
   2_adp:  40.287 0.6392  0.9304    39143.913
   2_occ:  40.323 0.6388  0.9294    39208.211
   3_bss:  40.126 0.6409  0.8604    38847.770
   3_xyz:  31.907 0.7361  0.9557    25164.133
   3_adp:  29.347 0.7652  0.9705    22382.511
   3_occ:  29.315 0.7656  0.9707    22354.281
   4_bss:  29.199 0.7667  0.9401    22122.361
   4_xyz:  23.300 0.8289  0.9906    14483.612
   4_adp:  20.999 0.8530  1.0108    12597.946
   4_occ:  20.941 0.8536  1.0110    12539.166
   5_bss:  20.935 0.8535  0.9812    12495.925
   5_xyz:  17.079 0.8892  0.9988     8701.639
   5_adp:  16.290 0.8963  0.9964     8118.203
   5_occ:  16.269 0.8965  0.9964     8093.889
   5_bss:  16.247 0.8967  0.9893     8102.636
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.085   5.2556e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.085   5.2556e+01
   1_xyz:   1.701  0.013  0.107 18.374  0.007  4.104   1.4683e-01
   1_adp:   1.701  0.013  0.107 18.374  0.007  4.104   1.4683e-01
   1_occ:   1.701  0.013  0.107 18.374  0.007  4.104   1.4683e-01
   2_bss:   1.701  0.013  0.107 18.374  0.007  4.104   1.4683e-01
   2_xyz:   1.268  0.009  0.086 16.941  0.006  4.103   1.0113e-01
   2_adp:   1.268  0.009  0.086 16.941  0.006  4.103   1.0113e-01
   2_occ:   1.268  0.009  0.086 16.941  0.006  4.103   1.0113e-01
   3_bss:   1.268  0.009  0.086 16.941  0.006  4.103   1.0113e-01
   3_xyz:   1.082  0.008  0.072 15.896  0.005  4.116   7.1528e-02
   3_adp:   1.082  0.008  0.072 15.896  0.005  4.116   7.1528e-02
   3_occ:   1.082  0.008  0.072 15.896  0.005  4.116   7.1528e-02
   4_bss:   1.082  0.008  0.072 15.896  0.005  4.116   7.1528e-02
   4_xyz:   0.938  0.006  0.066 15.573  0.003  4.108   5.8424e-02
   4_adp:   0.938  0.006  0.066 15.573  0.003  4.108   5.8424e-02
   4_occ:   0.938  0.006  0.066 15.573  0.003  4.108   5.8424e-02
   5_bss:   0.938  0.006  0.066 15.573  0.003  4.108   5.8424e-02
   5_xyz:   0.957  0.006  0.066 15.528  0.003  4.105   5.7964e-02
   5_adp:   0.957  0.006  0.066 15.528  0.003  4.105   5.7964e-02
   5_occ:   0.957  0.006  0.066 15.528  0.003  4.105   5.7964e-02
   5_bss:   0.957  0.006  0.066 15.528  0.003  4.105   5.7964e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.529   6.8050e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.529   6.8050e+00
   1_xyz:  14.278  0.165  0.454 84.504  0.057  2.156   9.6227e-02
   1_adp:  14.278  0.165  0.454 84.504  0.057  2.156   9.6227e-02
   1_occ:  14.278  0.165  0.454 84.504  0.057  2.156   9.6227e-02
   2_bss:  14.278  0.165  0.454 84.504  0.057  2.156   9.6227e-02
   2_xyz:   7.556  0.109  0.415 75.353  0.054  2.210   7.9527e-02
   2_adp:   7.556  0.109  0.415 75.353  0.054  2.210   7.9527e-02
   2_occ:   7.556  0.109  0.415 75.353  0.054  2.210   7.9527e-02
   3_bss:   7.556  0.109  0.415 75.353  0.054  2.210   7.9527e-02
   3_xyz:   7.970  0.064  0.272 85.915  0.027  2.297   5.9424e-02
   3_adp:   7.970  0.064  0.272 85.915  0.027  2.297   5.9424e-02
   3_occ:   7.970  0.064  0.272 85.915  0.027  2.297   5.9424e-02
   4_bss:   7.970  0.064  0.272 85.915  0.027  2.297   5.9424e-02
   4_xyz:   7.175  0.044  0.254 89.515  0.019  2.407   5.5722e-02
   4_adp:   7.175  0.044  0.254 89.515  0.019  2.407   5.5722e-02
   4_occ:   7.175  0.044  0.254 89.515  0.019  2.407   5.5722e-02
   5_bss:   7.175  0.044  0.254 89.515  0.019  2.407   5.5722e-02
   5_xyz:   6.433  0.040  0.217 83.085  0.028  2.325   7.1171e-02
   5_adp:   6.433  0.040  0.217 83.085  0.028  2.325   7.1171e-02
   5_occ:   6.433  0.040  0.217 83.085  0.028  2.325   7.1171e-02
   5_bss:   6.433  0.040  0.217 83.085  0.028  2.325   7.1171e-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:  81.07   0.00  15.89  73.19   0.00  14.41  81.07   0.00  23.93
   1_occ:  81.07   0.00  15.89  73.19   0.00  14.41  81.07   0.00  23.93
   2_bss:  81.07   0.00  15.89  73.19   0.00  14.41  81.07   0.00  23.93
   2_xyz:  81.07   0.00  15.89  73.19   0.00  14.41  81.07   0.00  23.93
   2_adp:  84.27   0.00  15.31  84.27   0.00  12.64  80.29   0.00  29.81
   2_occ:  84.27   0.00  15.31  84.27   0.00  12.64  80.29   0.00  29.81
   3_bss:  84.27   0.00  15.31  84.27   0.00  12.64  80.29   0.00  29.81
   3_xyz:  84.27   0.00  15.31  84.27   0.00  12.64  80.29   0.00  29.81
   3_adp: 100.49   0.00  15.79 100.49   0.00  11.65  81.27   1.20  38.33
   3_occ: 100.49   0.00  15.79 100.49   0.00  11.65  81.27   1.20  38.33
   4_bss: 100.49   0.00  15.79 100.49   0.00  11.65  81.27   1.20  38.33
   4_xyz: 100.49   0.00  15.79 100.49   0.00  11.65  81.27   1.20  38.33
   4_adp:  97.60   0.00  15.19  97.60   0.00  11.05  82.06   2.69  37.72
   4_occ:  97.60   0.00  15.19  97.60   0.00  11.05  82.06   2.69  37.72
   5_bss:  97.60   0.00  15.19  97.60   0.00  11.05  82.06   2.69  37.72
   5_xyz:  97.60   0.00  15.19  97.60   0.00  11.05  82.06   2.69  37.72
   5_adp:  98.86   0.00  15.42  98.86   0.00  10.69  84.97   4.19  41.17
   5_occ:  98.86   0.00  15.42  98.86   0.00  10.69  84.97   4.19  41.17
   5_bss:  99.16   0.30  15.72  99.16   0.30  10.99  85.27   4.49  41.47
------------------------------------------------------------------------
 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:    1.256    0.014    0.410
   1_adp:    1.256    0.014    0.410
   1_occ:    1.256    0.014    0.410
   2_bss:    1.256    0.014    0.410
   2_xyz:    1.637    0.037    0.591
   2_adp:    1.637    0.037    0.591
   2_occ:    1.637    0.037    0.591
   3_bss:    1.637    0.037    0.591
   3_xyz:    1.583    0.035    0.691
   3_adp:    1.583    0.035    0.691
   3_occ:    1.583    0.035    0.691
   4_bss:    1.583    0.035    0.691
   4_xyz:    1.671    0.052    0.780
   4_adp:    1.671    0.052    0.780
   4_occ:    1.671    0.052    0.780
   5_bss:    1.671    0.052    0.780
   5_xyz:    1.825    0.046    0.835
   5_adp:    1.825    0.046    0.835
   5_occ:    1.825    0.046    0.835
   5_bss:    1.825    0.046    0.835
------------------------------------------------------------------------

CPU time actual refinement: 345.40


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_264/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_264/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_264/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_264/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_264/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 345.25 
  Macro-tasks:
    bulk solvent and scale       = 40.97  
    individual site refinement   = 147.66 
    weights calculation          = 31.98  
    collect and process          = 6.32   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 227.03 
  Micro-tasks:
    mask                            = 2.93   
    f_calc                          = 108.02 
    alpha_beta                      = 8.17   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 119.73 
    fmodel                         = 7.05   
    r_factors                      = 0.22   
    phase_errors                   = 10.06  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 257.62 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.843 micro seconds
Total CPU time: 5.98 minutes
from_scatterers_fft:    647 calls, 107.79 s
gradients_fft:          593 calls, 106.46 s

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

# Date 2008-01-16 Time 01:09:40 PST -0800 (1200474580.00 s)
Start R-work = 0.5093, R-free = 0.5028 (no bulk solvent and anisotropic scale)
Final R-work = 0.1485, R-free = 0.1943 (no bulk solvent and anisotropic scale)

Start R-work = 0.5010, R-free = 0.4927
Final R-work = 0.1330, R-free = 0.1791