# Date 2008-01-16 Time 03:31:06 PST -0800 (1200483066.38 s)
#phil __OFF__

Command line arguments: "../1266.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 25625
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1266

-------------------------------------------------------------------------------
  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: (72.0062, 46.93, 84.6622, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (72.0062, 46.93, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1768 1.96127
Completeness in resolution range: 0.9265
Completeness with d_max=infinity: 0.923792

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1768
                             d_min =   1.9613

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: (72.0062, 46.93, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1768 1.96127
Completeness in resolution range: 0.9265
Completeness with d_max=infinity: 0.923792

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1772 -  4.1984 [2217/2247]  1998   219   9.9%
  bin  2:  4.1984 -  3.3441 [2132/2151]  1919   213  10.0%
  bin  3:  3.3441 -  2.9248 [2102/2122]  1886   216  10.3%
  bin  4:  2.9248 -  2.6590 [2095/2120]  1893   202   9.6%
  bin  5:  2.6590 -  2.4693 [2062/2081]  1853   209  10.1%
  bin  6:  2.4693 -  2.3242 [2050/2097]  1842   208  10.1%
  bin  7:  2.3242 -  2.2082 [2068/2100]  1859   209  10.1%
  bin  8:  2.2082 -  2.1123 [2027/2064]  1829   198   9.8%
  bin  9:  2.1123 -  2.0312 [2019/2094]  1817   202  10.0%
  bin 10:  2.0312 -  1.9613 [ 817/2067]   734    83  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1266/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.65 -     2.30: 22
        2.30 -     2.95: 1655
        2.95 -     3.60: 4530
        3.60 -     4.25: 9192
        4.25 -     4.90: 12937
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 107 " - " O   HOH Z 340 "  1.653 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.809 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.889 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 341 "  1.923 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28331 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_1266/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1266/model_refine_001.geo

CPU time processing inputs: 9.14


============================ 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 = 72.00625 46.93 84.6622 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4830   r_free= 0.4847   ksol= 0.00   Bsol= 0.00   scale= 0.789    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.283838                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1772 -  4.6835 0.99   1436  161 0.3972 0.4056       6.594      6.5875|
|  2:  4.6835 -  3.7357 0.99   1390  152 0.4012 0.4092      6.7901      6.8481|
|  3:  3.7357 -  3.2689 0.99   1356  151 0.4529 0.4187      6.6694      6.6666|
|  4:  3.2689 -  2.9724 0.99   1358  155 0.4652 0.4858      6.5152      6.5154|
|  5:  2.9724 -  2.7608 0.99   1333  147 0.5090 0.5349      6.3679      6.3533|
|  6:  2.7608 -  2.5988 0.98   1343  149 0.5135 0.5287      6.2763      6.2513|
|  7:  2.5988 -  2.4693 0.99   1333  144 0.5386 0.4718      6.2595       6.159|
|  8:  2.4693 -  2.3622 0.98   1324  151 0.5333 0.5305      6.1524      6.1858|
|  9:  2.3622 -  2.2716 0.98   1315  151 0.5208 0.5053      6.1318      6.0842|
| 10:  2.2716 -  2.1934 0.98   1307  148 0.5249 0.5268      6.0719      6.0949|
| 11:  2.1934 -  2.1250 0.99   1344  137 0.5257 0.5768      6.0365      6.0412|
| 12:  2.1250 -  2.0644 0.98   1298  146 0.5273 0.5594      5.9517      5.9876|
| 13:  2.0644 -  2.0102 0.84   1122  136 0.5358 0.4819      5.8684      5.8299|
| 14:  2.0102 -  1.9613 0.27    371   31 0.5582 0.5769      5.8125      5.8261|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1772 -  4.6835  1436   161  0.68  36.24   0.79     0.72      78958.63|
|  2:  4.6835 -  3.7357  1390   152  0.69  36.45   0.88     0.76     112108.70|
|  3:  3.7357 -  3.2689  1356   151  0.56  47.05   0.82     0.69     123137.18|
|  4:  3.2689 -  2.9724  1358   155  0.46  55.26   0.80     0.58     114542.99|
|  5:  2.9724 -  2.7608  1333   147  0.35  63.52   0.73     0.44      93690.38|
|  6:  2.7608 -  2.5988  1343   149  0.34  64.26   0.73     0.42      78355.76|
|  7:  2.5988 -  2.4693  1333   144  0.35  63.40   0.71     0.40      65896.22|
|  8:  2.4693 -  2.3622  1324   151  0.37  62.62   0.71     0.45      58462.88|
|  9:  2.3622 -  2.2716  1315   151  0.36  63.07   0.75     0.42      52193.60|
| 10:  2.2716 -  2.1934  1307   148  0.33  65.00   0.74     0.40      50118.66|
| 11:  2.1934 -  2.1250  1344   137  0.28  69.00   0.76     0.35      49170.55|
| 12:  2.1250 -  2.0644  1298   146  0.22  73.37   0.73     0.29      47049.34|
| 13:  2.0644 -  2.0102  1122   136  0.21  74.54   0.72     0.27      41558.15|
| 14:  2.0102 -  1.9613   371    31  0.23  72.83   0.68     0.29      34275.99|
|alpha:            min =        0.27 max =            0.76 mean =         0.48|
|beta:             min =    34275.99 max =       123137.18 mean =     74177.21|
|figures of merit: min =        0.00 max =            1.00 mean =         0.40|
|phase err.(work): min =        0.00 max =           89.95 mean =        59.36|
|phase err.(test): min =        0.00 max =           89.94 mean =        59.51|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.847099             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.292   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.490828              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.459   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       26 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      170 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      698 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1512 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2633 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3942 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5056 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6544 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7727 |
|-----------------------------------------------------------------------------|
|-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 |       53.746 |
| 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 |       1.837 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.947)------------------------------------------|
|    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 = 11.947)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4880   r_free= 0.4906   ksol= 0.00   Bsol= 0.00   scale= 0.760    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.81 A                  |
| x-ray target function (ml) for work reflections: 6.285795                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4748   r_free= 0.4727   ksol= 0.32   Bsol= 3.86   scale= 0.992    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (10.13,7.32,8.73,0.00,0.00,0.00); trace/3= 8.73                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.81 A                  |
| x-ray target function (ml) for work reflections: 6.280126                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.824398             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.027   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.307078              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.422   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4748      final r-factor (work) = 0.4010          |
| start r-factor (free) = 0.4727      final r-factor (free) = 0.4300          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 97.1662 = 13.82 * 0.50 * 6.2817 + 1.00 * 53.7461                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 43.0415 = 13.82 * 0.50 * 6.2059 + 1.00 * 0.1453                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4010      final r-factor (work) = 0.3583          |
| start r-factor (free) = 0.4300      final r-factor (free) = 0.4119          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.1259 = 1.31 * 1.00 * 6.2059 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.0349 = 1.31 * 1.00 * 6.1347 + 1.00 * 0.0163                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.947)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.22   13.62    None  None   None       |
|    all(noH): 2823   0      0.00    96.22   13.62    None  None   None       |
|    Sol.    : 438    0      0.00    80.80   26.33    None  None   None       |
|    Mac.    : 2385   0      0.00    96.22   11.29    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 -   9.622: 1381   |   5:    48.111 -  57.734:   40        |
|      1:     9.622 -  19.245:  729   |   6:    57.734 -  67.356:   13        |
|      2:    19.245 -  28.867:  390   |   7:    67.356 -  76.978:    7        |
|      3:    28.867 -  38.489:  178   |   8:    76.978 -  86.600:    2        |
|      4:    38.489 -  48.111:   80   |   9:    86.600 -  96.223:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3583 r_free = 0.4119             target_work(ml) = 6.115         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3573 r_free = 0.4126             target_work(ml) = 6.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3573   r_free= 0.4126   ksol= 0.32   Bsol= 3.86   scale= 1.102    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (10.13,7.32,8.73,0.00,0.00,0.00); trace/3= 8.73                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.114314                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3547   r_free= 0.4094   ksol= 0.33   Bsol= 32.17   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.99,3.86,5.71,0.00,0.00,0.00); trace/3= 5.18                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.113567                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.876484              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.631   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.616089              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.500  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3547      final r-factor (work) = 0.2812          |
| start r-factor (free) = 0.4094      final r-factor (free) = 0.3464          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.1554 = 5.88 * 0.50 * 6.1296 + 1.00 * 0.1453                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.7815 = 5.88 * 0.50 * 6.0247 + 1.00 * 0.0794                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2812      final r-factor (work) = 0.2619          |
| start r-factor (free) = 0.3464      final r-factor (free) = 0.3247          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7281 = 0.62 * 1.00 * 6.0247 + 1.00 * 0.0163                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6542 = 0.62 * 1.00 * 5.9121 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.947)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.06   13.45    None  None   None       |
|    all(noH): 2823   0      0.00    90.06   13.45    None  None   None       |
|    Sol.    : 438    0      0.00    80.56   31.89    None  None   None       |
|    Mac.    : 2385   0      0.00    90.06   10.06    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 -   9.006: 1409   |   5:    45.030 -  54.036:   71        |
|      1:     9.006 -  18.012:  716   |   6:    54.036 -  63.042:   28        |
|      2:    18.012 -  27.018:  304   |   7:    63.042 -  72.049:    7        |
|      3:    27.018 -  36.024:  171   |   8:    72.049 -  81.055:    1        |
|      4:    36.024 -  45.030:  113   |   9:    81.055 -  90.061:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2619 r_free = 0.3247             target_work(ml) = 5.886         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2618 r_free = 0.3247             target_work(ml) = 5.885         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2618   r_free= 0.3247   ksol= 0.33   Bsol= 32.17   scale= 1.054   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.99,3.86,5.71,0.00,0.00,0.00); trace/3= 5.18                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.885380                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2609   r_free= 0.3214   ksol= 0.33   Bsol= 41.39   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.72,2.51,3.77,0.00,0.00,0.00); trace/3= 3.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.883642                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.870104              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.006   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.551960              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.104  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2609      final r-factor (work) = 0.1858          |
| start r-factor (free) = 0.3214      final r-factor (free) = 0.2432          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.4351 = 5.87 * 0.50 * 5.9133 + 1.00 * 0.0794                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.9853 = 5.87 * 0.50 * 5.7616 + 1.00 * 0.0747                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1858      final r-factor (work) = 0.1675          |
| start r-factor (free) = 0.2432      final r-factor (free) = 0.2220          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1921 = 0.55 * 1.00 * 5.7616 + 1.00 * 0.0119                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0705 = 0.55 * 1.00 * 5.5417 + 1.00 * 0.0117                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.947)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.14   13.78    None  None   None       |
|    all(noH): 2823   0      0.00    89.14   13.78    None  None   None       |
|    Sol.    : 438    0      1.74    83.88   36.78    None  None   None       |
|    Mac.    : 2385   0      0.00    89.14   9.55     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 -   8.914: 1491   |   5:    44.572 -  53.486:   99        |
|      1:     8.914 -  17.829:  712   |   6:    53.486 -  62.401:   44        |
|      2:    17.829 -  26.743:  187   |   7:    62.401 -  71.315:   17        |
|      3:    26.743 -  35.657:  114   |   8:    71.315 -  80.229:    1        |
|      4:    35.657 -  44.572:  154   |   9:    80.229 -  89.144:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1675 r_free = 0.2220             target_work(ml) = 5.498         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1673 r_free = 0.2217             target_work(ml) = 5.497         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1673   r_free= 0.2217   ksol= 0.33   Bsol= 41.39   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.72,2.51,3.77,0.00,0.00,0.00); trace/3= 3.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.497389                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1668   r_free= 0.2206   ksol= 0.33   Bsol= 45.72   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.31,1.59,2.21,0.00,0.00,0.00); trace/3= 2.04                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.496462                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.853504              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.087  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.333388              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.116  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1668      final r-factor (work) = 0.1402          |
| start r-factor (free) = 0.2206      final r-factor (free) = 0.1899          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9949 = 2.85 * 0.50 * 5.5510 + 1.00 * 0.0750                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8067 = 2.85 * 0.50 * 5.4280 + 1.00 * 0.0623                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1402      final r-factor (work) = 0.1324          |
| start r-factor (free) = 0.1899      final r-factor (free) = 0.1852          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.2492 = 1.33 * 1.00 * 5.4280 + 1.00 * 0.0116                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1048 = 1.33 * 1.00 * 5.3179 + 1.00 * 0.0139                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.947)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.06  14.34    None  None   None       |
|    all(noH): 2823   0      0.00    101.06  14.34    None  None   None       |
|    Sol.    : 438    0      2.58    91.89   40.35    None  None   None       |
|    Mac.    : 2385   0      0.00    101.06  9.56     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 -  10.106: 1689   |   5:    50.531 -  60.637:   82        |
|      1:    10.106 -  20.212:  593   |   6:    60.637 -  70.743:   48        |
|      2:    20.212 -  30.319:  152   |   7:    70.743 -  80.849:   19        |
|      3:    30.319 -  40.425:  114   |   8:    80.849 -  90.956:    5        |
|      4:    40.425 -  50.531:  117   |   9:    90.956 - 101.062:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1324 r_free = 0.1852             target_work(ml) = 5.305         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1323 r_free = 0.1850             target_work(ml) = 5.304         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1323   r_free= 0.1850   ksol= 0.33   Bsol= 45.72   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.31,1.59,2.21,0.00,0.00,0.00); trace/3= 2.04                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.304258                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1325   r_free= 0.1854   ksol= 0.33   Bsol= 51.11   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.87,1.31,1.84,0.00,0.00,0.00); trace/3= 1.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.305544                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.814898              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 133.169  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.467093              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.219  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1325      final r-factor (work) = 0.1254          |
| start r-factor (free) = 0.1854      final r-factor (free) = 0.1770          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8891 = 1.81 * 0.50 * 5.3191 + 1.00 * 0.0623                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8528 = 1.81 * 0.50 * 5.2839 + 1.00 * 0.0579                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1254      final r-factor (work) = 0.1241          |
| start r-factor (free) = 0.1770      final r-factor (free) = 0.1748          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4819 = 0.47 * 1.00 * 5.2839 + 1.00 * 0.0138                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4664 = 0.47 * 1.00 * 5.2544 + 1.00 * 0.0121                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.947)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.05  14.01    None  None   None       |
|    all(noH): 2823   0      0.00    103.05  14.01    None  None   None       |
|    Sol.    : 438    0      2.60    92.94   38.83    None  None   None       |
|    Mac.    : 2385   0      0.00    103.05  9.45     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 -  10.305: 1732   |   5:    51.524 -  61.828:   64        |
|      1:    10.305 -  20.610:  576   |   6:    61.828 -  72.133:   41        |
|      2:    20.610 -  30.914:  149   |   7:    72.133 -  82.438:   15        |
|      3:    30.914 -  41.219:  133   |   8:    82.438 -  92.743:    5        |
|      4:    41.219 -  51.524:  105   |   9:    92.743 - 103.047:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1241 r_free = 0.1748             target_work(ml) = 5.246         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1240 r_free = 0.1746             target_work(ml) = 5.245         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1240   r_free= 0.1746   ksol= 0.33   Bsol= 51.11   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.87,1.31,1.84,0.00,0.00,0.00); trace/3= 1.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.245406                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1772 -  4.6835 0.99   1436  161 0.0994 0.1336      5.3897      5.5822|
|  2:  4.6835 -  3.7357 0.99   1390  152 0.0917 0.1191       5.487      5.7379|
|  3:  3.7357 -  3.2689 0.99   1356  151 0.1163 0.1787      5.5483      5.9408|
|  4:  3.2689 -  2.9724 0.99   1358  155 0.1394 0.1676      5.5576      5.6781|
|  5:  2.9724 -  2.7608 0.99   1333  147 0.1478 0.1917      5.4231      5.6009|
|  6:  2.7608 -  2.5988 0.98   1343  149 0.1401 0.2157      5.3228      5.5644|
|  7:  2.5988 -  2.4693 0.99   1333  144 0.1401 0.1929      5.2683      5.4886|
|  8:  2.4693 -  2.3622 0.98   1324  151 0.1301 0.1829      5.1525       5.331|
|  9:  2.3622 -  2.2716 0.98   1315  151 0.1298 0.2178      5.1125      5.4214|
| 10:  2.2716 -  2.1934 0.98   1307  148 0.1285 0.1829      5.0598      5.2929|
| 11:  2.1934 -  2.1250 0.99   1344  137 0.1332 0.2011      5.0467      5.3991|
| 12:  2.1250 -  2.0644 0.98   1298  146 0.1282 0.1874      4.9853      5.1724|
| 13:  2.0644 -  2.0102 0.84   1122  136 0.1314 0.1877      4.8836      5.1211|
| 14:  2.0102 -  1.9613 0.27    371   31 0.1114 0.1876      4.7116      4.9942|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1772 -  4.6835  1436   161  0.94   9.23   0.97     0.96       7546.32|
|  2:  4.6835 -  3.7357  1390   152  0.95   8.60   1.01     0.99       9961.34|
|  3:  3.7357 -  3.2689  1356   151  0.92  13.03   1.03     1.03      12273.58|
|  4:  3.2689 -  2.9724  1358   155  0.90  16.20   1.01     0.98      12821.18|
|  5:  2.9724 -  2.7608  1333   147  0.89  17.70   0.99     0.97      10143.05|
|  6:  2.7608 -  2.5988  1343   149  0.88  18.69   0.99     0.96       9124.70|
|  7:  2.5988 -  2.4693  1333   144  0.89  17.51   0.99     0.97       7643.89|
|  8:  2.4693 -  2.3622  1324   151  0.89  17.54   0.99     0.95       6501.49|
|  9:  2.3622 -  2.2716  1315   151  0.88  18.11   1.01     0.97       5989.04|
| 10:  2.2716 -  2.1934  1307   148  0.89  16.94   1.00     0.96       5310.19|
| 11:  2.1934 -  2.1250  1344   137  0.88  18.66   0.99     0.94       5429.30|
| 12:  2.1250 -  2.0644  1298   146  0.89  18.13   1.00     1.00       5026.96|
| 13:  2.0644 -  2.0102  1122   136  0.88  18.51   0.99     0.98       4129.57|
| 14:  2.0102 -  1.9613   371    31  0.89  17.31   0.98     0.96       2974.89|
|alpha:            min =        0.94 max =            1.03 mean =         0.97|
|beta:             min =     2974.89 max =        12821.18 mean =      7809.66|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.83 mean =        15.99|
|phase err.(test): min =        0.00 max =           89.85 mean =        15.45|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1240   r_free= 0.1746   ksol= 0.32   Bsol= 51.14   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.16,-0.31,0.15,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.245408                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1240   r_free= 0.1746   ksol= 0.32   Bsol= 51.14   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.16,-0.31,0.15,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.245408                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1772 -  4.6835 0.99   1436  161 0.0993 0.1336      5.3886      5.5816|
|  2:  4.6835 -  3.7357 0.99   1390  152 0.0916 0.1190      5.4863      5.7368|
|  3:  3.7357 -  3.2689 0.99   1356  151 0.1163 0.1787      5.5477      5.9403|
|  4:  3.2689 -  2.9724 0.99   1358  155 0.1394 0.1677      5.5577      5.6785|
|  5:  2.9724 -  2.7608 0.99   1333  147 0.1478 0.1917      5.4236      5.6012|
|  6:  2.7608 -  2.5988 0.98   1343  149 0.1402 0.2159      5.3233      5.5649|
|  7:  2.5988 -  2.4693 0.99   1333  144 0.1401 0.1929      5.2686      5.4887|
|  8:  2.4693 -  2.3622 0.98   1324  151 0.1302 0.1830      5.1529      5.3314|
|  9:  2.3622 -  2.2716 0.98   1315  151 0.1298 0.2178      5.1128      5.4216|
| 10:  2.2716 -  2.1934 0.98   1307  148 0.1286 0.1831        5.06      5.2929|
| 11:  2.1934 -  2.1250 0.99   1344  137 0.1333 0.2012      5.0468      5.3991|
| 12:  2.1250 -  2.0644 0.98   1298  146 0.1282 0.1875      4.9855      5.1726|
| 13:  2.0644 -  2.0102 0.84   1122  136 0.1313 0.1877      4.8835       5.121|
| 14:  2.0102 -  1.9613 0.27    371   31 0.1115 0.1882      4.7122      4.9957|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1772 -  4.6835  1436   161  0.94   9.23   0.97     0.96       7546.13|
|  2:  4.6835 -  3.7357  1390   152  0.95   8.60   1.01     0.99       9951.93|
|  3:  3.7357 -  3.2689  1356   151  0.92  13.01   1.03     1.03      12251.97|
|  4:  3.2689 -  2.9724  1358   155  0.90  16.19   1.01     0.98      12821.14|
|  5:  2.9724 -  2.7608  1333   147  0.89  17.71   0.99     0.97      10152.08|
|  6:  2.7608 -  2.5988  1343   149  0.88  18.70   0.99     0.96       9134.76|
|  7:  2.5988 -  2.4693  1333   144  0.89  17.52   0.99     0.96       7652.52|
|  8:  2.4693 -  2.3622  1324   151  0.89  17.55   0.99     0.95       6508.31|
|  9:  2.3622 -  2.2716  1315   151  0.88  18.11   1.00     0.97       5992.04|
| 10:  2.2716 -  2.1934  1307   148  0.89  16.94   1.00     0.96       5313.41|
| 11:  2.1934 -  2.1250  1344   137  0.88  18.66   0.99     0.94       5427.55|
| 12:  2.1250 -  2.0644  1298   146  0.89  18.13   1.00     1.00       5028.49|
| 13:  2.0644 -  2.0102  1122   136  0.88  18.52   0.99     0.98       4131.46|
| 14:  2.0102 -  1.9613   371    31  0.89  17.31   0.98     0.96       2978.88|
|alpha:            min =        0.94 max =            1.03 mean =         0.97|
|beta:             min =     2978.88 max =        12821.14 mean =      7810.50|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.86 mean =        15.99|
|phase err.(test): min =        0.00 max =           89.85 mean =        15.46|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.947)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.65    104.70  15.66    None  None   None       |
|    all(noH): 2823   0      1.65    104.70  15.66    None  None   None       |
|    Sol.    : 438    0      4.26    94.59   40.48    None  None   None       |
|    Mac.    : 2385   0      1.65    104.70  11.11    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:     1.654 -  11.959: 1732   |   5:    53.178 -  63.482:   64        |
|      1:    11.959 -  22.264:  576   |   6:    63.482 -  73.787:   41        |
|      2:    22.264 -  32.568:  149   |   7:    73.787 -  84.092:   15        |
|      3:    32.568 -  42.873:  133   |   8:    84.092 -  94.397:    5        |
|      4:    42.873 -  53.178:  105   |   9:    94.397 - 104.701:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 333         
Filter by distance & map next to the model:
   mapped sites are within: 0.523 - 5.863
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 327 from: 333
   mapped sites are within: 0.704 - 5.863

peak=   10.175 closest distance to " CB  VAL A 230 " =    1.449
peak=    9.513 closest distance to " CG2 VAL A 296 " =    1.465
peak=    7.852 closest distance to " O   HOH Z 179 " =    1.056
peak=    7.488 closest distance to " CG  ARG A 138 " =    1.275
peak=    5.999 closest distance to " CD2 LEU A   5 " =    1.240
peak=    5.965 closest distance to " O   HOH Z 278 " =    1.292
peak=    5.775 closest distance to " NH2AARG A 102 " =    1.061
peak=    5.763 closest distance to " O   HOH Z 111 " =    2.122
peak=    5.595 closest distance to " O   HOH Z 102 " =    1.082
peak=    5.542 closest distance to " O   HOH Z  37 " =    1.396
peak=    5.497 closest distance to " CG  LEU A   5 " =    1.246
peak=    5.358 closest distance to " CD1AILE A 234 " =    1.091
peak=    5.314 closest distance to " CB  GLN A 223 " =    1.465
peak=    5.136 closest distance to " CG  PRO A 213 " =    1.307
peak=    5.015 closest distance to " O   HOH Z 246 " =    1.583
peak=    4.990 closest distance to " NH1 ARG A 138 " =    1.054
peak=    4.872 closest distance to " O   HOH Z 193 " =    1.891
peak=    4.870 closest distance to " O   HOH Z 186 " =    1.534
peak=    4.847 closest distance to " O   HOH Z 112 " =    1.509
peak=    4.737 closest distance to " CB  VAL A 230 " =    1.261
peak=    4.714 closest distance to " CB  SER A  63 " =    1.412
peak=    4.709 closest distance to " O   HOH Z  48 " =    1.822
peak=    4.691 closest distance to " NH1 ARG A  56 " =    1.092
peak=    4.674 closest distance to " CG  PRO A 198 " =    1.309
peak=    4.674 closest distance to " NE2 GLN A  11 " =    1.138
peak=    4.635 closest distance to " O   HOH Z 298 " =    1.790
peak=    4.613 closest distance to " CD  ARG A 138 " =    1.064
peak=    4.540 closest distance to " O   HOH Z 183 " =    1.495
peak=    4.539 closest distance to " CD2 LEU A 228 " =    1.258
peak=    4.501 closest distance to " CB  GLN A 183 " =    1.234
peak=    4.496 closest distance to " O   HOH Z 236 " =    1.840
peak=    4.395 closest distance to " O   HOH Z 108 " =    1.657
peak=    4.393 closest distance to " O   HOH Z 303 " =    2.153
peak=    4.392 closest distance to " O   HOH Z 427 " =    3.382
peak=    4.389 closest distance to " CB  SER A   3 " =    1.510
peak=    4.385 closest distance to " CG  LEU A 228 " =    1.309
peak=    4.370 closest distance to " CB  ASN A 148 " =    1.358
peak=    4.365 closest distance to " O   PRO A 198 " =    1.524
peak=    4.321 closest distance to " O   HOH Z  78 " =    2.295
peak=    4.301 closest distance to " O   HOH Z 260 " =    1.319
peak=    4.297 closest distance to " CG  PRO A 243 " =    1.161
peak=    4.285 closest distance to " CG  PRO A 280 " =    0.814
peak=    4.283 closest distance to " CA  ALA A  21 " =    1.210
peak=    4.265 closest distance to " O   HOH Z 132 " =    1.051
peak=    4.251 closest distance to " O   HOH Z 124 " =    1.289
peak=    4.249 closest distance to " O   HOH Z 368 " =    1.960
peak=    4.226 closest distance to " OD1 ASN A 217 " =    1.634
peak=    4.222 closest distance to " O   HOH Z  80 " =    1.824
peak=    4.214 closest distance to " O   HOH Z 134 " =    1.507
peak=    4.211 closest distance to " O   HOH Z 369 " =    1.949
peak=    4.180 closest distance to " CG2 THR A 221 " =    0.909
peak=    4.157 closest distance to " O   HOH Z 316 " =    2.923
peak=    4.151 closest distance to " O   HOH Z 202 " =    1.392
peak=    4.149 closest distance to " CB  TYR A 169 " =    0.912
peak=    4.137 closest distance to " O   HOH Z  97 " =    1.992
peak=    4.135 closest distance to " CB  LEU A 228 " =    1.303
peak=    4.122 closest distance to " CB  GLU A 152 " =    1.245
peak=    4.120 closest distance to " CB  VAL A 202 " =    1.560
peak=    4.118 closest distance to " O   HOH Z 411 " =    3.434
peak=    4.110 closest distance to " O   HOH Z 232 " =    2.128
peak=    4.094 closest distance to " O   HOH Z 126 " =    1.588
peak=    4.073 closest distance to " O   HOH Z 227 " =    1.763
peak=    4.070 closest distance to " O   HOH Z  68 " =    1.574
peak=    4.057 closest distance to " CB  ARG A 275 " =    0.858
peak=    4.028 closest distance to " O   HOH Z 374 " =    1.086
peak=    4.022 closest distance to " O   HOH Z  63 " =    1.927
peak=    4.002 closest distance to " CB  TRP A 266 " =    0.979
peak=    3.985 closest distance to " OD2 ASP A 286 " =    2.860
peak=    3.964 closest distance to " O   HOH Z 263 " =    1.498
peak=    3.962 closest distance to " O   HOH Z 193 " =    2.128
peak=    3.959 closest distance to " O   HOH Z  92 " =    0.943
peak=    3.954 closest distance to " CD  ARG A 269 " =    0.889
peak=    3.951 closest distance to " CA  LEU A 282 " =    1.080
peak=    3.947 closest distance to " O   HOH Z 425 " =    1.520
peak=    3.945 closest distance to " O   HOH Z  15 " =    2.070
peak=    3.942 closest distance to " O   HOH Z 280 " =    3.060
peak=    3.941 closest distance to " CB  ASP A 124 " =    0.758
peak=    3.940 closest distance to " O   HOH Z  11 " =    1.219
peak=    3.927 closest distance to " CD1 LEU A 300 " =    1.203
peak=    3.920 closest distance to " O   HOH Z 184 " =    1.754
peak=    3.919 closest distance to " O   HOH Z 371 " =    3.368
peak=    3.910 closest distance to " O   HOH Z 272 " =    1.919
peak=    3.908 closest distance to " CB  PRO A  54 " =    0.716
peak=    3.899 closest distance to " CD2 LEU A 255 " =    1.553
peak=    3.897 closest distance to " CB  GLU A 128 " =    1.127
peak=    3.891 closest distance to " NH1AARG A 145 " =    1.082
peak=    3.875 closest distance to " O   HOH Z  88 " =    3.341
peak=    3.874 closest distance to " CB  TRP A 179 " =    1.397
peak=    3.873 closest distance to " CZ  PHE A 192 " =    1.063
peak=    3.873 closest distance to " OE1 GLN A  58 " =    1.309
peak=    3.862 closest distance to " CB  VAL A 265 " =    1.231
peak=    3.860 closest distance to " O   HOH Z  58 " =    1.834
peak=    3.855 closest distance to " O   HOH Z 243 " =    1.165
peak=    3.853 closest distance to " CB  ALA A 161 " =    0.980
peak=    3.852 closest distance to " O   HOH Z 144 " =    1.483
peak=    3.845 closest distance to " OD1 ASN A  69 " =    2.606
peak=    3.840 closest distance to " O   HOH Z   7 " =    1.199
peak=    3.837 closest distance to " CB  MET A  40 " =    0.824
peak=    3.824 closest distance to " O   HOH Z 281 " =    4.168
peak=    3.812 closest distance to " CA  THR A 221 " =    0.944
peak=    3.797 closest distance to " CG1 VAL A 153 " =    0.971
peak=    3.784 closest distance to " O   HOH Z 271 " =    2.081
peak=    3.769 closest distance to " O   HOH Z 126 " =    1.884
peak=    3.767 closest distance to " O   HOH Z 127 " =    1.282
peak=    3.762 closest distance to " CD  LYS A 119 " =    1.287
peak=    3.747 closest distance to " O   HOH Z 394 " =    1.745
peak=    3.743 closest distance to " OH  TYR A 186 " =    1.028
peak=    3.741 closest distance to " CA  TYR A  30 " =    0.984
peak=    3.727 closest distance to " O   HOH Z 128 " =    1.956
peak=    3.718 closest distance to " CB  SER A 216 " =    0.869
peak=    3.705 closest distance to " CG  GLN A  88 " =    1.055
peak=    3.702 closest distance to " CG  LEU A 167 " =    1.118
peak=    3.696 closest distance to " O   HOH Z 132 " =    2.496
peak=    3.693 closest distance to " CA  ASP A 124 " =    0.704
peak=    3.691 closest distance to " ND2 ASN A 249 " =    1.941
peak=    3.691 closest distance to " CD ALYS A 290 " =    1.057
peak=    3.690 closest distance to " O   HOH Z 295 " =    1.561
peak=    3.683 closest distance to " O   HOH Z 178 " =    1.140
peak=    3.676 closest distance to " CB  LEU A 143 " =    1.127
peak=    3.675 closest distance to " O   HOH Z   4 " =    1.684
peak=    3.667 closest distance to " CA  MET A  40 " =    1.083
peak=    3.655 closest distance to " CA  GLU A 152 " =    0.819
peak=    3.649 closest distance to " CA  TYR A 186 " =    1.526
peak=    3.642 closest distance to " O   HOH Z 182 " =    1.378
peak=    3.641 closest distance to " O   HOH Z  53 " =    2.605
peak=    3.640 closest distance to " O   HOH Z 171 " =    3.840
peak=    3.639 closest distance to " O   HOH Z 298 " =    2.437
peak=    3.630 closest distance to " O   MET A 105 " =    1.767
peak=    3.623 closest distance to " O   HOH Z 410 " =    1.498
peak=    3.621 closest distance to " CA  ARG A 102 " =    1.164
peak=    3.609 closest distance to " OG  SER A 206 " =    1.222
peak=    3.609 closest distance to " O   HOH Z 344 " =    2.989
peak=    3.608 closest distance to " O   ALA A 291 " =    1.758
peak=    3.607 closest distance to " O   SER A  87 " =    2.368
peak=    3.605 closest distance to " NE2 GLN A  58 " =    5.648
peak=    3.605 closest distance to " O   HOH Z 355 " =    1.911
peak=    3.605 closest distance to " CB  PRO A 198 " =    0.957
peak=    3.595 closest distance to " CB  ASN A 187 " =    1.159
peak=    3.592 closest distance to " O   HOH Z 437 " =    2.172
peak=    3.592 closest distance to " CB  ALA A 291 " =    1.370
peak=    3.589 closest distance to " NH1BARG A 275 " =    1.303
peak=    3.585 closest distance to " CA  ALA A  51 " =    1.059
peak=    3.584 closest distance to " O   HOH Z  49 " =    1.975
peak=    3.578 closest distance to " NZ  LYS A 117 " =    3.327
peak=    3.574 closest distance to " O   HOH Z 276 " =    1.306
peak=    3.567 closest distance to " CA  ALA A 160 " =    0.862
peak=    3.562 closest distance to " CB  TYR A  30 " =    1.424
peak=    3.562 closest distance to " CG1BVAL A  72 " =    1.519
peak=    3.550 closest distance to " O   HOH Z 327 " =    2.263
peak=    3.549 closest distance to " O   HOH Z 282 " =    1.426
peak=    3.548 closest distance to " O   HOH Z 345 " =    3.462
peak=    3.544 closest distance to " CG1 ILE A  33 " =    1.365
peak=    3.540 closest distance to " O   HOH Z 172 " =    3.793
peak=    3.536 closest distance to " O   HOH Z 180 " =    2.090
peak=    3.531 closest distance to " OE1 GLN A  11 " =    1.677
peak=    3.530 closest distance to " CD  ARG A  14 " =    1.297
peak=    3.527 closest distance to " C   ALA A 299 " =    0.984
peak=    3.526 closest distance to " O   HOH Z 236 " =    1.679
peak=    3.522 closest distance to " O   HOH Z 133 " =    2.322
peak=    3.508 closest distance to " O   HOH Z  63 " =    1.953
peak=    3.507 closest distance to " CA  VAL A 126 " =    1.221
peak=    3.504 closest distance to " O   HOH Z 130 " =    3.893
peak=    3.502 closest distance to " O   HOH Z 281 " =    1.618
peak=    3.499 closest distance to " CB  GLU A 236 " =    1.189
peak=    3.491 closest distance to " O   ASP A 132 " =    3.671
peak=    3.490 closest distance to " CB  ILE A 199 " =    0.850
peak=    3.489 closest distance to " O   HOH Z 109 " =    2.703
peak=    3.488 closest distance to " CE1 PHE A 208 " =    1.047
peak=    3.479 closest distance to " CB  MET A  47 " =    1.093
peak=    3.478 closest distance to " CA  ALA A 158 " =    1.091
peak=    3.473 closest distance to " CD  LYS A 166 " =    1.404
peak=    3.467 closest distance to " CG2 VAL A 257 " =    0.869
peak=    3.464 closest distance to " OD1 ASP A 238 " =    0.902
peak=    3.463 closest distance to " O   HOH Z 403 " =    1.849
peak=    3.462 closest distance to " O   HOH Z 332 " =    1.613
peak=    3.461 closest distance to " O   HOH Z 290 " =    1.261
peak=    3.461 closest distance to " NH2BARG A 145 " =    2.121
peak=    3.461 closest distance to " CA  ALA A 154 " =    1.243
peak=    3.453 closest distance to " CB  LYS A 117 " =    1.161
peak=    3.450 closest distance to " CD1 ILE A  33 " =    1.705
peak=    3.447 closest distance to " O   HOH Z 175 " =    2.226
peak=    3.440 closest distance to " N   ASN A  39 " =    1.248
peak=    3.433 closest distance to " O   HOH Z 189 " =    2.757
peak=    3.431 closest distance to " CB  LEU A 255 " =    0.964
peak=    3.431 closest distance to " CB  GLU A 277 " =    3.633
peak=    3.430 closest distance to " O   HOH Z 346 " =    1.436
peak=    3.422 closest distance to " OG1 THR A 246 " =    3.340
peak=    3.417 closest distance to " CD  ARG A 159 " =    0.813
peak=    3.413 closest distance to " NE AARG A 275 " =    1.449
peak=    3.413 closest distance to " O   TRP A 274 " =    1.776
peak=    3.411 closest distance to " CG  ARG A  66 " =    2.405
peak=    3.398 closest distance to " O   HOH Z  38 " =    1.938
peak=    3.395 closest distance to " O   HOH Z 392 " =    1.960
peak=    3.395 closest distance to " O   HOH Z  61 " =    1.497
peak=    3.392 closest distance to " O   HOH Z  63 " =    1.355
peak=    3.389 closest distance to " CD1 TRP A 266 " =    1.137
peak=    3.384 closest distance to " O   HOH Z 255 " =    1.847
peak=    3.375 closest distance to " O   HOH Z 120 " =    1.029
peak=    3.374 closest distance to " CB  TRP A 150 " =    1.501
peak=    3.373 closest distance to " NE AARG A 102 " =    1.265
peak=    3.372 closest distance to " CB  ILE A 234 " =    0.906
peak=    3.360 closest distance to " CA  GLY A 196 " =    0.853
peak=    3.359 closest distance to " O   HOH Z  57 " =    1.267
peak=    3.359 closest distance to " O   HOH Z 267 " =    1.366
peak=    3.352 closest distance to " O   HOH Z 313 " =    1.950
peak=    3.347 closest distance to " CB  ASN A 148 " =    1.917
peak=    3.345 closest distance to " CE1 TYR A 186 " =    1.245
peak=    3.342 closest distance to " N   ARG A 156 " =    1.484
peak=    3.342 closest distance to " CD  ARG A 219 " =    1.215
peak=    3.340 closest distance to " O   HOH Z   3 " =    1.519
peak=    3.336 closest distance to " O   HOH Z 116 " =    1.774
peak=    3.332 closest distance to " O   HOH Z 207 " =    2.365
peak=    3.329 closest distance to " CA  LEU A 101 " =    1.594
peak=    3.328 closest distance to " CG BARG A 102 " =    1.845
peak=    3.325 closest distance to " CA  ASN A 127 " =    1.053
peak=    3.325 closest distance to " CG2 VAL A  67 " =    1.023
peak=    3.324 closest distance to " CA  GLY A 211 " =    1.229
peak=    3.323 closest distance to " CA  GLU A 152 " =    1.405
peak=    3.322 closest distance to " O   HOH Z  71 " =    1.349
peak=    3.322 closest distance to " NH1 ARG A  14 " =    1.069
peak=    3.315 closest distance to " CB  ALA A 104 " =    0.872
peak=    3.313 closest distance to " O   HOH Z 217 " =    1.392
peak=    3.312 closest distance to " O   HOH Z  99 " =    2.385
peak=    3.306 closest distance to " O   HOH Z 108 " =    2.044
peak=    3.300 closest distance to " O   HOH Z 163 " =    1.589
peak=    3.291 closest distance to " O   HOH Z 286 " =    2.262
peak=    3.290 closest distance to " O   PRO A 198 " =    1.194
peak=    3.289 closest distance to " N   TYR A  15 " =    0.911
peak=    3.287 closest distance to " OG  SER A  22 " =    2.875
peak=    3.286 closest distance to " NZ  LYS A  48 " =    1.404
peak=    3.285 closest distance to " CG2 THR A  42 " =    0.922
peak=    3.284 closest distance to " CE  LYS A  76 " =    0.921
peak=    3.283 closest distance to " O   HOH Z 284 " =    1.456
peak=    3.282 closest distance to " CG  MET A 188 " =    1.432
peak=    3.279 closest distance to " CA  GLU A  46 " =    0.776
peak=    3.277 closest distance to " CB  ALA A  34 " =    0.900
peak=    3.277 closest distance to " CB  ALA A 248 " =    1.325
peak=    3.277 closest distance to " ND1 HIS A  86 " =    1.774
peak=    3.275 closest distance to " O   HOH Z 374 " =    2.370
peak=    3.275 closest distance to " O   HOH Z 126 " =    1.788
peak=    3.273 closest distance to " O   HOH Z  54 " =    2.339
peak=    3.272 closest distance to " O   HOH Z 151 " =    1.729
peak=    3.271 closest distance to " OG BSER A 164 " =    2.211
peak=    3.271 closest distance to " CB  ARG A 139 " =    0.821
peak=    3.269 closest distance to " O   HOH Z 435 " =    2.094
peak=    3.267 closest distance to " O   HOH Z 148 " =    1.972
peak=    3.266 closest distance to " CB  LYS A 193 " =    1.254
peak=    3.265 closest distance to " CA  VAL A  41 " =    0.961
peak=    3.264 closest distance to " CZ  PHE A 218 " =    1.017
peak=    3.263 closest distance to " CA  GLY A 267 " =    1.117
peak=    3.260 closest distance to " CB  SER A 212 " =    1.144
peak=    3.258 closest distance to " O   GLN A 278 " =    1.298
peak=    3.255 closest distance to " O   HOH Z 261 " =    1.790
peak=    3.255 closest distance to " NZ ALYS A 290 " =    1.165
peak=    3.253 closest distance to " CB BVAL A  41 " =    1.368
peak=    3.253 closest distance to " O   HOH Z 149 " =    2.018
peak=    3.253 closest distance to " O   HOH Z 374 " =    3.134
peak=    3.251 closest distance to " O   HOH Z 426 " =    1.451
peak=    3.251 closest distance to " CA  THR A 264 " =    0.780
peak=    3.247 closest distance to " CB  LEU A 237 " =    0.974
peak=    3.247 closest distance to " CA  ASP A 191 " =    0.864
peak=    3.246 closest distance to " O   HOH Z 214 " =    1.849
peak=    3.246 closest distance to " O   HOH Z 175 " =    3.648
peak=    3.242 closest distance to " CB  ARG A  79 " =    1.606
peak=    3.241 closest distance to " NZ  LYS A  76 " =    1.204
peak=    3.239 closest distance to " O   HOH Z   9 " =    2.010
peak=    3.237 closest distance to " O   HOH Z  93 " =    2.853
peak=    3.236 closest distance to " CH2 TRP A 150 " =    1.122
peak=    3.231 closest distance to " CG2 VAL A 174 " =    1.356
peak=    3.227 closest distance to " O   HOH Z 197 " =    2.606
peak=    3.227 closest distance to " CA  LYS A  48 " =    1.461
peak=    3.221 closest distance to " O   HOH Z 302 " =    1.917
peak=    3.221 closest distance to " O   HOH Z 203 " =    1.745
peak=    3.219 closest distance to " O   HOH Z 148 " =    3.720
peak=    3.219 closest distance to " O   HOH Z 273 " =    2.864
peak=    3.218 closest distance to " CB  PHE A  16 " =    1.078
peak=    3.218 closest distance to " CH2 TRP A 123 " =    1.209
peak=    3.218 closest distance to " O   HOH Z 195 " =    1.945
peak=    3.218 closest distance to " CB  ARG A 259 " =    1.905
peak=    3.217 closest distance to " CA  ASN A 215 " =    1.275
peak=    3.216 closest distance to " O   HOH Z 407 " =    2.067
peak=    3.213 closest distance to " O   ARG A  56 " =    1.751
peak=    3.212 closest distance to " O   HOH Z  21 " =    1.843
peak=    3.211 closest distance to " CA  ALA A 295 " =    1.098
peak=    3.211 closest distance to " CG2 THR A 264 " =    0.918
peak=    3.205 closest distance to " O   HOH Z 407 " =    3.171
peak=    3.205 closest distance to " CA  ASP A 140 " =    1.277
peak=    3.204 closest distance to " O   HOH Z 287 " =    1.716
peak=    3.202 closest distance to " CZ  PHE A 192 " =    0.765
peak=    3.200 closest distance to " O   HOH Z 151 " =    1.656
peak=    3.197 closest distance to " OD2 ASP A 200 " =    1.398
peak=    3.196 closest distance to " O   HOH Z 257 " =    1.069
peak=    3.193 closest distance to " O   HOH Z  30 " =    2.282
peak=    3.188 closest distance to " O   HOH Z 216 " =    2.545
peak=    3.186 closest distance to " CE2 PHE A 204 " =    0.775
peak=    3.185 closest distance to " CD1 LEU A 101 " =    1.184
peak=    3.180 closest distance to " O   ASP A 124 " =    1.138
peak=    3.177 closest distance to " CB  ALA A 100 " =    1.511
peak=    3.173 closest distance to " CG2 VAL A 112 " =    0.759
peak=    3.170 closest distance to " O   SER A  26 " =    1.615
peak=    3.162 closest distance to " CB  ARG A  56 " =    1.143
peak=    3.161 closest distance to " CG1 VAL A 174 " =    1.144
peak=    3.159 closest distance to " O   HOH Z 222 " =    2.404
peak=    3.155 closest distance to " N   PHE A 130 " =    1.382
peak=    3.153 closest distance to " O   HOH Z 344 " =    1.206
peak=    3.152 closest distance to " CE  MET A  40 " =    1.031
peak=    3.138 closest distance to " N   GLN A 278 " =    0.953
peak=    3.129 closest distance to " O   HOH Z  78 " =    1.777
peak=    3.129 closest distance to " NE  ARG A 156 " =    1.043
peak=    3.126 closest distance to " O   HOH Z 141 " =    1.502
peak=    3.125 closest distance to " CB  THR A  31 " =    1.558
peak=    3.119 closest distance to " O   HOH Z 329 " =    3.762
peak=    3.108 closest distance to " OH  TYR A 214 " =    1.259
peak=    3.105 closest distance to " O   HOH Z 350 " =    1.410
peak=    3.101 closest distance to " CA  LYS A 117 " =    1.261
peak=    3.097 closest distance to " O   ALA A   1 " =    1.463
peak=    3.082 closest distance to " CE3 TRP A 274 " =    1.113
peak=    3.079 closest distance to " O   HOH Z 426 " =    3.091
peak=    3.078 closest distance to " CB  ASN A  39 " =    0.880
peak=    3.071 closest distance to " O   HOH Z  49 " =    2.455
peak=    3.063 closest distance to " O   HOH Z 392 " =    2.503
peak=    3.060 closest distance to " CG1 ILE A  49 " =    1.571
peak=    3.053 closest distance to " O   HOH Z 365 " =    5.863
peak=    3.050 closest distance to " O   HOH Z 334 " =    1.627
peak=    3.040 closest distance to " CD  LYS A 119 " =    2.228
peak=    3.038 closest distance to " O   HOH Z 383 " =    2.261
peak=    3.032 closest distance to " CB  GLN A 194 " =    0.886

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 198         
Filter by distance & map next to the model:
   mapped sites are within: 0.760 - 5.448
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 197 from: 198
   mapped sites are within: 0.760 - 5.448

peak=   -5.550 closest distance to " CD  ARG A 138 " =    1.083
peak=   -5.339 closest distance to " CG2 VAL A 230 " =    0.883
peak=   -4.893 closest distance to " O   HOH Z 102 " =    1.206
peak=   -4.520 closest distance to " O   HOH Z 231 " =    1.310
peak=   -4.347 closest distance to " O   HOH Z  19 " =    2.481
peak=   -4.179 closest distance to " CG  ARG A 138 " =    0.833
peak=   -4.162 closest distance to " O   HOH Z 198 " =    2.622
peak=   -4.145 closest distance to " OG ASER A 134 " =    1.235
peak=   -4.057 closest distance to " CA  SER A 271 " =    2.447
peak=   -4.052 closest distance to " OE1 GLN A  88 " =    0.946
peak=   -4.044 closest distance to " O   HOH Z 290 " =    1.037
peak=   -4.044 closest distance to " O   ILE A 109 " =    2.681
peak=   -4.033 closest distance to " O   HOH Z 377 " =    1.297
peak=   -3.964 closest distance to " CG  ASP A 231 " =    0.854
peak=   -3.919 closest distance to " O   HOH Z 388 " =    1.867
peak=   -3.915 closest distance to " O   HOH Z 266 " =    4.478
peak=   -3.913 closest distance to " CG1 VAL A 250 " =    2.655
peak=   -3.905 closest distance to " CB  GLN A  55 " =    1.223
peak=   -3.882 closest distance to " O   HOH Z  43 " =    1.526
peak=   -3.881 closest distance to " OG  SER A  87 " =    1.524
peak=   -3.869 closest distance to " CG  GLN A 223 " =    2.276
peak=   -3.861 closest distance to " CB  TYR A  15 " =    2.232
peak=   -3.849 closest distance to " C   ALA A 158 " =    1.276
peak=   -3.844 closest distance to " CD  GLN A  88 " =    0.876
peak=   -3.842 closest distance to " NH2 ARG A  66 " =    1.993
peak=   -3.831 closest distance to " O   HOH Z 166 " =    1.885
peak=   -3.813 closest distance to " CB  TRP A  85 " =    2.399
peak=   -3.791 closest distance to " O   HOH Z  13 " =    1.374
peak=   -3.791 closest distance to " O   HOH Z  71 " =    0.925
peak=   -3.789 closest distance to " C   ASN A 285 " =    2.571
peak=   -3.777 closest distance to " CG  ASN A  45 " =    1.755
peak=   -3.756 closest distance to " O   HOH Z 198 " =    2.161
peak=   -3.746 closest distance to " O   HOH Z 407 " =    3.393
peak=   -3.736 closest distance to " O   HOH Z 177 " =    1.200
peak=   -3.730 closest distance to " O   HOH Z 275 " =    1.635
peak=   -3.722 closest distance to " O   HOH Z 266 " =    4.786
peak=   -3.719 closest distance to " N   GLN A  58 " =    1.587
peak=   -3.718 closest distance to " O   PRO A 198 " =    1.268
peak=   -3.717 closest distance to " CD1 PHE A  59 " =    1.863
peak=   -3.713 closest distance to " CD  GLN A  88 " =    2.292
peak=   -3.697 closest distance to " NH1 ARG A  56 " =    2.411
peak=   -3.686 closest distance to " CD1 LEU A 101 " =    2.700
peak=   -3.678 closest distance to " O   HOH Z  98 " =    1.763
peak=   -3.674 closest distance to " O   HOH Z 222 " =    0.981
peak=   -3.663 closest distance to " CD  ARG A  14 " =    3.184
peak=   -3.661 closest distance to " CD  ARG A 156 " =    2.008
peak=   -3.641 closest distance to " CG1 VAL A 296 " =    1.427
peak=   -3.639 closest distance to " N   THR A 157 " =    1.599
peak=   -3.629 closest distance to " C   ASN A 187 " =    1.718
peak=   -3.620 closest distance to " O   HOH Z  52 " =    1.913
peak=   -3.617 closest distance to " CG  MET A 105 " =    0.928
peak=   -3.610 closest distance to " O   HOH Z 243 " =    1.572
peak=   -3.598 closest distance to " O   PRO A 163 " =    2.014
peak=   -3.596 closest distance to " OG BSER A 134 " =    1.307
peak=   -3.593 closest distance to " OG  SER A  97 " =    2.192
peak=   -3.586 closest distance to " O   HOH Z 184 " =    1.586
peak=   -3.583 closest distance to " CG2 VAL A 112 " =    2.613
peak=   -3.555 closest distance to " CD1 LEU A   5 " =    2.570
peak=   -3.541 closest distance to " OG1 THR A   4 " =    1.932
peak=   -3.531 closest distance to " O   HOH Z  17 " =    1.393
peak=   -3.528 closest distance to " N   ALA A  43 " =    2.380
peak=   -3.528 closest distance to " O   HOH Z 389 " =    1.755
peak=   -3.519 closest distance to " OD1 ASN A 249 " =    1.225
peak=   -3.517 closest distance to " CD  LYS A 289 " =    2.558
peak=   -3.498 closest distance to " CB  ALA A 227 " =    2.394
peak=   -3.489 closest distance to " CD1 LEU A 228 " =    2.488
peak=   -3.487 closest distance to " CD2 LEU A   5 " =    1.095
peak=   -3.481 closest distance to " N   ALA A   9 " =    1.468
peak=   -3.479 closest distance to " CD2 LEU A 167 " =    1.835
peak=   -3.477 closest distance to " CB  PRO A 163 " =    2.611
peak=   -3.477 closest distance to " O   GLY A 196 " =    1.235
peak=   -3.473 closest distance to " N   ALA A 226 " =    2.131
peak=   -3.471 closest distance to " CA  GLY A  98 " =    2.099
peak=   -3.469 closest distance to " O   GLY A 211 " =    1.409
peak=   -3.467 closest distance to " CG  GLU A 152 " =    2.246
peak=   -3.467 closest distance to " ND2 ASN A  45 " =    0.953
peak=   -3.460 closest distance to " CB  CYS A 254 " =    2.053
peak=   -3.441 closest distance to " OG1 THR A 178 " =    1.302
peak=   -3.441 closest distance to " O   HOH Z 341 " =    1.216
peak=   -3.439 closest distance to " CA  ARG A  56 " =    1.223
peak=   -3.438 closest distance to " CG  GLU A  53 " =    1.541
peak=   -3.435 closest distance to " O   ASN A  60 " =    0.962
peak=   -3.434 closest distance to " OXT GLY A 302 " =    3.624
peak=   -3.434 closest distance to " O   HOH Z 103 " =    1.899
peak=   -3.431 closest distance to " CG  PRO A 163 " =    2.452
peak=   -3.424 closest distance to " O   HOH Z 353 " =    2.432
peak=   -3.394 closest distance to " O   HOH Z 179 " =    0.760
peak=   -3.391 closest distance to " O   GLY A  80 " =    2.478
peak=   -3.391 closest distance to " CA  ASN A 127 " =    1.035
peak=   -3.390 closest distance to " CB  SER A  63 " =    3.362
peak=   -3.384 closest distance to " CG  TYR A 186 " =    2.215
peak=   -3.382 closest distance to " CE3 TRP A 150 " =    2.110
peak=   -3.382 closest distance to " O   HOH Z  63 " =    0.927
peak=   -3.380 closest distance to " O   HOH Z 252 " =    1.269
peak=   -3.376 closest distance to " O   HOH Z  98 " =    1.436
peak=   -3.374 closest distance to " O   HOH Z 366 " =    1.737
peak=   -3.373 closest distance to " CG2 VAL A 296 " =    1.920
peak=   -3.363 closest distance to " CA  GLY A 241 " =    2.219
peak=   -3.361 closest distance to " O   HOH Z 292 " =    4.537
peak=   -3.358 closest distance to " CB  TYR A 172 " =    2.377
peak=   -3.356 closest distance to " O   HOH Z 221 " =    1.453
peak=   -3.355 closest distance to " OG  SER A 206 " =    1.844
peak=   -3.353 closest distance to " CA  GLY A 133 " =    1.936
peak=   -3.339 closest distance to " O   GLN A 194 " =    1.253
peak=   -3.338 closest distance to " O   HOH Z 119 " =    2.583
peak=   -3.338 closest distance to " CE2 TYR A  30 " =    2.819
peak=   -3.329 closest distance to " CG2 ILE A 151 " =    2.613
peak=   -3.328 closest distance to " O   HOH Z 396 " =    1.562
peak=   -3.325 closest distance to " O   SER A 135 " =    1.443
peak=   -3.318 closest distance to " O   HOH Z 205 " =    0.937
peak=   -3.316 closest distance to " CB  ASN A  39 " =    1.908
peak=   -3.315 closest distance to " O   HOH Z 166 " =    1.491
peak=   -3.313 closest distance to " CZ  TYR A 169 " =    1.875
peak=   -3.308 closest distance to " O   HOH Z 151 " =    1.278
peak=   -3.306 closest distance to " O   HOH Z 213 " =    1.423
peak=   -3.304 closest distance to " O   HOH Z  38 " =    1.639
peak=   -3.303 closest distance to " NH2AARG A 275 " =    5.448
peak=   -3.302 closest distance to " CD  GLU A 236 " =    1.018
peak=   -3.299 closest distance to " CD2 LEU A 237 " =    2.747
peak=   -3.296 closest distance to " CE2 PHE A 283 " =    2.484
peak=   -3.296 closest distance to " O   HOH Z 368 " =    1.694
peak=   -3.292 closest distance to " C   HIS A 108 " =    1.041
peak=   -3.292 closest distance to " O   HOH Z  11 " =    1.635
peak=   -3.288 closest distance to " O   HOH Z 189 " =    2.483
peak=   -3.284 closest distance to " CB  PRO A  54 " =    2.374
peak=   -3.283 closest distance to " O   HOH Z  55 " =    2.554
peak=   -3.282 closest distance to " C   GLN A 240 " =    2.242
peak=   -3.282 closest distance to " CB  ALA A  43 " =    2.518
peak=   -3.280 closest distance to " CD  ARG A 139 " =    1.735
peak=   -3.279 closest distance to " O   ALA A 158 " =    0.994
peak=   -3.278 closest distance to " O   HOH Z 317 " =    2.317
peak=   -3.277 closest distance to " O   HOH Z 210 " =    1.051
peak=   -3.268 closest distance to " OD2 ASP A 171 " =    1.833
peak=   -3.265 closest distance to " CE  MET A 105 " =    2.081
peak=   -3.262 closest distance to " O   HOH Z 186 " =    1.313
peak=   -3.261 closest distance to " O   HOH Z 298 " =    1.260
peak=   -3.259 closest distance to " CZ  PHE A 130 " =    0.963
peak=   -3.254 closest distance to " CH2 TRP A 179 " =    1.275
peak=   -3.253 closest distance to " CG  GLU A 277 " =    1.244
peak=   -3.248 closest distance to " O   HOH Z 221 " =    1.601
peak=   -3.247 closest distance to " SG ACYS A 201 " =    1.132
peak=   -3.244 closest distance to " O   HOH Z 128 " =    4.063
peak=   -3.241 closest distance to " O   HOH Z 306 " =    2.930
peak=   -3.238 closest distance to " O   HOH Z 431 " =    1.499
peak=   -3.237 closest distance to " OD2 ASP A  50 " =    1.733
peak=   -3.235 closest distance to " O   TYR A  30 " =    2.735
peak=   -3.234 closest distance to " O   HOH Z 411 " =    3.501
peak=   -3.233 closest distance to " O   HOH Z  60 " =    2.012
peak=   -3.231 closest distance to " OG BSER A 134 " =    1.831
peak=   -3.225 closest distance to " O   HOH Z 350 " =    1.742
peak=   -3.224 closest distance to " CB  ALA A 248 " =    1.905
peak=   -3.223 closest distance to " SG  CYS A 254 " =    2.969
peak=   -3.221 closest distance to " C   GLU A  46 " =    1.163
peak=   -3.217 closest distance to " O   ASN A 301 " =    1.857
peak=   -3.211 closest distance to " CA  ASN A 142 " =    1.312
peak=   -3.205 closest distance to " O   HOH Z 274 " =    2.660
peak=   -3.202 closest distance to " CG  TRP A 266 " =    1.638
peak=   -3.198 closest distance to " OH  TYR A 172 " =    1.613
peak=   -3.189 closest distance to " O   HOH Z 211 " =    1.656
peak=   -3.179 closest distance to " O   GLY A 203 " =    2.458
peak=   -3.178 closest distance to " N   VAL A 125 " =    0.894
peak=   -3.176 closest distance to " ND2 ASN A  60 " =    1.646
peak=   -3.175 closest distance to " O   HOH Z 124 " =    1.181
peak=   -3.174 closest distance to " O   ALA A   7 " =    1.643
peak=   -3.171 closest distance to " CB  ALA A 291 " =    2.242
peak=   -3.170 closest distance to " CB  ILE A 239 " =    2.067
peak=   -3.170 closest distance to " O   HOH Z  97 " =    1.854
peak=   -3.164 closest distance to " CE3 TRP A  70 " =    1.797
peak=   -3.163 closest distance to " O   HOH Z 295 " =    1.377
peak=   -3.156 closest distance to " CD2 TYR A 293 " =    2.065
peak=   -3.153 closest distance to " O   HOH Z 387 " =    3.515
peak=   -3.149 closest distance to " OH  TYR A 214 " =    1.272
peak=   -3.146 closest distance to " C   ALA A 165 " =    1.966
peak=   -3.139 closest distance to " O   HOH Z 417 " =    2.644
peak=   -3.133 closest distance to " OD1 ASN A 148 " =    1.605
peak=   -3.132 closest distance to " CB  ALA A   9 " =    2.710
peak=   -3.132 closest distance to " OG1 THR A  82 " =    2.123
peak=   -3.131 closest distance to " OE1 GLN A  88 " =    1.302
peak=   -3.128 closest distance to " O   HOH Z 149 " =    2.145
peak=   -3.118 closest distance to " N   GLY A  23 " =    2.129
peak=   -3.115 closest distance to " O   HOH Z 112 " =    1.362
peak=   -3.098 closest distance to " O   HOH Z 410 " =    1.770
peak=   -3.098 closest distance to " O   HOH Z 393 " =    4.633
peak=   -3.094 closest distance to " CB  PRO A 243 " =    2.675
peak=   -3.094 closest distance to " CG  ARG A 259 " =    2.749
peak=   -3.084 closest distance to " O   HOH Z 322 " =    0.889
peak=   -3.075 closest distance to " C   PRO A 213 " =    1.286
peak=   -3.073 closest distance to " CB  ALA A   8 " =    2.616
peak=   -3.069 closest distance to " O   HOH Z  10 " =    1.520
peak=   -3.068 closest distance to " CE2 PHE A 218 " =    2.621
peak=   -3.068 closest distance to " CG  GLU A   2 " =    2.038
peak=   -3.057 closest distance to " O   HOH Z 430 " =    1.660
peak=   -3.045 closest distance to " N   LEU A 261 " =    1.400
peak=   -3.044 closest distance to " O   HOH Z 310 " =    1.863
peak=   -3.043 closest distance to " OG  SER A  62 " =    4.464
peak=   -3.038 closest distance to " CD2 LEU A 237 " =    2.536
peak=   -2.901 closest distance to " O   HOH Z 102 " =    1.550

================= 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    :  0.4830 0.4847   6.283838e+00   6.278939e+00
   1_bss:  0.4748 0.4727   6.280126e+00   6.271413e+00
   1_xyz:  0.4010 0.4300   6.183442e+00   6.224880e+00
   1_adp:  0.3583 0.4119   6.114838e+00   6.202617e+00
   1_occ:  0.3573 0.4126   6.114314e+00   6.202465e+00
   2_bss:  0.3547 0.4094   6.113567e+00   6.200454e+00
   2_xyz:  0.2812 0.3464   5.938529e+00   6.085025e+00
   2_adp:  0.2619 0.3247   5.885957e+00   6.042443e+00
   2_occ:  0.2618 0.3247   5.885380e+00   6.042287e+00
   3_bss:  0.2609 0.3214   5.883642e+00   6.039260e+00
   3_xyz:  0.1858 0.2432   5.588489e+00   5.793030e+00
   3_adp:  0.1675 0.2220   5.498011e+00   5.712469e+00
   3_occ:  0.1673 0.2217   5.497389e+00   5.711559e+00
   4_bss:  0.1668 0.2206   5.496462e+00   5.708580e+00
   4_xyz:  0.1402 0.1899   5.341314e+00   5.567634e+00
   4_adp:  0.1324 0.1852   5.305107e+00   5.541634e+00
   4_occ:  0.1323 0.1850   5.304258e+00   5.540806e+00
   5_bss:  0.1325 0.1854   5.305544e+00   5.542679e+00
   5_xyz:  0.1254 0.1770   5.257470e+00   5.497662e+00
   5_adp:  0.1241 0.1748   5.246264e+00   5.485437e+00
   5_occ:  0.1240 0.1746   5.245406e+00   5.484400e+00
   5_bss:  0.1240 0.1746   5.245408e+00   5.484413e+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:  0.320   3.865  10.133   7.319   8.725   0.000   0.000   0.000
   1_xyz:  0.320   3.865  10.133   7.319   8.725   0.000   0.000   0.000
   1_adp:  0.320   3.865  10.133   7.319   8.725   0.000   0.000   0.000
   1_occ:  0.320   3.865  10.133   7.319   8.725   0.000   0.000   0.000
   2_bss:  0.330  32.168   5.991   3.858   5.705   0.000   0.000   0.000
   2_xyz:  0.330  32.168   5.991   3.858   5.705   0.000   0.000   0.000
   2_adp:  0.330  32.168   5.991   3.858   5.705   0.000   0.000   0.000
   2_occ:  0.330  32.168   5.991   3.858   5.705   0.000   0.000   0.000
   3_bss:  0.331  41.386   3.723   2.515   3.775   0.000   0.000   0.000
   3_xyz:  0.331  41.386   3.723   2.515   3.775   0.000   0.000   0.000
   3_adp:  0.331  41.386   3.723   2.515   3.775   0.000   0.000   0.000
   3_occ:  0.331  41.386   3.723   2.515   3.775   0.000   0.000   0.000
   4_bss:  0.326  45.723   2.309   1.592   2.208   0.000   0.000   0.000
   4_xyz:  0.326  45.723   2.309   1.592   2.208   0.000   0.000   0.000
   4_adp:  0.326  45.723   2.309   1.592   2.208   0.000   0.000   0.000
   4_occ:  0.326  45.723   2.309   1.592   2.208   0.000   0.000   0.000
   5_bss:  0.328  51.105   1.869   1.306   1.843   0.000   0.000   0.000
   5_xyz:  0.328  51.105   1.869   1.306   1.843   0.000   0.000   0.000
   5_adp:  0.328  51.105   1.869   1.306   1.843   0.000   0.000   0.000
   5_occ:  0.328  51.105   1.869   1.306   1.843   0.000   0.000   0.000
   5_bss:  0.324  51.144   0.160  -0.305   0.145   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  59.372 0.4018  0.4785    74185.932
   1_bss:  60.041 0.3908  0.5875    71276.636
   1_xyz:  52.242 0.4896  0.7264    56647.763
   1_adp:  48.463 0.5374  0.8403    51155.996
   1_occ:  48.596 0.5356  0.8361    51308.852
   2_bss:  48.203 0.5405  0.7533    50815.223
   2_xyz:  38.458 0.6591  0.9050    34446.697
   2_adp:  35.368 0.6959  0.9465    30305.806
   2_occ:  35.335 0.6963  0.9467    30262.050
   3_bss:  35.074 0.6989  0.8894    29876.187
   3_xyz:  24.440 0.8166  0.9926    15666.279
   3_adp:  21.792 0.8442  1.0118    13105.916
   3_occ:  21.770 0.8444  1.0119    13081.519
   4_bss:  21.634 0.8456  0.9667    12958.878
   4_xyz:  18.010 0.8802  0.9830     9375.577
   4_adp:  17.382 0.8861  0.9809     8875.664
   4_occ:  17.360 0.8863  0.9809     8846.689
   5_bss:  17.394 0.8861  0.9682     8907.053
   5_xyz:  16.317 0.8957  0.9737     8024.168
   5_adp:  15.955 0.8991  0.9738     7829.160
   5_occ:  15.934 0.8993  0.9739     7810.963
   5_bss:  15.937 0.8993  0.9731     7811.803
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3746e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3746e+01
   1_xyz:   1.709  0.013  0.109 18.376  0.007  4.111   1.4529e-01
   1_adp:   1.709  0.013  0.109 18.376  0.007  4.111   1.4529e-01
   1_occ:   1.709  0.013  0.109 18.376  0.007  4.111   1.4529e-01
   2_bss:   1.709  0.013  0.109 18.376  0.007  4.111   1.4529e-01
   2_xyz:   1.143  0.008  0.076 16.494  0.004  4.111   7.9359e-02
   2_adp:   1.143  0.008  0.076 16.494  0.004  4.111   7.9359e-02
   2_occ:   1.143  0.008  0.076 16.494  0.004  4.111   7.9359e-02
   3_bss:   1.143  0.008  0.076 16.494  0.004  4.111   7.9359e-02
   3_xyz:   1.130  0.008  0.081 15.755  0.004  4.130   7.4657e-02
   3_adp:   1.130  0.008  0.081 15.755  0.004  4.130   7.4657e-02
   3_occ:   1.130  0.008  0.081 15.755  0.004  4.130   7.4657e-02
   4_bss:   1.130  0.008  0.081 15.755  0.004  4.130   7.4657e-02
   4_xyz:   1.007  0.007  0.075 15.540  0.003  4.120   6.2340e-02
   4_adp:   1.007  0.007  0.075 15.540  0.003  4.120   6.2340e-02
   4_occ:   1.007  0.007  0.075 15.540  0.003  4.120   6.2340e-02
   5_bss:   1.007  0.007  0.075 15.540  0.003  4.120   6.2340e-02
   5_xyz:   0.968  0.006  0.071 15.432  0.003  4.124   5.7892e-02
   5_adp:   0.968  0.006  0.071 15.432  0.003  4.124   5.7892e-02
   5_occ:   0.968  0.006  0.071 15.432  0.003  4.124   5.7892e-02
   5_bss:   0.968  0.006  0.071 15.432  0.003  4.124   5.7892e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9675e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9675e+00
   1_xyz:  14.085  0.174  0.462 84.575  0.049  2.149   1.0174e-01
   1_adp:  14.085  0.174  0.462 84.575  0.049  2.149   1.0174e-01
   1_occ:  14.085  0.174  0.462 84.575  0.049  2.149   1.0174e-01
   2_bss:  14.085  0.174  0.462 84.575  0.049  2.149   1.0174e-01
   2_xyz:   8.057  0.084  0.300 81.861  0.030  2.254   5.9506e-02
   2_adp:   8.057  0.084  0.300 81.861  0.030  2.254   5.9506e-02
   2_occ:   8.057  0.084  0.300 81.861  0.030  2.254   5.9506e-02
   3_bss:   8.057  0.084  0.300 81.861  0.030  2.254   5.9506e-02
   3_xyz:   8.384  0.062  0.332 79.526  0.022  2.321   6.2466e-02
   3_adp:   8.384  0.062  0.332 79.526  0.022  2.321   6.2466e-02
   3_occ:   8.384  0.062  0.332 79.526  0.022  2.321   6.2466e-02
   4_bss:   8.384  0.062  0.332 79.526  0.022  2.321   6.2466e-02
   4_xyz:   8.436  0.052  0.317 81.257  0.032  2.340   3.9515e-02
   4_adp:   8.436  0.052  0.317 81.257  0.032  2.340   3.9515e-02
   4_occ:   8.436  0.052  0.317 81.257  0.032  2.340   3.9515e-02
   5_bss:   8.436  0.052  0.317 81.257  0.032  2.340   3.9515e-02
   5_xyz:   8.034  0.050  0.336 84.702  0.029  2.378   5.0465e-02
   5_adp:   8.034  0.050  0.336 84.702  0.029  2.378   5.0465e-02
   5_occ:   8.034  0.050  0.336 84.702  0.029  2.378   5.0465e-02
   5_bss:   8.034  0.050  0.336 84.702  0.029  2.378   5.0465e-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:  96.22   0.00  13.62  96.22   0.00  11.29  80.80   0.00  26.33
   1_occ:  96.22   0.00  13.62  96.22   0.00  11.29  80.80   0.00  26.33
   2_bss:  96.22   0.00  13.62  96.22   0.00  11.29  80.80   0.00  26.33
   2_xyz:  96.22   0.00  13.62  96.22   0.00  11.29  80.80   0.00  26.33
   2_adp:  90.06   0.00  13.45  90.06   0.00  10.06  80.56   0.00  31.89
   2_occ:  90.06   0.00  13.45  90.06   0.00  10.06  80.56   0.00  31.89
   3_bss:  90.06   0.00  13.45  90.06   0.00  10.06  80.56   0.00  31.89
   3_xyz:  90.06   0.00  13.45  90.06   0.00  10.06  80.56   0.00  31.89
   3_adp:  89.14   0.00  13.78  89.14   0.00   9.55  83.88   1.74  36.78
   3_occ:  89.14   0.00  13.78  89.14   0.00   9.55  83.88   1.74  36.78
   4_bss:  89.14   0.00  13.78  89.14   0.00   9.55  83.88   1.74  36.78
   4_xyz:  89.14   0.00  13.78  89.14   0.00   9.55  83.88   1.74  36.78
   4_adp: 101.06   0.00  14.34 101.06   0.00   9.56  91.89   2.58  40.35
   4_occ: 101.06   0.00  14.34 101.06   0.00   9.56  91.89   2.58  40.35
   5_bss: 101.06   0.00  14.34 101.06   0.00   9.56  91.89   2.58  40.35
   5_xyz: 101.06   0.00  14.34 101.06   0.00   9.56  91.89   2.58  40.35
   5_adp: 103.05   0.00  14.01 103.05   0.00   9.45  92.94   2.60  38.83
   5_occ: 103.05   0.00  14.01 103.05   0.00   9.45  92.94   2.60  38.83
   5_bss: 104.70   1.65  15.66 104.70   1.65  11.11  94.59   4.26  40.48
------------------------------------------------------------------------
 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:    1.237    0.033    0.411
   1_adp:    1.237    0.033    0.411
   1_occ:    1.237    0.033    0.411
   2_bss:    1.237    0.033    0.411
   2_xyz:    1.680    0.049    0.564
   2_adp:    1.680    0.049    0.564
   2_occ:    1.680    0.049    0.564
   3_bss:    1.680    0.049    0.564
   3_xyz:    1.699    0.047    0.672
   3_adp:    1.699    0.047    0.672
   3_occ:    1.699    0.047    0.672
   4_bss:    1.699    0.047    0.672
   4_xyz:    1.771    0.044    0.724
   4_adp:    1.771    0.044    0.724
   4_occ:    1.771    0.044    0.724
   5_bss:    1.771    0.044    0.724
   5_xyz:    1.935    0.037    0.746
   5_adp:    1.935    0.037    0.746
   5_occ:    1.935    0.037    0.746
   5_bss:    1.935    0.037    0.746
------------------------------------------------------------------------

CPU time actual refinement: 336.21


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1266/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_1266/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1266/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1266/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1266/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 336.05 
  Macro-tasks:
    bulk solvent and scale       = 41.39  
    individual site refinement   = 134.82 
    weights calculation          = 31.86  
    collect and process          = 6.35   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 214.53 
  Micro-tasks:
    mask                            = 2.39   
    f_calc                          = 105.98 
    alpha_beta                      = 8.02   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 114.30 
    fmodel                         = 6.73   
    r_factors                      = 0.25   
    phase_errors                   = 10.42  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 249.52 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.797 micro seconds
Total CPU time: 5.83 minutes
from_scatterers_fft:    633 calls, 105.73 s
gradients_fft:          578 calls, 101.71 s

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

# Date 2008-01-16 Time 03:36:54 PST -0800 (1200483414.86 s)
Start R-work = 0.4830, R-free = 0.4847 (no bulk solvent and anisotropic scale)
Final R-work = 0.1403, R-free = 0.1916 (no bulk solvent and anisotropic scale)

Start R-work = 0.4748, R-free = 0.4727
Final R-work = 0.1240, R-free = 0.1746