# Date 2008-01-16 Time 02:27:27 PST -0800 (1200479247.87 s)
#phil __OFF__

Command line arguments: "../842.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 21836
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 842

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 48.1033, 86.822, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 48.1033, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0689 2.01049
Completeness in resolution range: 0.967406
Completeness with d_max=infinity: 0.964358

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0689
                             d_min =   2.0105

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 48.1033, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0689 2.01049
Completeness in resolution range: 0.967406
Completeness with d_max=infinity: 0.964358

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0694 -  4.3010 [2122/2150]  1911   211   9.9%
  bin  2:  4.3010 -  3.4271 [2038/2057]  1832   206  10.1%
  bin  3:  3.4271 -  2.9978 [2024/2044]  1822   202  10.0%
  bin  4:  2.9978 -  2.7254 [1987/2012]  1792   195   9.8%
  bin  5:  2.7254 -  2.5311 [1987/2006]  1787   200  10.1%
  bin  6:  2.5311 -  2.3824 [1966/2011]  1771   195   9.9%
  bin  7:  2.3824 -  2.2635 [1962/1996]  1765   197  10.0%
  bin  8:  2.2635 -  2.1653 [1959/1994]  1758   201  10.3%
  bin  9:  2.1653 -  2.0822 [1945/1975]  1754   191   9.8%
  bin 10:  2.0822 -  2.0105 [1599/2004]  1438   161  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_842/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:
        1.72 -     2.35: 7
        2.35 -     2.99: 1824
        2.99 -     3.63: 4524
        3.63 -     4.26: 8958
        4.26 -     4.90: 12524
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.718 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 277 " - " O   HOH Z 343 "  1.794 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.840 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.983 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 27832 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_842/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_842/model_refine_001.geo

CPU time processing inputs: 9.72


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 48.10325 86.82195 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: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4941   r_free= 0.4788   ksol= 0.00   Bsol= 0.00   scale= 0.771    |
|                                                                             |
| 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:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.295646                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0694 -  4.7967 0.99   1380  154 0.4052 0.4137      6.6186      6.6101|
|  2:  4.7967 -  3.8278 0.99   1329  146 0.4241 0.4621      6.8402       6.914|
|  3:  3.8278 -  3.3500 0.99   1304  147 0.4645 0.4000      6.7314      6.6479|
|  4:  3.3500 -  3.0465 0.99   1293  138 0.4858 0.4338      6.5646      6.4706|
|  5:  3.0465 -  2.8297 0.99   1282  146 0.5368 0.5041      6.4057       6.419|
|  6:  2.8297 -  2.6638 0.98   1281  142 0.5232 0.4877      6.3007      6.1995|
|  7:  2.6638 -  2.5311 0.99   1275  141 0.5045 0.4849      6.2494       6.146|
|  8:  2.5311 -  2.4214 0.98   1266  142 0.5229 0.4840      6.1904      6.1866|
|  9:  2.4214 -  2.3285 0.98   1276  146 0.5311 0.5678      6.1235      6.1656|
| 10:  2.3285 -  2.2484 0.97   1232  132 0.5506 0.5419      6.1262      6.1326|
| 11:  2.2484 -  2.1783 0.99   1275  144 0.5397 0.5163      6.0439      6.0935|
| 12:  2.1783 -  2.1162 0.98   1271  133 0.5391 0.5102      5.9912      6.0065|
| 13:  2.1162 -  2.0607 0.97   1226  139 0.5224 0.5289      5.8915      5.8865|
| 14:  2.0607 -  2.0105 0.73    940  109 0.5443 0.5193      5.8605      5.7447|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0694 -  4.7967  1380   154  0.65  38.87   0.78     0.68      88141.77|
|  2:  4.7967 -  3.8278  1329   146  0.67  37.72   0.86     0.71     116566.79|
|  3:  3.8278 -  3.3500  1304   147  0.58  45.10   0.80     0.68     120215.12|
|  4:  3.3500 -  3.0465  1293   138  0.51  51.17   0.78     0.58     100467.01|
|  5:  3.0465 -  2.8297  1282   146  0.45  56.19   0.72     0.52      80033.13|
|  6:  2.8297 -  2.6638  1281   142  0.45  56.22   0.70     0.50      64740.10|
|  7:  2.6638 -  2.5311  1275   141  0.42  58.35   0.74     0.47      60882.94|
|  8:  2.5311 -  2.4214  1266   142  0.35  63.57   0.73     0.40      59500.90|
|  9:  2.4214 -  2.3285  1276   146  0.27  69.62   0.70     0.32      60293.48|
| 10:  2.3285 -  2.2484  1232   132  0.25  71.60   0.70     0.28      56590.42|
| 11:  2.2484 -  2.1783  1275   144  0.25  71.11   0.74     0.31      51625.26|
| 12:  2.1783 -  2.1162  1271   133  0.27  70.18   0.75     0.33      47186.07|
| 13:  2.1162 -  2.0607  1226   139  0.26  70.76   0.71     0.31      40022.34|
| 14:  2.0607 -  2.0105   940   109  0.22  73.87   0.71     0.23      31930.51|
|alpha:            min =        0.23 max =            0.71 mean =         0.46|
|beta:             min =    31930.51 max =       120215.12 mean =     71085.50|
|figures of merit: min =        0.00 max =            1.00 mean =         0.41|
|phase err.(work): min =        0.00 max =           89.98 mean =        59.03|
|phase err.(test): min =        0.00 max =           89.98 mean =        59.29|
|-----------------------------------------------------------------------------|

============================== 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 = 15.440971             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.444   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.472203              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.646   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      163 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      679 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1473 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2574 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3853 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4990 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6467 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7611 |
|-----------------------------------------------------------------------------|
|-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 |       54.464 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.788 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.282)------------------------------------------|
|    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 = 12.282)------------------------------------------|
|    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: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4997   r_free= 0.4831   ksol= 0.00   Bsol= 0.00   scale= 0.743    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.81 A                  |
| x-ray target function (ml) for work reflections: 6.296945                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4874   r_free= 0.4689   ksol= 0.32   Bsol= 20.00   scale= 0.962   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.99,12.33,7.50,0.00,0.00,0.00); trace/3= 8.61                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.290236                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.572445             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.454   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.345992              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.669   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4874      final r-factor (work) = 0.4169          |
| start r-factor (free) = 0.4689      final r-factor (free) = 0.4236          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 100.3389 = 14.57 * 0.50 * 6.2961 + 1.00 * 54.4644                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 45.5088 = 14.57 * 0.50 * 6.2267 + 1.00 * 0.1397                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4169      final r-factor (work) = 0.3728          |
| start r-factor (free) = 0.4236      final r-factor (free) = 0.4134          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.3958 = 1.35 * 1.00 * 6.2267 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.3127 = 1.35 * 1.00 * 6.1601 + 1.00 * 0.0213                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.282)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    119.59  15.00    None  None   None       |
|    all(noH): 2823   0      0.00    119.59  15.00    None  None   None       |
|    Sol.    : 438    0      0.00    119.59  26.94    None  None   None       |
|    Mac.    : 2385   0      0.00    77.37   12.81    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.959: 1455   |   5:    59.797 -  71.756:   22        |
|      1:    11.959 -  23.919:  800   |   6:    71.756 -  83.715:    9        |
|      2:    23.919 -  35.878:  346   |   7:    83.715 -  95.675:    3        |
|      3:    35.878 -  47.837:  135   |   8:    95.675 - 107.634:    0        |
|      4:    47.837 -  59.797:   51   |   9:   107.634 - 119.593:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3728 r_free = 0.4134             target_work(ml) = 6.145         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3720 r_free = 0.4120             target_work(ml) = 6.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3720   r_free= 0.4120   ksol= 0.32   Bsol= 20.00   scale= 1.085   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.99,12.33,7.50,0.00,0.00,0.00); trace/3= 8.61                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.143838                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3697   r_free= 0.4069   ksol= 0.32   Bsol= 41.99   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.76,7.89,4.38,0.00,0.00,0.00); trace/3= 5.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.145130                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.311442             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.132  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.484493              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.711  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3697      final r-factor (work) = 0.3083          |
| start r-factor (free) = 0.4069      final r-factor (free) = 0.3733          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.8652 = 10.31 * 0.50 * 6.1535 + 1.00 * 0.1392                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.3219 = 10.31 * 0.50 * 6.0543 + 1.00 * 0.1075                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3083      final r-factor (work) = 0.2981          |
| start r-factor (free) = 0.3733      final r-factor (free) = 0.3599          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9546 = 0.48 * 1.00 * 6.0543 + 1.00 * 0.0213                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9205 = 0.48 * 1.00 * 6.0053 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.282)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    111.93  13.55    None  None   None       |
|    all(noH): 2823   0      0.00    111.93  13.55    None  None   None       |
|    Sol.    : 438    0      0.00    111.93  27.29    None  None   None       |
|    Mac.    : 2385   0      0.00    65.79   11.02    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.193: 1577   |   5:    55.963 -  67.155:   22        |
|      1:    11.193 -  22.385:  734   |   6:    67.155 -  78.348:    5        |
|      2:    22.385 -  33.578:  312   |   7:    78.348 -  89.540:    2        |
|      3:    33.578 -  44.770:  125   |   8:    89.540 - 100.733:    1        |
|      4:    44.770 -  55.963:   44   |   9:   100.733 - 111.925:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2981 r_free = 0.3599             target_work(ml) = 5.996         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2978 r_free = 0.3599             target_work(ml) = 5.996         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2978   r_free= 0.3599   ksol= 0.32   Bsol= 41.99   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.76,7.89,4.38,0.00,0.00,0.00); trace/3= 5.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 5.995575                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2978   r_free= 0.3593   ksol= 0.30   Bsol= 41.99   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.28,5.61,3.38,0.00,0.00,0.00); trace/3= 3.76                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 5.997174                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.079385              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.702  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.426567              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 112.234  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2978      final r-factor (work) = 0.2490          |
| start r-factor (free) = 0.3593      final r-factor (free) = 0.2981          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.3592 = 5.08 * 0.50 * 6.0054 + 1.00 * 0.1075                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.1182 = 5.08 * 0.50 * 5.9223 + 1.00 * 0.0773                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2490      final r-factor (work) = 0.2391          |
| start r-factor (free) = 0.2981      final r-factor (free) = 0.2906          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5389 = 0.43 * 1.00 * 5.9223 + 1.00 * 0.0126                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5025 = 0.43 * 1.00 * 5.8080 + 1.00 * 0.0249                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.282)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    111.07  13.57    None  None   None       |
|    all(noH): 2823   0      0.00    111.07  13.57    None  None   None       |
|    Sol.    : 438    0      0.78    111.07  28.72    None  None   None       |
|    Mac.    : 2385   0      0.00    91.41   10.78    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.107: 1568   |   5:    55.537 -  66.644:   24        |
|      1:    11.107 -  22.215:  740   |   6:    66.644 -  77.752:    4        |
|      2:    22.215 -  33.322:  305   |   7:    77.752 -  88.859:    2        |
|      3:    33.322 -  44.430:  131   |   8:    88.859 -  99.966:    2        |
|      4:    44.430 -  55.537:   46   |   9:    99.966 - 111.074:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2391 r_free = 0.2906             target_work(ml) = 5.800         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2388 r_free = 0.2909             target_work(ml) = 5.800         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2388   r_free= 0.2909   ksol= 0.30   Bsol= 41.99   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.28,5.61,3.38,0.00,0.00,0.00); trace/3= 3.76                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.799701                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2386   r_free= 0.2905   ksol= 0.31   Bsol= 41.99   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.62,4.14,2.78,0.00,0.00,0.00); trace/3= 2.85                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.799608                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.177621              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.865  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.446121              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.305   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2386      final r-factor (work) = 0.1825          |
| start r-factor (free) = 0.2905      final r-factor (free) = 0.2329          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.0185 = 6.18 * 0.50 * 5.8084 + 1.00 * 0.0773                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.6429 = 6.18 * 0.50 * 5.6799 + 1.00 * 0.0988                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1825      final r-factor (work) = 0.1596          |
| start r-factor (free) = 0.2329      final r-factor (free) = 0.2051          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5520 = 0.45 * 1.00 * 5.6799 + 1.00 * 0.0181                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4629 = 0.45 * 1.00 * 5.4941 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.282)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    96.29   13.89    None  None   None       |
|    all(noH): 2823   0      0.00    96.29   13.89    None  None   None       |
|    Sol.    : 438    0      1.16    96.29   36.53    None  None   None       |
|    Mac.    : 2385   0      0.00    80.38   9.73     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.629: 1568   |   5:    48.144 -  57.773:   77        |
|      1:     9.629 -  19.258:  673   |   6:    57.773 -  67.402:   38        |
|      2:    19.258 -  28.886:  201   |   7:    67.402 -  77.030:   16        |
|      3:    28.886 -  38.515:  136   |   8:    77.030 -  86.659:    6        |
|      4:    38.515 -  48.144:  106   |   9:    86.659 -  96.288:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1596 r_free = 0.2051             target_work(ml) = 5.439         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1595 r_free = 0.2053             target_work(ml) = 5.439         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1595   r_free= 0.2053   ksol= 0.31   Bsol= 41.99   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.62,4.14,2.78,0.00,0.00,0.00); trace/3= 2.85                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.439242                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1592   r_free= 0.2058   ksol= 0.32   Bsol= 60.48   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.15,2.65,2.52,0.00,0.00,0.00); trace/3= 2.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.439059                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.521586              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.354   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.224924              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 108.584  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1592      final r-factor (work) = 0.1403          |
| start r-factor (free) = 0.2058      final r-factor (free) = 0.1866          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0284 = 2.52 * 0.50 * 5.4963 + 1.00 * 0.0988                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8543 = 2.52 * 0.50 * 5.3829 + 1.00 * 0.0676                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1403      final r-factor (work) = 0.1366          |
| start r-factor (free) = 0.1866      final r-factor (free) = 0.1825          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2232 = 0.22 * 1.00 * 5.3829 + 1.00 * 0.0125                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2184 = 0.22 * 1.00 * 5.3224 + 1.00 * 0.0213                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.282)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.88   13.62    None  None   None       |
|    all(noH): 2823   0      0.00    97.88   13.62    None  None   None       |
|    Sol.    : 438    0      1.77    97.88   36.76    None  None   None       |
|    Mac.    : 2385   0      0.00    81.81   9.37     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 -   9.788: 1655   |   5:    48.941 -  58.729:   70        |
|      1:     9.788 -  19.576:  634   |   6:    58.729 -  68.517:   40        |
|      2:    19.576 -  29.365:  159   |   7:    68.517 -  78.305:   11        |
|      3:    29.365 -  39.153:  124   |   8:    78.305 -  88.094:    4        |
|      4:    39.153 -  48.941:  125   |   9:    88.094 -  97.882:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1366 r_free = 0.1825             target_work(ml) = 5.310         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1365 r_free = 0.1825             target_work(ml) = 5.310         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1365   r_free= 0.1825   ksol= 0.32   Bsol= 60.48   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.15,2.65,2.52,0.00,0.00,0.00); trace/3= 2.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.309513                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0694 -  4.7967 0.99   1380  154 0.1073 0.1389      5.4704      5.6206|
|  2:  4.7967 -  3.8278 0.99   1329  146 0.0968 0.1237      5.5527      5.7332|
|  3:  3.8278 -  3.3500 0.99   1304  147 0.1265 0.1756      5.6353      5.9879|
|  4:  3.3500 -  3.0465 0.99   1293  138 0.1494 0.1867      5.6177      5.7675|
|  5:  3.0465 -  2.8297 0.99   1282  146 0.1645 0.1803      5.5171      5.6027|
|  6:  2.8297 -  2.6638 0.98   1281  142 0.1547 0.2308      5.3953      5.6282|
|  7:  2.6638 -  2.5311 0.99   1275  141 0.1537 0.1998      5.3372      5.5096|
|  8:  2.5311 -  2.4214 0.98   1266  142 0.1472 0.1973      5.2525      5.4917|
|  9:  2.4214 -  2.3285 0.98   1276  146 0.1527 0.2099      5.2127      5.4587|
| 10:  2.3285 -  2.2484 0.97   1232  132 0.1491 0.2080      5.1742      5.3702|
| 11:  2.2484 -  2.1783 0.99   1275  144 0.1454 0.2129      5.1195      5.4409|
| 12:  2.1783 -  2.1162 0.98   1271  133 0.1379 0.1907      5.0443      5.2779|
| 13:  2.1162 -  2.0607 0.97   1226  139 0.1456 0.2025      4.9735       5.184|
| 14:  2.0607 -  2.0105 0.73    940  109 0.1370 0.1999      4.8562      5.0869|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0694 -  4.7967  1380   154  0.93  10.41   0.96     0.93       8728.03|
|  2:  4.7967 -  3.8278  1329   146  0.94   9.63   1.00     0.99      11286.68|
|  3:  3.8278 -  3.3500  1304   147  0.91  13.81   1.01     1.01      13963.85|
|  4:  3.3500 -  3.0465  1293   138  0.90  15.90   1.00     0.98      13258.75|
|  5:  3.0465 -  2.8297  1282   146  0.87  18.96   0.99     0.98      11579.37|
|  6:  2.8297 -  2.6638  1281   142  0.88  18.77   0.98     0.94       9439.01|
|  7:  2.6638 -  2.5311  1275   141  0.88  18.45   0.99     0.96       8311.92|
|  8:  2.5311 -  2.4214  1266   142  0.89  17.92   0.99     0.95       7289.29|
|  9:  2.4214 -  2.3285  1276   146  0.87  19.46   1.00     0.96       6947.10|
| 10:  2.3285 -  2.2484  1232   132  0.87  19.09   1.00     0.96       6370.40|
| 11:  2.2484 -  2.1783  1275   144  0.87  19.37   0.99     0.94       5972.99|
| 12:  2.1783 -  2.1162  1271   133  0.89  17.95   0.99     0.98       5272.96|
| 13:  2.1162 -  2.0607  1226   139  0.88  19.01   0.99     0.98       4582.28|
| 14:  2.0607 -  2.0105   940   109  0.88  18.36   0.96     0.92       3567.45|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     3567.45 max =        13963.85 mean =      8460.62|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.98 mean =        16.83|
|phase err.(test): min =        0.00 max =           89.52 mean =        16.08|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1365   r_free= 0.1825   ksol= 0.32   Bsol= 62.42   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.90,0.34,0.56,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.309404                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1365   r_free= 0.1825   ksol= 0.32   Bsol= 62.42   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.90,0.34,0.56,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.309404                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0694 -  4.7967 0.99   1380  154 0.1074 0.1390      5.4709      5.6209|
|  2:  4.7967 -  3.8278 0.99   1329  146 0.0969 0.1236      5.5527      5.7332|
|  3:  3.8278 -  3.3500 0.99   1304  147 0.1265 0.1756      5.6357      5.9886|
|  4:  3.3500 -  3.0465 0.99   1293  138 0.1493 0.1868      5.6177      5.7674|
|  5:  3.0465 -  2.8297 0.99   1282  146 0.1646 0.1801      5.5169      5.6022|
|  6:  2.8297 -  2.6638 0.98   1281  142 0.1547 0.2299      5.3949       5.626|
|  7:  2.6638 -  2.5311 0.99   1275  141 0.1537 0.2001      5.3368      5.5105|
|  8:  2.5311 -  2.4214 0.98   1266  142 0.1471 0.1973      5.2522      5.4917|
|  9:  2.4214 -  2.3285 0.98   1276  146 0.1525 0.2102      5.2125      5.4581|
| 10:  2.3285 -  2.2484 0.97   1232  132 0.1490 0.2091      5.1743      5.3718|
| 11:  2.2484 -  2.1783 0.99   1275  144 0.1454 0.2127      5.1192      5.4401|
| 12:  2.1783 -  2.1162 0.98   1271  133 0.1377 0.1914       5.044      5.2809|
| 13:  2.1162 -  2.0607 0.97   1226  139 0.1457 0.2022      4.9735      5.1835|
| 14:  2.0607 -  2.0105 0.73    940  109 0.1370 0.1993      4.8553      5.0848|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0694 -  4.7967  1380   154  0.93  10.42   0.96     0.93       8740.24|
|  2:  4.7967 -  3.8278  1329   146  0.94   9.62   1.00     0.99      11286.97|
|  3:  3.8278 -  3.3500  1304   147  0.91  13.81   1.01     1.01      13971.07|
|  4:  3.3500 -  3.0465  1293   138  0.90  15.90   1.00     0.97      13256.55|
|  5:  3.0465 -  2.8297  1282   146  0.87  18.94   0.99     0.97      11554.12|
|  6:  2.8297 -  2.6638  1281   142  0.88  18.75   0.98     0.94       9424.98|
|  7:  2.6638 -  2.5311  1275   141  0.88  18.45   0.98     0.96       8309.23|
|  8:  2.5311 -  2.4214  1266   142  0.89  17.93   0.98     0.94       7295.84|
|  9:  2.4214 -  2.3285  1276   146  0.87  19.48   0.99     0.95       6953.26|
| 10:  2.3285 -  2.2484  1232   132  0.87  19.10   0.99     0.95       6374.72|
| 11:  2.2484 -  2.1783  1275   144  0.87  19.38   0.99     0.93       5982.06|
| 12:  2.1783 -  2.1162  1271   133  0.89  17.97   0.99     0.97       5279.59|
| 13:  2.1162 -  2.0607  1226   139  0.88  18.99   0.98     0.97       4578.96|
| 14:  2.0607 -  2.0105   940   109  0.88  18.33   0.95     0.91       3552.91|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     3552.91 max =        13971.07 mean =      8460.27|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.97 mean =        16.83|
|phase err.(test): min =        0.00 max =           89.51 mean =        16.08|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.282)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.94    99.82   15.56    None  None   None       |
|    all(noH): 2823   0      1.94    99.82   15.56    None  None   None       |
|    Sol.    : 438    0      3.70    99.82   38.70    None  None   None       |
|    Mac.    : 2385   0      1.94    83.75   11.31    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:     1.935 -  11.723: 1655   |   5:    50.876 -  60.664:   70        |
|      1:    11.723 -  21.511:  634   |   6:    60.664 -  70.452:   40        |
|      2:    21.511 -  31.300:  159   |   7:    70.452 -  80.240:   11        |
|      3:    31.300 -  41.088:  124   |   8:    80.240 -  90.028:    4        |
|      4:    41.088 -  50.876:  125   |   9:    90.028 -  99.817:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 326         
Filter by distance & map next to the model:
   mapped sites are within: 0.638 - 5.052
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 320 from: 326
   mapped sites are within: 0.708 - 5.052

peak=    7.368 closest distance to " O   HOH Z 120 " =    1.722
peak=    7.194 closest distance to " O   HOH Z  57 " =    1.143
peak=    6.891 closest distance to " CG2 VAL A 230 " =    1.244
peak=    6.745 closest distance to " CG1 ILE A 234 " =    1.496
peak=    6.149 closest distance to " CG2 VAL A 296 " =    1.171
peak=    6.093 closest distance to " O   HOH Z 210 " =    1.654
peak=    6.016 closest distance to " CG  LEU A   5 " =    1.405
peak=    5.868 closest distance to " OD1 ASN A 301 " =    1.114
peak=    5.306 closest distance to " O   HOH Z 111 " =    2.340
peak=    5.033 closest distance to " CG  PRO A 280 " =    0.935
peak=    4.889 closest distance to " CB  SER A  63 " =    1.240
peak=    4.851 closest distance to " O   HOH Z 388 " =    1.288
peak=    4.846 closest distance to " CB  VAL A 230 " =    1.250
peak=    4.762 closest distance to " O   HOH Z 426 " =    1.264
peak=    4.711 closest distance to " O   HOH Z 425 " =    1.769
peak=    4.685 closest distance to " O   HOH Z 128 " =    1.704
peak=    4.660 closest distance to " CG  PRO A 198 " =    1.275
peak=    4.640 closest distance to " O   HOH Z 422 " =    1.169
peak=    4.553 closest distance to " O   HOH Z 102 " =    1.569
peak=    4.548 closest distance to " O   HOH Z 412 " =    3.264
peak=    4.547 closest distance to " N   SER A 164 " =    0.977
peak=    4.415 closest distance to " N   ASP A 298 " =    0.946
peak=    4.415 closest distance to " NH2 ARG A 156 " =    1.195
peak=    4.409 closest distance to " O   HOH Z 154 " =    1.642
peak=    4.398 closest distance to " CB  GLN A 223 " =    1.370
peak=    4.395 closest distance to " CG  PRO A  54 " =    1.322
peak=    4.386 closest distance to " CB  ARG A 275 " =    0.892
peak=    4.334 closest distance to " CB  VAL A 296 " =    1.119
peak=    4.321 closest distance to " O   ASP A 124 " =    1.320
peak=    4.303 closest distance to " O   HOH Z 418 " =    1.864
peak=    4.280 closest distance to " O   HOH Z 395 " =    1.537
peak=    4.279 closest distance to " O   HOH Z  49 " =    1.484
peak=    4.274 closest distance to " O  BHOH Z 338 " =    1.056
peak=    4.271 closest distance to " O   HOH Z 234 " =    3.538
peak=    4.239 closest distance to " CG AARG A 275 " =    1.178
peak=    4.229 closest distance to " O   HOH Z 126 " =    1.565
peak=    4.226 closest distance to " CB  GLN A 183 " =    1.223
peak=    4.208 closest distance to " O   HOH Z 209 " =    2.273
peak=    4.196 closest distance to " O   HOH Z 357 " =    2.199
peak=    4.192 closest distance to " CG  GLN A  77 " =    0.957
peak=    4.188 closest distance to " CD  LYS A 166 " =    1.623
peak=    4.159 closest distance to " CB  PRO A  54 " =    0.946
peak=    4.141 closest distance to " O   HOH Z  48 " =    1.993
peak=    4.133 closest distance to " O   HOH Z 403 " =    1.988
peak=    4.124 closest distance to " CA  ARG A 195 " =    1.138
peak=    4.107 closest distance to " O   HOH Z  48 " =    2.010
peak=    4.083 closest distance to " CZ  PHE A 218 " =    1.122
peak=    4.053 closest distance to " CD2 LEU A 228 " =    1.218
peak=    4.046 closest distance to " O   HOH Z 433 " =    2.103
peak=    4.031 closest distance to " OD2 ASP A 298 " =    0.857
peak=    4.030 closest distance to " O   HOH Z  95 " =    1.740
peak=    3.990 closest distance to " O   GLN A  11 " =    0.974
peak=    3.989 closest distance to " O   HOH Z  44 " =    1.761
peak=    3.984 closest distance to " O   HOH Z 248 " =    1.889
peak=    3.975 closest distance to " O   HOH Z 246 " =    1.582
peak=    3.969 closest distance to " CB  PRO A 198 " =    1.048
peak=    3.963 closest distance to " O   HOH Z  80 " =    2.187
peak=    3.960 closest distance to " CB  VAL A 296 " =    1.453
peak=    3.960 closest distance to " CB  TRP A 266 " =    1.007
peak=    3.958 closest distance to " CB  ALA A 299 " =    1.140
peak=    3.954 closest distance to " O   HOH Z 261 " =    2.267
peak=    3.948 closest distance to " O   HOH Z 404 " =    1.409
peak=    3.944 closest distance to " O   HOH Z 415 " =    1.710
peak=    3.937 closest distance to " CG  LEU A 228 " =    1.422
peak=    3.935 closest distance to " OE1 GLU A   2 " =    1.573
peak=    3.921 closest distance to " O   PRO A 198 " =    1.618
peak=    3.912 closest distance to " C   VAL A 265 " =    1.099
peak=    3.908 closest distance to " CA  TYR A  30 " =    0.960
peak=    3.902 closest distance to " O   HOH Z 431 " =    1.793
peak=    3.901 closest distance to " CD2 TRP A 179 " =    2.500
peak=    3.897 closest distance to " O   HOH Z  57 " =    2.310
peak=    3.895 closest distance to " O   HOH Z  43 " =    1.823
peak=    3.892 closest distance to " CG2 THR A 221 " =    1.082
peak=    3.871 closest distance to " O   ASP A 298 " =    0.890
peak=    3.867 closest distance to " CG1 ILE A 120 " =    1.100
peak=    3.857 closest distance to " CB  TRP A 179 " =    1.420
peak=    3.856 closest distance to " CG  ARG A  66 " =    0.982
peak=    3.855 closest distance to " NE2 HIS A 115 " =    1.119
peak=    3.854 closest distance to " CB  ASN A 187 " =    1.082
peak=    3.839 closest distance to " O   HOH Z 394 " =    1.888
peak=    3.838 closest distance to " O   HOH Z 139 " =    1.236
peak=    3.827 closest distance to " O   HOH Z  40 " =    2.271
peak=    3.823 closest distance to " CB  SER A  28 " =    1.071
peak=    3.813 closest distance to " CA  ARG A  66 " =    0.959
peak=    3.802 closest distance to " CB  ASN A 285 " =    0.861
peak=    3.799 closest distance to " CG  PRO A 213 " =    1.281
peak=    3.797 closest distance to " O   HOH Z 193 " =    1.582
peak=    3.795 closest distance to " O   HOH Z 130 " =    2.735
peak=    3.783 closest distance to " O   HOH Z 423 " =    1.795
peak=    3.781 closest distance to " O   HOH Z 435 " =    1.774
peak=    3.765 closest distance to " CB  SER A 141 " =    1.016
peak=    3.754 closest distance to " NH1AARG A 145 " =    1.276
peak=    3.753 closest distance to " O   HOH Z 389 " =    2.199
peak=    3.753 closest distance to " N   ILE A  33 " =    1.008
peak=    3.752 closest distance to " O   HOH Z  54 " =    1.182
peak=    3.749 closest distance to " ND2 ASN A 301 " =    1.022
peak=    3.740 closest distance to " O   HOH Z  63 " =    2.502
peak=    3.727 closest distance to " CG1 ILE A  33 " =    1.267
peak=    3.723 closest distance to " OE1 GLN A  11 " =    2.095
peak=    3.717 closest distance to " O   HOH Z 176 " =    2.238
peak=    3.709 closest distance to " O   HOH Z 277 " =    2.804
peak=    3.693 closest distance to " O   HOH Z 134 " =    2.384
peak=    3.688 closest distance to " O   HOH Z 265 " =    2.175
peak=    3.682 closest distance to " O   HOH Z 232 " =    2.224
peak=    3.679 closest distance to " CB  ARG A 275 " =    1.245
peak=    3.678 closest distance to " CB BVAL A  41 " =    1.109
peak=    3.673 closest distance to " CA  ASP A 191 " =    0.800
peak=    3.672 closest distance to " N   ALA A 256 " =    1.119
peak=    3.665 closest distance to " CB  ASN A 148 " =    1.362
peak=    3.664 closest distance to " CD  ARG A  36 " =    1.015
peak=    3.664 closest distance to " CB  MET A 105 " =    1.222
peak=    3.658 closest distance to " CB  SER A  62 " =    0.991
peak=    3.657 closest distance to " CA  VAL A  41 " =    0.817
peak=    3.654 closest distance to " O   HOH Z 393 " =    3.715
peak=    3.652 closest distance to " O   HOH Z 146 " =    1.711
peak=    3.651 closest distance to " CG  GLN A  11 " =    1.253
peak=    3.646 closest distance to " O   HOH Z 418 " =    3.193
peak=    3.643 closest distance to " CG  PRO A 243 " =    1.279
peak=    3.642 closest distance to " O   HOH Z 124 " =    1.345
peak=    3.639 closest distance to " CB  GLN A  88 " =    1.214
peak=    3.637 closest distance to " O   HOH Z  38 " =    2.751
peak=    3.623 closest distance to " OE1 GLN A  88 " =    0.950
peak=    3.620 closest distance to " CE1 HIS A 108 " =    1.191
peak=    3.618 closest distance to " O   HOH Z  88 " =    3.119
peak=    3.618 closest distance to " C   ALA A 299 " =    0.899
peak=    3.617 closest distance to " O   HOH Z 155 " =    1.571
peak=    3.597 closest distance to " O   HOH Z 130 " =    1.162
peak=    3.586 closest distance to " NE2 GLN A 278 " =    2.328
peak=    3.586 closest distance to " CB  GLN A  73 " =    1.190
peak=    3.586 closest distance to " C   GLY A  80 " =    1.156
peak=    3.585 closest distance to " CA  ALA A 295 " =    1.113
peak=    3.566 closest distance to " O   HOH Z  67 " =    1.919
peak=    3.565 closest distance to " O   HOH Z 126 " =    2.651
peak=    3.563 closest distance to " CG1 VAL A 153 " =    1.127
peak=    3.563 closest distance to " O   ALA A 292 " =    1.550
peak=    3.549 closest distance to " O   HOH Z 234 " =    1.854
peak=    3.548 closest distance to " CE1 TYR A 186 " =    1.345
peak=    3.546 closest distance to " CB  VAL A 202 " =    1.462
peak=    3.544 closest distance to " CD BLYS A 290 " =    1.123
peak=    3.544 closest distance to " CA  SER A  12 " =    1.423
peak=    3.541 closest distance to " NZ  LYS A  76 " =    1.110
peak=    3.539 closest distance to " CB  ALA A 100 " =    1.369
peak=    3.538 closest distance to " CE  LYS A 119 " =    1.465
peak=    3.537 closest distance to " CA  ILE A 106 " =    0.754
peak=    3.533 closest distance to " O   ALA A 165 " =    1.348
peak=    3.533 closest distance to " O   HOH Z 196 " =    1.778
peak=    3.530 closest distance to " NE2 GLN A  11 " =    0.981
peak=    3.523 closest distance to " CB  MET A  40 " =    0.820
peak=    3.521 closest distance to " O   HOH Z 273 " =    2.987
peak=    3.519 closest distance to " CB  GLU A 128 " =    1.138
peak=    3.518 closest distance to " OG1 THR A 294 " =    2.380
peak=    3.518 closest distance to " O   HOH Z 285 " =    2.974
peak=    3.514 closest distance to " NH1 ARG A  14 " =    1.075
peak=    3.513 closest distance to " CB  GLU A 152 " =    1.328
peak=    3.510 closest distance to " O   HOH Z 139 " =    5.052
peak=    3.508 closest distance to " CA  GLY A 196 " =    0.836
peak=    3.504 closest distance to " N   TYR A  15 " =    0.819
peak=    3.497 closest distance to " CA  ASN A 217 " =    1.337
peak=    3.487 closest distance to " N   ASN A  39 " =    1.182
peak=    3.475 closest distance to " O   HOH Z 377 " =    1.471
peak=    3.473 closest distance to " CB  ASN A 142 " =    1.184
peak=    3.470 closest distance to " O   HOH Z 280 " =    2.876
peak=    3.470 closest distance to " CB  GLU A 277 " =    3.841
peak=    3.467 closest distance to " NZ  LYS A 181 " =    0.826
peak=    3.466 closest distance to " CE3 TRP A  85 " =    1.327
peak=    3.465 closest distance to " CD  PRO A  54 " =    1.041
peak=    3.465 closest distance to " O   HOH Z 359 " =    1.459
peak=    3.463 closest distance to " O   HOH Z 155 " =    2.844
peak=    3.458 closest distance to " CB  ALA A 248 " =    1.323
peak=    3.457 closest distance to " O   HOH Z 257 " =    2.494
peak=    3.453 closest distance to " O   HOH Z 133 " =    2.265
peak=    3.452 closest distance to " CG2 THR A 220 " =    0.747
peak=    3.451 closest distance to " O   HOH Z 227 " =    1.741
peak=    3.450 closest distance to " O   HOH Z 416 " =    1.345
peak=    3.450 closest distance to " CG2 ILE A 234 " =    1.116
peak=    3.448 closest distance to " CZ3 TRP A  85 " =    0.943
peak=    3.445 closest distance to " O   HOH Z 174 " =    1.885
peak=    3.441 closest distance to " O   HOH Z 214 " =    1.399
peak=    3.437 closest distance to " O   HOH Z  66 " =    1.749
peak=    3.435 closest distance to " CD2 TRP A 179 " =    1.235
peak=    3.434 closest distance to " CD  ARG A 269 " =    0.944
peak=    3.433 closest distance to " CD1 LEU A 222 " =    0.797
peak=    3.429 closest distance to " CD  ARG A 159 " =    0.835
peak=    3.407 closest distance to " O   HOH Z 128 " =    2.074
peak=    3.404 closest distance to " CG  ASP A 231 " =    1.235
peak=    3.402 closest distance to " CA  ALA A  51 " =    1.113
peak=    3.396 closest distance to " O   HOH Z 394 " =    4.278
peak=    3.395 closest distance to " O   HOH Z 117 " =    1.144
peak=    3.390 closest distance to " CB  SER A  97 " =    1.497
peak=    3.390 closest distance to " NH2 ARG A  79 " =    1.314
peak=    3.387 closest distance to " O   HOH Z 146 " =    1.631
peak=    3.386 closest distance to " O   GLY A  91 " =    1.190
peak=    3.381 closest distance to " N   GLY A  75 " =    1.607
peak=    3.372 closest distance to " O   HOH Z 301 " =    1.785
peak=    3.371 closest distance to " OG  SER A  62 " =    2.836
peak=    3.369 closest distance to " O   HOH Z 369 " =    1.823
peak=    3.366 closest distance to " O   HOH Z 415 " =    1.258
peak=    3.365 closest distance to " CB  THR A  31 " =    1.387
peak=    3.365 closest distance to " O   HOH Z 403 " =    1.410
peak=    3.362 closest distance to " O   HOH Z 148 " =    1.972
peak=    3.361 closest distance to " O   HOH Z   4 " =    1.536
peak=    3.358 closest distance to " O   HOH Z 419 " =    2.231
peak=    3.355 closest distance to " O   HOH Z 291 " =    1.537
peak=    3.352 closest distance to " CD  LYS A 289 " =    1.068
peak=    3.351 closest distance to " CB  ALA A   1 " =    1.421
peak=    3.351 closest distance to " CA  HIS A 115 " =    0.980
peak=    3.349 closest distance to " O   HOH Z 301 " =    2.317
peak=    3.346 closest distance to " O   HOH Z 299 " =    4.203
peak=    3.344 closest distance to " O   HOH Z  61 " =    1.479
peak=    3.342 closest distance to " CB  ALA A 291 " =    1.248
peak=    3.341 closest distance to " O   HOH Z 130 " =    2.493
peak=    3.341 closest distance to " CG  GLN A 205 " =    1.159
peak=    3.340 closest distance to " O   HOH Z 426 " =    3.409
peak=    3.339 closest distance to " CA  GLY A  23 " =    0.941
peak=    3.335 closest distance to " O   HOH Z   5 " =    1.950
peak=    3.323 closest distance to " O   HOH Z 174 " =    1.335
peak=    3.322 closest distance to " NH1 ARG A 269 " =    0.869
peak=    3.321 closest distance to " O   HOH Z 387 " =    2.987
peak=    3.321 closest distance to " CB  THR A 235 " =    1.217
peak=    3.318 closest distance to " O   HOH Z 189 " =    2.791
peak=    3.317 closest distance to " CB  GLU A  46 " =    1.002
peak=    3.313 closest distance to " CA  LEU A 282 " =    1.145
peak=    3.303 closest distance to " O   HOH Z 427 " =    3.013
peak=    3.303 closest distance to " CB  ALA A 226 " =    1.260
peak=    3.297 closest distance to " ND1 HIS A  81 " =    1.547
peak=    3.296 closest distance to " CA  THR A 246 " =    1.029
peak=    3.293 closest distance to " O   HOH Z 245 " =    1.417
peak=    3.291 closest distance to " OG  SER A  62 " =    3.100
peak=    3.288 closest distance to " OG  SER A 245 " =    1.615
peak=    3.286 closest distance to " OD2 ASP A 298 " =    3.338
peak=    3.282 closest distance to " O   ASP A 200 " =    1.580
peak=    3.281 closest distance to " O   GLU A   2 " =    1.777
peak=    3.281 closest distance to " CG1 ILE A 106 " =    1.167
peak=    3.280 closest distance to " CG  MET A 185 " =    1.242
peak=    3.276 closest distance to " O   HOH Z 420 " =    5.034
peak=    3.276 closest distance to " CB  GLU A 175 " =    1.341
peak=    3.268 closest distance to " CB  ALA A 137 " =    1.281
peak=    3.267 closest distance to " CG  ASN A 173 " =    1.233
peak=    3.265 closest distance to " O   HOH Z  15 " =    2.286
peak=    3.263 closest distance to " CA  SER A 210 " =    1.421
peak=    3.262 closest distance to " CB  PHE A  16 " =    1.246
peak=    3.262 closest distance to " O   HOH Z 417 " =    1.284
peak=    3.262 closest distance to " O   HOH Z  85 " =    2.043
peak=    3.261 closest distance to " O   HOH Z 383 " =    2.113
peak=    3.260 closest distance to " CA  THR A 264 " =    0.919
peak=    3.260 closest distance to " O   HOH Z 359 " =    1.871
peak=    3.256 closest distance to " O   HOH Z 371 " =    3.211
peak=    3.255 closest distance to " CA  GLN A 223 " =    0.750
peak=    3.254 closest distance to " O   HOH Z 316 " =    3.157
peak=    3.249 closest distance to " CA  ASP A 140 " =    1.265
peak=    3.248 closest distance to " CA  SER A  87 " =    0.885
peak=    3.247 closest distance to " O   LYS A 289 " =    0.943
peak=    3.246 closest distance to " O   HOH Z  78 " =    2.578
peak=    3.245 closest distance to " CD2 LEU A 297 " =    0.799
peak=    3.240 closest distance to " CA  TYR A 116 " =    1.490
peak=    3.233 closest distance to " CA  ALA A  21 " =    1.273
peak=    3.232 closest distance to " CG1BVAL A 121 " =    1.315
peak=    3.229 closest distance to " O   HOH Z 406 " =    1.544
peak=    3.229 closest distance to " CD  ARG A  24 " =    1.322
peak=    3.228 closest distance to " O   HOH Z 117 " =    1.958
peak=    3.226 closest distance to " O   HOH Z 344 " =    3.035
peak=    3.223 closest distance to " OD1 ASN A 217 " =    1.687
peak=    3.223 closest distance to " CB  ARG A 219 " =    1.422
peak=    3.223 closest distance to " O   HOH Z 236 " =    1.964
peak=    3.217 closest distance to " CB  PHE A 283 " =    0.905
peak=    3.216 closest distance to " N   ALA A 180 " =    0.989
peak=    3.211 closest distance to " O   SER A 273 " =    1.818
peak=    3.210 closest distance to " N   THR A  42 " =    1.298
peak=    3.209 closest distance to " CD  LYS A 119 " =    2.159
peak=    3.208 closest distance to " OG1 THR A 294 " =    1.579
peak=    3.203 closest distance to " CA  CYS A 260 " =    1.070
peak=    3.203 closest distance to " O   HOH Z 214 " =    2.310
peak=    3.203 closest distance to " CA  ALA A 291 " =    0.889
peak=    3.203 closest distance to " N   CYS A 260 " =    0.867
peak=    3.200 closest distance to " N   PHE A 130 " =    1.199
peak=    3.196 closest distance to " CB  TRP A 179 " =    1.423
peak=    3.196 closest distance to " OG BSER A 212 " =    2.609
peak=    3.194 closest distance to " CE BMET A  47 " =    1.533
peak=    3.190 closest distance to " CA  LYS A  48 " =    1.355
peak=    3.187 closest distance to " O   HOH Z 368 " =    3.182
peak=    3.186 closest distance to " CA  ALA A   9 " =    1.224
peak=    3.185 closest distance to " N   VAL A 126 " =    1.721
peak=    3.183 closest distance to " N   THR A  52 " =    1.065
peak=    3.180 closest distance to " NE  ARG A 195 " =    1.909
peak=    3.176 closest distance to " CB  GLU A 277 " =    0.850
peak=    3.175 closest distance to " O   HOH Z 374 " =    2.881
peak=    3.173 closest distance to " O   HOH Z 162 " =    3.989
peak=    3.170 closest distance to " CB  ARG A 190 " =    1.819
peak=    3.169 closest distance to " CB  PRO A 243 " =    1.253
peak=    3.165 closest distance to " O   HOH Z 281 " =    2.781
peak=    3.162 closest distance to " CB  ALA A 242 " =    0.900
peak=    3.158 closest distance to " CA  ALA A 248 " =    1.279
peak=    3.157 closest distance to " CG2 ILE A 106 " =    0.795
peak=    3.148 closest distance to " O   HOH Z 438 " =    2.018
peak=    3.143 closest distance to " CB  ASN A 301 " =    0.846
peak=    3.143 closest distance to " CB  LEU A  83 " =    0.708
peak=    3.142 closest distance to " O   SER A  87 " =    2.397
peak=    3.137 closest distance to " CB  ALA A 256 " =    1.458
peak=    3.137 closest distance to " O   HOH Z 327 " =    2.924
peak=    3.135 closest distance to " CB  ARG A 269 " =    1.788
peak=    3.128 closest distance to " CB  VAL A 265 " =    1.340
peak=    3.125 closest distance to " O   HOH Z 193 " =    2.126
peak=    3.123 closest distance to " CB  GLN A  73 " =    1.148
peak=    3.122 closest distance to " N   ALA A 292 " =    1.113
peak=    3.112 closest distance to " CA  ASN A 249 " =    1.398
peak=    3.110 closest distance to " O   HOH Z 350 " =    1.290
peak=    3.110 closest distance to " OH  TYR A 116 " =    1.339
peak=    3.107 closest distance to " N   ALA A   1 " =    1.360
peak=    3.102 closest distance to " O   HOH Z 271 " =    2.260
peak=    3.101 closest distance to " O   HOH Z 185 " =    1.746
peak=    3.092 closest distance to " O   HOH Z 433 " =    3.753
peak=    3.085 closest distance to " CB  SER A  26 " =    1.635
peak=    3.065 closest distance to " CB  PRO A  90 " =    1.078
peak=    3.061 closest distance to " CG1 ILE A  20 " =    1.296
peak=    3.059 closest distance to " O   HOH Z 193 " =    1.891
peak=    3.054 closest distance to " CG1 VAL A 250 " =    1.504
peak=    3.051 closest distance to " CD  GLN A  73 " =    1.068
peak=    3.047 closest distance to " CA  ASN A 176 " =    1.176
peak=    3.046 closest distance to " O   HOH Z 187 " =    2.337
peak=    3.046 closest distance to " CB  ARG A  79 " =    0.936

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 225         
Filter by distance & map next to the model:
   mapped sites are within: 0.440 - 5.277
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 219 from: 225
   mapped sites are within: 0.714 - 5.277

peak=   -4.908 closest distance to " CG2 VAL A 230 " =    0.910
peak=   -4.730 closest distance to " O   HOH Z 400 " =    0.819
peak=   -4.608 closest distance to " O   HOH Z 166 " =    1.454
peak=   -4.552 closest distance to " OD1 ASN A 301 " =    0.803
peak=   -4.451 closest distance to " CD1 PHE A  59 " =    1.959
peak=   -4.395 closest distance to " CA  ASP A 298 " =    1.065
peak=   -4.365 closest distance to " CB  ALA A 291 " =    2.504
peak=   -4.323 closest distance to " CD  GLN A  58 " =    0.982
peak=   -4.235 closest distance to " CG2BVAL A  41 " =    2.580
peak=   -4.165 closest distance to " OXT GLY A 302 " =    2.865
peak=   -4.156 closest distance to " CA  TYR A  68 " =    2.825
peak=   -4.111 closest distance to " O   HOH Z 151 " =    1.126
peak=   -4.105 closest distance to " CD  GLN A 223 " =    1.370
peak=   -4.093 closest distance to " O   GLN A  11 " =    0.957
peak=   -4.061 closest distance to " CD  GLN A  58 " =    0.935
peak=   -4.036 closest distance to " O   HOH Z 411 " =    5.277
peak=   -4.023 closest distance to " CD  ARG A  14 " =    3.210
peak=   -4.001 closest distance to " CG  PRO A 243 " =    1.733
peak=   -3.996 closest distance to " O   HOH Z  13 " =    1.669
peak=   -3.994 closest distance to " CG  LEU A   5 " =    1.129
peak=   -3.989 closest distance to " O   HOH Z 184 " =    1.056
peak=   -3.953 closest distance to " CA  VAL A 197 " =    0.986
peak=   -3.923 closest distance to " O   HOH Z 231 " =    1.738
peak=   -3.909 closest distance to " O   HOH Z 351 " =    1.646
peak=   -3.902 closest distance to " CD  GLN A  73 " =    0.714
peak=   -3.901 closest distance to " O   HOH Z 196 " =    1.828
peak=   -3.900 closest distance to " O   HOH Z 290 " =    0.993
peak=   -3.898 closest distance to " O   PRO A 198 " =    1.286
peak=   -3.897 closest distance to " O   SER A  95 " =    2.074
peak=   -3.880 closest distance to " O   HOH Z   5 " =    1.693
peak=   -3.877 closest distance to " CD1 LEU A  25 " =    2.590
peak=   -3.863 closest distance to " OE2 GLU A 277 " =    2.859
peak=   -3.853 closest distance to " O   HOH Z  52 " =    2.043
peak=   -3.850 closest distance to " CG  ASP A 231 " =    0.748
peak=   -3.833 closest distance to " CA  SER A 164 " =    2.010
peak=   -3.832 closest distance to " O   HOH Z 426 " =    0.860
peak=   -3.823 closest distance to " O   HOH Z 210 " =    0.740
peak=   -3.807 closest distance to " NH2 ARG A  36 " =    1.185
peak=   -3.805 closest distance to " OD2 ASP A 298 " =    0.918
peak=   -3.799 closest distance to " O   HOH Z 388 " =    1.827
peak=   -3.777 closest distance to " CG1 VAL A 112 " =    2.475
peak=   -3.763 closest distance to " O   HOH Z  58 " =    0.962
peak=   -3.762 closest distance to " CB  SER A 146 " =    2.120
peak=   -3.755 closest distance to " OD1 ASN A 148 " =    1.437
peak=   -3.745 closest distance to " CB  LEU A 167 " =    2.121
peak=   -3.740 closest distance to " NH2 ARG A  66 " =    1.261
peak=   -3.737 closest distance to " O   HOH Z  19 " =    2.168
peak=   -3.732 closest distance to " O   ASP A 298 " =    0.872
peak=   -3.729 closest distance to " O   HOH Z 120 " =    1.557
peak=   -3.725 closest distance to " O   HOH Z 174 " =    1.683
peak=   -3.720 closest distance to " CB  ALA A 161 " =    2.582
peak=   -3.702 closest distance to " O   HOH Z 265 " =    1.078
peak=   -3.702 closest distance to " O   HOH Z 377 " =    0.735
peak=   -3.701 closest distance to " O   HOH Z 103 " =    2.192
peak=   -3.698 closest distance to " CD2 PHE A  59 " =    2.494
peak=   -3.697 closest distance to " C   ASN A 285 " =    2.295
peak=   -3.696 closest distance to " O   HOH Z  60 " =    1.750
peak=   -3.694 closest distance to " O   HOH Z 422 " =    1.143
peak=   -3.685 closest distance to " CZ  ARG A 259 " =    0.882
peak=   -3.685 closest distance to " O   HOH Z 407 " =    1.630
peak=   -3.674 closest distance to " CG1 VAL A 250 " =    2.583
peak=   -3.670 closest distance to " O   SER A 135 " =    1.945
peak=   -3.667 closest distance to " CG1 VAL A 197 " =    2.417
peak=   -3.665 closest distance to " CD  GLN A 223 " =    0.793
peak=   -3.662 closest distance to " N   ALA A   1 " =    2.475
peak=   -3.655 closest distance to " CA  TRP A 274 " =    1.155
peak=   -3.623 closest distance to " CB  PRO A 243 " =    2.861
peak=   -3.618 closest distance to " CG1 VAL A 296 " =    1.182
peak=   -3.615 closest distance to " O   HOH Z  57 " =    0.863
peak=   -3.609 closest distance to " O   HOH Z 301 " =    2.327
peak=   -3.607 closest distance to " OG  SER A  87 " =    1.778
peak=   -3.605 closest distance to " O   HOH Z 407 " =    1.426
peak=   -3.600 closest distance to " O   HOH Z 109 " =    3.283
peak=   -3.581 closest distance to " CD  GLN A  11 " =    0.763
peak=   -3.569 closest distance to " CA  ASN A 127 " =    1.032
peak=   -3.561 closest distance to " OG1 THR A  82 " =    1.594
peak=   -3.560 closest distance to " N   SER A 134 " =    1.219
peak=   -3.556 closest distance to " CG  ASP A  50 " =    2.273
peak=   -3.539 closest distance to " O   SER A 164 " =    1.900
peak=   -3.533 closest distance to " O   HOH Z 109 " =    3.483
peak=   -3.533 closest distance to " SG  CYS A 168 " =    1.191
peak=   -3.507 closest distance to " O   HOH Z 222 " =    1.329
peak=   -3.501 closest distance to " O   HOH Z 198 " =    1.144
peak=   -3.500 closest distance to " CA  SER A 276 " =    1.449
peak=   -3.499 closest distance to " O  BHOH Z 338 " =    1.178
peak=   -3.498 closest distance to " O   HOH Z   6 " =    2.084
peak=   -3.495 closest distance to " O   HOH Z  37 " =    1.331
peak=   -3.492 closest distance to " OD1 ASP A 298 " =    2.408
peak=   -3.492 closest distance to " C   THR A 279 " =    1.099
peak=   -3.480 closest distance to " O   HOH Z 275 " =    1.475
peak=   -3.478 closest distance to " O   HOH Z 252 " =    1.220
peak=   -3.477 closest distance to " O   HOH Z 423 " =    2.586
peak=   -3.476 closest distance to " CE  MET A 105 " =    2.111
peak=   -3.475 closest distance to " CA  GLU A 277 " =    1.349
peak=   -3.474 closest distance to " O   HOH Z 171 " =    2.338
peak=   -3.473 closest distance to " OG1 THR A  82 " =    1.287
peak=   -3.462 closest distance to " OH  TYR A 169 " =    0.912
peak=   -3.460 closest distance to " O   HOH Z 189 " =    1.907
peak=   -3.459 closest distance to " CD2 LEU A 143 " =    2.505
peak=   -3.455 closest distance to " N   ASP A 272 " =    1.199
peak=   -3.455 closest distance to " O   HOH Z 120 " =    0.774
peak=   -3.450 closest distance to " N   SER A   3 " =    2.506
peak=   -3.436 closest distance to " N   VAL A 230 " =    0.979
peak=   -3.436 closest distance to " O   HOH Z 426 " =    2.160
peak=   -3.435 closest distance to " CG  GLN A 103 " =    2.372
peak=   -3.430 closest distance to " OE1 GLN A  88 " =    1.197
peak=   -3.425 closest distance to " O   TYR A  15 " =    1.638
peak=   -3.423 closest distance to " CG2 VAL A 296 " =    0.859
peak=   -3.421 closest distance to " O   ALA A 256 " =    1.714
peak=   -3.415 closest distance to " CB  ALA A 248 " =    2.291
peak=   -3.415 closest distance to " O   HOH Z 384 " =    1.808
peak=   -3.414 closest distance to " O   HOH Z 368 " =    1.950
peak=   -3.414 closest distance to " O   HOH Z 252 " =    3.973
peak=   -3.412 closest distance to " O   HOH Z  92 " =    1.369
peak=   -3.405 closest distance to " O   ALA A   1 " =    2.142
peak=   -3.400 closest distance to " O   HOH Z 132 " =    1.478
peak=   -3.399 closest distance to " CD  GLN A  88 " =    0.758
peak=   -3.398 closest distance to " CD  PRO A 213 " =    2.263
peak=   -3.396 closest distance to " CD2 PHE A  61 " =    2.128
peak=   -3.395 closest distance to " O   HOH Z 418 " =    1.389
peak=   -3.395 closest distance to " O   HOH Z 111 " =    2.849
peak=   -3.390 closest distance to " O   HOH Z 165 " =    1.693
peak=   -3.387 closest distance to " O   HOH Z 308 " =    1.440
peak=   -3.387 closest distance to " CA  ALA A 137 " =    2.622
peak=   -3.381 closest distance to " O   HOH Z   7 " =    1.346
peak=   -3.376 closest distance to " CG  ARG A 269 " =    2.479
peak=   -3.374 closest distance to " O   GLY A  80 " =    2.536
peak=   -3.372 closest distance to " O   HOH Z 401 " =    1.526
peak=   -3.366 closest distance to " CD2 HIS A 115 " =    1.084
peak=   -3.356 closest distance to " CG2 THR A 221 " =    2.421
peak=   -3.344 closest distance to " O   HOH Z 238 " =    1.005
peak=   -3.342 closest distance to " CB  ALA A 291 " =    2.276
peak=   -3.339 closest distance to " CB  ALA A  10 " =    2.101
peak=   -3.338 closest distance to " O   HOH Z 200 " =    1.342
peak=   -3.334 closest distance to " N   ALA A 226 " =    2.159
peak=   -3.332 closest distance to " CD  GLN A  77 " =    0.972
peak=   -3.331 closest distance to " O   ASP A 298 " =    1.412
peak=   -3.324 closest distance to " O   TRP A  92 " =    2.179
peak=   -3.324 closest distance to " OH  TYR A 247 " =    2.034
peak=   -3.320 closest distance to " O  BHOH Z  74 " =    1.550
peak=   -3.320 closest distance to " OD1 ASP A 171 " =    1.510
peak=   -3.319 closest distance to " C   VAL A 265 " =    0.903
peak=   -3.319 closest distance to " CH2 TRP A 150 " =    1.005
peak=   -3.318 closest distance to " OD2 ASP A 171 " =    1.915
peak=   -3.317 closest distance to " CG2 ILE A  49 " =    2.686
peak=   -3.315 closest distance to " N   ALA A 242 " =    1.832
peak=   -3.313 closest distance to " CB  ALA A 291 " =    2.514
peak=   -3.313 closest distance to " C   ALA A 158 " =    1.351
peak=   -3.312 closest distance to " CE  LYS A 119 " =    1.882
peak=   -3.311 closest distance to " CG  ARG A 259 " =    2.470
peak=   -3.303 closest distance to " CG  MET A  93 " =    2.540
peak=   -3.302 closest distance to " CA  GLY A 203 " =    2.242
peak=   -3.295 closest distance to " O   HOH Z 411 " =    1.853
peak=   -3.293 closest distance to " O   HOH Z  64 " =    1.569
peak=   -3.293 closest distance to " O   HOH Z 114 " =    1.572
peak=   -3.290 closest distance to " O   HOH Z 185 " =    2.490
peak=   -3.290 closest distance to " CD  GLU A 236 " =    1.038
peak=   -3.290 closest distance to " O   HOH Z 396 " =    1.911
peak=   -3.286 closest distance to " O   PHE A  59 " =    2.330
peak=   -3.285 closest distance to " O   ASN A 301 " =    1.068
peak=   -3.283 closest distance to " CB  HIS A  86 " =    2.397
peak=   -3.282 closest distance to " CD1 LEU A 228 " =    2.402
peak=   -3.274 closest distance to " OE2 GLU A 128 " =    1.939
peak=   -3.268 closest distance to " OG BSER A 210 " =    1.141
peak=   -3.267 closest distance to " O   HOH Z  50 " =    1.138
peak=   -3.265 closest distance to " O   HOH Z 285 " =    1.529
peak=   -3.260 closest distance to " O   HOH Z 369 " =    2.454
peak=   -3.257 closest distance to " O   HOH Z  39 " =    2.272
peak=   -3.255 closest distance to " O   HOH Z  56 " =    1.797
peak=   -3.252 closest distance to " O   HOH Z 108 " =    2.101
peak=   -3.248 closest distance to " O   HOH Z 311 " =    3.304
peak=   -3.243 closest distance to " CZ  TYR A 169 " =    1.786
peak=   -3.241 closest distance to " N   THR A 235 " =    1.270
peak=   -3.240 closest distance to " O   HOH Z  11 " =    1.844
peak=   -3.239 closest distance to " O   HOH Z 264 " =    1.940
peak=   -3.237 closest distance to " ND2 ASN A  60 " =    1.703
peak=   -3.236 closest distance to " N   ARG A 275 " =    1.097
peak=   -3.234 closest distance to " O   HOH Z 234 " =    4.118
peak=   -3.229 closest distance to " O   HOH Z 231 " =    2.164
peak=   -3.227 closest distance to " NH2 ARG A 159 " =    2.338
peak=   -3.226 closest distance to " O   HOH Z 423 " =    1.281
peak=   -3.224 closest distance to " O   VAL A 121 " =    0.891
peak=   -3.223 closest distance to " CD2 PHE A 192 " =    2.114
peak=   -3.211 closest distance to " O   HOH Z 150 " =    1.795
peak=   -3.207 closest distance to " CA  GLY A 241 " =    3.373
peak=   -3.206 closest distance to " NH1 ARG A 219 " =    1.886
peak=   -3.203 closest distance to " OG  SER A  97 " =    2.435
peak=   -3.197 closest distance to " CE2 TYR A  30 " =    2.637
peak=   -3.194 closest distance to " O   GLN A  94 " =    2.353
peak=   -3.187 closest distance to " CD2 LEU A 237 " =    2.752
peak=   -3.179 closest distance to " CD1 TYR A 247 " =    2.283
peak=   -3.174 closest distance to " O   HOH Z 221 " =    1.138
peak=   -3.174 closest distance to " O   ALA A  34 " =    2.459
peak=   -3.173 closest distance to " O   HOH Z 205 " =    0.890
peak=   -3.164 closest distance to " O   HOH Z 435 " =    1.354
peak=   -3.163 closest distance to " ND2 ASN A  60 " =    1.594
peak=   -3.161 closest distance to " O   HOH Z  90 " =    1.878
peak=   -3.147 closest distance to " O   HOH Z 432 " =    1.076
peak=   -3.147 closest distance to " CE  MET A 105 " =    2.178
peak=   -3.142 closest distance to " CG  ARG A 259 " =    1.445
peak=   -3.128 closest distance to " O   HOH Z 414 " =    2.823
peak=   -3.117 closest distance to " ND2 ASN A  45 " =    1.123
peak=   -3.109 closest distance to " OE2 GLU A   2 " =    1.559
peak=   -3.105 closest distance to " CG  PHE A 283 " =    2.567
peak=   -3.100 closest distance to " O   HOH Z  39 " =    0.769
peak=   -3.100 closest distance to " O   HOH Z 136 " =    0.918
peak=   -3.098 closest distance to " CB  PHE A 130 " =    1.256
peak=   -3.096 closest distance to " O   HOH Z 253 " =    2.256
peak=   -3.096 closest distance to " N   ALA A  43 " =    2.622
peak=   -3.080 closest distance to " NH2BARG A 145 " =    2.371
peak=   -3.078 closest distance to " O   HOH Z 137 " =    1.474
peak=   -3.074 closest distance to " N   ASN A  60 " =    1.832
peak=   -3.069 closest distance to " CD2 LEU A 222 " =    2.136
peak=   -3.067 closest distance to " O   LEU A 282 " =    2.123
peak=   -3.067 closest distance to " OD1 ASP A 272 " =    1.632
peak=   -3.065 closest distance to " OH  TYR A 172 " =    1.835
peak=   -3.053 closest distance to " O   HOH Z 210 " =    1.236
peak=   -3.039 closest distance to " CB  MET A 188 " =    1.727
peak=   -3.015 closest distance to " CD2 TYR A 293 " =    1.932

================= 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    :  0.4941 0.4788   6.295646e+00   6.273904e+00
   1_bss:  0.4874 0.4689   6.290236e+00   6.267884e+00
   1_xyz:  0.4169 0.4236   6.215087e+00   6.217917e+00
   1_adp:  0.3728 0.4134   6.144737e+00   6.202047e+00
   1_occ:  0.3720 0.4120   6.143838e+00   6.201870e+00
   2_bss:  0.3697 0.4069   6.145130e+00   6.201692e+00
   2_xyz:  0.3083 0.3733   6.016001e+00   6.132549e+00
   2_adp:  0.2981 0.3599   5.996040e+00   6.114419e+00
   2_occ:  0.2978 0.3599   5.995575e+00   6.114439e+00
   3_bss:  0.2978 0.3593   5.997174e+00   6.115203e+00
   3_xyz:  0.2490 0.2981   5.828609e+00   5.965835e+00
   3_adp:  0.2391 0.2906   5.799778e+00   5.944860e+00
   3_occ:  0.2388 0.2909   5.799701e+00   5.945461e+00
   4_bss:  0.2386 0.2905   5.799608e+00   5.943738e+00
   4_xyz:  0.1825 0.2329   5.559778e+00   5.749956e+00
   4_adp:  0.1596 0.2051   5.439402e+00   5.639479e+00
   4_occ:  0.1595 0.2053   5.439242e+00   5.639858e+00
   5_bss:  0.1592 0.2058   5.439059e+00   5.639829e+00
   5_xyz:  0.1403 0.1866   5.333586e+00   5.545801e+00
   5_adp:  0.1366 0.1825   5.309953e+00   5.522890e+00
   5_occ:  0.1365 0.1825   5.309513e+00   5.522710e+00
   5_bss:  0.1365 0.1825   5.309404e+00   5.522691e+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:  0.317  20.001   5.992  12.333   7.502   0.000   0.000   0.000
   1_xyz:  0.317  20.001   5.992  12.333   7.502   0.000   0.000   0.000
   1_adp:  0.317  20.001   5.992  12.333   7.502   0.000   0.000   0.000
   1_occ:  0.317  20.001   5.992  12.333   7.502   0.000   0.000   0.000
   2_bss:  0.315  41.995   2.764   7.887   4.381   0.000   0.000   0.000
   2_xyz:  0.315  41.995   2.764   7.887   4.381   0.000   0.000   0.000
   2_adp:  0.315  41.995   2.764   7.887   4.381   0.000   0.000   0.000
   2_occ:  0.315  41.995   2.764   7.887   4.381   0.000   0.000   0.000
   3_bss:  0.299  41.995   2.284   5.610   3.378   0.000   0.000   0.000
   3_xyz:  0.299  41.995   2.284   5.610   3.378   0.000   0.000   0.000
   3_adp:  0.299  41.995   2.284   5.610   3.378   0.000   0.000   0.000
   3_occ:  0.299  41.995   2.284   5.610   3.378   0.000   0.000   0.000
   4_bss:  0.311  41.995   1.622   4.139   2.777   0.000   0.000   0.000
   4_xyz:  0.311  41.995   1.622   4.139   2.777   0.000   0.000   0.000
   4_adp:  0.311  41.995   1.622   4.139   2.777   0.000   0.000   0.000
   4_occ:  0.311  41.995   1.622   4.139   2.777   0.000   0.000   0.000
   5_bss:  0.323  60.482   1.146   2.651   2.520   0.000   0.000   0.000
   5_xyz:  0.323  60.482   1.146   2.651   2.520   0.000   0.000   0.000
   5_adp:  0.323  60.482   1.146   2.651   2.520   0.000   0.000   0.000
   5_occ:  0.323  60.482   1.146   2.651   2.520   0.000   0.000   0.000
   5_bss:  0.325  62.417  -0.905   0.340   0.565   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  59.060 0.4061  0.4594    71075.789
   1_bss:  58.393 0.4136  0.5985    69095.613
   1_xyz:  49.856 0.5216  0.7386    53940.055
   1_adp:  46.831 0.5597  0.8529    49683.645
   1_occ:  46.778 0.5603  0.8524    49557.952
   2_bss:  46.502 0.5637  0.7609    49242.702
   2_xyz:  41.579 0.6231  0.8417    40059.464
   2_adp:  39.988 0.6426  0.8533    37725.650
   2_occ:  39.969 0.6428  0.8531    37689.071
   3_bss:  39.869 0.6441  0.8198    37628.571
   3_xyz:  30.990 0.7470  0.9276    24119.360
   3_adp:  29.901 0.7594  0.9405    22921.756
   3_occ:  29.925 0.7592  0.9402    22963.592
   4_bss:  29.811 0.7604  0.9116    22785.830
   4_xyz:  22.833 0.8336  0.9667    13787.867
   4_adp:  19.842 0.8631  0.9734    10810.137
   4_occ:  19.842 0.8631  0.9736    10829.809
   5_bss:  19.791 0.8637  0.9499    10818.259
   5_xyz:  17.411 0.8860  0.9633     8804.082
   5_adp:  16.763 0.8922  0.9628     8456.560
   5_occ:  16.756 0.8922  0.9628     8459.621
   5_bss:  16.755 0.8923  0.9573     8459.258
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4464e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4464e+01
   1_xyz:   1.665  0.013  0.106 18.120  0.006  4.125   1.3968e-01
   1_adp:   1.665  0.013  0.106 18.120  0.006  4.125   1.3968e-01
   1_occ:   1.665  0.013  0.106 18.120  0.006  4.125   1.3968e-01
   2_bss:   1.665  0.013  0.106 18.120  0.006  4.125   1.3968e-01
   2_xyz:   1.345  0.010  0.088 17.026  0.005  4.110   1.0746e-01
   2_adp:   1.345  0.010  0.088 17.026  0.005  4.110   1.0746e-01
   2_occ:   1.345  0.010  0.088 17.026  0.005  4.110   1.0746e-01
   3_bss:   1.345  0.010  0.088 17.026  0.005  4.110   1.0746e-01
   3_xyz:   1.172  0.009  0.080 15.255  0.004  4.112   7.7276e-02
   3_adp:   1.172  0.009  0.080 15.255  0.004  4.112   7.7276e-02
   3_occ:   1.172  0.009  0.080 15.255  0.004  4.112   7.7276e-02
   4_bss:   1.172  0.009  0.080 15.255  0.004  4.112   7.7276e-02
   4_xyz:   1.247  0.011  0.087 15.736  0.005  4.132   9.8761e-02
   4_adp:   1.247  0.011  0.087 15.736  0.005  4.132   9.8761e-02
   4_occ:   1.247  0.011  0.087 15.736  0.005  4.132   9.8761e-02
   5_bss:   1.247  0.011  0.087 15.736  0.005  4.132   9.8761e-02
   5_xyz:   1.057  0.008  0.081 15.350  0.004  4.118   6.7570e-02
   5_adp:   1.057  0.008  0.081 15.350  0.004  4.118   6.7570e-02
   5_occ:   1.057  0.008  0.081 15.350  0.004  4.118   6.7570e-02
   5_bss:   1.057  0.008  0.081 15.350  0.004  4.118   6.7570e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0609e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0609e+00
   1_xyz:  14.504  0.115  0.461 88.703  0.041  2.233   1.0003e-01
   1_adp:  14.504  0.115  0.461 88.703  0.041  2.233   1.0003e-01
   1_occ:  14.504  0.115  0.461 88.703  0.041  2.233   1.0003e-01
   2_bss:  14.504  0.115  0.461 88.703  0.041  2.233   1.0003e-01
   2_xyz:   7.636  0.082  0.306 86.832  0.030  2.002   9.1752e-02
   2_adp:   7.636  0.082  0.306 86.832  0.030  2.002   9.1752e-02
   2_occ:   7.636  0.082  0.306 86.832  0.030  2.002   9.1752e-02
   3_bss:   7.636  0.082  0.306 86.832  0.030  2.002   9.1752e-02
   3_xyz:   7.190  0.061  0.294 86.514  0.046  2.190   6.5740e-02
   3_adp:   7.190  0.061  0.294 86.514  0.046  2.190   6.5740e-02
   3_occ:   7.190  0.061  0.294 86.514  0.046  2.190   6.5740e-02
   4_bss:   7.190  0.061  0.294 86.514  0.046  2.190   6.5740e-02
   4_xyz:   8.176  0.069  0.351 89.567  0.047  2.126   1.8894e-01
   4_adp:   8.176  0.069  0.351 89.567  0.047  2.126   1.8894e-01
   4_occ:   8.176  0.069  0.351 89.567  0.047  2.126   1.8894e-01
   5_bss:   8.176  0.069  0.351 89.567  0.047  2.126   1.8894e-01
   5_xyz:   7.123  0.050  0.477 81.442  0.038  2.246   3.9550e-02
   5_adp:   7.123  0.050  0.477 81.442  0.038  2.246   3.9550e-02
   5_occ:   7.123  0.050  0.477 81.442  0.038  2.246   3.9550e-02
   5_bss:   7.123  0.050  0.477 81.442  0.038  2.246   3.9550e-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: 119.59   0.00  15.00  77.37   0.00  12.81 119.59   0.00  26.94
   1_occ: 119.59   0.00  15.00  77.37   0.00  12.81 119.59   0.00  26.94
   2_bss: 119.59   0.00  15.00  77.37   0.00  12.81 119.59   0.00  26.94
   2_xyz: 119.59   0.00  15.00  77.37   0.00  12.81 119.59   0.00  26.94
   2_adp: 111.93   0.00  13.55  65.79   0.00  11.02 111.93   0.00  27.29
   2_occ: 111.93   0.00  13.55  65.79   0.00  11.02 111.93   0.00  27.29
   3_bss: 111.93   0.00  13.55  65.79   0.00  11.02 111.93   0.00  27.29
   3_xyz: 111.93   0.00  13.55  65.79   0.00  11.02 111.93   0.00  27.29
   3_adp: 111.07   0.00  13.57  91.41   0.00  10.78 111.07   0.78  28.72
   3_occ: 111.07   0.00  13.57  91.41   0.00  10.78 111.07   0.78  28.72
   4_bss: 111.07   0.00  13.57  91.41   0.00  10.78 111.07   0.78  28.72
   4_xyz: 111.07   0.00  13.57  91.41   0.00  10.78 111.07   0.78  28.72
   4_adp:  96.29   0.00  13.89  80.38   0.00   9.73  96.29   1.16  36.53
   4_occ:  96.29   0.00  13.89  80.38   0.00   9.73  96.29   1.16  36.53
   5_bss:  96.29   0.00  13.89  80.38   0.00   9.73  96.29   1.16  36.53
   5_xyz:  96.29   0.00  13.89  80.38   0.00   9.73  96.29   1.16  36.53
   5_adp:  97.88   0.00  13.62  81.81   0.00   9.37  97.88   1.77  36.76
   5_occ:  97.88   0.00  13.62  81.81   0.00   9.37  97.88   1.77  36.76
   5_bss:  99.82   1.94  15.56  83.75   1.94  11.31  99.82   3.70  38.70
------------------------------------------------------------------------
 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:    1.102    0.027    0.407
   1_adp:    1.102    0.027    0.407
   1_occ:    1.102    0.027    0.407
   2_bss:    1.102    0.027    0.407
   2_xyz:    1.653    0.067    0.587
   2_adp:    1.653    0.067    0.587
   2_occ:    1.653    0.067    0.587
   3_bss:    1.653    0.067    0.587
   3_xyz:    1.662    0.048    0.683
   3_adp:    1.662    0.048    0.683
   3_occ:    1.662    0.048    0.683
   4_bss:    1.662    0.048    0.683
   4_xyz:    1.978    0.070    0.820
   4_adp:    1.978    0.070    0.820
   4_occ:    1.978    0.070    0.820
   5_bss:    1.978    0.070    0.820
   5_xyz:    2.012    0.040    0.856
   5_adp:    2.012    0.040    0.856
   5_occ:    2.012    0.040    0.856
   5_bss:    2.012    0.040    0.856
------------------------------------------------------------------------

CPU time actual refinement: 333.78


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_842/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_842/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_842/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_842/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_842/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 333.62 
  Macro-tasks:
    bulk solvent and scale       = 41.98  
    individual site refinement   = 137.63 
    weights calculation          = 32.51  
    collect and process          = 6.45   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 218.69 
  Micro-tasks:
    mask                            = 2.41   
    f_calc                          = 102.16 
    alpha_beta                      = 8.33   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 112.25 
    fmodel                         = 7.25   
    r_factors                      = 0.32   
    phase_errors                   = 9.99   
    foms                           = 0.31   
    TOTAL for micro-tasks          = 244.16 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.711 micro seconds
Total CPU time: 5.79 minutes
from_scatterers_fft:    641 calls, 101.82 s
gradients_fft:          585 calls,  99.10 s

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

# Date 2008-01-16 Time 02:33:13 PST -0800 (1200479593.51 s)
Start R-work = 0.4941, R-free = 0.4788 (no bulk solvent and anisotropic scale)
Final R-work = 0.1525, R-free = 0.1987 (no bulk solvent and anisotropic scale)

Start R-work = 0.4874, R-free = 0.4689
Final R-work = 0.1365, R-free = 0.1825