# Date 2008-01-16 Time 01:57:53 PST -0800 (1200477473.47 s)
#phil __OFF__

Command line arguments: "../637.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 6501
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 637

-------------------------------------------------------------------------------
  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: (70.25, 46.2261, 88.5498, 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: 3.31, per 1000 atoms: 1.17


================================== 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: (70.25, 46.2261, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0929 1.97297
Completeness in resolution range: 0.937856
Completeness with d_max=infinity: 0.93508

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0929
                             d_min =   1.9730

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: (70.25, 46.2261, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0929 1.97297
Completeness in resolution range: 0.937856
Completeness with d_max=infinity: 0.93508

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0933 -  4.2225 [2192/2217]  1971   221  10.1%
  bin  2:  4.2225 -  3.3637 [2110/2130]  1902   208   9.9%
  bin  3:  3.3637 -  2.9421 [2088/2107]  1879   209  10.0%
  bin  4:  2.9421 -  2.6748 [2057/2087]  1844   213  10.4%
  bin  5:  2.6748 -  2.4839 [2050/2069]  1851   199   9.7%
  bin  6:  2.4839 -  2.3381 [2040/2065]  1835   205  10.0%
  bin  7:  2.3381 -  2.2213 [2015/2043]  1811   204  10.1%
  bin  8:  2.2213 -  2.1249 [2025/2061]  1823   202  10.0%
  bin  9:  2.1249 -  2.0433 [2013/2061]  1818   195   9.7%
  bin 10:  2.0433 -  1.9730 [ 999/2047]   896   103  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_637/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: 0.15 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:
        1.53 -     2.20: 13
        2.20 -     2.88: 1238
        2.88 -     3.55: 4443
        3.55 -     4.23: 9168
        4.23 -     4.90: 13332
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.525 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.550 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.564 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.745 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.745 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28189 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_637/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_637/model_refine_001.geo

CPU time processing inputs: 9.34


============================ 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 = 70.25 46.22605 88.54975 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


============================= ml refinement start =============================


   ----------structure factors based statistics (before refinement)----------  


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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4985   r_free= 0.4833   ksol= 0.00   Bsol= 0.00   scale= 0.776    |
|                                                                             |
| 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:   0.82 A                  |
| x-ray target function (ml) for work reflections: 6.298018                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7100 0.99   1424  156 0.4195 0.3915      6.6384      6.5958|
|  2:  4.7100 -  3.7574 0.99   1376  156 0.4246 0.4334       6.826      6.8413|
|  3:  3.7574 -  3.2881 0.99   1343  147 0.4562 0.4057      6.6934      6.6615|
|  4:  3.2881 -  2.9900 0.99   1335  153 0.5026 0.4647      6.5579       6.487|
|  5:  2.9900 -  2.7771 0.99   1320  145 0.5349 0.5006       6.374      6.4046|
|  6:  2.7771 -  2.6143 0.99   1329  143 0.5305 0.5532      6.2837      6.2139|
|  7:  2.6143 -  2.4839 0.99   1320  150 0.5363 0.5074      6.2458      6.2055|
|  8:  2.4839 -  2.3762 0.98   1307  146 0.5500 0.5192      6.1899      6.1793|
|  9:  2.3762 -  2.2851 0.98   1296  140 0.5305 0.5496      6.1277      6.1778|
| 10:  2.2851 -  2.2065 1.00   1307  149 0.5422 0.5412      6.0968      6.1107|
| 11:  2.2065 -  2.1377 0.98   1305  144 0.5253 0.5205      6.0338       6.037|
| 12:  2.1377 -  2.0767 0.98   1294  142 0.5359 0.5524      5.9554      5.9718|
| 13:  2.0767 -  2.0222 0.93   1218  136 0.5440 0.4993      5.8905       5.817|
| 14:  2.0222 -  1.9730 0.35    456   52 0.5318 0.5362      5.8771      5.8293|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0933 -  4.7100  1424   156  0.68  36.20   0.78     0.73      79209.34|
|  2:  4.7100 -  3.7574  1376   156  0.69  36.03   0.85     0.77     113394.08|
|  3:  3.7574 -  3.2881  1343   147  0.58  45.57   0.83     0.71     120124.38|
|  4:  3.2881 -  2.9900  1335   153  0.48  53.47   0.76     0.58     107785.51|
|  5:  2.9900 -  2.7771  1320   145  0.37  62.32   0.72     0.45      88169.22|
|  6:  2.7771 -  2.6143  1329   143  0.31  66.61   0.70     0.36      79460.38|
|  7:  2.6143 -  2.4839  1320   150  0.25  71.15   0.72     0.30      75171.08|
|  8:  2.4839 -  2.3762  1307   146  0.24  71.79   0.71     0.30      67458.49|
|  9:  2.3762 -  2.2851  1296   140  0.24  71.77   0.72     0.29      62360.52|
| 10:  2.2851 -  2.2065  1307   149  0.26  70.41   0.72     0.31      53583.32|
| 11:  2.2065 -  2.1377  1305   144  0.24  71.97   0.75     0.31      52955.19|
| 12:  2.1377 -  2.0767  1294   142  0.24  71.80   0.73     0.31      46700.23|
| 13:  2.0767 -  2.0222  1218   136  0.24  72.19   0.71     0.31      41456.17|
| 14:  2.0222 -  1.9730   456    52  0.28  69.15   0.74     0.32      32874.84|
|alpha:            min =        0.29 max =            0.77 mean =         0.44|
|beta:             min =    32874.84 max =       120124.38 mean =     75399.84|
|figures of merit: min =        0.00 max =            1.00 mean =         0.37|
|phase err.(work): min =        0.00 max =           89.99 mean =        61.46|
|phase err.(test): min =        0.00 max =           89.85 mean =        61.70|
|-----------------------------------------------------------------------------|

============================== 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 = 18.654183             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.184   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.824679              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.242   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       32 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      171 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      687 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1507 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2619 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3909 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5044 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6549 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7705 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.881 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.977 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.925)------------------------------------------|
|    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 = 11.925)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

*********************** REFINEMENT MACRO_CYCLE 1 OF 5 *************************

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5039   r_free= 0.4847   ksol= 0.00   Bsol= 0.00   scale= 0.747    |
|                                                                             |
| 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:   0.81 A                  |
| x-ray target function (ml) for work reflections: 6.299409                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4897   r_free= 0.4702   ksol= 0.33   Bsol= 0.00   scale= 0.990    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.71,8.87,12.11,0.00,0.00,0.00); trace/3= 9.23                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.291612                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.189488             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.157   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.475891              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.585   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4897      final r-factor (work) = 0.4174          |
| start r-factor (free) = 0.4702      final r-factor (free) = 0.4439          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 101.6632 = 15.19 * 0.50 * 6.2915 + 1.00 * 53.8810                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 47.4484 = 15.19 * 0.50 * 6.2277 + 1.00 * 0.1507                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4174      final r-factor (work) = 0.3772          |
| start r-factor (free) = 0.4439      final r-factor (free) = 0.4344          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.2058 = 1.48 * 1.00 * 6.2277 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.1126 = 1.48 * 1.00 * 6.1611 + 1.00 * 0.0195                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.925)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.57   15.46    None  None   None       |
|    all(noH): 2823   0      0.00    85.57   15.46    None  None   None       |
|    Sol.    : 438    0      0.00    85.57   25.47    None  None   None       |
|    Mac.    : 2385   0      0.00    75.80   13.62    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 -   8.557: 1017   |   5:    42.787 -  51.344:   63        |
|      1:     8.557 -  17.115:  812   |   6:    51.344 -  59.902:   33        |
|      2:    17.115 -  25.672:  491   |   7:    59.902 -  68.459:   21        |
|      3:    25.672 -  34.230:  250   |   8:    68.459 -  77.016:    5        |
|      4:    34.230 -  42.787:  130   |   9:    77.016 -  85.574:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3772 r_free = 0.4344             target_work(ml) = 6.149         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3767 r_free = 0.4349             target_work(ml) = 6.149         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3767   r_free= 0.4349   ksol= 0.33   Bsol= 0.00   scale= 1.133    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.71,8.87,12.11,0.00,0.00,0.00); trace/3= 9.23                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.148625                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3730   r_free= 0.4307   ksol= 0.35   Bsol= 50.00   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.98,4.41,7.48,0.00,0.00,0.00); trace/3= 4.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.149908                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.621938              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.024  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.613361              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.092  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3730      final r-factor (work) = 0.3044          |
| start r-factor (free) = 0.4307      final r-factor (free) = 0.3708          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.6171 = 7.62 * 0.50 * 6.1576 + 1.00 * 0.1507                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.1967 = 7.62 * 0.50 * 6.0635 + 1.00 * 0.0890                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3044      final r-factor (work) = 0.2829          |
| start r-factor (free) = 0.3708      final r-factor (free) = 0.3550          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7391 = 0.61 * 1.00 * 6.0635 + 1.00 * 0.0200                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6692 = 0.61 * 1.00 * 5.9607 + 1.00 * 0.0131                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.925)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.79   14.61    None  None   None       |
|    all(noH): 2823   0      0.00    89.79   14.61    None  None   None       |
|    Sol.    : 438    0      0.00    89.79   31.40    None  None   None       |
|    Mac.    : 2385   0      0.00    60.28   11.52    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.979: 1168   |   5:    44.894 -  53.873:   58        |
|      1:     8.979 -  17.958:  864   |   6:    53.873 -  62.852:   31        |
|      2:    17.958 -  26.937:  396   |   7:    62.852 -  71.831:    9        |
|      3:    26.937 -  35.915:  189   |   8:    71.831 -  80.809:    5        |
|      4:    35.915 -  44.894:  102   |   9:    80.809 -  89.788:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2829 r_free = 0.3550             target_work(ml) = 5.944         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2827 r_free = 0.3548             target_work(ml) = 5.944         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2827   r_free= 0.3548   ksol= 0.35   Bsol= 50.00   scale= 1.063   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.98,4.41,7.48,0.00,0.00,0.00); trace/3= 4.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.943778                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2818   r_free= 0.3545   ksol= 0.34   Bsol= 50.00   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.78,2.39,5.13,0.00,0.00,0.00); trace/3= 3.10                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 5.944622                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.682921              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.632  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.505295              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 119.798  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2818      final r-factor (work) = 0.2206          |
| start r-factor (free) = 0.3545      final r-factor (free) = 0.2806          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.0664 = 3.68 * 0.50 * 5.9612 + 1.00 * 0.0890                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.8420 = 3.68 * 0.50 * 5.8514 + 1.00 * 0.0668                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2206      final r-factor (work) = 0.2041          |
| start r-factor (free) = 0.2806      final r-factor (free) = 0.2646          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9698 = 0.51 * 1.00 * 5.8514 + 1.00 * 0.0131                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8977 = 0.51 * 1.00 * 5.6991 + 1.00 * 0.0179                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.925)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    118.10  14.42    None  None   None       |
|    all(noH): 2823   0      0.00    118.10  14.42    None  None   None       |
|    Sol.    : 438    0      0.00    90.11   34.66    None  None   None       |
|    Mac.    : 2385   0      0.00    118.10  10.71    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 -  11.810: 1637   |   5:    59.050 -  70.860:   18        |
|      1:    11.810 -  23.620:  664   |   6:    70.860 -  82.670:    6        |
|      2:    23.620 -  35.430:  266   |   7:    82.670 -  94.481:    1        |
|      3:    35.430 -  47.240:  160   |   8:    94.481 - 106.291:    0        |
|      4:    47.240 -  59.050:   70   |   9:   106.291 - 118.101:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2041 r_free = 0.2646             target_work(ml) = 5.670         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2039 r_free = 0.2644             target_work(ml) = 5.669         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2039   r_free= 0.2644   ksol= 0.34   Bsol= 50.00   scale= 1.040   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.78,2.39,5.13,0.00,0.00,0.00); trace/3= 3.10                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.669125                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2034   r_free= 0.2639   ksol= 0.32   Bsol= 50.00   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.79,1.22,3.63,0.00,0.00,0.00); trace/3= 1.88                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.669951                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.627498              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.419  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.155739              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 109.231  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2034      final r-factor (work) = 0.1657          |
| start r-factor (free) = 0.2639      final r-factor (free) = 0.2221          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5581 = 2.63 * 0.50 * 5.7022 + 1.00 * 0.0668                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3953 = 2.63 * 0.50 * 5.5838 + 1.00 * 0.0597                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1657      final r-factor (work) = 0.1524          |
| start r-factor (free) = 0.2221      final r-factor (free) = 0.2094          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.0743 = 2.16 * 1.00 * 5.5838 + 1.00 * 0.0372                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.7739 = 2.16 * 1.00 * 5.4542 + 1.00 * 0.0162                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.925)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.27   15.26    None  None   None       |
|    all(noH): 2823   0      0.00    98.27   15.26    None  None   None       |
|    Sol.    : 438    0      2.35    98.27   42.08    None  None   None       |
|    Mac.    : 2385   0      0.00    83.29   10.33    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 -   9.827: 1526   |   5:    49.133 -  58.960:   98        |
|      1:     9.827 -  19.653:  687   |   6:    58.960 -  68.787:   58        |
|      2:    19.653 -  29.480:  188   |   7:    68.787 -  78.613:   27        |
|      3:    29.480 -  39.307:  119   |   8:    78.613 -  88.440:   12        |
|      4:    39.307 -  49.133:  106   |   9:    88.440 -  98.267:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1524 r_free = 0.2094             target_work(ml) = 5.424         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1523 r_free = 0.2094             target_work(ml) = 5.424         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1523   r_free= 0.2094   ksol= 0.32   Bsol= 50.00   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.79,1.22,3.63,0.00,0.00,0.00); trace/3= 1.88                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.423882                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1523   r_free= 0.2096   ksol= 0.33   Bsol= 64.39   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.72,0.83,3.22,0.00,0.00,0.00); trace/3= 1.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.422756                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.070166              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.192  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.953423              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.500  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1523      final r-factor (work) = 0.1366          |
| start r-factor (free) = 0.2096      final r-factor (free) = 0.1907          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7053 = 2.07 * 0.50 * 5.4542 + 1.00 * 0.0597                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6257 = 2.07 * 0.50 * 5.3791 + 1.00 * 0.0579                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1366      final r-factor (work) = 0.1328          |
| start r-factor (free) = 0.1907      final r-factor (free) = 0.1866          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.9028 = 2.95 * 1.00 * 5.3791 + 1.00 * 0.0160                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.7194 = 2.95 * 1.00 * 5.3168 + 1.00 * 0.0166                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.925)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.82  15.34    None  None   None       |
|    all(noH): 2823   0      0.00    101.82  15.34    None  None   None       |
|    Sol.    : 438    0      2.90    101.82  43.90    None  None   None       |
|    Mac.    : 2385   0      0.00    99.93   10.09    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.182: 1595   |   5:    50.910 -  61.092:   89        |
|      1:    10.182 -  20.364:  663   |   6:    61.092 -  71.274:   53        |
|      2:    20.364 -  30.546:  166   |   7:    71.274 -  81.456:   35        |
|      3:    30.546 -  40.728:  109   |   8:    81.456 -  91.638:   16        |
|      4:    40.728 -  50.910:   87   |   9:    91.638 - 101.820:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1328 r_free = 0.1866             target_work(ml) = 5.305         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1327 r_free = 0.1866             target_work(ml) = 5.305         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1327   r_free= 0.1866   ksol= 0.33   Bsol= 64.39   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.72,0.83,3.22,0.00,0.00,0.00); trace/3= 1.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.304602                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7100 0.99   1424  156 0.0994 0.1317      5.4168      5.6067|
|  2:  4.7100 -  3.7574 0.99   1376  156 0.0927 0.1274      5.5234      5.7308|
|  3:  3.7574 -  3.2881 0.99   1343  147 0.1241 0.1778      5.6225       5.967|
|  4:  3.2881 -  2.9900 0.99   1335  153 0.1491 0.2031      5.6155      5.8115|
|  5:  2.9900 -  2.7771 0.99   1320  145 0.1610 0.2000      5.4963       5.674|
|  6:  2.7771 -  2.6143 0.99   1329  143 0.1511 0.2566       5.382      5.7117|
|  7:  2.6143 -  2.4839 0.99   1320  150 0.1547 0.1812      5.3454      5.4481|
|  8:  2.4839 -  2.3762 0.98   1307  146 0.1526 0.2061      5.2963       5.513|
|  9:  2.3762 -  2.2851 0.98   1296  140 0.1497 0.2340      5.2297      5.5142|
| 10:  2.2851 -  2.2065 1.00   1307  149 0.1396 0.2007      5.1268      5.3344|
| 11:  2.2065 -  2.1377 0.98   1305  144 0.1368 0.2220      5.0907       5.476|
| 12:  2.1377 -  2.0767 0.98   1294  142 0.1403 0.2100      5.0401      5.3209|
| 13:  2.0767 -  2.0222 0.93   1218  136 0.1246 0.1758      4.9057      5.0665|
| 14:  2.0222 -  1.9730 0.35    456   52 0.1074 0.1704      4.7233      5.0034|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0933 -  4.7100  1424   156  0.93  10.23   0.97     0.94       8424.87|
|  2:  4.7100 -  3.7574  1376   156  0.94   9.47   1.02     1.00      11069.63|
|  3:  3.7574 -  3.2881  1343   147  0.91  14.09   1.04     1.03      14177.37|
|  4:  3.2881 -  2.9900  1335   153  0.89  17.39   1.02     1.00      14606.27|
|  5:  2.9900 -  2.7771  1320   145  0.87  19.57   1.00     0.97      12036.83|
|  6:  2.7771 -  2.6143  1329   143  0.86  20.14   0.98     0.94      10174.77|
|  7:  2.6143 -  2.4839  1320   150  0.86  20.02   0.99     0.95       9283.50|
|  8:  2.4839 -  2.3762  1307   146  0.86  20.74   0.99     0.95       8692.02|
|  9:  2.3762 -  2.2851  1296   140  0.87  19.97   0.99     0.93       7476.46|
| 10:  2.2851 -  2.2065  1307   149  0.87  19.41   1.00     0.95       6250.67|
| 11:  2.2065 -  2.1377  1305   144  0.87  19.67   0.99     0.93       5976.16|
| 12:  2.1377 -  2.0767  1294   142  0.87  19.70   1.00     0.98       5672.33|
| 13:  2.0767 -  2.0222  1218   136  0.87  19.37   0.99     0.96       4472.78|
| 14:  2.0222 -  1.9730   456    52  0.91  15.27   0.98     0.95       2914.76|
|alpha:            min =        0.93 max =            1.03 mean =         0.97|
|beta:             min =     2914.76 max =        14606.27 mean =      8994.27|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.93 mean =        17.52|
|phase err.(test): min =        0.00 max =           89.52 mean =        16.89|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1327   r_free= 0.1866   ksol= 0.33   Bsol= 66.07   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.78,-0.75,1.53,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.304654                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1327   r_free= 0.1866   ksol= 0.33   Bsol= 66.07   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.78,-0.75,1.53,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.304654                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7100 0.99   1424  156 0.0994 0.1317      5.4171      5.6073|
|  2:  4.7100 -  3.7574 0.99   1376  156 0.0927 0.1275      5.5238      5.7312|
|  3:  3.7574 -  3.2881 0.99   1343  147 0.1241 0.1778      5.6229      5.9677|
|  4:  3.2881 -  2.9900 0.99   1335  153 0.1491 0.2032      5.6156      5.8118|
|  5:  2.9900 -  2.7771 0.99   1320  145 0.1610 0.1999      5.4963      5.6741|
|  6:  2.7771 -  2.6143 0.99   1329  143 0.1511 0.2567      5.3822      5.7126|
|  7:  2.6143 -  2.4839 0.99   1320  150 0.1547 0.1815      5.3457      5.4487|
|  8:  2.4839 -  2.3762 0.98   1307  146 0.1526 0.2061      5.2967      5.5129|
|  9:  2.3762 -  2.2851 0.98   1296  140 0.1497 0.2343      5.2297      5.5151|
| 10:  2.2851 -  2.2065 1.00   1307  149 0.1396 0.2002      5.1268      5.3334|
| 11:  2.2065 -  2.1377 0.98   1305  144 0.1368 0.2216      5.0903      5.4751|
| 12:  2.1377 -  2.0767 0.98   1294  142 0.1403 0.2102      5.0398      5.3214|
| 13:  2.0767 -  2.0222 0.93   1218  136 0.1246 0.1755      4.9051      5.0655|
| 14:  2.0222 -  1.9730 0.35    456   52 0.1075 0.1699      4.7229      5.0026|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0933 -  4.7100  1424   156  0.93  10.24   0.97     0.94       8433.55|
|  2:  4.7100 -  3.7574  1376   156  0.94   9.48   1.02     1.00      11080.36|
|  3:  3.7574 -  3.2881  1343   147  0.91  14.11   1.04     1.04      14194.76|
|  4:  3.2881 -  2.9900  1335   153  0.89  17.42   1.03     1.01      14615.68|
|  5:  2.9900 -  2.7771  1320   145  0.87  19.57   1.01     0.98      12049.54|
|  6:  2.7771 -  2.6143  1329   143  0.86  20.15   0.98     0.94      10180.44|
|  7:  2.6143 -  2.4839  1320   150  0.86  20.03   1.00     0.95       9290.19|
|  8:  2.4839 -  2.3762  1307   146  0.86  20.75   1.00     0.96       8702.89|
|  9:  2.3762 -  2.2851  1296   140  0.87  19.98   1.00     0.93       7481.66|
| 10:  2.2851 -  2.2065  1307   149  0.87  19.39   1.01     0.96       6244.20|
| 11:  2.2065 -  2.1377  1305   144  0.87  19.64   0.99     0.93       5965.10|
| 12:  2.1377 -  2.0767  1294   142  0.87  19.68   1.00     0.99       5665.51|
| 13:  2.0767 -  2.0222  1218   136  0.87  19.36   0.99     0.97       4463.43|
| 14:  2.0222 -  1.9730   456    52  0.91  15.25   0.99     0.95       2905.89|
|alpha:            min =        0.93 max =            1.04 mean =         0.97|
|beta:             min =     2905.89 max =        14615.68 mean =      8998.24|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.93 mean =        17.52|
|phase err.(test): min =        0.00 max =           89.52 mean =        16.89|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.925)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.68    103.50  17.02    None  None   None       |
|    all(noH): 2823   0      1.68    103.50  17.02    None  None   None       |
|    Sol.    : 438    0      4.58    103.50  45.58    None  None   None       |
|    Mac.    : 2385   0      1.68    101.61  11.77    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.679 -  11.861: 1595   |   5:    52.589 -  62.771:   89        |
|      1:    11.861 -  22.043:  663   |   6:    62.771 -  72.953:   53        |
|      2:    22.043 -  32.225:  166   |   7:    72.953 -  83.135:   35        |
|      3:    32.225 -  42.407:  109   |   8:    83.135 -  93.317:   16        |
|      4:    42.407 -  52.589:   87   |   9:    93.317 - 103.499:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 327         
Filter by distance & map next to the model:
   mapped sites are within: 0.300 - 5.397
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 320 from: 327
   mapped sites are within: 0.719 - 5.397

peak=    9.321 closest distance to " CB  VAL A 230 " =    1.403
peak=    8.183 closest distance to " CB  VAL A 296 " =    1.565
peak=    6.937 closest distance to " CD2 LEU A   5 " =    1.366
peak=    6.713 closest distance to " CG  ARG A 138 " =    1.301
peak=    6.510 closest distance to " O   HOH Z 130 " =    1.309
peak=    5.981 closest distance to " O   HOH Z 103 " =    1.185
peak=    5.815 closest distance to " NH1 ARG A 138 " =    1.058
peak=    5.754 closest distance to " CD1AILE A 234 " =    1.086
peak=    5.370 closest distance to " O   HOH Z  70 " =    1.130
peak=    5.248 closest distance to " CG  PRO A  54 " =    1.536
peak=    5.152 closest distance to " O   HOH Z 425 " =    1.741
peak=    5.135 closest distance to " CB  VAL A 230 " =    1.245
peak=    5.075 closest distance to " O   HOH Z 246 " =    1.196
peak=    5.043 closest distance to " CB  ASN A 148 " =    1.437
peak=    4.996 closest distance to " CG  LEU A 228 " =    1.212
peak=    4.975 closest distance to " O   HOH Z 427 " =    2.344
peak=    4.939 closest distance to " O   HOH Z 255 " =    1.020
peak=    4.879 closest distance to " NE2 GLN A  11 " =    1.026
peak=    4.834 closest distance to " O   HOH Z 222 " =    1.317
peak=    4.730 closest distance to " O   HOH Z 127 " =    1.289
peak=    4.710 closest distance to " O   HOH Z 287 " =    2.004
peak=    4.662 closest distance to " CB  ASN A 142 " =    1.003
peak=    4.633 closest distance to " CZ3 TRP A 266 " =    1.227
peak=    4.596 closest distance to " O   HOH Z  69 " =    1.260
peak=    4.571 closest distance to " OE1 GLN A  73 " =    2.162
peak=    4.563 closest distance to " O  BHOH Z  74 " =    1.158
peak=    4.560 closest distance to " CD  ARG A 138 " =    1.052
peak=    4.557 closest distance to " O   HOH Z 369 " =    2.146
peak=    4.550 closest distance to " O   HOH Z 232 " =    2.268
peak=    4.530 closest distance to " C   GLN A  73 " =    1.083
peak=    4.510 closest distance to " O   PRO A 198 " =    1.455
peak=    4.508 closest distance to " O   HOH Z 331 " =    0.968
peak=    4.482 closest distance to " CG  PRO A 198 " =    1.268
peak=    4.459 closest distance to " O   HOH Z 427 " =    1.256
peak=    4.457 closest distance to " O   HOH Z  65 " =    1.219
peak=    4.419 closest distance to " CB  PRO A  54 " =    1.158
peak=    4.398 closest distance to " CG  PRO A 243 " =    1.176
peak=    4.390 closest distance to " O   HOH Z 207 " =    1.153
peak=    4.378 closest distance to " O   HOH Z 248 " =    1.152
peak=    4.326 closest distance to " O   HOH Z   7 " =    1.571
peak=    4.311 closest distance to " O   HOH Z 417 " =    1.342
peak=    4.265 closest distance to " CB  GLN A 223 " =    1.560
peak=    4.251 closest distance to " CG BARG A 275 " =    1.323
peak=    4.251 closest distance to " NH2 ARG A  56 " =    2.031
peak=    4.221 closest distance to " CG  LEU A 167 " =    1.261
peak=    4.210 closest distance to " CB  SER A 216 " =    1.017
peak=    4.196 closest distance to " CG2 ILE A 234 " =    0.952
peak=    4.181 closest distance to " CG  LEU A   5 " =    1.318
peak=    4.174 closest distance to " CB  SER A  63 " =    1.258
peak=    4.157 closest distance to " O   SER A  87 " =    2.505
peak=    4.144 closest distance to " CD  LYS A  76 " =    1.799
peak=    4.139 closest distance to " ND2BASN A 224 " =    0.855
peak=    4.138 closest distance to " O   HOH Z 112 " =    1.101
peak=    4.136 closest distance to " NH2AARG A 190 " =    1.916
peak=    4.107 closest distance to " O   HOH Z 258 " =    1.136
peak=    4.101 closest distance to " O   HOH Z 423 " =    1.687
peak=    4.066 closest distance to " CG2 VAL A 257 " =    0.896
peak=    4.059 closest distance to " O   HOH Z   9 " =    2.377
peak=    4.032 closest distance to " CB  GLN A 183 " =    1.197
peak=    4.028 closest distance to " O   HOH Z 126 " =    1.903
peak=    4.027 closest distance to " O   HOH Z 437 " =    1.777
peak=    3.984 closest distance to " O   HOH Z 298 " =    1.691
peak=    3.936 closest distance to " O   HOH Z 362 " =    2.279
peak=    3.916 closest distance to " NH1AARG A 145 " =    1.163
peak=    3.899 closest distance to " CB  ASN A  39 " =    0.969
peak=    3.893 closest distance to " O   HOH Z 422 " =    1.079
peak=    3.889 closest distance to " O   HOH Z 365 " =    3.180
peak=    3.876 closest distance to " CB  PRO A  90 " =    1.124
peak=    3.874 closest distance to " CB  TYR A 169 " =    0.786
peak=    3.871 closest distance to " CA  ALA A  51 " =    1.067
peak=    3.865 closest distance to " O   HOH Z 389 " =    1.619
peak=    3.848 closest distance to " N   ALA A 256 " =    1.096
peak=    3.829 closest distance to " CB  ARG A 275 " =    1.069
peak=    3.823 closest distance to " O   HOH Z 126 " =    1.600
peak=    3.816 closest distance to " O   HOH Z 211 " =    1.230
peak=    3.810 closest distance to " O   HOH Z 303 " =    2.107
peak=    3.807 closest distance to " O   HOH Z 361 " =    1.295
peak=    3.805 closest distance to " CA  ARG A 195 " =    1.229
peak=    3.794 closest distance to " CA  ALA A 160 " =    1.118
peak=    3.793 closest distance to " O   HOH Z  59 " =    1.872
peak=    3.778 closest distance to " O   HOH Z  78 " =    1.775
peak=    3.769 closest distance to " OD1 ASN A  69 " =    0.907
peak=    3.767 closest distance to " ND2 ASN A 249 " =    0.847
peak=    3.754 closest distance to " CE3 TRP A 274 " =    1.242
peak=    3.754 closest distance to " CE  LYS A  76 " =    0.908
peak=    3.744 closest distance to " CD  ARG A 159 " =    0.736
peak=    3.741 closest distance to " CB  ALA A  10 " =    0.963
peak=    3.738 closest distance to " O   HOH Z 236 " =    1.496
peak=    3.736 closest distance to " CG  PRO A 213 " =    1.284
peak=    3.732 closest distance to " O   HOH Z 411 " =    3.362
peak=    3.722 closest distance to " CD2 LEU A 228 " =    1.250
peak=    3.718 closest distance to " O   HOH Z 148 " =    1.501
peak=    3.718 closest distance to " NH2AARG A 145 " =    1.193
peak=    3.716 closest distance to " O   HOH Z 419 " =    1.757
peak=    3.712 closest distance to " O   HOH Z  49 " =    1.191
peak=    3.712 closest distance to " CB  TRP A 179 " =    1.492
peak=    3.710 closest distance to " CG2 ILE A 120 " =    1.130
peak=    3.709 closest distance to " O   HOH Z  66 " =    2.371
peak=    3.707 closest distance to " CG1 ILE A 151 " =    1.147
peak=    3.704 closest distance to " CE3 TRP A 150 " =    1.177
peak=    3.695 closest distance to " N   TYR A  15 " =    1.032
peak=    3.694 closest distance to " CB  SER A   3 " =    1.587
peak=    3.694 closest distance to " CZ  PHE A 218 " =    1.198
peak=    3.690 closest distance to " O   HOH Z 403 " =    1.552
peak=    3.688 closest distance to " O   HOH Z  80 " =    1.600
peak=    3.685 closest distance to " CB  THR A  52 " =    0.971
peak=    3.683 closest distance to " O   HOH Z 130 " =    2.571
peak=    3.672 closest distance to " O   HOH Z 359 " =    1.599
peak=    3.670 closest distance to " O   HOH Z 316 " =    3.080
peak=    3.667 closest distance to " CB  LYS A 117 " =    1.224
peak=    3.667 closest distance to " CG2 THR A 221 " =    1.316
peak=    3.666 closest distance to " CG  GLN A  58 " =    1.209
peak=    3.664 closest distance to " O   HOH Z 143 " =    1.374
peak=    3.661 closest distance to " O   TYR A 116 " =    1.185
peak=    3.653 closest distance to " OG  SER A 135 " =    1.302
peak=    3.648 closest distance to " O   PHE A 192 " =    1.292
peak=    3.647 closest distance to " CB  ASP A 107 " =    1.117
peak=    3.638 closest distance to " O   HOH Z 265 " =    1.956
peak=    3.638 closest distance to " CB  ASN A 110 " =    1.114
peak=    3.636 closest distance to " O   HOH Z 124 " =    1.254
peak=    3.624 closest distance to " O   HOH Z 258 " =    1.825
peak=    3.624 closest distance to " O   HOH Z 368 " =    3.420
peak=    3.621 closest distance to " CD1 LEU A   5 " =    1.433
peak=    3.621 closest distance to " N   PHE A 130 " =    1.362
peak=    3.614 closest distance to " CE  MET A  93 " =    1.451
peak=    3.613 closest distance to " O   HOH Z 422 " =    2.442
peak=    3.611 closest distance to " CD2 TRP A 179 " =    1.334
peak=    3.611 closest distance to " CB  MET A  40 " =    0.889
peak=    3.608 closest distance to " NZ  LYS A 117 " =    2.875
peak=    3.603 closest distance to " CB  VAL A 202 " =    1.572
peak=    3.602 closest distance to " O   HOH Z  39 " =    1.103
peak=    3.580 closest distance to " CB  ARG A 138 " =    1.151
peak=    3.578 closest distance to " CB  LEU A 237 " =    0.870
peak=    3.572 closest distance to " O   HOH Z 180 " =    2.215
peak=    3.567 closest distance to " O   HOH Z 380 " =    1.733
peak=    3.559 closest distance to " ND1 HIS A  86 " =    1.813
peak=    3.559 closest distance to " O   HOH Z   3 " =    2.237
peak=    3.542 closest distance to " O   HOH Z 272 " =    1.782
peak=    3.533 closest distance to " O   HOH Z 218 " =    1.667
peak=    3.526 closest distance to " O   HOH Z 251 " =    1.551
peak=    3.524 closest distance to " CB  ASP A 124 " =    0.805
peak=    3.523 closest distance to " O  BHOH Z 338 " =    2.388
peak=    3.517 closest distance to " O   HOH Z 423 " =    2.272
peak=    3.515 closest distance to " CA  ILE A 234 " =    1.066
peak=    3.515 closest distance to " O   HOH Z 153 " =    3.732
peak=    3.512 closest distance to " O   HOH Z 406 " =    1.411
peak=    3.510 closest distance to " O   HOH Z 193 " =    1.636
peak=    3.510 closest distance to " CA  PHE A 283 " =    1.182
peak=    3.508 closest distance to " CA  ASP A 124 " =    0.763
peak=    3.502 closest distance to " O   HOH Z 278 " =    0.935
peak=    3.501 closest distance to " CB  GLN A  89 " =    1.111
peak=    3.500 closest distance to " O   HOH Z 290 " =    1.590
peak=    3.499 closest distance to " O   HOH Z  88 " =    3.615
peak=    3.498 closest distance to " O   HOH Z 145 " =    1.711
peak=    3.496 closest distance to " CD1 ILE A  33 " =    1.899
peak=    3.491 closest distance to " CB  VAL A 265 " =    1.329
peak=    3.486 closest distance to " O   HOH Z 119 " =    1.571
peak=    3.471 closest distance to " OE2 GLU A   2 " =    2.141
peak=    3.467 closest distance to " O   HOH Z 346 " =    1.588
peak=    3.466 closest distance to " CB  GLU A 277 " =    3.571
peak=    3.458 closest distance to " CZ3 TRP A 177 " =    1.140
peak=    3.457 closest distance to " O   HOH Z   1 " =    1.793
peak=    3.456 closest distance to " O   HOH Z  20 " =    1.595
peak=    3.454 closest distance to " CA  ARG A 156 " =    1.088
peak=    3.452 closest distance to " O   HOH Z 303 " =    2.426
peak=    3.446 closest distance to " O   HOH Z 193 " =    1.770
peak=    3.441 closest distance to " O   HOH Z 116 " =    1.015
peak=    3.436 closest distance to " NZ  LYS A 119 " =    2.739
peak=    3.435 closest distance to " N   ASP A 162 " =    1.083
peak=    3.434 closest distance to " O   HOH Z 392 " =    1.043
peak=    3.432 closest distance to " OG1 THR A 279 " =    1.478
peak=    3.428 closest distance to " CA  TYR A  30 " =    1.017
peak=    3.427 closest distance to " CB  SER A 210 " =    0.876
peak=    3.424 closest distance to " CB  ALA A 114 " =    0.824
peak=    3.415 closest distance to " CA  ARG A  36 " =    0.970
peak=    3.414 closest distance to " CZ3 TRP A  92 " =    1.160
peak=    3.408 closest distance to " O   HOH Z  26 " =    1.340
peak=    3.407 closest distance to " O   HOH Z 147 " =    1.306
peak=    3.404 closest distance to " O   HOH Z 193 " =    1.540
peak=    3.404 closest distance to " CZ  PHE A  38 " =    1.197
peak=    3.403 closest distance to " O   HOH Z 281 " =    2.246
peak=    3.402 closest distance to " O   ASP A 124 " =    0.949
peak=    3.402 closest distance to " OG  SER A 276 " =    1.036
peak=    3.401 closest distance to " CB  ASN A 215 " =    1.277
peak=    3.400 closest distance to " CB  SER A  62 " =    0.949
peak=    3.398 closest distance to " OG ASER A 212 " =    1.518
peak=    3.398 closest distance to " N   GLN A 278 " =    1.302
peak=    3.397 closest distance to " ND2 ASN A 176 " =    0.920
peak=    3.397 closest distance to " O   HOH Z  53 " =    2.358
peak=    3.396 closest distance to " O   HOH Z  63 " =    1.227
peak=    3.392 closest distance to " CB  ARG A 102 " =    0.883
peak=    3.387 closest distance to " O   HOH Z 162 " =    1.202
peak=    3.386 closest distance to " O   HOH Z  40 " =    1.620
peak=    3.374 closest distance to " O   HOH Z   4 " =    1.523
peak=    3.371 closest distance to " O   ASP A 200 " =    1.663
peak=    3.362 closest distance to " O   HOH Z 342 " =    0.955
peak=    3.359 closest distance to " O   HOH Z 329 " =    4.248
peak=    3.356 closest distance to " CB  ARG A  79 " =    0.853
peak=    3.352 closest distance to " CG2 ILE A  20 " =    1.626
peak=    3.351 closest distance to " C   VAL A  72 " =    0.887
peak=    3.345 closest distance to " CG1 VAL A 257 " =    1.394
peak=    3.345 closest distance to " O   HOH Z 357 " =    2.303
peak=    3.343 closest distance to " O   HOH Z 214 " =    2.593
peak=    3.340 closest distance to " CB  THR A  31 " =    1.489
peak=    3.340 closest distance to " CB  GLU A 236 " =    1.256
peak=    3.340 closest distance to " O   HOH Z 293 " =    1.548
peak=    3.339 closest distance to " CA  ASN A 127 " =    1.197
peak=    3.336 closest distance to " CB  HIS A 108 " =    0.832
peak=    3.336 closest distance to " CA  ASP A 162 " =    0.917
peak=    3.336 closest distance to " O   HOH Z 371 " =    2.921
peak=    3.336 closest distance to " N   TRP A  70 " =    0.841
peak=    3.335 closest distance to " CG1BVAL A  72 " =    0.726
peak=    3.334 closest distance to " CD1 LEU A 300 " =    0.990
peak=    3.330 closest distance to " C   ASN A 209 " =    1.576
peak=    3.330 closest distance to " O   HOH Z  21 " =    1.506
peak=    3.329 closest distance to " OE2 GLU A  53 " =    1.932
peak=    3.327 closest distance to " CG  LEU A 281 " =    0.983
peak=    3.326 closest distance to " N   ASN A  74 " =    1.367
peak=    3.324 closest distance to " O   HOH Z 158 " =    2.833
peak=    3.321 closest distance to " CA  TYR A 116 " =    1.504
peak=    3.318 closest distance to " CB  PHE A 204 " =    0.877
peak=    3.317 closest distance to " O   HOH Z 148 " =    2.394
peak=    3.315 closest distance to " CA  ALA A 129 " =    1.260
peak=    3.312 closest distance to " CD  ARG A  66 " =    2.278
peak=    3.311 closest distance to " O   HOH Z 189 " =    3.341
peak=    3.311 closest distance to " CA  MET A 105 " =    0.987
peak=    3.306 closest distance to " CB  GLU A 175 " =    1.399
peak=    3.306 closest distance to " OG  SER A  62 " =    2.492
peak=    3.303 closest distance to " O   HOH Z 368 " =    1.982
peak=    3.303 closest distance to " CD  ARG A 269 " =    0.962
peak=    3.301 closest distance to " CD1 LEU A 167 " =    1.210
peak=    3.300 closest distance to " O   HOH Z 438 " =    2.352
peak=    3.298 closest distance to " O   PRO A 213 " =    1.226
peak=    3.298 closest distance to " O   HOH Z 270 " =    1.330
peak=    3.298 closest distance to " CD  GLN A  77 " =    1.195
peak=    3.295 closest distance to " O   HOH Z 392 " =    1.000
peak=    3.294 closest distance to " N   ASN A 127 " =    1.322
peak=    3.292 closest distance to " OE1 GLN A 240 " =    1.625
peak=    3.291 closest distance to " CA  ALA A 154 " =    1.087
peak=    3.286 closest distance to " O   HOH Z 261 " =    1.729
peak=    3.286 closest distance to " CB  LEU A 300 " =    1.002
peak=    3.283 closest distance to " O   HOH Z 146 " =    1.546
peak=    3.273 closest distance to " O   HOH Z 220 " =    1.518
peak=    3.272 closest distance to " OD1 ASN A 301 " =    1.522
peak=    3.272 closest distance to " O   HOH Z  42 " =    1.384
peak=    3.269 closest distance to " O   HOH Z  61 " =    1.690
peak=    3.269 closest distance to " O   HOH Z 139 " =    1.114
peak=    3.264 closest distance to " CB  ARG A 156 " =    1.074
peak=    3.262 closest distance to " CB  TYR A  30 " =    1.385
peak=    3.256 closest distance to " C   ALA A 299 " =    0.905
peak=    3.255 closest distance to " CB  ALA A  43 " =    0.843
peak=    3.249 closest distance to " O   HOH Z 216 " =    3.583
peak=    3.246 closest distance to " O   HOH Z 330 " =    1.001
peak=    3.242 closest distance to " CG  PRO A  90 " =    1.831
peak=    3.239 closest distance to " NH1AARG A 102 " =    0.948
peak=    3.235 closest distance to " CB  SER A 276 " =    1.092
peak=    3.231 closest distance to " CB  SER A  26 " =    1.576
peak=    3.231 closest distance to " O   HOH Z 261 " =    1.789
peak=    3.227 closest distance to " CG BARG A 102 " =    1.999
peak=    3.227 closest distance to " CA  ARG A 159 " =    1.230
peak=    3.227 closest distance to " O   THR A 157 " =    1.307
peak=    3.226 closest distance to " O   HOH Z  40 " =    1.887
peak=    3.226 closest distance to " CA  VAL A 125 " =    1.109
peak=    3.225 closest distance to " O   HOH Z 425 " =    1.971
peak=    3.220 closest distance to " OG  SER A 146 " =    0.881
peak=    3.219 closest distance to " O   HOH Z  71 " =    1.452
peak=    3.219 closest distance to " ND2 ASN A 187 " =    1.927
peak=    3.218 closest distance to " O   HOH Z 222 " =    2.031
peak=    3.216 closest distance to " CA  GLY A 267 " =    1.298
peak=    3.216 closest distance to " CE2 PHE A  16 " =    0.860
peak=    3.215 closest distance to " N   THR A 221 " =    0.727
peak=    3.208 closest distance to " O   HOH Z 172 " =    5.397
peak=    3.207 closest distance to " CD  LYS A 119 " =    1.763
peak=    3.207 closest distance to " CB  LEU A 228 " =    1.377
peak=    3.207 closest distance to " O   HOH Z 110 " =    1.633
peak=    3.204 closest distance to " CA  TRP A 150 " =    1.033
peak=    3.202 closest distance to " O   HOH Z 368 " =    4.197
peak=    3.201 closest distance to " CA  GLY A  80 " =    0.738
peak=    3.201 closest distance to " CB  TRP A 266 " =    1.069
peak=    3.201 closest distance to " NE2 HIS A 207 " =    1.033
peak=    3.200 closest distance to " CA  THR A 221 " =    0.908
peak=    3.197 closest distance to " NE2 GLN A  58 " =    4.577
peak=    3.196 closest distance to " O   MET A 105 " =    1.770
peak=    3.195 closest distance to " CA  GLY A 136 " =    1.086
peak=    3.194 closest distance to " O   THR A 182 " =    1.540
peak=    3.192 closest distance to " N   VAL A 296 " =    1.808
peak=    3.183 closest distance to " CB  LEU A 143 " =    1.122
peak=    3.173 closest distance to " O   HOH Z 188 " =    2.942
peak=    3.168 closest distance to " O   HOH Z 328 " =    1.628
peak=    3.163 closest distance to " CG  GLN A  89 " =    1.576
peak=    3.162 closest distance to " O   HOH Z 280 " =    3.009
peak=    3.157 closest distance to " O   THR A 294 " =    1.084
peak=    3.155 closest distance to " O   HOH Z 424 " =    2.720
peak=    3.152 closest distance to " CA  LEU A 282 " =    1.277
peak=    3.149 closest distance to " CD  GLU A 236 " =    0.871
peak=    3.147 closest distance to " OG1 THR A 221 " =    1.125
peak=    3.145 closest distance to " CG  ARG A 159 " =    0.941
peak=    3.144 closest distance to " CB  ASN A 173 " =    0.995
peak=    3.138 closest distance to " O   HOH Z 123 " =    1.003
peak=    3.136 closest distance to " O   HOH Z 323 " =    1.607
peak=    3.134 closest distance to " CG ALYS A 290 " =    0.993
peak=    3.134 closest distance to " CD  ARG A 195 " =    3.526
peak=    3.128 closest distance to " O   HOH Z  28 " =    1.264
peak=    3.128 closest distance to " N   PHE A  59 " =    0.719
peak=    3.125 closest distance to " OD1 ASN A  45 " =    1.526
peak=    3.124 closest distance to " NH2 ARG A 269 " =    0.961
peak=    3.121 closest distance to " OE2 GLU A  53 " =    1.262
peak=    3.120 closest distance to " ND2 ASN A  60 " =    2.993
peak=    3.116 closest distance to " CG2 THR A  42 " =    1.302
peak=    3.116 closest distance to " CA  ALA A 184 " =    1.282
peak=    3.109 closest distance to " CA  CYS A 201 " =    1.196
peak=    3.105 closest distance to " CA  CYS A 260 " =    1.390
peak=    3.096 closest distance to " O   HOH Z 122 " =    2.087
peak=    3.076 closest distance to " O   HOH Z 238 " =    1.539
peak=    3.073 closest distance to " O   HOH Z 343 " =    2.816
peak=    3.070 closest distance to " O   HOH Z 172 " =    2.880
peak=    3.066 closest distance to " O   HOH Z 213 " =    1.908
peak=    3.033 closest distance to " CA  SER A  87 " =    1.000
peak=    3.030 closest distance to " OG BSER A 164 " =    2.290
peak=    3.003 closest distance to " N   ARG A 156 " =    1.558

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 211         
Filter by distance & map next to the model:
   mapped sites are within: 0.595 - 5.234
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 208 from: 211
   mapped sites are within: 0.758 - 5.234

peak=   -5.494 closest distance to " CD  ARG A 138 " =    1.220
peak=   -4.762 closest distance to " CB  VAL A 230 " =    1.022
peak=   -4.708 closest distance to " CB  GLN A  55 " =    1.147
peak=   -4.615 closest distance to " O   PRO A 198 " =    1.235
peak=   -4.417 closest distance to " CZ2 TRP A  92 " =    2.810
peak=   -4.282 closest distance to " O   HOH Z 147 " =    1.896
peak=   -4.211 closest distance to " O   HOH Z 276 " =    1.128
peak=   -4.209 closest distance to " CA  ASP A  27 " =    2.461
peak=   -4.196 closest distance to " O   HOH Z  69 " =    1.708
peak=   -4.094 closest distance to " CD  ARG A  14 " =    3.087
peak=   -4.057 closest distance to " C   HIS A 108 " =    1.372
peak=   -4.007 closest distance to " OG BSER A 134 " =    1.452
peak=   -3.995 closest distance to " CG  ARG A 219 " =    2.386
peak=   -3.961 closest distance to " O   HOH Z  44 " =    0.871
peak=   -3.918 closest distance to " CG2 VAL A 202 " =    2.706
peak=   -3.908 closest distance to " O   HOH Z 231 " =    0.758
peak=   -3.905 closest distance to " CD  ARG A 156 " =    1.971
peak=   -3.890 closest distance to " CG  LEU A 281 " =    1.941
peak=   -3.867 closest distance to " O   HOH Z  39 " =    0.883
peak=   -3.859 closest distance to " O   HOH Z  70 " =    0.895
peak=   -3.856 closest distance to " CD  PRO A 213 " =    2.203
peak=   -3.840 closest distance to " O   HOH Z  60 " =    1.562
peak=   -3.828 closest distance to " O   HOH Z 359 " =    3.171
peak=   -3.794 closest distance to " O   HOH Z 411 " =    5.234
peak=   -3.781 closest distance to " O   HOH Z 193 " =    0.777
peak=   -3.778 closest distance to " O   HOH Z 131 " =    4.004
peak=   -3.755 closest distance to " O   HOH Z 275 " =    1.805
peak=   -3.748 closest distance to " O   HOH Z 105 " =    1.973
peak=   -3.746 closest distance to " CG2 ILE A  20 " =    2.626
peak=   -3.731 closest distance to " NZ  LYS A 166 " =    1.248
peak=   -3.725 closest distance to " CG2 VAL A 230 " =    0.834
peak=   -3.721 closest distance to " O   HOH Z 368 " =    1.477
peak=   -3.720 closest distance to " CB  ALA A  43 " =    2.649
peak=   -3.699 closest distance to " C   ARG A 269 " =    1.360
peak=   -3.690 closest distance to " CD1 ILE A 151 " =    2.081
peak=   -3.682 closest distance to " CA  HIS A 207 " =    1.101
peak=   -3.658 closest distance to " O   HOH Z 389 " =    1.354
peak=   -3.657 closest distance to " NE2 GLN A 223 " =    1.760
peak=   -3.653 closest distance to " O   HOH Z 177 " =    2.573
peak=   -3.642 closest distance to " OE1 GLU A 277 " =    2.178
peak=   -3.640 closest distance to " CE2 TYR A  30 " =    2.664
peak=   -3.622 closest distance to " O   HOH Z 216 " =    1.625
peak=   -3.621 closest distance to " CB  ALA A   7 " =    2.072
peak=   -3.621 closest distance to " CG1 VAL A 112 " =    2.632
peak=   -3.618 closest distance to " O   HOH Z 100 " =    0.950
peak=   -3.616 closest distance to " CA  ASN A 127 " =    1.104
peak=   -3.616 closest distance to " CB  PRO A 243 " =    2.735
peak=   -3.615 closest distance to " CG  ARG A 259 " =    2.456
peak=   -3.605 closest distance to " CD1 LEU A 255 " =    2.868
peak=   -3.603 closest distance to " CB  ASP A 132 " =    2.558
peak=   -3.585 closest distance to " CG1 VAL A 125 " =    2.464
peak=   -3.582 closest distance to " O   GLU A 152 " =    1.610
peak=   -3.581 closest distance to " O   HOH Z 111 " =    1.933
peak=   -3.578 closest distance to " O   ILE A  49 " =    1.728
peak=   -3.571 closest distance to " C   ILE A 239 " =    2.124
peak=   -3.571 closest distance to " O   SER A 276 " =    1.671
peak=   -3.566 closest distance to " CZ  PHE A 130 " =    1.040
peak=   -3.565 closest distance to " O   HOH Z 144 " =    1.000
peak=   -3.562 closest distance to " OG  SER A  97 " =    2.161
peak=   -3.562 closest distance to " O   HOH Z 286 " =    1.529
peak=   -3.538 closest distance to " O   LEU A 300 " =    2.325
peak=   -3.537 closest distance to " O   PRO A 163 " =    1.858
peak=   -3.535 closest distance to " O   VAL A  67 " =    2.567
peak=   -3.529 closest distance to " NE2 GLN A  55 " =    1.174
peak=   -3.527 closest distance to " O   HOH Z  66 " =    1.048
peak=   -3.524 closest distance to " OG  SER A  28 " =    2.145
peak=   -3.521 closest distance to " N   ALA A 244 " =    1.231
peak=   -3.516 closest distance to " NH2 ARG A 219 " =    1.767
peak=   -3.512 closest distance to " O   HOH Z  64 " =    1.278
peak=   -3.509 closest distance to " ND2 ASN A  69 " =    1.791
peak=   -3.500 closest distance to " O   ALA A  84 " =    1.722
peak=   -3.498 closest distance to " O   ALA A  51 " =    1.362
peak=   -3.495 closest distance to " CD2 TYR A 293 " =    1.925
peak=   -3.491 closest distance to " O   HOH Z 292 " =    1.664
peak=   -3.488 closest distance to " O   HOH Z 201 " =    1.962
peak=   -3.488 closest distance to " CD2 HIS A 207 " =    2.212
peak=   -3.488 closest distance to " CB  TRP A  85 " =    2.361
peak=   -3.486 closest distance to " CG2 VAL A 189 " =    1.924
peak=   -3.484 closest distance to " OE1 GLN A  88 " =    1.118
peak=   -3.481 closest distance to " N   THR A 157 " =    1.415
peak=   -3.478 closest distance to " CB  HIS A  81 " =    1.015
peak=   -3.476 closest distance to " O   HOH Z 105 " =    1.106
peak=   -3.474 closest distance to " CG  MET A 105 " =    1.013
peak=   -3.469 closest distance to " O   LYS A  76 " =    1.590
peak=   -3.466 closest distance to " CA  ASN A 110 " =    0.955
peak=   -3.460 closest distance to " N   ALA A  43 " =    2.575
peak=   -3.459 closest distance to " CB  ALA A 248 " =    2.087
peak=   -3.457 closest distance to " O   HOH Z 257 " =    1.001
peak=   -3.454 closest distance to " ND2 ASN A 285 " =    2.186
peak=   -3.450 closest distance to " CA  GLY A 241 " =    2.302
peak=   -3.443 closest distance to " O   HOH Z 394 " =    1.668
peak=   -3.442 closest distance to " O   HOH Z  65 " =    1.484
peak=   -3.436 closest distance to " O   HOH Z 427 " =    1.939
peak=   -3.433 closest distance to " O   HOH Z 179 " =    2.081
peak=   -3.431 closest distance to " CD1 TYR A 247 " =    2.800
peak=   -3.431 closest distance to " CG2 THR A 178 " =    2.292
peak=   -3.425 closest distance to " CD2 TYR A 116 " =    2.275
peak=   -3.419 closest distance to " O   HOH Z 255 " =    1.127
peak=   -3.415 closest distance to " CZ  ARG A 259 " =    0.865
peak=   -3.413 closest distance to " CA  GLN A  58 " =    1.057
peak=   -3.408 closest distance to " CG1 VAL A 265 " =    2.503
peak=   -3.402 closest distance to " O   HOH Z   9 " =    2.214
peak=   -3.401 closest distance to " OH  TYR A 247 " =    1.648
peak=   -3.397 closest distance to " OG  SER A  87 " =    1.597
peak=   -3.396 closest distance to " CG1 VAL A 250 " =    2.669
peak=   -3.386 closest distance to " O   HOH Z 398 " =    1.280
peak=   -3.383 closest distance to " CA  GLY A 241 " =    3.163
peak=   -3.376 closest distance to " O   HOH Z 107 " =    0.847
peak=   -3.376 closest distance to " CE2 TRP A  70 " =    2.480
peak=   -3.375 closest distance to " C   GLU A   2 " =    1.881
peak=   -3.367 closest distance to " O   SER A 135 " =    1.540
peak=   -3.366 closest distance to " O   SER A  22 " =    2.532
peak=   -3.363 closest distance to " O   HOH Z 149 " =    2.017
peak=   -3.358 closest distance to " O   HOH Z 352 " =    1.527
peak=   -3.358 closest distance to " O   HOH Z 134 " =    4.502
peak=   -3.355 closest distance to " CE1 PHE A 218 " =    1.386
peak=   -3.348 closest distance to " CG1 VAL A 125 " =    2.009
peak=   -3.345 closest distance to " CD2 LEU A   5 " =    1.024
peak=   -3.345 closest distance to " C   GLN A 205 " =    1.895
peak=   -3.344 closest distance to " CB  TYR A  68 " =    1.279
peak=   -3.338 closest distance to " CD  GLU A  44 " =    1.104
peak=   -3.338 closest distance to " CG  GLN A  58 " =    1.268
peak=   -3.337 closest distance to " O   HOH Z 231 " =    2.097
peak=   -3.332 closest distance to " CZ  TYR A 169 " =    1.929
peak=   -3.315 closest distance to " O   HOH Z 198 " =    1.516
peak=   -3.310 closest distance to " N   GLN A  58 " =    1.420
peak=   -3.309 closest distance to " O   HOH Z 214 " =    1.696
peak=   -3.308 closest distance to " O   HOH Z 368 " =    1.631
peak=   -3.307 closest distance to " ND2 ASN A 173 " =    1.744
peak=   -3.303 closest distance to " O   HOH Z  32 " =    1.847
peak=   -3.300 closest distance to " O   HOH Z  68 " =    1.505
peak=   -3.299 closest distance to " CE  MET A 188 " =    2.245
peak=   -3.296 closest distance to " CG  GLN A  88 " =    0.808
peak=   -3.294 closest distance to " O   HOH Z 100 " =    1.566
peak=   -3.292 closest distance to " CD1 LEU A 101 " =    2.165
peak=   -3.292 closest distance to " O   HOH Z 281 " =    2.631
peak=   -3.289 closest distance to " OE2 GLU A 152 " =    1.228
peak=   -3.288 closest distance to " ND2 ASN A  39 " =    1.731
peak=   -3.288 closest distance to " O   HOH Z 163 " =    1.899
peak=   -3.286 closest distance to " O   HOH Z 434 " =    1.656
peak=   -3.280 closest distance to " O   HOH Z 238 " =    0.862
peak=   -3.280 closest distance to " O   HOH Z 389 " =    2.525
peak=   -3.269 closest distance to " OD2 ASP A 171 " =    1.702
peak=   -3.268 closest distance to " O   HOH Z 108 " =    1.396
peak=   -3.268 closest distance to " O   HOH Z  11 " =    1.584
peak=   -3.265 closest distance to " C   ASN A 285 " =    2.200
peak=   -3.262 closest distance to " O   HOH Z 236 " =    1.322
peak=   -3.260 closest distance to " SG BCYS A 201 " =    0.848
peak=   -3.258 closest distance to " O   HOH Z 155 " =    1.178
peak=   -3.256 closest distance to " O   PRO A 243 " =    1.859
peak=   -3.256 closest distance to " CD  LYS A 166 " =    2.435
peak=   -3.253 closest distance to " NE2 GLN A  11 " =    1.690
peak=   -3.246 closest distance to " CD1 LEU A   5 " =    2.390
peak=   -3.236 closest distance to " O   GLN A 144 " =    1.437
peak=   -3.235 closest distance to " CG2AVAL A  41 " =    2.804
peak=   -3.233 closest distance to " CE3 TRP A 150 " =    2.391
peak=   -3.231 closest distance to " O   HOH Z 128 " =    2.460
peak=   -3.231 closest distance to " CD1 LEU A 228 " =    2.224
peak=   -3.219 closest distance to " O   HOH Z 285 " =    2.016
peak=   -3.217 closest distance to " O   HOH Z 165 " =    2.271
peak=   -3.217 closest distance to " CG  ARG A 138 " =    1.198
peak=   -3.215 closest distance to " NH2AARG A 275 " =    5.126
peak=   -3.210 closest distance to " CG2 ILE A 151 " =    2.564
peak=   -3.210 closest distance to " O   HOH Z 219 " =    4.787
peak=   -3.204 closest distance to " CB  HIS A  86 " =    1.098
peak=   -3.203 closest distance to " SG BCYS A 201 " =    2.278
peak=   -3.196 closest distance to " C   VAL A  72 " =    0.867
peak=   -3.196 closest distance to " CG1 VAL A 257 " =    2.205
peak=   -3.196 closest distance to " N   ASP A 191 " =    1.444
peak=   -3.195 closest distance to " CG  GLU A 277 " =    1.237
peak=   -3.191 closest distance to " CD  LYS A 289 " =    2.322
peak=   -3.187 closest distance to " NH2BARG A 102 " =    0.954
peak=   -3.177 closest distance to " O   HOH Z  53 " =    1.636
peak=   -3.173 closest distance to " CE1 TYR A 186 " =    2.315
peak=   -3.172 closest distance to " CG2 THR A  52 " =    3.105
peak=   -3.167 closest distance to " OE1 GLN A 183 " =    1.647
peak=   -3.164 closest distance to " CB  PRO A 163 " =    2.324
peak=   -3.164 closest distance to " CD2 LEU A 237 " =    2.213
peak=   -3.161 closest distance to " CB  ALA A 291 " =    2.087
peak=   -3.159 closest distance to " O   HOH Z 262 " =    2.412
peak=   -3.159 closest distance to " CG  PRO A 163 " =    2.815
peak=   -3.158 closest distance to " O   PHE A 218 " =    1.546
peak=   -3.158 closest distance to " OH  TYR A 169 " =    0.953
peak=   -3.157 closest distance to " CG  TRP A 266 " =    1.661
peak=   -3.156 closest distance to " CB  ALA A 129 " =    2.629
peak=   -3.153 closest distance to " O   HOH Z 357 " =    1.671
peak=   -3.150 closest distance to " O  BHOH Z  74 " =    0.951
peak=   -3.148 closest distance to " CE2 PHE A 218 " =    2.560
peak=   -3.144 closest distance to " ND2 ASN A  45 " =    2.471
peak=   -3.141 closest distance to " CG2BVAL A  72 " =    1.980
peak=   -3.141 closest distance to " O   GLY A  80 " =    2.575
peak=   -3.139 closest distance to " OE1 GLU A  37 " =    1.446
peak=   -3.137 closest distance to " CD1 TYR A 214 " =    1.588
peak=   -3.135 closest distance to " OG ASER A 134 " =    1.305
peak=   -3.134 closest distance to " CE1 TYR A 247 " =    2.622
peak=   -3.117 closest distance to " O   HOH Z  24 " =    1.048
peak=   -3.111 closest distance to " N   ILE A 120 " =    1.067
peak=   -3.110 closest distance to " CG2 VAL A 296 " =    2.121
peak=   -3.109 closest distance to " CE BMET A  47 " =    1.279
peak=   -3.108 closest distance to " CZ  PHE A  38 " =    2.381
peak=   -3.103 closest distance to " O   ALA A  10 " =    1.532
peak=   -3.096 closest distance to " OD1 ASP A 107 " =    1.155
peak=   -3.092 closest distance to " O   THR A  52 " =    1.217
peak=   -3.089 closest distance to " O   HOH Z 407 " =    2.612
peak=   -3.082 closest distance to " O   HOH Z 295 " =    1.675
peak=   -3.080 closest distance to " CG1 VAL A 112 " =    2.557
peak=   -3.073 closest distance to " C   MET A 188 " =    1.471
peak=   -3.058 closest distance to " CB  ALA A 161 " =    1.619

================= 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    :  0.4985 0.4833   6.298018e+00   6.281348e+00
   1_bss:  0.4897 0.4702   6.291612e+00   6.273989e+00
   1_xyz:  0.4174 0.4439   6.208422e+00   6.230075e+00
   1_adp:  0.3772 0.4344   6.149063e+00   6.220516e+00
   1_occ:  0.3767 0.4349   6.148625e+00   6.221268e+00
   2_bss:  0.3730 0.4307   6.149908e+00   6.220832e+00
   2_xyz:  0.3044 0.3708   5.986671e+00   6.113368e+00
   2_adp:  0.2829 0.3550   5.943616e+00   6.082463e+00
   2_occ:  0.2827 0.3548   5.943778e+00   6.082736e+00
   3_bss:  0.2818 0.3545   5.944622e+00   6.083666e+00
   3_xyz:  0.2206 0.2806   5.733668e+00   5.918071e+00
   3_adp:  0.2041 0.2646   5.669938e+00   5.866579e+00
   3_occ:  0.2039 0.2644   5.669125e+00   5.865626e+00
   4_bss:  0.2034 0.2639   5.669951e+00   5.866341e+00
   4_xyz:  0.1657 0.2221   5.491367e+00   5.707570e+00
   4_adp:  0.1524 0.2094   5.424206e+00   5.650505e+00
   4_occ:  0.1523 0.2094   5.423882e+00   5.650188e+00
   5_bss:  0.1523 0.2096   5.422756e+00   5.649370e+00
   5_xyz:  0.1366 0.1907   5.328858e+00   5.564663e+00
   5_adp:  0.1328 0.1866   5.304678e+00   5.541784e+00
   5_occ:  0.1327 0.1866   5.304602e+00   5.541982e+00
   5_bss:  0.1327 0.1866   5.304654e+00   5.542096e+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:  0.329   0.000   6.706   8.874  12.107   0.000   0.000   0.000
   1_xyz:  0.329   0.000   6.706   8.874  12.107   0.000   0.000   0.000
   1_adp:  0.329   0.000   6.706   8.874  12.107   0.000   0.000   0.000
   1_occ:  0.329   0.000   6.706   8.874  12.107   0.000   0.000   0.000
   2_bss:  0.352  50.000   2.982   4.411   7.478   0.000   0.000   0.000
   2_xyz:  0.352  50.000   2.982   4.411   7.478   0.000   0.000   0.000
   2_adp:  0.352  50.000   2.982   4.411   7.478   0.000   0.000   0.000
   2_occ:  0.352  50.000   2.982   4.411   7.478   0.000   0.000   0.000
   3_bss:  0.341  50.000   1.784   2.392   5.130   0.000   0.000   0.000
   3_xyz:  0.341  50.000   1.784   2.392   5.130   0.000   0.000   0.000
   3_adp:  0.341  50.000   1.784   2.392   5.130   0.000   0.000   0.000
   3_occ:  0.341  50.000   1.784   2.392   5.130   0.000   0.000   0.000
   4_bss:  0.323  50.000   0.786   1.224   3.626   0.000   0.000   0.000
   4_xyz:  0.323  50.000   0.786   1.224   3.626   0.000   0.000   0.000
   4_adp:  0.323  50.000   0.786   1.224   3.626   0.000   0.000   0.000
   4_occ:  0.323  50.000   0.786   1.224   3.626   0.000   0.000   0.000
   5_bss:  0.329  64.387   0.721   0.831   3.218   0.000   0.000   0.000
   5_xyz:  0.329  64.387   0.721   0.831   3.218   0.000   0.000   0.000
   5_adp:  0.329  64.387   0.721   0.831   3.218   0.000   0.000   0.000
   5_occ:  0.329  64.387   0.721   0.831   3.218   0.000   0.000   0.000
   5_bss:  0.329  66.067  -0.783  -0.745   1.528   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  61.487 0.3737  0.4436    75403.830
   1_bss:  60.526 0.3856  0.5942    73443.029
   1_xyz:  52.287 0.4904  0.7399    58407.608
   1_adp:  49.664 0.5238  0.8696    55788.855
   1_occ:  49.811 0.5220  0.8654    56022.985
   2_bss:  49.388 0.5273  0.7594    55488.251
   2_xyz:  40.248 0.6383  0.8956    37547.165
   2_adp:  37.865 0.6672  0.9192    34374.692
   2_occ:  37.927 0.6664  0.9176    34414.533
   3_bss:  37.855 0.6672  0.8612    34393.451
   3_xyz:  28.905 0.7688  0.9657    21110.033
   3_adp:  26.483 0.7957  0.9846    18455.672
   3_occ:  26.465 0.7958  0.9842    18399.154
   4_bss:  26.449 0.7960  0.9421    18443.917
   4_xyz:  21.803 0.8436  0.9735    12873.622
   4_adp:  20.231 0.8592  0.9697    11464.240
   4_occ:  20.222 0.8592  0.9696    11443.796
   5_bss:  20.180 0.8597  0.9603    11405.993
   5_xyz:  18.093 0.8794  0.9720     9460.314
   5_adp:  17.454 0.8856  0.9656     8998.443
   5_occ:  17.455 0.8856  0.9656     8994.578
   5_bss:  17.456 0.8856  0.9687     8998.545
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3881e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3881e+01
   1_xyz:   1.759  0.014  0.109 18.539  0.006  4.108   1.5073e-01
   1_adp:   1.759  0.014  0.109 18.539  0.006  4.108   1.5073e-01
   1_occ:   1.759  0.014  0.109 18.539  0.006  4.108   1.5073e-01
   2_bss:   1.759  0.014  0.109 18.539  0.006  4.108   1.5073e-01
   2_xyz:   1.202  0.008  0.083 16.596  0.005  4.124   8.8988e-02
   2_adp:   1.202  0.008  0.083 16.596  0.005  4.124   8.8988e-02
   2_occ:   1.202  0.008  0.083 16.596  0.005  4.124   8.8988e-02
   3_bss:   1.202  0.008  0.083 16.596  0.005  4.124   8.8988e-02
   3_xyz:   1.068  0.007  0.078 15.693  0.003  4.120   6.6797e-02
   3_adp:   1.068  0.007  0.078 15.693  0.003  4.120   6.6797e-02
   3_occ:   1.068  0.007  0.078 15.693  0.003  4.120   6.6797e-02
   4_bss:   1.068  0.007  0.078 15.693  0.003  4.120   6.6797e-02
   4_xyz:   0.978  0.007  0.073 15.680  0.003  4.129   5.9693e-02
   4_adp:   0.978  0.007  0.073 15.680  0.003  4.129   5.9693e-02
   4_occ:   0.978  0.007  0.073 15.680  0.003  4.129   5.9693e-02
   5_bss:   0.978  0.007  0.073 15.680  0.003  4.129   5.9693e-02
   5_xyz:   0.948  0.006  0.071 15.481  0.003  4.115   5.7853e-02
   5_adp:   0.948  0.006  0.071 15.481  0.003  4.115   5.7853e-02
   5_occ:   0.948  0.006  0.071 15.481  0.003  4.115   5.7853e-02
   5_bss:   0.948  0.006  0.071 15.481  0.003  4.115   5.7853e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9838e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9838e+00
   1_xyz:  14.135  0.194  0.426 85.288  0.032  2.080   1.0472e-01
   1_adp:  14.135  0.194  0.426 85.288  0.032  2.080   1.0472e-01
   1_occ:  14.135  0.194  0.426 85.288  0.032  2.080   1.0472e-01
   2_bss:  14.135  0.194  0.426 85.288  0.032  2.080   1.0472e-01
   2_xyz:   6.417  0.075  0.311 87.307  0.051  2.224   6.2005e-02
   2_adp:   6.417  0.075  0.311 87.307  0.051  2.224   6.2005e-02
   2_occ:   6.417  0.075  0.311 87.307  0.051  2.224   6.2005e-02
   3_bss:   6.417  0.075  0.311 87.307  0.051  2.224   6.2005e-02
   3_xyz:   7.855  0.048  0.333 81.751  0.032  2.312   6.0091e-02
   3_adp:   7.855  0.048  0.333 81.751  0.032  2.312   6.0091e-02
   3_occ:   7.855  0.048  0.333 81.751  0.032  2.312   6.0091e-02
   4_bss:   7.855  0.048  0.333 81.751  0.032  2.312   6.0091e-02
   4_xyz:   6.264  0.062  0.232 88.986  0.036  2.348   4.1148e-02
   4_adp:   6.264  0.062  0.232 88.986  0.036  2.348   4.1148e-02
   4_occ:   6.264  0.062  0.232 88.986  0.036  2.348   4.1148e-02
   5_bss:   6.264  0.062  0.232 88.986  0.036  2.348   4.1148e-02
   5_xyz:   7.009  0.044  0.245 80.743  0.039  2.339   5.5241e-02
   5_adp:   7.009  0.044  0.245 80.743  0.039  2.339   5.5241e-02
   5_occ:   7.009  0.044  0.245 80.743  0.039  2.339   5.5241e-02
   5_bss:   7.009  0.044  0.245 80.743  0.039  2.339   5.5241e-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:  85.57   0.00  15.46  75.80   0.00  13.62  85.57   0.00  25.47
   1_occ:  85.57   0.00  15.46  75.80   0.00  13.62  85.57   0.00  25.47
   2_bss:  85.57   0.00  15.46  75.80   0.00  13.62  85.57   0.00  25.47
   2_xyz:  85.57   0.00  15.46  75.80   0.00  13.62  85.57   0.00  25.47
   2_adp:  89.79   0.00  14.61  60.28   0.00  11.52  89.79   0.00  31.40
   2_occ:  89.79   0.00  14.61  60.28   0.00  11.52  89.79   0.00  31.40
   3_bss:  89.79   0.00  14.61  60.28   0.00  11.52  89.79   0.00  31.40
   3_xyz:  89.79   0.00  14.61  60.28   0.00  11.52  89.79   0.00  31.40
   3_adp: 118.10   0.00  14.42 118.10   0.00  10.71  90.11   0.00  34.66
   3_occ: 118.10   0.00  14.42 118.10   0.00  10.71  90.11   0.00  34.66
   4_bss: 118.10   0.00  14.42 118.10   0.00  10.71  90.11   0.00  34.66
   4_xyz: 118.10   0.00  14.42 118.10   0.00  10.71  90.11   0.00  34.66
   4_adp:  98.27   0.00  15.26  83.29   0.00  10.33  98.27   2.35  42.08
   4_occ:  98.27   0.00  15.26  83.29   0.00  10.33  98.27   2.35  42.08
   5_bss:  98.27   0.00  15.26  83.29   0.00  10.33  98.27   2.35  42.08
   5_xyz:  98.27   0.00  15.26  83.29   0.00  10.33  98.27   2.35  42.08
   5_adp: 101.82   0.00  15.34  99.93   0.00  10.09 101.82   2.90  43.90
   5_occ: 101.82   0.00  15.34  99.93   0.00  10.09 101.82   2.90  43.90
   5_bss: 103.50   1.68  17.02 101.61   1.68  11.77 103.50   4.58  45.58
------------------------------------------------------------------------
 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:    1.299    0.022    0.413
   1_adp:    1.299    0.022    0.413
   1_occ:    1.299    0.022    0.413
   2_bss:    1.299    0.022    0.413
   2_xyz:    1.848    0.040    0.575
   2_adp:    1.848    0.040    0.575
   2_occ:    1.848    0.040    0.575
   3_bss:    1.848    0.040    0.575
   3_xyz:    1.574    0.051    0.677
   3_adp:    1.574    0.051    0.677
   3_occ:    1.574    0.051    0.677
   4_bss:    1.574    0.051    0.677
   4_xyz:    1.739    0.069    0.756
   4_adp:    1.739    0.069    0.756
   4_occ:    1.739    0.069    0.756
   5_bss:    1.739    0.069    0.756
   5_xyz:    1.764    0.067    0.784
   5_adp:    1.764    0.067    0.784
   5_occ:    1.764    0.067    0.784
   5_bss:    1.764    0.067    0.784
------------------------------------------------------------------------

CPU time actual refinement: 331.67


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_637/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_637/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_637/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_637/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_637/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 331.52 
  Macro-tasks:
    bulk solvent and scale       = 40.27  
    individual site refinement   = 133.94 
    weights calculation          = 32.06  
    collect and process          = 6.45   
    model show statistics        = 0.15   
    TOTAL for macro-tasks        = 212.87 
  Micro-tasks:
    mask                            = 2.40   
    f_calc                          = 102.88 
    alpha_beta                      = 8.36   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 111.88 
    fmodel                         = 7.13   
    r_factors                      = 0.22   
    phase_errors                   = 9.96   
    foms                           = 0.26   
    TOTAL for micro-tasks          = 244.26 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.733 micro seconds
Total CPU time: 5.75 minutes
from_scatterers_fft:    633 calls, 102.48 s
gradients_fft:          578 calls,  99.12 s

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

# Date 2008-01-16 Time 02:03:38 PST -0800 (1200477818.31 s)
Start R-work = 0.4985, R-free = 0.4833 (no bulk solvent and anisotropic scale)
Final R-work = 0.1496, R-free = 0.2024 (no bulk solvent and anisotropic scale)

Start R-work = 0.4897, R-free = 0.4702
Final R-work = 0.1327, R-free = 0.1866