# Date 2008-01-16 Time 01:21:32 PST -0800 (1200475292.36 s)
#phil __OFF__

Command line arguments: "../382.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 5128
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 382

-------------------------------------------------------------------------------
  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: (69.5475, 45.9914, 87.6859, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.31, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 45.9914, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9429 1.96261
Completeness in resolution range: 0.94578
Completeness with d_max=infinity: 0.942912

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9429
                             d_min =   1.9626

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: (69.5475, 45.9914, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9429 1.96261
Completeness in resolution range: 0.94578
Completeness with d_max=infinity: 0.942912

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9433 -  4.2000 [2177/2201]  1957   220  10.1%
  bin  2:  4.2000 -  3.3459 [2084/2104]  1876   208  10.0%
  bin  3:  3.3459 -  2.9266 [2070/2089]  1865   205   9.9%
  bin  4:  2.9266 -  2.6607 [2023/2053]  1817   206  10.2%
  bin  5:  2.6607 -  2.4709 [2053/2072]  1852   201   9.8%
  bin  6:  2.4709 -  2.3258 [2009/2034]  1805   204  10.2%
  bin  7:  2.3258 -  2.2097 [2014/2042]  1816   198   9.8%
  bin  8:  2.2097 -  2.1138 [2002/2038]  1799   203  10.1%
  bin  9:  2.1138 -  2.0326 [1994/2036]  1800   194   9.7%
  bin 10:  2.0326 -  1.9626 [1163/2043]  1043   120  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_382/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:
        1.42 -     2.12: 18
        2.12 -     2.81: 829
        2.81 -     3.51: 4542
        3.51 -     4.20: 9396
        4.20 -     4.90: 13788
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.420 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.717 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.927 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28568 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_382/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_382/model_refine_001.geo

CPU time processing inputs: 9.28


============================ 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 = 69.5475 45.9914 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4967   r_free= 0.4882   ksol= 0.00   Bsol= 0.00   scale= 0.785    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.82 A                  |
| x-ray target function (ml) for work reflections: 6.297211                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9433 -  4.6846 0.99   1414  154 0.4155 0.4034      6.6225      6.6214|
|  2:  4.6846 -  3.7375 0.99   1359  154 0.4231 0.4107      6.8227      6.8066|
|  3:  3.7375 -  3.2707 0.99   1331  146 0.4587 0.3944      6.7013       6.661|
|  4:  3.2707 -  2.9742 0.99   1324  150 0.4886 0.4881      6.5573      6.5206|
|  5:  2.9742 -  2.7625 0.99   1311  148 0.5292 0.4996      6.3781      6.4107|
|  6:  2.7625 -  2.6005 0.99   1315  144 0.5315 0.5507      6.2961      6.2205|
|  7:  2.6005 -  2.4709 0.99   1313  144 0.5247 0.5257      6.2398      6.2055|
|  8:  2.4709 -  2.3637 0.98   1291  142 0.5549 0.5066      6.2015      6.1833|
|  9:  2.3637 -  2.2731 0.98   1288  144 0.5310 0.5595      6.1193      6.2013|
| 10:  2.2731 -  2.1949 1.00   1287  145 0.5453 0.5636      6.1106      6.1008|
| 11:  2.1949 -  2.1265 0.98   1294  146 0.5284 0.5290       6.035      6.0558|
| 12:  2.1265 -  2.0658 0.98   1274  140 0.5329 0.5293      5.9725      5.9669|
| 13:  2.0658 -  2.0116 0.96   1263  141 0.5383 0.5329      5.8815      5.8236|
| 14:  2.0116 -  1.9626 0.43    566   61 0.5577 0.5080      5.9178       5.801|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9433 -  4.6846  1414   154  0.66  37.77   0.78     0.72      85410.44|
|  2:  4.6846 -  3.7375  1359   154  0.68  36.74   0.86     0.77     115239.21|
|  3:  3.7375 -  3.2707  1331   146  0.57  45.88   0.84     0.71     121663.03|
|  4:  3.2707 -  2.9742  1324   150  0.47  54.21   0.78     0.57     110764.34|
|  5:  2.9742 -  2.7625  1311   148  0.33  64.76   0.73     0.41      92384.83|
|  6:  2.7625 -  2.6005  1315   144  0.28  68.76   0.71     0.33      82696.33|
|  7:  2.6005 -  2.4709  1313   144  0.20  74.74   0.73     0.24      78022.24|
|  8:  2.4709 -  2.3637  1291   142  0.20  74.89   0.71     0.25      70155.59|
|  9:  2.3637 -  2.2731  1288   144  0.19  75.76   0.73     0.23      64809.11|
| 10:  2.2731 -  2.1949  1287   145  0.24  72.49   0.74     0.28      55220.28|
| 11:  2.1949 -  2.1265  1294   146  0.22  73.39   0.76     0.29      53894.78|
| 12:  2.1265 -  2.0658  1274   140  0.25  71.76   0.76     0.32      46591.65|
| 13:  2.0658 -  2.0116  1263   141  0.26  70.53   0.71     0.34      40374.56|
| 14:  2.0116 -  1.9626   566    61  0.34  64.47   0.73     0.40      31385.98|
|alpha:            min =        0.23 max =            0.77 mean =         0.42|
|beta:             min =    31385.98 max =       121663.03 mean =     77211.57|
|figures of merit: min =        0.00 max =            1.00 mean =         0.36|
|phase err.(work): min =        0.00 max =           90.00 mean =        62.91|
|phase err.(test): min =        0.00 max =           89.88 mean =        63.18|
|-----------------------------------------------------------------------------|

============================== 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 = 20.314405             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.354   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.893765              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.407   (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:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       39 |
| 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:      700 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1538 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2663 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3947 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5145 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6612 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7728 |
|-----------------------------------------------------------------------------|
|-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 |       53.413 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.087    4.900  1.196 |       2.221 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.634)------------------------------------------|
|    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 = 11.634)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5028   r_free= 0.4890   ksol= 0.00   Bsol= 0.00   scale= 0.755    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.81 A                  |
| x-ray target function (ml) for work reflections: 6.297912                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4886   r_free= 0.4753   ksol= 0.38   Bsol= 20.00   scale= 0.982   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.37,9.26,9.49,0.00,0.00,0.00); trace/3= 8.37                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.291733                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.155502             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.626   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.608300              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.487   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4886      final r-factor (work) = 0.4195          |
| start r-factor (free) = 0.4753      final r-factor (free) = 0.4424          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 101.0935 = 15.16 * 0.50 * 6.2921 + 1.00 * 53.4133                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 47.3800 = 15.16 * 0.50 * 6.2332 + 1.00 * 0.1465                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4195      final r-factor (work) = 0.3786          |
| start r-factor (free) = 0.4424      final r-factor (free) = 0.4407          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.0393 = 1.61 * 1.00 * 6.2332 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.9435 = 1.61 * 1.00 * 6.1699 + 1.00 * 0.0205                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.634)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.38   15.44    None  None   None       |
|    all(noH): 2823   0      0.00    85.38   15.44    None  None   None       |
|    Sol.    : 438    0      0.00    85.38   25.24    None  None   None       |
|    Mac.    : 2385   0      0.00    67.47   13.65    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.539:  975   |   5:    42.693 -  51.231:   78        |
|      1:     8.539 -  17.077:  834   |   6:    51.231 -  59.769:   35        |
|      2:    17.077 -  25.616:  518   |   7:    59.769 -  68.308:   11        |
|      3:    25.616 -  34.154:  257   |   8:    68.308 -  76.846:    2        |
|      4:    34.154 -  42.693:  110   |   9:    76.846 -  85.385:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3786 r_free = 0.4407             target_work(ml) = 6.162         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3783 r_free = 0.4418             target_work(ml) = 6.162         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3783   r_free= 0.4418   ksol= 0.38   Bsol= 20.00   scale= 1.123   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.37,9.26,9.49,0.00,0.00,0.00); trace/3= 8.37                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.161547                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3765   r_free= 0.4375   ksol= 0.35   Bsol= 35.39   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.45,5.46,5.96,0.00,0.00,0.00); trace/3= 4.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.162545                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.958557              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.472  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.719789              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.315  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3765      final r-factor (work) = 0.3108          |
| start r-factor (free) = 0.4375      final r-factor (free) = 0.3783          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.7638 = 8.96 * 0.50 * 6.1656 + 1.00 * 0.1465                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.3672 = 8.96 * 0.50 * 6.0898 + 1.00 * 0.0893                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3108      final r-factor (work) = 0.2902          |
| start r-factor (free) = 0.3783      final r-factor (free) = 0.3652          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4039 = 0.72 * 1.00 * 6.0898 + 1.00 * 0.0205                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3273 = 0.72 * 1.00 * 5.9933 + 1.00 * 0.0134                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 33     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.634)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.18   14.79    None  None   None       |
|    all(noH): 2823   0      0.00    90.18   14.79    None  None   None       |
|    Sol.    : 438    0      0.00    90.18   30.05    None  None   None       |
|    Mac.    : 2385   0      0.00    69.88   11.98    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 -   9.018: 1131   |   5:    45.092 -  54.110:   44        |
|      1:     9.018 -  18.037:  830   |   6:    54.110 -  63.128:   22        |
|      2:    18.037 -  27.055:  464   |   7:    63.128 -  72.147:    7        |
|      3:    27.055 -  36.073:  207   |   8:    72.147 -  81.165:    1        |
|      4:    36.073 -  45.092:  116   |   9:    81.165 -  90.183:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2902 r_free = 0.3652             target_work(ml) = 5.974         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2899 r_free = 0.3653             target_work(ml) = 5.974         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2899   r_free= 0.3653   ksol= 0.35   Bsol= 35.39   scale= 1.078   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.45,5.46,5.96,0.00,0.00,0.00); trace/3= 4.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 5.974172                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2882   r_free= 0.3634   ksol= 0.33   Bsol= 43.71   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.58,2.91,3.70,0.00,0.00,0.00); trace/3= 2.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 5.973429                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.945724              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.780  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.917971              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.183  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2882      final r-factor (work) = 0.2232          |
| start r-factor (free) = 0.3634      final r-factor (free) = 0.2854          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.9066 = 5.95 * 0.50 * 5.9933 + 1.00 * 0.0893                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.5542 = 5.95 * 0.50 * 5.8781 + 1.00 * 0.0794                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2232      final r-factor (work) = 0.1996          |
| start r-factor (free) = 0.2854      final r-factor (free) = 0.2701          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.2875 = 1.92 * 1.00 * 5.8781 + 1.00 * 0.0135                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.9334 = 1.92 * 1.00 * 5.6910 + 1.00 * 0.0182                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.634)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.86  15.98    None  None   None       |
|    all(noH): 2823   0      0.00    101.86  15.98    None  None   None       |
|    Sol.    : 438    0      0.00    101.86  40.89    None  None   None       |
|    Mac.    : 2385   0      0.00    87.99   11.40    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.186: 1413   |   5:    50.929 -  61.114:   94        |
|      1:    10.186 -  20.371:  725   |   6:    61.114 -  71.300:   44        |
|      2:    20.371 -  30.557:  252   |   7:    71.300 -  81.486:   19        |
|      3:    30.557 -  40.743:  145   |   8:    81.486 -  91.671:    7        |
|      4:    40.743 -  50.929:  122   |   9:    91.671 - 101.857:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1996 r_free = 0.2701             target_work(ml) = 5.662         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1994 r_free = 0.2698             target_work(ml) = 5.662         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1994   r_free= 0.2698   ksol= 0.33   Bsol= 43.71   scale= 1.048   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.58,2.91,3.70,0.00,0.00,0.00); trace/3= 2.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.661524                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1988   r_free= 0.2699   ksol= 0.33   Bsol= 52.86   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.69,1.47,2.87,0.00,0.00,0.00); trace/3= 1.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.661401                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.360522              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.520  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.765272              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.515  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1988      final r-factor (work) = 0.1609          |
| start r-factor (free) = 0.2699      final r-factor (free) = 0.2215          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6460 = 3.36 * 0.50 * 5.6935 + 1.00 * 0.0794                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4324 = 3.36 * 0.50 * 5.5781 + 1.00 * 0.0598                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1609      final r-factor (work) = 0.1495          |
| start r-factor (free) = 0.2215      final r-factor (free) = 0.2065          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2866 = 0.77 * 1.00 * 5.5781 + 1.00 * 0.0179                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1824 = 0.77 * 1.00 * 5.4447 + 1.00 * 0.0158                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.634)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.34  15.35    None  None   None       |
|    all(noH): 2823   0      0.00    104.34  15.35    None  None   None       |
|    Sol.    : 438    0      2.48    104.34  42.60    None  None   None       |
|    Mac.    : 2385   0      0.00    95.78   10.34    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.434: 1621   |   5:    52.171 -  62.606:   90        |
|      1:    10.434 -  20.869:  628   |   6:    62.606 -  73.040:   48        |
|      2:    20.869 -  31.303:  172   |   7:    73.040 -  83.474:   20        |
|      3:    31.303 -  41.737:  119   |   8:    83.474 -  93.909:    6        |
|      4:    41.737 -  52.171:  115   |   9:    93.909 - 104.343:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1495 r_free = 0.2065             target_work(ml) = 5.405         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1494 r_free = 0.2062             target_work(ml) = 5.404         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1494   r_free= 0.2062   ksol= 0.33   Bsol= 52.86   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.69,1.47,2.87,0.00,0.00,0.00); trace/3= 1.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.404059                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1496   r_free= 0.2063   ksol= 0.32   Bsol= 51.70   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.65,0.94,2.73,0.00,0.00,0.00); trace/3= 1.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.402885                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.590043              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 117.089  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.426429              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.793   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1496      final r-factor (work) = 0.1319          |
| start r-factor (free) = 0.2063      final r-factor (free) = 0.1840          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1106 = 2.59 * 0.50 * 5.4445 + 1.00 * 0.0598                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9909 = 2.59 * 0.50 * 5.3532 + 1.00 * 0.0583                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1319      final r-factor (work) = 0.1285          |
| start r-factor (free) = 0.1840      final r-factor (free) = 0.1771          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3004 = 0.43 * 1.00 * 5.3532 + 1.00 * 0.0177                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2803 = 0.43 * 1.00 * 5.2804 + 1.00 * 0.0286                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.634)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.13  14.63    None  None   None       |
|    all(noH): 2823   0      0.00    101.13  14.63    None  None   None       |
|    Sol.    : 438    0      3.03    101.13  40.75    None  None   None       |
|    Mac.    : 2385   0      0.00    99.60   9.83     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.114: 1653   |   5:    50.567 -  60.681:   88        |
|      1:    10.114 -  20.227:  623   |   6:    60.681 -  70.794:   46        |
|      2:    20.227 -  30.340:  165   |   7:    70.794 -  80.908:   22        |
|      3:    30.340 -  40.454:  117   |   8:    80.908 -  91.021:    5        |
|      4:    40.454 -  50.567:   98   |   9:    91.021 - 101.134:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1285 r_free = 0.1771             target_work(ml) = 5.260         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1283 r_free = 0.1769             target_work(ml) = 5.259         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1283   r_free= 0.1769   ksol= 0.32   Bsol= 51.70   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.65,0.94,2.73,0.00,0.00,0.00); trace/3= 1.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.258790                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9433 -  4.6846 0.99   1414  154 0.1014 0.1330      5.4195      5.5967|
|  2:  4.6846 -  3.7375 0.99   1359  154 0.0928 0.1268      5.5144      5.7487|
|  3:  3.7375 -  3.2707 0.99   1331  146 0.1211 0.1582      5.5902      5.8788|
|  4:  3.2707 -  2.9742 0.99   1324  150 0.1409 0.2015      5.5675       5.769|
|  5:  2.9742 -  2.7625 0.99   1311  148 0.1540 0.1865      5.4563      5.6454|
|  6:  2.7625 -  2.6005 0.99   1315  144 0.1410 0.2282       5.324       5.599|
|  7:  2.6005 -  2.4709 0.99   1313  144 0.1495 0.1834      5.2897      5.4271|
|  8:  2.4709 -  2.3637 0.98   1291  142 0.1430 0.1868       5.221      5.4208|
|  9:  2.3637 -  2.2731 0.98   1288  144 0.1393 0.2030      5.1486      5.4433|
| 10:  2.2731 -  2.1949 1.00   1287  145 0.1335 0.1931      5.0828       5.284|
| 11:  2.1949 -  2.1265 0.98   1294  146 0.1329 0.2048      5.0576      5.3924|
| 12:  2.1265 -  2.0658 0.98   1274  140 0.1349 0.2015       5.012      5.3268|
| 13:  2.0658 -  2.0116 0.96   1263  141 0.1262 0.1739        4.86       5.001|
| 14:  2.0116 -  1.9626 0.43    566   61 0.1097 0.1593      4.7038      4.9488|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9433 -  4.6846  1414   154  0.93  10.14   0.98     0.95       8235.78|
|  2:  4.6846 -  3.7375  1359   154  0.94   9.28   1.03     1.01      10734.78|
|  3:  3.7375 -  3.2707  1331   146  0.92  13.72   1.05     1.04      13253.97|
|  4:  3.2707 -  2.9742  1324   150  0.90  16.16   1.02     1.00      12997.20|
|  5:  2.9742 -  2.7625  1311   148  0.88  18.08   1.01     0.98      10713.35|
|  6:  2.7625 -  2.6005  1315   144  0.88  18.67   0.99     0.95       8832.34|
|  7:  2.6005 -  2.4709  1313   144  0.88  18.28   1.00     0.97       7757.23|
|  8:  2.4709 -  2.3637  1291   142  0.88  18.29   1.01     0.98       7153.46|
|  9:  2.3637 -  2.2731  1288   144  0.89  17.79   1.00     0.95       6146.53|
| 10:  2.2731 -  2.1949  1287   145  0.88  18.27   1.01     0.96       5662.21|
| 11:  2.1949 -  2.1265  1294   146  0.87  19.16   1.01     0.96       5594.28|
| 12:  2.1265 -  2.0658  1274   140  0.88  18.63   1.01     1.00       5195.69|
| 13:  2.0658 -  2.0116  1263   141  0.89  17.85   1.00     0.98       3809.29|
| 14:  2.0116 -  1.9626   566    61  0.93  13.20   1.00     0.98       2544.86|
|alpha:            min =        0.95 max =            1.04 mean =         0.98|
|beta:             min =     2544.86 max =        13253.97 mean =      8024.80|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.98 mean =        16.30|
|phase err.(test): min =        0.00 max =           89.91 mean =        15.60|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1283   r_free= 0.1769   ksol= 0.32   Bsol= 53.10   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.77,-0.59,1.35,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.258637                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1283   r_free= 0.1769   ksol= 0.32   Bsol= 53.10   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.77,-0.59,1.35,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.258637                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9433 -  4.6846 0.99   1414  154 0.1014 0.1330      5.4194      5.5966|
|  2:  4.6846 -  3.7375 0.99   1359  154 0.0929 0.1268      5.5145      5.7486|
|  3:  3.7375 -  3.2707 0.99   1331  146 0.1211 0.1581      5.5903      5.8788|
|  4:  3.2707 -  2.9742 0.99   1324  150 0.1409 0.2014      5.5674      5.7689|
|  5:  2.9742 -  2.7625 0.99   1311  148 0.1539 0.1865      5.4562      5.6451|
|  6:  2.7625 -  2.6005 0.99   1315  144 0.1409 0.2280      5.3235      5.5982|
|  7:  2.6005 -  2.4709 0.99   1313  144 0.1495 0.1836      5.2896      5.4273|
|  8:  2.4709 -  2.3637 0.98   1291  142 0.1430 0.1868      5.2209      5.4208|
|  9:  2.3637 -  2.2731 0.98   1288  144 0.1393 0.2026      5.1486      5.4423|
| 10:  2.2731 -  2.1949 1.00   1287  145 0.1334 0.1932      5.0825      5.2851|
| 11:  2.1949 -  2.1265 0.98   1294  146 0.1328 0.2050      5.0577      5.3935|
| 12:  2.1265 -  2.0658 0.98   1274  140 0.1349 0.2013       5.012      5.3263|
| 13:  2.0658 -  2.0116 0.96   1263  141 0.1262 0.1733      4.8594      4.9993|
| 14:  2.0116 -  1.9626 0.43    566   61 0.1097 0.1592       4.703      4.9483|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9433 -  4.6846  1414   154  0.93  10.13   0.98     0.95       8231.99|
|  2:  4.6846 -  3.7375  1359   154  0.94   9.27   1.02     1.01      10733.09|
|  3:  3.7375 -  3.2707  1331   146  0.92  13.72   1.05     1.04      13256.77|
|  4:  3.2707 -  2.9742  1324   150  0.90  16.16   1.02     1.00      12991.88|
|  5:  2.9742 -  2.7625  1311   148  0.88  18.07   1.01     0.98      10701.69|
|  6:  2.7625 -  2.6005  1315   144  0.88  18.66   0.98     0.95       8827.22|
|  7:  2.6005 -  2.4709  1313   144  0.88  18.27   1.00     0.96       7753.86|
|  8:  2.4709 -  2.3637  1291   142  0.88  18.28   1.01     0.98       7151.28|
|  9:  2.3637 -  2.2731  1288   144  0.89  17.78   1.00     0.95       6145.55|
| 10:  2.2731 -  2.1949  1287   145  0.88  18.27   1.01     0.96       5664.33|
| 11:  2.1949 -  2.1265  1294   146  0.87  19.17   1.00     0.96       5600.31|
| 12:  2.1265 -  2.0658  1274   140  0.88  18.63   1.01     1.00       5196.54|
| 13:  2.0658 -  2.0116  1263   141  0.89  17.83   1.00     0.98       3802.75|
| 14:  2.0116 -  1.9626   566    61  0.93  13.17   1.00     0.97       2535.45|
|alpha:            min =        0.95 max =            1.04 mean =         0.98|
|beta:             min =     2535.45 max =        13256.77 mean =      8022.33|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.97 mean =        16.30|
|phase err.(test): min =        0.00 max =           89.91 mean =        15.60|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.634)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.40    102.54  16.03    None  None   None       |
|    all(noH): 2823   0      1.40    102.54  16.03    None  None   None       |
|    Sol.    : 438    0      4.44    102.54  42.15    None  None   None       |
|    Mac.    : 2385   0      1.40    101.00  11.23    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.403 -  11.516: 1653   |   5:    51.970 -  62.083:   88        |
|      1:    11.516 -  21.630:  623   |   6:    62.083 -  72.197:   46        |
|      2:    21.630 -  31.743:  165   |   7:    72.197 -  82.310:   22        |
|      3:    31.743 -  41.856:  117   |   8:    82.310 -  92.424:    5        |
|      4:    41.856 -  51.970:   98   |   9:    92.424 - 102.537:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 328         
Filter by distance & map next to the model:
   mapped sites are within: 0.209 - 4.300
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 324 from: 328
   mapped sites are within: 0.781 - 4.300

peak=    9.550 closest distance to " CB  VAL A 230 " =    1.433
peak=    9.267 closest distance to " CB  VAL A 296 " =    1.520
peak=    7.898 closest distance to " O   HOH Z 130 " =    1.807
peak=    7.400 closest distance to " CD2 LEU A   5 " =    1.422
peak=    6.927 closest distance to " CG  ARG A 138 " =    1.156
peak=    5.492 closest distance to " O   HOH Z 375 " =    1.340
peak=    5.471 closest distance to " O   HOH Z 415 " =    1.258
peak=    5.363 closest distance to " O   HOH Z  65 " =    1.665
peak=    5.328 closest distance to " CD1AILE A 234 " =    1.046
peak=    5.276 closest distance to " NE2 GLN A  11 " =    1.150
peak=    5.234 closest distance to " O   HOH Z 385 " =    1.178
peak=    5.219 closest distance to " CG  PRO A  54 " =    1.525
peak=    5.206 closest distance to " NH1 ARG A 138 " =    0.995
peak=    5.173 closest distance to " O   HOH Z 424 " =    1.244
peak=    5.110 closest distance to " CB  VAL A 230 " =    1.257
peak=    5.086 closest distance to " O   HOH Z 232 " =    2.202
peak=    5.079 closest distance to " NH2 ARG A  56 " =    2.083
peak=    5.021 closest distance to " O   HOH Z 222 " =    1.334
peak=    4.935 closest distance to " O   HOH Z 417 " =    1.958
peak=    4.923 closest distance to " O   HOH Z   9 " =    2.162
peak=    4.919 closest distance to " O   HOH Z 427 " =    1.218
peak=    4.908 closest distance to " O   HOH Z 124 " =    1.466
peak=    4.838 closest distance to " O   HOH Z 427 " =    2.076
peak=    4.827 closest distance to " CB  PRO A  54 " =    1.139
peak=    4.779 closest distance to " CB  ARG A 275 " =    1.098
peak=    4.654 closest distance to " O   HOH Z 425 " =    1.560
peak=    4.633 closest distance to " CG  LEU A 228 " =    1.090
peak=    4.612 closest distance to " O   HOH Z 142 " =    1.945
peak=    4.596 closest distance to " O   HOH Z 418 " =    1.173
peak=    4.583 closest distance to " O   HOH Z 287 " =    1.816
peak=    4.562 closest distance to " CG  LEU A   5 " =    1.200
peak=    4.539 closest distance to " O   HOH Z 126 " =    1.982
peak=    4.532 closest distance to " CG2 ILE A 120 " =    1.208
peak=    4.477 closest distance to " O   HOH Z  69 " =    1.308
peak=    4.454 closest distance to " O   HOH Z 369 " =    2.214
peak=    4.453 closest distance to " CB  SER A   3 " =    1.405
peak=    4.446 closest distance to " CG2 ILE A 234 " =    0.915
peak=    4.440 closest distance to " O   HOH Z  59 " =    1.697
peak=    4.424 closest distance to " O   HOH Z  49 " =    1.048
peak=    4.379 closest distance to " O   HOH Z 389 " =    1.513
peak=    4.378 closest distance to " O   HOH Z  78 " =    1.727
peak=    4.375 closest distance to " O   HOH Z 112 " =    1.355
peak=    4.375 closest distance to " O  BHOH Z  74 " =    1.071
peak=    4.373 closest distance to " O   HOH Z   7 " =    1.383
peak=    4.357 closest distance to " O   HOH Z  11 " =    1.264
peak=    4.351 closest distance to " O   HOH Z 127 " =    1.137
peak=    4.326 closest distance to " C   GLN A  73 " =    1.034
peak=    4.315 closest distance to " CZ3 TRP A 266 " =    1.199
peak=    4.307 closest distance to " O   HOH Z 258 " =    1.196
peak=    4.299 closest distance to " O   HOH Z 419 " =    2.091
peak=    4.297 closest distance to " CG  PRO A 280 " =    0.956
peak=    4.279 closest distance to " O   HOH Z 366 " =    2.932
peak=    4.278 closest distance to " CB  GLN A 223 " =    1.498
peak=    4.235 closest distance to " O   PRO A 198 " =    1.398
peak=    4.229 closest distance to " O   HOH Z 316 " =    3.035
peak=    4.223 closest distance to " O   HOH Z  63 " =    1.511
peak=    4.223 closest distance to " O   HOH Z 423 " =    1.793
peak=    4.200 closest distance to " O   HOH Z  66 " =    1.191
peak=    4.187 closest distance to " O   HOH Z 123 " =    1.295
peak=    4.162 closest distance to " O   HOH Z  24 " =    1.893
peak=    4.153 closest distance to " NH2AARG A 145 " =    1.077
peak=    4.144 closest distance to " CA  PHE A 283 " =    1.229
peak=    4.140 closest distance to " O   HOH Z  39 " =    1.557
peak=    4.135 closest distance to " CD  ARG A 138 " =    0.874
peak=    4.122 closest distance to " CD2 LEU A 228 " =    1.183
peak=    4.116 closest distance to " O   HOH Z 422 " =    1.015
peak=    4.109 closest distance to " O   HOH Z 139 " =    1.230
peak=    4.096 closest distance to " O   HOH Z 225 " =    1.682
peak=    4.095 closest distance to " O   HOH Z 303 " =    2.152
peak=    4.093 closest distance to " O   HOH Z 425 " =    2.113
peak=    4.079 closest distance to " CG  PRO A 198 " =    1.305
peak=    4.063 closest distance to " CB  ASN A  39 " =    0.921
peak=    4.053 closest distance to " O   HOH Z 298 " =    1.677
peak=    4.016 closest distance to " CB  ASN A 142 " =    1.047
peak=    4.013 closest distance to " O   HOH Z 258 " =    2.069
peak=    4.012 closest distance to " CB  SER A 216 " =    0.973
peak=    4.009 closest distance to " O   HOH Z 380 " =    1.933
peak=    4.007 closest distance to " CG  PRO A 243 " =    1.166
peak=    4.005 closest distance to " O   HOH Z 371 " =    2.835
peak=    4.004 closest distance to " CB  SER A 276 " =    1.166
peak=    3.995 closest distance to " O   HOH Z  11 " =    1.916
peak=    3.977 closest distance to " O   HOH Z  91 " =    2.383
peak=    3.974 closest distance to " ND2BASN A 224 " =    0.851
peak=    3.971 closest distance to " CB  GLU A 277 " =    3.473
peak=    3.968 closest distance to " O   HOH Z 293 " =    1.457
peak=    3.961 closest distance to " O   HOH Z 392 " =    1.179
peak=    3.950 closest distance to " CB  SER A  63 " =    1.277
peak=    3.950 closest distance to " CB  ASN A 148 " =    1.363
peak=    3.936 closest distance to " CA  ILE A 234 " =    1.023
peak=    3.933 closest distance to " O   HOH Z 272 " =    1.809
peak=    3.919 closest distance to " O   HOH Z 143 " =    1.512
peak=    3.914 closest distance to " CB  GLN A 183 " =    1.186
peak=    3.909 closest distance to " O   HOH Z 422 " =    2.363
peak=    3.903 closest distance to " CG  GLN A  58 " =    1.042
peak=    3.899 closest distance to " O   HOH Z   1 " =    1.787
peak=    3.844 closest distance to " CB  VAL A 265 " =    1.343
peak=    3.844 closest distance to " O   HOH Z  61 " =    1.620
peak=    3.840 closest distance to " O   VAL A  72 " =    0.884
peak=    3.840 closest distance to " O   HOH Z 214 " =    2.569
peak=    3.822 closest distance to " O   HOH Z 193 " =    1.511
peak=    3.817 closest distance to " O   HOH Z 236 " =    1.586
peak=    3.815 closest distance to " O   HOH Z 146 " =    1.661
peak=    3.803 closest distance to " CA  ASN A 127 " =    1.082
peak=    3.797 closest distance to " O   HOH Z  69 " =    1.720
peak=    3.794 closest distance to " O   HOH Z 362 " =    1.794
peak=    3.792 closest distance to " CD  GLN A  77 " =    1.262
peak=    3.788 closest distance to " CG  LYS A  76 " =    1.749
peak=    3.784 closest distance to " O   HOH Z 423 " =    1.718
peak=    3.776 closest distance to " CG  LEU A 167 " =    1.238
peak=    3.775 closest distance to " CB  ASN A 215 " =    1.205
peak=    3.773 closest distance to " NE2 GLN A  58 " =    4.300
peak=    3.769 closest distance to " CE3 TRP A 150 " =    1.079
peak=    3.764 closest distance to " O   HOH Z 153 " =    3.634
peak=    3.763 closest distance to " O   HOH Z  26 " =    1.531
peak=    3.750 closest distance to " ND2 ASN A 249 " =    0.924
peak=    3.735 closest distance to " O   HOH Z 145 " =    2.449
peak=    3.731 closest distance to " O   HOH Z 130 " =    2.136
peak=    3.724 closest distance to " N   ARG A 156 " =    1.274
peak=    3.723 closest distance to " CB  ASP A 124 " =    0.881
peak=    3.707 closest distance to " OG BSER A 212 " =    2.837
peak=    3.690 closest distance to " NH2BARG A 190 " =    1.361
peak=    3.689 closest distance to " NZ  LYS A 119 " =    2.537
peak=    3.686 closest distance to " O   HOH Z  51 " =    1.812
peak=    3.678 closest distance to " CB  LYS A 117 " =    1.202
peak=    3.658 closest distance to " NH2AARG A 190 " =    1.746
peak=    3.647 closest distance to " CB  VAL A 202 " =    1.623
peak=    3.637 closest distance to " N   GLN A 278 " =    1.257
peak=    3.634 closest distance to " CB  ALA A  43 " =    0.891
peak=    3.629 closest distance to " O   HOH Z 218 " =    2.081
peak=    3.621 closest distance to " O   HOH Z 359 " =    1.369
peak=    3.621 closest distance to " CG  PRO A 213 " =    1.171
peak=    3.617 closest distance to " O   HOH Z 346 " =    1.563
peak=    3.611 closest distance to " CG AARG A 275 " =    1.225
peak=    3.607 closest distance to " O   HOH Z 406 " =    1.403
peak=    3.605 closest distance to " ND1 HIS A  81 " =    1.552
peak=    3.600 closest distance to " NH1AARG A 145 " =    1.097
peak=    3.599 closest distance to " O   HOH Z 116 " =    1.125
peak=    3.589 closest distance to " O   HOH Z  83 " =    1.160
peak=    3.586 closest distance to " O   HOH Z  44 " =    1.783
peak=    3.585 closest distance to " NE1 TRP A 274 " =    1.009
peak=    3.585 closest distance to " CB  TRP A 266 " =    1.129
peak=    3.581 closest distance to " CA  ARG A 195 " =    1.268
peak=    3.579 closest distance to " NE2 GLN A  73 " =    1.472
peak=    3.579 closest distance to " O   HOH Z 368 " =    3.341
peak=    3.571 closest distance to " O   ARG A 275 " =    1.333
peak=    3.564 closest distance to " O   HOH Z 350 " =    1.504
peak=    3.563 closest distance to " CB  SER A 212 " =    1.444
peak=    3.561 closest distance to " CG BARG A 102 " =    1.928
peak=    3.547 closest distance to " O   HOH Z  46 " =    1.096
peak=    3.547 closest distance to " O   HOH Z 411 " =    3.404
peak=    3.544 closest distance to " O   HOH Z  40 " =    1.482
peak=    3.542 closest distance to " O   HOH Z 437 " =    2.183
peak=    3.541 closest distance to " CA  GLY A 136 " =    1.050
peak=    3.539 closest distance to " O   HOH Z 379 " =    1.432
peak=    3.534 closest distance to " CB  LEU A 300 " =    0.978
peak=    3.530 closest distance to " CD1 LEU A 281 " =    1.003
peak=    3.529 closest distance to " O   HOH Z 148 " =    2.344
peak=    3.528 closest distance to " O   HOH Z  47 " =    1.499
peak=    3.524 closest distance to " O   HOH Z 331 " =    1.122
peak=    3.518 closest distance to " CD  ARG A 269 " =    1.000
peak=    3.514 closest distance to " O   HOH Z  22 " =    1.887
peak=    3.511 closest distance to " CD  ARG A 159 " =    0.781
peak=    3.509 closest distance to " N   PHE A 130 " =    1.276
peak=    3.500 closest distance to " CB  ARG A 138 " =    0.926
peak=    3.495 closest distance to " CB  TRP A 179 " =    1.424
peak=    3.494 closest distance to " CE3 TRP A 274 " =    1.358
peak=    3.494 closest distance to " O   HOH Z 403 " =    1.635
peak=    3.483 closest distance to " CA  ALA A 160 " =    1.525
peak=    3.478 closest distance to " CB  ARG A 190 " =    1.721
peak=    3.477 closest distance to " CB  ALA A 114 " =    1.174
peak=    3.472 closest distance to " O   HOH Z  76 " =    1.084
peak=    3.466 closest distance to " ND2 ASN A 187 " =    1.725
peak=    3.463 closest distance to " O   HOH Z 423 " =    1.970
peak=    3.457 closest distance to " CD1 LEU A   5 " =    1.555
peak=    3.457 closest distance to " O   HOH Z 233 " =    1.705
peak=    3.455 closest distance to " OE2 GLU A   2 " =    2.138
peak=    3.448 closest distance to " CB  PHE A 204 " =    0.940
peak=    3.445 closest distance to " O   HOH Z  30 " =    1.359
peak=    3.434 closest distance to " O   HOH Z 410 " =    1.621
peak=    3.433 closest distance to " O   HOH Z 329 " =    4.076
peak=    3.430 closest distance to " CB  MET A  47 " =    1.112
peak=    3.428 closest distance to " NZ  LYS A 117 " =    2.715
peak=    3.424 closest distance to " N   ASP A 162 " =    1.136
peak=    3.419 closest distance to " O   HOH Z 343 " =    2.824
peak=    3.418 closest distance to " O   HOH Z  48 " =    1.540
peak=    3.418 closest distance to " O   HOH Z 344 " =    1.163
peak=    3.417 closest distance to " O   HOH Z 352 " =    1.749
peak=    3.416 closest distance to " O   HOH Z 117 " =    1.963
peak=    3.416 closest distance to " O   HOH Z 193 " =    1.577
peak=    3.415 closest distance to " CB  SER A  62 " =    1.084
peak=    3.414 closest distance to " O   HOH Z   4 " =    1.382
peak=    3.414 closest distance to " OG  SER A  62 " =    2.957
peak=    3.412 closest distance to " CA  VAL A 125 " =    1.082
peak=    3.412 closest distance to " O   HOH Z   1 " =    1.655
peak=    3.411 closest distance to " CB  PRO A  90 " =    1.110
peak=    3.407 closest distance to " CA  ALA A  51 " =    1.098
peak=    3.402 closest distance to " CG2 ILE A  20 " =    1.650
peak=    3.397 closest distance to " CG2 THR A 221 " =    1.202
peak=    3.394 closest distance to " O   HOH Z 222 " =    2.106
peak=    3.393 closest distance to " OG1 THR A 221 " =    1.220
peak=    3.393 closest distance to " O   HOH Z 361 " =    1.253
peak=    3.387 closest distance to " O   HOH Z 327 " =    1.615
peak=    3.385 closest distance to " NH1 ARG A  14 " =    1.093
peak=    3.384 closest distance to " O   HOH Z  32 " =    2.242
peak=    3.380 closest distance to " CE AMET A  47 " =    1.436
peak=    3.372 closest distance to " CD1 ILE A  33 " =    1.868
peak=    3.368 closest distance to " O   HOH Z 272 " =    2.188
peak=    3.361 closest distance to " CE2 PHE A  16 " =    0.886
peak=    3.360 closest distance to " O   HOH Z  88 " =    3.491
peak=    3.356 closest distance to " O   HOH Z 172 " =    2.479
peak=    3.352 closest distance to " O   HOH Z 176 " =    1.769
peak=    3.348 closest distance to " O   HOH Z 181 " =    2.284
peak=    3.346 closest distance to " CA  ASN A 215 " =    0.966
peak=    3.343 closest distance to " O   HOH Z 393 " =    1.383
peak=    3.341 closest distance to " CB  LEU A 237 " =    0.870
peak=    3.338 closest distance to " CB  GLN A  88 " =    1.449
peak=    3.335 closest distance to " O  BHOH Z 338 " =    2.454
peak=    3.328 closest distance to " O   HOH Z 158 " =    2.785
peak=    3.324 closest distance to " CB  SER A 210 " =    0.927
peak=    3.323 closest distance to " O   HOH Z  58 " =    1.797
peak=    3.320 closest distance to " OD1 ASN A  45 " =    1.271
peak=    3.315 closest distance to " O   HOH Z  85 " =    1.267
peak=    3.315 closest distance to " N   SER A 271 " =    1.107
peak=    3.314 closest distance to " O   HOH Z 414 " =    1.123
peak=    3.313 closest distance to " CG  LYS A 119 " =    1.016
peak=    3.313 closest distance to " OG BSER A 164 " =    2.126
peak=    3.312 closest distance to " CG2 THR A 220 " =    0.861
peak=    3.307 closest distance to " O   HOH Z 150 " =    1.268
peak=    3.307 closest distance to " NZ  LYS A 117 " =    1.084
peak=    3.307 closest distance to " O   HOH Z  68 " =    2.018
peak=    3.305 closest distance to " O   HOH Z 425 " =    2.151
peak=    3.302 closest distance to " O   HOH Z 418 " =    2.077
peak=    3.300 closest distance to " O   HOH Z 356 " =    1.370
peak=    3.300 closest distance to " CG2 VAL A 257 " =    0.947
peak=    3.293 closest distance to " CB  THR A  31 " =    1.484
peak=    3.292 closest distance to " O   HOH Z 193 " =    1.181
peak=    3.291 closest distance to " CB  ALA A  10 " =    0.864
peak=    3.288 closest distance to " CB  SER A  99 " =    0.840
peak=    3.285 closest distance to " CB  SER A  26 " =    1.626
peak=    3.285 closest distance to " CE  MET A  40 " =    0.993
peak=    3.284 closest distance to " O   HOH Z 378 " =    1.053
peak=    3.283 closest distance to " N   GLU A   2 " =    1.405
peak=    3.281 closest distance to " CD  PRO A 243 " =    1.651
peak=    3.280 closest distance to " CB  ILE A 234 " =    1.326
peak=    3.270 closest distance to " O   HOH Z 388 " =    2.277
peak=    3.266 closest distance to " O   HOH Z 234 " =    3.655
peak=    3.265 closest distance to " O   HOH Z 392 " =    1.668
peak=    3.259 closest distance to " O   HOH Z 357 " =    2.082
peak=    3.257 closest distance to " CA  SER A  87 " =    1.000
peak=    3.257 closest distance to " CA  ALA A 129 " =    1.327
peak=    3.256 closest distance to " O   HOH Z   9 " =    2.179
peak=    3.255 closest distance to " NH1AARG A 275 " =    0.907
peak=    3.254 closest distance to " O   ASP A 124 " =    0.991
peak=    3.251 closest distance to " O   HOH Z 260 " =    2.328
peak=    3.250 closest distance to " O   HOH Z 368 " =    2.003
peak=    3.250 closest distance to " O   HOH Z 118 " =    1.530
peak=    3.249 closest distance to " N   ASN A 127 " =    1.371
peak=    3.248 closest distance to " CB  ARG A 219 " =    0.959
peak=    3.246 closest distance to " O   HOH Z  71 " =    1.215
peak=    3.246 closest distance to " O   HOH Z  40 " =    1.996
peak=    3.242 closest distance to " O   HOH Z 251 " =    1.407
peak=    3.239 closest distance to " CB  ALA A 248 " =    1.312
peak=    3.237 closest distance to " OD2 ASP A 286 " =    2.371
peak=    3.233 closest distance to " N   SER A  97 " =    0.852
peak=    3.231 closest distance to " C   ASN A 209 " =    1.602
peak=    3.228 closest distance to " O   HOH Z 330 " =    1.251
peak=    3.228 closest distance to " O   HOH Z 389 " =    2.946
peak=    3.225 closest distance to " O   HOH Z  55 " =    1.817
peak=    3.225 closest distance to " O   HOH Z 244 " =    1.623
peak=    3.224 closest distance to " CB  ARG A  79 " =    1.377
peak=    3.222 closest distance to " O   HOH Z 159 " =    0.878
peak=    3.221 closest distance to " O   HOH Z  10 " =    1.747
peak=    3.221 closest distance to " O   HOH Z 177 " =    1.112
peak=    3.220 closest distance to " CE1 TYR A 116 " =    1.471
peak=    3.211 closest distance to " O   HOH Z   6 " =    1.577
peak=    3.210 closest distance to " CZ  PHE A  38 " =    1.229
peak=    3.206 closest distance to " CA  ASP A 162 " =    0.936
peak=    3.205 closest distance to " CB  ARG A  79 " =    0.830
peak=    3.197 closest distance to " O   HOH Z 305 " =    3.533
peak=    3.194 closest distance to " CG2 THR A 178 " =    1.071
peak=    3.186 closest distance to " CB BVAL A  41 " =    1.379
peak=    3.183 closest distance to " O   HOH Z 302 " =    1.594
peak=    3.183 closest distance to " O   HOH Z 332 " =    1.475
peak=    3.182 closest distance to " N   ALA A 256 " =    1.028
peak=    3.181 closest distance to " CA  LEU A 282 " =    1.220
peak=    3.179 closest distance to " CB  GLU A 128 " =    0.993
peak=    3.173 closest distance to " CD  LYS A 166 " =    1.370
peak=    3.171 closest distance to " O   HOH Z 148 " =    1.599
peak=    3.170 closest distance to " O   HOH Z 128 " =    2.059
peak=    3.170 closest distance to " N   CYS A 260 " =    0.970
peak=    3.163 closest distance to " O   HOH Z 125 " =    1.561
peak=    3.163 closest distance to " O   HOH Z  44 " =    2.352
peak=    3.160 closest distance to " O   HOH Z 147 " =    1.315
peak=    3.159 closest distance to " N   TYR A  15 " =    1.105
peak=    3.159 closest distance to " CE  LYS A  76 " =    0.902
peak=    3.156 closest distance to " O   PHE A 192 " =    1.429
peak=    3.155 closest distance to " O   HOH Z 207 " =    2.659
peak=    3.151 closest distance to " O   ILE A  20 " =    1.855
peak=    3.147 closest distance to " OE1 GLN A 240 " =    1.462
peak=    3.143 closest distance to " CA  PHE A 155 " =    1.017
peak=    3.142 closest distance to " CB  HIS A 108 " =    0.830
peak=    3.139 closest distance to " CG2 VAL A 197 " =    1.108
peak=    3.137 closest distance to " O   HOH Z 371 " =    2.110
peak=    3.134 closest distance to " O   HOH Z 402 " =    1.416
peak=    3.133 closest distance to " O   HOH Z   3 " =    2.233
peak=    3.126 closest distance to " O   GLY A 302 " =    2.082
peak=    3.123 closest distance to " O   HOH Z 323 " =    1.702
peak=    3.122 closest distance to " CA  VAL A 153 " =    1.153
peak=    3.120 closest distance to " OE1 GLU A   2 " =    1.495
peak=    3.115 closest distance to " O   HOH Z 291 " =    1.696
peak=    3.114 closest distance to " O   HOH Z 162 " =    1.372
peak=    3.112 closest distance to " O   HOH Z  41 " =    2.560
peak=    3.106 closest distance to " O   HOH Z 245 " =    1.222
peak=    3.101 closest distance to " CB  ASN A 187 " =    1.019
peak=    3.100 closest distance to " O   HOH Z 119 " =    1.620
peak=    3.099 closest distance to " CB  ARG A  79 " =    0.893
peak=    3.082 closest distance to " O   HOH Z 222 " =    1.935
peak=    3.081 closest distance to " CG1 ILE A 263 " =    1.266
peak=    3.077 closest distance to " O   HOH Z 193 " =    1.643
peak=    3.071 closest distance to " O   HOH Z 216 " =    3.775
peak=    3.058 closest distance to " CG2BVAL A  72 " =    1.240
peak=    3.047 closest distance to " O   HOH Z 154 " =    1.721
peak=    3.041 closest distance to " O   HOH Z 109 " =    2.485
peak=    3.041 closest distance to " CA  ALA A 184 " =    1.137

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 212         
Filter by distance & map next to the model:
   mapped sites are within: 0.582 - 5.595
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 211 from: 212
   mapped sites are within: 0.752 - 5.595

peak=   -5.332 closest distance to " CG2 VAL A 230 " =    0.792
peak=   -4.892 closest distance to " O   HOH Z  69 " =    1.693
peak=   -4.793 closest distance to " O   PRO A 198 " =    1.072
peak=   -4.642 closest distance to " O   HOH Z 131 " =    3.985
peak=   -4.634 closest distance to " O   HOH Z 100 " =    0.853
peak=   -4.387 closest distance to " CD  ARG A 138 " =    1.245
peak=   -4.374 closest distance to " OG BSER A 134 " =    1.420
peak=   -4.157 closest distance to " O   HOH Z 231 " =    0.752
peak=   -4.140 closest distance to " CB  VAL A 230 " =    0.957
peak=   -4.126 closest distance to " O   HOH Z  24 " =    1.032
peak=   -4.099 closest distance to " CD1 LEU A 255 " =    2.874
peak=   -4.050 closest distance to " O   HOH Z 211 " =    1.000
peak=   -4.049 closest distance to " CB  ALA A  43 " =    2.381
peak=   -4.044 closest distance to " CE2 PHE A 218 " =    2.503
peak=   -4.036 closest distance to " CB  GLN A  55 " =    1.167
peak=   -4.008 closest distance to " O   HOH Z 415 " =    0.980
peak=   -4.000 closest distance to " O   SER A 135 " =    1.546
peak=   -3.985 closest distance to " N   THR A 157 " =    1.475
peak=   -3.970 closest distance to " CG  ARG A 138 " =    0.961
peak=   -3.928 closest distance to " O   HOH Z  52 " =    0.800
peak=   -3.880 closest distance to " O   HOH Z 385 " =    1.235
peak=   -3.867 closest distance to " CG  TRP A 266 " =    1.784
peak=   -3.866 closest distance to " C   HIS A 108 " =    1.187
peak=   -3.853 closest distance to " O   HOH Z 266 " =    5.077
peak=   -3.852 closest distance to " CB  ASP A  27 " =    2.370
peak=   -3.852 closest distance to " O   HOH Z 100 " =    1.005
peak=   -3.845 closest distance to " O   HOH Z 359 " =    3.331
peak=   -3.773 closest distance to " O   HOH Z 193 " =    1.000
peak=   -3.749 closest distance to " O   HOH Z 331 " =    0.986
peak=   -3.745 closest distance to " O   HOH Z 427 " =    1.879
peak=   -3.732 closest distance to " CD  ARG A  14 " =    2.989
peak=   -3.726 closest distance to " CB  ALA A 248 " =    2.184
peak=   -3.708 closest distance to " NE2 GLN A  55 " =    1.083
peak=   -3.704 closest distance to " CA  ASN A 127 " =    1.253
peak=   -3.691 closest distance to " CD2 LEU A   5 " =    0.937
peak=   -3.679 closest distance to " N   VAL A  72 " =    2.050
peak=   -3.675 closest distance to " OE1 GLU A 277 " =    2.166
peak=   -3.672 closest distance to " O   HOH Z  39 " =    0.991
peak=   -3.667 closest distance to " CB  TYR A  68 " =    1.376
peak=   -3.665 closest distance to " CD2 TYR A 293 " =    1.861
peak=   -3.658 closest distance to " O   HOH Z 185 " =    1.953
peak=   -3.652 closest distance to " CB  ASP A 132 " =    2.411
peak=   -3.651 closest distance to " ND2 ASN A 249 " =    2.377
peak=   -3.646 closest distance to " CG  ARG A 219 " =    2.281
peak=   -3.644 closest distance to " O   HOH Z  53 " =    1.670
peak=   -3.638 closest distance to " CG2 VAL A 296 " =    2.328
peak=   -3.635 closest distance to " CB  PRO A 243 " =    2.642
peak=   -3.634 closest distance to " OG  SER A  97 " =    2.146
peak=   -3.620 closest distance to " O   HOH Z  60 " =    1.807
peak=   -3.612 closest distance to " OG  SER A  87 " =    1.621
peak=   -3.606 closest distance to " CA  GLY A  35 " =    2.073
peak=   -3.603 closest distance to " O   SER A  22 " =    2.558
peak=   -3.601 closest distance to " CE2 TYR A  30 " =    2.731
peak=   -3.600 closest distance to " O   PRO A 163 " =    1.850
peak=   -3.597 closest distance to " O   HOH Z 359 " =    1.752
peak=   -3.592 closest distance to " NH2 ARG A  79 " =    2.202
peak=   -3.585 closest distance to " O   HOH Z 238 " =    0.944
peak=   -3.583 closest distance to " O   HOH Z 368 " =    2.462
peak=   -3.575 closest distance to " C   GLU A   2 " =    1.921
peak=   -3.570 closest distance to " O   HOH Z 286 " =    1.576
peak=   -3.556 closest distance to " O   HOH Z 407 " =    2.567
peak=   -3.552 closest distance to " CD  ARG A 156 " =    1.898
peak=   -3.545 closest distance to " N   GLN A  58 " =    1.281
peak=   -3.545 closest distance to " CB  ALA A 114 " =    2.406
peak=   -3.534 closest distance to " ND2 ASN A 187 " =    1.492
peak=   -3.534 closest distance to " N   PRO A 163 " =    1.493
peak=   -3.532 closest distance to " CD2 LEU A 237 " =    2.695
peak=   -3.531 closest distance to " CA  GLY A 133 " =    2.053
peak=   -3.525 closest distance to " N   ALA A  43 " =    2.565
peak=   -3.516 closest distance to " O   HOH Z  65 " =    1.277
peak=   -3.513 closest distance to " O   HOH Z 166 " =    1.489
peak=   -3.511 closest distance to " N   ALA A   1 " =    1.324
peak=   -3.508 closest distance to " O   VAL A  67 " =    2.511
peak=   -3.508 closest distance to " CG2 VAL A 202 " =    2.721
peak=   -3.507 closest distance to " ND2 ASN A  45 " =    2.387
peak=   -3.501 closest distance to " C   ARG A 269 " =    1.319
peak=   -3.499 closest distance to " O   ILE A  49 " =    1.558
peak=   -3.491 closest distance to " OG  SER A 245 " =    1.394
peak=   -3.484 closest distance to " CA  GLY A 241 " =    2.346
peak=   -3.482 closest distance to " C   GLN A 205 " =    2.015
peak=   -3.474 closest distance to " CE1 TYR A 247 " =    2.557
peak=   -3.474 closest distance to " O   HOH Z 377 " =    0.947
peak=   -3.468 closest distance to " CG  GLN A  58 " =    0.860
peak=   -3.467 closest distance to " CZ2 TRP A 274 " =    0.955
peak=   -3.462 closest distance to " O   HOH Z 389 " =    1.272
peak=   -3.458 closest distance to " O   PRO A 243 " =    2.534
peak=   -3.456 closest distance to " O   HOH Z 231 " =    2.050
peak=   -3.451 closest distance to " O   HOH Z 183 " =    1.651
peak=   -3.451 closest distance to " O   HOH Z 298 " =    2.942
peak=   -3.450 closest distance to " O   HOH Z 404 " =    1.558
peak=   -3.445 closest distance to " CG2 ILE A  20 " =    2.710
peak=   -3.444 closest distance to " CB  LYS A 290 " =    2.164
peak=   -3.428 closest distance to " ND2 ASN A 285 " =    1.980
peak=   -3.428 closest distance to " O   HOH Z 276 " =    1.333
peak=   -3.414 closest distance to " O   HOH Z 134 " =    4.172
peak=   -3.409 closest distance to " CG2 THR A  52 " =    2.888
peak=   -3.409 closest distance to " O   HOH Z 352 " =    1.586
peak=   -3.408 closest distance to " O   HOH Z 435 " =    2.325
peak=   -3.407 closest distance to " O   HOH Z 159 " =    0.844
peak=   -3.402 closest distance to " CB  ASN A  39 " =    2.310
peak=   -3.401 closest distance to " O   HOH Z 414 " =    2.163
peak=   -3.399 closest distance to " CZ  TYR A 169 " =    1.868
peak=   -3.397 closest distance to " C   VAL A  72 " =    0.913
peak=   -3.394 closest distance to " O   ALA A  10 " =    1.566
peak=   -3.393 closest distance to " O   ALA A  84 " =    1.662
peak=   -3.390 closest distance to " O   HOH Z  11 " =    1.863
peak=   -3.388 closest distance to " O   ASP A 270 " =    1.598
peak=   -3.384 closest distance to " O   HOH Z 313 " =    1.424
peak=   -3.382 closest distance to " CB  ASP A 132 " =    2.470
peak=   -3.379 closest distance to " O   HOH Z 295 " =    2.022
peak=   -3.367 closest distance to " O   ASN A 301 " =    1.343
peak=   -3.366 closest distance to " O   ALA A  51 " =    1.188
peak=   -3.354 closest distance to " O   HOH Z 339 " =    1.719
peak=   -3.353 closest distance to " O   HOH Z 232 " =    2.306
peak=   -3.352 closest distance to " O   HOH Z  64 " =    1.292
peak=   -3.349 closest distance to " O   GLN A 240 " =    1.969
peak=   -3.349 closest distance to " O   HOH Z 275 " =    1.778
peak=   -3.348 closest distance to " OD2 ASP A 171 " =    2.163
peak=   -3.338 closest distance to " O   HOH Z 128 " =    2.373
peak=   -3.337 closest distance to " OG  SER A  62 " =    4.134
peak=   -3.336 closest distance to " CG  PRO A 243 " =    1.568
peak=   -3.335 closest distance to " CD  PRO A 213 " =    2.107
peak=   -3.333 closest distance to " O   HOH Z 292 " =    1.384
peak=   -3.325 closest distance to " CD2 PHE A  61 " =    1.994
peak=   -3.324 closest distance to " C   MET A 188 " =    1.639
peak=   -3.323 closest distance to " O   HOH Z  66 " =    0.784
peak=   -3.323 closest distance to " CA  GLY A  23 " =    2.015
peak=   -3.312 closest distance to " CB  ALA A   7 " =    2.093
peak=   -3.312 closest distance to " O   HOH Z   9 " =    2.128
peak=   -3.304 closest distance to " O   HOH Z 151 " =    1.219
peak=   -3.302 closest distance to " O   SER A 271 " =    2.158
peak=   -3.302 closest distance to " CG  MET A 105 " =    0.943
peak=   -3.302 closest distance to " O   HOH Z 189 " =    1.079
peak=   -3.301 closest distance to " CD1 LEU A 101 " =    2.238
peak=   -3.292 closest distance to " O   HOH Z 111 " =    4.694
peak=   -3.291 closest distance to " CE  MET A 188 " =    2.236
peak=   -3.290 closest distance to " CB  ALA A   9 " =    2.444
peak=   -3.289 closest distance to " O   HOH Z  52 " =    1.572
peak=   -3.289 closest distance to " CA  GLY A  57 " =    2.213
peak=   -3.283 closest distance to " O   HOH Z 186 " =    1.461
peak=   -3.282 closest distance to " O   HOH Z 159 " =    1.613
peak=   -3.280 closest distance to " OXT GLY A 302 " =    4.203
peak=   -3.277 closest distance to " CB  ASN A  45 " =    2.043
peak=   -3.272 closest distance to " O   HOH Z 216 " =    1.528
peak=   -3.269 closest distance to " C   ALA A 158 " =    1.382
peak=   -3.267 closest distance to " O   HOH Z 428 " =    1.608
peak=   -3.262 closest distance to " CA  GLY A  98 " =    1.845
peak=   -3.258 closest distance to " CE BMET A  47 " =    1.124
peak=   -3.256 closest distance to " CD  GLU A 277 " =    0.887
peak=   -3.242 closest distance to " O   ASP A 191 " =    1.871
peak=   -3.242 closest distance to " CB  TRP A  85 " =    2.557
peak=   -3.239 closest distance to " O   HOH Z 350 " =    2.147
peak=   -3.239 closest distance to " C   ASN A 285 " =    2.028
peak=   -3.227 closest distance to " N   ASP A 171 " =    2.544
peak=   -3.227 closest distance to " CD1 TRP A 179 " =    1.074
peak=   -3.223 closest distance to " CE  MET A 105 " =    2.462
peak=   -3.220 closest distance to " OH  TYR A 172 " =    1.732
peak=   -3.216 closest distance to " O   HOH Z 414 " =    1.670
peak=   -3.215 closest distance to " OE2 GLU A 152 " =    1.178
peak=   -3.211 closest distance to " CB  ALA A 291 " =    2.228
peak=   -3.211 closest distance to " O   HOH Z 406 " =    0.883
peak=   -3.208 closest distance to " CG  LEU A  83 " =    2.159
peak=   -3.199 closest distance to " CE2 TRP A  70 " =    2.373
peak=   -3.196 closest distance to " O   HOH Z 283 " =    2.271
peak=   -3.189 closest distance to " CG  PRO A 163 " =    2.693
peak=   -3.187 closest distance to " O   HOH Z 235 " =    1.166
peak=   -3.187 closest distance to " O   HOH Z 208 " =    2.186
peak=   -3.184 closest distance to " OG  SER A  63 " =    1.425
peak=   -3.184 closest distance to " O   GLN A 144 " =    1.360
peak=   -3.183 closest distance to " CB  PHE A 130 " =    1.219
peak=   -3.182 closest distance to " O   GLU A 152 " =    1.500
peak=   -3.176 closest distance to " CG  GLN A 240 " =    2.352
peak=   -3.176 closest distance to " CG2AVAL A  41 " =    2.856
peak=   -3.174 closest distance to " CZ  PHE A  38 " =    2.343
peak=   -3.167 closest distance to " O   HOH Z 149 " =    1.559
peak=   -3.166 closest distance to " NE2 GLN A 223 " =    1.694
peak=   -3.162 closest distance to " O   HOH Z 374 " =    1.826
peak=   -3.160 closest distance to " C   ILE A 239 " =    2.014
peak=   -3.159 closest distance to " O   HOH Z 159 " =    1.083
peak=   -3.158 closest distance to " O   GLY A  80 " =    2.534
peak=   -3.152 closest distance to " O   HOH Z  37 " =    1.545
peak=   -3.149 closest distance to " OG BSER A  99 " =    1.216
peak=   -3.149 closest distance to " O   HOH Z 300 " =    1.250
peak=   -3.147 closest distance to " O   HOH Z  69 " =    2.099
peak=   -3.141 closest distance to " O   HOH Z 105 " =    1.867
peak=   -3.141 closest distance to " CD  LYS A 289 " =    2.275
peak=   -3.140 closest distance to " CG2 VAL A 189 " =    1.950
peak=   -3.133 closest distance to " CG2 ILE A 120 " =    1.254
peak=   -3.132 closest distance to " O   VAL A  72 " =    1.085
peak=   -3.130 closest distance to " CZ3 TRP A 274 " =    2.333
peak=   -3.129 closest distance to " CZ2 TRP A  92 " =    2.799
peak=   -3.128 closest distance to " O   HOH Z 251 " =    1.731
peak=   -3.121 closest distance to " O   HOH Z 292 " =    1.563
peak=   -3.115 closest distance to " O   HOH Z 262 " =    2.591
peak=   -3.102 closest distance to " O   HOH Z 191 " =    5.595
peak=   -3.095 closest distance to " ND2 ASN A  39 " =    1.346
peak=   -3.093 closest distance to " NH2 ARG A 219 " =    1.748
peak=   -3.092 closest distance to " O   HOH Z 144 " =    0.914
peak=   -3.091 closest distance to " O   THR A  82 " =    1.179
peak=   -3.085 closest distance to " CD  LYS A 166 " =    2.589
peak=   -3.074 closest distance to " CD2 HIS A 207 " =    2.221
peak=   -3.073 closest distance to " OE1 GLN A 183 " =    1.595
peak=   -3.069 closest distance to " O   HOH Z 401 " =    1.352
peak=   -3.064 closest distance to " CG  ARG A 259 " =    2.281
peak=   -3.059 closest distance to " O   ARG A 156 " =    1.011
peak=   -3.055 closest distance to " O   ASP A 124 " =    1.374
peak=   -3.052 closest distance to " CB  TRP A 274 " =    2.656
peak=   -3.047 closest distance to " O   HOH Z 353 " =    1.549
peak=   -3.044 closest distance to " NH2AARG A 275 " =    5.008
peak=   -3.044 closest distance to " OD1 ASN A 301 " =    2.016
peak=   -3.029 closest distance to " CE BMET A  47 " =    1.301

================= 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    :  0.4967 0.4882   6.297211e+00   6.282146e+00
   1_bss:  0.4886 0.4753   6.291733e+00   6.273040e+00
   1_xyz:  0.4195 0.4424   6.212942e+00   6.235151e+00
   1_adp:  0.3786 0.4407   6.161776e+00   6.232015e+00
   1_occ:  0.3783 0.4418   6.161547e+00   6.232651e+00
   2_bss:  0.3765 0.4375   6.162545e+00   6.231921e+00
   2_xyz:  0.3108 0.3783   6.015930e+00   6.140583e+00
   2_adp:  0.2902 0.3652   5.973884e+00   6.108475e+00
   2_occ:  0.2899 0.3653   5.974172e+00   6.109277e+00
   3_bss:  0.2882 0.3634   5.973429e+00   6.108713e+00
   3_xyz:  0.2232 0.2854   5.744880e+00   5.920006e+00
   3_adp:  0.1996 0.2701   5.662344e+00   5.870472e+00
   3_occ:  0.1994 0.2698   5.661524e+00   5.869961e+00
   4_bss:  0.1988 0.2699   5.661401e+00   5.869958e+00
   4_xyz:  0.1609 0.2215   5.475025e+00   5.704849e+00
   4_adp:  0.1495 0.2065   5.404927e+00   5.635499e+00
   4_occ:  0.1494 0.2062   5.404059e+00   5.634453e+00
   5_bss:  0.1496 0.2063   5.402885e+00   5.633759e+00
   5_xyz:  0.1319 0.1840   5.289299e+00   5.528670e+00
   5_adp:  0.1285 0.1771   5.259528e+00   5.490400e+00
   5_occ:  0.1283 0.1769   5.258790e+00   5.489509e+00
   5_bss:  0.1283 0.1769   5.258637e+00   5.489340e+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:  0.375  20.001   6.373   9.258   9.495   0.000   0.000   0.000
   1_xyz:  0.375  20.001   6.373   9.258   9.495   0.000   0.000   0.000
   1_adp:  0.375  20.001   6.373   9.258   9.495   0.000   0.000   0.000
   1_occ:  0.375  20.001   6.373   9.258   9.495   0.000   0.000   0.000
   2_bss:  0.351  35.387   3.451   5.463   5.959   0.000   0.000   0.000
   2_xyz:  0.351  35.387   3.451   5.463   5.959   0.000   0.000   0.000
   2_adp:  0.351  35.387   3.451   5.463   5.959   0.000   0.000   0.000
   2_occ:  0.351  35.387   3.451   5.463   5.959   0.000   0.000   0.000
   3_bss:  0.325  43.705   1.577   2.906   3.695   0.000   0.000   0.000
   3_xyz:  0.325  43.705   1.577   2.906   3.695   0.000   0.000   0.000
   3_adp:  0.325  43.705   1.577   2.906   3.695   0.000   0.000   0.000
   3_occ:  0.325  43.705   1.577   2.906   3.695   0.000   0.000   0.000
   4_bss:  0.328  52.860   0.688   1.470   2.866   0.000   0.000   0.000
   4_xyz:  0.328  52.860   0.688   1.470   2.866   0.000   0.000   0.000
   4_adp:  0.328  52.860   0.688   1.470   2.866   0.000   0.000   0.000
   4_occ:  0.328  52.860   0.688   1.470   2.866   0.000   0.000   0.000
   5_bss:  0.323  51.700   0.653   0.937   2.733   0.000   0.000   0.000
   5_xyz:  0.323  51.700   0.653   0.937   2.733   0.000   0.000   0.000
   5_adp:  0.323  51.700   0.653   0.937   2.733   0.000   0.000   0.000
   5_occ:  0.323  51.700   0.653   0.937   2.733   0.000   0.000   0.000
   5_bss:  0.323  53.103  -0.765  -0.586   1.351   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  62.940 0.3549  0.4232    77218.553
   1_bss:  62.441 0.3602  0.5441    74814.561
   1_xyz:  53.613 0.4734  0.7028    60192.818
   1_adp:  52.815 0.4833  0.7821    59298.525
   1_occ:  52.950 0.4815  0.7780    59525.566
   2_bss:  52.608 0.4857  0.6997    58861.144
   2_xyz:  42.298 0.6138  0.8817    41352.273
   2_adp:  39.576 0.6471  0.9226    37414.687
   2_occ:  39.640 0.6464  0.9211    37495.623
   3_bss:  39.427 0.6488  0.8532    37200.823
   3_xyz:  29.086 0.7669  0.9764    21576.309
   3_adp:  26.885 0.7912  0.9833    19025.922
   3_occ:  26.874 0.7914  0.9831    18978.279
   4_bss:  26.824 0.7920  0.9474    18994.460
   4_xyz:  21.847 0.8428  0.9793    12671.865
   4_adp:  19.809 0.8634  0.9788    10943.620
   4_occ:  19.785 0.8636  0.9787    10912.415
   5_bss:  19.743 0.8639  0.9706    10873.807
   5_xyz:  17.237 0.8870  0.9832     8607.112
   5_adp:  16.242 0.8963  0.9798     8047.500
   5_occ:  16.233 0.8964  0.9795     8025.740
   5_bss:  16.229 0.8964  0.9782     8023.275
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.087   5.3413e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.087   5.3413e+01
   1_xyz:   1.725  0.013  0.106 18.343  0.006  4.104   1.4653e-01
   1_adp:   1.725  0.013  0.106 18.343  0.006  4.104   1.4653e-01
   1_occ:   1.725  0.013  0.106 18.343  0.006  4.104   1.4653e-01
   2_bss:   1.725  0.013  0.106 18.343  0.006  4.104   1.4653e-01
   2_xyz:   1.195  0.008  0.083 16.068  0.005  4.105   8.9322e-02
   2_adp:   1.195  0.008  0.083 16.068  0.005  4.105   8.9322e-02
   2_occ:   1.195  0.008  0.083 16.068  0.005  4.105   8.9322e-02
   3_bss:   1.195  0.008  0.083 16.068  0.005  4.105   8.9322e-02
   3_xyz:   1.154  0.009  0.085 15.884  0.005  4.122   7.9446e-02
   3_adp:   1.154  0.009  0.085 15.884  0.005  4.122   7.9446e-02
   3_occ:   1.154  0.009  0.085 15.884  0.005  4.122   7.9446e-02
   4_bss:   1.154  0.009  0.085 15.884  0.005  4.122   7.9446e-02
   4_xyz:   0.964  0.007  0.071 15.577  0.004  4.110   5.9759e-02
   4_adp:   0.964  0.007  0.071 15.577  0.004  4.110   5.9759e-02
   4_occ:   0.964  0.007  0.071 15.577  0.004  4.110   5.9759e-02
   5_bss:   0.964  0.007  0.071 15.577  0.004  4.110   5.9759e-02
   5_xyz:   0.963  0.006  0.071 15.474  0.003  4.115   5.8322e-02
   5_adp:   0.963  0.006  0.071 15.474  0.003  4.115   5.8322e-02
   5_occ:   0.963  0.006  0.071 15.474  0.003  4.115   5.8322e-02
   5_bss:   0.963  0.006  0.071 15.474  0.003  4.115   5.8322e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9214e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9214e+00
   1_xyz:  13.658  0.189  0.411 84.808  0.037  2.128   9.9207e-02
   1_adp:  13.658  0.189  0.411 84.808  0.037  2.128   9.9207e-02
   1_occ:  13.658  0.189  0.411 84.808  0.037  2.128   9.9207e-02
   2_bss:  13.658  0.189  0.411 84.808  0.037  2.128   9.9207e-02
   2_xyz:   6.907  0.067  0.316 81.850  0.041  2.121   6.7698e-02
   2_adp:   6.907  0.067  0.316 81.850  0.041  2.121   6.7698e-02
   2_occ:   6.907  0.067  0.316 81.850  0.041  2.121   6.7698e-02
   3_bss:   6.907  0.067  0.316 81.850  0.041  2.121   6.7698e-02
   3_xyz:   7.591  0.066  0.354 83.472  0.030  2.315   6.1109e-02
   3_adp:   7.591  0.066  0.354 83.472  0.030  2.315   6.1109e-02
   3_occ:   7.591  0.066  0.354 83.472  0.030  2.315   6.1109e-02
   4_bss:   7.591  0.066  0.354 83.472  0.030  2.315   6.1109e-02
   4_xyz:   6.537  0.046  0.217 84.171  0.033  2.395   4.5954e-02
   4_adp:   6.537  0.046  0.217 84.171  0.033  2.395   4.5954e-02
   4_occ:   6.537  0.046  0.217 84.171  0.033  2.395   4.5954e-02
   5_bss:   6.537  0.046  0.217 84.171  0.033  2.395   4.5954e-02
   5_xyz:   7.608  0.049  0.254 81.633  0.027  2.374   4.0012e-02
   5_adp:   7.608  0.049  0.254 81.633  0.027  2.374   4.0012e-02
   5_occ:   7.608  0.049  0.254 81.633  0.027  2.374   4.0012e-02
   5_bss:   7.608  0.049  0.254 81.633  0.027  2.374   4.0012e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  85.38   0.00  15.44  67.47   0.00  13.65  85.38   0.00  25.24
   1_occ:  85.38   0.00  15.44  67.47   0.00  13.65  85.38   0.00  25.24
   2_bss:  85.38   0.00  15.44  67.47   0.00  13.65  85.38   0.00  25.24
   2_xyz:  85.38   0.00  15.44  67.47   0.00  13.65  85.38   0.00  25.24
   2_adp:  90.18   0.00  14.79  69.88   0.00  11.98  90.18   0.00  30.05
   2_occ:  90.18   0.00  14.79  69.88   0.00  11.98  90.18   0.00  30.05
   3_bss:  90.18   0.00  14.79  69.88   0.00  11.98  90.18   0.00  30.05
   3_xyz:  90.18   0.00  14.79  69.88   0.00  11.98  90.18   0.00  30.05
   3_adp: 101.86   0.00  15.98  87.99   0.00  11.40 101.86   0.00  40.89
   3_occ: 101.86   0.00  15.98  87.99   0.00  11.40 101.86   0.00  40.89
   4_bss: 101.86   0.00  15.98  87.99   0.00  11.40 101.86   0.00  40.89
   4_xyz: 101.86   0.00  15.98  87.99   0.00  11.40 101.86   0.00  40.89
   4_adp: 104.34   0.00  15.35  95.78   0.00  10.34 104.34   2.48  42.60
   4_occ: 104.34   0.00  15.35  95.78   0.00  10.34 104.34   2.48  42.60
   5_bss: 104.34   0.00  15.35  95.78   0.00  10.34 104.34   2.48  42.60
   5_xyz: 104.34   0.00  15.35  95.78   0.00  10.34 104.34   2.48  42.60
   5_adp: 101.13   0.00  14.63  99.60   0.00   9.83 101.13   3.03  40.75
   5_occ: 101.13   0.00  14.63  99.60   0.00   9.83 101.13   3.03  40.75
   5_bss: 102.54   1.40  16.03 101.00   1.40  11.23 102.54   4.44  42.15
------------------------------------------------------------------------
 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:    1.298    0.040    0.411
   1_adp:    1.298    0.040    0.411
   1_occ:    1.298    0.040    0.411
   2_bss:    1.298    0.040    0.411
   2_xyz:    1.750    0.023    0.572
   2_adp:    1.750    0.023    0.572
   2_occ:    1.750    0.023    0.572
   3_bss:    1.750    0.023    0.572
   3_xyz:    1.590    0.071    0.690
   3_adp:    1.590    0.071    0.690
   3_occ:    1.590    0.071    0.690
   4_bss:    1.590    0.071    0.690
   4_xyz:    1.687    0.071    0.770
   4_adp:    1.687    0.071    0.770
   4_occ:    1.687    0.071    0.770
   5_bss:    1.687    0.071    0.770
   5_xyz:    1.764    0.037    0.804
   5_adp:    1.764    0.037    0.804
   5_occ:    1.764    0.037    0.804
   5_bss:    1.764    0.037    0.804
------------------------------------------------------------------------

CPU time actual refinement: 333.10


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_382/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_382/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_382/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_382/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_382/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 332.94 
  Macro-tasks:
    bulk solvent and scale       = 41.58  
    individual site refinement   = 134.63 
    weights calculation          = 31.64  
    collect and process          = 6.46   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 214.43 
  Micro-tasks:
    mask                            = 2.37   
    f_calc                          = 103.31 
    alpha_beta                      = 8.29   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 112.49 
    fmodel                         = 7.25   
    r_factors                      = 0.21   
    phase_errors                   = 10.08  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 245.43 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.757 micro seconds
Total CPU time: 5.78 minutes
from_scatterers_fft:    634 calls, 102.97 s
gradients_fft:          580 calls,  99.95 s

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

# Date 2008-01-16 Time 01:27:20 PST -0800 (1200475640.46 s)
Start R-work = 0.4967, R-free = 0.4882 (no bulk solvent and anisotropic scale)
Final R-work = 0.1448, R-free = 0.1914 (no bulk solvent and anisotropic scale)

Start R-work = 0.4886, R-free = 0.4753
Final R-work = 0.1283, R-free = 0.1769