# Date 2008-01-16 Time 01:32:49 PST -0800 (1200475969.38 s)
#phil __OFF__

Command line arguments: "../457.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 30445
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 457

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.5475, 47.6339, 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: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 47.6339, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9118 1.98069
Completeness in resolution range: 0.949954
Completeness with d_max=infinity: 0.947015

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9118
                             d_min =   1.9807

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 47.6339, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9118 1.98069
Completeness in resolution range: 0.949954
Completeness with d_max=infinity: 0.947015

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9122 -  4.2377 [2178/2206]  1957   221  10.1%
  bin  2:  4.2377 -  3.3764 [2063/2086]  1859   204   9.9%
  bin  3:  3.3764 -  2.9534 [2061/2083]  1855   206  10.0%
  bin  4:  2.9534 -  2.6851 [2032/2051]  1831   201   9.9%
  bin  5:  2.6851 -  2.4936 [2023/2052]  1811   212  10.5%
  bin  6:  2.4936 -  2.3471 [2008/2050]  1814   194   9.7%
  bin  7:  2.3471 -  2.2300 [2000/2036]  1803   197   9.8%
  bin  8:  2.2300 -  2.1332 [1997/2034]  1795   202  10.1%
  bin  9:  2.1332 -  2.0513 [1987/2019]  1790   197   9.9%
  bin 10:  2.0513 -  1.9807 [1240/2004]  1115   125  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_457/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: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 20
        2.42 -     3.04: 2180
        3.04 -     3.66: 4670
        3.66 -     4.28: 8982
        4.28 -     4.90: 12334
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.900 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.968 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.980 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 296 "  2.034 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28181 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_457/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_457/model_refine_001.geo

CPU time processing inputs: 9.08


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.5475 47.63395 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: 1.98 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4658   r_free= 0.4505   ksol= 0.00   Bsol= 0.00   scale= 0.800    |
|                                                                             |
| 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:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.267026                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9122 -  4.7262 0.99   1403  157 0.3744 0.3687      6.5505      6.5691|
|  2:  4.7262 -  3.7713 0.99   1362  151 0.3797 0.3999      6.7412      6.8016|
|  3:  3.7713 -  3.3005 0.99   1328  149 0.4200 0.3807      6.6417      6.6165|
|  4:  3.3005 -  3.0014 0.99   1313  137 0.4501 0.4048      6.4988       6.408|
|  5:  3.0014 -  2.7878 0.99   1305  148 0.5003 0.4922      6.3634      6.3896|
|  6:  2.7878 -  2.6244 0.98   1305  149 0.4936 0.5150      6.2692      6.1889|
|  7:  2.6244 -  2.4936 0.99   1297  153 0.4854 0.4691      6.2296       6.154|
|  8:  2.4936 -  2.3855 0.99   1307  131 0.5149 0.4408      6.1782      6.1314|
|  9:  2.3855 -  2.2940 0.98   1294  147 0.5178 0.5468      6.1057      6.1489|
| 10:  2.2940 -  2.2151 0.98   1275  143 0.5293 0.4696      6.1237       6.092|
| 11:  2.2151 -  2.1460 0.98   1285  147 0.5250 0.4860      6.0226      6.0368|
| 12:  2.1460 -  2.0849 0.99   1288  137 0.5212 0.5222      5.9649      5.9847|
| 13:  2.0849 -  2.0301 0.97   1268  137 0.5209 0.5281       5.888      5.8346|
| 14:  2.0301 -  1.9807 0.48    600   73 0.5572 0.4789      5.8771      5.7475|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9122 -  4.7262  1403   157  0.70  34.37   0.81     0.71      69587.91|
|  2:  4.7262 -  3.7713  1362   151  0.72  33.18   0.90     0.77      94321.51|
|  3:  3.7713 -  3.3005  1328   149  0.65  39.62   0.84     0.74      96734.35|
|  4:  3.3005 -  3.0014  1313   137  0.59  44.90   0.81     0.66      80740.30|
|  5:  3.0014 -  2.7878  1305   148  0.49  52.76   0.74     0.56      70079.73|
|  6:  2.7878 -  2.6244  1305   149  0.47  54.65   0.73     0.53      62229.64|
|  7:  2.6244 -  2.4936  1297   153  0.45  55.86   0.76     0.50      57241.25|
|  8:  2.4936 -  2.3855  1307   131  0.47  54.89   0.74     0.53      49995.56|
|  9:  2.3855 -  2.2940  1294   147  0.44  56.62   0.72     0.52      47022.74|
| 10:  2.2940 -  2.2151  1275   143  0.44  56.87   0.73     0.51      43821.74|
| 11:  2.2151 -  2.1460  1285   147  0.39  60.46   0.74     0.48      43175.49|
| 12:  2.1460 -  2.0849  1288   137  0.36  63.13   0.77     0.46      41302.84|
| 13:  2.0849 -  2.0301  1268   137  0.34  64.75   0.73     0.41      36175.90|
| 14:  2.0301 -  1.9807   600    73  0.34  64.61   0.71     0.37      27723.13|
|alpha:            min =        0.37 max =            0.77 mean =         0.56|
|beta:             min =    27723.13 max =        96734.35 mean =     60165.99|
|figures of merit: min =        0.00 max =            1.00 mean =         0.50|
|phase err.(work): min =        0.00 max =           90.00 mean =        51.90|
|phase err.(test): min =        0.00 max =           89.91 mean =        52.08|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.719909             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.262   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.913960              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.512   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      164 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      691 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1502 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2624 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3877 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5062 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6567 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7705 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.884 |
| 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 |       1.819 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.973)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

                ----------Modify initial isotropic ADP----------               

Randomizing
|-ADP statistics (Wilson B = 11.973)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4717   r_free= 0.4573   ksol= 0.00   Bsol= 0.00   scale= 0.770    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.269897                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4579   r_free= 0.4431   ksol= 0.33   Bsol= 20.00   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.30,10.29,7.68,0.00,0.00,0.00); trace/3= 8.09                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.259038                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.187932             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.567   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.879806              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.250   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4579      final r-factor (work) = 0.3599          |
| start r-factor (free) = 0.4431      final r-factor (free) = 0.3777          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 85.8230 = 10.19 * 0.50 * 6.2700 + 1.00 * 53.8838                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.4350 = 10.19 * 0.50 * 6.1440 + 1.00 * 0.1376                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3599      final r-factor (work) = 0.3050          |
| start r-factor (free) = 0.3777      final r-factor (free) = 0.3480          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4199 = 0.88 * 1.00 * 6.1440 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3127 = 0.88 * 1.00 * 6.0218 + 1.00 * 0.0146                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.973)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.79   12.21    None  None   None       |
|    all(noH): 2823   0      0.00    82.79   12.21    None  None   None       |
|    Sol.    : 438    0      0.00    82.79   27.21    None  None   None       |
|    Mac.    : 2385   0      0.00    72.84   9.45     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.279: 1383   |   5:    41.397 -  49.676:   66        |
|      1:     8.279 -  16.559:  753   |   6:    49.676 -  57.955:   28        |
|      2:    16.559 -  24.838:  313   |   7:    57.955 -  66.235:   15        |
|      3:    24.838 -  33.117:  178   |   8:    66.235 -  74.514:    2        |
|      4:    33.117 -  41.397:   81   |   9:    74.514 -  82.793:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3050 r_free = 0.3480             target_work(ml) = 5.992         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3046 r_free = 0.3482             target_work(ml) = 5.991         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3046   r_free= 0.3482   ksol= 0.33   Bsol= 20.00   scale= 1.080   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.30,10.29,7.68,0.00,0.00,0.00); trace/3= 8.09                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.990735                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3023   r_free= 0.3454   ksol= 0.32   Bsol= 36.44   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.41,6.64,4.90,0.00,0.00,0.00); trace/3= 4.98                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 5.991923                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.411259              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.966   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.377827              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.792  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3023      final r-factor (work) = 0.2096          |
| start r-factor (free) = 0.3454      final r-factor (free) = 0.2559          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.4399 = 6.41 * 0.50 * 6.0214 + 1.00 * 0.1376                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.7643 = 6.41 * 0.50 * 5.8285 + 1.00 * 0.0804                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2096      final r-factor (work) = 0.1878          |
| start r-factor (free) = 0.2559      final r-factor (free) = 0.2333          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2169 = 0.38 * 1.00 * 5.8285 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1328 = 0.38 * 1.00 * 5.6165 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.973)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.65   12.02    None  None   None       |
|    all(noH): 2823   0      0.00    77.65   12.02    None  None   None       |
|    Sol.    : 438    0      1.25    77.65   31.64    None  None   None       |
|    Mac.    : 2385   0      0.00    68.09   8.41     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.765: 1463   |   5:    38.825 -  46.590:  108        |
|      1:     7.765 -  15.530:  709   |   6:    46.590 -  54.355:   45        |
|      2:    15.530 -  23.295:  226   |   7:    54.355 -  62.120:   22        |
|      3:    23.295 -  31.060:  138   |   8:    62.120 -  69.885:    8        |
|      4:    31.060 -  38.825:  102   |   9:    69.885 -  77.649:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1878 r_free = 0.2333             target_work(ml) = 5.580         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1875 r_free = 0.2336             target_work(ml) = 5.580         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1875   r_free= 0.2336   ksol= 0.32   Bsol= 36.44   scale= 1.038   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.41,6.64,4.90,0.00,0.00,0.00); trace/3= 4.98                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.579854                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1859   r_free= 0.2325   ksol= 0.32   Bsol= 51.60   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.12,4.10,3.90,0.00,0.00,0.00); trace/3= 3.37                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.578335                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.083120              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.540  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.261668              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.713  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1859      final r-factor (work) = 0.1494          |
| start r-factor (free) = 0.2325      final r-factor (free) = 0.1850          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9380 = 2.08 * 0.50 * 5.6237 + 1.00 * 0.0805                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7687 = 2.08 * 0.50 * 5.4849 + 1.00 * 0.0558                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1494      final r-factor (work) = 0.1417          |
| start r-factor (free) = 0.1850      final r-factor (free) = 0.1774          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4459 = 0.26 * 1.00 * 5.4849 + 1.00 * 0.0107                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4077 = 0.26 * 1.00 * 5.3411 + 1.00 * 0.0101                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.973)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.31   12.12    None  None   None       |
|    all(noH): 2823   0      0.00    76.31   12.12    None  None   None       |
|    Sol.    : 438    0      1.47    76.31   33.23    None  None   None       |
|    Mac.    : 2385   0      0.00    69.24   8.24     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.631: 1486   |   5:    38.157 -  45.788:  118        |
|      1:     7.631 -  15.263:  705   |   6:    45.788 -  53.419:   51        |
|      2:    15.263 -  22.894:  181   |   7:    53.419 -  61.051:   33        |
|      3:    22.894 -  30.525:  122   |   8:    61.051 -  68.682:    9        |
|      4:    30.525 -  38.157:  115   |   9:    68.682 -  76.313:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1417 r_free = 0.1774             target_work(ml) = 5.323         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1415 r_free = 0.1774             target_work(ml) = 5.322         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1415   r_free= 0.1774   ksol= 0.32   Bsol= 51.60   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.12,4.10,3.90,0.00,0.00,0.00); trace/3= 3.37                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.322364                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1415   r_free= 0.1772   ksol= 0.33   Bsol= 51.60   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.70,3.16,3.58,0.00,0.00,0.00); trace/3= 2.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.322531                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.816025              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 122.694  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.025452              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.031  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1415      final r-factor (work) = 0.1216          |
| start r-factor (free) = 0.1772      final r-factor (free) = 0.1633          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5789 = 2.82 * 0.50 * 5.3431 + 1.00 * 0.0558                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4638 = 2.82 * 0.50 * 5.2502 + 1.00 * 0.0716                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1216      final r-factor (work) = 0.1174          |
| start r-factor (free) = 0.1633      final r-factor (free) = 0.1615          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3939 = 1.03 * 1.00 * 5.2502 + 1.00 * 0.0101                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3352 = 1.03 * 1.00 * 5.1904 + 1.00 * 0.0126                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.973)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.37   12.42    None  None   None       |
|    all(noH): 2823   0      0.00    75.37   12.42    None  None   None       |
|    Sol.    : 438    0      1.45    75.03   35.52    None  None   None       |
|    Mac.    : 2385   0      0.00    75.37   8.18     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.537: 1508   |   5:    37.685 -  45.222:   96        |
|      1:     7.537 -  15.074:  679   |   6:    45.222 -  52.759:   84        |
|      2:    15.074 -  22.611:  177   |   7:    52.759 -  60.296:   48        |
|      3:    22.611 -  30.148:  105   |   8:    60.296 -  67.833:   23        |
|      4:    30.148 -  37.685:   96   |   9:    67.833 -  75.370:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1174 r_free = 0.1615             target_work(ml) = 5.186         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1173 r_free = 0.1615             target_work(ml) = 5.185         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1173   r_free= 0.1615   ksol= 0.33   Bsol= 51.60   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.70,3.16,3.58,0.00,0.00,0.00); trace/3= 2.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.185451                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1172   r_free= 0.1614   ksol= 0.33   Bsol= 51.60   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.89,3.05,3.70,0.00,0.00,0.00); trace/3= 2.88                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.185322                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.622772              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 140.480  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.934473              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.769  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1172      final r-factor (work) = 0.1181          |
| start r-factor (free) = 0.1614      final r-factor (free) = 0.1610          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2831 = 1.62 * 0.50 * 5.1905 + 1.00 * 0.0716                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2675 = 1.62 * 0.50 * 5.1899 + 1.00 * 0.0565                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1181      final r-factor (work) = 0.1176          |
| start r-factor (free) = 0.1610      final r-factor (free) = 0.1612          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8624 = 0.93 * 1.00 * 5.1899 + 1.00 * 0.0126                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8610 = 0.93 * 1.00 * 5.1878 + 1.00 * 0.0131                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.973)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.51   12.41    None  None   None       |
|    all(noH): 2823   0      0.00    78.51   12.41    None  None   None       |
|    Sol.    : 438    0      1.13    73.64   35.73    None  None   None       |
|    Mac.    : 2385   0      0.00    78.51   8.13     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.851: 1587   |   5:    39.253 -  47.104:   90        |
|      1:     7.851 -  15.701:  618   |   6:    47.104 -  54.954:   80        |
|      2:    15.701 -  23.552:  171   |   7:    54.954 -  62.805:   41        |
|      3:    23.552 -  31.402:  112   |   8:    62.805 -  70.655:   16        |
|      4:    31.402 -  39.253:  101   |   9:    70.655 -  78.506:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1176 r_free = 0.1612             target_work(ml) = 5.188         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1176 r_free = 0.1612             target_work(ml) = 5.188         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1176   r_free= 0.1612   ksol= 0.33   Bsol= 51.60   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.89,3.05,3.70,0.00,0.00,0.00); trace/3= 2.88                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.188261                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9122 -  4.7262 0.99   1403  157 0.1016 0.1290      5.4055      5.5498|
|  2:  4.7262 -  3.7713 0.99   1362  151 0.0875 0.1046      5.4471      5.6254|
|  3:  3.7713 -  3.3005 0.99   1328  149 0.1093 0.1488      5.4921      5.8667|
|  4:  3.3005 -  3.0014 0.99   1313  137 0.1259 0.1601      5.4766      5.6311|
|  5:  3.0014 -  2.7878 0.99   1305  148 0.1409 0.1707      5.3815      5.5176|
|  6:  2.7878 -  2.6244 0.98   1305  149 0.1339 0.2207      5.2698      5.5797|
|  7:  2.6244 -  2.4936 0.99   1297  153 0.1311 0.1606      5.2145      5.3767|
|  8:  2.4936 -  2.3855 0.99   1307  131 0.1239 0.1794      5.1363      5.3631|
|  9:  2.3855 -  2.2940 0.98   1294  147 0.1268 0.2038      5.0747      5.3886|
| 10:  2.2940 -  2.2151 0.98   1275  143 0.1220 0.1626      5.0198      5.1961|
| 11:  2.2151 -  2.1460 0.98   1285  147 0.1199 0.1810      4.9605      5.2559|
| 12:  2.1460 -  2.0849 0.99   1288  137 0.1156 0.1697      4.8816      5.1779|
| 13:  2.0849 -  2.0301 0.97   1268  137 0.1179 0.1746      4.8241      5.0582|
| 14:  2.0301 -  1.9807 0.48    600   73 0.1171 0.1946      4.7667      5.0172|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9122 -  4.7262  1403   157  0.94   9.22   0.97     0.95       7448.99|
|  2:  4.7262 -  3.7713  1362   151  0.95   8.09   1.01     1.00       9022.01|
|  3:  3.7713 -  3.3005  1328   149  0.93  11.28   1.02     1.02      10546.82|
|  4:  3.3005 -  3.0014  1313   137  0.92  14.15   1.00     0.99      10722.49|
|  5:  3.0014 -  2.7878  1305   148  0.89  16.68   1.00     0.97       9040.42|
|  6:  2.7878 -  2.6244  1305   149  0.89  17.37   0.97     0.94       7816.83|
|  7:  2.6244 -  2.4936  1297   153  0.90  16.12   0.98     0.95       6748.77|
|  8:  2.4936 -  2.3855  1307   131  0.90  16.16   0.99     0.96       6099.07|
|  9:  2.3855 -  2.2940  1294   147  0.89  17.16   1.00     0.96       5524.76|
| 10:  2.2940 -  2.2151  1275   143  0.89  16.68   0.99     0.95       4909.15|
| 11:  2.2151 -  2.1460  1285   147  0.90  16.46   0.99     0.95       4508.06|
| 12:  2.1460 -  2.0849  1288   137  0.91  15.59   1.00     0.99       3927.28|
| 13:  2.0849 -  2.0301  1268   137  0.90  16.38   0.98     0.97       3576.84|
| 14:  2.0301 -  1.9807   600    73  0.89  17.29   0.96     0.91       3163.05|
|alpha:            min =        0.91 max =            1.02 mean =         0.97|
|beta:             min =     3163.05 max =        10722.49 mean =      6820.18|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.74|
|phase err.(test): min =        0.00 max =           89.84 mean =        14.20|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1176   r_free= 0.1614   ksol= 0.33   Bsol= 54.56   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.96,0.12,0.84,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.189513                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1176   r_free= 0.1614   ksol= 0.33   Bsol= 54.56   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.96,0.12,0.84,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.189513                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9122 -  4.7262 0.99   1403  157 0.1009 0.1323      5.4134      5.5685|
|  2:  4.7262 -  3.7713 0.99   1362  151 0.0883 0.1032      5.4552      5.6245|
|  3:  3.7713 -  3.3005 0.99   1328  149 0.1092 0.1496      5.4924      5.8645|
|  4:  3.3005 -  3.0014 0.99   1313  137 0.1264 0.1593      5.4778      5.6289|
|  5:  3.0014 -  2.7878 0.99   1305  148 0.1411 0.1706      5.3818      5.5184|
|  6:  2.7878 -  2.6244 0.98   1305  149 0.1336 0.2212        5.27      5.5808|
|  7:  2.6244 -  2.4936 0.99   1297  153 0.1308 0.1606      5.2139      5.3748|
|  8:  2.4936 -  2.3855 0.99   1307  131 0.1238 0.1793      5.1356      5.3639|
|  9:  2.3855 -  2.2940 0.98   1294  147 0.1267 0.2038      5.0744      5.3875|
| 10:  2.2940 -  2.2151 0.98   1275  143 0.1219 0.1627      5.0196      5.1966|
| 11:  2.2151 -  2.1460 0.98   1285  147 0.1199 0.1810      4.9604      5.2552|
| 12:  2.1460 -  2.0849 0.99   1288  137 0.1155 0.1702      4.8816      5.1797|
| 13:  2.0849 -  2.0301 0.97   1268  137 0.1178 0.1745      4.8242       5.058|
| 14:  2.0301 -  1.9807 0.48    600   73 0.1170 0.1946      4.7661      5.0163|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9122 -  4.7262  1403   157  0.94   9.65   0.97     0.94       7731.59|
|  2:  4.7262 -  3.7713  1362   151  0.95   8.28   1.01     1.00       9187.62|
|  3:  3.7713 -  3.3005  1328   149  0.93  11.27   1.02     1.02      10555.19|
|  4:  3.3005 -  3.0014  1313   137  0.92  14.15   1.01     0.99      10691.58|
|  5:  3.0014 -  2.7878  1305   148  0.89  16.68   1.00     0.97       9039.67|
|  6:  2.7878 -  2.6244  1305   149  0.89  17.40   0.98     0.94       7823.16|
|  7:  2.6244 -  2.4936  1297   153  0.90  16.15   0.99     0.95       6760.01|
|  8:  2.4936 -  2.3855  1307   131  0.90  16.15   0.99     0.96       6087.89|
|  9:  2.3855 -  2.2940  1294   147  0.89  17.17   1.00     0.97       5524.60|
| 10:  2.2940 -  2.2151  1275   143  0.89  16.67   0.99     0.96       4906.06|
| 11:  2.2151 -  2.1460  1285   147  0.90  16.47   0.99     0.95       4511.87|
| 12:  2.1460 -  2.0849  1288   137  0.91  15.60   1.00     0.99       3932.38|
| 13:  2.0849 -  2.0301  1268   137  0.90  16.39   0.99     0.97       3578.51|
| 14:  2.0301 -  1.9807   600    73  0.89  17.28   0.97     0.92       3157.14|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     3157.14 max =        10691.58 mean =      6854.53|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           90.00 mean =        14.79|
|phase err.(test): min =        0.00 max =           89.04 mean =        14.23|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.973)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.96    81.47   15.37    None  None   None       |
|    all(noH): 2823   0      2.96    81.47   15.37    None  None   None       |
|    Sol.    : 438    0      4.09    76.60   38.69    None  None   None       |
|    Mac.    : 2385   0      2.96    81.47   11.09    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.960 -  10.810: 1587   |   5:    42.213 -  50.063:   90        |
|      1:    10.810 -  18.661:  618   |   6:    50.063 -  57.914:   80        |
|      2:    18.661 -  26.511:  171   |   7:    57.914 -  65.764:   41        |
|      3:    26.511 -  34.362:  112   |   8:    65.764 -  73.615:   16        |
|      4:    34.362 -  42.213:  101   |   9:    73.615 -  81.466:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 313         
Filter by distance & map next to the model:
   mapped sites are within: 0.330 - 4.356
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 307 from: 313
   mapped sites are within: 0.729 - 4.356

peak=   10.679 closest distance to " CB  VAL A 230 " =    1.433
peak=    6.123 closest distance to " CG  LEU A   5 " =    1.200
peak=    5.734 closest distance to " CG2 VAL A 296 " =    1.027
peak=    5.552 closest distance to " CG1 VAL A 296 " =    1.189
peak=    5.543 closest distance to " NH2 ARG A  56 " =    2.222
peak=    5.423 closest distance to " CD1AILE A 234 " =    1.051
peak=    5.409 closest distance to " CB  VAL A 296 " =    1.117
peak=    5.237 closest distance to " CB  GLN A 223 " =    1.397
peak=    5.173 closest distance to " CG  PRO A  54 " =    1.317
peak=    5.121 closest distance to " O   HOH Z 403 " =    1.909
peak=    5.074 closest distance to " CG  PRO A 198 " =    1.203
peak=    5.034 closest distance to " CB  PRO A  54 " =    0.983
peak=    5.030 closest distance to " CG  LEU A 228 " =    1.192
peak=    4.898 closest distance to " CB  SER A  63 " =    1.221
peak=    4.770 closest distance to " CD2 LEU A   5 " =    1.112
peak=    4.769 closest distance to " CB  ARG A 275 " =    0.956
peak=    4.646 closest distance to " O   HOH Z 232 " =    2.271
peak=    4.578 closest distance to " O   HOH Z  44 " =    2.322
peak=    4.574 closest distance to " O   HOH Z 128 " =    1.513
peak=    4.527 closest distance to " O   HOH Z 402 " =    1.519
peak=    4.522 closest distance to " CA  TYR A  30 " =    0.955
peak=    4.489 closest distance to " O   HOH Z 248 " =    1.542
peak=    4.432 closest distance to " C   PRO A 198 " =    1.505
peak=    4.424 closest distance to " CB  GLN A 183 " =    1.308
peak=    4.397 closest distance to " CG  PRO A 213 " =    1.255
peak=    4.397 closest distance to " CD2 LEU A 228 " =    1.246
peak=    4.349 closest distance to " O   HOH Z  49 " =    1.147
peak=    4.344 closest distance to " O   HOH Z  63 " =    2.025
peak=    4.343 closest distance to " O   HOH Z  85 " =    1.396
peak=    4.335 closest distance to " O   HOH Z 265 " =    2.208
peak=    4.320 closest distance to " CB  VAL A 230 " =    1.220
peak=    4.315 closest distance to " O   HOH Z 193 " =    1.679
peak=    4.286 closest distance to " CG  PRO A 243 " =    1.169
peak=    4.284 closest distance to " O   HOH Z  43 " =    2.171
peak=    4.265 closest distance to " O   HOH Z 130 " =    2.611
peak=    4.249 closest distance to " O   HOH Z 234 " =    3.725
peak=    4.246 closest distance to " O   SER A  87 " =    2.212
peak=    4.241 closest distance to " CB  ARG A 190 " =    1.760
peak=    4.222 closest distance to " O   HOH Z 298 " =    1.801
peak=    4.212 closest distance to " CA  ALA A  51 " =    1.044
peak=    4.208 closest distance to " O   HOH Z 189 " =    2.468
peak=    4.176 closest distance to " O   HOH Z 126 " =    1.888
peak=    4.169 closest distance to " O   HOH Z 102 " =    1.358
peak=    4.168 closest distance to " CZ  PHE A 218 " =    1.143
peak=    4.164 closest distance to " O   HOH Z 247 " =    1.387
peak=    4.152 closest distance to " O   HOH Z 346 " =    1.563
peak=    4.142 closest distance to " NE2 GLN A  11 " =    1.018
peak=    4.130 closest distance to " O   HOH Z 272 " =    1.899
peak=    4.120 closest distance to " CB  GLU A 128 " =    1.164
peak=    4.104 closest distance to " O   HOH Z 368 " =    2.325
peak=    4.104 closest distance to " O   HOH Z 142 " =    1.602
peak=    4.080 closest distance to " CB  TRP A 179 " =    1.266
peak=    4.078 closest distance to " O   HOH Z  59 " =    2.325
peak=    4.060 closest distance to " O   HOH Z 124 " =    1.321
peak=    4.059 closest distance to " CD  LYS A 166 " =    1.404
peak=    4.048 closest distance to " CD  ARG A 269 " =    1.075
peak=    4.036 closest distance to " CB  GLU A 152 " =    1.133
peak=    4.029 closest distance to " NH2 ARG A 156 " =    1.096
peak=    4.028 closest distance to " CB  ARG A  79 " =    1.329
peak=    4.025 closest distance to " CB  GLU A 277 " =    3.649
peak=    3.990 closest distance to " CA  VAL A  41 " =    0.805
peak=    3.984 closest distance to " O   HOH Z 327 " =    1.642
peak=    3.974 closest distance to " O   HOH Z 369 " =    2.180
peak=    3.969 closest distance to " O   HOH Z  80 " =    1.894
peak=    3.964 closest distance to " O   HOH Z  40 " =    1.898
peak=    3.962 closest distance to " O   HOH Z 261 " =    2.092
peak=    3.960 closest distance to " CB  ASN A 148 " =    1.370
peak=    3.957 closest distance to " CB  TYR A 169 " =    0.767
peak=    3.947 closest distance to " CD2 TRP A 179 " =    1.319
peak=    3.939 closest distance to " CG1 ILE A  33 " =    1.267
peak=    3.938 closest distance to " O   HOH Z  97 " =    1.992
peak=    3.928 closest distance to " O   HOH Z 214 " =    2.652
peak=    3.928 closest distance to " O   HOH Z 316 " =    2.934
peak=    3.916 closest distance to " O   HOH Z 423 " =    1.744
peak=    3.895 closest distance to " O   HOH Z 417 " =    3.232
peak=    3.882 closest distance to " NZ  LYS A 117 " =    3.081
peak=    3.877 closest distance to " O   HOH Z 154 " =    1.520
peak=    3.870 closest distance to " CB  SER A   3 " =    1.275
peak=    3.836 closest distance to " O   HOH Z 210 " =    0.893
peak=    3.836 closest distance to " CA  ALA A 295 " =    1.034
peak=    3.835 closest distance to " O   HOH Z   4 " =    1.663
peak=    3.833 closest distance to " O   HOH Z 357 " =    2.035
peak=    3.811 closest distance to " O   HOH Z 284 " =    3.006
peak=    3.807 closest distance to " OG  SER A 276 " =    1.536
peak=    3.802 closest distance to " ND2 ASN A 187 " =    1.585
peak=    3.801 closest distance to " O   HOH Z 433 " =    1.465
peak=    3.796 closest distance to " O   HOH Z 287 " =    1.745
peak=    3.791 closest distance to " O   HOH Z 414 " =    1.714
peak=    3.784 closest distance to " CA  ARG A 195 " =    1.169
peak=    3.781 closest distance to " O   HOH Z 426 " =    1.445
peak=    3.780 closest distance to " O   HOH Z 412 " =    3.805
peak=    3.772 closest distance to " N   ASN A  39 " =    1.215
peak=    3.770 closest distance to " CA  ARG A  36 " =    1.036
peak=    3.761 closest distance to " O   HOH Z 126 " =    1.546
peak=    3.758 closest distance to " OG BSER A 164 " =    2.204
peak=    3.754 closest distance to " O   HOH Z  48 " =    1.719
peak=    3.749 closest distance to " CG AARG A 275 " =    1.193
peak=    3.749 closest distance to " O   HOH Z 203 " =    1.787
peak=    3.747 closest distance to " O   HOH Z 371 " =    3.296
peak=    3.744 closest distance to " CZ  PHE A  38 " =    1.191
peak=    3.740 closest distance to " O   HOH Z 359 " =    1.497
peak=    3.731 closest distance to " CD1 LEU A  96 " =    0.806
peak=    3.710 closest distance to " OD1 ASN A  69 " =    2.462
peak=    3.707 closest distance to " O   HOH Z 303 " =    2.203
peak=    3.703 closest distance to " CG1BVAL A  72 " =    1.808
peak=    3.700 closest distance to " CD2 LEU A 297 " =    0.855
peak=    3.693 closest distance to " CG2 ILE A  20 " =    1.403
peak=    3.691 closest distance to " ND2 ASN A 249 " =    1.927
peak=    3.678 closest distance to " CB  SER A  26 " =    1.732
peak=    3.676 closest distance to " O   HOH Z 251 " =    1.380
peak=    3.675 closest distance to " CB  VAL A 202 " =    1.457
peak=    3.671 closest distance to " O   HOH Z 422 " =    2.611
peak=    3.666 closest distance to " O   HOH Z 345 " =    3.023
peak=    3.656 closest distance to " O   HOH Z 134 " =    1.528
peak=    3.654 closest distance to " O   HOH Z 158 " =    3.096
peak=    3.647 closest distance to " O  BHOH Z  74 " =    1.343
peak=    3.645 closest distance to " O   TRP A 274 " =    1.849
peak=    3.643 closest distance to " CB  ASN A  39 " =    0.873
peak=    3.638 closest distance to " CB  ALA A 248 " =    1.339
peak=    3.636 closest distance to " O   HOH Z 130 " =    1.102
peak=    3.633 closest distance to " O   ASP A 124 " =    1.341
peak=    3.627 closest distance to " O   HOH Z 383 " =    2.110
peak=    3.627 closest distance to " O   HOH Z 250 " =    1.409
peak=    3.625 closest distance to " CG  MET A 185 " =    1.160
peak=    3.625 closest distance to " CB BVAL A  41 " =    1.099
peak=    3.621 closest distance to " O   HOH Z 394 " =    1.464
peak=    3.615 closest distance to " O   HOH Z 245 " =    1.401
peak=    3.614 closest distance to " CB  THR A  52 " =    0.885
peak=    3.611 closest distance to " NH1AARG A 145 " =    1.232
peak=    3.611 closest distance to " CB  ASN A 187 " =    1.458
peak=    3.604 closest distance to " CA  ALA A  21 " =    1.198
peak=    3.604 closest distance to " CB  TRP A 266 " =    1.040
peak=    3.602 closest distance to " ND2 ASN A 249 " =    0.915
peak=    3.588 closest distance to " O   HOH Z  15 " =    2.267
peak=    3.581 closest distance to " CE  LYS A 119 " =    1.048
peak=    3.580 closest distance to " O   HOH Z  44 " =    1.866
peak=    3.579 closest distance to " CB  VAL A 265 " =    1.235
peak=    3.577 closest distance to " CE1 HIS A 108 " =    1.144
peak=    3.576 closest distance to " O   HOH Z  54 " =    1.572
peak=    3.560 closest distance to " CG2 ILE A 120 " =    1.189
peak=    3.559 closest distance to " O   HOH Z 258 " =    2.262
peak=    3.548 closest distance to " O   ASN A  74 " =    1.772
peak=    3.546 closest distance to " O   HOH Z  97 " =    2.426
peak=    3.545 closest distance to " O   HOH Z 185 " =    1.690
peak=    3.542 closest distance to " O   HOH Z 145 " =    2.344
peak=    3.527 closest distance to " O   HOH Z 344 " =    3.005
peak=    3.514 closest distance to " CB  PRO A 198 " =    1.071
peak=    3.512 closest distance to " O   GLY A  91 " =    1.320
peak=    3.508 closest distance to " CG1 VAL A 153 " =    1.014
peak=    3.501 closest distance to " CD  ARG A 159 " =    0.777
peak=    3.499 closest distance to " O   HOH Z 427 " =    2.863
peak=    3.498 closest distance to " OE1 GLN A  11 " =    1.766
peak=    3.492 closest distance to " OE1 GLU A   2 " =    2.036
peak=    3.491 closest distance to " O   HOH Z  78 " =    1.654
peak=    3.479 closest distance to " NZ  LYS A  48 " =    1.243
peak=    3.473 closest distance to " NE2 GLN A  77 " =    3.246
peak=    3.471 closest distance to " CB  ASN A 142 " =    1.181
peak=    3.467 closest distance to " CA  ASN A 176 " =    1.092
peak=    3.466 closest distance to " CD  LYS A 119 " =    1.995
peak=    3.461 closest distance to " O   HOH Z 313 " =    1.679
peak=    3.461 closest distance to " CB  GLU A  46 " =    1.021
peak=    3.461 closest distance to " CA  ASP A 140 " =    1.178
peak=    3.459 closest distance to " O   HOH Z 421 " =    1.813
peak=    3.454 closest distance to " CB  HIS A 108 " =    0.821
peak=    3.454 closest distance to " O   ALA A 165 " =    1.407
peak=    3.451 closest distance to " CE1 TYR A 186 " =    1.250
peak=    3.451 closest distance to " N   SER A 288 " =    1.773
peak=    3.448 closest distance to " O   HOH Z 189 " =    2.697
peak=    3.440 closest distance to " O   HOH Z 366 " =    2.772
peak=    3.438 closest distance to " O   HOH Z 273 " =    2.934
peak=    3.435 closest distance to " CA  LYS A 117 " =    1.281
peak=    3.434 closest distance to " CG  ARG A  66 " =    0.920
peak=    3.432 closest distance to " CG2 ILE A 106 " =    0.883
peak=    3.424 closest distance to " CA  TRP A  85 " =    1.213
peak=    3.424 closest distance to " CG2 THR A 221 " =    1.211
peak=    3.424 closest distance to " CB  GLN A  89 " =    1.156
peak=    3.416 closest distance to " O   HOH Z 263 " =    1.718
peak=    3.416 closest distance to " CA  ALA A 160 " =    0.892
peak=    3.415 closest distance to " CB  ASP A 140 " =    1.045
peak=    3.412 closest distance to " NH2BARG A 145 " =    2.178
peak=    3.411 closest distance to " O   HOH Z 301 " =    1.947
peak=    3.409 closest distance to " CB  MET A  47 " =    1.087
peak=    3.407 closest distance to " CB  TRP A 150 " =    1.454
peak=    3.407 closest distance to " CZ3 TRP A  85 " =    0.969
peak=    3.400 closest distance to " O   HOH Z 271 " =    2.407
peak=    3.400 closest distance to " O   HOH Z 403 " =    1.357
peak=    3.395 closest distance to " CA  ASP A 191 " =    1.132
peak=    3.394 closest distance to " CD1 LEU A 222 " =    0.729
peak=    3.393 closest distance to " CB  ALA A   9 " =    1.638
peak=    3.392 closest distance to " CB  PRO A 243 " =    1.166
peak=    3.391 closest distance to " NH1BARG A 190 " =    2.162
peak=    3.385 closest distance to " CG  LEU A 167 " =    1.083
peak=    3.381 closest distance to " CA  TYR A 116 " =    1.382
peak=    3.381 closest distance to " O   HOH Z  61 " =    1.547
peak=    3.380 closest distance to " CB  ARG A 219 " =    1.263
peak=    3.374 closest distance to " NH1 ARG A  14 " =    1.105
peak=    3.367 closest distance to " O   HOH Z 162 " =    1.664
peak=    3.365 closest distance to " OH  TYR A 116 " =    1.163
peak=    3.365 closest distance to " CB  MET A  40 " =    0.893
peak=    3.356 closest distance to " O   HOH Z  48 " =    1.486
peak=    3.351 closest distance to " CA  GLY A  80 " =    0.914
peak=    3.351 closest distance to " O   HOH Z 291 " =    1.485
peak=    3.349 closest distance to " O   HOH Z 285 " =    2.914
peak=    3.347 closest distance to " O   HOH Z  66 " =    2.247
peak=    3.345 closest distance to " O   HOH Z 336 " =    1.796
peak=    3.342 closest distance to " C   ALA A 299 " =    0.911
peak=    3.341 closest distance to " O   HOH Z 368 " =    3.494
peak=    3.341 closest distance to " CD1 ILE A 199 " =    0.957
peak=    3.341 closest distance to " O   HOH Z 435 " =    1.940
peak=    3.339 closest distance to " CB  SER A 273 " =    0.922
peak=    3.338 closest distance to " O   PRO A 213 " =    1.375
peak=    3.335 closest distance to " O   HOH Z 409 " =    3.728
peak=    3.329 closest distance to " O   HOH Z 214 " =    1.384
peak=    3.321 closest distance to " CB  TYR A 247 " =    1.014
peak=    3.320 closest distance to " N   ASP A 231 " =    1.630
peak=    3.318 closest distance to " CA  VAL A 125 " =    1.333
peak=    3.316 closest distance to " CG2 ILE A 234 " =    1.018
peak=    3.310 closest distance to " O   HOH Z 419 " =    1.791
peak=    3.309 closest distance to " CB  SER A  62 " =    0.847
peak=    3.307 closest distance to " NH1 ARG A 269 " =    0.819
peak=    3.295 closest distance to " O   HOH Z 193 " =    2.048
peak=    3.285 closest distance to " O   HOH Z 417 " =    2.206
peak=    3.281 closest distance to " O   HOH Z 353 " =    2.738
peak=    3.281 closest distance to " OD2 ASP A 298 " =    3.804
peak=    3.280 closest distance to " O   HOH Z 227 " =    2.084
peak=    3.278 closest distance to " CZ3 TRP A 266 " =    1.086
peak=    3.278 closest distance to " CB  ARG A 139 " =    0.853
peak=    3.275 closest distance to " N   ALA A 256 " =    1.090
peak=    3.272 closest distance to " CA  ASN A 215 " =    1.121
peak=    3.270 closest distance to " O   HOH Z 128 " =    2.533
peak=    3.267 closest distance to " CE  LYS A  76 " =    0.833
peak=    3.266 closest distance to " CA  ASN A 217 " =    1.183
peak=    3.265 closest distance to " O   HOH Z  68 " =    1.778
peak=    3.265 closest distance to " CB  ASP A 124 " =    0.738
peak=    3.264 closest distance to " O   HOH Z 416 " =    2.844
peak=    3.264 closest distance to " O   HOH Z  21 " =    1.832
peak=    3.263 closest distance to " CG  GLN A  58 " =    2.758
peak=    3.262 closest distance to " CG1 ILE A  49 " =    1.514
peak=    3.261 closest distance to " CB  SER A 141 " =    1.135
peak=    3.253 closest distance to " CG BARG A 102 " =    1.846
peak=    3.252 closest distance to " N   CYS A 260 " =    0.770
peak=    3.248 closest distance to " O   HOH Z 408 " =    1.592
peak=    3.247 closest distance to " CB  ALA A 291 " =    1.313
peak=    3.244 closest distance to " CB  LEU A   5 " =    1.298
peak=    3.244 closest distance to " O   HOH Z 112 " =    1.678
peak=    3.242 closest distance to " CD1 LEU A 300 " =    1.257
peak=    3.242 closest distance to " CB  ASN A 110 " =    1.131
peak=    3.241 closest distance to " O   HOH Z 141 " =    1.579
peak=    3.238 closest distance to " CG  GLN A  11 " =    1.361
peak=    3.233 closest distance to " O   HOH Z 345 " =    1.591
peak=    3.232 closest distance to " CB  ASN A 285 " =    0.945
peak=    3.231 closest distance to " O   HOH Z 109 " =    2.296
peak=    3.230 closest distance to " CB  ALA A 100 " =    1.234
peak=    3.225 closest distance to " O   HOH Z 227 " =    1.564
peak=    3.221 closest distance to " CB  THR A  31 " =    1.473
peak=    3.220 closest distance to " CB  ASN A  45 " =    1.088
peak=    3.215 closest distance to " CA  SER A  87 " =    0.983
peak=    3.215 closest distance to " CB  ALA A 295 " =    1.280
peak=    3.212 closest distance to " CD  ARG A  66 " =    2.361
peak=    3.205 closest distance to " CB  PHE A  16 " =    1.011
peak=    3.203 closest distance to " O   HOH Z  68 " =    1.842
peak=    3.198 closest distance to " CB  ALA A 242 " =    0.935
peak=    3.197 closest distance to " O   HOH Z 329 " =    4.025
peak=    3.189 closest distance to " CD1 LEU A   5 " =    1.445
peak=    3.188 closest distance to " O   HOH Z 197 " =    1.854
peak=    3.188 closest distance to " CB  LEU A  83 " =    0.751
peak=    3.182 closest distance to " O   HOH Z 420 " =    1.804
peak=    3.180 closest distance to " CG2 VAL A 197 " =    1.123
peak=    3.176 closest distance to " O   HOH Z  88 " =    2.647
peak=    3.176 closest distance to " O   HOH Z 147 " =    1.844
peak=    3.170 closest distance to " CB  GLN A  88 " =    1.191
peak=    3.169 closest distance to " O   HOH Z 238 " =    0.836
peak=    3.167 closest distance to " O   HOH Z 163 " =    1.382
peak=    3.161 closest distance to " NH2 ARG A  79 " =    1.330
peak=    3.160 closest distance to " O   HOH Z 391 " =    2.994
peak=    3.159 closest distance to " O   HOH Z 404 " =    2.159
peak=    3.158 closest distance to " CA  LYS A 290 " =    1.118
peak=    3.158 closest distance to " CB  GLN A 278 " =    0.972
peak=    3.157 closest distance to " OG  SER A  62 " =    2.816
peak=    3.155 closest distance to " O   HOH Z 133 " =    2.893
peak=    3.154 closest distance to " N   SER A 135 " =    1.383
peak=    3.153 closest distance to " CA  MET A 105 " =    1.071
peak=    3.152 closest distance to " O   HOH Z   1 " =    1.933
peak=    3.145 closest distance to " O   HOH Z 367 " =    3.498
peak=    3.143 closest distance to " O   HOH Z 173 " =    2.538
peak=    3.142 closest distance to " O   HOH Z 438 " =    3.000
peak=    3.137 closest distance to " CG  MET A 185 " =    0.968
peak=    3.135 closest distance to " CG2 THR A  29 " =    1.343
peak=    3.131 closest distance to " OG  SER A 245 " =    1.520
peak=    3.125 closest distance to " O   HOH Z 299 " =    4.356
peak=    3.124 closest distance to " CB  ASN A 215 " =    1.118
peak=    3.120 closest distance to " C   SER A  32 " =    1.083
peak=    3.119 closest distance to " O   ALA A 242 " =    1.062
peak=    3.115 closest distance to " O   ALA A 292 " =    1.191
peak=    3.114 closest distance to " C   ILE A 106 " =    1.857
peak=    3.113 closest distance to " CG2 VAL A 257 " =    0.822
peak=    3.099 closest distance to " N   ASP A 162 " =    1.287
peak=    3.098 closest distance to " CG  GLU A  37 " =    0.879
peak=    3.094 closest distance to " CZ2 TRP A 150 " =    1.148
peak=    3.090 closest distance to " CG1 ILE A  20 " =    1.275
peak=    3.081 closest distance to " CB  ALA A 104 " =    0.761
peak=    3.071 closest distance to " O   HOH Z 406 " =    1.598
peak=    3.069 closest distance to " O   HOH Z 403 " =    1.266
peak=    3.066 closest distance to " O   HOH Z   9 " =    2.400
peak=    3.065 closest distance to " N   TYR A 247 " =    1.179
peak=    3.064 closest distance to " O   HOH Z 387 " =    2.859
peak=    3.041 closest distance to " O   ALA A 158 " =    1.211

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 195         
Filter by distance & map next to the model:
   mapped sites are within: 0.762 - 5.663
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 194 from: 195
   mapped sites are within: 0.762 - 5.663

peak=   -5.336 closest distance to " CG2 VAL A 230 " =    0.762
peak=   -4.552 closest distance to " CG1 VAL A 296 " =    1.046
peak=   -4.548 closest distance to " CD  GLN A  58 " =    1.072
peak=   -4.453 closest distance to " O   HOH Z 166 " =    1.528
peak=   -4.400 closest distance to " O   HOH Z 266 " =    5.171
peak=   -4.399 closest distance to " SG  CYS A 254 " =    3.267
peak=   -4.350 closest distance to " CD  ARG A 156 " =    2.077
peak=   -4.279 closest distance to " O   HOH Z 351 " =    1.557
peak=   -4.267 closest distance to " C   HIS A 108 " =    1.198
peak=   -4.264 closest distance to " O   HOH Z 210 " =    0.975
peak=   -4.148 closest distance to " O   PRO A 163 " =    2.170
peak=   -4.117 closest distance to " OXT GLY A 302 " =    2.861
peak=   -4.016 closest distance to " CA  ASP A 298 " =    1.054
peak=   -4.008 closest distance to " CB  PHE A 208 " =    2.336
peak=   -3.996 closest distance to " CD2 LEU A 237 " =    2.624
peak=   -3.977 closest distance to " CZ2 TRP A  92 " =    2.800
peak=   -3.974 closest distance to " O   HOH Z  13 " =    1.736
peak=   -3.974 closest distance to " CD1 LEU A 101 " =    2.381
peak=   -3.945 closest distance to " CE2 TYR A  30 " =    2.747
peak=   -3.931 closest distance to " O   HOH Z 196 " =    2.267
peak=   -3.884 closest distance to " CB  PHE A 192 " =    2.078
peak=   -3.880 closest distance to " CG1 VAL A 112 " =    2.684
peak=   -3.859 closest distance to " O   HOH Z 290 " =    1.001
peak=   -3.852 closest distance to " ND2 ASN A 187 " =    1.649
peak=   -3.838 closest distance to " O   VAL A  67 " =    2.712
peak=   -3.827 closest distance to " O   HOH Z 394 " =    1.618
peak=   -3.816 closest distance to " CH2 TRP A 179 " =    1.241
peak=   -3.779 closest distance to " C   THR A 279 " =    1.167
peak=   -3.776 closest distance to " OG BSER A 134 " =    1.301
peak=   -3.775 closest distance to " CG  GLU A  53 " =    1.469
peak=   -3.772 closest distance to " O   PRO A 198 " =    1.245
peak=   -3.770 closest distance to " O   HOH Z 426 " =    1.846
peak=   -3.758 closest distance to " O   HOH Z 165 " =    1.977
peak=   -3.746 closest distance to " O   ASN A  45 " =    1.857
peak=   -3.735 closest distance to " CB  PRO A 243 " =    2.701
peak=   -3.724 closest distance to " O   HOH Z  60 " =    2.211
peak=   -3.719 closest distance to " CD  LYS A 289 " =    2.526
peak=   -3.717 closest distance to " CB  ALA A 248 " =    2.246
peak=   -3.717 closest distance to " CD1 PHE A  59 " =    1.975
peak=   -3.716 closest distance to " OG  SER A  97 " =    2.352
peak=   -3.698 closest distance to " CG  ASP A 231 " =    0.867
peak=   -3.686 closest distance to " O   HOH Z 231 " =    2.169
peak=   -3.685 closest distance to " CE3 TRP A 150 " =    2.223
peak=   -3.673 closest distance to " N   ALA A 226 " =    2.022
peak=   -3.649 closest distance to " O   HOH Z  37 " =    1.920
peak=   -3.636 closest distance to " CB  ALA A 161 " =    2.558
peak=   -3.627 closest distance to " O   SER A  95 " =    1.721
peak=   -3.623 closest distance to " CD2 LEU A 167 " =    1.792
peak=   -3.618 closest distance to " CB  ALA A  10 " =    2.252
peak=   -3.618 closest distance to " ND2 ASN A  45 " =    1.088
peak=   -3.611 closest distance to " OE1 GLN A 223 " =    2.323
peak=   -3.603 closest distance to " O   HOH Z 114 " =    3.292
peak=   -3.596 closest distance to " O   SER A 210 " =    1.801
peak=   -3.585 closest distance to " CD2 TYR A 293 " =    1.813
peak=   -3.575 closest distance to " ND2 ASN A  39 " =    1.167
peak=   -3.572 closest distance to " CZ  TYR A 169 " =    1.766
peak=   -3.571 closest distance to " O   HOH Z 423 " =    2.301
peak=   -3.569 closest distance to " CD1 LEU A  25 " =    2.477
peak=   -3.534 closest distance to " CB  ALA A 248 " =    2.050
peak=   -3.530 closest distance to " O   VAL A  67 " =    2.861
peak=   -3.523 closest distance to " O   SER A 271 " =    1.960
peak=   -3.521 closest distance to " N   ALA A 248 " =    1.824
peak=   -3.513 closest distance to " O   HOH Z  10 " =    1.559
peak=   -3.501 closest distance to " O   HOH Z 174 " =    2.134
peak=   -3.500 closest distance to " O   GLY A  75 " =    1.931
peak=   -3.500 closest distance to " NE2 GLN A  88 " =    1.027
peak=   -3.496 closest distance to " O   ALA A 161 " =    1.770
peak=   -3.489 closest distance to " O   HOH Z 435 " =    2.646
peak=   -3.482 closest distance to " C   ASN A 285 " =    2.331
peak=   -3.469 closest distance to " CG  GLN A  58 " =    1.248
peak=   -3.467 closest distance to " C   SER A 206 " =    1.526
peak=   -3.462 closest distance to " CD  GLN A 223 " =    0.783
peak=   -3.449 closest distance to " O   HOH Z  44 " =    2.217
peak=   -3.448 closest distance to " O   HOH Z 171 " =    2.173
peak=   -3.448 closest distance to " OD1 ASN A 148 " =    1.431
peak=   -3.432 closest distance to " ND2 ASN A  69 " =    1.777
peak=   -3.428 closest distance to " OG1 THR A  82 " =    1.365
peak=   -3.425 closest distance to " O   HOH Z 283 " =    1.974
peak=   -3.424 closest distance to " CA  GLY A 203 " =    2.381
peak=   -3.423 closest distance to " CA  GLY A 241 " =    2.391
peak=   -3.423 closest distance to " CG  ARG A 269 " =    2.225
peak=   -3.419 closest distance to " N   THR A 235 " =    1.282
peak=   -3.411 closest distance to " C   ALA A 158 " =    1.299
peak=   -3.410 closest distance to " OD1 ASN A 249 " =    2.445
peak=   -3.408 closest distance to " CA  VAL A 296 " =    0.932
peak=   -3.405 closest distance to " O   HOH Z 252 " =    3.909
peak=   -3.404 closest distance to " O   HOH Z  11 " =    1.876
peak=   -3.400 closest distance to " CD  ARG A 139 " =    1.643
peak=   -3.399 closest distance to " O   HOH Z 185 " =    2.431
peak=   -3.398 closest distance to " O   HOH Z 193 " =    2.146
peak=   -3.397 closest distance to " OG  SER A  63 " =    1.089
peak=   -3.392 closest distance to " CG2 ILE A 263 " =    2.332
peak=   -3.392 closest distance to " O   GLY A 196 " =    1.062
peak=   -3.392 closest distance to " CG  GLN A  11 " =    1.676
peak=   -3.390 closest distance to " CE  LYS A 166 " =    2.999
peak=   -3.387 closest distance to " CB  PRO A 163 " =    2.588
peak=   -3.379 closest distance to " O   HOH Z  92 " =    1.640
peak=   -3.377 closest distance to " N   THR A  52 " =    1.613
peak=   -3.373 closest distance to " NE  ARG A  66 " =    4.270
peak=   -3.370 closest distance to " CG  TRP A 266 " =    1.899
peak=   -3.368 closest distance to " CG2 VAL A 296 " =    1.397
peak=   -3.364 closest distance to " O   HOH Z 353 " =    2.161
peak=   -3.356 closest distance to " NE2 GLN A 103 " =    1.712
peak=   -3.353 closest distance to " OXT GLY A 302 " =    3.468
peak=   -3.349 closest distance to " O   HOH Z 131 " =    4.087
peak=   -3.349 closest distance to " O   GLY A  80 " =    2.435
peak=   -3.348 closest distance to " CG  ASP A 132 " =    2.360
peak=   -3.347 closest distance to " ND2BASN A 224 " =    1.777
peak=   -3.344 closest distance to " O   HOH Z 119 " =    2.083
peak=   -3.339 closest distance to " O   HOH Z 177 " =    1.756
peak=   -3.338 closest distance to " O   HOH Z 222 " =    1.515
peak=   -3.335 closest distance to " O   HOH Z 136 " =    2.420
peak=   -3.333 closest distance to " O   VAL A  67 " =    2.081
peak=   -3.330 closest distance to " CA  VAL A 197 " =    0.970
peak=   -3.330 closest distance to " O   HOH Z 407 " =    2.945
peak=   -3.330 closest distance to " CD2 LEU A 300 " =    2.686
peak=   -3.329 closest distance to " O   HOH Z 193 " =    1.488
peak=   -3.328 closest distance to " CA  GLY A 133 " =    2.373
peak=   -3.318 closest distance to " O   ARG A  24 " =    2.079
peak=   -3.316 closest distance to " NH2 ARG A  66 " =    1.627
peak=   -3.313 closest distance to " O   LEU A 282 " =    2.066
peak=   -3.311 closest distance to " O   HOH Z 150 " =    1.911
peak=   -3.307 closest distance to " O   HOH Z   6 " =    1.794
peak=   -3.306 closest distance to " O   HOH Z 139 " =    5.143
peak=   -3.305 closest distance to " CB  SER A 210 " =    1.140
peak=   -3.305 closest distance to " CG  PRO A 243 " =    1.604
peak=   -3.304 closest distance to " CH2 TRP A 150 " =    1.020
peak=   -3.304 closest distance to " OD2 ASP A 171 " =    2.219
peak=   -3.301 closest distance to " O   HOH Z 191 " =    5.663
peak=   -3.300 closest distance to " O   HOH Z 301 " =    2.384
peak=   -3.296 closest distance to " OG  SER A   3 " =    1.735
peak=   -3.293 closest distance to " O   HOH Z 422 " =    1.643
peak=   -3.290 closest distance to " O   HOH Z  52 " =    1.851
peak=   -3.286 closest distance to " O   HOH Z 377 " =    1.680
peak=   -3.284 closest distance to " CE  MET A 105 " =    2.241
peak=   -3.273 closest distance to " C   MET A 188 " =    1.550
peak=   -3.272 closest distance to " CD  GLN A 223 " =    1.604
peak=   -3.270 closest distance to " O   HOH Z 154 " =    1.565
peak=   -3.268 closest distance to " CE BMET A  47 " =    1.529
peak=   -3.266 closest distance to " O   HOH Z 285 " =    1.592
peak=   -3.249 closest distance to " ND2 ASN A  45 " =    1.875
peak=   -3.245 closest distance to " O   ALA A  34 " =    2.551
peak=   -3.244 closest distance to " CG  GLU A 277 " =    1.168
peak=   -3.243 closest distance to " CG  ASP A  50 " =    2.295
peak=   -3.243 closest distance to " O   HOH Z 311 " =    3.684
peak=   -3.239 closest distance to " ND2 ASN A  45 " =    1.134
peak=   -3.233 closest distance to " O   HOH Z 208 " =    1.762
peak=   -3.224 closest distance to " CB  TRP A  85 " =    2.535
peak=   -3.218 closest distance to " N   SER A 276 " =    1.416
peak=   -3.216 closest distance to " O   HOH Z 388 " =    2.016
peak=   -3.215 closest distance to " CD  ARG A 195 " =    5.103
peak=   -3.202 closest distance to " CD1 PHE A  59 " =    2.140
peak=   -3.201 closest distance to " NE2 GLN A 194 " =    1.813
peak=   -3.198 closest distance to " CE3 TRP A 274 " =    2.453
peak=   -3.198 closest distance to " NH2 ARG A  79 " =    1.590
peak=   -3.198 closest distance to " O   HOH Z 139 " =    3.207
peak=   -3.195 closest distance to " O   HOH Z 431 " =    2.274
peak=   -3.187 closest distance to " O   PHE A 218 " =    1.546
peak=   -3.183 closest distance to " CD  PRO A 243 " =    1.979
peak=   -3.178 closest distance to " C   VAL A 265 " =    0.873
peak=   -3.176 closest distance to " CE2 PHE A  61 " =    2.549
peak=   -3.176 closest distance to " OD1 ASN A  39 " =    2.146
peak=   -3.168 closest distance to " N   ALA A  43 " =    2.658
peak=   -3.167 closest distance to " O   ALA A  10 " =    1.745
peak=   -3.162 closest distance to " CD1 TYR A 247 " =    2.589
peak=   -3.162 closest distance to " O   HOH Z 110 " =    1.490
peak=   -3.158 closest distance to " O   HOH Z  43 " =    1.935
peak=   -3.158 closest distance to " CB  ALA A  43 " =    2.514
peak=   -3.157 closest distance to " O   VAL A 189 " =    2.589
peak=   -3.156 closest distance to " O  BHOH Z 338 " =    1.185
peak=   -3.150 closest distance to " O   HOH Z 251 " =    5.045
peak=   -3.134 closest distance to " O   HOH Z 265 " =    2.259
peak=   -3.134 closest distance to " O   HOH Z 244 " =    1.396
peak=   -3.121 closest distance to " O   HOH Z   6 " =    2.130
peak=   -3.121 closest distance to " O   HOH Z  71 " =    1.919
peak=   -3.119 closest distance to " O   GLU A 152 " =    1.658
peak=   -3.118 closest distance to " O   HOH Z 197 " =    5.160
peak=   -3.115 closest distance to " CG1 VAL A 112 " =    2.746
peak=   -3.113 closest distance to " CG  LEU A   5 " =    1.525
peak=   -3.113 closest distance to " O   TRP A  92 " =    1.976
peak=   -3.105 closest distance to " CZ  PHE A  38 " =    2.026
peak=   -3.102 closest distance to " O   HOH Z 234 " =    4.275
peak=   -3.100 closest distance to " O   HOH Z 136 " =    1.438
peak=   -3.099 closest distance to " O   ASP A 171 " =    1.905
peak=   -3.093 closest distance to " O   HOH Z 166 " =    1.741
peak=   -3.087 closest distance to " O   GLY A 203 " =    2.346
peak=   -3.082 closest distance to " OG ASER A 134 " =    1.354
peak=   -3.078 closest distance to " O   SER A 276 " =    1.761
peak=   -3.064 closest distance to " O   HOH Z 421 " =    3.891
peak=   -3.062 closest distance to " N   VAL A 230 " =    1.053
peak=   -3.051 closest distance to " O   SER A   3 " =    1.116
peak=   -3.041 closest distance to " CZ  TYR A  68 " =    1.180
peak=   -3.002 closest distance to " N   GLN A  58 " =    2.069
peak=   -3.001 closest distance to " CA  SER A  62 " =    2.298

================= 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    :  0.4658 0.4505   6.267026e+00   6.246040e+00
   1_bss:  0.4579 0.4431   6.259038e+00   6.239745e+00
   1_xyz:  0.3599 0.3777   6.107813e+00   6.136321e+00
   1_adp:  0.3050 0.3480   5.991687e+00   6.080212e+00
   1_occ:  0.3046 0.3482   5.990735e+00   6.080613e+00
   2_bss:  0.3023 0.3454   5.991923e+00   6.079687e+00
   2_xyz:  0.2096 0.2559   5.670434e+00   5.833737e+00
   2_adp:  0.1878 0.2333   5.579975e+00   5.755794e+00
   2_occ:  0.1875 0.2336   5.579854e+00   5.756863e+00
   3_bss:  0.1859 0.2325   5.578335e+00   5.753256e+00
   3_xyz:  0.1494 0.1850   5.368982e+00   5.547141e+00
   3_adp:  0.1417 0.1774   5.322791e+00   5.507050e+00
   3_occ:  0.1415 0.1774   5.322364e+00   5.507081e+00
   4_bss:  0.1415 0.1772   5.322531e+00   5.506283e+00
   4_xyz:  0.1216 0.1633   5.207230e+00   5.429269e+00
   4_adp:  0.1174 0.1615   5.185657e+00   5.417654e+00
   4_occ:  0.1173 0.1615   5.185451e+00   5.417572e+00
   5_bss:  0.1172 0.1614   5.185322e+00   5.417541e+00
   5_xyz:  0.1181 0.1610   5.190654e+00   5.419002e+00
   5_adp:  0.1176 0.1612   5.188367e+00   5.419083e+00
   5_occ:  0.1176 0.1612   5.188261e+00   5.419051e+00
   5_bss:  0.1176 0.1614   5.189513e+00   5.420193e+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:  0.334  20.001   6.302  10.292   7.681   0.000   0.000   0.000
   1_xyz:  0.334  20.001   6.302  10.292   7.681   0.000   0.000   0.000
   1_adp:  0.334  20.001   6.302  10.292   7.681   0.000   0.000   0.000
   1_occ:  0.334  20.001   6.302  10.292   7.681   0.000   0.000   0.000
   2_bss:  0.319  36.445   3.414   6.636   4.897   0.000   0.000   0.000
   2_xyz:  0.319  36.445   3.414   6.636   4.897   0.000   0.000   0.000
   2_adp:  0.319  36.445   3.414   6.636   4.897   0.000   0.000   0.000
   2_occ:  0.319  36.445   3.414   6.636   4.897   0.000   0.000   0.000
   3_bss:  0.315  51.604   2.118   4.101   3.901   0.000   0.000   0.000
   3_xyz:  0.315  51.604   2.118   4.101   3.901   0.000   0.000   0.000
   3_adp:  0.315  51.604   2.118   4.101   3.901   0.000   0.000   0.000
   3_occ:  0.315  51.604   2.118   4.101   3.901   0.000   0.000   0.000
   4_bss:  0.326  51.604   1.697   3.161   3.578   0.000   0.000   0.000
   4_xyz:  0.326  51.604   1.697   3.161   3.578   0.000   0.000   0.000
   4_adp:  0.326  51.604   1.697   3.161   3.578   0.000   0.000   0.000
   4_occ:  0.326  51.604   1.697   3.161   3.578   0.000   0.000   0.000
   5_bss:  0.325  51.604   1.894   3.048   3.697   0.000   0.000   0.000
   5_xyz:  0.325  51.604   1.894   3.048   3.697   0.000   0.000   0.000
   5_adp:  0.325  51.604   1.894   3.048   3.697   0.000   0.000   0.000
   5_occ:  0.325  51.604   1.894   3.048   3.697   0.000   0.000   0.000
   5_bss:  0.325  54.563  -0.958   0.123   0.835   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  51.918 0.4979  0.5640    60160.523
   1_bss:  51.570 0.5009  0.7222    58261.138
   1_xyz:  42.021 0.6173  0.8666    39987.528
   1_adp:  37.045 0.6777  0.9642    33472.522
   1_occ:  37.071 0.6774  0.9629    33477.718
   2_bss:  36.837 0.6802  0.8674    33217.875
   2_xyz:  26.151 0.7985  0.9824    17153.072
   2_adp:  23.401 0.8278  1.0015    14353.281
   2_occ:  23.417 0.8277  1.0012    14375.407
   3_bss:  23.242 0.8295  0.9472    14234.268
   3_xyz:  17.601 0.8841  0.9815     8851.012
   3_adp:  16.556 0.8938  0.9869     8156.977
   3_occ:  16.554 0.8938  0.9869     8160.288
   4_bss:  16.554 0.8938  0.9677     8154.282
   4_xyz:  14.995 0.9069  0.9722     6979.255
   4_adp:  14.771 0.9089  0.9679     6832.293
   4_occ:  14.764 0.9089  0.9679     6833.483
   5_bss:  14.760 0.9090  0.9705     6833.798
   5_xyz:  14.699 0.9096  0.9706     6818.726
   5_adp:  14.684 0.9098  0.9665     6819.257
   5_occ:  14.684 0.9098  0.9665     6819.237
   5_bss:  14.733 0.9094  0.9685     6853.632
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.3884e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.3884e+01
   1_xyz:   1.674  0.013  0.109 17.868  0.007  4.110   1.3761e-01
   1_adp:   1.674  0.013  0.109 17.868  0.007  4.110   1.3761e-01
   1_occ:   1.674  0.013  0.109 17.868  0.007  4.110   1.3761e-01
   2_bss:   1.674  0.013  0.109 17.868  0.007  4.110   1.3761e-01
   2_xyz:   1.185  0.009  0.077 16.008  0.004  4.127   8.0419e-02
   2_adp:   1.185  0.009  0.077 16.008  0.004  4.127   8.0419e-02
   2_occ:   1.185  0.009  0.077 16.008  0.004  4.127   8.0419e-02
   3_bss:   1.185  0.009  0.077 16.008  0.004  4.127   8.0419e-02
   3_xyz:   0.944  0.006  0.071 15.576  0.004  4.124   5.5846e-02
   3_adp:   0.944  0.006  0.071 15.576  0.004  4.124   5.5846e-02
   3_occ:   0.944  0.006  0.071 15.576  0.004  4.124   5.5846e-02
   4_bss:   0.944  0.006  0.071 15.576  0.004  4.124   5.5846e-02
   4_xyz:   1.109  0.009  0.086 15.677  0.004  4.134   7.1554e-02
   4_adp:   1.109  0.009  0.086 15.677  0.004  4.134   7.1554e-02
   4_occ:   1.109  0.009  0.086 15.677  0.004  4.134   7.1554e-02
   5_bss:   1.109  0.009  0.086 15.677  0.004  4.134   7.1554e-02
   5_xyz:   0.954  0.007  0.075 15.299  0.003  4.133   5.6452e-02
   5_adp:   0.954  0.007  0.075 15.299  0.003  4.133   5.6452e-02
   5_occ:   0.954  0.007  0.075 15.299  0.003  4.133   5.6452e-02
   5_bss:   0.954  0.007  0.075 15.299  0.003  4.133   5.6452e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9854e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9854e+00
   1_xyz:  15.743  0.160  0.527 85.389  0.038  2.282   1.0318e-01
   1_adp:  15.743  0.160  0.527 85.389  0.038  2.282   1.0318e-01
   1_occ:  15.743  0.160  0.527 85.389  0.038  2.282   1.0318e-01
   2_bss:  15.743  0.160  0.527 85.389  0.038  2.282   1.0318e-01
   2_xyz:   8.294  0.117  0.268 83.288  0.036  2.078   7.2174e-02
   2_adp:   8.294  0.117  0.268 83.288  0.036  2.078   7.2174e-02
   2_occ:   8.294  0.117  0.268 83.288  0.036  2.078   7.2174e-02
   3_bss:   8.294  0.117  0.268 83.288  0.036  2.078   7.2174e-02
   3_xyz:   6.430  0.043  0.273 79.690  0.047  2.284   3.1334e-02
   3_adp:   6.430  0.043  0.273 79.690  0.047  2.284   3.1334e-02
   3_occ:   6.430  0.043  0.273 79.690  0.047  2.284   3.1334e-02
   4_bss:   6.430  0.043  0.273 79.690  0.047  2.284   3.1334e-02
   4_xyz:   7.994  0.053  0.507 83.600  0.039  2.225   4.9788e-02
   4_adp:   7.994  0.053  0.507 83.600  0.039  2.225   4.9788e-02
   4_occ:   7.994  0.053  0.507 83.600  0.039  2.225   4.9788e-02
   5_bss:   7.994  0.053  0.507 83.600  0.039  2.225   4.9788e-02
   5_xyz:   6.721  0.044  0.372 81.292  0.035  2.341   3.1837e-02
   5_adp:   6.721  0.044  0.372 81.292  0.035  2.341   3.1837e-02
   5_occ:   6.721  0.044  0.372 81.292  0.035  2.341   3.1837e-02
   5_bss:   6.721  0.044  0.372 81.292  0.035  2.341   3.1837e-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:  82.79   0.00  12.21  72.84   0.00   9.45  82.79   0.00  27.21
   1_occ:  82.79   0.00  12.21  72.84   0.00   9.45  82.79   0.00  27.21
   2_bss:  82.79   0.00  12.21  72.84   0.00   9.45  82.79   0.00  27.21
   2_xyz:  82.79   0.00  12.21  72.84   0.00   9.45  82.79   0.00  27.21
   2_adp:  77.65   0.00  12.02  68.09   0.00   8.41  77.65   1.25  31.64
   2_occ:  77.65   0.00  12.02  68.09   0.00   8.41  77.65   1.25  31.64
   3_bss:  77.65   0.00  12.02  68.09   0.00   8.41  77.65   1.25  31.64
   3_xyz:  77.65   0.00  12.02  68.09   0.00   8.41  77.65   1.25  31.64
   3_adp:  76.31   0.00  12.12  69.24   0.00   8.24  76.31   1.47  33.23
   3_occ:  76.31   0.00  12.12  69.24   0.00   8.24  76.31   1.47  33.23
   4_bss:  76.31   0.00  12.12  69.24   0.00   8.24  76.31   1.47  33.23
   4_xyz:  76.31   0.00  12.12  69.24   0.00   8.24  76.31   1.47  33.23
   4_adp:  75.37   0.00  12.42  75.37   0.00   8.18  75.03   1.45  35.52
   4_occ:  75.37   0.00  12.42  75.37   0.00   8.18  75.03   1.45  35.52
   5_bss:  75.37   0.00  12.42  75.37   0.00   8.18  75.03   1.45  35.52
   5_xyz:  75.37   0.00  12.42  75.37   0.00   8.18  75.03   1.45  35.52
   5_adp:  78.51   0.00  12.41  78.51   0.00   8.13  73.64   1.13  35.73
   5_occ:  78.51   0.00  12.41  78.51   0.00   8.13  73.64   1.13  35.73
   5_bss:  81.47   2.96  15.37  81.47   2.96  11.09  76.60   4.09  38.69
------------------------------------------------------------------------
 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:    1.219    0.013    0.413
   1_adp:    1.219    0.013    0.413
   1_occ:    1.219    0.013    0.413
   2_bss:    1.219    0.013    0.413
   2_xyz:    1.697    0.028    0.582
   2_adp:    1.697    0.028    0.582
   2_occ:    1.697    0.028    0.582
   3_bss:    1.697    0.028    0.582
   3_xyz:    1.750    0.033    0.624
   3_adp:    1.750    0.033    0.624
   3_occ:    1.750    0.033    0.624
   4_bss:    1.750    0.033    0.624
   4_xyz:    1.832    0.065    0.669
   4_adp:    1.832    0.065    0.669
   4_occ:    1.832    0.065    0.669
   5_bss:    1.832    0.065    0.669
   5_xyz:    1.982    0.055    0.675
   5_adp:    1.982    0.055    0.675
   5_occ:    1.982    0.055    0.675
   5_bss:    1.982    0.055    0.675
------------------------------------------------------------------------

CPU time actual refinement: 324.57


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_457/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_457/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_457/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_457/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_457/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 324.42 
  Macro-tasks:
    bulk solvent and scale       = 41.98  
    individual site refinement   = 126.93 
    weights calculation          = 32.84  
    collect and process          = 6.71   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 208.60 
  Micro-tasks:
    mask                            = 2.36   
    f_calc                          = 98.18  
    alpha_beta                      = 8.21   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 107.17 
    fmodel                         = 7.28   
    r_factors                      = 0.24   
    phase_errors                   = 10.85  
    foms                           = 0.30   
    TOTAL for micro-tasks          = 235.77 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.636 micro seconds
Total CPU time: 5.63 minutes
from_scatterers_fft:    627 calls, 97.87 s
gradients_fft:          571 calls, 94.69 s

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

# Date 2008-01-16 Time 01:38:27 PST -0800 (1200476307.79 s)
Start R-work = 0.4658, R-free = 0.4505 (no bulk solvent and anisotropic scale)
Final R-work = 0.1347, R-free = 0.1766 (no bulk solvent and anisotropic scale)

Start R-work = 0.4579, R-free = 0.4431
Final R-work = 0.1176, R-free = 0.1614