# Date 2008-01-16 Time 01:09:45 PST -0800 (1200474585.35 s)
#phil __OFF__

Command line arguments: "../306.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 22010
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 306

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 46.93, 88.1178, 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: 3.29, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 46.93, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.906 1.97083
Completeness in resolution range: 0.939746
Completeness with d_max=infinity: 0.936869

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9060
                             d_min =   1.9708

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 46.93, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.906 1.97083
Completeness in resolution range: 0.939746
Completeness with d_max=infinity: 0.936869

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9064 -  4.2170 [2195/2222]  1974   221  10.1%
  bin  2:  4.2170 -  3.3598 [2097/2113]  1883   214  10.2%
  bin  3:  3.3598 -  2.9388 [2078/2097]  1877   201   9.7%
  bin  4:  2.9388 -  2.6717 [2054/2084]  1847   207  10.1%
  bin  5:  2.6717 -  2.4812 [2029/2048]  1824   205  10.1%
  bin  6:  2.4812 -  2.3355 [2033/2069]  1828   205  10.1%
  bin  7:  2.3355 -  2.2189 [2023/2056]  1829   194   9.6%
  bin  8:  2.2189 -  2.1226 [2021/2056]  1808   213  10.5%
  bin  9:  2.1226 -  2.0411 [2016/2043]  1820   196   9.7%
  bin 10:  2.0411 -  1.9708 [1043/2057]   940   103   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_306/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:
        1.39 -     2.10: 13
        2.10 -     2.80: 710
        2.80 -     3.50: 4447
        3.50 -     4.20: 9329
        4.20 -     4.90: 13782
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.394 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.538 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.660 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.743 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.776 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28276 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_306/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_306/model_refine_001.geo

CPU time processing inputs: 9.22


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 46.93 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4675   r_free= 0.4533   ksol= 0.00   Bsol= 0.00   scale= 0.801    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.269721                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9064 -  4.7033 0.99   1421  158 0.3757 0.3591      6.5715      6.5373|
|  2:  4.7033 -  3.7528 0.99   1375  153 0.3661 0.4108      6.7093      6.8377|
|  3:  3.7528 -  3.2842 0.99   1337  148 0.4343 0.3853      6.6492      6.6083|
|  4:  3.2842 -  2.9866 0.99   1335  144 0.4575 0.4664      6.4978      6.4724|
|  5:  2.9866 -  2.7740 0.99   1310  153 0.4923 0.4761      6.3488       6.375|
|  6:  2.7740 -  2.6113 0.99   1329  145 0.4935 0.5364      6.2675      6.2086|
|  7:  2.6113 -  2.4812 0.99   1298  147 0.4948 0.4838      6.2186       6.148|
|  8:  2.4812 -  2.3736 0.98   1314  142 0.5236 0.4696      6.1865      6.1546|
|  9:  2.3736 -  2.2826 0.98   1315  145 0.5281 0.4796      6.1241      6.1324|
| 10:  2.2826 -  2.2041 0.98   1291  138 0.5284 0.4703      6.1084      6.0761|
| 11:  2.2041 -  2.1354 1.00   1307  158 0.5155 0.5269      6.0191      6.0359|
| 12:  2.1354 -  2.0745 0.97   1288  133 0.5268 0.4685      5.9556      5.9631|
| 13:  2.0745 -  2.0200 0.94   1242  138 0.5291 0.4907      5.8965      5.8149|
| 14:  2.0200 -  1.9708 0.36    468   57 0.4948 0.4193      5.8967      5.7152|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9064 -  4.7033  1421   158  0.72  32.48   0.81     0.73      64584.94|
|  2:  4.7033 -  3.7528  1375   153  0.72  33.16   0.89     0.78      95255.61|
|  3:  3.7528 -  3.2842  1337   148  0.64  40.91   0.84     0.74     100744.61|
|  4:  3.2842 -  2.9866  1335   144  0.55  48.26   0.80     0.63      91141.57|
|  5:  2.9866 -  2.7740  1310   153  0.44  57.00   0.75     0.51      78652.80|
|  6:  2.7740 -  2.6113  1329   145  0.38  61.54   0.72     0.44      73344.87|
|  7:  2.6113 -  2.4812  1298   147  0.38  61.44   0.75     0.44      65507.59|
|  8:  2.4812 -  2.3736  1314   142  0.42  58.71   0.73     0.49      54433.23|
|  9:  2.3736 -  2.2826  1315   145  0.45  56.05   0.72     0.54      47500.78|
| 10:  2.2826 -  2.2041  1291   138  0.46  55.48   0.73     0.53      40961.64|
| 11:  2.2041 -  2.1354  1307   158  0.41  59.23   0.76     0.52      42696.90|
| 12:  2.1354 -  2.0745  1288   133  0.40  60.39   0.75     0.50      38664.58|
| 13:  2.0745 -  2.0200  1242   138  0.41  59.47   0.73     0.51      33467.77|
| 14:  2.0200 -  1.9708   468    57  0.51  51.17   0.77     0.52      22551.16|
|alpha:            min =        0.44 max =            0.78 mean =         0.57|
|beta:             min =    22551.16 max =       100744.61 mean =     62918.70|
|figures of merit: min =        0.00 max =            1.00 mean =         0.49|
|phase err.(work): min =        0.00 max =           89.98 mean =        52.33|
|phase err.(test): min =        0.00 max =           89.94 mean =        52.64|
|-----------------------------------------------------------------------------|

============================== 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 = 10.946206             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.112   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.864976              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.002   (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:        6 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       24 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      175 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      701 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1509 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2613 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3935 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5075 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6542 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7729 |
|-----------------------------------------------------------------------------|
|-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 |       53.762 |
| 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 |       2.052 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.858)------------------------------------------|
|    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 = 11.858)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4743   r_free= 0.4563   ksol= 0.00   Bsol= 0.00   scale= 0.770    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.272659                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4574   r_free= 0.4446   ksol= 0.34   Bsol= 11.31   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.63,7.64,11.62,0.00,0.00,0.00); trace/3= 8.97                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.259913                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.862320              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.438   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.859118              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 74.928   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4574      final r-factor (work) = 0.3678          |
| start r-factor (free) = 0.4446      final r-factor (free) = 0.3853          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 84.6821 = 9.86 * 0.50 * 6.2703 + 1.00 * 53.7624                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.4960 = 9.86 * 0.50 * 6.1572 + 1.00 * 0.1337                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3678      final r-factor (work) = 0.3184          |
| start r-factor (free) = 0.3853      final r-factor (free) = 0.3607          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3042 = 0.86 * 1.00 * 6.1572 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2036 = 0.86 * 1.00 * 6.0405 + 1.00 * 0.0141                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.858)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    68.07   12.41    None  None   None       |
|    all(noH): 2823   0      0.00    68.07   12.41    None  None   None       |
|    Sol.    : 438    0      0.00    68.07   26.81    None  None   None       |
|    Mac.    : 2385   0      0.00    60.11   9.77     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.807: 1122   |   5:    34.033 -  40.840:   75        |
|      1:     6.807 -  13.613:  745   |   6:    40.840 -  47.646:   48        |
|      2:    13.613 -  20.420:  414   |   7:    47.646 -  54.453:   38        |
|      3:    20.420 -  27.226:  227   |   8:    54.453 -  61.259:    8        |
|      4:    27.226 -  34.033:  142   |   9:    61.259 -  68.066:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3184 r_free = 0.3607             target_work(ml) = 6.014         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3180 r_free = 0.3617             target_work(ml) = 6.013         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3180   r_free= 0.3617   ksol= 0.34   Bsol= 11.31   scale= 1.110   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.63,7.64,11.62,0.00,0.00,0.00); trace/3= 8.97                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 6.012783                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3132   r_free= 0.3567   ksol= 0.34   Bsol= 40.06   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.77,3.69,7.61,0.00,0.00,0.00); trace/3= 5.03                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 6.012750                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.436630              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.829   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.398646              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 120.010  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3132      final r-factor (work) = 0.2267          |
| start r-factor (free) = 0.3567      final r-factor (free) = 0.2742          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.5351 = 4.44 * 0.50 * 6.0412 + 1.00 * 0.1337                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.0902 = 4.44 * 0.50 * 5.8690 + 1.00 * 0.0710                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2267      final r-factor (work) = 0.2068          |
| start r-factor (free) = 0.2742      final r-factor (free) = 0.2585          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3539 = 0.40 * 1.00 * 5.8690 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2802 = 0.40 * 1.00 * 5.6901 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.858)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    67.40   12.56    None  None   None       |
|    all(noH): 2823   0      0.00    67.40   12.56    None  None   None       |
|    Sol.    : 438    0      0.00    67.40   32.59    None  None   None       |
|    Mac.    : 2385   0      0.00    63.11   8.88     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.740: 1195   |   5:    33.700 -  40.440:  113        |
|      1:     6.740 -  13.480:  780   |   6:    40.440 -  47.180:   79        |
|      2:    13.480 -  20.220:  337   |   7:    47.180 -  53.920:   46        |
|      3:    20.220 -  26.960:  125   |   8:    53.920 -  60.660:   19        |
|      4:    26.960 -  33.700:  120   |   9:    60.660 -  67.400:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2068 r_free = 0.2585             target_work(ml) = 5.663         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2066 r_free = 0.2583             target_work(ml) = 5.663         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2066   r_free= 0.2583   ksol= 0.34   Bsol= 40.06   scale= 1.051   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.77,3.69,7.61,0.00,0.00,0.00); trace/3= 5.03                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.663010                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2045   r_free= 0.2577   ksol= 0.32   Bsol= 48.01   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.94,2.59,4.92,0.00,0.00,0.00); trace/3= 3.15                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.661860                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.770745              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.219  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.491259              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 117.030  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2045      final r-factor (work) = 0.1456          |
| start r-factor (free) = 0.2577      final r-factor (free) = 0.1943          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.6657 = 4.77 * 0.50 * 5.6993 + 1.00 * 0.0708                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.2577 = 4.77 * 0.50 * 5.5259 + 1.00 * 0.0764                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1456      final r-factor (work) = 0.1332          |
| start r-factor (free) = 0.1943      final r-factor (free) = 0.1821          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7277 = 0.49 * 1.00 * 5.5259 + 1.00 * 0.0130                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6272 = 0.49 * 1.00 * 5.3237 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.858)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    69.73   12.71    None  None   None       |
|    all(noH): 2823   0      0.00    69.73   12.71    None  None   None       |
|    Sol.    : 438    0      1.77    67.84   35.35    None  None   None       |
|    Mac.    : 2385   0      0.00    69.73   8.55     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 -   6.973: 1323   |   5:    34.866 -  41.839:  103        |
|      1:     6.973 -  13.946:  769   |   6:    41.839 -  48.812:  100        |
|      2:    13.946 -  20.919:  235   |   7:    48.812 -  55.785:   54        |
|      3:    20.919 -  27.893:  107   |   8:    55.785 -  62.758:   27        |
|      4:    27.893 -  34.866:   95   |   9:    62.758 -  69.731:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1332 r_free = 0.1821             target_work(ml) = 5.293         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1331 r_free = 0.1818             target_work(ml) = 5.292         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1331   r_free= 0.1818   ksol= 0.32   Bsol= 48.01   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.94,2.59,4.92,0.00,0.00,0.00); trace/3= 3.15                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.291839                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1333   r_free= 0.1821   ksol= 0.33   Bsol= 52.89   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.43,2.17,4.07,0.00,0.00,0.00); trace/3= 2.55                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.293362                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.971350              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 128.815  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.292913              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.771   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1333      final r-factor (work) = 0.1243          |
| start r-factor (free) = 0.1821      final r-factor (free) = 0.1694          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3285 = 1.97 * 0.50 * 5.3281 + 1.00 * 0.0768                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2515 = 1.97 * 0.50 * 5.2682 + 1.00 * 0.0588                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1243      final r-factor (work) = 0.1216          |
| start r-factor (free) = 0.1694      final r-factor (free) = 0.1684          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8245 = 1.29 * 1.00 * 5.2682 + 1.00 * 0.0132                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8112 = 1.29 * 1.00 * 5.2256 + 1.00 * 0.0550                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.858)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.74   13.04    None  None   None       |
|    all(noH): 2823   0      0.00    86.74   13.04    None  None   None       |
|    Sol.    : 438    0      0.95    80.16   37.24    None  None   None       |
|    Mac.    : 2385   0      0.00    86.74   8.60     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 -   8.674: 1628   |   5:    43.368 -  52.041:  108        |
|      1:     8.674 -  17.347:  602   |   6:    52.041 -  60.715:   67        |
|      2:    17.347 -  26.021:  170   |   7:    60.715 -  69.388:   26        |
|      3:    26.021 -  34.694:  112   |   8:    69.388 -  78.062:   11        |
|      4:    34.694 -  43.368:   97   |   9:    78.062 -  86.735:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1216 r_free = 0.1684             target_work(ml) = 5.224         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1214 r_free = 0.1686             target_work(ml) = 5.224         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1214   r_free= 0.1686   ksol= 0.33   Bsol= 52.89   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.43,2.17,4.07,0.00,0.00,0.00); trace/3= 2.55                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.223502                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1213   r_free= 0.1685   ksol= 0.33   Bsol= 52.89   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.58,2.32,4.07,0.00,0.00,0.00); trace/3= 2.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.223643                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.495705              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 139.856  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.932839              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.445   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1213      final r-factor (work) = 0.1193          |
| start r-factor (free) = 0.1685      final r-factor (free) = 0.1656          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9664 = 1.50 * 0.50 * 5.2252 + 1.00 * 0.0587                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9549 = 1.50 * 0.50 * 5.2156 + 1.00 * 0.0544                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1193      final r-factor (work) = 0.1184          |
| start r-factor (free) = 0.1656      final r-factor (free) = 0.1661          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.3250 = 2.93 * 1.00 * 5.2156 + 1.00 * 0.0285                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 15.2774 = 2.93 * 1.00 * 5.2039 + 1.00 * 0.0152                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.858)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.79   13.03    None  None   None       |
|    all(noH): 2823   0      0.00    92.79   13.03    None  None   None       |
|    Sol.    : 438    0      0.95    92.79   37.62    None  None   None       |
|    Mac.    : 2385   0      0.00    89.15   8.52     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.279: 1728   |   5:    46.396 -  55.675:   81        |
|      1:     9.279 -  18.558:  531   |   6:    55.675 -  64.954:   59        |
|      2:    18.558 -  27.837:  171   |   7:    64.954 -  74.233:   22        |
|      3:    27.837 -  37.117:  117   |   8:    74.233 -  83.512:   14        |
|      4:    37.117 -  46.396:   97   |   9:    83.512 -  92.791:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1184 r_free = 0.1661             target_work(ml) = 5.206         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1183 r_free = 0.1661             target_work(ml) = 5.206         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1183   r_free= 0.1661   ksol= 0.33   Bsol= 52.89   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.58,2.32,4.07,0.00,0.00,0.00); trace/3= 2.66                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.206027                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9064 -  4.7033 0.99   1421  158 0.1029 0.1370      5.4365      5.5998|
|  2:  4.7033 -  3.7528 0.99   1375  153 0.0869 0.1109      5.4602      5.6577|
|  3:  3.7528 -  3.2842 0.99   1337  148 0.1121 0.1554       5.514      5.8439|
|  4:  3.2842 -  2.9866 0.99   1335  144 0.1263 0.1704      5.4776      5.6661|
|  5:  2.9866 -  2.7740 0.99   1310  153 0.1359 0.1587      5.3634       5.533|
|  6:  2.7740 -  2.6113 0.99   1329  145 0.1321 0.2246       5.266      5.5749|
|  7:  2.6113 -  2.4812 0.99   1298  147 0.1356 0.1715      5.2309      5.3689|
|  8:  2.4812 -  2.3736 0.98   1314  142 0.1212 0.1808      5.1352      5.3686|
|  9:  2.3736 -  2.2826 0.98   1315  145 0.1253 0.2093      5.0872      5.4248|
| 10:  2.2826 -  2.2041 0.98   1291  138 0.1215 0.1629      5.0241      5.2074|
| 11:  2.2041 -  2.1354 1.00   1307  158 0.1256 0.2059      5.0021      5.3681|
| 12:  2.1354 -  2.0745 0.97   1288  133 0.1267 0.1661      4.9569      5.1698|
| 13:  2.0745 -  2.0200 0.94   1242  138 0.1165 0.1871      4.8351      5.0656|
| 14:  2.0200 -  1.9708 0.36    468   57 0.1012 0.1807      4.6993      4.9889|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9064 -  4.7033  1421   158  0.93   9.95   0.97     0.94       8230.92|
|  2:  4.7033 -  3.7528  1375   153  0.95   8.50   1.01     1.00       9762.15|
|  3:  3.7528 -  3.2842  1337   148  0.93  11.99   1.03     1.03      11132.74|
|  4:  3.2842 -  2.9866  1335   144  0.92  14.00   1.01     1.00      10810.84|
|  5:  2.9866 -  2.7740  1310   153  0.89  16.70   1.00     0.98       9198.41|
|  6:  2.7740 -  2.6113  1329   145  0.88  17.81   0.98     0.95       8021.91|
|  7:  2.6113 -  2.4812  1298   147  0.90  16.66   0.98     0.94       6915.90|
|  8:  2.4812 -  2.3736  1314   142  0.90  16.61   0.99     0.95       6257.56|
|  9:  2.3736 -  2.2826  1315   145  0.89  17.25   1.00     0.96       5767.62|
| 10:  2.2826 -  2.2041  1291   138  0.89  17.52   0.99     0.95       5175.81|
| 11:  2.2041 -  2.1354  1307   158  0.88  18.06   0.99     0.94       5100.87|
| 12:  2.1354 -  2.0745  1288   133  0.89  17.52   0.99     0.98       4639.81|
| 13:  2.0745 -  2.0200  1242   138  0.89  17.37   0.98     0.95       3769.64|
| 14:  2.0200 -  1.9708   468    57  0.92  14.29   0.97     0.93       2749.65|
|alpha:            min =        0.93 max =            1.03 mean =         0.97|
|beta:             min =     2749.65 max =        11132.74 mean =      7216.36|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.98 mean =        15.27|
|phase err.(test): min =        0.00 max =           89.80 mean =        14.85|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1182   r_free= 0.1660   ksol= 0.33   Bsol= 55.74   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.05,-0.32,1.38,0.00,0.00,0.00); trace/3= -0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.206207                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1182   r_free= 0.1660   ksol= 0.33   Bsol= 55.74   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.05,-0.32,1.38,0.00,0.00,0.00); trace/3= -0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.206207                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9064 -  4.7033 0.99   1421  158 0.1029 0.1372      5.4373      5.6012|
|  2:  4.7033 -  3.7528 0.99   1375  153 0.0869 0.1109      5.4607      5.6576|
|  3:  3.7528 -  3.2842 0.99   1337  148 0.1121 0.1554      5.5141      5.8442|
|  4:  3.2842 -  2.9866 0.99   1335  144 0.1263 0.1704      5.4777      5.6664|
|  5:  2.9866 -  2.7740 0.99   1310  153 0.1359 0.1586      5.3633      5.5327|
|  6:  2.7740 -  2.6113 0.99   1329  145 0.1321 0.2246      5.2661       5.575|
|  7:  2.6113 -  2.4812 0.99   1298  147 0.1356 0.1715      5.2311       5.369|
|  8:  2.4812 -  2.3736 0.98   1314  142 0.1212 0.1809      5.1356      5.3689|
|  9:  2.3736 -  2.2826 0.98   1315  145 0.1252 0.2093      5.0874      5.4248|
| 10:  2.2826 -  2.2041 0.98   1291  138 0.1215 0.1629      5.0243      5.2072|
| 11:  2.2041 -  2.1354 1.00   1307  158 0.1256 0.2058       5.002      5.3678|
| 12:  2.1354 -  2.0745 0.97   1288  133 0.1268 0.1660      4.9568      5.1696|
| 13:  2.0745 -  2.0200 0.94   1242  138 0.1165 0.1872       4.835      5.0658|
| 14:  2.0200 -  1.9708 0.36    468   57 0.1012 0.1806      4.6998      4.9888|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9064 -  4.7033  1421   158  0.93   9.96   0.97     0.94       8247.52|
|  2:  4.7033 -  3.7528  1375   153  0.95   8.51   1.02     1.00       9772.78|
|  3:  3.7528 -  3.2842  1337   148  0.93  12.00   1.03     1.03      11138.26|
|  4:  3.2842 -  2.9866  1335   144  0.92  14.00   1.02     1.00      10813.45|
|  5:  2.9866 -  2.7740  1310   153  0.89  16.71   1.01     0.98       9200.70|
|  6:  2.7740 -  2.6113  1329   145  0.88  17.81   0.98     0.95       8021.98|
|  7:  2.6113 -  2.4812  1298   147  0.90  16.66   0.99     0.95       6918.57|
|  8:  2.4812 -  2.3736  1314   142  0.90  16.62   1.00     0.96       6262.13|
|  9:  2.3736 -  2.2826  1315   145  0.89  17.26   1.01     0.97       5770.02|
| 10:  2.2826 -  2.2041  1291   138  0.89  17.52   1.00     0.95       5175.04|
| 11:  2.2041 -  2.1354  1307   158  0.88  18.05   1.00     0.95       5096.78|
| 12:  2.1354 -  2.0745  1288   133  0.89  17.52   1.00     0.99       4638.93|
| 13:  2.0745 -  2.0200  1242   138  0.89  17.38   0.99     0.96       3768.97|
| 14:  2.0200 -  1.9708   468    57  0.92  14.31   0.98     0.94       2749.87|
|alpha:            min =        0.94 max =            1.03 mean =         0.97|
|beta:             min =     2749.87 max =        11138.26 mean =      7219.57|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.98 mean =        15.28|
|phase err.(test): min =        0.00 max =           89.80 mean =        14.86|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.858)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.85    95.64   15.88    None  None   None       |
|    all(noH): 2823   0      2.85    95.64   15.88    None  None   None       |
|    Sol.    : 438    0      3.80    95.64   40.47    None  None   None       |
|    Mac.    : 2385   0      2.85    92.00   11.37    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.848 -  12.127: 1728   |   5:    49.244 -  58.523:   81        |
|      1:    12.127 -  21.406:  531   |   6:    58.523 -  67.802:   59        |
|      2:    21.406 -  30.685:  171   |   7:    67.802 -  77.081:   22        |
|      3:    30.685 -  39.965:  117   |   8:    77.081 -  86.360:   14        |
|      4:    39.965 -  49.244:   97   |   9:    86.360 -  95.639:    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)= 288         
Filter by distance & map next to the model:
   mapped sites are within: 0.208 - 4.215
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 281 from: 288
   mapped sites are within: 0.702 - 4.215

peak=   10.900 closest distance to " CB  VAL A 230 " =    1.451
peak=    5.814 closest distance to " CG  LEU A   5 " =    1.216
peak=    5.805 closest distance to " CG  PRO A  54 " =    1.375
peak=    5.707 closest distance to " CD2 LEU A   5 " =    1.214
peak=    5.678 closest distance to " NH2 ARG A  56 " =    2.144
peak=    5.503 closest distance to " CG2 VAL A 296 " =    1.083
peak=    5.261 closest distance to " CB  VAL A 296 " =    1.073
peak=    5.254 closest distance to " NE2 GLN A  11 " =    1.153
peak=    5.249 closest distance to " CG1 VAL A 296 " =    1.198
peak=    5.228 closest distance to " CG  LEU A 228 " =    1.210
peak=    5.151 closest distance to " CB  GLN A 223 " =    1.452
peak=    4.950 closest distance to " CB  ARG A 275 " =    0.990
peak=    4.935 closest distance to " O   HOH Z 142 " =    1.792
peak=    4.814 closest distance to " O   HOH Z 232 " =    2.379
peak=    4.759 closest distance to " CG  PRO A 198 " =    1.223
peak=    4.713 closest distance to " CG  PRO A 243 " =    1.109
peak=    4.693 closest distance to " CB  PRO A  54 " =    0.992
peak=    4.585 closest distance to " O   HOH Z 248 " =    1.270
peak=    4.538 closest distance to " O   HOH Z 265 " =    2.065
peak=    4.522 closest distance to " CG  PRO A 213 " =    1.238
peak=    4.419 closest distance to " CB  ASN A 148 " =    1.430
peak=    4.410 closest distance to " O   HOH Z 251 " =    1.636
peak=    4.399 closest distance to " O   HOH Z 313 " =    2.005
peak=    4.398 closest distance to " O   HOH Z  78 " =    1.699
peak=    4.379 closest distance to " CB  GLN A 183 " =    1.269
peak=    4.321 closest distance to " CZ  PHE A 218 " =    1.161
peak=    4.319 closest distance to " O   SER A  87 " =    2.407
peak=    4.308 closest distance to " O   HOH Z 427 " =    3.025
peak=    4.292 closest distance to " O   HOH Z 402 " =    1.391
peak=    4.291 closest distance to " CB  VAL A 230 " =    1.144
peak=    4.271 closest distance to " CB  ASN A 142 " =    1.141
peak=    4.270 closest distance to " ND2 ASN A 249 " =    0.924
peak=    4.243 closest distance to " O   HOH Z 126 " =    1.536
peak=    4.197 closest distance to " O   HOH Z  43 " =    2.083
peak=    4.193 closest distance to " O   HOH Z 369 " =    2.340
peak=    4.172 closest distance to " O   HOH Z 425 " =    1.409
peak=    4.159 closest distance to " O   HOH Z 188 " =    2.756
peak=    4.145 closest distance to " CB  ARG A 190 " =    1.679
peak=    4.133 closest distance to " O   HOH Z 346 " =    1.563
peak=    4.108 closest distance to " O   HOH Z 287 " =    1.906
peak=    4.101 closest distance to " CD2 TRP A 179 " =    1.352
peak=    4.098 closest distance to " O   HOH Z 193 " =    1.529
peak=    4.083 closest distance to " CB  VAL A 265 " =    1.259
peak=    4.075 closest distance to " O   HOH Z 126 " =    2.058
peak=    4.067 closest distance to " CB  SER A  63 " =    1.165
peak=    4.062 closest distance to " O   HOH Z 403 " =    1.632
peak=    4.054 closest distance to " CA  TYR A  30 " =    0.945
peak=    4.053 closest distance to " O   HOH Z 303 " =    2.101
peak=    4.040 closest distance to " O  BHOH Z 338 " =    2.301
peak=    4.024 closest distance to " CG  GLN A  58 " =    0.840
peak=    4.020 closest distance to " O   HOH Z  59 " =    2.002
peak=    4.015 closest distance to " CA  ARG A  36 " =    1.035
peak=    4.009 closest distance to " CE  LYS A  76 " =    0.914
peak=    4.008 closest distance to " N   ASN A  39 " =    1.261
peak=    4.000 closest distance to " O   HOH Z 209 " =    2.299
peak=    3.995 closest distance to " OG ASER A 258 " =    3.063
peak=    3.995 closest distance to " CB  ARG A  79 " =    1.439
peak=    3.995 closest distance to " ND2 ASN A 187 " =    1.573
peak=    3.978 closest distance to " O   HOH Z 188 " =    1.417
peak=    3.978 closest distance to " CG  ARG A  66 " =    2.503
peak=    3.976 closest distance to " CB  ASN A  39 " =    0.952
peak=    3.966 closest distance to " O   HOH Z 411 " =    3.978
peak=    3.941 closest distance to " CA  ALA A  51 " =    0.973
peak=    3.939 closest distance to " CD2 LEU A 228 " =    1.278
peak=    3.930 closest distance to " CA  ARG A 195 " =    1.202
peak=    3.924 closest distance to " O   HOH Z  92 " =    2.098
peak=    3.923 closest distance to " O   HOH Z 359 " =    1.624
peak=    3.919 closest distance to " CD  ARG A 269 " =    1.045
peak=    3.917 closest distance to " CZ3 TRP A 266 " =    1.113
peak=    3.916 closest distance to " NH2AARG A 145 " =    1.166
peak=    3.910 closest distance to " O   HOH Z  85 " =    1.378
peak=    3.906 closest distance to " O   HOH Z 423 " =    1.844
peak=    3.895 closest distance to " CB  GLU A 277 " =    3.663
peak=    3.881 closest distance to " CG2 VAL A 257 " =    0.823
peak=    3.852 closest distance to " CG AARG A 275 " =    1.188
peak=    3.850 closest distance to " O   HOH Z 272 " =    1.816
peak=    3.849 closest distance to " CB  ASN A 110 " =    1.116
peak=    3.848 closest distance to " O   HOH Z   9 " =    1.249
peak=    3.836 closest distance to " CA  ALA A 160 " =    0.939
peak=    3.824 closest distance to " CG  MET A 185 " =    1.265
peak=    3.817 closest distance to " O   HOH Z 261 " =    2.296
peak=    3.817 closest distance to " O   HOH Z  61 " =    1.793
peak=    3.816 closest distance to " O   PRO A 198 " =    1.571
peak=    3.811 closest distance to " CD2 LEU A 297 " =    0.923
peak=    3.807 closest distance to " O   HOH Z 371 " =    2.809
peak=    3.802 closest distance to " CB  THR A  52 " =    0.816
peak=    3.799 closest distance to " CB  THR A  31 " =    1.502
peak=    3.793 closest distance to " O   HOH Z  80 " =    1.848
peak=    3.785 closest distance to " O   HOH Z 368 " =    2.209
peak=    3.782 closest distance to " CZ  PHE A  38 " =    1.129
peak=    3.775 closest distance to " CG  LYS A  76 " =    2.031
peak=    3.761 closest distance to " CG2AVAL A 121 " =    2.361
peak=    3.744 closest distance to " O   HOH Z 214 " =    2.554
peak=    3.733 closest distance to " O   HOH Z 365 " =    2.711
peak=    3.732 closest distance to " O   HOH Z 298 " =    1.709
peak=    3.728 closest distance to " NH1AARG A 145 " =    1.245
peak=    3.727 closest distance to " CB  TRP A 266 " =    1.106
peak=    3.717 closest distance to " O   HOH Z 422 " =    2.615
peak=    3.709 closest distance to " CB AVAL A  41 " =    0.987
peak=    3.701 closest distance to " NH2AARG A 190 " =    2.095
peak=    3.694 closest distance to " CB  VAL A 202 " =    1.587
peak=    3.684 closest distance to " CB  SER A  26 " =    1.868
peak=    3.678 closest distance to " O   HOH Z  88 " =    3.621
peak=    3.677 closest distance to " O   HOH Z 406 " =    1.518
peak=    3.676 closest distance to " O   HOH Z 172 " =    3.794
peak=    3.664 closest distance to " CB  TRP A 179 " =    1.445
peak=    3.662 closest distance to " O   HOH Z 290 " =    1.072
peak=    3.659 closest distance to " O   HOH Z 353 " =    2.670
peak=    3.655 closest distance to " O   HOH Z   3 " =    1.989
peak=    3.641 closest distance to " CD  LYS A 166 " =    1.356
peak=    3.633 closest distance to " O   HOH Z 280 " =    2.968
peak=    3.621 closest distance to " O   HOH Z  63 " =    1.769
peak=    3.619 closest distance to " CB  ASP A 124 " =    0.851
peak=    3.618 closest distance to " O   HOH Z 258 " =    2.043
peak=    3.611 closest distance to " NZ  LYS A 117 " =    2.990
peak=    3.607 closest distance to " CG  LEU A 167 " =    1.237
peak=    3.599 closest distance to " O   HOH Z 329 " =    4.157
peak=    3.594 closest distance to " N   ALA A 256 " =    1.050
peak=    3.576 closest distance to " CB  PHE A 204 " =    0.943
peak=    3.576 closest distance to " CA  ASN A 217 " =    1.130
peak=    3.576 closest distance to " CB  PRO A  90 " =    1.002
peak=    3.574 closest distance to " CB  GLU A 152 " =    1.152
peak=    3.574 closest distance to " O   HOH Z 124 " =    1.256
peak=    3.574 closest distance to " OG BSER A 164 " =    2.170
peak=    3.567 closest distance to " O   HOH Z 187 " =    2.316
peak=    3.564 closest distance to " O   HOH Z 128 " =    2.429
peak=    3.563 closest distance to " CE1 TYR A 186 " =    1.295
peak=    3.549 closest distance to " O   HOH Z 234 " =    3.572
peak=    3.548 closest distance to " CD  ARG A 159 " =    0.702
peak=    3.548 closest distance to " O   HOH Z 273 " =    3.041
peak=    3.544 closest distance to " CB  ALA A 248 " =    1.391
peak=    3.543 closest distance to " CA  ILE A 234 " =    1.002
peak=    3.543 closest distance to " CB  GLU A  46 " =    0.997
peak=    3.539 closest distance to " CB  LYS A 117 " =    1.184
peak=    3.530 closest distance to " O   HOH Z 337 " =    1.923
peak=    3.529 closest distance to " CB  PRO A 198 " =    1.099
peak=    3.517 closest distance to " O   HOH Z   9 " =    1.962
peak=    3.505 closest distance to " O   HOH Z  97 " =    2.255
peak=    3.502 closest distance to " CB  GLU A 128 " =    1.023
peak=    3.499 closest distance to " O   HOH Z 337 " =    3.562
peak=    3.499 closest distance to " CB  SER A 273 " =    0.928
peak=    3.489 closest distance to " CA  ALA A 129 " =    1.542
peak=    3.487 closest distance to " CA  PHE A 283 " =    1.165
peak=    3.484 closest distance to " CA  ASN A 127 " =    1.028
peak=    3.483 closest distance to " CE  LYS A  48 " =    1.164
peak=    3.483 closest distance to " CB  ASP A 140 " =    1.178
peak=    3.481 closest distance to " NE2 HIS A 207 " =    1.121
peak=    3.480 closest distance to " O   HOH Z 361 " =    3.481
peak=    3.476 closest distance to " CG2 ILE A  20 " =    1.514
peak=    3.470 closest distance to " CA  ALA A 295 " =    1.028
peak=    3.463 closest distance to " NZ  LYS A  48 " =    1.080
peak=    3.461 closest distance to " CB  ALA A 114 " =    0.808
peak=    3.457 closest distance to " CB  GLN A  89 " =    1.313
peak=    3.456 closest distance to " CD1 LEU A  96 " =    0.725
peak=    3.454 closest distance to " CA  LYS A 290 " =    1.182
peak=    3.452 closest distance to " CB  ALA A   9 " =    1.596
peak=    3.444 closest distance to " CG  PHE A 204 " =    1.031
peak=    3.441 closest distance to " CB  HIS A 108 " =    0.845
peak=    3.438 closest distance to " CB  SER A 212 " =    1.310
peak=    3.437 closest distance to " O   ASP A 124 " =    1.161
peak=    3.432 closest distance to " CD  LYS A 119 " =    1.864
peak=    3.430 closest distance to " CB  SER A   3 " =    1.233
peak=    3.426 closest distance to " O   HOH Z 246 " =    1.295
peak=    3.425 closest distance to " CB  SER A  62 " =    0.955
peak=    3.424 closest distance to " O   HOH Z 145 " =    2.476
peak=    3.421 closest distance to " N   ASP A 162 " =    1.181
peak=    3.420 closest distance to " O   HOH Z 162 " =    1.449
peak=    3.414 closest distance to " O   HOH Z 345 " =    3.304
peak=    3.408 closest distance to " O   HOH Z 117 " =    2.130
peak=    3.406 closest distance to " CG  GLU A  37 " =    0.900
peak=    3.398 closest distance to " CA  VAL A 125 " =    1.085
peak=    3.387 closest distance to " CD1 ILE A 199 " =    1.100
peak=    3.384 closest distance to " CA  SER A  87 " =    1.011
peak=    3.383 closest distance to " CG2 ILE A 120 " =    1.207
peak=    3.380 closest distance to " N   PHE A 130 " =    1.305
peak=    3.375 closest distance to " CB  ASN A 215 " =    1.187
peak=    3.374 closest distance to " CA  ASN A 215 " =    1.076
peak=    3.370 closest distance to " O   HOH Z 244 " =    1.630
peak=    3.369 closest distance to " O   ASN A  74 " =    1.404
peak=    3.367 closest distance to " O   HOH Z 361 " =    3.587
peak=    3.367 closest distance to " CB  SER A 216 " =    0.930
peak=    3.364 closest distance to " O   HOH Z  44 " =    1.858
peak=    3.360 closest distance to " CA  ALA A 291 " =    0.843
peak=    3.346 closest distance to " CA  MET A 105 " =    1.020
peak=    3.344 closest distance to " O   HOH Z 299 " =    4.215
peak=    3.343 closest distance to " NH2BARG A 190 " =    1.764
peak=    3.337 closest distance to " O   HOH Z 158 " =    3.122
peak=    3.335 closest distance to " CA  LYS A 117 " =    1.259
peak=    3.333 closest distance to " N   ARG A 190 " =    1.028
peak=    3.331 closest distance to " O   HOH Z   4 " =    1.519
peak=    3.329 closest distance to " CG2 ILE A 234 " =    0.892
peak=    3.323 closest distance to " CB  GLN A  88 " =    1.269
peak=    3.318 closest distance to " O   HOH Z 207 " =    1.117
peak=    3.313 closest distance to " O   HOH Z 203 " =    1.593
peak=    3.310 closest distance to " O   HOH Z 435 " =    1.984
peak=    3.310 closest distance to " O   HOH Z  68 " =    2.223
peak=    3.310 closest distance to " O   HOH Z 357 " =    2.079
peak=    3.308 closest distance to " CB  SER A 210 " =    0.780
peak=    3.308 closest distance to " O   HOH Z 403 " =    1.544
peak=    3.305 closest distance to " CB  SER A  62 " =    1.173
peak=    3.304 closest distance to " O   HOH Z  40 " =    1.837
peak=    3.303 closest distance to " CA  ASP A 191 " =    1.247
peak=    3.299 closest distance to " CG1 ILE A 120 " =    1.009
peak=    3.298 closest distance to " O   THR A 182 " =    1.408
peak=    3.298 closest distance to " O   HOH Z  76 " =    1.048
peak=    3.296 closest distance to " CG BARG A 102 " =    1.803
peak=    3.296 closest distance to " O   HOH Z 171 " =    3.973
peak=    3.293 closest distance to " OG  SER A 276 " =    1.263
peak=    3.291 closest distance to " OE2 GLU A  53 " =    1.938
peak=    3.289 closest distance to " CA  ARG A 139 " =    1.006
peak=    3.288 closest distance to " CG1 ILE A 151 " =    1.037
peak=    3.286 closest distance to " O   HOH Z 325 " =    2.087
peak=    3.284 closest distance to " CB  PRO A 243 " =    1.152
peak=    3.284 closest distance to " O   HOH Z 180 " =    2.133
peak=    3.281 closest distance to " OD1 ASN A  69 " =    2.467
peak=    3.278 closest distance to " O   HOH Z 222 " =    2.382
peak=    3.271 closest distance to " CB  ARG A 145 " =    0.888
peak=    3.268 closest distance to " O   THR A 220 " =    1.321
peak=    3.262 closest distance to " O   HOH Z 380 " =    1.922
peak=    3.250 closest distance to " O   HOH Z 183 " =    1.797
peak=    3.250 closest distance to " O   HOH Z 285 " =    2.406
peak=    3.249 closest distance to " CA  LEU A 282 " =    1.245
peak=    3.247 closest distance to " OG1 THR A 221 " =    1.329
peak=    3.247 closest distance to " CB  THR A 235 " =    1.442
peak=    3.240 closest distance to " CA  ALA A 154 " =    1.038
peak=    3.235 closest distance to " O   HOH Z 389 " =    1.760
peak=    3.234 closest distance to " CA  ALA A 233 " =    1.430
peak=    3.225 closest distance to " O   HOH Z 352 " =    1.360
peak=    3.221 closest distance to " OG BSER A 134 " =    2.954
peak=    3.217 closest distance to " O   HOH Z 403 " =    2.092
peak=    3.215 closest distance to " O   HOH Z   1 " =    1.798
peak=    3.214 closest distance to " CA  VAL A  41 " =    0.726
peak=    3.212 closest distance to " O   HOH Z 133 " =    2.769
peak=    3.211 closest distance to " CB  ARG A 219 " =    1.071
peak=    3.203 closest distance to " CB  ALA A 227 " =    1.122
peak=    3.202 closest distance to " N   SER A 135 " =    1.416
peak=    3.195 closest distance to " O   HOH Z 322 " =    1.907
peak=    3.195 closest distance to " CB  SER A  22 " =    0.922
peak=    3.194 closest distance to " CD1 LEU A 261 " =    1.135
peak=    3.191 closest distance to " CA  GLY A 133 " =    3.747
peak=    3.190 closest distance to " CE3 TRP A 150 " =    1.133
peak=    3.187 closest distance to " O   HOH Z 250 " =    1.251
peak=    3.178 closest distance to " CB  VAL A 268 " =    0.846
peak=    3.172 closest distance to " OG  SER A  62 " =    2.779
peak=    3.169 closest distance to " CG1 VAL A 126 " =    1.359
peak=    3.166 closest distance to " CB  ASN A 173 " =    1.029
peak=    3.165 closest distance to " O   HOH Z 421 " =    3.065
peak=    3.163 closest distance to " O   SER A 164 " =    1.355
peak=    3.163 closest distance to " C   PHE A  59 " =    0.899
peak=    3.157 closest distance to " CG  MET A 185 " =    0.969
peak=    3.155 closest distance to " O   HOH Z 294 " =    1.545
peak=    3.153 closest distance to " O   HOH Z 156 " =    3.376
peak=    3.153 closest distance to " O   PRO A 198 " =    1.280
peak=    3.150 closest distance to " CA  ARG A 102 " =    1.145
peak=    3.149 closest distance to " O   HOH Z 344 " =    2.787
peak=    3.146 closest distance to " O   HOH Z 421 " =    2.157
peak=    3.144 closest distance to " CG1BVAL A  72 " =    1.754
peak=    3.144 closest distance to " O   HOH Z 193 " =    1.577
peak=    3.143 closest distance to " O   HOH Z 281 " =    2.791
peak=    3.135 closest distance to " NE2 GLN A  77 " =    3.265
peak=    3.133 closest distance to " O   ASP A 200 " =    1.615
peak=    3.129 closest distance to " O   HOH Z 128 " =    1.471
peak=    3.128 closest distance to " O   HOH Z 238 " =    1.150
peak=    3.126 closest distance to " O   HOH Z  66 " =    2.232
peak=    3.125 closest distance to " O   HOH Z 293 " =    1.972
peak=    3.125 closest distance to " O   HOH Z 227 " =    1.395
peak=    3.125 closest distance to " OH  TYR A  30 " =    1.014
peak=    3.124 closest distance to " O   HOH Z 162 " =    2.986
peak=    3.121 closest distance to " CG  LEU A 281 " =    1.018
peak=    3.120 closest distance to " O   HOH Z 375 " =    2.550
peak=    3.108 closest distance to " CG2 THR A 220 " =    0.705
peak=    3.105 closest distance to " CG1 VAL A 153 " =    0.939
peak=    3.097 closest distance to " O   HOH Z 305 " =    3.429
peak=    3.096 closest distance to " O   HOH Z 371 " =    1.326
peak=    3.078 closest distance to " CA  ASP A 149 " =    1.178
peak=    3.066 closest distance to " CA  LEU A  83 " =    1.097
peak=    3.063 closest distance to " CD  ARG A  66 " =    2.504
peak=    3.053 closest distance to " CG1 ILE A  20 " =    1.261
peak=    3.042 closest distance to " CD1 LEU A  96 " =    1.238
peak=    3.021 closest distance to " O   HOH Z 109 " =    1.026
peak=    3.018 closest distance to " O   HOH Z 109 " =    2.524

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 217         
Filter by distance & map next to the model:
   mapped sites are within: 0.747 - 5.627
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 216 from: 217
   mapped sites are within: 0.747 - 5.627

peak=   -5.004 closest distance to " CD  ARG A  14 " =    3.374
peak=   -4.581 closest distance to " OG BSER A 134 " =    1.421
peak=   -4.408 closest distance to " O   VAL A  67 " =    2.457
peak=   -4.405 closest distance to " CG2 VAL A 230 " =    0.747
peak=   -4.369 closest distance to " CG  GLN A  58 " =    1.076
peak=   -4.339 closest distance to " C   HIS A 108 " =    1.137
peak=   -4.337 closest distance to " CB  PHE A 192 " =    1.991
peak=   -4.258 closest distance to " CG2 ILE A  49 " =    2.864
peak=   -4.222 closest distance to " O   HOH Z 267 " =    5.627
peak=   -4.144 closest distance to " OE1 GLN A 223 " =    2.293
peak=   -4.135 closest distance to " O   HOH Z 231 " =    2.229
peak=   -4.129 closest distance to " CD1 LEU A 101 " =    2.366
peak=   -4.120 closest distance to " CG2 VAL A 296 " =    1.297
peak=   -4.115 closest distance to " CD  ARG A 156 " =    2.062
peak=   -4.060 closest distance to " O   HOH Z 193 " =    1.047
peak=   -4.038 closest distance to " O   PRO A 198 " =    1.201
peak=   -4.019 closest distance to " CG1 VAL A 112 " =    2.797
peak=   -3.959 closest distance to " CD2 TYR A 293 " =    1.922
peak=   -3.952 closest distance to " O   HOH Z 211 " =    1.251
peak=   -3.927 closest distance to " O   HOH Z 387 " =    2.732
peak=   -3.905 closest distance to " O   HOH Z 166 " =    1.890
peak=   -3.902 closest distance to " O   HOH Z 394 " =    1.657
peak=   -3.898 closest distance to " CE  MET A 105 " =    2.336
peak=   -3.898 closest distance to " O   SER A 271 " =    2.111
peak=   -3.855 closest distance to " CG1 VAL A 296 " =    1.065
peak=   -3.849 closest distance to " CG1 VAL A 250 " =    2.708
peak=   -3.847 closest distance to " CE2 TYR A  30 " =    2.678
peak=   -3.831 closest distance to " O   HOH Z 351 " =    1.421
peak=   -3.821 closest distance to " CA  VAL A  67 " =    2.993
peak=   -3.817 closest distance to " OXT GLY A 302 " =    2.926
peak=   -3.807 closest distance to " O   PRO A 163 " =    2.176
peak=   -3.796 closest distance to " CE BMET A  47 " =    1.216
peak=   -3.794 closest distance to " CB  ALA A  43 " =    2.504
peak=   -3.772 closest distance to " O   ASN A 252 " =    1.359
peak=   -3.741 closest distance to " CA  ASP A 298 " =    1.066
peak=   -3.719 closest distance to " O   ALA A 227 " =    1.360
peak=   -3.715 closest distance to " O   PHE A 218 " =    1.475
peak=   -3.696 closest distance to " O   HOH Z 100 " =    0.957
peak=   -3.678 closest distance to " CG1 VAL A 112 " =    2.667
peak=   -3.671 closest distance to " O   HOH Z 371 " =    2.222
peak=   -3.668 closest distance to " CG2 THR A 178 " =    2.494
peak=   -3.659 closest distance to " O   HOH Z 107 " =    0.905
peak=   -3.644 closest distance to " O   HOH Z 216 " =    1.275
peak=   -3.643 closest distance to " OG  SER A  97 " =    2.325
peak=   -3.604 closest distance to " N   THR A  52 " =    1.694
peak=   -3.598 closest distance to " O   HOH Z 191 " =    5.595
peak=   -3.597 closest distance to " O   HOH Z 128 " =    1.174
peak=   -3.592 closest distance to " NE2 GLN A  11 " =    1.834
peak=   -3.585 closest distance to " CB  ALA A 161 " =    2.471
peak=   -3.583 closest distance to " CB  ALA A 248 " =    2.293
peak=   -3.582 closest distance to " CG  TRP A 266 " =    1.797
peak=   -3.578 closest distance to " CB  HIS A  86 " =    1.146
peak=   -3.577 closest distance to " ND2 ASN A 249 " =    2.321
peak=   -3.558 closest distance to " NH2AARG A 275 " =    5.005
peak=   -3.544 closest distance to " O   HOH Z 345 " =    2.098
peak=   -3.543 closest distance to " O   HOH Z  11 " =    2.236
peak=   -3.533 closest distance to " O   MET A  40 " =    2.818
peak=   -3.530 closest distance to " O   HOH Z 103 " =    1.750
peak=   -3.526 closest distance to " O   HOH Z 166 " =    2.218
peak=   -3.523 closest distance to " CA  GLY A 241 " =    2.376
peak=   -3.518 closest distance to " O   ILE A 106 " =    1.891
peak=   -3.493 closest distance to " CG1 VAL A  78 " =    2.623
peak=   -3.492 closest distance to " ND2 ASN A 187 " =    1.459
peak=   -3.489 closest distance to " CD2 PHE A  61 " =    2.196
peak=   -3.488 closest distance to " O   HOH Z 114 " =    3.087
peak=   -3.487 closest distance to " ND2 ASN A  45 " =    1.099
peak=   -3.481 closest distance to " CE3 TRP A 150 " =    2.206
peak=   -3.476 closest distance to " CB  ALA A 248 " =    2.071
peak=   -3.469 closest distance to " O   HOH Z 131 " =    4.100
peak=   -3.467 closest distance to " O   HOH Z  73 " =    2.422
peak=   -3.466 closest distance to " O   HOH Z 102 " =    1.615
peak=   -3.460 closest distance to " CD1 LEU A 255 " =    2.799
peak=   -3.457 closest distance to " CB  ALA A  10 " =    2.325
peak=   -3.448 closest distance to " C   SER A 206 " =    1.491
peak=   -3.445 closest distance to " CE2 TRP A  70 " =    2.090
peak=   -3.444 closest distance to " CG  GLU A 277 " =    1.257
peak=   -3.431 closest distance to " O   HOH Z 359 " =    2.913
peak=   -3.429 closest distance to " O   LYS A  76 " =    1.740
peak=   -3.428 closest distance to " O   HOH Z  11 " =    1.834
peak=   -3.419 closest distance to " CG2 VAL A 189 " =    2.009
peak=   -3.419 closest distance to " O   HOH Z 429 " =    1.541
peak=   -3.411 closest distance to " O   HOH Z 236 " =    1.440
peak=   -3.406 closest distance to " O   HOH Z   9 " =    1.544
peak=   -3.402 closest distance to " NE2 GLN A  88 " =    1.247
peak=   -3.400 closest distance to " O   HOH Z 238 " =    0.865
peak=   -3.397 closest distance to " CG1 VAL A 125 " =    1.864
peak=   -3.396 closest distance to " CE2 PHE A  61 " =    2.673
peak=   -3.393 closest distance to " CD2 HIS A 207 " =    2.384
peak=   -3.391 closest distance to " CZ2 TRP A 274 " =    0.968
peak=   -3.387 closest distance to " OG  SER A  63 " =    1.153
peak=   -3.386 closest distance to " CG2 ILE A 263 " =    2.327
peak=   -3.381 closest distance to " CG2 VAL A 202 " =    2.722
peak=   -3.372 closest distance to " O   HOH Z 357 " =    2.206
peak=   -3.369 closest distance to " CA  ASN A 127 " =    1.279
peak=   -3.367 closest distance to " NE  ARG A  66 " =    4.189
peak=   -3.366 closest distance to " CD2 PHE A 225 " =    1.112
peak=   -3.364 closest distance to " O   HOH Z 407 " =    2.824
peak=   -3.360 closest distance to " CA  GLY A 133 " =    1.907
peak=   -3.356 closest distance to " CA  GLY A 133 " =    2.285
peak=   -3.354 closest distance to " O   HOH Z 252 " =    3.899
peak=   -3.350 closest distance to " O   HOH Z 295 " =    1.545
peak=   -3.347 closest distance to " O   TRP A  70 " =    1.570
peak=   -3.342 closest distance to " CA  VAL A 296 " =    0.972
peak=   -3.342 closest distance to " O   HOH Z 185 " =    2.349
peak=   -3.339 closest distance to " NE2 GLN A  88 " =    2.019
peak=   -3.338 closest distance to " CG1BVAL A  72 " =    2.315
peak=   -3.337 closest distance to " O   SER A 210 " =    1.882
peak=   -3.336 closest distance to " N   ALA A 248 " =    1.673
peak=   -3.332 closest distance to " O   HOH Z 431 " =    1.934
peak=   -3.332 closest distance to " O   HOH Z 377 " =    2.088
peak=   -3.327 closest distance to " CB  PRO A 163 " =    2.484
peak=   -3.323 closest distance to " OH  TYR A 172 " =    1.822
peak=   -3.321 closest distance to " O   HOH Z 275 " =    1.817
peak=   -3.321 closest distance to " O   HOH Z 285 " =    2.021
peak=   -3.320 closest distance to " O   HOH Z 265 " =    2.366
peak=   -3.314 closest distance to " O   HOH Z 256 " =    1.422
peak=   -3.314 closest distance to " ND2 ASN A  39 " =    1.242
peak=   -3.309 closest distance to " O   GLY A  17 " =    1.123
peak=   -3.308 closest distance to " CB  SER A 210 " =    1.004
peak=   -3.307 closest distance to " CD1 ILE A 199 " =    2.405
peak=   -3.302 closest distance to " O   HOH Z 251 " =    5.014
peak=   -3.302 closest distance to " OD1 ASN A 249 " =    2.505
peak=   -3.301 closest distance to " CZ3 TRP A 179 " =    1.320
peak=   -3.300 closest distance to " CA  ASP A  27 " =    2.449
peak=   -3.297 closest distance to " CD2 LEU A 237 " =    2.823
peak=   -3.292 closest distance to " CA  GLY A 241 " =    3.155
peak=   -3.292 closest distance to " OG  SER A  62 " =    4.238
peak=   -3.292 closest distance to " O   HOH Z 351 " =    1.620
peak=   -3.291 closest distance to " O   HOH Z 106 " =    1.761
peak=   -3.289 closest distance to " CD  PRO A 243 " =    1.872
peak=   -3.287 closest distance to " N   THR A 157 " =    1.489
peak=   -3.285 closest distance to " O   HOH Z 286 " =    1.881
peak=   -3.279 closest distance to " N   ALA A 226 " =    1.960
peak=   -3.275 closest distance to " CB  ALA A  51 " =    1.940
peak=   -3.273 closest distance to " O   HOH Z  38 " =    1.856
peak=   -3.272 closest distance to " O   HOH Z 198 " =    1.828
peak=   -3.272 closest distance to " O   HOH Z 421 " =    3.094
peak=   -3.270 closest distance to " O   HOH Z 110 " =    1.483
peak=   -3.269 closest distance to " O   HOH Z 290 " =    1.205
peak=   -3.268 closest distance to " O   HOH Z 123 " =    2.620
peak=   -3.266 closest distance to " CB  ASN A  39 " =    2.354
peak=   -3.265 closest distance to " CE3 TRP A 274 " =    2.245
peak=   -3.252 closest distance to " O   HOH Z 201 " =    2.152
peak=   -3.250 closest distance to " ND2 ASN A  69 " =    1.956
peak=   -3.249 closest distance to " O   ILE A 234 " =    1.129
peak=   -3.248 closest distance to " O   GLY A  80 " =    2.511
peak=   -3.246 closest distance to " O   HOH Z 179 " =    1.995
peak=   -3.238 closest distance to " OD1 ASN A 148 " =    1.310
peak=   -3.236 closest distance to " CG  LEU A   5 " =    0.986
peak=   -3.232 closest distance to " CG  PRO A 243 " =    1.638
peak=   -3.229 closest distance to " O   HOH Z 340 " =    1.897
peak=   -3.228 closest distance to " O   HOH Z 113 " =    2.007
peak=   -3.228 closest distance to " CB  ALA A   9 " =    2.485
peak=   -3.227 closest distance to " O   HOH Z  52 " =    1.634
peak=   -3.224 closest distance to " O   HOH Z  69 " =    1.980
peak=   -3.218 closest distance to " C   MET A 188 " =    1.344
peak=   -3.209 closest distance to " O   HOH Z 136 " =    2.544
peak=   -3.208 closest distance to " O   HOH Z 128 " =    2.207
peak=   -3.206 closest distance to " NH2 ARG A  79 " =    1.503
peak=   -3.205 closest distance to " C   ALA A 158 " =    1.252
peak=   -3.203 closest distance to " OXT GLY A 302 " =    3.553
peak=   -3.203 closest distance to " ND2 ASN A  45 " =    1.205
peak=   -3.197 closest distance to " CZ  PHE A  38 " =    2.400
peak=   -3.191 closest distance to " O   HOH Z  64 " =    1.700
peak=   -3.186 closest distance to " O   ARG A 219 " =    1.833
peak=   -3.184 closest distance to " N   HIS A 115 " =    2.245
peak=   -3.184 closest distance to " CB  ASP A 132 " =    2.408
peak=   -3.183 closest distance to " O   ASP A  27 " =    2.090
peak=   -3.182 closest distance to " CE1 PHE A 192 " =    2.062
peak=   -3.181 closest distance to " O   HOH Z 165 " =    1.928
peak=   -3.178 closest distance to " O   ALA A 180 " =    1.426
peak=   -3.176 closest distance to " CD2 LEU A   5 " =    1.214
peak=   -3.173 closest distance to " O   HOH Z 210 " =    1.182
peak=   -3.170 closest distance to " O   HOH Z 364 " =    2.936
peak=   -3.168 closest distance to " CG2 THR A  42 " =    1.683
peak=   -3.168 closest distance to " O   HOH Z 174 " =    3.864
peak=   -3.168 closest distance to " CG  ASP A 231 " =    0.895
peak=   -3.167 closest distance to " O   SER A  95 " =    1.588
peak=   -3.166 closest distance to " CB  VAL A 296 " =    1.386
peak=   -3.166 closest distance to " O   ALA A  51 " =    1.264
peak=   -3.165 closest distance to " CB  ASP A 171 " =    2.288
peak=   -3.160 closest distance to " CD1 ILE A 239 " =    2.293
peak=   -3.158 closest distance to " OE1 GLN A 183 " =    1.495
peak=   -3.154 closest distance to " CB  TRP A  85 " =    2.546
peak=   -3.152 closest distance to " O   HOH Z 392 " =    1.930
peak=   -3.151 closest distance to " OD1 ASN A  39 " =    1.306
peak=   -3.146 closest distance to " CB  ALA A 291 " =    2.256
peak=   -3.146 closest distance to " O   HOH Z 174 " =    2.318
peak=   -3.143 closest distance to " O   HOH Z 139 " =    5.156
peak=   -3.142 closest distance to " CG1BVAL A  72 " =    2.734
peak=   -3.138 closest distance to " CB  GLN A  55 " =    1.229
peak=   -3.132 closest distance to " O   HOH Z 244 " =    2.029
peak=   -3.130 closest distance to " O   HOH Z 166 " =    1.692
peak=   -3.129 closest distance to " O   HOH Z 423 " =    2.302
peak=   -3.128 closest distance to " N   SER A 276 " =    1.322
peak=   -3.128 closest distance to " NE2 GLN A 194 " =    1.960
peak=   -3.127 closest distance to " O   HOH Z 231 " =    2.088
peak=   -3.124 closest distance to " CA  GLY A 203 " =    2.540
peak=   -3.123 closest distance to " O   ALA A  10 " =    1.723
peak=   -3.116 closest distance to " O   HOH Z 111 " =    4.458
peak=   -3.112 closest distance to " O   HOH Z 350 " =    2.224
peak=   -3.104 closest distance to " O   HOH Z 265 " =    1.963
peak=   -3.098 closest distance to " O   VAL A 189 " =    2.736
peak=   -3.097 closest distance to " CB  ASP A 132 " =    2.343
peak=   -3.096 closest distance to " O   TYR A 186 " =    1.710
peak=   -3.092 closest distance to " N   ASP A 286 " =    2.199
peak=   -3.091 closest distance to " O   HOH Z 137 " =    1.632
peak=   -3.085 closest distance to " O   HOH Z 313 " =    1.651
peak=   -3.085 closest distance to " O   HOH Z 139 " =    3.106
peak=   -3.071 closest distance to " CG  MET A 105 " =    0.928
peak=   -3.070 closest distance to " O   HOH Z  89 " =    2.694
peak=   -3.060 closest distance to " O   TYR A  15 " =    1.845
peak=   -3.060 closest distance to " O   HOH Z  68 " =    1.269
peak=   -3.040 closest distance to " O   HOH Z 352 " =    1.558
peak=   -3.031 closest distance to " CG  ARG A 269 " =    2.204
peak=   -3.016 closest distance to " O   GLY A  80 " =    2.461

================= 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    :  0.4675 0.4533   6.269721e+00   6.250704e+00
   1_bss:  0.4574 0.4446   6.259913e+00   6.241579e+00
   1_xyz:  0.3678 0.3853   6.120986e+00   6.155172e+00
   1_adp:  0.3184 0.3607   6.013646e+00   6.101634e+00
   1_occ:  0.3180 0.3617   6.012783e+00   6.103605e+00
   2_bss:  0.3132 0.3567   6.012750e+00   6.102814e+00
   2_xyz:  0.2267 0.2742   5.737659e+00   5.892572e+00
   2_adp:  0.2068 0.2585   5.663353e+00   5.838397e+00
   2_occ:  0.2066 0.2583   5.663010e+00   5.837923e+00
   3_bss:  0.2045 0.2577   5.661860e+00   5.836390e+00
   3_xyz:  0.1456 0.1943   5.364957e+00   5.579053e+00
   3_adp:  0.1332 0.1821   5.292507e+00   5.519316e+00
   3_occ:  0.1331 0.1818   5.291839e+00   5.518957e+00
   4_bss:  0.1333 0.1821   5.293362e+00   5.518804e+00
   4_xyz:  0.1243 0.1694   5.236107e+00   5.461207e+00
   4_adp:  0.1216 0.1684   5.224025e+00   5.454983e+00
   4_occ:  0.1214 0.1686   5.223502e+00   5.455162e+00
   5_bss:  0.1213 0.1685   5.223643e+00   5.455374e+00
   5_xyz:  0.1193 0.1656   5.208244e+00   5.441439e+00
   5_adp:  0.1184 0.1661   5.206349e+00   5.442770e+00
   5_occ:  0.1183 0.1661   5.206027e+00   5.442596e+00
   5_bss:  0.1182 0.1660   5.206207e+00   5.442716e+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:  0.340  11.315   7.632   7.643  11.622   0.000   0.000   0.000
   1_xyz:  0.340  11.315   7.632   7.643  11.622   0.000   0.000   0.000
   1_adp:  0.340  11.315   7.632   7.643  11.622   0.000   0.000   0.000
   1_occ:  0.340  11.315   7.632   7.643  11.622   0.000   0.000   0.000
   2_bss:  0.338  40.062   3.774   3.691   7.610   0.000   0.000   0.000
   2_xyz:  0.338  40.062   3.774   3.691   7.610   0.000   0.000   0.000
   2_adp:  0.338  40.062   3.774   3.691   7.610   0.000   0.000   0.000
   2_occ:  0.338  40.062   3.774   3.691   7.610   0.000   0.000   0.000
   3_bss:  0.319  48.009   1.936   2.590   4.917   0.000   0.000   0.000
   3_xyz:  0.319  48.009   1.936   2.590   4.917   0.000   0.000   0.000
   3_adp:  0.319  48.009   1.936   2.590   4.917   0.000   0.000   0.000
   3_occ:  0.319  48.009   1.936   2.590   4.917   0.000   0.000   0.000
   4_bss:  0.326  52.893   1.426   2.169   4.067   0.000   0.000   0.000
   4_xyz:  0.326  52.893   1.426   2.169   4.067   0.000   0.000   0.000
   4_adp:  0.326  52.893   1.426   2.169   4.067   0.000   0.000   0.000
   4_occ:  0.326  52.893   1.426   2.169   4.067   0.000   0.000   0.000
   5_bss:  0.326  52.893   1.579   2.323   4.072   0.000   0.000   0.000
   5_xyz:  0.326  52.893   1.579   2.323   4.072   0.000   0.000   0.000
   5_adp:  0.326  52.893   1.579   2.323   4.072   0.000   0.000   0.000
   5_occ:  0.326  52.893   1.579   2.323   4.072   0.000   0.000   0.000
   5_bss:  0.326  55.741  -1.055  -0.323   1.377   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  52.360 0.4922  0.5688    62914.418
   1_bss:  52.290 0.4917  0.7456    61086.704
   1_xyz:  42.700 0.6098  0.8906    42103.761
   1_adp:  38.209 0.6643  0.9938    35800.351
   1_occ:  38.299 0.6632  0.9908    35930.056
   2_bss:  38.012 0.6665  0.8678    35635.021
   2_xyz:  27.687 0.7830  0.9874    19707.626
   2_adp:  25.405 0.8078  1.0119    17274.588
   2_occ:  25.400 0.8079  1.0117    17253.858
   3_bss:  25.272 0.8092  0.9465    17139.829
   3_xyz:  18.438 0.8762  0.9893     9632.924
   3_adp:  17.068 0.8889  0.9894     8575.327
   3_occ:  17.064 0.8889  0.9895     8566.849
   4_bss:  17.038 0.8892  0.9688     8566.338
   4_xyz:  15.650 0.9015  0.9737     7538.538
   4_adp:  15.507 0.9029  0.9677     7456.154
   4_occ:  15.517 0.9028  0.9675     7458.182
   5_bss:  15.521 0.9028  0.9711     7462.041
   5_xyz:  15.229 0.9052  0.9724     7209.708
   5_adp:  15.238 0.9052  0.9660     7221.368
   5_occ:  15.231 0.9053  0.9659     7215.742
   5_bss:  15.236 0.9053  0.9724     7218.949
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3762e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3762e+01
   1_xyz:   1.648  0.013  0.105 18.015  0.006  4.108   1.3370e-01
   1_adp:   1.648  0.013  0.105 18.015  0.006  4.108   1.3370e-01
   1_occ:   1.648  0.013  0.105 18.015  0.006  4.108   1.3370e-01
   2_bss:   1.648  0.013  0.105 18.015  0.006  4.108   1.3370e-01
   2_xyz:   1.095  0.007  0.077 15.970  0.004  4.123   7.0977e-02
   2_adp:   1.095  0.007  0.077 15.970  0.004  4.123   7.0977e-02
   2_occ:   1.095  0.007  0.077 15.970  0.004  4.123   7.0977e-02
   3_bss:   1.095  0.007  0.077 15.970  0.004  4.123   7.0977e-02
   3_xyz:   1.151  0.009  0.085 16.040  0.004  4.129   7.6399e-02
   3_adp:   1.151  0.009  0.085 16.040  0.004  4.129   7.6399e-02
   3_occ:   1.151  0.009  0.085 16.040  0.004  4.129   7.6399e-02
   4_bss:   1.151  0.009  0.085 16.040  0.004  4.129   7.6399e-02
   4_xyz:   0.970  0.007  0.076 15.530  0.004  4.118   5.8756e-02
   4_adp:   0.970  0.007  0.076 15.530  0.004  4.118   5.8756e-02
   4_occ:   0.970  0.007  0.076 15.530  0.004  4.118   5.8756e-02
   5_bss:   0.970  0.007  0.076 15.530  0.004  4.118   5.8756e-02
   5_xyz:   0.936  0.006  0.074 15.154  0.003  4.122   5.4365e-02
   5_adp:   0.936  0.006  0.074 15.154  0.003  4.122   5.4365e-02
   5_occ:   0.936  0.006  0.074 15.154  0.003  4.122   5.4365e-02
   5_bss:   0.936  0.006  0.074 15.154  0.003  4.122   5.4365e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9677e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9677e+00
   1_xyz:  13.661  0.162  0.414 87.665  0.039  2.168   9.8944e-02
   1_adp:  13.661  0.162  0.414 87.665  0.039  2.168   9.8944e-02
   1_occ:  13.661  0.162  0.414 87.665  0.039  2.168   9.8944e-02
   2_bss:  13.661  0.162  0.414 87.665  0.039  2.168   9.8944e-02
   2_xyz:   7.136  0.069  0.280 82.362  0.030  2.327   6.0642e-02
   2_adp:   7.136  0.069  0.280 82.362  0.030  2.327   6.0642e-02
   2_occ:   7.136  0.069  0.280 82.362  0.030  2.327   6.0642e-02
   3_bss:   7.136  0.069  0.280 82.362  0.030  2.327   6.0642e-02
   3_xyz:   9.213  0.063  0.423 86.503  0.042  2.251   5.2442e-02
   3_adp:   9.213  0.063  0.423 86.503  0.042  2.251   5.2442e-02
   3_occ:   9.213  0.063  0.423 86.503  0.042  2.251   5.2442e-02
   4_bss:   9.213  0.063  0.423 86.503  0.042  2.251   5.2442e-02
   4_xyz:   6.043  0.045  0.346 81.848  0.036  2.382   4.0004e-02
   4_adp:   6.043  0.045  0.346 81.848  0.036  2.382   4.0004e-02
   4_occ:   6.043  0.045  0.346 81.848  0.036  2.382   4.0004e-02
   5_bss:   6.043  0.045  0.346 81.848  0.036  2.382   4.0004e-02
   5_xyz:   6.220  0.046  0.345 82.630  0.037  2.374   3.1521e-02
   5_adp:   6.220  0.046  0.345 82.630  0.037  2.374   3.1521e-02
   5_occ:   6.220  0.046  0.345 82.630  0.037  2.374   3.1521e-02
   5_bss:   6.220  0.046  0.345 82.630  0.037  2.374   3.1521e-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:  68.07   0.00  12.41  60.11   0.00   9.77  68.07   0.00  26.81
   1_occ:  68.07   0.00  12.41  60.11   0.00   9.77  68.07   0.00  26.81
   2_bss:  68.07   0.00  12.41  60.11   0.00   9.77  68.07   0.00  26.81
   2_xyz:  68.07   0.00  12.41  60.11   0.00   9.77  68.07   0.00  26.81
   2_adp:  67.40   0.00  12.56  63.11   0.00   8.88  67.40   0.00  32.59
   2_occ:  67.40   0.00  12.56  63.11   0.00   8.88  67.40   0.00  32.59
   3_bss:  67.40   0.00  12.56  63.11   0.00   8.88  67.40   0.00  32.59
   3_xyz:  67.40   0.00  12.56  63.11   0.00   8.88  67.40   0.00  32.59
   3_adp:  69.73   0.00  12.71  69.73   0.00   8.55  67.84   1.77  35.35
   3_occ:  69.73   0.00  12.71  69.73   0.00   8.55  67.84   1.77  35.35
   4_bss:  69.73   0.00  12.71  69.73   0.00   8.55  67.84   1.77  35.35
   4_xyz:  69.73   0.00  12.71  69.73   0.00   8.55  67.84   1.77  35.35
   4_adp:  86.74   0.00  13.04  86.74   0.00   8.60  80.16   0.95  37.24
   4_occ:  86.74   0.00  13.04  86.74   0.00   8.60  80.16   0.95  37.24
   5_bss:  86.74   0.00  13.04  86.74   0.00   8.60  80.16   0.95  37.24
   5_xyz:  86.74   0.00  13.04  86.74   0.00   8.60  80.16   0.95  37.24
   5_adp:  92.79   0.00  13.03  89.15   0.00   8.52  92.79   0.95  37.62
   5_occ:  92.79   0.00  13.03  89.15   0.00   8.52  92.79   0.95  37.62
   5_bss:  95.64   2.85  15.88  92.00   2.85  11.37  95.64   3.80  40.47
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.282    0.026    0.409
   1_adp:    1.282    0.026    0.409
   1_occ:    1.282    0.026    0.409
   2_bss:    1.282    0.026    0.409
   2_xyz:    1.789    0.039    0.543
   2_adp:    1.789    0.039    0.543
   2_occ:    1.789    0.039    0.543
   3_bss:    1.789    0.039    0.543
   3_xyz:    1.739    0.053    0.624
   3_adp:    1.739    0.053    0.624
   3_occ:    1.739    0.053    0.624
   4_bss:    1.739    0.053    0.624
   4_xyz:    1.842    0.044    0.644
   4_adp:    1.842    0.044    0.644
   4_occ:    1.842    0.044    0.644
   5_bss:    1.842    0.044    0.644
   5_xyz:    1.882    0.058    0.660
   5_adp:    1.882    0.058    0.660
   5_occ:    1.882    0.058    0.660
   5_bss:    1.882    0.058    0.660
------------------------------------------------------------------------

CPU time actual refinement: 325.02


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_306/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_306/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_306/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_306/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_306/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 324.85 
  Macro-tasks:
    bulk solvent and scale       = 42.60  
    individual site refinement   = 126.43 
    weights calculation          = 33.28  
    collect and process          = 6.55   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 209.00 
  Micro-tasks:
    mask                            = 1.72   
    f_calc                          = 97.85  
    alpha_beta                      = 8.32   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 107.10 
    fmodel                         = 7.33   
    r_factors                      = 0.21   
    phase_errors                   = 10.83  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 234.74 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.642 micro seconds
Total CPU time: 5.64 minutes
from_scatterers_fft:    639 calls, 97.48 s
gradients_fft:          583 calls, 94.38 s

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

# Date 2008-01-16 Time 01:15:23 PST -0800 (1200474923.50 s)
Start R-work = 0.4675, R-free = 0.4533 (no bulk solvent and anisotropic scale)
Final R-work = 0.1355, R-free = 0.1818 (no bulk solvent and anisotropic scale)

Start R-work = 0.4574, R-free = 0.4446
Final R-work = 0.1182, R-free = 0.1660