# Date 2008-01-16 Time 02:56:41 PST -0800 (1200481001.41 s)
#phil __OFF__

Command line arguments: "../1037.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 14856
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1037

-------------------------------------------------------------------------------
  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: (71.3037, 47.1647, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.29, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.1647, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1145 1.98118
Completeness in resolution range: 0.94954
Completeness with d_max=infinity: 0.946694

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1145
                             d_min =   1.9812

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: (71.3037, 47.1647, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1145 1.98118
Completeness in resolution range: 0.94954
Completeness with d_max=infinity: 0.946694

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1149 -  4.2399 [2167/2196]  1953   214   9.9%
  bin  2:  4.2399 -  3.3777 [2074/2090]  1864   210  10.1%
  bin  3:  3.3777 -  2.9543 [2048/2067]  1842   206  10.1%
  bin  4:  2.9543 -  2.6858 [2047/2077]  1849   198   9.7%
  bin  5:  2.6858 -  2.4943 [2034/2053]  1830   204  10.0%
  bin  6:  2.4943 -  2.3478 [2011/2047]  1803   208  10.3%
  bin  7:  2.3478 -  2.2306 [1986/2019]  1786   200  10.1%
  bin  8:  2.2306 -  2.1338 [2002/2036]  1806   196   9.8%
  bin  9:  2.1338 -  2.0518 [1984/2012]  1784   200  10.1%
  bin 10:  2.0518 -  1.9812 [1236/2033]  1113   123  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1037/model_refine_data.mtz


========================== Anomalous scatterer groups =========================

All atoms refined with f_prime=0 and f_double_prime=0.

========================== Set up restraints manager ==========================

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 15
        2.42 -     3.04: 2187
        3.04 -     3.66: 4651
        3.66 -     4.28: 8986
        4.28 -     4.90: 12339
  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 207 " - " O   HOH Z 341 "  1.852 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  2.149 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  2.162 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.163 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28173 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_1037/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1037/model_refine_001.geo

CPU time processing inputs: 9.26


============================ 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 = 71.30375 47.16465 85.5261 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 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4407   r_free= 0.4302   ksol= 0.00   Bsol= 0.00   scale= 0.815    |
|                                                                             |
| 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:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.238003                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1149 -  4.7292 0.99   1402  157 0.3705 0.3551       6.537       6.498|
|  2:  4.7292 -  3.7729 0.99   1359  145 0.3387 0.3546      6.6746      6.6858|
|  3:  3.7729 -  3.3017 0.99   1322  152 0.3875 0.3541      6.5745      6.5821|
|  4:  3.3017 -  3.0024 0.99   1328  149 0.4166 0.4049       6.459      6.3986|
|  5:  3.0024 -  2.7886 0.99   1315  143 0.4599 0.4835      6.3236      6.3544|
|  6:  2.7886 -  2.6251 0.99   1298  145 0.4654 0.4715      6.2339        6.22|
|  7:  2.6251 -  2.4943 0.99   1314  141 0.4930 0.4705      6.2345      6.1765|
|  8:  2.4943 -  2.3861 0.98   1275  150 0.4908 0.4618      6.1393      6.1487|
|  9:  2.3861 -  2.2946 0.98   1295  147 0.4853 0.4910      6.1046      6.0971|
| 10:  2.2946 -  2.2157 0.98   1279  134 0.4888 0.4994      6.0768       6.085|
| 11:  2.2157 -  2.1466 1.00   1285  143 0.4873 0.4538      6.0207      5.9858|
| 12:  2.1466 -  2.0854 0.97   1259  139 0.5076 0.5136      5.9569      6.0184|
| 13:  2.0854 -  2.0306 0.98   1284  143 0.5173 0.4926      5.8732      5.8042|
| 14:  2.0306 -  1.9812 0.47    615   71 0.5113 0.4548       5.836      5.7649|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1149 -  4.7292  1402   157  0.74  31.01   0.81     0.76      58579.13|
|  2:  4.7292 -  3.7729  1359   145  0.76  29.64   0.91     0.81      78389.59|
|  3:  3.7729 -  3.3017  1322   152  0.68  37.30   0.86     0.78      84528.91|
|  4:  3.3017 -  3.0024  1328   149  0.61  43.24   0.83     0.69      78834.78|
|  5:  3.0024 -  2.7886  1315   143  0.51  51.06   0.76     0.60      68449.89|
|  6:  2.7886 -  2.6251  1298   145  0.49  52.67   0.77     0.56      59788.45|
|  7:  2.6251 -  2.4943  1314   141  0.50  51.92   0.75     0.56      52539.41|
|  8:  2.4943 -  2.3861  1275   150  0.49  53.21   0.73     0.57      47951.66|
|  9:  2.3861 -  2.2946  1295   147  0.48  53.48   0.75     0.55      43580.24|
| 10:  2.2946 -  2.2157  1279   134  0.46  55.22   0.77     0.53      41667.62|
| 11:  2.2157 -  2.1466  1285   143  0.43  57.69   0.78     0.50      39648.86|
| 12:  2.1466 -  2.0854  1259   139  0.40  60.44   0.75     0.47      39207.30|
| 13:  2.0854 -  2.0306  1284   143  0.38  61.46   0.73     0.46      33659.74|
| 14:  2.0306 -  1.9812   615    71  0.45  56.62   0.74     0.49      25830.43|
|alpha:            min =        0.46 max =            0.81 mean =         0.60|
|beta:             min =    25830.43 max =        84528.91 mean =     55135.35|
|figures of merit: min =        0.00 max =            1.00 mean =         0.53|
|phase err.(work): min =        0.00 max =           89.99 mean =        49.12|
|phase err.(test): min =        0.00 max =           90.00 mean =        49.01|
|-----------------------------------------------------------------------------|

============================== 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 = 9.567451              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 75.900   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.726617              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.340   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       22 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      162 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      685 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1504 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2618 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3886 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5046 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6551 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7682 |
|-----------------------------------------------------------------------------|
|-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 |       53.964 |
| 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 |       1.663 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.045)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.045)------------------------------------------|
|    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 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4485   r_free= 0.4392   ksol= 0.00   Bsol= 0.00   scale= 0.784    |
|                                                                             |
| 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:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.241221                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4327   r_free= 0.4209   ksol= 0.30   Bsol= 20.00   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.45,8.05,7.79,0.00,0.00,0.00); trace/3= 8.10                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.234585                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.672516              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.040   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.727276              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.246   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4327      final r-factor (work) = 0.3288          |
| start r-factor (free) = 0.4209      final r-factor (free) = 0.3620          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 81.0362 = 8.67 * 0.50 * 6.2432 + 1.00 * 53.9640                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.5485 = 8.67 * 0.50 * 6.0931 + 1.00 * 0.1274                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3288      final r-factor (work) = 0.2727          |
| start r-factor (free) = 0.3620      final r-factor (free) = 0.3203          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4457 = 0.73 * 1.00 * 6.0931 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3353 = 0.73 * 1.00 * 5.9442 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 11      |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.045)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    52.32   10.38    None  None   None       |
|    all(noH): 2823   0      0.00    52.32   10.38    None  None   None       |
|    Sol.    : 438    0      0.00    52.32   26.00    None  None   None       |
|    Mac.    : 2385   0      0.00    48.03   7.51     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 -   5.232: 1095   |   5:    26.160 -  31.392:  107        |
|      1:     5.232 -  10.464:  783   |   6:    31.392 -  36.624:   87        |
|      2:    10.464 -  15.696:  352   |   7:    36.624 -  41.856:   62        |
|      3:    15.696 -  20.928:  175   |   8:    41.856 -  47.088:   31        |
|      4:    20.928 -  26.160:  124   |   9:    47.088 -  52.320:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2727 r_free = 0.3203             target_work(ml) = 5.893         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2722 r_free = 0.3208             target_work(ml) = 5.892         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2722   r_free= 0.3208   ksol= 0.30   Bsol= 20.00   scale= 1.073   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.45,8.05,7.79,0.00,0.00,0.00); trace/3= 8.10                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.892480                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2690   r_free= 0.3156   ksol= 0.32   Bsol= 49.08   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.06,4.60,5.12,0.00,0.00,0.00); trace/3= 4.93                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.892921                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.149940              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.130   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.407898              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 119.658  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2690      final r-factor (work) = 0.1897          |
| start r-factor (free) = 0.3156      final r-factor (free) = 0.2379          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4942 = 3.15 * 0.50 * 5.9473 + 1.00 * 0.1274                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1094 = 3.15 * 0.50 * 5.7467 + 1.00 * 0.0585                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1897      final r-factor (work) = 0.1749          |
| start r-factor (free) = 0.2379      final r-factor (free) = 0.2206          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3680 = 0.41 * 1.00 * 5.7467 + 1.00 * 0.0239                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3367 = 0.41 * 1.00 * 5.5529 + 1.00 * 0.0717                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.045)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.73   10.97    None  None   None       |
|    all(noH): 2823   0      0.00    87.73   10.97    None  None   None       |
|    Sol.    : 438    0      1.24    55.72   29.74    None  None   None       |
|    Mac.    : 2385   0      0.00    87.73   7.52     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.773: 1719   |   5:    43.865 -  52.638:   43        |
|      1:     8.773 -  17.546:  573   |   6:    52.638 -  61.411:    4        |
|      2:    17.546 -  26.319:  165   |   7:    61.411 -  70.185:    0        |
|      3:    26.319 -  35.092:  175   |   8:    70.185 -  78.958:    0        |
|      4:    35.092 -  43.865:  143   |   9:    78.958 -  87.731:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1749 r_free = 0.2206             target_work(ml) = 5.519         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1748 r_free = 0.2206             target_work(ml) = 5.518         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1748   r_free= 0.2206   ksol= 0.32   Bsol= 49.08   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.06,4.60,5.12,0.00,0.00,0.00); trace/3= 4.93                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.518037                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1736   r_free= 0.2186   ksol= 0.34   Bsol= 49.08   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.47,3.40,3.98,0.00,0.00,0.00); trace/3= 3.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.518425                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.563144              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.329  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.320948              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.496   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1736      final r-factor (work) = 0.1360          |
| start r-factor (free) = 0.2186      final r-factor (free) = 0.1817          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1839 = 2.56 * 0.50 * 5.5599 + 1.00 * 0.0585                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0039 = 2.56 * 0.50 * 5.4163 + 1.00 * 0.0626                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1360      final r-factor (work) = 0.1264          |
| start r-factor (free) = 0.1817      final r-factor (free) = 0.1727          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1871 = 1.32 * 1.00 * 5.4163 + 1.00 * 0.0324                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.9847 = 1.32 * 1.00 * 5.2770 + 1.00 * 0.0141                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.045)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.66   12.22    None  None   None       |
|    all(noH): 2823   0      0.00    77.66   12.22    None  None   None       |
|    Sol.    : 438    0      0.69    77.66   36.15    None  None   None       |
|    Mac.    : 2385   0      0.00    76.24   7.83     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.766: 1606   |   5:    38.830 -  46.596:   91        |
|      1:     7.766 -  15.532:  596   |   6:    46.596 -  54.362:   77        |
|      2:    15.532 -  23.298:  172   |   7:    54.362 -  62.128:   49        |
|      3:    23.298 -  31.064:   99   |   8:    62.128 -  69.894:   19        |
|      4:    31.064 -  38.830:  104   |   9:    69.894 -  77.660:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1264 r_free = 0.1727             target_work(ml) = 5.253         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1263 r_free = 0.1725             target_work(ml) = 5.252         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1263   r_free= 0.1725   ksol= 0.34   Bsol= 49.08   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.47,3.40,3.98,0.00,0.00,0.00); trace/3= 3.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.252199                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1267   r_free= 0.1727   ksol= 0.32   Bsol= 49.08   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.09,3.07,3.67,0.00,0.00,0.00); trace/3= 3.28                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.253169                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.506466              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 128.410  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.247200              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.499  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1267      final r-factor (work) = 0.1171          |
| start r-factor (free) = 0.1727      final r-factor (free) = 0.1641          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6768 = 2.51 * 0.50 * 5.2777 + 1.00 * 0.0626                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6100 = 2.51 * 0.50 * 5.2208 + 1.00 * 0.0672                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1171      final r-factor (work) = 0.1168          |
| start r-factor (free) = 0.1641      final r-factor (free) = 0.1616          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3046 = 0.25 * 1.00 * 5.2208 + 1.00 * 0.0140                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2950 = 0.25 * 1.00 * 5.1927 + 1.00 * 0.0113                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.045)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.85   11.91    None  None   None       |
|    all(noH): 2823   0      0.00    76.85   11.91    None  None   None       |
|    Sol.    : 438    0      0.95    74.55   34.89    None  None   None       |
|    Mac.    : 2385   0      0.00    76.85   7.70     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 -   7.685: 1644   |   5:    38.423 -  46.107:   88        |
|      1:     7.685 -  15.369:  574   |   6:    46.107 -  53.792:   77        |
|      2:    15.369 -  23.054:  175   |   7:    53.792 -  61.477:   44        |
|      3:    23.054 -  30.738:   93   |   8:    61.477 -  69.161:   14        |
|      4:    30.738 -  38.423:  104   |   9:    69.161 -  76.846:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1168 r_free = 0.1616             target_work(ml) = 5.183         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1168 r_free = 0.1614             target_work(ml) = 5.183         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1168   r_free= 0.1614   ksol= 0.32   Bsol= 49.08   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.09,3.07,3.67,0.00,0.00,0.00); trace/3= 3.28                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.182757                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1168   r_free= 0.1614   ksol= 0.32   Bsol= 48.04   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.09,3.07,3.67,0.00,0.00,0.00); trace/3= 3.28                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.182731                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.599030              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 149.506  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.193577              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.042  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1168      final r-factor (work) = 0.1109          |
| start r-factor (free) = 0.1614      final r-factor (free) = 0.1584          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4109 = 3.60 * 0.50 * 5.1924 + 1.00 * 0.0671                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3691 = 3.60 * 0.50 * 5.1610 + 1.00 * 0.0818                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1109      final r-factor (work) = 0.1094          |
| start r-factor (free) = 0.1584      final r-factor (free) = 0.1598          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.3324 = 2.19 * 1.00 * 5.1610 + 1.00 * 0.0113                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.2936 = 2.19 * 1.00 * 5.1422 + 1.00 * 0.0137                              |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.045)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.96   12.00    None  None   None       |
|    all(noH): 2823   0      0.00    83.96   12.00    None  None   None       |
|    Sol.    : 438    0      1.06    79.58   35.39    None  None   None       |
|    Mac.    : 2385   0      0.00    83.96   7.71     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 -   8.396: 1713   |   5:    41.980 -  50.376:   91        |
|      1:     8.396 -  16.792:  537   |   6:    50.376 -  58.771:   58        |
|      2:    16.792 -  25.188:  156   |   7:    58.771 -  67.167:   31        |
|      3:    25.188 -  33.584:  119   |   8:    67.167 -  75.563:    9        |
|      4:    33.584 -  41.980:  101   |   9:    75.563 -  83.959:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1094 r_free = 0.1598             target_work(ml) = 5.149         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1094 r_free = 0.1598             target_work(ml) = 5.149         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1094   r_free= 0.1598   ksol= 0.32   Bsol= 48.04   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.09,3.07,3.67,0.00,0.00,0.00); trace/3= 3.28                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.148731                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1149 -  4.7292 0.99   1402  157 0.0966 0.1326      5.3706      5.5526|
|  2:  4.7292 -  3.7729 0.99   1359  145 0.0831 0.1109      5.4197      5.6291|
|  3:  3.7729 -  3.3017 0.99   1322  152 0.1048 0.1574      5.4678      5.8746|
|  4:  3.3017 -  3.0024 0.99   1328  149 0.1171 0.1523      5.4462      5.5865|
|  5:  3.0024 -  2.7886 0.99   1315  143 0.1295 0.1798      5.3304      5.5383|
|  6:  2.7886 -  2.6251 0.99   1298  145 0.1194 0.1851      5.2109      5.4993|
|  7:  2.6251 -  2.4943 0.99   1314  141 0.1236 0.1657      5.1685      5.3732|
|  8:  2.4943 -  2.3861 0.98   1275  150 0.1153 0.1750      5.0666      5.3466|
|  9:  2.3861 -  2.2946 0.98   1295  147 0.1157 0.1877      5.0471      5.3517|
| 10:  2.2946 -  2.2157 0.98   1279  134 0.1094 0.1743      4.9725      5.2227|
| 11:  2.2157 -  2.1466 1.00   1285  143 0.1125 0.1782      4.9491      5.2847|
| 12:  2.1466 -  2.0854 0.97   1259  139 0.1054 0.1665      4.8744      5.1137|
| 13:  2.0854 -  2.0306 0.98   1284  143 0.1172 0.1762      4.7878      5.0428|
| 14:  2.0306 -  1.9812 0.47    615   71 0.0970 0.1803      4.6377       4.973|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1149 -  4.7292  1402   157  0.94   8.90   0.98     0.95       7207.65|
|  2:  4.7292 -  3.7729  1359   145  0.95   7.97   1.01     1.00       9050.49|
|  3:  3.7729 -  3.3017  1322   152  0.93  11.55   1.02     1.02      10511.84|
|  4:  3.3017 -  3.0024  1328   149  0.92  13.98   1.00     0.98      10622.01|
|  5:  3.0024 -  2.7886  1315   143  0.89  16.66   0.99     0.96       8727.43|
|  6:  2.7886 -  2.6251  1298   145  0.90  16.21   0.98     0.96       7338.74|
|  7:  2.6251 -  2.4943  1314   141  0.91  15.55   0.98     0.95       6347.59|
|  8:  2.4943 -  2.3861  1275   150  0.90  16.02   0.99     0.96       5552.05|
|  9:  2.3861 -  2.2946  1295   147  0.90  16.10   1.00     0.97       5377.47|
| 10:  2.2946 -  2.2157  1279   134  0.90  16.20   0.99     0.95       4670.71|
| 11:  2.2157 -  2.1466  1285   143  0.90  16.67   0.99     0.95       4545.06|
| 12:  2.1466 -  2.0854  1259   139  0.91  15.23   1.00     0.99       4125.35|
| 13:  2.0854 -  2.0306  1284   143  0.89  17.11   1.00     0.97       3408.13|
| 14:  2.0306 -  1.9812   615    71  0.91  14.87   0.98     0.95       2565.29|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2565.29 max =        10622.01 mean =      6622.51|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.42|
|phase err.(test): min =        0.00 max =           88.46 mean =        13.91|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1093   r_free= 0.1598   ksol= 0.32   Bsol= 51.42   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.21,-0.19,0.40,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.148793                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.11 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1093   r_free= 0.1598   ksol= 0.32   Bsol= 51.42   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.21,-0.19,0.40,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.148793                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1149 -  4.7292 0.99   1402  157 0.0966 0.1327      5.3711      5.5532|
|  2:  4.7292 -  3.7729 0.99   1359  145 0.0832 0.1109      5.4199      5.6289|
|  3:  3.7729 -  3.3017 0.99   1322  152 0.1048 0.1573      5.4676      5.8744|
|  4:  3.3017 -  3.0024 0.99   1328  149 0.1171 0.1523      5.4461      5.5865|
|  5:  3.0024 -  2.7886 0.99   1315  143 0.1295 0.1799      5.3304      5.5384|
|  6:  2.7886 -  2.6251 0.99   1298  145 0.1194 0.1851      5.2109      5.4992|
|  7:  2.6251 -  2.4943 0.99   1314  141 0.1236 0.1656      5.1684      5.3732|
|  8:  2.4943 -  2.3861 0.98   1275  150 0.1153 0.1750      5.0666      5.3466|
|  9:  2.3861 -  2.2946 0.98   1295  147 0.1158 0.1877      5.0471      5.3515|
| 10:  2.2946 -  2.2157 0.98   1279  134 0.1093 0.1743      4.9725      5.2228|
| 11:  2.2157 -  2.1466 1.00   1285  143 0.1125 0.1782      4.9492       5.285|
| 12:  2.1466 -  2.0854 0.97   1259  139 0.1054 0.1665      4.8745      5.1138|
| 13:  2.0854 -  2.0306 0.98   1284  143 0.1172 0.1762      4.7878      5.0428|
| 14:  2.0306 -  1.9812 0.47    615   71 0.0970 0.1803      4.6377      4.9729|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1149 -  4.7292  1402   157  0.94   8.90   0.98     0.95       7214.75|
|  2:  4.7292 -  3.7729  1359   145  0.95   7.97   1.01     1.00       9053.43|
|  3:  3.7729 -  3.3017  1322   152  0.93  11.54   1.03     1.02      10507.92|
|  4:  3.3017 -  3.0024  1328   149  0.92  13.98   1.01     0.99      10622.30|
|  5:  3.0024 -  2.7886  1315   143  0.89  16.66   1.00     0.97       8727.29|
|  6:  2.7886 -  2.6251  1298   145  0.90  16.21   0.99     0.96       7339.09|
|  7:  2.6251 -  2.4943  1314   141  0.91  15.55   0.99     0.96       6346.56|
|  8:  2.4943 -  2.3861  1275   150  0.90  16.02   0.99     0.96       5551.43|
|  9:  2.3861 -  2.2946  1295   147  0.90  16.10   1.00     0.97       5376.17|
| 10:  2.2946 -  2.2157  1279   134  0.90  16.21   1.00     0.95       4671.04|
| 11:  2.2157 -  2.1466  1285   143  0.90  16.67   1.00     0.96       4545.33|
| 12:  2.1466 -  2.0854  1259   139  0.91  15.24   1.01     1.00       4126.83|
| 13:  2.0854 -  2.0306  1284   143  0.89  17.11   1.00     0.98       3408.37|
| 14:  2.0306 -  1.9812   615    71  0.91  14.87   0.98     0.96       2565.16|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2565.16 max =        10622.30 mean =      6622.99|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        14.42|
|phase err.(test): min =        0.00 max =           88.46 mean =        13.91|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.045)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.38    87.34   15.38    None  None   None       |
|    all(noH): 2823   0      3.38    87.34   15.38    None  None   None       |
|    Sol.    : 438    0      4.44    82.96   38.77    None  None   None       |
|    Mac.    : 2385   0      3.38    87.34   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:     3.378 -  11.774: 1713   |   5:    45.357 -  53.753:   91        |
|      1:    11.774 -  20.169:  537   |   6:    53.753 -  62.149:   58        |
|      2:    20.169 -  28.565:  156   |   7:    62.149 -  70.545:   31        |
|      3:    28.565 -  36.961:  119   |   8:    70.545 -  78.941:    9        |
|      4:    36.961 -  45.357:  101   |   9:    78.941 -  87.337:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 332         
Filter by distance & map next to the model:
   mapped sites are within: 0.359 - 5.934
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 328 from: 332
   mapped sites are within: 0.701 - 5.934

peak=   10.423 closest distance to " CG2 VAL A 230 " =    1.338
peak=    6.190 closest distance to " CG  LEU A   5 " =    1.129
peak=    5.946 closest distance to " NH2 ARG A  56 " =    2.235
peak=    5.920 closest distance to " CG2 VAL A 296 " =    1.043
peak=    5.673 closest distance to " CG  LEU A 228 " =    1.163
peak=    5.430 closest distance to " CB  GLN A 223 " =    1.454
peak=    5.415 closest distance to " CB  VAL A 296 " =    1.058
peak=    5.155 closest distance to " CB  SER A  63 " =    1.306
peak=    5.035 closest distance to " CG  PRO A  54 " =    1.172
peak=    5.035 closest distance to " CD2 LEU A   5 " =    1.123
peak=    4.880 closest distance to " CB  GLN A 183 " =    1.293
peak=    4.868 closest distance to " NE2 GLN A  11 " =    1.095
peak=    4.817 closest distance to " CB  VAL A 230 " =    1.198
peak=    4.704 closest distance to " O   HOH Z 232 " =    2.314
peak=    4.603 closest distance to " OD1 ASN A  69 " =    2.661
peak=    4.578 closest distance to " CB  PRO A  54 " =    0.846
peak=    4.525 closest distance to " O   HOH Z 126 " =    1.871
peak=    4.524 closest distance to " O   HOH Z 316 " =    2.992
peak=    4.491 closest distance to " O   HOH Z 272 " =    1.882
peak=    4.472 closest distance to " CB  GLU A 152 " =    1.194
peak=    4.467 closest distance to " O   HOH Z 298 " =    1.801
peak=    4.429 closest distance to " C   PRO A 198 " =    1.529
peak=    4.415 closest distance to " O   HOH Z 369 " =    2.154
peak=    4.411 closest distance to " O   HOH Z 427 " =    3.037
peak=    4.368 closest distance to " O   HOH Z 403 " =    1.739
peak=    4.366 closest distance to " O   HOH Z 368 " =    2.275
peak=    4.325 closest distance to " O   HOH Z 303 " =    2.094
peak=    4.268 closest distance to " CB  ARG A 275 " =    0.857
peak=    4.251 closest distance to " CG  PRO A 213 " =    1.165
peak=    4.242 closest distance to " O   HOH Z  54 " =    2.409
peak=    4.216 closest distance to " CB  TYR A 169 " =    0.757
peak=    4.180 closest distance to " CB  ASN A 148 " =    1.346
peak=    4.167 closest distance to " O   HOH Z 203 " =    1.762
peak=    4.148 closest distance to " O   HOH Z 236 " =    1.924
peak=    4.145 closest distance to " CB  GLU A 277 " =    3.624
peak=    4.137 closest distance to " CB  GLU A 128 " =    1.107
peak=    4.112 closest distance to " O   HOH Z 193 " =    1.814
peak=    4.104 closest distance to " CB  ARG A  79 " =    1.463
peak=    4.100 closest distance to " O   HOH Z  88 " =    3.314
peak=    4.096 closest distance to " CA  TYR A  30 " =    0.950
peak=    4.096 closest distance to " CB  SER A   3 " =    1.353
peak=    4.089 closest distance to " O   HOH Z 144 " =    1.590
peak=    4.077 closest distance to " CB  ASP A 140 " =    1.010
peak=    4.073 closest distance to " O   HOH Z 158 " =    3.005
peak=    4.072 closest distance to " O   HOH Z  78 " =    1.733
peak=    4.044 closest distance to " O   HOH Z 280 " =    2.928
peak=    4.031 closest distance to " O   HOH Z 112 " =    1.635
peak=    4.005 closest distance to " O   HOH Z 423 " =    1.772
peak=    4.005 closest distance to " O   SER A  87 " =    2.246
peak=    3.987 closest distance to " CG  ARG A  66 " =    2.688
peak=    3.980 closest distance to " CB  TRP A 266 " =    0.991
peak=    3.966 closest distance to " O   HOH Z  61 " =    1.650
peak=    3.948 closest distance to " CB  VAL A 265 " =    1.260
peak=    3.946 closest distance to " O   HOH Z 263 " =    1.670
peak=    3.926 closest distance to " CD2 LEU A 228 " =    1.141
peak=    3.923 closest distance to " O   HOH Z 371 " =    3.260
peak=    3.918 closest distance to " CA  ALA A  51 " =    1.035
peak=    3.906 closest distance to " OD2 ASP A 286 " =    2.847
peak=    3.901 closest distance to " CB  TRP A 179 " =    1.417
peak=    3.899 closest distance to " O   HOH Z 425 " =    1.351
peak=    3.895 closest distance to " NH2 ARG A 156 " =    1.167
peak=    3.875 closest distance to " O   HOH Z  97 " =    2.027
peak=    3.875 closest distance to " O   HOH Z  63 " =    1.916
peak=    3.873 closest distance to " ND2 ASN A 249 " =    1.896
peak=    3.873 closest distance to " CG1BVAL A  72 " =    1.651
peak=    3.864 closest distance to " O   HOH Z 247 " =    1.282
peak=    3.862 closest distance to " ND2 ASN A 187 " =    1.495
peak=    3.862 closest distance to " O   HOH Z 411 " =    3.646
peak=    3.845 closest distance to " CB  ARG A 190 " =    1.646
peak=    3.842 closest distance to " CG  ARG A 138 " =    1.113
peak=    3.840 closest distance to " OG BSER A 164 " =    2.171
peak=    3.836 closest distance to " CG1 ILE A  33 " =    1.237
peak=    3.824 closest distance to " O   HOH Z  80 " =    1.680
peak=    3.819 closest distance to " O   HOH Z 234 " =    3.680
peak=    3.818 closest distance to " O   HOH Z  20 " =    1.909
peak=    3.815 closest distance to " CB  LEU A 228 " =    1.270
peak=    3.799 closest distance to " O   HOH Z  15 " =    2.111
peak=    3.799 closest distance to " CD BLYS A 290 " =    1.031
peak=    3.795 closest distance to " O   HOH Z 193 " =    2.088
peak=    3.793 closest distance to " O   MET A 105 " =    1.844
peak=    3.783 closest distance to " CA  THR A 221 " =    0.948
peak=    3.778 closest distance to " CG  PRO A 243 " =    1.215
peak=    3.772 closest distance to " O   HOH Z 128 " =    2.155
peak=    3.771 closest distance to " O   HOH Z 261 " =    2.063
peak=    3.771 closest distance to " O   HOH Z 135 " =    1.927
peak=    3.764 closest distance to " CG2 THR A 221 " =    1.138
peak=    3.759 closest distance to " O   HOH Z 197 " =    2.905
peak=    3.755 closest distance to " O   TRP A 274 " =    1.895
peak=    3.739 closest distance to " O   HOH Z  44 " =    2.196
peak=    3.727 closest distance to " CB  SER A 212 " =    1.150
peak=    3.724 closest distance to " NZ  LYS A 117 " =    3.300
peak=    3.724 closest distance to " O   HOH Z 425 " =    2.022
peak=    3.716 closest distance to " CA  ALA A  21 " =    1.193
peak=    3.713 closest distance to " CB  ARG A 139 " =    0.965
peak=    3.711 closest distance to " O   HOH Z 189 " =    2.819
peak=    3.704 closest distance to " CG  MET A 185 " =    1.254
peak=    3.701 closest distance to " O   HOH Z 346 " =    1.576
peak=    3.694 closest distance to " CD  ARG A 159 " =    0.781
peak=    3.694 closest distance to " O   HOH Z 134 " =    1.419
peak=    3.691 closest distance to " O   HOH Z 133 " =    2.379
peak=    3.689 closest distance to " O   HOH Z 180 " =    2.083
peak=    3.685 closest distance to " O   HOH Z  43 " =    1.981
peak=    3.682 closest distance to " CA  THR A 264 " =    0.718
peak=    3.680 closest distance to " CA  MET A  40 " =    1.150
peak=    3.676 closest distance to " CA  ASN A 215 " =    1.259
peak=    3.676 closest distance to " CA  LYS A 117 " =    1.223
peak=    3.660 closest distance to " O   HOH Z 133 " =    1.723
peak=    3.660 closest distance to " O   HOH Z 245 " =    1.383
peak=    3.655 closest distance to " CA  GLY A 267 " =    0.713
peak=    3.653 closest distance to " NH1AARG A 145 " =    1.119
peak=    3.647 closest distance to " O   HOH Z 145 " =    1.999
peak=    3.643 closest distance to " CB  ASN A 187 " =    1.145
peak=    3.638 closest distance to " O   HOH Z 345 " =    3.463
peak=    3.634 closest distance to " ND1 HIS A  81 " =    1.668
peak=    3.633 closest distance to " CB  ALA A   9 " =    1.589
peak=    3.627 closest distance to " O   HOH Z 420 " =    2.059
peak=    3.626 closest distance to " CD1 LEU A 300 " =    1.161
peak=    3.619 closest distance to " CD  ARG A 269 " =    0.932
peak=    3.617 closest distance to " CB  SER A 216 " =    0.854
peak=    3.607 closest distance to " CB BVAL A  41 " =    1.153
peak=    3.603 closest distance to " O   ALA A 158 " =    1.418
peak=    3.596 closest distance to " CG  GLN A  88 " =    1.047
peak=    3.594 closest distance to " CD2 LEU A 255 " =    1.510
peak=    3.592 closest distance to " CB  VAL A 202 " =    1.574
peak=    3.591 closest distance to " CB  LEU A 143 " =    1.175
peak=    3.589 closest distance to " O   HOH Z 271 " =    2.567
peak=    3.584 closest distance to " CD1 LEU A   5 " =    1.306
peak=    3.583 closest distance to " CG  PRO A 198 " =    1.256
peak=    3.577 closest distance to " CB  ASN A  39 " =    0.908
peak=    3.566 closest distance to " O   HOH Z 437 " =    1.885
peak=    3.555 closest distance to " CE1 TYR A 186 " =    1.279
peak=    3.549 closest distance to " O   HOH Z  49 " =    2.462
peak=    3.546 closest distance to " CG2 THR A 220 " =    0.956
peak=    3.543 closest distance to " O   HOH Z  66 " =    2.132
peak=    3.532 closest distance to " O   HOH Z 329 " =    3.845
peak=    3.531 closest distance to " CB  THR A  82 " =    1.364
peak=    3.523 closest distance to " O   HOH Z 344 " =    2.976
peak=    3.520 closest distance to " O   HOH Z 126 " =    1.552
peak=    3.518 closest distance to " OG  SER A  22 " =    2.881
peak=    3.516 closest distance to " O   HOH Z  97 " =    2.774
peak=    3.516 closest distance to " O   HOH Z 193 " =    1.662
peak=    3.516 closest distance to " O   HOH Z 132 " =    2.626
peak=    3.513 closest distance to " ND2 ASN A 110 " =    1.764
peak=    3.512 closest distance to " N   VAL A 126 " =    1.331
peak=    3.510 closest distance to " O   HOH Z 213 " =    1.653
peak=    3.509 closest distance to " O   HOH Z 295 " =    1.470
peak=    3.499 closest distance to " O   HOH Z 313 " =    1.800
peak=    3.497 closest distance to " CA  ARG A 195 " =    1.244
peak=    3.494 closest distance to " O   HOH Z 171 " =    3.843
peak=    3.493 closest distance to " O   HOH Z 422 " =    2.697
peak=    3.484 closest distance to " O   HOH Z 128 " =    1.887
peak=    3.483 closest distance to " CZ  PHE A 218 " =    1.081
peak=    3.478 closest distance to " O   HOH Z  21 " =    1.637
peak=    3.478 closest distance to " CA  ALA A 158 " =    1.203
peak=    3.478 closest distance to " O   HOH Z 383 " =    2.168
peak=    3.476 closest distance to " N   SER A 135 " =    1.480
peak=    3.467 closest distance to " O   HOH Z  10 " =    1.820
peak=    3.465 closest distance to " CD2 HIS A  81 " =    1.016
peak=    3.460 closest distance to " O   HOH Z  61 " =    1.574
peak=    3.459 closest distance to " O   HOH Z 426 " =    1.535
peak=    3.457 closest distance to " O   HOH Z 172 " =    3.658
peak=    3.444 closest distance to " O   HOH Z  58 " =    1.256
peak=    3.440 closest distance to " CB  ASN A 110 " =    1.267
peak=    3.439 closest distance to " O   HOH Z 227 " =    1.658
peak=    3.438 closest distance to " O   HOH Z 281 " =    4.529
peak=    3.437 closest distance to " ND1 HIS A  86 " =    1.730
peak=    3.436 closest distance to " O   HOH Z  40 " =    2.417
peak=    3.431 closest distance to " CB  TRP A 150 " =    1.367
peak=    3.430 closest distance to " O   HOH Z 214 " =    2.114
peak=    3.425 closest distance to " O   HOH Z 368 " =    3.613
peak=    3.415 closest distance to " CB  GLN A  88 " =    1.278
peak=    3.413 closest distance to " O   HOH Z 147 " =    1.745
peak=    3.406 closest distance to " O   ALA A 165 " =    1.412
peak=    3.406 closest distance to " CD  LYS A 166 " =    1.303
peak=    3.405 closest distance to " CA  LEU A 282 " =    1.084
peak=    3.404 closest distance to " O   HOH Z  48 " =    1.407
peak=    3.403 closest distance to " CA  ALA A 295 " =    1.028
peak=    3.402 closest distance to " CA  ALA A 291 " =    0.952
peak=    3.400 closest distance to " CZ  PHE A 192 " =    0.996
peak=    3.398 closest distance to " O   HOH Z  63 " =    0.989
peak=    3.393 closest distance to " O   HOH Z  68 " =    1.541
peak=    3.388 closest distance to " CG  GLN A  58 " =    2.765
peak=    3.384 closest distance to " OD1 ASN A 217 " =    1.651
peak=    3.384 closest distance to " CG BARG A 102 " =    1.873
peak=    3.381 closest distance to " O   ASP A 124 " =    1.081
peak=    3.379 closest distance to " CB  LYS A 117 " =    1.134
peak=    3.379 closest distance to " N   ASN A 127 " =    1.238
peak=    3.379 closest distance to " CA  ASP A 140 " =    1.181
peak=    3.378 closest distance to " CB  THR A  31 " =    1.674
peak=    3.375 closest distance to " CG  MET A 185 " =    1.117
peak=    3.372 closest distance to " O   HOH Z 130 " =    2.240
peak=    3.370 closest distance to " NH2 ARG A 219 " =    1.844
peak=    3.368 closest distance to " O   HOH Z 163 " =    1.501
peak=    3.368 closest distance to " O   HOH Z 250 " =    1.335
peak=    3.366 closest distance to " CB  VAL A 268 " =    0.852
peak=    3.366 closest distance to " CB  MET A  47 " =    1.156
peak=    3.359 closest distance to " CG1 ILE A  49 " =    1.470
peak=    3.359 closest distance to " O   HOH Z 290 " =    0.957
peak=    3.359 closest distance to " O   HOH Z 116 " =    1.793
peak=    3.357 closest distance to " O   HOH Z  54 " =    1.584
peak=    3.353 closest distance to " O   HOH Z 248 " =    1.782
peak=    3.345 closest distance to " OG1 THR A 294 " =    2.384
peak=    3.342 closest distance to " CE  LYS A  76 " =    0.812
peak=    3.340 closest distance to " CG2AVAL A 121 " =    2.343
peak=    3.340 closest distance to " O   HOH Z  19 " =    2.394
peak=    3.335 closest distance to " CG1 VAL A 296 " =    1.207
peak=    3.330 closest distance to " CB  ALA A 161 " =    0.839
peak=    3.328 closest distance to " CB  ALA A 291 " =    1.487
peak=    3.327 closest distance to " CB  THR A 157 " =    1.140
peak=    3.324 closest distance to " O   HOH Z 407 " =    2.467
peak=    3.323 closest distance to " CB  LEU A 255 " =    0.754
peak=    3.321 closest distance to " O   HOH Z 420 " =    5.934
peak=    3.321 closest distance to " OD1 ASP A 231 " =    1.867
peak=    3.319 closest distance to " CB  ALA A 248 " =    1.006
peak=    3.317 closest distance to " OG BSER A 134 " =    3.019
peak=    3.317 closest distance to " CB  ASN A 142 " =    1.088
peak=    3.312 closest distance to " O   HOH Z 402 " =    1.460
peak=    3.311 closest distance to " O   HOH Z 271 " =    2.135
peak=    3.309 closest distance to " O   HOH Z 128 " =    2.151
peak=    3.309 closest distance to " NH2 ARG A  79 " =    1.373
peak=    3.308 closest distance to " CG1 VAL A 153 " =    0.965
peak=    3.299 closest distance to " CD1 LEU A  96 " =    0.701
peak=    3.294 closest distance to " O   HOH Z 313 " =    1.789
peak=    3.287 closest distance to " O   HOH Z 244 " =    1.673
peak=    3.281 closest distance to " CB  HIS A 108 " =    0.830
peak=    3.279 closest distance to " NE2 HIS A 207 " =    1.682
peak=    3.274 closest distance to " CG BARG A 275 " =    1.473
peak=    3.273 closest distance to " OE1 GLU A 152 " =    0.847
peak=    3.269 closest distance to " O   HOH Z 171 " =    2.377
peak=    3.266 closest distance to " N   SER A 134 " =    1.648
peak=    3.266 closest distance to " CA  ARG A  36 " =    1.111
peak=    3.258 closest distance to " O   HOH Z 102 " =    1.283
peak=    3.257 closest distance to " CD1 ILE A 106 " =    1.029
peak=    3.256 closest distance to " C   SER A  32 " =    1.041
peak=    3.256 closest distance to " O   HOH Z 299 " =    4.383
peak=    3.252 closest distance to " CB  MET A  40 " =    0.828
peak=    3.251 closest distance to " O   HOH Z 409 " =    3.336
peak=    3.251 closest distance to " NZ  LYS A 166 " =    3.180
peak=    3.251 closest distance to " O   HOH Z  30 " =    1.072
peak=    3.249 closest distance to " CB  GLU A 277 " =    3.802
peak=    3.247 closest distance to " CD2 TRP A 179 " =    1.396
peak=    3.246 closest distance to " CA  GLY A 211 " =    1.250
peak=    3.245 closest distance to " O   HOH Z 109 " =    2.595
peak=    3.244 closest distance to " CB  MET A 113 " =    1.784
peak=    3.239 closest distance to " CG  LEU A 167 " =    1.178
peak=    3.238 closest distance to " CB  ALA A 248 " =    1.408
peak=    3.237 closest distance to " O   HOH Z 189 " =    3.043
peak=    3.233 closest distance to " CA  ASN A  74 " =    1.281
peak=    3.233 closest distance to " CD1AILE A 234 " =    0.821
peak=    3.232 closest distance to " O   HOH Z 184 " =    1.391
peak=    3.229 closest distance to " O   HOH Z 155 " =    3.272
peak=    3.229 closest distance to " CB  ASN A 224 " =    1.063
peak=    3.229 closest distance to " CB  ILE A 120 " =    1.413
peak=    3.229 closest distance to " O  BHOH Z 338 " =    2.378
peak=    3.226 closest distance to " O   HOH Z  35 " =    2.621
peak=    3.224 closest distance to " NH1 ARG A  56 " =    1.050
peak=    3.224 closest distance to " O   HOH Z  15 " =    1.447
peak=    3.222 closest distance to " CA  VAL A  41 " =    0.938
peak=    3.219 closest distance to " O   THR A  31 " =    1.551
peak=    3.219 closest distance to " CG2 ILE A 120 " =    1.199
peak=    3.217 closest distance to " CA  TYR A 116 " =    1.442
peak=    3.217 closest distance to " CB  TYR A 116 " =    0.896
peak=    3.216 closest distance to " CB  GLU A  46 " =    1.087
peak=    3.214 closest distance to " O   ALA A   1 " =    1.575
peak=    3.209 closest distance to " O   HOH Z 301 " =    1.878
peak=    3.207 closest distance to " N   PHE A 130 " =    1.335
peak=    3.205 closest distance to " C   LYS A 290 " =    1.313
peak=    3.204 closest distance to " NZ  LYS A  48 " =    1.461
peak=    3.201 closest distance to " O   HOH Z 353 " =    2.817
peak=    3.200 closest distance to " O   HOH Z 227 " =    2.080
peak=    3.200 closest distance to " NE2 GLN A  58 " =    5.862
peak=    3.196 closest distance to " CB  ALA A 100 " =    1.252
peak=    3.196 closest distance to " CG1 VAL A 174 " =    1.219
peak=    3.195 closest distance to " ND2 ASN A 301 " =    1.763
peak=    3.194 closest distance to " CB  TYR A  30 " =    1.498
peak=    3.193 closest distance to " O   HOH Z 302 " =    1.963
peak=    3.192 closest distance to " O   HOH Z 367 " =    3.446
peak=    3.192 closest distance to " CA  ASN A 176 " =    1.192
peak=    3.190 closest distance to " NE  ARG A  79 " =    1.224
peak=    3.189 closest distance to " OE2 GLU A  53 " =    2.072
peak=    3.188 closest distance to " CD  LYS A 119 " =    1.808
peak=    3.187 closest distance to " CG  ARG A 138 " =    1.116
peak=    3.186 closest distance to " O   HOH Z 166 " =    3.512
peak=    3.184 closest distance to " CG  GLN A  77 " =    2.203
peak=    3.181 closest distance to " O   HOH Z 291 " =    1.568
peak=    3.179 closest distance to " N   ASN A  39 " =    1.256
peak=    3.179 closest distance to " CG2 VAL A 257 " =    0.873
peak=    3.174 closest distance to " O   HOH Z 279 " =    2.236
peak=    3.174 closest distance to " CA  ALA A 154 " =    0.995
peak=    3.172 closest distance to " CD1 LEU A 228 " =    1.658
peak=    3.161 closest distance to " O   HOH Z  48 " =    1.519
peak=    3.158 closest distance to " O   HOH Z 305 " =    3.579
peak=    3.157 closest distance to " O   HOH Z 118 " =    1.386
peak=    3.156 closest distance to " CG  MET A 188 " =    1.116
peak=    3.153 closest distance to " O   HOH Z 417 " =    3.224
peak=    3.150 closest distance to " O   HOH Z 238 " =    2.268
peak=    3.149 closest distance to " O   HOH Z 175 " =    3.518
peak=    3.148 closest distance to " O   HOH Z  85 " =    2.136
peak=    3.148 closest distance to " O   HOH Z  59 " =    2.286
peak=    3.147 closest distance to " NH2BARG A 145 " =    2.042
peak=    3.145 closest distance to " O   HOH Z 423 " =    2.999
peak=    3.144 closest distance to " OD1 ASN A 148 " =    1.737
peak=    3.144 closest distance to " O   HOH Z 273 " =    2.660
peak=    3.143 closest distance to " CD1 ILE A  33 " =    1.576
peak=    3.140 closest distance to " O   HOH Z  48 " =    1.801
peak=    3.136 closest distance to " O   HOH Z 128 " =    1.996
peak=    3.134 closest distance to " C   ALA A 299 " =    0.976
peak=    3.133 closest distance to " CB  ARG A 138 " =    0.912
peak=    3.132 closest distance to " CG2 THR A 294 " =    1.661
peak=    3.128 closest distance to " CA  VAL A 126 " =    0.962
peak=    3.127 closest distance to " O   GLN A 278 " =    1.528
peak=    3.120 closest distance to " O   HOH Z 374 " =    2.668
peak=    3.119 closest distance to " O   HOH Z 391 " =    3.036
peak=    3.118 closest distance to " CA  SER A  87 " =    0.957
peak=    3.116 closest distance to " O   HOH Z 207 " =    2.042
peak=    3.113 closest distance to " CG2 ILE A 234 " =    0.907
peak=    3.113 closest distance to " O   GLU A   2 " =    1.706
peak=    3.104 closest distance to " CA  SER A 146 " =    1.738
peak=    3.102 closest distance to " CG2 ILE A  20 " =    1.498
peak=    3.100 closest distance to " CA  ILE A 106 " =    0.810
peak=    3.095 closest distance to " O   HOH Z 156 " =    2.926
peak=    3.094 closest distance to " O   HOH Z 327 " =    1.803
peak=    3.085 closest distance to " O   HOH Z 146 " =    2.383
peak=    3.062 closest distance to " OH  TYR A 214 " =    1.227
peak=    3.060 closest distance to " CB  SER A 245 " =    3.083
peak=    3.025 closest distance to " O   HOH Z   9 " =    2.055
peak=    3.019 closest distance to " O   HOH Z  46 " =    1.520
peak=    3.008 closest distance to " OE1 GLU A   2 " =    2.202

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.774 - 5.562
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 204
   mapped sites are within: 0.774 - 5.562

peak=   -4.939 closest distance to " CG2 VAL A 230 " =    0.914
peak=   -4.649 closest distance to " CD  ARG A 156 " =    1.970
peak=   -4.325 closest distance to " SG  CYS A 254 " =    3.166
peak=   -4.319 closest distance to " O   HOH Z 266 " =    4.748
peak=   -4.299 closest distance to " O   HOH Z  52 " =    1.559
peak=   -4.224 closest distance to " OE1 GLN A 223 " =    2.146
peak=   -4.169 closest distance to " CB  ALA A 161 " =    2.625
peak=   -4.112 closest distance to " O   PRO A 163 " =    2.083
peak=   -4.012 closest distance to " CB  PRO A 243 " =    2.613
peak=   -3.992 closest distance to " CG2BVAL A  41 " =    2.591
peak=   -3.950 closest distance to " NE2 GLN A  88 " =    2.202
peak=   -3.893 closest distance to " O   HOH Z 198 " =    2.527
peak=   -3.887 closest distance to " N   ALA A  43 " =    2.468
peak=   -3.883 closest distance to " O   HOH Z 290 " =    1.267
peak=   -3.882 closest distance to " O   HOH Z 389 " =    1.870
peak=   -3.876 closest distance to " CD1 LEU A 228 " =    2.354
peak=   -3.870 closest distance to " CD2 LEU A 300 " =    2.867
peak=   -3.855 closest distance to " CE2 TYR A  30 " =    2.812
peak=   -3.845 closest distance to " O   HOH Z 196 " =    2.232
peak=   -3.812 closest distance to " O   HOH Z 231 " =    1.965
peak=   -3.790 closest distance to " OG  SER A  87 " =    1.482
peak=   -3.786 closest distance to " O   HOH Z 103 " =    1.824
peak=   -3.771 closest distance to " OXT GLY A 302 " =    2.963
peak=   -3.751 closest distance to " OG ASER A 134 " =    1.222
peak=   -3.749 closest distance to " CB  ALA A  43 " =    2.511
peak=   -3.745 closest distance to " CG1 VAL A 250 " =    2.700
peak=   -3.743 closest distance to " O   HOH Z  43 " =    1.663
peak=   -3.739 closest distance to " CD  ARG A 139 " =    1.565
peak=   -3.735 closest distance to " O   HOH Z 426 " =    1.665
peak=   -3.730 closest distance to " CD  ARG A  14 " =    3.009
peak=   -3.707 closest distance to " C   HIS A 108 " =    1.164
peak=   -3.703 closest distance to " CD  LYS A 289 " =    2.467
peak=   -3.693 closest distance to " O   HOH Z 353 " =    2.235
peak=   -3.692 closest distance to " OG  SER A  26 " =    1.332
peak=   -3.691 closest distance to " O   HOH Z 377 " =    2.029
peak=   -3.688 closest distance to " C   ASN A 187 " =    1.815
peak=   -3.685 closest distance to " O   SER A 271 " =    2.137
peak=   -3.679 closest distance to " CG  TRP A 266 " =    1.758
peak=   -3.679 closest distance to " OG  SER A  97 " =    2.218
peak=   -3.673 closest distance to " O   HOH Z 166 " =    1.911
peak=   -3.661 closest distance to " CA  ASP A 298 " =    1.038
peak=   -3.658 closest distance to " CD1 PHE A  59 " =    1.876
peak=   -3.653 closest distance to " O   HOH Z  19 " =    2.283
peak=   -3.649 closest distance to " CZ3 TRP A 179 " =    1.187
peak=   -3.642 closest distance to " O   HOH Z 118 " =    3.025
peak=   -3.636 closest distance to " NH2AARG A 275 " =    5.297
peak=   -3.636 closest distance to " CE2 PHE A 218 " =    2.584
peak=   -3.634 closest distance to " OG BSER A 134 " =    1.231
peak=   -3.627 closest distance to " O   HOH Z  17 " =    1.550
peak=   -3.626 closest distance to " O   HOH Z  11 " =    1.954
peak=   -3.626 closest distance to " OD1 ASN A 148 " =    1.547
peak=   -3.613 closest distance to " CG1 VAL A 296 " =    1.430
peak=   -3.609 closest distance to " CG  ARG A 269 " =    2.426
peak=   -3.604 closest distance to " O   HOH Z 283 " =    1.965
peak=   -3.603 closest distance to " CB  ALA A 291 " =    2.149
peak=   -3.601 closest distance to " O   VAL A  67 " =    2.654
peak=   -3.598 closest distance to " NH2 ARG A  66 " =    1.912
peak=   -3.596 closest distance to " CG2 VAL A 296 " =    1.364
peak=   -3.593 closest distance to " O   HOH Z 311 " =    3.772
peak=   -3.590 closest distance to " O   HOH Z  13 " =    1.438
peak=   -3.589 closest distance to " CG  ASP A 231 " =    0.798
peak=   -3.588 closest distance to " CG1 VAL A 112 " =    2.964
peak=   -3.587 closest distance to " C   ALA A 158 " =    1.254
peak=   -3.581 closest distance to " O   HOH Z 394 " =    1.519
peak=   -3.580 closest distance to " O   HOH Z 350 " =    1.742
peak=   -3.580 closest distance to " OG  SER A  62 " =    1.692
peak=   -3.578 closest distance to " ND2 ASN A  45 " =    1.306
peak=   -3.578 closest distance to " O   HOH Z 407 " =    3.183
peak=   -3.577 closest distance to " N   ALA A 226 " =    2.146
peak=   -3.559 closest distance to " O   HOH Z 292 " =    4.545
peak=   -3.549 closest distance to " CG1 VAL A 197 " =    2.282
peak=   -3.545 closest distance to " CB  ALA A 291 " =    2.328
peak=   -3.541 closest distance to " O   HOH Z 351 " =    1.526
peak=   -3.536 closest distance to " CD1 LEU A 101 " =    2.523
peak=   -3.527 closest distance to " O   HOH Z 275 " =    1.419
peak=   -3.517 closest distance to " O   HOH Z 211 " =    1.586
peak=   -3.514 closest distance to " CB  PRO A 163 " =    2.563
peak=   -3.500 closest distance to " CG  PHE A 283 " =    2.828
peak=   -3.492 closest distance to " OG BSER A 134 " =    1.700
peak=   -3.492 closest distance to " O   HOH Z  60 " =    1.983
peak=   -3.491 closest distance to " O   HOH Z  38 " =    1.529
peak=   -3.472 closest distance to " CG1 VAL A 112 " =    2.636
peak=   -3.471 closest distance to " CA  GLY A 241 " =    3.043
peak=   -3.463 closest distance to " O   HOH Z 166 " =    1.495
peak=   -3.462 closest distance to " O   HOH Z 102 " =    1.638
peak=   -3.448 closest distance to " O   VAL A 189 " =    2.630
peak=   -3.447 closest distance to " O   SER A 210 " =    2.089
peak=   -3.445 closest distance to " O   VAL A 125 " =    2.278
peak=   -3.430 closest distance to " N   GLN A  58 " =    1.652
peak=   -3.423 closest distance to " CD2 LEU A 167 " =    1.697
peak=   -3.420 closest distance to " O   HOH Z  10 " =    1.563
peak=   -3.419 closest distance to " OD1 ASN A 187 " =    1.602
peak=   -3.415 closest distance to " CA  GLY A 203 " =    2.338
peak=   -3.411 closest distance to " O   HOH Z 435 " =    2.699
peak=   -3.410 closest distance to " NH2 ARG A  79 " =    1.959
peak=   -3.397 closest distance to " CG  PRO A 163 " =    2.526
peak=   -3.395 closest distance to " CB  PHE A 192 " =    1.841
peak=   -3.390 closest distance to " O   HOH Z 241 " =    1.281
peak=   -3.388 closest distance to " CD  GLN A  58 " =    1.173
peak=   -3.388 closest distance to " N   THR A 235 " =    1.364
peak=   -3.379 closest distance to " CG  ASP A  50 " =    2.415
peak=   -3.372 closest distance to " O   PRO A 198 " =    1.378
peak=   -3.371 closest distance to " CG2 VAL A 112 " =    2.531
peak=   -3.364 closest distance to " CZ  PHE A  59 " =    1.619
peak=   -3.353 closest distance to " CE BMET A  47 " =    1.921
peak=   -3.350 closest distance to " O   HOH Z 189 " =    1.887
peak=   -3.341 closest distance to " O   HOH Z 185 " =    2.355
peak=   -3.338 closest distance to " CB  ALA A 248 " =    2.008
peak=   -3.335 closest distance to " O   HOH Z 431 " =    1.747
peak=   -3.328 closest distance to " CE  MET A 105 " =    2.081
peak=   -3.327 closest distance to " N   SER A 276 " =    1.380
peak=   -3.325 closest distance to " O   GLY A 211 " =    1.547
peak=   -3.324 closest distance to " O   HOH Z 353 " =    2.212
peak=   -3.323 closest distance to " CG2 ILE A 263 " =    2.387
peak=   -3.318 closest distance to " O   HOH Z 207 " =    2.152
peak=   -3.316 closest distance to " CB  TYR A  15 " =    2.262
peak=   -3.312 closest distance to " CG  MET A 105 " =    0.966
peak=   -3.311 closest distance to " CD2 TYR A 293 " =    2.103
peak=   -3.306 closest distance to " N   THR A 157 " =    1.467
peak=   -3.299 closest distance to " O   HOH Z 198 " =    1.511
peak=   -3.295 closest distance to " CA  GLY A 133 " =    2.247
peak=   -3.295 closest distance to " ND2 ASN A 187 " =    1.730
peak=   -3.292 closest distance to " O   GLY A  80 " =    2.548
peak=   -3.288 closest distance to " CZ  TYR A 169 " =    1.678
peak=   -3.287 closest distance to " O   ASN A 301 " =    1.437
peak=   -3.286 closest distance to " O   GLY A 196 " =    1.136
peak=   -3.286 closest distance to " CB  ASP A 132 " =    2.289
peak=   -3.272 closest distance to " CB  ASP A 132 " =    2.286
peak=   -3.271 closest distance to " N   ASP A 171 " =    2.384
peak=   -3.270 closest distance to " O   LYS A 117 " =    1.754
peak=   -3.269 closest distance to " O   HOH Z 417 " =    2.822
peak=   -3.266 closest distance to " C   LEU A 222 " =    0.774
peak=   -3.263 closest distance to " O   HOH Z 128 " =    2.540
peak=   -3.263 closest distance to " O   HOH Z 372 " =    2.471
peak=   -3.262 closest distance to " O   HOH Z 113 " =    2.113
peak=   -3.261 closest distance to " O   HOH Z 234 " =    4.293
peak=   -3.261 closest distance to " O   HOH Z 139 " =    3.054
peak=   -3.260 closest distance to " C   ASN A 285 " =    2.538
peak=   -3.254 closest distance to " O   HOH Z 191 " =    5.562
peak=   -3.252 closest distance to " CA  ASN A 127 " =    1.039
peak=   -3.251 closest distance to " N   MET A 105 " =    2.675
peak=   -3.249 closest distance to " CG  ARG A  66 " =    2.401
peak=   -3.249 closest distance to " CD1 TYR A 247 " =    2.380
peak=   -3.245 closest distance to " ND2 ASN A  60 " =    1.447
peak=   -3.243 closest distance to " CD1 LEU A 101 " =    2.614
peak=   -3.240 closest distance to " O   HOH Z 388 " =    2.057
peak=   -3.238 closest distance to " CG  GLU A   2 " =    1.825
peak=   -3.236 closest distance to " NE2 GLN A 103 " =    1.675
peak=   -3.232 closest distance to " O   HOH Z 165 " =    1.973
peak=   -3.232 closest distance to " O   HOH Z 117 " =    4.579
peak=   -3.231 closest distance to " CZ  PHE A  38 " =    2.362
peak=   -3.229 closest distance to " O   HOH Z  90 " =    3.087
peak=   -3.226 closest distance to " O   GLN A 240 " =    2.404
peak=   -3.222 closest distance to " O   HOH Z 184 " =    1.649
peak=   -3.217 closest distance to " O   HOH Z 120 " =    4.270
peak=   -3.215 closest distance to " O   HOH Z 278 " =    1.988
peak=   -3.214 closest distance to " CE1 TYR A 169 " =    2.490
peak=   -3.213 closest distance to " N   PHE A  59 " =    2.135
peak=   -3.210 closest distance to " CD  ARG A 195 " =    5.096
peak=   -3.210 closest distance to " O   HOH Z 359 " =    3.058
peak=   -3.207 closest distance to " ND2BASN A 224 " =    1.635
peak=   -3.203 closest distance to " OD1 ASP A 191 " =    1.548
peak=   -3.202 closest distance to " O   MET A  40 " =    2.705
peak=   -3.199 closest distance to " CE3 TRP A 150 " =    2.161
peak=   -3.198 closest distance to " O   PRO A 198 " =    1.268
peak=   -3.194 closest distance to " CB  ALA A 227 " =    2.356
peak=   -3.186 closest distance to " O   HOH Z 310 " =    1.841
peak=   -3.183 closest distance to " NH2 ARG A 159 " =    2.385
peak=   -3.181 closest distance to " O   LEU A 167 " =    1.520
peak=   -3.177 closest distance to " NH1 ARG A 195 " =    2.628
peak=   -3.173 closest distance to " O   HOH Z 193 " =    1.744
peak=   -3.169 closest distance to " O   HOH Z 177 " =    1.622
peak=   -3.163 closest distance to " CG  ARG A 259 " =    2.539
peak=   -3.163 closest distance to " CA  SER A 135 " =    1.354
peak=   -3.162 closest distance to " C   LEU A 143 " =    1.142
peak=   -3.160 closest distance to " O   HOH Z 393 " =    1.497
peak=   -3.158 closest distance to " O   HOH Z 313 " =    1.873
peak=   -3.155 closest distance to " CB  TRP A  85 " =    2.505
peak=   -3.154 closest distance to " CD2 PHE A  61 " =    2.400
peak=   -3.151 closest distance to " CD1 ILE A 199 " =    2.512
peak=   -3.149 closest distance to " O   HOH Z  60 " =    1.911
peak=   -3.144 closest distance to " CG  GLU A 277 " =    1.132
peak=   -3.139 closest distance to " O   HOH Z 222 " =    1.533
peak=   -3.132 closest distance to " NE2 GLN A 194 " =    1.828
peak=   -3.120 closest distance to " O   HOH Z  37 " =    2.225
peak=   -3.115 closest distance to " OD2 ASP A 171 " =    2.268
peak=   -3.114 closest distance to " C   MET A 188 " =    1.398
peak=   -3.110 closest distance to " OE1 GLN A  77 " =    1.824
peak=   -3.109 closest distance to " CG  LEU A 228 " =    1.047
peak=   -3.106 closest distance to " CD2 TYR A 247 " =    2.259
peak=   -3.104 closest distance to " O   HOH Z 231 " =    1.404
peak=   -3.104 closest distance to " O   HOH Z 111 " =    2.457
peak=   -3.099 closest distance to " O   HOH Z 148 " =    1.730
peak=   -3.084 closest distance to " OG1 THR A 279 " =    1.333
peak=   -3.078 closest distance to " O   HOH Z 396 " =    1.748
peak=   -3.070 closest distance to " NE2 GLN A  88 " =    1.011
peak=   -3.069 closest distance to " CZ2 TRP A  92 " =    2.773
peak=   -3.047 closest distance to " N   ALA A 248 " =    1.592
peak=   -3.045 closest distance to " OXT GLY A 302 " =    3.401
peak=   -3.042 closest distance to " N   ALA A 248 " =    2.461
peak=   -3.019 closest distance to " CA  TYR A  68 " =    2.912
peak=   -3.016 closest distance to " O   HOH Z 417 " =    2.765
peak=   -3.001 closest distance to " CG2 ILE A  20 " =    2.810

================= 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    :  0.4407 0.4302   6.238003e+00   6.222954e+00
   1_bss:  0.4327 0.4209   6.234585e+00   6.215682e+00
   1_xyz:  0.3288 0.3620   6.042284e+00   6.106512e+00
   1_adp:  0.2727 0.3203   5.893135e+00   6.016594e+00
   1_occ:  0.2722 0.3208   5.892480e+00   6.017459e+00
   2_bss:  0.2690 0.3156   5.892921e+00   6.014739e+00
   2_xyz:  0.1897 0.2379   5.593182e+00   5.774160e+00
   2_adp:  0.1749 0.2206   5.518546e+00   5.708515e+00
   2_occ:  0.1748 0.2206   5.518037e+00   5.708431e+00
   3_bss:  0.1736 0.2186   5.518425e+00   5.707325e+00
   3_xyz:  0.1360 0.1817   5.309363e+00   5.531715e+00
   3_adp:  0.1264 0.1727   5.252583e+00   5.483638e+00
   3_occ:  0.1263 0.1725   5.252199e+00   5.483342e+00
   4_bss:  0.1267 0.1727   5.253169e+00   5.484239e+00
   4_xyz:  0.1171 0.1641   5.191737e+00   5.433453e+00
   4_adp:  0.1168 0.1616   5.183271e+00   5.417598e+00
   4_occ:  0.1168 0.1614   5.182757e+00   5.417153e+00
   5_bss:  0.1168 0.1614   5.182731e+00   5.417156e+00
   5_xyz:  0.1109 0.1584   5.148734e+00   5.396931e+00
   5_adp:  0.1094 0.1598   5.148614e+00   5.405386e+00
   5_occ:  0.1094 0.1598   5.148731e+00   5.405592e+00
   5_bss:  0.1093 0.1598   5.148793e+00   5.405632e+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:  0.300  20.000   8.447   8.054   7.792   0.000   0.000   0.000
   1_xyz:  0.300  20.000   8.447   8.054   7.792   0.000   0.000   0.000
   1_adp:  0.300  20.000   8.447   8.054   7.792   0.000   0.000   0.000
   1_occ:  0.300  20.000   8.447   8.054   7.792   0.000   0.000   0.000
   2_bss:  0.323  49.084   5.064   4.604   5.116   0.000   0.000   0.000
   2_xyz:  0.323  49.084   5.064   4.604   5.116   0.000   0.000   0.000
   2_adp:  0.323  49.084   5.064   4.604   5.116   0.000   0.000   0.000
   2_occ:  0.323  49.084   5.064   4.604   5.116   0.000   0.000   0.000
   3_bss:  0.341  49.084   3.469   3.398   3.981   0.000   0.000   0.000
   3_xyz:  0.341  49.084   3.469   3.398   3.981   0.000   0.000   0.000
   3_adp:  0.341  49.084   3.469   3.398   3.981   0.000   0.000   0.000
   3_occ:  0.341  49.084   3.469   3.398   3.981   0.000   0.000   0.000
   4_bss:  0.325  49.084   3.086   3.074   3.665   0.000   0.000   0.000
   4_xyz:  0.325  49.084   3.086   3.074   3.665   0.000   0.000   0.000
   4_adp:  0.325  49.084   3.086   3.074   3.665   0.000   0.000   0.000
   4_occ:  0.325  49.084   3.086   3.074   3.665   0.000   0.000   0.000
   5_bss:  0.322  48.039   3.086   3.074   3.665   0.000   0.000   0.000
   5_xyz:  0.322  48.039   3.086   3.074   3.665   0.000   0.000   0.000
   5_adp:  0.322  48.039   3.086   3.074   3.665   0.000   0.000   0.000
   5_occ:  0.322  48.039   3.086   3.074   3.665   0.000   0.000   0.000
   5_bss:  0.322  51.416  -0.207  -0.190   0.397   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  49.106 0.5328  0.6022    55133.472
   1_bss:  49.417 0.5265  0.7536    53158.573
   1_xyz:  39.780 0.6438  0.9003    36415.420
   1_adp:  33.361 0.7199  0.9947    27424.259
   1_occ:  33.420 0.7191  0.9934    27492.044
   2_bss:  33.213 0.7215  0.8917    27297.818
   2_xyz:  23.628 0.8252  0.9841    14711.738
   2_adp:  21.377 0.8487  1.0044    12667.461
   2_occ:  21.378 0.8486  1.0042    12665.354
   3_bss:  21.342 0.8490  0.9574    12631.169
   3_xyz:  17.061 0.8890  0.9794     8596.325
   3_adp:  16.017 0.8983  0.9823     7800.884
   3_occ:  16.008 0.8984  0.9822     7794.122
   4_bss:  16.017 0.8984  0.9698     7818.522
   4_xyz:  14.935 0.9076  0.9735     7007.331
   4_adp:  14.550 0.9109  0.9741     6800.566
   4_occ:  14.538 0.9110  0.9741     6793.712
   5_bss:  14.538 0.9110  0.9740     6792.754
   5_xyz:  14.175 0.9138  0.9752     6530.816
   5_adp:  14.365 0.9123  0.9706     6620.425
   5_occ:  14.368 0.9123  0.9705     6622.516
   5_bss:  14.370 0.9122  0.9740     6622.991
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.3964e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.3964e+01
   1_xyz:   1.606  0.012  0.104 17.849  0.006  4.112   1.2741e-01
   1_adp:   1.606  0.012  0.104 17.849  0.006  4.112   1.2741e-01
   1_occ:   1.606  0.012  0.104 17.849  0.006  4.112   1.2741e-01
   2_bss:   1.606  0.012  0.104 17.849  0.006  4.112   1.2741e-01
   2_xyz:   0.950  0.006  0.069 15.915  0.004  4.127   5.8537e-02
   2_adp:   0.950  0.006  0.069 15.915  0.004  4.127   5.8537e-02
   2_occ:   0.950  0.006  0.069 15.915  0.004  4.127   5.8537e-02
   3_bss:   0.950  0.006  0.069 15.915  0.004  4.127   5.8537e-02
   3_xyz:   1.028  0.007  0.078 15.638  0.003  4.115   6.2558e-02
   3_adp:   1.028  0.007  0.078 15.638  0.003  4.115   6.2558e-02
   3_occ:   1.028  0.007  0.078 15.638  0.003  4.115   6.2558e-02
   4_bss:   1.028  0.007  0.078 15.638  0.003  4.115   6.2558e-02
   4_xyz:   1.051  0.008  0.084 15.755  0.004  4.119   6.7170e-02
   4_adp:   1.051  0.008  0.084 15.755  0.004  4.119   6.7170e-02
   4_occ:   1.051  0.008  0.084 15.755  0.004  4.119   6.7170e-02
   5_bss:   1.051  0.008  0.084 15.755  0.004  4.119   6.7170e-02
   5_xyz:   1.163  0.011  0.095 15.799  0.005  4.122   8.1795e-02
   5_adp:   1.163  0.011  0.095 15.799  0.005  4.122   8.1795e-02
   5_occ:   1.163  0.011  0.095 15.799  0.005  4.122   8.1795e-02
   5_bss:   1.163  0.011  0.095 15.799  0.005  4.122   8.1795e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9971e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9971e+00
   1_xyz:  14.237  0.153  0.469 85.931  0.045  2.293   9.5808e-02
   1_adp:  14.237  0.153  0.469 85.931  0.045  2.293   9.5808e-02
   1_occ:  14.237  0.153  0.469 85.931  0.045  2.293   9.5808e-02
   2_bss:  14.237  0.153  0.469 85.931  0.045  2.293   9.5808e-02
   2_xyz:   6.153  0.043  0.234 88.991  0.033  2.330   5.0947e-02
   2_adp:   6.153  0.043  0.234 88.991  0.033  2.330   5.0947e-02
   2_occ:   6.153  0.043  0.234 88.991  0.033  2.330   5.0947e-02
   3_bss:   6.153  0.043  0.234 88.991  0.033  2.330   5.0947e-02
   3_xyz:   7.478  0.056  0.455 81.284  0.039  2.399   3.8367e-02
   3_adp:   7.478  0.056  0.455 81.284  0.039  2.399   3.8367e-02
   3_occ:   7.478  0.056  0.455 81.284  0.039  2.399   3.8367e-02
   4_bss:   7.478  0.056  0.455 81.284  0.039  2.399   3.8367e-02
   4_xyz:   8.164  0.059  0.540 84.118  0.039  2.331   4.6606e-02
   4_adp:   8.164  0.059  0.540 84.118  0.039  2.331   4.6606e-02
   4_occ:   8.164  0.059  0.540 84.118  0.039  2.331   4.6606e-02
   5_bss:   8.164  0.059  0.540 84.118  0.039  2.331   4.6606e-02
   5_xyz:   7.382  0.054  0.707 82.767  0.043  2.293   6.4216e-02
   5_adp:   7.382  0.054  0.707 82.767  0.043  2.293   6.4216e-02
   5_occ:   7.382  0.054  0.707 82.767  0.043  2.293   6.4216e-02
   5_bss:   7.382  0.054  0.707 82.767  0.043  2.293   6.4216e-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:  52.32   0.00  10.38  48.03   0.00   7.51  52.32   0.00  26.00
   1_occ:  52.32   0.00  10.38  48.03   0.00   7.51  52.32   0.00  26.00
   2_bss:  52.32   0.00  10.38  48.03   0.00   7.51  52.32   0.00  26.00
   2_xyz:  52.32   0.00  10.38  48.03   0.00   7.51  52.32   0.00  26.00
   2_adp:  87.73   0.00  10.97  87.73   0.00   7.52  55.72   1.24  29.74
   2_occ:  87.73   0.00  10.97  87.73   0.00   7.52  55.72   1.24  29.74
   3_bss:  87.73   0.00  10.97  87.73   0.00   7.52  55.72   1.24  29.74
   3_xyz:  87.73   0.00  10.97  87.73   0.00   7.52  55.72   1.24  29.74
   3_adp:  77.66   0.00  12.22  76.24   0.00   7.83  77.66   0.69  36.15
   3_occ:  77.66   0.00  12.22  76.24   0.00   7.83  77.66   0.69  36.15
   4_bss:  77.66   0.00  12.22  76.24   0.00   7.83  77.66   0.69  36.15
   4_xyz:  77.66   0.00  12.22  76.24   0.00   7.83  77.66   0.69  36.15
   4_adp:  76.85   0.00  11.91  76.85   0.00   7.70  74.55   0.95  34.89
   4_occ:  76.85   0.00  11.91  76.85   0.00   7.70  74.55   0.95  34.89
   5_bss:  76.85   0.00  11.91  76.85   0.00   7.70  74.55   0.95  34.89
   5_xyz:  76.85   0.00  11.91  76.85   0.00   7.70  74.55   0.95  34.89
   5_adp:  83.96   0.00  12.00  83.96   0.00   7.71  79.58   1.06  35.39
   5_occ:  83.96   0.00  12.00  83.96   0.00   7.71  79.58   1.06  35.39
   5_bss:  87.34   3.38  15.38  87.34   3.38  11.09  82.96   4.44  38.77
------------------------------------------------------------------------
 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:    1.195    0.017    0.410
   1_adp:    1.195    0.017    0.410
   1_occ:    1.195    0.017    0.410
   2_bss:    1.195    0.017    0.410
   2_xyz:    1.508    0.019    0.517
   2_adp:    1.508    0.019    0.517
   2_occ:    1.508    0.019    0.517
   3_bss:    1.508    0.019    0.517
   3_xyz:    1.502    0.018    0.566
   3_adp:    1.502    0.018    0.566
   3_occ:    1.502    0.018    0.566
   4_bss:    1.502    0.018    0.566
   4_xyz:    1.571    0.026    0.589
   4_adp:    1.571    0.026    0.589
   4_occ:    1.571    0.026    0.589
   5_bss:    1.571    0.026    0.589
   5_xyz:    1.625    0.021    0.600
   5_adp:    1.625    0.021    0.600
   5_occ:    1.625    0.021    0.600
   5_bss:    1.625    0.021    0.600
------------------------------------------------------------------------

CPU time actual refinement: 339.39


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1037/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_1037/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1037/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1037/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1037/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 339.24 
  Macro-tasks:
    bulk solvent and scale       = 43.05  
    individual site refinement   = 138.26 
    weights calculation          = 32.92  
    collect and process          = 6.70   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 221.07 
  Micro-tasks:
    mask                            = 1.72   
    f_calc                          = 102.76 
    alpha_beta                      = 8.45   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 113.78 
    fmodel                         = 7.88   
    r_factors                      = 0.23   
    phase_errors                   = 10.84  
    foms                           = 0.18   
    TOTAL for micro-tasks          = 247.02 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.737 micro seconds
Total CPU time: 5.88 minutes
from_scatterers_fft:    660 calls, 102.43 s
gradients_fft:          605 calls, 100.12 s

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

# Date 2008-01-16 Time 03:02:33 PST -0800 (1200481353.97 s)
Start R-work = 0.4407, R-free = 0.4302 (no bulk solvent and anisotropic scale)
Final R-work = 0.1262, R-free = 0.1754 (no bulk solvent and anisotropic scale)

Start R-work = 0.4327, R-free = 0.4209
Final R-work = 0.1093, R-free = 0.1598