# Date 2008-01-16 Time 03:26:38 PST -0800 (1200482798.23 s)
#phil __OFF__

Command line arguments: "../1237.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 24442
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1237

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (72.0062, 46.2261, 86.39, 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: (72.0062, 46.2261, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2644 1.97392
Completeness in resolution range: 0.9388
Completeness with d_max=infinity: 0.936108

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2644
                             d_min =   1.9739

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (72.0062, 46.2261, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2644 1.97392
Completeness in resolution range: 0.9388
Completeness with d_max=infinity: 0.936108

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2649 -  4.2254 [2193/2220]  1976   217   9.9%
  bin  2:  4.2254 -  3.3657 [2103/2123]  1892   211  10.0%
  bin  3:  3.3657 -  2.9437 [2074/2093]  1864   210  10.1%
  bin  4:  2.9437 -  2.6761 [2049/2079]  1842   207  10.1%
  bin  5:  2.6761 -  2.4852 [2056/2075]  1860   196   9.5%
  bin  6:  2.4852 -  2.3392 [2037/2062]  1823   214  10.5%
  bin  7:  2.3392 -  2.2224 [2032/2060]  1827   205  10.1%
  bin  8:  2.2224 -  2.1260 [2006/2042]  1812   194   9.7%
  bin  9:  2.1260 -  2.0443 [2006/2055]  1806   200  10.0%
  bin 10:  2.0443 -  1.9739 [1033/2057]   928   105  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1237/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:
        1.81 -     2.42: 30
        2.42 -     3.04: 2182
        3.04 -     3.66: 4700
        3.66 -     4.28: 9022
        4.28 -     4.90: 12292
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 208 " - " O   HOH Z 342 "  1.926 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.948 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.051 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.091 3.040 x,y+1,z
  ... (remaining 28221 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_1237/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1237/model_refine_001.geo

CPU time processing inputs: 9.15


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 72.00625 46.22605 86.39 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4881   r_free= 0.4818   ksol= 0.00   Bsol= 0.00   scale= 0.783    |
|                                                                             |
| 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:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.290032                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2649 -  4.7137 0.99   1420  160 0.4073 0.4134      6.6045      6.6197|
|  2:  4.7137 -  3.7598 0.99   1365  150 0.4086 0.4181      6.8217      6.8063|
|  3:  3.7598 -  3.2899 0.99   1337  146 0.4451 0.4192      6.6672      6.6762|
|  4:  3.2899 -  2.9916 0.99   1348  155 0.4800 0.4781      6.5387       6.522|
|  5:  2.9916 -  2.7786 0.99   1327  146 0.5178 0.4957      6.3779      6.3907|
|  6:  2.7786 -  2.6156 0.99   1331  142 0.5172 0.5208      6.2794       6.216|
|  7:  2.6156 -  2.4852 0.99   1306  142 0.5416 0.4936      6.2532       6.197|
|  8:  2.4852 -  2.3774 0.98   1295  153 0.5310 0.5048      6.1794      6.1959|
|  9:  2.3774 -  2.2862 0.98   1308  148 0.5272 0.5002      6.1315      6.1274|
| 10:  2.2862 -  2.2076 1.00   1294  153 0.5311 0.4828      6.0924      6.0534|
| 11:  2.2076 -  2.1387 0.98   1313  130 0.5234 0.5434       6.039      6.0569|
| 12:  2.1387 -  2.0777 0.98   1278  154 0.5328 0.5968      5.9566      6.0024|
| 13:  2.0777 -  2.0232 0.93   1232  125 0.5467 0.5042      5.8773        5.81|
| 14:  2.0232 -  1.9739 0.36    476   55 0.5529 0.5251      5.8794      5.8212|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2649 -  4.7137  1420   160  0.66  37.72   0.78     0.72      86155.11|
|  2:  4.7137 -  3.7598  1365   150  0.69  36.55   0.87     0.76     115470.35|
|  3:  3.7598 -  3.2899  1337   146  0.57  46.16   0.83     0.70     122430.66|
|  4:  3.2899 -  2.9916  1348   155  0.48  53.39   0.77     0.59     110216.06|
|  5:  2.9916 -  2.7786  1327   146  0.38  61.18   0.73     0.46      89293.31|
|  6:  2.7786 -  2.6156  1331   142  0.35  63.81   0.72     0.41      76952.60|
|  7:  2.6156 -  2.4852  1306   142  0.33  65.55   0.72     0.38      68360.88|
|  8:  2.4852 -  2.3774  1295   153  0.33  65.09   0.72     0.39      60924.47|
|  9:  2.3774 -  2.2862  1308   148  0.36  63.07   0.72     0.41      52758.67|
| 10:  2.2862 -  2.2076  1294   153  0.36  62.99   0.74     0.43      48035.81|
| 11:  2.2076 -  2.1387  1313   130  0.30  67.42   0.76     0.37      48981.84|
| 12:  2.1387 -  2.0777  1278   154  0.24  71.87   0.74     0.32      47170.94|
| 13:  2.0777 -  2.0232  1232   125  0.24  72.04   0.70     0.32      40439.33|
| 14:  2.0232 -  1.9739   476    55  0.39  60.99   0.70     0.43      28535.63|
|alpha:            min =        0.32 max =            0.76 mean =         0.48|
|beta:             min =    28535.63 max =       122430.66 mean =     73765.14|
|figures of merit: min =        0.00 max =            1.00 mean =         0.41|
|phase err.(work): min =        0.00 max =           90.00 mean =        58.72|
|phase err.(test): min =        0.00 max =           89.87 mean =        58.77|
|-----------------------------------------------------------------------------|

============================== 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 = 17.353003             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.554   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.451745              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.391   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       28 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      166 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      688 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1508 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2630 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3934 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5041 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6526 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7678 |
|-----------------------------------------------------------------------------|
|-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 |       53.908 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.196 |       1.796 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.993)------------------------------------------|
|    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 = 11.993)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4924   r_free= 0.4837   ksol= 0.00   Bsol= 0.00   scale= 0.754    |
|                                                                             |
| 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:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.291213                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4802   r_free= 0.4684   ksol= 0.34   Bsol= 20.00   scale= 0.979   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (9.72,8.66,6.93,0.00,0.00,0.00); trace/3= 8.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.284409                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.904236             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.759   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.364756              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.612   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4802      final r-factor (work) = 0.4053          |
| start r-factor (free) = 0.4684      final r-factor (free) = 0.4226          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 100.7537 = 14.90 * 0.50 * 6.2862 + 1.00 * 53.9080                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 46.4635 = 14.90 * 0.50 * 6.2156 + 1.00 * 0.1444                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4053      final r-factor (work) = 0.3613          |
| start r-factor (free) = 0.4226      final r-factor (free) = 0.4135          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.4972 = 1.36 * 1.00 * 6.2156 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.3989 = 1.36 * 1.00 * 6.1402 + 1.00 * 0.0190                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.993)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    73.77   14.31    None  None   None       |
|    all(noH): 2823   0      0.00    73.77   14.31    None  None   None       |
|    Sol.    : 438    0      0.00    73.77   25.83    None  None   None       |
|    Mac.    : 2385   0      0.00    71.21   12.20    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 -   7.377:  999   |   5:    36.883 -  44.260:   95        |
|      1:     7.377 -  14.753:  747   |   6:    44.260 -  51.637:   60        |
|      2:    14.753 -  22.130:  480   |   7:    51.637 -  59.013:   18        |
|      3:    22.130 -  29.507:  262   |   8:    59.013 -  66.390:    8        |
|      4:    29.507 -  36.883:  147   |   9:    66.390 -  73.767:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3613 r_free = 0.4135             target_work(ml) = 6.126         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3606 r_free = 0.4141             target_work(ml) = 6.126         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3606   r_free= 0.4141   ksol= 0.34   Bsol= 20.00   scale= 1.103   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (9.72,8.66,6.93,0.00,0.00,0.00); trace/3= 8.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.125718                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3576   r_free= 0.4093   ksol= 0.34   Bsol= 40.44   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.10,4.71,4.24,0.00,0.00,0.00); trace/3= 5.02                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.125618                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.595734              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.715   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.562793              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.321  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3576      final r-factor (work) = 0.2758          |
| start r-factor (free) = 0.4093      final r-factor (free) = 0.3359          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.5805 = 9.60 * 0.50 * 6.1353 + 1.00 * 0.1444                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.0006 = 9.60 * 0.50 * 6.0249 + 1.00 * 0.0940                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2758      final r-factor (work) = 0.2479          |
| start r-factor (free) = 0.3359      final r-factor (free) = 0.3137          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4096 = 0.56 * 1.00 * 6.0249 + 1.00 * 0.0188                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3147 = 0.56 * 1.00 * 5.8678 + 1.00 * 0.0123                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.993)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.68   13.89    None  None   None       |
|    all(noH): 2823   0      0.00    82.68   13.89    None  None   None       |
|    Sol.    : 438    0      0.00    79.24   33.04    None  None   None       |
|    Mac.    : 2385   0      0.00    82.68   10.37    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.268: 1255   |   5:    41.340 -  49.608:   89        |
|      1:     8.268 -  16.536:  796   |   6:    49.608 -  57.876:   44        |
|      2:    16.536 -  24.804:  310   |   7:    57.876 -  66.144:   17        |
|      3:    24.804 -  33.072:  175   |   8:    66.144 -  74.412:    4        |
|      4:    33.072 -  41.340:  130   |   9:    74.412 -  82.680:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2479 r_free = 0.3137             target_work(ml) = 5.836         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2478 r_free = 0.3135             target_work(ml) = 5.835         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2478   r_free= 0.3135   ksol= 0.34   Bsol= 40.44   scale= 1.062   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.10,4.71,4.24,0.00,0.00,0.00); trace/3= 5.02                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.835231                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2455   r_free= 0.3108   ksol= 0.34   Bsol= 53.81   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.26,2.20,3.13,0.00,0.00,0.00); trace/3= 2.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.831803                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.038177              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.215  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.261858              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.511  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2455      final r-factor (work) = 0.1909          |
| start r-factor (free) = 0.3108      final r-factor (free) = 0.2472          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0119 = 3.04 * 0.50 * 5.8706 + 1.00 * 0.0940                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7740 = 3.04 * 0.50 * 5.7338 + 1.00 * 0.0638                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1909      final r-factor (work) = 0.1801          |
| start r-factor (free) = 0.2472      final r-factor (free) = 0.2310          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5138 = 0.26 * 1.00 * 5.7338 + 1.00 * 0.0123                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4708 = 0.26 * 1.00 * 5.5801 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.993)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.83   13.79    None  None   None       |
|    all(noH): 2823   0      0.00    79.83   13.79    None  None   None       |
|    Sol.    : 438    0      1.86    76.90   35.14    None  None   None       |
|    Mac.    : 2385   0      0.00    79.83   9.87     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 -   7.983: 1243   |   5:    39.916 -  47.899:  108        |
|      1:     7.983 -  15.966:  872   |   6:    47.899 -  55.882:   71        |
|      2:    15.966 -  23.950:  237   |   7:    55.882 -  63.865:   19        |
|      3:    23.950 -  31.933:  137   |   8:    63.865 -  71.848:    6        |
|      4:    31.933 -  39.916:  126   |   9:    71.848 -  79.832:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1801 r_free = 0.2310             target_work(ml) = 5.554         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1801 r_free = 0.2305             target_work(ml) = 5.553         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1801   r_free= 0.2305   ksol= 0.34   Bsol= 53.81   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.26,2.20,3.13,0.00,0.00,0.00); trace/3= 2.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.553278                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1797   r_free= 0.2298   ksol= 0.34   Bsol= 53.81   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.92,1.05,2.25,0.00,0.00,0.00); trace/3= 1.74                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.554297                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.533751              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.339   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.378123              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.051  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1797      final r-factor (work) = 0.1409          |
| start r-factor (free) = 0.2298      final r-factor (free) = 0.1885          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9330 = 3.53 * 0.50 * 5.5857 + 1.00 * 0.0638                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7009 = 3.53 * 0.50 * 5.4515 + 1.00 * 0.0688                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1409      final r-factor (work) = 0.1326          |
| start r-factor (free) = 0.1885      final r-factor (free) = 0.1819          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0709 = 0.38 * 1.00 * 5.4515 + 1.00 * 0.0096                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0212 = 0.38 * 1.00 * 5.3170 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.993)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.09   14.12    None  None   None       |
|    all(noH): 2823   0      0.00    84.09   14.12    None  None   None       |
|    Sol.    : 438    0      3.16    75.44   37.95    None  None   None       |
|    Mac.    : 2385   0      0.00    84.09   9.74     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 -   8.409: 1380   |   5:    42.043 -  50.451:   98        |
|      1:     8.409 -  16.817:  793   |   6:    50.451 -  58.860:   71        |
|      2:    16.817 -  25.226:  208   |   7:    58.860 -  67.268:   38        |
|      3:    25.226 -  33.634:  112   |   8:    67.268 -  75.677:   16        |
|      4:    33.634 -  42.043:  105   |   9:    75.677 -  84.086:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1326 r_free = 0.1819             target_work(ml) = 5.298         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1325 r_free = 0.1818             target_work(ml) = 5.297         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1325   r_free= 0.1818   ksol= 0.34   Bsol= 53.81   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.92,1.05,2.25,0.00,0.00,0.00); trace/3= 1.74                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.297019                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1327   r_free= 0.1817   ksol= 0.33   Bsol= 53.81   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.46,0.64,1.99,0.00,0.00,0.00); trace/3= 1.36                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.296505                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.677125              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 123.183  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.149971              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 159.153  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1327      final r-factor (work) = 0.1229          |
| start r-factor (free) = 0.1817      final r-factor (free) = 0.1697          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1870 = 2.68 * 0.50 * 5.3178 + 1.00 * 0.0688                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1152 = 2.68 * 0.50 * 5.2659 + 1.00 * 0.0664                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1229      final r-factor (work) = 0.1230          |
| start r-factor (free) = 0.1697      final r-factor (free) = 0.1677          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8002 = 0.15 * 1.00 * 5.2659 + 1.00 * 0.0105                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7931 = 0.15 * 1.00 * 5.2313 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 33     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.993)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.93   13.67    None  None   None       |
|    all(noH): 2823   0      0.00    82.93   13.67    None  None   None       |
|    Sol.    : 438    0      3.53    75.84   35.76    None  None   None       |
|    Mac.    : 2385   0      0.00    82.93   9.61     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 -   8.293: 1340   |   5:    41.466 -  49.759:   96        |
|      1:     8.293 -  16.586:  850   |   6:    49.759 -  58.052:   64        |
|      2:    16.586 -  24.880:  208   |   7:    58.052 -  66.346:   26        |
|      3:    24.880 -  33.173:  123   |   8:    66.346 -  74.639:   10        |
|      4:    33.173 -  41.466:  103   |   9:    74.639 -  82.932:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1230 r_free = 0.1677             target_work(ml) = 5.224         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1229 r_free = 0.1676             target_work(ml) = 5.223         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1229   r_free= 0.1676   ksol= 0.33   Bsol= 53.81   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.46,0.64,1.99,0.00,0.00,0.00); trace/3= 1.36                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.222977                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2649 -  4.7137 0.99   1420  160 0.1021 0.1404      5.4153      5.6271|
|  2:  4.7137 -  3.7598 0.99   1365  150 0.0916 0.1129      5.4959      5.6428|
|  3:  3.7598 -  3.2899 0.99   1337  146 0.1142 0.1637      5.5262      5.8809|
|  4:  3.2899 -  2.9916 0.99   1348  155 0.1373 0.1663      5.5233      5.6319|
|  5:  2.9916 -  2.7786 0.99   1327  146 0.1444 0.1880       5.392      5.6293|
|  6:  2.7786 -  2.6156 0.99   1331  142 0.1359 0.2017      5.2682      5.5166|
|  7:  2.6156 -  2.4852 0.99   1306  142 0.1407 0.1755      5.2444       5.393|
|  8:  2.4852 -  2.3774 0.98   1295  153 0.1283 0.1919      5.1398      5.4178|
|  9:  2.3774 -  2.2862 0.98   1308  148 0.1353 0.1981      5.1375      5.4012|
| 10:  2.2862 -  2.2076 1.00   1294  153 0.1257 0.1698      5.0339      5.2105|
| 11:  2.2076 -  2.1387 0.98   1313  130 0.1280 0.2003      5.0196       5.386|
| 12:  2.1387 -  2.0777 0.98   1278  154 0.1242 0.1802      4.9366      5.1623|
| 13:  2.0777 -  2.0232 0.93   1232  125 0.1319 0.1767      4.8703      5.0822|
| 14:  2.0232 -  1.9739 0.36    476   55 0.1128 0.1605      4.7262      4.9301|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2649 -  4.7137  1420   160  0.94   9.75   0.97     0.96       8030.91|
|  2:  4.7137 -  3.7598  1365   150  0.95   8.64   1.01     1.00      10094.85|
|  3:  3.7598 -  3.2899  1337   146  0.93  11.93   1.02     1.02      11256.30|
|  4:  3.2899 -  2.9916  1348   155  0.91  15.30   1.00     0.98      11408.23|
|  5:  2.9916 -  2.7786  1327   146  0.90  16.53   0.99     0.98       9116.22|
|  6:  2.7786 -  2.6156  1331   142  0.89  17.23   0.98     0.95       7725.46|
|  7:  2.6156 -  2.4852  1306   142  0.89  16.91   1.00     0.98       7101.16|
|  8:  2.4852 -  2.3774  1295   153  0.89  16.88   0.98     0.96       6108.09|
|  9:  2.3774 -  2.2862  1308   148  0.89  17.71   1.01     0.96       6062.33|
| 10:  2.2862 -  2.2076  1294   153  0.90  16.77   1.00     0.97       5033.32|
| 11:  2.2076 -  2.1387  1313   130  0.89  17.35   1.00     0.95       4883.50|
| 12:  2.1387 -  2.0777  1278   154  0.90  16.88   1.01     1.01       4446.25|
| 13:  2.0777 -  2.0232  1232   125  0.89  17.88   1.00     0.99       3826.93|
| 14:  2.0232 -  1.9739   476    55  0.90  15.79   0.98     0.96       2909.78|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2909.78 max =        11408.23 mean =      7249.69|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           90.00 mean =        15.30|
|phase err.(test): min =        0.00 max =           89.28 mean =        14.74|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1228   r_free= 0.1676   ksol= 0.32   Bsol= 50.65   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.03,-0.71,0.68,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.222911                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1228   r_free= 0.1676   ksol= 0.32   Bsol= 50.65   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.03,-0.71,0.68,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.222911                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2649 -  4.7137 0.99   1420  160 0.1017 0.1399       5.412      5.6237|
|  2:  4.7137 -  3.7598 0.99   1365  150 0.0914 0.1125      5.4931      5.6399|
|  3:  3.7598 -  3.2899 0.99   1337  146 0.1141 0.1633      5.5247      5.8785|
|  4:  3.2899 -  2.9916 0.99   1348  155 0.1374 0.1664      5.5233      5.6324|
|  5:  2.9916 -  2.7786 0.99   1327  146 0.1446 0.1882      5.3928      5.6303|
|  6:  2.7786 -  2.6156 0.99   1331  142 0.1361 0.2020      5.2693      5.5172|
|  7:  2.6156 -  2.4852 0.99   1306  142 0.1407 0.1756      5.2452      5.3936|
|  8:  2.4852 -  2.3774 0.98   1295  153 0.1284 0.1920      5.1406      5.4183|
|  9:  2.3774 -  2.2862 0.98   1308  148 0.1354 0.1983       5.138      5.4016|
| 10:  2.2862 -  2.2076 1.00   1294  153 0.1259 0.1697      5.0347      5.2113|
| 11:  2.2076 -  2.1387 0.98   1313  130 0.1281 0.2005        5.02      5.3867|
| 12:  2.1387 -  2.0777 0.98   1278  154 0.1243 0.1806      4.9378      5.1638|
| 13:  2.0777 -  2.0232 0.93   1232  125 0.1319 0.1766      4.8708      5.0826|
| 14:  2.0232 -  1.9739 0.36    476   55 0.1127 0.1606      4.7263      4.9304|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2649 -  4.7137  1420   160  0.94   9.72   0.97     0.96       7983.84|
|  2:  4.7137 -  3.7598  1365   150  0.95   8.61   1.01     0.99      10034.29|
|  3:  3.7598 -  3.2899  1337   146  0.93  11.90   1.02     1.02      11203.87|
|  4:  3.2899 -  2.9916  1348   155  0.91  15.28   1.00     0.98      11395.21|
|  5:  2.9916 -  2.7786  1327   146  0.90  16.53   0.99     0.97       9125.41|
|  6:  2.7786 -  2.6156  1331   142  0.89  17.24   0.97     0.95       7743.38|
|  7:  2.6156 -  2.4852  1306   142  0.89  16.93   0.99     0.97       7116.57|
|  8:  2.4852 -  2.3774  1295   153  0.89  16.89   0.98     0.95       6118.58|
|  9:  2.3774 -  2.2862  1308   148  0.89  17.71   1.00     0.95       6069.66|
| 10:  2.2862 -  2.2076  1294   153  0.89  16.78   1.00     0.96       5040.57|
| 11:  2.2076 -  2.1387  1313   130  0.89  17.36   0.99     0.94       4891.25|
| 12:  2.1387 -  2.0777  1278   154  0.90  16.90   1.00     1.01       4457.81|
| 13:  2.0777 -  2.0232  1232   125  0.89  17.90   1.00     0.98       3833.27|
| 14:  2.0232 -  1.9739   476    55  0.90  15.80   0.97     0.95       2912.22|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2912.22 max =        11395.21 mean =      7243.19|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.94 mean =        15.30|
|phase err.(test): min =        0.00 max =           89.22 mean =        14.74|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.993)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.22    84.15   14.88    None  None   None       |
|    all(noH): 2823   0      1.22    84.15   14.88    None  None   None       |
|    Sol.    : 438    0      4.75    77.06   36.98    None  None   None       |
|    Mac.    : 2385   0      1.22    84.15   10.83    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:     1.219 -   9.512: 1340   |   5:    42.685 -  50.978:   96        |
|      1:     9.512 -  17.805:  850   |   6:    50.978 -  59.271:   64        |
|      2:    17.805 -  26.098:  208   |   7:    59.271 -  67.564:   26        |
|      3:    26.098 -  34.391:  123   |   8:    67.564 -  75.857:   10        |
|      4:    34.391 -  42.685:  103   |   9:    75.857 -  84.151:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 320         
Filter by distance & map next to the model:
   mapped sites are within: 0.398 - 4.866
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 313 from: 320
   mapped sites are within: 0.706 - 4.866

peak=   10.313 closest distance to " CB  VAL A 230 " =    1.494
peak=    7.133 closest distance to " CG  ARG A 138 " =    1.241
peak=    6.700 closest distance to " CD2 LEU A   5 " =    1.353
peak=    6.411 closest distance to " CG2 VAL A 296 " =    1.083
peak=    5.657 closest distance to " NE2 GLN A  11 " =    1.159
peak=    5.330 closest distance to " O   HOH Z 222 " =    1.348
peak=    5.283 closest distance to " O   HOH Z   7 " =    1.607
peak=    5.274 closest distance to " CG  LEU A   5 " =    1.251
peak=    5.271 closest distance to " CG  PRO A  54 " =    1.457
peak=    5.154 closest distance to " O   HOH Z 232 " =    2.245
peak=    5.076 closest distance to " O   HOH Z 111 " =    1.742
peak=    4.987 closest distance to " O   HOH Z   2 " =    1.965
peak=    4.973 closest distance to " NH1 ARG A 138 " =    1.044
peak=    4.958 closest distance to " NH1AARG A 145 " =    1.212
peak=    4.910 closest distance to " CB  GLN A 223 " =    1.443
peak=    4.887 closest distance to " CD1AILE A 234 " =    1.086
peak=    4.808 closest distance to " CB  PRO A  54 " =    1.000
peak=    4.801 closest distance to " CD  ARG A 138 " =    1.185
peak=    4.791 closest distance to " O   HOH Z 144 " =    1.939
peak=    4.772 closest distance to " CG  LEU A 228 " =    1.204
peak=    4.748 closest distance to " NH1 ARG A  56 " =    1.072
peak=    4.679 closest distance to " O   HOH Z 183 " =    1.476
peak=    4.647 closest distance to " O   HOH Z 410 " =    1.630
peak=    4.642 closest distance to " O   HOH Z 369 " =    1.967
peak=    4.632 closest distance to " CB  ASP A 124 " =    0.736
peak=    4.599 closest distance to " CB  VAL A 296 " =    1.233
peak=    4.536 closest distance to " O   HOH Z 425 " =    1.627
peak=    4.511 closest distance to " O   HOH Z 236 " =    1.982
peak=    4.508 closest distance to " O   PRO A 198 " =    1.566
peak=    4.480 closest distance to " CB  SER A  63 " =    1.272
peak=    4.461 closest distance to " CB  ASN A 148 " =    1.314
peak=    4.461 closest distance to " O   HOH Z  55 " =    2.159
peak=    4.458 closest distance to " O   HOH Z  57 " =    1.444
peak=    4.428 closest distance to " O   HOH Z 298 " =    2.056
peak=    4.411 closest distance to " CB  SER A   3 " =    1.530
peak=    4.393 closest distance to " O   HOH Z 427 " =    2.853
peak=    4.389 closest distance to " CB  ARG A 275 " =    0.941
peak=    4.332 closest distance to " CD2 LEU A 228 " =    1.247
peak=    4.323 closest distance to " CG  PRO A 198 " =    1.281
peak=    4.320 closest distance to " CB  GLN A 183 " =    1.173
peak=    4.300 closest distance to " O   HOH Z 186 " =    1.330
peak=    4.288 closest distance to " CG  PRO A 213 " =    1.302
peak=    4.263 closest distance to " CG  LEU A 167 " =    1.228
peak=    4.249 closest distance to " CB  GLU A 152 " =    1.266
peak=    4.228 closest distance to " CG  PRO A 280 " =    0.919
peak=    4.223 closest distance to " O   HOH Z 193 " =    1.746
peak=    4.169 closest distance to " O   HOH Z 126 " =    2.136
peak=    4.162 closest distance to " CB  ASN A  39 " =    0.959
peak=    4.160 closest distance to " O   HOH Z 126 " =    1.592
peak=    4.147 closest distance to " O   HOH Z 316 " =    3.012
peak=    4.134 closest distance to " CB  VAL A 230 " =    1.220
peak=    4.133 closest distance to " CA  SER A  87 " =    0.854
peak=    4.088 closest distance to " CG  PRO A 243 " =    1.132
peak=    4.085 closest distance to " O   HOH Z 411 " =    3.249
peak=    4.068 closest distance to " CB  ASN A 187 " =    1.142
peak=    4.059 closest distance to " O   HOH Z 303 " =    2.344
peak=    4.029 closest distance to " O   ASP A 132 " =    3.892
peak=    4.025 closest distance to " ND2 ASN A 187 " =    1.506
peak=    4.019 closest distance to " O   HOH Z 112 " =    1.398
peak=    4.009 closest distance to " O   HOH Z 272 " =    1.888
peak=    4.006 closest distance to " NE AARG A 275 " =    1.436
peak=    4.004 closest distance to " CD1 LEU A 300 " =    1.226
peak=    3.999 closest distance to " CB  TRP A 266 " =    0.967
peak=    3.988 closest distance to " O   HOH Z 368 " =    2.087
peak=    3.985 closest distance to " ND1 HIS A  86 " =    1.749
peak=    3.977 closest distance to " CG  GLN A  88 " =    1.107
peak=    3.967 closest distance to " OD2 ASP A 286 " =    2.852
peak=    3.957 closest distance to " O   HOH Z 437 " =    2.324
peak=    3.932 closest distance to " CA  ALA A  51 " =    1.001
peak=    3.913 closest distance to " CB  SER A 210 " =    0.877
peak=    3.907 closest distance to " NH1 ARG A  14 " =    0.956
peak=    3.894 closest distance to " O   HOH Z 217 " =    2.836
peak=    3.887 closest distance to " O   HOH Z  58 " =    2.012
peak=    3.870 closest distance to " O   HOH Z 170 " =    1.218
peak=    3.868 closest distance to " O   HOH Z 281 " =    4.791
peak=    3.856 closest distance to " CB  SER A 216 " =    0.908
peak=    3.846 closest distance to " O   HOH Z 334 " =    1.722
peak=    3.844 closest distance to " CB  LEU A 237 " =    0.865
peak=    3.844 closest distance to " OD1 ASN A  69 " =    2.556
peak=    3.842 closest distance to " CZ  PHE A 192 " =    1.002
peak=    3.839 closest distance to " O   HOH Z   9 " =    1.364
peak=    3.838 closest distance to " O   HOH Z 146 " =    1.610
peak=    3.824 closest distance to " O   HOH Z 184 " =    1.470
peak=    3.820 closest distance to " O   HOH Z 373 " =    2.031
peak=    3.819 closest distance to " CB  ASN A 142 " =    0.962
peak=    3.808 closest distance to " CB  MET A  40 " =    0.870
peak=    3.800 closest distance to " CA  ILE A 234 " =    1.026
peak=    3.790 closest distance to " CG2 THR A 221 " =    1.029
peak=    3.786 closest distance to " CG1 ILE A 151 " =    1.202
peak=    3.782 closest distance to " CD1 ILE A  33 " =    1.708
peak=    3.782 closest distance to " NH2AARG A 145 " =    1.153
peak=    3.780 closest distance to " O   HOH Z  40 " =    2.282
peak=    3.777 closest distance to " CB  SER A 212 " =    1.259
peak=    3.776 closest distance to " CB  GLU A 128 " =    1.144
peak=    3.772 closest distance to " O   HOH Z  59 " =    1.776
peak=    3.769 closest distance to " CG1 ILE A  33 " =    1.238
peak=    3.763 closest distance to " CB  ALA A 104 " =    0.792
peak=    3.761 closest distance to " CD  GLN A 240 " =    1.675
peak=    3.750 closest distance to " CB  VAL A 265 " =    1.340
peak=    3.750 closest distance to " CB  LEU A 228 " =    1.204
peak=    3.748 closest distance to " O   HOH Z  88 " =    2.928
peak=    3.733 closest distance to " CB  GLN A  88 " =    1.347
peak=    3.733 closest distance to " O   HOH Z 148 " =    1.646
peak=    3.731 closest distance to " O   HOH Z 132 " =    2.444
peak=    3.727 closest distance to " O   HOH Z 332 " =    1.596
peak=    3.714 closest distance to " O   HOH Z 350 " =    1.649
peak=    3.713 closest distance to " O   HOH Z  44 " =    2.327
peak=    3.713 closest distance to " CE3 TRP A 274 " =    2.423
peak=    3.695 closest distance to " O   HOH Z 359 " =    3.997
peak=    3.693 closest distance to " O   HOH Z 102 " =    0.706
peak=    3.692 closest distance to " O   HOH Z 282 " =    1.856
peak=    3.681 closest distance to " O   SER A  87 " =    2.337
peak=    3.668 closest distance to " O   HOH Z 409 " =    2.569
peak=    3.667 closest distance to " O   HOH Z 193 " =    1.968
peak=    3.666 closest distance to " CA  ALA A 299 " =    0.918
peak=    3.663 closest distance to " CD  ARG A 159 " =    0.750
peak=    3.662 closest distance to " CA  TYR A 116 " =    1.481
peak=    3.656 closest distance to " CB  VAL A 202 " =    1.482
peak=    3.649 closest distance to " O   HOH Z 423 " =    1.658
peak=    3.643 closest distance to " O   PRO A 198 " =    1.333
peak=    3.635 closest distance to " O   MET A 105 " =    1.733
peak=    3.618 closest distance to " CE3 TRP A 274 " =    1.395
peak=    3.606 closest distance to " CB  MET A  47 " =    1.080
peak=    3.593 closest distance to " OG  SER A  62 " =    2.857
peak=    3.590 closest distance to " O   HOH Z 245 " =    1.342
peak=    3.590 closest distance to " NE  ARG A  56 " =    3.598
peak=    3.589 closest distance to " CG BARG A 275 " =    1.539
peak=    3.589 closest distance to " N   PHE A 130 " =    1.306
peak=    3.589 closest distance to " O   HOH Z   9 " =    1.780
peak=    3.579 closest distance to " O   HOH Z 371 " =    1.669
peak=    3.579 closest distance to " O   HOH Z 133 " =    1.798
peak=    3.578 closest distance to " O   TYR A 116 " =    1.159
peak=    3.576 closest distance to " O   HOH Z   1 " =    2.011
peak=    3.572 closest distance to " O   HOH Z  98 " =    1.934
peak=    3.571 closest distance to " CB  ILE A 234 " =    0.986
peak=    3.566 closest distance to " O   HOH Z  78 " =    1.478
peak=    3.563 closest distance to " O   HOH Z 261 " =    2.248
peak=    3.561 closest distance to " O   HOH Z  80 " =    1.647
peak=    3.556 closest distance to " CD BLYS A 290 " =    1.066
peak=    3.553 closest distance to " O   HOH Z 284 " =    3.057
peak=    3.552 closest distance to " O   HOH Z 222 " =    2.256
peak=    3.547 closest distance to " O   HOH Z  61 " =    1.629
peak=    3.541 closest distance to " O   HOH Z 193 " =    1.910
peak=    3.539 closest distance to " O   HOH Z 158 " =    2.838
peak=    3.539 closest distance to " CB  ARG A  79 " =    1.471
peak=    3.535 closest distance to " O   HOH Z 175 " =    3.669
peak=    3.534 closest distance to " O   HOH Z  10 " =    1.763
peak=    3.527 closest distance to " CG1 VAL A 153 " =    0.929
peak=    3.526 closest distance to " O   HOH Z 185 " =    1.923
peak=    3.524 closest distance to " O   HOH Z 389 " =    1.941
peak=    3.521 closest distance to " O   HOH Z 156 " =    2.848
peak=    3.519 closest distance to " O   HOH Z 313 " =    1.734
peak=    3.515 closest distance to " O   HOH Z  40 " =    2.209
peak=    3.515 closest distance to " C   GLU A 277 " =    1.422
peak=    3.513 closest distance to " O   HOH Z 273 " =    2.555
peak=    3.513 closest distance to " CB  THR A 157 " =    1.136
peak=    3.509 closest distance to " CB  GLU A 236 " =    1.081
peak=    3.501 closest distance to " O   HOH Z  30 " =    1.888
peak=    3.500 closest distance to " OH  TYR A 186 " =    1.028
peak=    3.495 closest distance to " CA  ALA A  21 " =    1.226
peak=    3.489 closest distance to " CG1 ILE A  49 " =    1.478
peak=    3.489 closest distance to " O   HOH Z 346 " =    1.591
peak=    3.487 closest distance to " CA  PRO A  54 " =    1.361
peak=    3.476 closest distance to " O   HOH Z  97 " =    1.553
peak=    3.472 closest distance to " O   HOH Z 392 " =    1.356
peak=    3.467 closest distance to " O   HOH Z 305 " =    3.502
peak=    3.465 closest distance to " CB  GLN A 103 " =    1.135
peak=    3.464 closest distance to " CB  ASP A 140 " =    0.846
peak=    3.457 closest distance to " CB  ARG A 138 " =    1.387
peak=    3.447 closest distance to " OG  SER A  22 " =    2.965
peak=    3.438 closest distance to " O   HOH Z 115 " =    1.801
peak=    3.420 closest distance to " CA  MET A  47 " =    1.115
peak=    3.415 closest distance to " O   ASN A 209 " =    1.465
peak=    3.413 closest distance to " O   HOH Z 124 " =    1.806
peak=    3.411 closest distance to " OG BSER A 212 " =    2.736
peak=    3.409 closest distance to " O   HOH Z 258 " =    2.183
peak=    3.409 closest distance to " NH2 ARG A 219 " =    1.841
peak=    3.406 closest distance to " CB  LEU A 143 " =    1.137
peak=    3.406 closest distance to " CA  ARG A 102 " =    1.120
peak=    3.402 closest distance to " O   HOH Z 105 " =    1.632
peak=    3.400 closest distance to " CB  VAL A 250 " =    1.045
peak=    3.398 closest distance to " CD  ARG A 195 " =    3.503
peak=    3.383 closest distance to " ND2 ASN A 110 " =    1.682
peak=    3.383 closest distance to " N   SER A 271 " =    0.969
peak=    3.381 closest distance to " O   HOH Z 207 " =    2.332
peak=    3.377 closest distance to " O   ALA A 291 " =    1.481
peak=    3.374 closest distance to " CA  LEU A 282 " =    1.023
peak=    3.373 closest distance to " CA  GLY A 267 " =    1.052
peak=    3.371 closest distance to " CD  ARG A 269 " =    0.956
peak=    3.361 closest distance to " O   HOH Z 302 " =    1.639
peak=    3.361 closest distance to " ND1 HIS A  81 " =    1.763
peak=    3.356 closest distance to " O   HOH Z 371 " =    2.708
peak=    3.354 closest distance to " O   ALA A  10 " =    1.518
peak=    3.352 closest distance to " O   HOH Z 130 " =    1.063
peak=    3.351 closest distance to " CB  TRP A 150 " =    1.510
peak=    3.351 closest distance to " O   HOH Z 345 " =    3.340
peak=    3.350 closest distance to " CB  HIS A 108 " =    0.782
peak=    3.349 closest distance to " CA  MET A  40 " =    1.071
peak=    3.345 closest distance to " OG BSER A 210 " =    1.166
peak=    3.338 closest distance to " O   HOH Z 109 " =    2.422
peak=    3.337 closest distance to " NH2AARG A 190 " =    1.565
peak=    3.336 closest distance to " CD  ARG A  14 " =    1.285
peak=    3.330 closest distance to " CA  TYR A 186 " =    1.552
peak=    3.323 closest distance to " CB  ILE A 120 " =    1.312
peak=    3.321 closest distance to " CB  ALA A  34 " =    0.999
peak=    3.320 closest distance to " O   HOH Z 255 " =    1.767
peak=    3.319 closest distance to " O   HOH Z 133 " =    2.478
peak=    3.317 closest distance to " CE1 TYR A 186 " =    1.346
peak=    3.317 closest distance to " O   HOH Z 271 " =    2.126
peak=    3.311 closest distance to " O   HOH Z 424 " =    2.921
peak=    3.311 closest distance to " CA  ASN A 127 " =    1.070
peak=    3.311 closest distance to " CB  THR A  82 " =    1.231
peak=    3.310 closest distance to " CB  GLU A 236 " =    0.913
peak=    3.309 closest distance to " O   HOH Z 195 " =    1.416
peak=    3.306 closest distance to " OD1 ASN A 217 " =    1.463
peak=    3.304 closest distance to " O   HOH Z 263 " =    1.578
peak=    3.304 closest distance to " CA  LYS A 117 " =    1.042
peak=    3.303 closest distance to " CB  PRO A 243 " =    1.210
peak=    3.301 closest distance to " O   HOH Z 380 " =    1.745
peak=    3.301 closest distance to " NE1 TRP A 274 " =    0.996
peak=    3.300 closest distance to " O   HOH Z  44 " =    2.542
peak=    3.288 closest distance to " O   HOH Z 122 " =    1.979
peak=    3.286 closest distance to " O   HOH Z  63 " =    1.260
peak=    3.284 closest distance to " CD2 LEU A 255 " =    1.724
peak=    3.284 closest distance to " O   HOH Z 174 " =    1.227
peak=    3.283 closest distance to " O   HOH Z 252 " =    1.715
peak=    3.277 closest distance to " CA  LEU A 101 " =    1.354
peak=    3.277 closest distance to " N   ASN A 127 " =    1.323
peak=    3.275 closest distance to " CG  ARG A 159 " =    1.019
peak=    3.275 closest distance to " CB  SER A 273 " =    0.955
peak=    3.272 closest distance to " O   HOH Z 128 " =    2.017
peak=    3.269 closest distance to " O   HOH Z 235 " =    1.665
peak=    3.263 closest distance to " CB  GLN A  89 " =    1.181
peak=    3.259 closest distance to " O   HOH Z  68 " =    1.934
peak=    3.258 closest distance to " CA  ALA A 295 " =    1.026
peak=    3.252 closest distance to " CA  TYR A  30 " =    0.995
peak=    3.251 closest distance to " CB  TYR A  30 " =    1.349
peak=    3.250 closest distance to " CG BARG A 102 " =    1.947
peak=    3.247 closest distance to " O   HOH Z 173 " =    1.753
peak=    3.247 closest distance to " CB  ARG A 259 " =    1.002
peak=    3.245 closest distance to " N   TYR A  15 " =    0.886
peak=    3.244 closest distance to " CA  GLU A 152 " =    0.978
peak=    3.244 closest distance to " CB  TRP A 179 " =    1.488
peak=    3.242 closest distance to " O   HOH Z 126 " =    1.658
peak=    3.239 closest distance to " CG  GLN A 144 " =    0.920
peak=    3.236 closest distance to " O   HOH Z 175 " =    2.192
peak=    3.233 closest distance to " CE  MET A  93 " =    1.490
peak=    3.231 closest distance to " N   ARG A 156 " =    1.332
peak=    3.227 closest distance to " O   HOH Z 180 " =    2.093
peak=    3.227 closest distance to " CZ  PHE A 218 " =    1.054
peak=    3.226 closest distance to " O   HOH Z 391 " =    2.981
peak=    3.225 closest distance to " O   HOH Z 130 " =    2.060
peak=    3.225 closest distance to " O   HOH Z  22 " =    2.085
peak=    3.224 closest distance to " CA  ALA A 154 " =    1.040
peak=    3.221 closest distance to " CD  LYS A 166 " =    1.323
peak=    3.220 closest distance to " ND2 ASN A 249 " =    0.768
peak=    3.217 closest distance to " O   HOH Z 248 " =    1.925
peak=    3.215 closest distance to " CG2 VAL A 257 " =    0.984
peak=    3.215 closest distance to " O   HOH Z 225 " =    1.711
peak=    3.211 closest distance to " CB  GLU A 277 " =    3.584
peak=    3.208 closest distance to " CG1 VAL A 296 " =    1.229
peak=    3.207 closest distance to " CA  ALA A 160 " =    1.073
peak=    3.206 closest distance to " O   ALA A 233 " =    1.859
peak=    3.202 closest distance to " CG  LYS A 119 " =    1.164
peak=    3.201 closest distance to " CG AARG A 275 " =    1.227
peak=    3.200 closest distance to " CG2BVAL A  41 " =    1.256
peak=    3.198 closest distance to " O   HOH Z  39 " =    2.559
peak=    3.196 closest distance to " CE3 TRP A  85 " =    1.110
peak=    3.196 closest distance to " O   HOH Z 295 " =    1.592
peak=    3.190 closest distance to " NH2BARG A 145 " =    2.009
peak=    3.189 closest distance to " O   HOH Z 119 " =    1.675
peak=    3.186 closest distance to " O   HOH Z 110 " =    1.612
peak=    3.183 closest distance to " CG  GLN A  55 " =    1.849
peak=    3.182 closest distance to " O   THR A 294 " =    1.086
peak=    3.180 closest distance to " O   HOH Z  51 " =    1.879
peak=    3.180 closest distance to " O   HOH Z 303 " =    1.814
peak=    3.179 closest distance to " CD1 LEU A   5 " =    1.272
peak=    3.178 closest distance to " CB  ALA A  43 " =    0.995
peak=    3.176 closest distance to " O   HOH Z 327 " =    1.901
peak=    3.175 closest distance to " NZ ALYS A 290 " =    0.963
peak=    3.172 closest distance to " NZ  LYS A  48 " =    1.508
peak=    3.166 closest distance to " CB  ARG A 139 " =    1.314
peak=    3.162 closest distance to " O   HOH Z 353 " =    2.616
peak=    3.161 closest distance to " O   HOH Z 419 " =    1.718
peak=    3.160 closest distance to " CG1BVAL A  72 " =    1.580
peak=    3.156 closest distance to " CB  SER A 276 " =    1.284
peak=    3.154 closest distance to " O   HOH Z 135 " =    2.049
peak=    3.151 closest distance to " O   HOH Z 145 " =    3.646
peak=    3.150 closest distance to " CA  GLN A  88 " =    1.180
peak=    3.144 closest distance to " O   HOH Z 403 " =    1.262
peak=    3.142 closest distance to " O   HOH Z 244 " =    1.600
peak=    3.142 closest distance to " O   HOH Z  61 " =    1.529
peak=    3.137 closest distance to " O   LEU A 300 " =    1.229
peak=    3.136 closest distance to " CA  ARG A 195 " =    1.281
peak=    3.135 closest distance to " CG2 ILE A 109 " =    0.885
peak=    3.135 closest distance to " OG  SER A  97 " =    3.056
peak=    3.129 closest distance to " O   HOH Z 344 " =    2.969
peak=    3.126 closest distance to " CB  ASN A 110 " =    1.073
peak=    3.114 closest distance to " CB  LEU A  83 " =    0.783
peak=    3.103 closest distance to " OG BSER A 164 " =    2.361
peak=    3.101 closest distance to " O   HOH Z 216 " =    2.777
peak=    3.097 closest distance to " CA  VAL A  41 " =    0.889
peak=    3.095 closest distance to " NE2 GLN A  58 " =    3.407
peak=    3.092 closest distance to " O   HOH Z 425 " =    2.119
peak=    3.091 closest distance to " O   HOH Z 217 " =    1.695
peak=    3.077 closest distance to " CZ3 TRP A  92 " =    1.463
peak=    3.076 closest distance to " O   HOH Z 294 " =    1.485
peak=    3.074 closest distance to " O   HOH Z 116 " =    1.751
peak=    3.073 closest distance to " O   HOH Z 218 " =    4.866
peak=    3.072 closest distance to " CA  ALA A 184 " =    1.039
peak=    3.069 closest distance to " CA  ILE A 106 " =    0.772
peak=    3.060 closest distance to " O   HOH Z 153 " =    3.819
peak=    3.038 closest distance to " O   HOH Z 172 " =    2.867

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 201         
Filter by distance & map next to the model:
   mapped sites are within: 0.241 - 5.986
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 196 from: 201
   mapped sites are within: 0.727 - 5.986

peak=   -5.773 closest distance to " CG2 VAL A 230 " =    0.760
peak=   -4.776 closest distance to " CD  ARG A 138 " =    1.046
peak=   -4.479 closest distance to " OE1 GLN A  88 " =    0.924
peak=   -4.437 closest distance to " O   HOH Z 231 " =    1.534
peak=   -4.435 closest distance to " CD  ARG A  14 " =    3.077
peak=   -4.432 closest distance to " O   HOH Z 290 " =    1.127
peak=   -4.418 closest distance to " O   HOH Z 102 " =    1.135
peak=   -4.253 closest distance to " CG  ARG A 138 " =    0.884
peak=   -4.145 closest distance to " O   PRO A 198 " =    1.267
peak=   -4.142 closest distance to " O   HOH Z  65 " =    1.095
peak=   -4.067 closest distance to " NH2 ARG A  79 " =    1.931
peak=   -4.066 closest distance to " CB  PRO A 243 " =    2.615
peak=   -4.064 closest distance to " CD1 TYR A 247 " =    2.851
peak=   -4.051 closest distance to " OG  SER A  87 " =    1.467
peak=   -4.037 closest distance to " O   HOH Z 377 " =    1.085
peak=   -4.019 closest distance to " CD2 LEU A   5 " =    0.892
peak=   -4.016 closest distance to " CD  ARG A 156 " =    2.023
peak=   -3.942 closest distance to " N   ALA A  43 " =    2.399
peak=   -3.933 closest distance to " N   THR A 157 " =    1.573
peak=   -3.922 closest distance to " CE1 TYR A 169 " =    2.613
peak=   -3.916 closest distance to " CG  LEU A 101 " =    2.539
peak=   -3.885 closest distance to " CD1 LEU A 228 " =    2.460
peak=   -3.862 closest distance to " O   HOH Z 435 " =    2.834
peak=   -3.852 closest distance to " C   ALA A 158 " =    1.378
peak=   -3.812 closest distance to " CZ3 TRP A 179 " =    1.166
peak=   -3.803 closest distance to " CA  ASP A  27 " =    2.509
peak=   -3.788 closest distance to " CB  ALA A   9 " =    2.581
peak=   -3.786 closest distance to " NH2AARG A 275 " =    5.665
peak=   -3.782 closest distance to " CA  GLY A 241 " =    2.346
peak=   -3.768 closest distance to " CG  MET A 105 " =    0.959
peak=   -3.749 closest distance to " CB  PRO A 163 " =    2.416
peak=   -3.748 closest distance to " C   LEU A 222 " =    0.908
peak=   -3.744 closest distance to " O   HOH Z 211 " =    1.446
peak=   -3.736 closest distance to " CG1 VAL A 296 " =    1.344
peak=   -3.735 closest distance to " O   HOH Z  43 " =    1.736
peak=   -3.728 closest distance to " OG BSER A 134 " =    1.588
peak=   -3.727 closest distance to " CG  GLN A 223 " =    2.413
peak=   -3.724 closest distance to " CB  ALA A  43 " =    2.452
peak=   -3.724 closest distance to " O   HOH Z  52 " =    1.884
peak=   -3.673 closest distance to " CD1 PHE A  59 " =    1.915
peak=   -3.644 closest distance to " O   HOH Z 351 " =    1.337
peak=   -3.632 closest distance to " O   HOH Z  51 " =    0.964
peak=   -3.630 closest distance to " CG2 VAL A 296 " =    1.013
peak=   -3.627 closest distance to " C   ASN A 285 " =    2.406
peak=   -3.613 closest distance to " O   HOH Z 359 " =    1.619
peak=   -3.611 closest distance to " CB  VAL A 296 " =    0.964
peak=   -3.592 closest distance to " O   HOH Z 166 " =    1.246
peak=   -3.560 closest distance to " O   HOH Z 362 " =    5.986
peak=   -3.557 closest distance to " O   GLY A 203 " =    2.499
peak=   -3.546 closest distance to " O   HOH Z 389 " =    2.021
peak=   -3.541 closest distance to " O   HOH Z  53 " =    1.784
peak=   -3.536 closest distance to " O   GLY A  80 " =    2.526
peak=   -3.535 closest distance to " CD1 LEU A 101 " =    2.501
peak=   -3.528 closest distance to " CD  LYS A 289 " =    2.453
peak=   -3.527 closest distance to " O   HOH Z 266 " =    5.068
peak=   -3.523 closest distance to " O   HOH Z  52 " =    1.104
peak=   -3.522 closest distance to " O   HOH Z  90 " =    2.995
peak=   -3.516 closest distance to " O   HOH Z 275 " =    1.521
peak=   -3.515 closest distance to " CD1 ILE A 239 " =    2.151
peak=   -3.513 closest distance to " C   MET A 188 " =    1.464
peak=   -3.509 closest distance to " CD  GLU A 277 " =    0.934
peak=   -3.502 closest distance to " CG2 VAL A 202 " =    2.766
peak=   -3.501 closest distance to " CB  ALA A 248 " =    1.927
peak=   -3.499 closest distance to " OG ASER A 134 " =    1.268
peak=   -3.495 closest distance to " CG  TRP A 266 " =    1.716
peak=   -3.492 closest distance to " O   HOH Z 281 " =    4.958
peak=   -3.492 closest distance to " O   HOH Z 103 " =    1.366
peak=   -3.487 closest distance to " CA  GLY A  98 " =    1.984
peak=   -3.487 closest distance to " O   SER A 135 " =    1.431
peak=   -3.482 closest distance to " CB  VAL A 230 " =    1.057
peak=   -3.480 closest distance to " O   HOH Z 111 " =    2.088
peak=   -3.474 closest distance to " O   PRO A 163 " =    1.977
peak=   -3.469 closest distance to " O   HOH Z 394 " =    1.479
peak=   -3.465 closest distance to " O   SER A  22 " =    2.459
peak=   -3.454 closest distance to " OG  SER A  63 " =    0.968
peak=   -3.441 closest distance to " O   HOH Z 275 " =    1.832
peak=   -3.437 closest distance to " CD  GLN A  58 " =    0.894
peak=   -3.437 closest distance to " OD1 ASN A  60 " =    0.903
peak=   -3.429 closest distance to " CG  TYR A 186 " =    2.311
peak=   -3.425 closest distance to " O   HOH Z 390 " =    2.351
peak=   -3.419 closest distance to " O   VAL A  67 " =    2.611
peak=   -3.418 closest distance to " C   LYS A  76 " =    1.362
peak=   -3.416 closest distance to " CB  ALA A 161 " =    2.665
peak=   -3.409 closest distance to " CE2 TYR A  30 " =    2.727
peak=   -3.407 closest distance to " OG  SER A 206 " =    1.631
peak=   -3.405 closest distance to " CB  TYR A  15 " =    2.127
peak=   -3.403 closest distance to " O   HOH Z 353 " =    2.364
peak=   -3.396 closest distance to " CB  CYS A 254 " =    1.842
peak=   -3.390 closest distance to " O   HOH Z 298 " =    1.189
peak=   -3.387 closest distance to " OG  SER A  97 " =    2.261
peak=   -3.385 closest distance to " OH  TYR A 214 " =    1.070
peak=   -3.384 closest distance to " O   ILE A  49 " =    1.740
peak=   -3.383 closest distance to " O   HOH Z 407 " =    3.403
peak=   -3.382 closest distance to " CG  PRO A 163 " =    2.406
peak=   -3.369 closest distance to " CB  TRP A  85 " =    2.529
peak=   -3.366 closest distance to " CG  GLU A 152 " =    0.764
peak=   -3.366 closest distance to " O   HOH Z 179 " =    2.116
peak=   -3.365 closest distance to " CB  ASN A  39 " =    2.122
peak=   -3.365 closest distance to " O   HOH Z 185 " =    2.271
peak=   -3.363 closest distance to " CZ  PHE A 130 " =    0.950
peak=   -3.360 closest distance to " O   HOH Z 108 " =    1.549
peak=   -3.352 closest distance to " O   HOH Z  60 " =    1.604
peak=   -3.351 closest distance to " CB  ASP A 132 " =    2.321
peak=   -3.351 closest distance to " CG  GLN A  88 " =    0.828
peak=   -3.343 closest distance to " CD2 LEU A 143 " =    2.608
peak=   -3.340 closest distance to " CB  PHE A 130 " =    1.308
peak=   -3.339 closest distance to " CA  GLY A 203 " =    2.389
peak=   -3.334 closest distance to " CB  ALA A 114 " =    2.374
peak=   -3.329 closest distance to " OE1 GLN A 278 " =    1.051
peak=   -3.325 closest distance to " O   HOH Z  11 " =    1.945
peak=   -3.324 closest distance to " O   GLY A 211 " =    1.236
peak=   -3.314 closest distance to " CB  PRO A  54 " =    2.483
peak=   -3.314 closest distance to " N   GLN A  58 " =    1.788
peak=   -3.313 closest distance to " CE  LYS A  76 " =    2.727
peak=   -3.312 closest distance to " O   VAL A 197 " =    1.625
peak=   -3.312 closest distance to " CG  GLN A 278 " =    2.305
peak=   -3.312 closest distance to " CD1 LEU A   5 " =    2.581
peak=   -3.308 closest distance to " CB  ALA A 248 " =    2.479
peak=   -3.304 closest distance to " O   HOH Z 417 " =    2.885
peak=   -3.296 closest distance to " O   HOH Z 368 " =    2.432
peak=   -3.290 closest distance to " O   HOH Z 241 " =    1.301
peak=   -3.287 closest distance to " CE BMET A  47 " =    1.699
peak=   -3.285 closest distance to " C   GLN A 240 " =    2.453
peak=   -3.282 closest distance to " O   HOH Z 143 " =    1.311
peak=   -3.280 closest distance to " O   HOH Z 359 " =    3.441
peak=   -3.279 closest distance to " CG1 VAL A 112 " =    3.020
peak=   -3.278 closest distance to " O   HOH Z 170 " =    2.606
peak=   -3.277 closest distance to " OG ASER A 134 " =    1.826
peak=   -3.275 closest distance to " O   HOH Z 176 " =    0.747
peak=   -3.274 closest distance to " CZ2 TRP A 274 " =    0.792
peak=   -3.273 closest distance to " CB  ALA A 227 " =    2.422
peak=   -3.269 closest distance to " O   HOH Z 198 " =    2.252
peak=   -3.266 closest distance to " O   HOH Z 166 " =    1.853
peak=   -3.263 closest distance to " O   HOH Z 309 " =    2.324
peak=   -3.259 closest distance to " O   HOH Z 385 " =    2.119
peak=   -3.257 closest distance to " NE2 GLN A 278 " =    0.920
peak=   -3.251 closest distance to " O   HOH Z  13 " =    1.649
peak=   -3.249 closest distance to " O   HOH Z 371 " =    1.206
peak=   -3.246 closest distance to " CG  ASP A 231 " =    0.756
peak=   -3.239 closest distance to " O   HOH Z 322 " =    0.943
peak=   -3.238 closest distance to " O   HOH Z 128 " =    2.565
peak=   -3.236 closest distance to " O   HOH Z  56 " =    0.833
peak=   -3.235 closest distance to " ND2 ASN A  45 " =    1.853
peak=   -3.234 closest distance to " O   HOH Z 281 " =    2.918
peak=   -3.233 closest distance to " O   HOH Z 198 " =    1.430
peak=   -3.232 closest distance to " N   ARG A 138 " =    1.575
peak=   -3.230 closest distance to " O   HOH Z 140 " =    1.374
peak=   -3.226 closest distance to " O   ARG A 145 " =    1.579
peak=   -3.224 closest distance to " O   HOH Z  60 " =    0.727
peak=   -3.221 closest distance to " O   HOH Z 300 " =    2.068
peak=   -3.217 closest distance to " OD2 ASP A 171 " =    1.838
peak=   -3.210 closest distance to " O   GLN A 194 " =    1.362
peak=   -3.208 closest distance to " CE2 PHE A 218 " =    2.533
peak=   -3.202 closest distance to " N   GLY A  23 " =    2.360
peak=   -3.201 closest distance to " O   HOH Z 168 " =    1.885
peak=   -3.200 closest distance to " CD2 LEU A 237 " =    2.683
peak=   -3.198 closest distance to " O   HOH Z 295 " =    1.427
peak=   -3.194 closest distance to " ND2 ASN A 209 " =    2.043
peak=   -3.185 closest distance to " O   ASN A  60 " =    0.999
peak=   -3.183 closest distance to " O   HOH Z   2 " =    1.720
peak=   -3.178 closest distance to " CB  ALA A 244 " =    2.042
peak=   -3.173 closest distance to " OG1 THR A 246 " =    1.442
peak=   -3.172 closest distance to " O   HOH Z 118 " =    1.511
peak=   -3.166 closest distance to " O   ASP A 231 " =    2.549
peak=   -3.160 closest distance to " O   HOH Z 191 " =    5.242
peak=   -3.159 closest distance to " CG2 THR A 178 " =    2.318
peak=   -3.156 closest distance to " C   GLU A 236 " =    0.806
peak=   -3.156 closest distance to " ND2 ASN A  60 " =    1.653
peak=   -3.154 closest distance to " OG1 THR A 178 " =    1.219
peak=   -3.143 closest distance to " OG  SER A   3 " =    1.645
peak=   -3.143 closest distance to " O   HOH Z 401 " =    0.911
peak=   -3.136 closest distance to " O   TYR A 214 " =    2.318
peak=   -3.128 closest distance to " O   HOH Z  88 " =    1.290
peak=   -3.124 closest distance to " O   HOH Z 351 " =    1.692
peak=   -3.119 closest distance to " CD2 TYR A 293 " =    2.665
peak=   -3.114 closest distance to " OG1 THR A 157 " =    1.711
peak=   -3.113 closest distance to " CB  SER A  63 " =    3.302
peak=   -3.108 closest distance to " O   HOH Z 313 " =    1.544
peak=   -3.105 closest distance to " O   SER A  62 " =    2.332
peak=   -3.104 closest distance to " CD1 ILE A 199 " =    2.694
peak=   -3.100 closest distance to " CZ BARG A 275 " =    1.463
peak=   -3.097 closest distance to " CA  GLY A 133 " =    2.090
peak=   -3.096 closest distance to " CD1 TRP A 179 " =    0.780
peak=   -3.096 closest distance to " O   HOH Z 114 " =    1.689
peak=   -3.095 closest distance to " ND2 ASN A 285 " =    2.192
peak=   -3.094 closest distance to " CE2 TRP A  70 " =    2.379
peak=   -3.092 closest distance to " O   HOH Z 292 " =    1.490
peak=   -3.088 closest distance to " OD1 ASN A 148 " =    1.501
peak=   -3.080 closest distance to " O   HOH Z  49 " =    1.990
peak=   -3.070 closest distance to " CZ2 TRP A 179 " =    2.382
peak=   -3.066 closest distance to " N   ASP A 191 " =    1.060
peak=   -3.063 closest distance to " OE1 GLN A 223 " =    2.394
peak=   -3.056 closest distance to " CA  ARG A 139 " =    0.953
peak=   -3.050 closest distance to " O   HOH Z 147 " =    1.368
peak=   -3.036 closest distance to " O   HOH Z 426 " =    2.207
peak=   -3.021 closest distance to " CG1 VAL A 174 " =    2.877

================= 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    :  0.4881 0.4818   6.290032e+00   6.279022e+00
   1_bss:  0.4802 0.4684   6.284409e+00   6.271838e+00
   1_xyz:  0.4053 0.4226   6.191441e+00   6.216304e+00
   1_adp:  0.3613 0.4135   6.126139e+00   6.204741e+00
   1_occ:  0.3606 0.4141   6.125718e+00   6.205212e+00
   2_bss:  0.3576 0.4093   6.125618e+00   6.203733e+00
   2_xyz:  0.2758 0.3359   5.912023e+00   6.047230e+00
   2_adp:  0.2479 0.3137   5.836004e+00   5.992466e+00
   2_occ:  0.2478 0.3135   5.835231e+00   5.991522e+00
   3_bss:  0.2455 0.3108   5.831803e+00   5.986368e+00
   3_xyz:  0.1909 0.2472   5.606404e+00   5.795946e+00
   3_adp:  0.1801 0.2310   5.553741e+00   5.742524e+00
   3_occ:  0.1801 0.2305   5.553278e+00   5.741805e+00
   4_bss:  0.1797 0.2298   5.554297e+00   5.741791e+00
   4_xyz:  0.1409 0.1885   5.343260e+00   5.562088e+00
   4_adp:  0.1326 0.1819   5.297840e+00   5.525000e+00
   4_occ:  0.1325 0.1818   5.297019e+00   5.523834e+00
   5_bss:  0.1327 0.1817   5.296505e+00   5.522423e+00
   5_xyz:  0.1229 0.1697   5.228723e+00   5.461256e+00
   5_adp:  0.1230 0.1677   5.223955e+00   5.451218e+00
   5_occ:  0.1229 0.1676   5.222977e+00   5.449950e+00
   5_bss:  0.1228 0.1676   5.222911e+00   5.449821e+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:  0.342  20.000   9.720   8.663   6.930   0.000   0.000   0.000
   1_xyz:  0.342  20.000   9.720   8.663   6.930   0.000   0.000   0.000
   1_adp:  0.342  20.000   9.720   8.663   6.930   0.000   0.000   0.000
   1_occ:  0.342  20.000   9.720   8.663   6.930   0.000   0.000   0.000
   2_bss:  0.338  40.441   6.101   4.714   4.237   0.000   0.000   0.000
   2_xyz:  0.338  40.441   6.101   4.714   4.237   0.000   0.000   0.000
   2_adp:  0.338  40.441   6.101   4.714   4.237   0.000   0.000   0.000
   2_occ:  0.338  40.441   6.101   4.714   4.237   0.000   0.000   0.000
   3_bss:  0.342  53.810   3.262   2.198   3.133   0.000   0.000   0.000
   3_xyz:  0.342  53.810   3.262   2.198   3.133   0.000   0.000   0.000
   3_adp:  0.342  53.810   3.262   2.198   3.133   0.000   0.000   0.000
   3_occ:  0.342  53.810   3.262   2.198   3.133   0.000   0.000   0.000
   4_bss:  0.342  53.810   1.923   1.053   2.248   0.000   0.000   0.000
   4_xyz:  0.342  53.810   1.923   1.053   2.248   0.000   0.000   0.000
   4_adp:  0.342  53.810   1.923   1.053   2.248   0.000   0.000   0.000
   4_occ:  0.342  53.810   1.923   1.053   2.248   0.000   0.000   0.000
   5_bss:  0.329  53.810   1.458   0.639   1.985   0.000   0.000   0.000
   5_xyz:  0.329  53.810   1.458   0.639   1.985   0.000   0.000   0.000
   5_adp:  0.329  53.810   1.458   0.639   1.985   0.000   0.000   0.000
   5_occ:  0.329  53.810   1.458   0.639   1.985   0.000   0.000   0.000
   5_bss:  0.322  50.654   0.034  -0.714   0.679   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  58.729 0.4104  0.4843    73763.341
   1_bss:  58.875 0.4075  0.6136    72352.037
   1_xyz:  50.638 0.5114  0.7532    56022.006
   1_adp:  47.803 0.5473  0.8635    52942.183
   1_occ:  47.901 0.5460  0.8607    53035.965
   2_bss:  47.546 0.5504  0.7719    52533.734
   2_xyz:  36.156 0.6868  0.9376    31141.517
   2_adp:  32.759 0.7267  0.9705    26612.499
   2_occ:  32.743 0.7268  0.9698    26552.253
   3_bss:  32.482 0.7295  0.9021    26151.261
   3_xyz:  24.389 0.8171  0.9798    15624.389
   3_adp:  22.551 0.8366  0.9953    13848.972
   3_occ:  22.548 0.8366  0.9948    13811.629
   4_bss:  22.513 0.8370  0.9558    13796.522
   4_xyz:  17.993 0.8802  0.9813     9206.830
   4_adp:  17.097 0.8887  0.9824     8573.011
   4_occ:  17.078 0.8889  0.9823     8551.062
   5_bss:  17.052 0.8890  0.9690     8513.087
   5_xyz:  15.597 0.9018  0.9747     7410.316
   5_adp:  15.270 0.9049  0.9758     7282.620
   5_occ:  15.247 0.9050  0.9758     7249.942
   5_bss:  15.247 0.9050  0.9707     7243.447
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3908e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3908e+01
   1_xyz:   1.700  0.013  0.108 18.382  0.007  4.109   1.4438e-01
   1_adp:   1.700  0.013  0.108 18.382  0.007  4.109   1.4438e-01
   1_occ:   1.700  0.013  0.108 18.382  0.007  4.109   1.4438e-01
   2_bss:   1.700  0.013  0.108 18.382  0.007  4.109   1.4438e-01
   2_xyz:   1.209  0.009  0.087 16.844  0.005  4.109   9.3974e-02
   2_adp:   1.209  0.009  0.087 16.844  0.005  4.109   9.3974e-02
   2_occ:   1.209  0.009  0.087 16.844  0.005  4.109   9.3974e-02
   3_bss:   1.209  0.009  0.087 16.844  0.005  4.109   9.3974e-02
   3_xyz:   0.986  0.007  0.071 15.415  0.004  4.123   6.3792e-02
   3_adp:   0.986  0.007  0.071 15.415  0.004  4.123   6.3792e-02
   3_occ:   0.986  0.007  0.071 15.415  0.004  4.123   6.3792e-02
   4_bss:   0.986  0.007  0.071 15.415  0.004  4.123   6.3792e-02
   4_xyz:   1.057  0.008  0.081 15.421  0.004  4.113   6.8838e-02
   4_adp:   1.057  0.008  0.081 15.421  0.004  4.113   6.8838e-02
   4_occ:   1.057  0.008  0.081 15.421  0.004  4.113   6.8838e-02
   5_bss:   1.057  0.008  0.081 15.421  0.004  4.113   6.8838e-02
   5_xyz:   1.054  0.008  0.081 15.494  0.003  4.121   6.6407e-02
   5_adp:   1.054  0.008  0.081 15.494  0.003  4.121   6.6407e-02
   5_occ:   1.054  0.008  0.081 15.494  0.003  4.121   6.6407e-02
   5_bss:   1.054  0.008  0.081 15.494  0.003  4.121   6.6407e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9888e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9888e+00
   1_xyz:  13.604  0.169  0.442 88.644  0.052  2.203   1.0320e-01
   1_adp:  13.604  0.169  0.442 88.644  0.052  2.203   1.0320e-01
   1_occ:  13.604  0.169  0.442 88.644  0.052  2.203   1.0320e-01
   2_bss:  13.604  0.169  0.442 88.644  0.052  2.203   1.0320e-01
   2_xyz:   6.519  0.071  0.343 83.360  0.046  2.136   7.1188e-02
   2_adp:   6.519  0.071  0.343 83.360  0.046  2.136   7.1188e-02
   2_occ:   6.519  0.071  0.343 83.360  0.046  2.136   7.1188e-02
   3_bss:   6.519  0.071  0.343 83.360  0.046  2.136   7.1188e-02
   3_xyz:   7.753  0.056  0.302 80.733  0.050  2.302   1.1740e-01
   3_adp:   7.753  0.056  0.302 80.733  0.050  2.302   1.1740e-01
   3_occ:   7.753  0.056  0.302 80.733  0.050  2.302   1.1740e-01
   4_bss:   7.753  0.056  0.302 80.733  0.050  2.302   1.1740e-01
   4_xyz:   8.613  0.073  0.430 81.155  0.030  2.311   5.5968e-02
   4_adp:   8.613  0.073  0.430 81.155  0.030  2.311   5.5968e-02
   4_occ:   8.613  0.073  0.430 81.155  0.030  2.311   5.5968e-02
   5_bss:   8.613  0.073  0.430 81.155  0.030  2.311   5.5968e-02
   5_xyz:   8.552  0.069  0.507 84.184  0.034  2.317   4.6535e-02
   5_adp:   8.552  0.069  0.507 84.184  0.034  2.317   4.6535e-02
   5_occ:   8.552  0.069  0.507 84.184  0.034  2.317   4.6535e-02
   5_bss:   8.552  0.069  0.507 84.184  0.034  2.317   4.6535e-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:  73.77   0.00  14.31  71.21   0.00  12.20  73.77   0.00  25.83
   1_occ:  73.77   0.00  14.31  71.21   0.00  12.20  73.77   0.00  25.83
   2_bss:  73.77   0.00  14.31  71.21   0.00  12.20  73.77   0.00  25.83
   2_xyz:  73.77   0.00  14.31  71.21   0.00  12.20  73.77   0.00  25.83
   2_adp:  82.68   0.00  13.89  82.68   0.00  10.37  79.24   0.00  33.04
   2_occ:  82.68   0.00  13.89  82.68   0.00  10.37  79.24   0.00  33.04
   3_bss:  82.68   0.00  13.89  82.68   0.00  10.37  79.24   0.00  33.04
   3_xyz:  82.68   0.00  13.89  82.68   0.00  10.37  79.24   0.00  33.04
   3_adp:  79.83   0.00  13.79  79.83   0.00   9.87  76.90   1.86  35.14
   3_occ:  79.83   0.00  13.79  79.83   0.00   9.87  76.90   1.86  35.14
   4_bss:  79.83   0.00  13.79  79.83   0.00   9.87  76.90   1.86  35.14
   4_xyz:  79.83   0.00  13.79  79.83   0.00   9.87  76.90   1.86  35.14
   4_adp:  84.09   0.00  14.12  84.09   0.00   9.74  75.44   3.16  37.95
   4_occ:  84.09   0.00  14.12  84.09   0.00   9.74  75.44   3.16  37.95
   5_bss:  84.09   0.00  14.12  84.09   0.00   9.74  75.44   3.16  37.95
   5_xyz:  84.09   0.00  14.12  84.09   0.00   9.74  75.44   3.16  37.95
   5_adp:  82.93   0.00  13.67  82.93   0.00   9.61  75.84   3.53  35.76
   5_occ:  82.93   0.00  13.67  82.93   0.00   9.61  75.84   3.53  35.76
   5_bss:  84.15   1.22  14.88  84.15   1.22  10.83  77.06   4.75  36.98
------------------------------------------------------------------------
 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:    1.238    0.013    0.410
   1_adp:    1.238    0.013    0.410
   1_occ:    1.238    0.013    0.410
   2_bss:    1.238    0.013    0.410
   2_xyz:    1.597    0.029    0.609
   2_adp:    1.597    0.029    0.609
   2_occ:    1.597    0.029    0.609
   3_bss:    1.597    0.029    0.609
   3_xyz:    1.707    0.064    0.672
   3_adp:    1.707    0.064    0.672
   3_occ:    1.707    0.064    0.672
   4_bss:    1.707    0.064    0.672
   4_xyz:    1.940    0.063    0.751
   4_adp:    1.940    0.063    0.751
   4_occ:    1.940    0.063    0.751
   5_bss:    1.940    0.063    0.751
   5_xyz:    2.086    0.053    0.771
   5_adp:    2.086    0.053    0.771
   5_occ:    2.086    0.053    0.771
   5_bss:    2.086    0.053    0.771
------------------------------------------------------------------------

CPU time actual refinement: 346.86


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1237/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_1237/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1237/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1237/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1237/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 346.69 
  Macro-tasks:
    bulk solvent and scale       = 38.61  
    individual site refinement   = 147.23 
    weights calculation          = 31.85  
    collect and process          = 6.45   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 224.26 
  Micro-tasks:
    mask                            = 2.44   
    f_calc                          = 111.05 
    alpha_beta                      = 8.16   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 121.04 
    fmodel                         = 7.27   
    r_factors                      = 0.15   
    phase_errors                   = 10.48  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 261.99 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.864 micro seconds
Total CPU time: 6.01 minutes
from_scatterers_fft:    650 calls, 110.69 s
gradients_fft:          595 calls, 107.60 s

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

# Date 2008-01-16 Time 03:32:38 PST -0800 (1200483158.02 s)
Start R-work = 0.4881, R-free = 0.4818 (no bulk solvent and anisotropic scale)
Final R-work = 0.1397, R-free = 0.1848 (no bulk solvent and anisotropic scale)

Start R-work = 0.4802, R-free = 0.4684
Final R-work = 0.1228, R-free = 0.1676