# Date 2008-01-16 Time 02:51:32 PST -0800 (1200480692.43 s)
#phil __OFF__

Command line arguments: "../1005.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 18947
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1005

-------------------------------------------------------------------------------
  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, 46.4607, 85.9581, 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: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 46.4607, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1358 1.98157
Completeness in resolution range: 0.959728
Completeness with d_max=infinity: 0.956868

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1358
                             d_min =   1.9816

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, 46.4607, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1358 1.98157
Completeness in resolution range: 0.959728
Completeness with d_max=infinity: 0.956868

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1362 -  4.2408 [2136/2162]  1926   210   9.8%
  bin  2:  4.2408 -  3.3784 [2067/2087]  1857   210  10.2%
  bin  3:  3.3784 -  2.9549 [2032/2051]  1828   204  10.0%
  bin  4:  2.9549 -  2.6864 [2014/2044]  1814   200   9.9%
  bin  5:  2.6864 -  2.4948 [2017/2036]  1818   199   9.9%
  bin  6:  2.4948 -  2.3482 [1991/2016]  1784   207  10.4%
  bin  7:  2.3482 -  2.2310 [1973/2001]  1778   195   9.9%
  bin  8:  2.2310 -  2.1342 [1981/2017]  1783   198  10.0%
  bin  9:  2.1342 -  2.0522 [1959/2001]  1765   194   9.9%
  bin 10:  2.0522 -  1.9816 [1419/1996]  1277   142  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1005/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: 19
        2.42 -     3.04: 2188
        3.04 -     3.66: 4705
        3.66 -     4.28: 9067
        4.28 -     4.90: 12307
  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 204 " - " O   HOH Z 296 "  2.187 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.195 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 201 " - " O   HOH Z 349 "  2.231 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28281 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_1005/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1005/model_refine_001.geo

CPU time processing inputs: 9.18


============================ 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 46.4607 85.95805 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 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4516   r_free= 0.4367   ksol= 0.00   Bsol= 0.00   scale= 0.811    |
|                                                                             |
| 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:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.249790                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1362 -  4.7303 0.99   1392  156 0.3816 0.3757      6.5507      6.5247|
|  2:  4.7303 -  3.7738 0.99   1338  146 0.3540 0.3654      6.7151      6.6846|
|  3:  3.7738 -  3.3024 0.99   1321  144 0.3955 0.3600      6.5907      6.6268|
|  4:  3.3024 -  3.0030 0.99   1307  153 0.4273 0.3880      6.4893      6.4191|
|  5:  3.0030 -  2.7892 0.99   1295  142 0.4792 0.4825      6.3399      6.3614|
|  6:  2.7892 -  2.6256 0.99   1293  142 0.4720 0.4677       6.248      6.1868|
|  7:  2.6256 -  2.4948 0.99   1297  140 0.5046 0.4895      6.2401      6.2389|
|  8:  2.4948 -  2.3866 0.98   1253  144 0.5007 0.4295      6.1577      6.1258|
|  9:  2.3866 -  2.2950 0.98   1290  148 0.4783 0.4813      6.0968      6.1166|
| 10:  2.2950 -  2.2161 1.00   1279  138 0.5099 0.4730      6.0977      6.0793|
| 11:  2.2161 -  2.1470 0.98   1270  136 0.5100 0.4714      6.0335      5.9982|
| 12:  2.1470 -  2.0858 0.98   1251  145 0.4906 0.5620       5.967      6.0242|
| 13:  2.0858 -  2.0310 1.00   1284  137 0.5314 0.5104      5.8838      5.8079|
| 14:  2.0310 -  1.9816 0.59    760   88 0.5321 0.4663      5.8537      5.7861|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1362 -  4.7303  1392   156  0.71  33.50   0.80     0.75      67719.45|
|  2:  4.7303 -  3.7738  1338   146  0.76  30.22   0.90     0.82      84254.79|
|  3:  3.7738 -  3.3024  1321   144  0.68  37.19   0.87     0.79      87031.42|
|  4:  3.3024 -  3.0030  1307   153  0.62  42.25   0.82     0.71      77809.07|
|  5:  3.0030 -  2.7892  1295   142  0.51  51.28   0.75     0.60      68438.47|
|  6:  2.7892 -  2.6256  1293   142  0.48  53.83   0.75     0.54      62700.88|
|  7:  2.6256 -  2.4948  1297   140  0.45  55.70   0.75     0.51      57619.53|
|  8:  2.4948 -  2.3866  1253   144  0.45  55.88   0.74     0.53      51286.33|
|  9:  2.3866 -  2.2950  1290   148  0.48  53.52   0.74     0.53      43878.83|
| 10:  2.2950 -  2.2161  1279   138  0.46  55.32   0.77     0.53      40588.81|
| 11:  2.2161 -  2.1470  1270   136  0.43  57.50   0.77     0.51      40197.74|
| 12:  2.1470 -  2.0858  1251   145  0.40  60.10   0.78     0.48      39830.53|
| 13:  2.0858 -  2.0310  1284   137  0.37  62.32   0.73     0.47      34740.52|
| 14:  2.0310 -  1.9816   760    88  0.44  57.38   0.71     0.47      25878.62|
|alpha:            min =        0.47 max =            0.82 mean =         0.59|
|beta:             min =    25878.62 max =        87031.42 mean =     57063.42|
|figures of merit: min =        0.00 max =            1.00 mean =         0.52|
|phase err.(work): min =        0.00 max =           89.99 mean =        49.99|
|phase err.(test): min =        0.00 max =           89.98 mean =        50.06|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.008967             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.556   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.806475              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.722   (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:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      170 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      684 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1505 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2650 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3924 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5056 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6563 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7730 |
|-----------------------------------------------------------------------------|
|-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 |       53.744 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.697 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.921)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.921)------------------------------------------|
|    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 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4583   r_free= 0.4433   ksol= 0.00   Bsol= 0.00   scale= 0.780    |
|                                                                             |
| 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:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.253439                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4429   r_free= 0.4271   ksol= 0.34   Bsol= 13.86   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.77,8.93,7.62,0.00,0.00,0.00); trace/3= 8.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.243552                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.080891              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.277   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.789347              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.082   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4429      final r-factor (work) = 0.3432          |
| start r-factor (free) = 0.4271      final r-factor (free) = 0.3658          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 82.1407 = 9.08 * 0.50 * 6.2541 + 1.00 * 53.7441                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.9060 = 9.08 * 0.50 * 6.1178 + 1.00 * 0.1285                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3432      final r-factor (work) = 0.2879          |
| start r-factor (free) = 0.3658      final r-factor (free) = 0.3322          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8438 = 0.79 * 1.00 * 6.1178 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7338 = 0.79 * 1.00 * 5.9807 + 1.00 * 0.0129                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.921)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    70.30   11.36    None  None   None       |
|    all(noH): 2823   0      0.00    70.30   11.36    None  None   None       |
|    Sol.    : 438    0      0.00    70.30   27.26    None  None   None       |
|    Mac.    : 2385   0      0.00    68.94   8.44     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 -   7.030: 1287   |   5:    35.152 -  42.182:   75        |
|      1:     7.030 -  14.061:  771   |   6:    42.182 -  49.213:   40        |
|      2:    14.061 -  21.091:  312   |   7:    49.213 -  56.243:   25        |
|      3:    21.091 -  28.122:  184   |   8:    56.243 -  63.273:    6        |
|      4:    28.122 -  35.152:  119   |   9:    63.273 -  70.304:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2879 r_free = 0.3322             target_work(ml) = 5.940         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2875 r_free = 0.3322             target_work(ml) = 5.939         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2875   r_free= 0.3322   ksol= 0.34   Bsol= 13.86   scale= 1.095   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.77,8.93,7.62,0.00,0.00,0.00); trace/3= 8.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.939058                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2831   r_free= 0.3259   ksol= 0.36   Bsol= 50.00   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.19,4.81,4.54,0.00,0.00,0.00); trace/3= 4.85                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.936938                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.342185              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.491   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.408559              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.138  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2831      final r-factor (work) = 0.1814          |
| start r-factor (free) = 0.3259      final r-factor (free) = 0.2305          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.0983 = 6.34 * 0.50 * 5.9823 + 1.00 * 0.1280                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.3384 = 6.34 * 0.50 * 5.7584 + 1.00 * 0.0781                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1814      final r-factor (work) = 0.1576          |
| start r-factor (free) = 0.2305      final r-factor (free) = 0.2058          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3654 = 0.41 * 1.00 * 5.7584 + 1.00 * 0.0128                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2489 = 0.41 * 1.00 * 5.4777 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.921)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    71.63   11.72    None  None   None       |
|    all(noH): 2823   0      0.00    71.63   11.72    None  None   None       |
|    Sol.    : 438    0      0.64    69.88   33.00    None  None   None       |
|    Mac.    : 2385   0      0.00    71.63   7.81     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.163: 1490   |   5:    35.815 -  42.978:  115        |
|      1:     7.163 -  14.326:  665   |   6:    42.978 -  50.141:   75        |
|      2:    14.326 -  21.489:  209   |   7:    50.141 -  57.304:   40        |
|      3:    21.489 -  28.652:  109   |   8:    57.304 -  64.467:   11        |
|      4:    28.652 -  35.815:  104   |   9:    64.467 -  71.629:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1576 r_free = 0.2058             target_work(ml) = 5.423         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1575 r_free = 0.2057             target_work(ml) = 5.422         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1575   r_free= 0.2057   ksol= 0.36   Bsol= 50.00   scale= 1.040   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.19,4.81,4.54,0.00,0.00,0.00); trace/3= 4.85                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.422240                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1561   r_free= 0.2032   ksol= 0.34   Bsol= 50.00   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.49,2.98,3.86,0.00,0.00,0.00); trace/3= 3.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.419488                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.672425              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.506   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.981403              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.197  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1561      final r-factor (work) = 0.1351          |
| start r-factor (free) = 0.2032      final r-factor (free) = 0.1792          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6670 = 1.67 * 0.50 * 5.4877 + 1.00 * 0.0781                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5331 = 1.67 * 0.50 * 5.3566 + 1.00 * 0.0538                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1351      final r-factor (work) = 0.1294          |
| start r-factor (free) = 0.1792      final r-factor (free) = 0.1750          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2679 = 0.98 * 1.00 * 5.3566 + 1.00 * 0.0109                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1893 = 0.98 * 1.00 * 5.2730 + 1.00 * 0.0144                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.921)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.79   12.53    None  None   None       |
|    all(noH): 2823   0      0.00    84.79   12.53    None  None   None       |
|    Sol.    : 438    0      1.01    84.79   36.90    None  None   None       |
|    Mac.    : 2385   0      0.00    82.15   8.05     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 -   8.479: 1673   |   5:    42.396 -  50.875:   83        |
|      1:     8.479 -  16.958:  575   |   6:    50.875 -  59.354:   76        |
|      2:    16.958 -  25.437:  155   |   7:    59.354 -  67.833:   30        |
|      3:    25.437 -  33.917:  108   |   8:    67.833 -  76.312:   12        |
|      4:    33.917 -  42.396:  103   |   9:    76.312 -  84.791:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1294 r_free = 0.1750             target_work(ml) = 5.262         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1294 r_free = 0.1750             target_work(ml) = 5.262         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1294   r_free= 0.1750   ksol= 0.34   Bsol= 50.00   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.49,2.98,3.86,0.00,0.00,0.00); trace/3= 3.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.261525                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1293   r_free= 0.1748   ksol= 0.33   Bsol= 49.97   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.08,2.63,3.73,0.00,0.00,0.00); trace/3= 3.14                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.260736                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.398667              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 131.094  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.190050              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 117.247  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1293      final r-factor (work) = 0.1147          |
| start r-factor (free) = 0.1748      final r-factor (free) = 0.1629          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0142 = 3.40 * 0.50 * 5.2728 + 1.00 * 0.0539                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9280 = 3.40 * 0.50 * 5.2089 + 1.00 * 0.0764                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1147      final r-factor (work) = 0.1147          |
| start r-factor (free) = 0.1629      final r-factor (free) = 0.1601          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0039 = 0.19 * 1.00 * 5.2089 + 1.00 * 0.0139                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9935 = 0.19 * 1.00 * 5.1746 + 1.00 * 0.0100                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.921)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.58   11.83    None  None   None       |
|    all(noH): 2823   0      0.00    81.58   11.83    None  None   None       |
|    Sol.    : 438    0      1.61    78.13   33.74    None  None   None       |
|    Mac.    : 2385   0      0.00    81.58   7.81     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.159: 1689   |   5:    40.792 -  48.951:   88        |
|      1:     8.159 -  16.317:  584   |   6:    48.951 -  57.109:   56        |
|      2:    16.317 -  24.475:  140   |   7:    57.109 -  65.268:   23        |
|      3:    24.475 -  32.634:  138   |   8:    65.268 -  73.426:    8        |
|      4:    32.634 -  40.792:   91   |   9:    73.426 -  81.585:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1147 r_free = 0.1601             target_work(ml) = 5.163         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1147 r_free = 0.1598             target_work(ml) = 5.162         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1147   r_free= 0.1598   ksol= 0.33   Bsol= 49.97   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.08,2.63,3.73,0.00,0.00,0.00); trace/3= 3.14                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.161955                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1148   r_free= 0.1593   ksol= 0.33   Bsol= 49.97   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.89,2.48,3.65,0.00,0.00,0.00); trace/3= 3.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.161669                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.061526              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 152.518  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.198433              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.325  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1148      final r-factor (work) = 0.1116          |
| start r-factor (free) = 0.1593      final r-factor (free) = 0.1574          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9964 = 3.06 * 0.50 * 5.1739 + 1.00 * 0.0763                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9559 = 3.06 * 0.50 * 5.1502 + 1.00 * 0.0721                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1116      final r-factor (work) = 0.1116          |
| start r-factor (free) = 0.1574      final r-factor (free) = 0.1576          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0319 = 0.20 * 1.00 * 5.1502 + 1.00 * 0.0099                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0313 = 0.20 * 1.00 * 5.1429 + 1.00 * 0.0108                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.921)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.77   11.55    None  None   None       |
|    all(noH): 2823   0      0.00    80.77   11.55    None  None   None       |
|    Sol.    : 438    0      1.89    74.34   32.44    None  None   None       |
|    Mac.    : 2385   0      0.00    80.77   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 -   8.078: 1680   |   5:    40.387 -  48.465:   91        |
|      1:     8.078 -  16.155:  590   |   6:    48.465 -  56.542:   42        |
|      2:    16.155 -  24.232:  147   |   7:    56.542 -  64.620:   14        |
|      3:    24.232 -  32.310:  134   |   8:    64.620 -  72.697:    6        |
|      4:    32.310 -  40.387:  114   |   9:    72.697 -  80.775:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1116 r_free = 0.1576             target_work(ml) = 5.144         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1116 r_free = 0.1575             target_work(ml) = 5.143         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1116   r_free= 0.1575   ksol= 0.33   Bsol= 49.97   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.89,2.48,3.65,0.00,0.00,0.00); trace/3= 3.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.143367                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1362 -  4.7303 0.99   1392  156 0.0994 0.1281      5.3823      5.5275|
|  2:  4.7303 -  3.7738 0.99   1338  146 0.0878 0.1160      5.4585      5.6427|
|  3:  3.7738 -  3.3024 0.99   1321  144 0.1073 0.1546      5.4808      5.8757|
|  4:  3.3024 -  3.0030 0.99   1307  153 0.1184 0.1573      5.4457      5.5793|
|  5:  3.0030 -  2.7892 0.99   1295  142 0.1323 0.1762      5.3246      5.5757|
|  6:  2.7892 -  2.6256 0.99   1293  142 0.1196 0.1769       5.196      5.4481|
|  7:  2.6256 -  2.4948 0.99   1297  140 0.1264 0.1573      5.1742      5.3359|
|  8:  2.4948 -  2.3866 0.98   1253  144 0.1160 0.1790      5.0541      5.3782|
|  9:  2.3866 -  2.2950 0.98   1290  148 0.1189 0.1714      5.0512      5.2903|
| 10:  2.2950 -  2.2161 1.00   1279  138 0.1120 0.1799      4.9545      5.2559|
| 11:  2.2161 -  2.1470 0.98   1270  136 0.1132 0.1751      4.9511      5.2532|
| 12:  2.1470 -  2.0858 0.98   1251  145 0.1075 0.1636      4.8611      5.1398|
| 13:  2.0858 -  2.0310 1.00   1284  137 0.1156 0.1732      4.7751      5.0573|
| 14:  2.0310 -  1.9816 0.59    760   88 0.1003 0.1549       4.623      4.8488|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1362 -  4.7303  1392   156  0.94   9.00   0.98     0.96       7008.91|
|  2:  4.7303 -  3.7738  1338   146  0.95   8.15   1.01     1.00       9307.01|
|  3:  3.7738 -  3.3024  1321   144  0.93  11.40   1.02     1.02      10475.67|
|  4:  3.3024 -  3.0030  1307   153  0.92  13.61   1.00     0.97      10268.32|
|  5:  3.0030 -  2.7892  1295   142  0.90  15.99   0.99     0.97       8210.14|
|  6:  2.7892 -  2.6256  1293   142  0.90  15.60   0.98     0.96       6890.31|
|  7:  2.6256 -  2.4948  1297   140  0.91  15.38   0.99     0.97       6192.14|
|  8:  2.4948 -  2.3866  1253   144  0.91  15.35   0.98     0.96       5146.57|
|  9:  2.3866 -  2.2950  1290   148  0.91  15.64   1.00     0.98       5162.78|
| 10:  2.2950 -  2.2161  1279   138  0.91  15.40   1.01     0.97       4327.17|
| 11:  2.2161 -  2.1470  1270   136  0.90  15.96   0.99     0.94       4319.22|
| 12:  2.1470 -  2.0858  1251   145  0.91  14.85   1.02     1.02       3872.58|
| 13:  2.0858 -  2.0310  1284   137  0.90  15.84   1.01     1.00       3205.92|
| 14:  2.0310 -  1.9816   760    88  0.92  13.93   0.99     0.96       2349.31|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2349.31 max =        10475.67 mean =      6348.03|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.82 mean =        13.95|
|phase err.(test): min =        0.00 max =           87.34 mean =        13.45|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1116   r_free= 0.1574   ksol= 0.33   Bsol= 52.97   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.12,-0.52,0.64,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.143407                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1116   r_free= 0.1574   ksol= 0.33   Bsol= 52.97   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.12,-0.52,0.64,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.143407                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1362 -  4.7303 0.99   1392  156 0.0994 0.1281      5.3828      5.5279|
|  2:  4.7303 -  3.7738 0.99   1338  146 0.0877 0.1160      5.4584      5.6424|
|  3:  3.7738 -  3.3024 0.99   1321  144 0.1073 0.1546      5.4807      5.8756|
|  4:  3.3024 -  3.0030 0.99   1307  153 0.1184 0.1573      5.4457      5.5793|
|  5:  3.0030 -  2.7892 0.99   1295  142 0.1323 0.1762      5.3246      5.5757|
|  6:  2.7892 -  2.6256 0.99   1293  142 0.1196 0.1769      5.1961      5.4481|
|  7:  2.6256 -  2.4948 0.99   1297  140 0.1264 0.1573      5.1743      5.3359|
|  8:  2.4948 -  2.3866 0.98   1253  144 0.1160 0.1790      5.0541      5.3783|
|  9:  2.3866 -  2.2950 0.98   1290  148 0.1189 0.1714      5.0512      5.2903|
| 10:  2.2950 -  2.2161 1.00   1279  138 0.1120 0.1799      4.9545      5.2559|
| 11:  2.2161 -  2.1470 0.98   1270  136 0.1132 0.1751      4.9511      5.2532|
| 12:  2.1470 -  2.0858 0.98   1251  145 0.1075 0.1636      4.8611      5.1398|
| 13:  2.0858 -  2.0310 1.00   1284  137 0.1156 0.1732      4.7752      5.0573|
| 14:  2.0310 -  1.9816 0.59    760   88 0.1003 0.1549      4.6231      4.8488|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1362 -  4.7303  1392   156  0.94   9.00   0.98     0.96       7020.16|
|  2:  4.7303 -  3.7738  1338   146  0.95   8.16   1.01     1.00       9310.03|
|  3:  3.7738 -  3.3024  1321   144  0.93  11.40   1.02     1.02      10471.99|
|  4:  3.3024 -  3.0030  1307   153  0.92  13.61   1.00     0.97      10267.93|
|  5:  3.0030 -  2.7892  1295   142  0.90  15.99   0.99     0.97       8210.48|
|  6:  2.7892 -  2.6256  1293   142  0.90  15.60   0.98     0.96       6890.84|
|  7:  2.6256 -  2.4948  1297   140  0.91  15.38   0.99     0.97       6192.62|
|  8:  2.4948 -  2.3866  1253   144  0.91  15.35   0.98     0.96       5146.86|
|  9:  2.3866 -  2.2950  1290   148  0.91  15.64   1.00     0.98       5162.98|
| 10:  2.2950 -  2.2161  1279   138  0.91  15.40   1.01     0.97       4327.31|
| 11:  2.2161 -  2.1470  1270   136  0.90  15.96   0.99     0.94       4319.35|
| 12:  2.1470 -  2.0858  1251   145  0.91  14.85   1.02     1.02       3872.69|
| 13:  2.0858 -  2.0310  1284   137  0.90  15.84   1.01     1.00       3206.01|
| 14:  2.0310 -  1.9816   760    88  0.92  13.93   0.99     0.96       2349.38|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2349.38 max =        10471.99 mean =      6349.01|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.82 mean =        13.95|
|phase err.(test): min =        0.00 max =           87.35 mean =        13.45|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.921)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.01    83.78   14.56    None  None   None       |
|    all(noH): 2823   0      3.01    83.78   14.56    None  None   None       |
|    Sol.    : 438    0      4.90    77.34   35.45    None  None   None       |
|    Mac.    : 2385   0      3.01    83.78   10.72    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:     3.007 -  11.085: 1680   |   5:    43.394 -  51.472:   91        |
|      1:    11.085 -  19.162:  590   |   6:    51.472 -  59.549:   42        |
|      2:    19.162 -  27.239:  147   |   7:    59.549 -  67.627:   14        |
|      3:    27.239 -  35.317:  134   |   8:    67.627 -  75.704:    6        |
|      4:    35.317 -  43.394:  114   |   9:    75.704 -  83.782:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 308         
Filter by distance & map next to the model:
   mapped sites are within: 0.416 - 4.746
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 301 from: 308
   mapped sites are within: 0.714 - 4.746

peak=   11.094 closest distance to " CB  VAL A 230 " =    1.478
peak=    6.147 closest distance to " NH2 ARG A  56 " =    2.166
peak=    6.094 closest distance to " CG  LEU A   5 " =    1.216
peak=    6.029 closest distance to " CG2 VAL A 296 " =    1.042
peak=    5.986 closest distance to " CD2 LEU A   5 " =    1.268
peak=    5.715 closest distance to " NE2 GLN A  11 " =    1.197
peak=    5.475 closest distance to " CG  LEU A 228 " =    1.173
peak=    5.334 closest distance to " CG  PRO A  54 " =    1.290
peak=    5.243 closest distance to " CB  VAL A 296 " =    1.153
peak=    5.131 closest distance to " O   HOH Z 144 " =    1.858
peak=    4.995 closest distance to " O   HOH Z 232 " =    2.325
peak=    4.951 closest distance to " CB  SER A  63 " =    1.295
peak=    4.898 closest distance to " CB  GLN A 183 " =    1.177
peak=    4.873 closest distance to " C   PRO A 198 " =    1.550
peak=    4.837 closest distance to " CB  GLN A 223 " =    1.437
peak=    4.777 closest distance to " O   HOH Z 126 " =    1.860
peak=    4.732 closest distance to " CB  GLU A 152 " =    1.186
peak=    4.703 closest distance to " CD2 LEU A 228 " =    1.151
peak=    4.637 closest distance to " CB  VAL A 230 " =    1.207
peak=    4.593 closest distance to " CB  PRO A  54 " =    0.977
peak=    4.582 closest distance to " CB  SER A   3 " =    1.423
peak=    4.567 closest distance to " O   HOH Z 427 " =    2.825
peak=    4.542 closest distance to " O   HOH Z 236 " =    1.928
peak=    4.528 closest distance to " O   HOH Z 425 " =    1.475
peak=    4.486 closest distance to " O   HOH Z 298 " =    1.801
peak=    4.482 closest distance to " O   HOH Z 272 " =    1.892
peak=    4.415 closest distance to " CG  PRO A 213 " =    1.173
peak=    4.395 closest distance to " ND2 ASN A 187 " =    1.505
peak=    4.380 closest distance to " O   HOH Z 369 " =    2.049
peak=    4.370 closest distance to " CB  ASN A 148 " =    1.351
peak=    4.336 closest distance to " O   HOH Z 316 " =    3.062
peak=    4.331 closest distance to " O   HOH Z 193 " =    1.920
peak=    4.325 closest distance to " O   HOH Z 209 " =    2.345
peak=    4.258 closest distance to " O   HOH Z 193 " =    1.758
peak=    4.252 closest distance to " OD1 ASN A  69 " =    2.691
peak=    4.250 closest distance to " CB  ARG A  79 " =    1.426
peak=    4.210 closest distance to " O   HOH Z  61 " =    1.629
peak=    4.208 closest distance to " CG  PRO A 243 " =    1.111
peak=    4.189 closest distance to " O   HOH Z 126 " =    1.558
peak=    4.163 closest distance to " O   HOH Z   9 " =    2.116
peak=    4.144 closest distance to " CB  TRP A 266 " =    0.919
peak=    4.135 closest distance to " CD  ARG A  66 " =    2.429
peak=    4.117 closest distance to " O   HOH Z  55 " =    2.402
peak=    4.099 closest distance to " CB  ARG A 275 " =    0.894
peak=    4.081 closest distance to " O   HOH Z 368 " =    2.107
peak=    4.067 closest distance to " O   HOH Z 346 " =    1.635
peak=    4.065 closest distance to " O   HOH Z 234 " =    3.709
peak=    4.020 closest distance to " O   SER A  87 " =    2.324
peak=    4.017 closest distance to " O   HOH Z  78 " =    1.780
peak=    4.014 closest distance to " N   PHE A 130 " =    1.282
peak=    4.013 closest distance to " CB  ASN A  39 " =    0.851
peak=    4.012 closest distance to " CB  VAL A 265 " =    1.331
peak=    3.999 closest distance to " CG  LEU A 167 " =    1.221
peak=    3.972 closest distance to " O   HOH Z 403 " =    1.684
peak=    3.956 closest distance to " O   HOH Z   7 " =    1.265
peak=    3.948 closest distance to " O   HOH Z  30 " =    1.532
peak=    3.935 closest distance to " O   HOH Z 263 " =    1.606
peak=    3.930 closest distance to " O   HOH Z 303 " =    2.180
peak=    3.909 closest distance to " O   HOH Z 411 " =    3.730
peak=    3.892 closest distance to " CB  GLU A 128 " =    0.930
peak=    3.888 closest distance to " CB  SER A 216 " =    0.779
peak=    3.873 closest distance to " O   HOH Z   2 " =    1.668
peak=    3.873 closest distance to " CB  ASN A 142 " =    0.933
peak=    3.871 closest distance to " CB  ASN A 187 " =    0.990
peak=    3.867 closest distance to " O   HOH Z  10 " =    1.815
peak=    3.862 closest distance to " CA  ASN A 215 " =    1.164
peak=    3.860 closest distance to " O   HOH Z 193 " =    1.935
peak=    3.857 closest distance to " CB  SER A 212 " =    1.233
peak=    3.844 closest distance to " OD2 ASP A 286 " =    2.869
peak=    3.842 closest distance to " CA  ALA A  51 " =    0.998
peak=    3.829 closest distance to " CA  TYR A  30 " =    0.980
peak=    3.827 closest distance to " O   HOH Z 158 " =    3.145
peak=    3.822 closest distance to " CB  ASP A 140 " =    0.814
peak=    3.819 closest distance to " O   HOH Z 371 " =    2.780
peak=    3.806 closest distance to " NH2AARG A 190 " =    1.793
peak=    3.804 closest distance to " CD  ARG A 159 " =    0.733
peak=    3.780 closest distance to " O   HOH Z 132 " =    2.588
peak=    3.780 closest distance to " O   HOH Z 203 " =    1.751
peak=    3.777 closest distance to " O   HOH Z  88 " =    3.320
peak=    3.775 closest distance to " CG2 THR A 221 " =    1.034
peak=    3.774 closest distance to " CG  PRO A 198 " =    1.325
peak=    3.773 closest distance to " O   HOH Z 273 " =    2.760
peak=    3.771 closest distance to " O   HOH Z 248 " =    1.696
peak=    3.740 closest distance to " O   HOH Z 261 " =    2.148
peak=    3.735 closest distance to " CG2AVAL A  72 " =    1.609
peak=    3.710 closest distance to " CD1 LEU A 300 " =    1.172
peak=    3.707 closest distance to " O   HOH Z 133 " =    1.720
peak=    3.682 closest distance to " CZ  PHE A 218 " =    1.078
peak=    3.677 closest distance to " O   HOH Z  68 " =    2.122
peak=    3.674 closest distance to " O   HOH Z 280 " =    2.982
peak=    3.672 closest distance to " NH2 ARG A 156 " =    1.077
peak=    3.670 closest distance to " O   HOH Z 197 " =    3.235
peak=    3.665 closest distance to " O   HOH Z  97 " =    1.911
peak=    3.663 closest distance to " CB  LEU A 228 " =    1.169
peak=    3.660 closest distance to " ND2 ASN A 249 " =    1.929
peak=    3.658 closest distance to " CG  GLN A  88 " =    1.075
peak=    3.658 closest distance to " CD2 LEU A 255 " =    1.541
peak=    3.653 closest distance to " O   HOH Z  43 " =    1.832
peak=    3.652 closest distance to " CA  SER A  87 " =    0.902
peak=    3.648 closest distance to " O   HOH Z  61 " =    1.602
peak=    3.640 closest distance to " CA  LYS A 117 " =    1.169
peak=    3.635 closest distance to " O   HOH Z 171 " =    3.992
peak=    3.631 closest distance to " NH1AARG A 145 " =    1.168
peak=    3.626 closest distance to " O   HOH Z 437 " =    2.023
peak=    3.622 closest distance to " O   HOH Z   1 " =    1.818
peak=    3.618 closest distance to " CG  ARG A 138 " =    1.119
peak=    3.618 closest distance to " O   HOH Z  58 " =    1.658
peak=    3.616 closest distance to " CG BARG A 275 " =    1.482
peak=    3.613 closest distance to " O   HOH Z   1 " =    1.790
peak=    3.602 closest distance to " CB  TRP A 179 " =    1.509
peak=    3.601 closest distance to " CB  GLU A 277 " =    3.524
peak=    3.601 closest distance to " O   HOH Z  21 " =    1.697
peak=    3.598 closest distance to " NZ  LYS A 117 " =    3.285
peak=    3.595 closest distance to " CB  ASN A 224 " =    1.032
peak=    3.589 closest distance to " O   HOH Z 344 " =    2.879
peak=    3.587 closest distance to " CB  VAL A 250 " =    1.133
peak=    3.584 closest distance to " O   HOH Z 128 " =    2.018
peak=    3.573 closest distance to " CB  LEU A 143 " =    1.133
peak=    3.571 closest distance to " O   HOH Z 286 " =    2.323
peak=    3.568 closest distance to " O   HOH Z 145 " =    3.519
peak=    3.566 closest distance to " O   HOH Z 367 " =    2.328
peak=    3.553 closest distance to " O   HOH Z 135 " =    1.863
peak=    3.547 closest distance to " C   ALA A 299 " =    0.954
peak=    3.545 closest distance to " CB  VAL A 202 " =    1.533
peak=    3.534 closest distance to " ND1 HIS A  86 " =    1.669
peak=    3.527 closest distance to " CG2 VAL A 257 " =    0.922
peak=    3.525 closest distance to " O   HOH Z 189 " =    2.861
peak=    3.525 closest distance to " CD BLYS A 290 " =    1.147
peak=    3.514 closest distance to " O   HOH Z 175 " =    2.132
peak=    3.514 closest distance to " CA  ASP A 162 " =    0.986
peak=    3.513 closest distance to " CA  THR A 264 " =    0.761
peak=    3.508 closest distance to " CB  THR A 157 " =    1.155
peak=    3.507 closest distance to " O   HOH Z  63 " =    1.338
peak=    3.502 closest distance to " CD1 ILE A  33 " =    1.678
peak=    3.500 closest distance to " CB  THR A  82 " =    1.309
peak=    3.500 closest distance to " CB  GLN A  88 " =    1.249
peak=    3.497 closest distance to " CG1 VAL A 153 " =    0.944
peak=    3.490 closest distance to " O   HOH Z 148 " =    3.304
peak=    3.486 closest distance to " O   HOH Z 180 " =    2.095
peak=    3.477 closest distance to " O   HOH Z 366 " =    2.829
peak=    3.477 closest distance to " O   HOH Z 419 " =    1.830
peak=    3.475 closest distance to " CA  ALA A  21 " =    1.149
peak=    3.473 closest distance to " N   SER A 135 " =    1.321
peak=    3.470 closest distance to " CA  THR A 221 " =    0.902
peak=    3.469 closest distance to " O   HOH Z 410 " =    1.509
peak=    3.466 closest distance to " CB  ALA A 291 " =    1.395
peak=    3.463 closest distance to " CA  MET A  40 " =    1.115
peak=    3.459 closest distance to " O   HOH Z 291 " =    1.621
peak=    3.459 closest distance to " OG  SER A  22 " =    2.880
peak=    3.454 closest distance to " O   HOH Z 214 " =    1.912
peak=    3.452 closest distance to " CB  ALA A  34 " =    0.816
peak=    3.444 closest distance to " O   HOH Z 184 " =    1.470
peak=    3.444 closest distance to " O   HOH Z 112 " =    1.598
peak=    3.443 closest distance to " CB  ARG A 190 " =    1.642
peak=    3.441 closest distance to " CB  HIS A 108 " =    0.773
peak=    3.440 closest distance to " CE  LYS A  76 " =    0.896
peak=    3.440 closest distance to " N   ALA A   1 " =    2.137
peak=    3.438 closest distance to " O   HOH Z 271 " =    2.139
peak=    3.437 closest distance to " O   HOH Z 147 " =    1.766
peak=    3.436 closest distance to " OG BSER A 164 " =    2.253
peak=    3.435 closest distance to " CA  TYR A 116 " =    1.414
peak=    3.432 closest distance to " O   HOH Z   3 " =    1.813
peak=    3.431 closest distance to " CB  ALA A   9 " =    1.577
peak=    3.429 closest distance to " N   VAL A 126 " =    1.276
peak=    3.427 closest distance to " O   HOH Z 368 " =    3.628
peak=    3.420 closest distance to " CB  ARG A 139 " =    1.018
peak=    3.418 closest distance to " CD1 ILE A 106 " =    1.012
peak=    3.417 closest distance to " CB  ALA A 104 " =    0.714
peak=    3.411 closest distance to " CG1 ILE A  49 " =    1.371
peak=    3.408 closest distance to " CB  MET A  40 " =    0.828
peak=    3.406 closest distance to " CG  GLN A 278 " =    1.349
peak=    3.404 closest distance to " NE AARG A 275 " =    1.350
peak=    3.401 closest distance to " OG  SER A 206 " =    1.216
peak=    3.398 closest distance to " O   HOH Z 425 " =    1.935
peak=    3.396 closest distance to " O   HOH Z 126 " =    1.463
peak=    3.394 closest distance to " CD  LYS A 166 " =    1.309
peak=    3.391 closest distance to " CG1 ILE A  33 " =    1.306
peak=    3.386 closest distance to " O   HOH Z 303 " =    1.871
peak=    3.382 closest distance to " O   HOH Z 329 " =    3.870
peak=    3.379 closest distance to " N   SER A 146 " =    1.752
peak=    3.379 closest distance to " NH2BARG A 190 " =    1.685
peak=    3.376 closest distance to " O   HOH Z 409 " =    2.863
peak=    3.373 closest distance to " NE2 HIS A 207 " =    1.390
peak=    3.361 closest distance to " O   HOH Z 185 " =    2.152
peak=    3.356 closest distance to " O   HOH Z 350 " =    1.642
peak=    3.355 closest distance to " CZ  PHE A 192 " =    0.884
peak=    3.351 closest distance to " CB  ILE A 120 " =    1.297
peak=    3.348 closest distance to " CA  GLY A 267 " =    0.984
peak=    3.348 closest distance to " O   HOH Z 145 " =    1.696
peak=    3.346 closest distance to " CA  ALA A 295 " =    0.973
peak=    3.338 closest distance to " O   HOH Z 305 " =    3.427
peak=    3.328 closest distance to " CD1 LEU A   5 " =    1.350
peak=    3.328 closest distance to " NH2BARG A 145 " =    1.965
peak=    3.327 closest distance to " CZ3 TRP A 123 " =    1.374
peak=    3.327 closest distance to " O   HOH Z 302 " =    1.884
peak=    3.326 closest distance to " CA  ALA A 233 " =    1.166
peak=    3.323 closest distance to " CA  ALA A 158 " =    1.169
peak=    3.322 closest distance to " CD2 TRP A 179 " =    1.356
peak=    3.321 closest distance to " CB BVAL A  41 " =    1.287
peak=    3.318 closest distance to " O   HOH Z 345 " =    3.416
peak=    3.318 closest distance to " O   HOH Z 353 " =    2.637
peak=    3.317 closest distance to " O   HOH Z  40 " =    1.945
peak=    3.317 closest distance to " CA  TYR A 186 " =    1.499
peak=    3.313 closest distance to " OE2 GLU A  53 " =    2.109
peak=    3.312 closest distance to " O   HOH Z 313 " =    1.691
peak=    3.311 closest distance to " O   HOH Z 216 " =    2.657
peak=    3.311 closest distance to " CA  LEU A 282 " =    1.128
peak=    3.310 closest distance to " O  BHOH Z 338 " =    2.474
peak=    3.306 closest distance to " O   HOH Z 371 " =    1.755
peak=    3.305 closest distance to " CB  GLU A  46 " =    1.068
peak=    3.304 closest distance to " N   ARG A 156 " =    1.275
peak=    3.302 closest distance to " O   HOH Z 207 " =    1.754
peak=    3.298 closest distance to " CB  TRP A 150 " =    1.493
peak=    3.296 closest distance to " O   HOH Z  59 " =    1.937
peak=    3.295 closest distance to " CG2 ILE A  20 " =    1.591
peak=    3.295 closest distance to " O   HOH Z 411 " =    1.931
peak=    3.294 closest distance to " O   HOH Z 250 " =    1.374
peak=    3.293 closest distance to " O   HOH Z 422 " =    2.630
peak=    3.292 closest distance to " O   HOH Z  88 " =    2.682
peak=    3.289 closest distance to " O   HOH Z 227 " =    1.681
peak=    3.287 closest distance to " O   HOH Z 227 " =    2.132
peak=    3.287 closest distance to " OG BSER A 134 " =    3.005
peak=    3.282 closest distance to " O   HOH Z 435 " =    2.000
peak=    3.281 closest distance to " CB  ALA A   1 " =    4.746
peak=    3.271 closest distance to " CA  ILE A 234 " =    0.924
peak=    3.268 closest distance to " CB  ASN A 110 " =    1.099
peak=    3.265 closest distance to " CA  ALA A 291 " =    0.951
peak=    3.264 closest distance to " CA  VAL A  41 " =    0.910
peak=    3.263 closest distance to " O   HOH Z 116 " =    1.669
peak=    3.262 closest distance to " CB  GLN A 103 " =    1.003
peak=    3.261 closest distance to " O   HOH Z 383 " =    1.902
peak=    3.261 closest distance to " O   ALA A 158 " =    1.392
peak=    3.259 closest distance to " CD1 LEU A 228 " =    1.893
peak=    3.255 closest distance to " CB  MET A  47 " =    1.075
peak=    3.255 closest distance to " N   ASN A  39 " =    1.143
peak=    3.253 closest distance to " O   HOH Z 402 " =    1.431
peak=    3.251 closest distance to " CA  ARG A 195 " =    1.226
peak=    3.250 closest distance to " CG1 ILE A 151 " =    1.101
peak=    3.249 closest distance to " CD1 ILE A 263 " =    1.272
peak=    3.246 closest distance to " CE1 TYR A 186 " =    1.330
peak=    3.245 closest distance to " CG  MET A 185 " =    0.980
peak=    3.242 closest distance to " O   HOH Z 273 " =    1.614
peak=    3.242 closest distance to " O   HOH Z 423 " =    2.734
peak=    3.240 closest distance to " CG BARG A 102 " =    1.839
peak=    3.239 closest distance to " CB  GLN A 278 " =    0.835
peak=    3.235 closest distance to " N   SER A 134 " =    1.334
peak=    3.227 closest distance to " CB  SER A 245 " =    3.092
peak=    3.226 closest distance to " CB  SER A  62 " =    1.191
peak=    3.221 closest distance to " O   ASN A 209 " =    1.330
peak=    3.220 closest distance to " O   HOH Z 188 " =    2.003
peak=    3.218 closest distance to " CD  LYS A 119 " =    1.554
peak=    3.216 closest distance to " O   HOH Z 380 " =    1.685
peak=    3.216 closest distance to " O   HOH Z 141 " =    1.641
peak=    3.214 closest distance to " O   HOH Z 130 " =    2.184
peak=    3.213 closest distance to " O   HOH Z 423 " =    1.692
peak=    3.206 closest distance to " CB  ALA A 114 " =    1.319
peak=    3.203 closest distance to " OG  SER A  62 " =    2.951
peak=    3.199 closest distance to " CA  LYS A 290 " =    1.294
peak=    3.199 closest distance to " CG1 VAL A 174 " =    1.021
peak=    3.197 closest distance to " CG  MET A 185 " =    1.239
peak=    3.197 closest distance to " O   HOH Z 334 " =    1.490
peak=    3.197 closest distance to " O   HOH Z 151 " =    1.869
peak=    3.189 closest distance to " O   HOH Z 271 " =    2.565
peak=    3.186 closest distance to " ND1 HIS A  81 " =    1.759
peak=    3.183 closest distance to " O   HOH Z 173 " =    2.085
peak=    3.178 closest distance to " O   TYR A 116 " =    1.289
peak=    3.176 closest distance to " CB  ALA A 248 " =    0.985
peak=    3.174 closest distance to " O   HOH Z  85 " =    2.093
peak=    3.172 closest distance to " O   HOH Z  49 " =    2.459
peak=    3.172 closest distance to " O   HOH Z 109 " =    2.558
peak=    3.165 closest distance to " CA  ALA A 154 " =    1.021
peak=    3.165 closest distance to " O   HOH Z 327 " =    1.860
peak=    3.162 closest distance to " O   HOH Z 219 " =    2.238
peak=    3.159 closest distance to " O   HOH Z 285 " =    2.854
peak=    3.151 closest distance to " O   HOH Z 426 " =    1.748
peak=    3.151 closest distance to " O   MET A 105 " =    1.748
peak=    3.143 closest distance to " O   HOH Z 128 " =    2.263
peak=    3.136 closest distance to " O   GLN A 278 " =    1.530
peak=    3.136 closest distance to " CD  ARG A 219 " =    1.130
peak=    3.129 closest distance to " CA  VAL A 126 " =    0.852
peak=    3.127 closest distance to " O   SER A 164 " =    1.158
peak=    3.119 closest distance to " NH1 ARG A  56 " =    1.011
peak=    3.114 closest distance to " O   HOH Z 252 " =    1.666
peak=    3.112 closest distance to " CD  ARG A 138 " =    0.913
peak=    3.107 closest distance to " CA  ILE A 106 " =    0.755
peak=    3.103 closest distance to " CB  ASN A 173 " =    1.034
peak=    3.102 closest distance to " O   TRP A 274 " =    1.856
peak=    3.099 closest distance to " N   ASN A 127 " =    1.257
peak=    3.096 closest distance to " CB  LYS A 117 " =    1.225
peak=    3.095 closest distance to " CB  GLN A 205 " =    0.993
peak=    3.094 closest distance to " O   HOH Z 144 " =    1.715
peak=    3.093 closest distance to " CB  TYR A 116 " =    0.872
peak=    3.090 closest distance to " CG  GLN A 240 " =    3.535
peak=    3.089 closest distance to " CB  VAL A 268 " =    0.857
peak=    3.086 closest distance to " N   TYR A  15 " =    0.808
peak=    3.083 closest distance to " O   HOH Z 367 " =    3.588
peak=    3.077 closest distance to " O   HOH Z 294 " =    1.512
peak=    3.073 closest distance to " CG  GLN A  77 " =    2.129
peak=    3.065 closest distance to " NZ ALYS A 290 " =    1.001
peak=    3.065 closest distance to " O   HOH Z 163 " =    1.914
peak=    3.061 closest distance to " CG  ARG A 269 " =    1.787

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 199         
Filter by distance & map next to the model:
   mapped sites are within: 0.544 - 5.419
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 194 from: 199
   mapped sites are within: 0.720 - 5.419

peak=   -5.758 closest distance to " CG2 VAL A 230 " =    0.751
peak=   -4.596 closest distance to " CB  PRO A 243 " =    2.584
peak=   -4.461 closest distance to " O   HOH Z 290 " =    1.198
peak=   -4.326 closest distance to " CD  ARG A 156 " =    1.985
peak=   -4.281 closest distance to " O   HOH Z 231 " =    1.561
peak=   -4.224 closest distance to " CD  ARG A  14 " =    3.194
peak=   -4.172 closest distance to " CZ3 TRP A 179 " =    1.183
peak=   -4.165 closest distance to " O   HOH Z 231 " =    0.953
peak=   -4.046 closest distance to " O   HOH Z 266 " =    4.947
peak=   -4.023 closest distance to " CB  PRO A 163 " =    2.565
peak=   -3.958 closest distance to " CA  ASN A 110 " =    2.521
peak=   -3.937 closest distance to " O   VAL A  67 " =    2.549
peak=   -3.928 closest distance to " OG BSER A 134 " =    1.289
peak=   -3.915 closest distance to " O   HOH Z 435 " =    2.878
peak=   -3.914 closest distance to " CG1 VAL A 296 " =    1.425
peak=   -3.906 closest distance to " O   HOH Z 389 " =    1.946
peak=   -3.904 closest distance to " N   ALA A  43 " =    2.460
peak=   -3.864 closest distance to " O   HOH Z 351 " =    1.484
peak=   -3.833 closest distance to " OG  SER A  87 " =    1.387
peak=   -3.816 closest distance to " CB  ALA A 248 " =    2.055
peak=   -3.807 closest distance to " ND2 ASN A  45 " =    1.893
peak=   -3.805 closest distance to " O   HOH Z 211 " =    1.539
peak=   -3.804 closest distance to " CD1 LEU A 228 " =    2.325
peak=   -3.796 closest distance to " CD1 LEU A 101 " =    2.416
peak=   -3.786 closest distance to " CG  GLN A 223 " =    1.935
peak=   -3.776 closest distance to " C   LEU A 222 " =    0.806
peak=   -3.770 closest distance to " O   HOH Z  52 " =    1.295
peak=   -3.766 closest distance to " C   ALA A 158 " =    1.377
peak=   -3.752 closest distance to " CA  GLY A 241 " =    2.290
peak=   -3.745 closest distance to " C   HIS A 108 " =    1.200
peak=   -3.725 closest distance to " CG2 VAL A 296 " =    1.024
peak=   -3.720 closest distance to " OG BSER A 134 " =    1.669
peak=   -3.703 closest distance to " CB  VAL A 296 " =    1.075
peak=   -3.703 closest distance to " O   PRO A 198 " =    1.216
peak=   -3.699 closest distance to " O   PRO A 163 " =    2.001
peak=   -3.658 closest distance to " CG1 VAL A 197 " =    2.247
peak=   -3.657 closest distance to " O   GLY A  80 " =    2.510
peak=   -3.647 closest distance to " O   HOH Z 417 " =    2.980
peak=   -3.644 closest distance to " O   TYR A 247 " =    2.862
peak=   -3.619 closest distance to " CG  ASP A 231 " =    0.720
peak=   -3.599 closest distance to " CG2 THR A   4 " =    1.917
peak=   -3.584 closest distance to " NH2 ARG A  79 " =    1.887
peak=   -3.584 closest distance to " CD1 LEU A 101 " =    2.804
peak=   -3.574 closest distance to " O   HOH Z 140 " =    1.372
peak=   -3.573 closest distance to " O   HOH Z 407 " =    3.187
peak=   -3.556 closest distance to " N   THR A 157 " =    1.463
peak=   -3.555 closest distance to " NH2AARG A 275 " =    5.288
peak=   -3.542 closest distance to " CB  VAL A 230 " =    1.083
peak=   -3.538 closest distance to " CG  MET A 105 " =    0.960
peak=   -3.532 closest distance to " CB  ALA A 291 " =    2.307
peak=   -3.521 closest distance to " O   HOH Z  60 " =    2.237
peak=   -3.521 closest distance to " O   HOH Z  38 " =    1.712
peak=   -3.520 closest distance to " CD  GLN A  58 " =    0.933
peak=   -3.520 closest distance to " CA  ASP A  27 " =    2.446
peak=   -3.519 closest distance to " O   ARG A 145 " =    1.630
peak=   -3.505 closest distance to " ND2 ASN A 249 " =    2.354
peak=   -3.503 closest distance to " N   GLN A  58 " =    1.814
peak=   -3.499 closest distance to " O   HOH Z 185 " =    2.189
peak=   -3.499 closest distance to " O   VAL A  67 " =    2.629
peak=   -3.498 closest distance to " O   HOH Z 198 " =    1.440
peak=   -3.498 closest distance to " O   HOH Z  51 " =    1.110
peak=   -3.496 closest distance to " CG  LYS A 193 " =    2.469
peak=   -3.496 closest distance to " O   HOH Z 275 " =    1.474
peak=   -3.483 closest distance to " O   ALA A 161 " =    1.575
peak=   -3.475 closest distance to " CG  LEU A 101 " =    2.506
peak=   -3.472 closest distance to " CG1 VAL A 112 " =    2.854
peak=   -3.470 closest distance to " O   HOH Z  43 " =    1.704
peak=   -3.467 closest distance to " N   ASP A 171 " =    2.364
peak=   -3.463 closest distance to " CB  PHE A 192 " =    1.759
peak=   -3.461 closest distance to " CG1 VAL A 112 " =    2.602
peak=   -3.461 closest distance to " ND2 ASN A  60 " =    1.864
peak=   -3.461 closest distance to " O   PRO A 198 " =    1.319
peak=   -3.460 closest distance to " O   HOH Z 377 " =    2.057
peak=   -3.451 closest distance to " CG  TRP A 266 " =    1.727
peak=   -3.448 closest distance to " O   HOH Z 359 " =    3.259
peak=   -3.438 closest distance to " O   HOH Z 196 " =    2.296
peak=   -3.429 closest distance to " CD1 PHE A  59 " =    1.963
peak=   -3.421 closest distance to " CG1 VAL A 250 " =    2.780
peak=   -3.421 closest distance to " O   VAL A 189 " =    2.597
peak=   -3.420 closest distance to " CD2 LEU A 300 " =    2.788
peak=   -3.414 closest distance to " O   HOH Z 241 " =    1.259
peak=   -3.413 closest distance to " CD2 PHE A  61 " =    1.831
peak=   -3.413 closest distance to " CB  ALA A 248 " =    2.478
peak=   -3.410 closest distance to " CB  ASP A 132 " =    2.315
peak=   -3.409 closest distance to " OD1 ASN A 187 " =    1.612
peak=   -3.405 closest distance to " CG2 THR A 178 " =    2.218
peak=   -3.404 closest distance to " CG  PRO A 163 " =    2.524
peak=   -3.400 closest distance to " O   LYS A 289 " =    3.095
peak=   -3.398 closest distance to " O   HOH Z 394 " =    1.493
peak=   -3.395 closest distance to " CD  LYS A 289 " =    2.520
peak=   -3.394 closest distance to " O   HOH Z 166 " =    1.468
peak=   -3.393 closest distance to " CE BMET A  47 " =    1.695
peak=   -3.385 closest distance to " O   HOH Z  90 " =    2.906
peak=   -3.381 closest distance to " CA  GLY A 241 " =    3.072
peak=   -3.368 closest distance to " CA  GLY A 203 " =    2.237
peak=   -3.366 closest distance to " CE2 PHE A 218 " =    2.501
peak=   -3.364 closest distance to " O   HOH Z 281 " =    2.765
peak=   -3.363 closest distance to " O   HOH Z 118 " =    3.045
peak=   -3.360 closest distance to " OXT GLY A 302 " =    3.014
peak=   -3.358 closest distance to " CG  PHE A 283 " =    2.659
peak=   -3.355 closest distance to " OG  SER A  97 " =    2.240
peak=   -3.349 closest distance to " O   HOH Z 176 " =    0.796
peak=   -3.346 closest distance to " O   SER A  22 " =    2.177
peak=   -3.345 closest distance to " O   HOH Z 290 " =    0.824
peak=   -3.343 closest distance to " O   HOH Z  73 " =    2.259
peak=   -3.342 closest distance to " O   HOH Z 191 " =    5.419
peak=   -3.341 closest distance to " CB  TRP A  85 " =    2.477
peak=   -3.337 closest distance to " CD2 TYR A 293 " =    2.088
peak=   -3.336 closest distance to " N   PHE A  59 " =    2.147
peak=   -3.329 closest distance to " C   MET A 188 " =    1.456
peak=   -3.319 closest distance to " O   HOH Z  98 " =    2.199
peak=   -3.312 closest distance to " O   HOH Z 111 " =    1.122
peak=   -3.305 closest distance to " O   GLY A 211 " =    1.355
peak=   -3.305 closest distance to " O   HOH Z 103 " =    1.846
peak=   -3.295 closest distance to " OD2 ASP A  50 " =    2.190
peak=   -3.294 closest distance to " CB  ALA A 244 " =    2.044
peak=   -3.292 closest distance to " CG  GLU A 152 " =    1.113
peak=   -3.292 closest distance to " CD  GLN A  88 " =    0.767
peak=   -3.289 closest distance to " O   HOH Z   2 " =    1.834
peak=   -3.289 closest distance to " O   HOH Z 313 " =    1.711
peak=   -3.286 closest distance to " CE  MET A 105 " =    2.157
peak=   -3.282 closest distance to " O   HOH Z 317 " =    1.541
peak=   -3.281 closest distance to " C   ASN A 187 " =    1.733
peak=   -3.276 closest distance to " O   HOH Z 423 " =    1.123
peak=   -3.276 closest distance to " OXT GLY A 302 " =    3.489
peak=   -3.273 closest distance to " CB  ALA A  43 " =    2.437
peak=   -3.271 closest distance to " CE2 TYR A  30 " =    2.682
peak=   -3.270 closest distance to " OH  TYR A 214 " =    1.183
peak=   -3.269 closest distance to " O   HOH Z 350 " =    1.987
peak=   -3.263 closest distance to " CZ  TYR A 169 " =    1.524
peak=   -3.256 closest distance to " O   GLY A  17 " =    1.339
peak=   -3.256 closest distance to " O   GLY A 196 " =    1.202
peak=   -3.250 closest distance to " O   HOH Z 148 " =    1.758
peak=   -3.249 closest distance to " NH2BARG A 275 " =    1.655
peak=   -3.247 closest distance to " C   ASN A 285 " =    2.433
peak=   -3.244 closest distance to " CD  PRO A 243 " =    2.136
peak=   -3.238 closest distance to " O   HOH Z 281 " =    3.174
peak=   -3.237 closest distance to " C   ASP A 231 " =    2.625
peak=   -3.237 closest distance to " O   HOH Z 390 " =    2.388
peak=   -3.231 closest distance to " O   HOH Z 128 " =    4.088
peak=   -3.229 closest distance to " CG  GLU A 152 " =    0.783
peak=   -3.227 closest distance to " O   HOH Z 359 " =    1.589
peak=   -3.223 closest distance to " N   ALA A 248 " =    1.705
peak=   -3.218 closest distance to " NE2 GLN A  88 " =    2.092
peak=   -3.215 closest distance to " CD  GLU A 277 " =    1.000
peak=   -3.213 closest distance to " OE1 GLN A  88 " =    1.283
peak=   -3.210 closest distance to " CE3 TRP A 274 " =    0.991
peak=   -3.209 closest distance to " CA  GLY A  98 " =    1.955
peak=   -3.209 closest distance to " O   HOH Z  65 " =    1.255
peak=   -3.207 closest distance to " OG1 THR A 178 " =    1.260
peak=   -3.206 closest distance to " O   HOH Z 426 " =    1.634
peak=   -3.200 closest distance to " OD1 ASN A 301 " =    1.923
peak=   -3.198 closest distance to " O   SER A 135 " =    1.468
peak=   -3.198 closest distance to " CD2 LEU A   5 " =    1.041
peak=   -3.195 closest distance to " NH1AARG A 275 " =    1.872
peak=   -3.187 closest distance to " O   HOH Z 322 " =    0.931
peak=   -3.184 closest distance to " NZ  LYS A 119 " =    3.349
peak=   -3.178 closest distance to " C   VAL A 174 " =    1.794
peak=   -3.172 closest distance to " C   LYS A  76 " =    1.674
peak=   -3.170 closest distance to " SG BCYS A 201 " =    1.949
peak=   -3.170 closest distance to " O   HOH Z 168 " =    1.762
peak=   -3.165 closest distance to " O   HOH Z  63 " =    1.571
peak=   -3.161 closest distance to " SG BCYS A 201 " =    2.274
peak=   -3.160 closest distance to " CD  ARG A 139 " =    1.638
peak=   -3.153 closest distance to " O   SER A 210 " =    1.981
peak=   -3.152 closest distance to " O   VAL A 121 " =    1.416
peak=   -3.151 closest distance to " O   HOH Z 371 " =    1.189
peak=   -3.148 closest distance to " O   HOH Z 175 " =    4.232
peak=   -3.147 closest distance to " CB  ALA A 291 " =    2.151
peak=   -3.146 closest distance to " O   HOH Z 353 " =    2.110
peak=   -3.143 closest distance to " O   HOH Z 423 " =    2.076
peak=   -3.139 closest distance to " N   ASP A 270 " =    1.513
peak=   -3.138 closest distance to " CB  ALA A 114 " =    2.408
peak=   -3.134 closest distance to " O   HOH Z 234 " =    4.191
peak=   -3.133 closest distance to " CG2 VAL A 202 " =    2.734
peak=   -3.132 closest distance to " O   PRO A 243 " =    2.570
peak=   -3.129 closest distance to " O   MET A  40 " =    2.773
peak=   -3.128 closest distance to " O   HOH Z 111 " =    2.229
peak=   -3.127 closest distance to " O   HOH Z 417 " =    2.703
peak=   -3.122 closest distance to " O   HOH Z 313 " =    1.045
peak=   -3.121 closest distance to " O   HOH Z 336 " =    5.418
peak=   -3.121 closest distance to " CD1 ILE A 199 " =    2.580
peak=   -3.119 closest distance to " N   ALA A 248 " =    2.352
peak=   -3.119 closest distance to " CG2 ILE A  20 " =    2.732
peak=   -3.115 closest distance to " OG  SER A 206 " =    1.743
peak=   -3.113 closest distance to " O   HOH Z 171 " =    1.954
peak=   -3.099 closest distance to " CE  LYS A  76 " =    2.782
peak=   -3.092 closest distance to " O   HOH Z 298 " =    1.272
peak=   -3.091 closest distance to " O   LYS A 117 " =    1.851
peak=   -3.076 closest distance to " CB  ASN A 252 " =    1.795
peak=   -3.069 closest distance to " CD1 LEU A 297 " =    2.541
peak=   -3.066 closest distance to " O   HOH Z 210 " =    0.891
peak=   -3.056 closest distance to " CG2AVAL A  72 " =    4.418
peak=   -3.052 closest distance to " O   HOH Z 139 " =    3.020

================= 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    :  0.4516 0.4367   6.249790e+00   6.230686e+00
   1_bss:  0.4429 0.4271   6.243552e+00   6.221855e+00
   1_xyz:  0.3432 0.3658   6.072424e+00   6.116904e+00
   1_adp:  0.2879 0.3322   5.939841e+00   6.044237e+00
   1_occ:  0.2875 0.3322   5.939058e+00   6.045194e+00
   2_bss:  0.2831 0.3259   5.936938e+00   6.041767e+00
   2_xyz:  0.1814 0.2305   5.547541e+00   5.729925e+00
   2_adp:  0.1576 0.2058   5.423049e+00   5.625568e+00
   2_occ:  0.1575 0.2057   5.422240e+00   5.624878e+00
   3_bss:  0.1561 0.2032   5.419488e+00   5.621040e+00
   3_xyz:  0.1351 0.1792   5.293657e+00   5.506896e+00
   3_adp:  0.1294 0.1750   5.261506e+00   5.482892e+00
   3_occ:  0.1294 0.1750   5.261525e+00   5.482985e+00
   4_bss:  0.1293 0.1748   5.260736e+00   5.482427e+00
   4_xyz:  0.1147 0.1629   5.171713e+00   5.420142e+00
   4_adp:  0.1147 0.1601   5.162766e+00   5.403847e+00
   4_occ:  0.1147 0.1598   5.161955e+00   5.402696e+00
   5_bss:  0.1148 0.1593   5.161669e+00   5.401087e+00
   5_xyz:  0.1116 0.1574   5.142678e+00   5.389166e+00
   5_adp:  0.1116 0.1576   5.143552e+00   5.390829e+00
   5_occ:  0.1116 0.1575   5.143367e+00   5.390628e+00
   5_bss:  0.1116 0.1574   5.143407e+00   5.390648e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.342  13.858   8.769   8.930   7.620   0.000   0.000   0.000
   1_xyz:  0.342  13.858   8.769   8.930   7.620   0.000   0.000   0.000
   1_adp:  0.342  13.858   8.769   8.930   7.620   0.000   0.000   0.000
   1_occ:  0.342  13.858   8.769   8.930   7.620   0.000   0.000   0.000
   2_bss:  0.355  50.000   5.193   4.811   4.541   0.000   0.000   0.000
   2_xyz:  0.355  50.000   5.193   4.811   4.541   0.000   0.000   0.000
   2_adp:  0.355  50.000   5.193   4.811   4.541   0.000   0.000   0.000
   2_occ:  0.355  50.000   5.193   4.811   4.541   0.000   0.000   0.000
   3_bss:  0.338  50.000   3.492   2.976   3.856   0.000   0.000   0.000
   3_xyz:  0.338  50.000   3.492   2.976   3.856   0.000   0.000   0.000
   3_adp:  0.338  50.000   3.492   2.976   3.856   0.000   0.000   0.000
   3_occ:  0.338  50.000   3.492   2.976   3.856   0.000   0.000   0.000
   4_bss:  0.328  49.966   3.076   2.628   3.728   0.000   0.000   0.000
   4_xyz:  0.328  49.966   3.076   2.628   3.728   0.000   0.000   0.000
   4_adp:  0.328  49.966   3.076   2.628   3.728   0.000   0.000   0.000
   4_occ:  0.328  49.966   3.076   2.628   3.728   0.000   0.000   0.000
   5_bss:  0.330  49.966   2.887   2.483   3.651   0.000   0.000   0.000
   5_xyz:  0.330  49.966   2.887   2.483   3.651   0.000   0.000   0.000
   5_adp:  0.330  49.966   2.887   2.483   3.651   0.000   0.000   0.000
   5_occ:  0.330  49.966   2.887   2.483   3.651   0.000   0.000   0.000
   5_bss:  0.331  52.973  -0.120  -0.524   0.644   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  49.999 0.5218  0.5947    57061.569
   1_bss:  50.288 0.5163  0.7539    55097.760
   1_xyz:  40.582 0.6350  0.9042    38150.799
   1_adp:  34.621 0.7063  1.0099    30359.470
   1_occ:  34.683 0.7055  1.0080    30412.837
   2_bss:  34.345 0.7093  0.8918    29953.020
   2_xyz:  22.353 0.8381  1.0039    13225.592
   2_adp:  19.388 0.8678  1.0234    10686.283
   2_occ:  19.370 0.8679  1.0233    10663.779
   3_bss:  19.244 0.8690  0.9730    10530.486
   3_xyz:  16.427 0.8947  0.9858     8120.035
   3_adp:  15.881 0.8997  0.9867     7754.620
   3_occ:  15.886 0.8997  0.9865     7752.828
   4_bss:  15.870 0.8998  0.9760     7733.022
   4_xyz:  14.645 0.9097  0.9809     6756.439
   4_adp:  14.194 0.9136  0.9830     6560.035
   4_occ:  14.174 0.9137  0.9830     6539.684
   5_bss:  14.165 0.9138  0.9777     6506.398
   5_xyz:  13.906 0.9159  0.9778     6328.359
   5_adp:  13.903 0.9160  0.9763     6352.530
   5_occ:  13.901 0.9160  0.9762     6348.249
   5_bss:  13.903 0.9160  0.9762     6349.235
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.3744e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.3744e+01
   1_xyz:   1.590  0.012  0.103 18.143  0.006  4.121   1.2848e-01
   1_adp:   1.590  0.012  0.103 18.143  0.006  4.121   1.2848e-01
   1_occ:   1.590  0.012  0.103 18.143  0.006  4.121   1.2848e-01
   2_bss:   1.590  0.012  0.103 18.143  0.006  4.121   1.2848e-01
   2_xyz:   1.106  0.009  0.083 16.361  0.005  4.123   7.8106e-02
   2_adp:   1.106  0.009  0.083 16.361  0.005  4.123   7.8106e-02
   2_occ:   1.106  0.009  0.083 16.361  0.005  4.123   7.8106e-02
   3_bss:   1.106  0.009  0.083 16.361  0.005  4.123   7.8106e-02
   3_xyz:   0.907  0.005  0.071 15.683  0.003  4.127   5.3798e-02
   3_adp:   0.907  0.005  0.071 15.683  0.003  4.127   5.3798e-02
   3_occ:   0.907  0.005  0.071 15.683  0.003  4.127   5.3798e-02
   4_bss:   0.907  0.005  0.071 15.683  0.003  4.127   5.3798e-02
   4_xyz:   1.127  0.009  0.091 16.103  0.004  4.124   7.6371e-02
   4_adp:   1.127  0.009  0.091 16.103  0.004  4.124   7.6371e-02
   4_occ:   1.127  0.009  0.091 16.103  0.004  4.124   7.6371e-02
   5_bss:   1.127  0.009  0.091 16.103  0.004  4.124   7.6371e-02
   5_xyz:   1.080  0.009  0.088 15.706  0.004  4.111   7.2128e-02
   5_adp:   1.080  0.009  0.088 15.706  0.004  4.111   7.2128e-02
   5_occ:   1.080  0.009  0.088 15.706  0.004  4.111   7.2128e-02
   5_bss:   1.080  0.009  0.088 15.706  0.004  4.111   7.2128e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9683e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9683e+00
   1_xyz:  13.152  0.157  0.432 86.985  0.034  2.258   9.6761e-02
   1_adp:  13.152  0.157  0.432 86.985  0.034  2.258   9.6761e-02
   1_occ:  13.152  0.157  0.432 86.985  0.034  2.258   9.6761e-02
   2_bss:  13.152  0.157  0.432 86.985  0.034  2.258   9.6761e-02
   2_xyz:   7.956  0.080  0.319 86.734  0.047  2.324   1.1316e-01
   2_adp:   7.956  0.080  0.319 86.734  0.047  2.324   1.1316e-01
   2_occ:   7.956  0.080  0.319 86.734  0.047  2.324   1.1316e-01
   3_bss:   7.956  0.080  0.319 86.734  0.047  2.324   1.1316e-01
   3_xyz:   7.976  0.050  0.365 82.468  0.023  2.346   3.2063e-02
   3_adp:   7.976  0.050  0.365 82.468  0.023  2.346   3.2063e-02
   3_occ:   7.976  0.050  0.365 82.468  0.023  2.346   3.2063e-02
   4_bss:   7.976  0.050  0.365 82.468  0.023  2.346   3.2063e-02
   4_xyz:   9.752  0.068  0.613 84.069  0.040  2.295   5.5264e-02
   4_adp:   9.752  0.068  0.613 84.069  0.040  2.295   5.5264e-02
   4_occ:   9.752  0.068  0.613 84.069  0.040  2.295   5.5264e-02
   5_bss:   9.752  0.068  0.613 84.069  0.040  2.295   5.5264e-02
   5_xyz:   7.862  0.046  0.641 84.350  0.041  2.257   5.5058e-02
   5_adp:   7.862  0.046  0.641 84.350  0.041  2.257   5.5058e-02
   5_occ:   7.862  0.046  0.641 84.350  0.041  2.257   5.5058e-02
   5_bss:   7.862  0.046  0.641 84.350  0.041  2.257   5.5058e-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:  70.30   0.00  11.36  68.94   0.00   8.44  70.30   0.00  27.26
   1_occ:  70.30   0.00  11.36  68.94   0.00   8.44  70.30   0.00  27.26
   2_bss:  70.30   0.00  11.36  68.94   0.00   8.44  70.30   0.00  27.26
   2_xyz:  70.30   0.00  11.36  68.94   0.00   8.44  70.30   0.00  27.26
   2_adp:  71.63   0.00  11.72  71.63   0.00   7.81  69.88   0.64  33.00
   2_occ:  71.63   0.00  11.72  71.63   0.00   7.81  69.88   0.64  33.00
   3_bss:  71.63   0.00  11.72  71.63   0.00   7.81  69.88   0.64  33.00
   3_xyz:  71.63   0.00  11.72  71.63   0.00   7.81  69.88   0.64  33.00
   3_adp:  84.79   0.00  12.53  82.15   0.00   8.05  84.79   1.01  36.90
   3_occ:  84.79   0.00  12.53  82.15   0.00   8.05  84.79   1.01  36.90
   4_bss:  84.79   0.00  12.53  82.15   0.00   8.05  84.79   1.01  36.90
   4_xyz:  84.79   0.00  12.53  82.15   0.00   8.05  84.79   1.01  36.90
   4_adp:  81.58   0.00  11.83  81.58   0.00   7.81  78.13   1.61  33.74
   4_occ:  81.58   0.00  11.83  81.58   0.00   7.81  78.13   1.61  33.74
   5_bss:  81.58   0.00  11.83  81.58   0.00   7.81  78.13   1.61  33.74
   5_xyz:  81.58   0.00  11.83  81.58   0.00   7.81  78.13   1.61  33.74
   5_adp:  80.77   0.00  11.55  80.77   0.00   7.71  74.34   1.89  32.44
   5_occ:  80.77   0.00  11.55  80.77   0.00   7.71  74.34   1.89  32.44
   5_bss:  83.78   3.01  14.56  83.78   3.01  10.72  77.34   4.90  35.45
------------------------------------------------------------------------
 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:    1.190    0.022    0.408
   1_adp:    1.190    0.022    0.408
   1_occ:    1.190    0.022    0.408
   2_bss:    1.190    0.022    0.408
   2_xyz:    1.302    0.034    0.567
   2_adp:    1.302    0.034    0.567
   2_occ:    1.302    0.034    0.567
   3_bss:    1.302    0.034    0.567
   3_xyz:    1.570    0.041    0.581
   3_adp:    1.570    0.041    0.581
   3_occ:    1.570    0.041    0.581
   4_bss:    1.570    0.041    0.581
   4_xyz:    1.755    0.045    0.614
   4_adp:    1.755    0.045    0.614
   4_occ:    1.755    0.045    0.614
   5_bss:    1.755    0.045    0.614
   5_xyz:    1.822    0.054    0.623
   5_adp:    1.822    0.054    0.623
   5_occ:    1.822    0.054    0.623
   5_bss:    1.822    0.054    0.623
------------------------------------------------------------------------

CPU time actual refinement: 333.73


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1005/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_1005/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1005/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1005/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1005/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 333.57 
  Macro-tasks:
    bulk solvent and scale       = 41.39  
    individual site refinement   = 139.81 
    weights calculation          = 32.82  
    collect and process          = 6.47   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 220.60 
  Micro-tasks:
    mask                            = 1.79   
    f_calc                          = 101.86 
    alpha_beta                      = 8.12   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 113.31 
    fmodel                         = 7.45   
    r_factors                      = 0.16   
    phase_errors                   = 10.86  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 244.97 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.618 micro seconds
Total CPU time: 5.79 minutes
from_scatterers_fft:    664 calls, 101.47 s
gradients_fft:          608 calls,  99.16 s

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

# Date 2008-01-16 Time 02:57:19 PST -0800 (1200481039.45 s)
Start R-work = 0.4516, R-free = 0.4367 (no bulk solvent and anisotropic scale)
Final R-work = 0.1291, R-free = 0.1749 (no bulk solvent and anisotropic scale)

Start R-work = 0.4429, R-free = 0.4271
Final R-work = 0.1116, R-free = 0.1574