# Date 2008-01-16 Time 01:22:19 PST -0800 (1200475339.63 s)
#phil __OFF__

Command line arguments: "../396.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 4386
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 396

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.5475, 46.4607, 84.2302, 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: 2.79, per 1000 atoms: 0.99


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 46.4607, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.782 1.95115
Completeness in resolution range: 0.958038
Completeness with d_max=infinity: 0.955095

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7820
                             d_min =   1.9511

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 46.4607, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.782 1.95115
Completeness in resolution range: 0.958038
Completeness with d_max=infinity: 0.955095

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7824 -  4.1750 [2141/2169]  1929   212   9.9%
  bin  2:  4.1750 -  3.3262 [2059/2075]  1850   209  10.2%
  bin  3:  3.3262 -  2.9094 [2036/2055]  1833   203  10.0%
  bin  4:  2.9094 -  2.6451 [2022/2052]  1824   198   9.8%
  bin  5:  2.6451 -  2.4564 [2008/2027]  1807   201  10.0%
  bin  6:  2.4564 -  2.3122 [1987/2023]  1788   199  10.0%
  bin  7:  2.3122 -  2.1968 [1963/1996]  1764   199  10.1%
  bin  8:  2.1968 -  2.1014 [1997/2031]  1798   199  10.0%
  bin  9:  2.1014 -  2.0207 [1978/2006]  1780   198  10.0%
  bin 10:  2.0207 -  1.9511 [1398/2013]  1257   141  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_396/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.43 -     2.12: 22
        2.12 -     2.82: 907
        2.82 -     3.51: 4578
        3.51 -     4.21: 9505
        4.21 -     4.90: 13970
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.429 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.454 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.597 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.722 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.748 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28977 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_396/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_396/model_refine_001.geo

CPU time processing inputs: 8.18


============================ 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 = 69.5475 46.4607 84.23025 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: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4889   r_free= 0.4801   ksol= 0.00   Bsol= 0.00   scale= 0.801    |
|                                                                             |
| 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:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.287013                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7824 -  4.6566 0.99   1387  154 0.4044 0.4077      6.6025      6.6166|
|  2:  4.6566 -  3.7154 0.99   1354  147 0.4211 0.4046      6.8056      6.8107|
|  3:  3.7154 -  3.2514 0.99   1307  150 0.4503 0.4248      6.6939      6.7692|
|  4:  3.2514 -  2.9568 0.99   1310  146 0.4647 0.4717      6.5391      6.4946|
|  5:  2.9568 -  2.7463 0.99   1304  142 0.5174 0.5153      6.3884      6.3645|
|  6:  2.7463 -  2.5853 0.99   1286  145 0.5126 0.5601      6.2789      6.2768|
|  7:  2.5853 -  2.4564 0.99   1295  139 0.5128 0.4669      6.2498      6.2035|
|  8:  2.4564 -  2.3499 0.98   1273  149 0.5413 0.5476       6.185      6.1714|
|  9:  2.3499 -  2.2598 0.98   1281  142 0.5265 0.4959      6.1226      6.1145|
| 10:  2.2598 -  2.1821 0.98   1275  134 0.5504 0.5133      6.1212      6.1191|
| 11:  2.1821 -  2.1140 1.00   1265  147 0.5363 0.5307      6.0594      6.0777|
| 12:  2.1140 -  2.0538 0.97   1261  134 0.5185 0.4866       5.976      5.9966|
| 13:  2.0538 -  1.9998 0.98   1268  145 0.5445 0.5092      5.8893      5.8367|
| 14:  1.9998 -  1.9511 0.59    764   85 0.5568 0.5399      5.8432      5.7635|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7824 -  4.6566  1387   154  0.64  39.23   0.80     0.69      87310.92|
|  2:  4.6566 -  3.7154  1354   147  0.66  38.81   0.87     0.75     124734.76|
|  3:  3.7154 -  3.2514  1307   150  0.56  47.37   0.85     0.70     131322.66|
|  4:  3.2514 -  2.9568  1310   146  0.48  53.19   0.82     0.60     111625.86|
|  5:  2.9568 -  2.7463  1304   142  0.40  60.04   0.74     0.50      88208.23|
|  6:  2.7463 -  2.5853  1286   145  0.37  61.90   0.73     0.44      74258.43|
|  7:  2.5853 -  2.4564  1295   139  0.35  63.55   0.74     0.40      67532.55|
|  8:  2.4564 -  2.3499  1273   149  0.34  64.72   0.73     0.41      61114.33|
|  9:  2.3499 -  2.2598  1281   142  0.35  63.62   0.74     0.42      54318.70|
| 10:  2.2598 -  2.1821  1275   134  0.35  63.47   0.75     0.44      49251.29|
| 11:  2.1821 -  2.1140  1265   147  0.34  64.50   0.78     0.43      45731.85|
| 12:  2.1140 -  2.0538  1261   134  0.32  65.74   0.76     0.41      44203.92|
| 13:  2.0538 -  1.9998  1268   145  0.27  69.76   0.75     0.36      38532.79|
| 14:  1.9998 -  1.9511   764    85  0.25  71.66   0.72     0.29      32532.66|
|alpha:            min =        0.29 max =            0.75 mean =         0.50|
|beta:             min =    32532.66 max =       131322.66 mean =     73926.08|
|figures of merit: min =        0.00 max =            1.00 mean =         0.41|
|phase err.(work): min =        0.00 max =           90.00 mean =        58.49|
|phase err.(test): min =        0.00 max =           89.95 mean =        58.76|
|-----------------------------------------------------------------------------|

============================== 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 = 14.358897             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.179   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.450037              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 83.007   (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 |  0.798 -  1.208:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.208 -  1.618:        6 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.618 -  2.028:       41 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.028 -  2.439:      365 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.439 -  2.849:     1120 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.849 -  3.259:     2352 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.259 -  3.669:     3935 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.669 -  4.080:     5382 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.080 -  4.490:     7165 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.490 -  4.900:     8602 |
|-----------------------------------------------------------------------------|
|-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 |       52.808 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.087    4.900  0.798 |       2.391 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.373)------------------------------------------|
|    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 = 11.373)------------------------------------------|
|    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: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4945   r_free= 0.4862   ksol= 0.00   Bsol= 0.00   scale= 0.769    |
|                                                                             |
| 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:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.288605                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4806   r_free= 0.4714   ksol= 0.40   Bsol= 20.00   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.33,8.18,9.27,0.00,0.00,0.00); trace/3= 7.93                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.281564                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.135303             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.244   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.332228              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.220   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4806      final r-factor (work) = 0.4119          |
| start r-factor (free) = 0.4714      final r-factor (free) = 0.4267          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 90.9415 = 12.14 * 0.50 * 6.2848 + 1.00 * 52.8078                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 37.8566 = 12.14 * 0.50 * 6.2167 + 1.00 * 0.1358                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4119      final r-factor (work) = 0.3690          |
| start r-factor (free) = 0.4267      final r-factor (free) = 0.4209          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.2964 = 1.33 * 1.00 * 6.2167 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.2040 = 1.33 * 1.00 * 6.1442 + 1.00 * 0.0184                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.373)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.38   14.04    None  None   None       |
|    all(noH): 2823   0      0.00    78.38   14.04    None  None   None       |
|    Sol.    : 438    0      0.00    75.98   25.94    None  None   None       |
|    Mac.    : 2385   0      0.00    78.38   11.85    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 -   7.838: 1043   |   5:    39.191 -  47.029:   76        |
|      1:     7.838 -  15.676:  794   |   6:    47.029 -  54.867:   29        |
|      2:    15.676 -  23.515:  462   |   7:    54.867 -  62.706:   16        |
|      3:    23.515 -  31.353:  261   |   8:    62.706 -  70.544:    4        |
|      4:    31.353 -  39.191:  133   |   9:    70.544 -  78.382:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3690 r_free = 0.4209             target_work(ml) = 6.134         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3683 r_free = 0.4213             target_work(ml) = 6.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3683   r_free= 0.4213   ksol= 0.40   Bsol= 20.00   scale= 1.109   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.33,8.18,9.27,0.00,0.00,0.00); trace/3= 7.93                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.133806                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3650   r_free= 0.4171   ksol= 0.36   Bsol= 29.67   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.99,4.00,5.84,0.00,0.00,0.00); trace/3= 4.28                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.133564                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.069732              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.595   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.526377              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.573  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3650      final r-factor (work) = 0.2818          |
| start r-factor (free) = 0.4171      final r-factor (free) = 0.3378          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.9070 = 8.07 * 0.50 * 6.1393 + 1.00 * 0.1358                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.4262 = 8.07 * 0.50 * 6.0319 + 1.00 * 0.0882                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2818      final r-factor (work) = 0.2584          |
| start r-factor (free) = 0.3378      final r-factor (free) = 0.3186          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1929 = 0.53 * 1.00 * 6.0319 + 1.00 * 0.0179                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1419 = 0.53 * 1.00 * 5.8926 + 1.00 * 0.0402                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.373)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.82   13.76    None  None   None       |
|    all(noH): 2823   0      0.00    80.82   13.76    None  None   None       |
|    Sol.    : 438    0      0.00    74.84   31.03    None  None   None       |
|    Mac.    : 2385   0      0.00    80.82   10.58    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 -   8.082: 1220   |   5:    40.411 -  48.493:   65        |
|      1:     8.082 -  16.165:  752   |   6:    48.493 -  56.576:   32        |
|      2:    16.165 -  24.247:  355   |   7:    56.576 -  64.658:   13        |
|      3:    24.247 -  32.329:  221   |   8:    64.658 -  72.740:    2        |
|      4:    32.329 -  40.411:  158   |   9:    72.740 -  80.822:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2584 r_free = 0.3186             target_work(ml) = 5.867         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2581 r_free = 0.3192             target_work(ml) = 5.867         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2581   r_free= 0.3192   ksol= 0.36   Bsol= 29.67   scale= 1.064   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.99,4.00,5.84,0.00,0.00,0.00); trace/3= 4.28                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.867490                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2568   r_free= 0.3183   ksol= 0.33   Bsol= 29.67   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.60,2.47,3.93,0.00,0.00,0.00); trace/3= 2.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.865996                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.463904              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.316  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.026935              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.466   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2568      final r-factor (work) = 0.1834          |
| start r-factor (free) = 0.3183      final r-factor (free) = 0.2376          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.1318 = 6.46 * 0.50 * 5.8923 + 1.00 * 0.0882                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.6182 = 6.46 * 0.50 * 5.7370 + 1.00 * 0.0766                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1834      final r-factor (work) = 0.1590          |
| start r-factor (free) = 0.2376      final r-factor (free) = 0.2131          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.9224 = 1.03 * 1.00 * 5.7370 + 1.00 * 0.0310                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6717 = 1.03 * 1.00 * 5.5106 + 1.00 * 0.0127                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.373)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.76   14.25    None  None   None       |
|    all(noH): 2823   0      0.00    89.76   14.25    None  None   None       |
|    Sol.    : 438    0      1.87    81.18   38.67    None  None   None       |
|    Mac.    : 2385   0      0.00    89.76   9.77     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 -   8.976: 1531   |   5:    44.879 -  53.855:   94        |
|      1:     8.976 -  17.952:  644   |   6:    53.855 -  62.831:   69        |
|      2:    17.952 -  26.927:  204   |   7:    62.831 -  71.806:   25        |
|      3:    26.927 -  35.903:  117   |   8:    71.806 -  80.782:   10        |
|      4:    35.903 -  44.879:  125   |   9:    80.782 -  89.758:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1590 r_free = 0.2131             target_work(ml) = 5.448         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1587 r_free = 0.2129             target_work(ml) = 5.447         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1587   r_free= 0.2129   ksol= 0.33   Bsol= 29.67   scale= 1.044   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.60,2.47,3.93,0.00,0.00,0.00); trace/3= 2.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.446865                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1582   r_free= 0.2111   ksol= 0.31   Bsol= 32.69   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.10,1.52,2.41,0.00,0.00,0.00); trace/3= 1.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.440475                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.285191              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.133  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.296719              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.124  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1582      final r-factor (work) = 0.1344          |
| start r-factor (free) = 0.2111      final r-factor (free) = 0.1823          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3783 = 2.29 * 0.50 * 5.5152 + 1.00 * 0.0766                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1990 = 2.29 * 0.50 * 5.3760 + 1.00 * 0.0564                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1344      final r-factor (work) = 0.1288          |
| start r-factor (free) = 0.1823      final r-factor (free) = 0.1731          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6077 = 0.30 * 1.00 * 5.3760 + 1.00 * 0.0126                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5760 = 0.30 * 1.00 * 5.2775 + 1.00 * 0.0100                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.373)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.24   13.78    None  None   None       |
|    all(noH): 2823   0      0.00    88.24   13.78    None  None   None       |
|    Sol.    : 438    0      2.79    85.86   37.61    None  None   None       |
|    Mac.    : 2385   0      0.00    88.24   9.40     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 -   8.824: 1554   |   5:    44.118 -  52.941:   88        |
|      1:     8.824 -  17.647:  670   |   6:    52.941 -  61.765:   63        |
|      2:    17.647 -  26.471:  175   |   7:    61.765 -  70.589:   19        |
|      3:    26.471 -  35.294:  121   |   8:    70.589 -  79.412:   11        |
|      4:    35.294 -  44.118:  116   |   9:    79.412 -  88.236:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1288 r_free = 0.1731             target_work(ml) = 5.251         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1286 r_free = 0.1729             target_work(ml) = 5.250         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1286   r_free= 0.1729   ksol= 0.31   Bsol= 32.69   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.10,1.52,2.41,0.00,0.00,0.00); trace/3= 1.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.249690                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1287   r_free= 0.1734   ksol= 0.32   Bsol= 33.39   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.05,1.38,2.01,0.00,0.00,0.00); trace/3= 1.48                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.249710                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.184841              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 122.775  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.417479              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.218  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1287      final r-factor (work) = 0.1174          |
| start r-factor (free) = 0.1734      final r-factor (free) = 0.1625          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8212 = 2.18 * 0.50 * 5.2771 + 1.00 * 0.0564                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7503 = 2.18 * 0.50 * 5.2088 + 1.00 * 0.0600                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1174      final r-factor (work) = 0.1155          |
| start r-factor (free) = 0.1625      final r-factor (free) = 0.1623          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1846 = 0.42 * 1.00 * 5.2088 + 1.00 * 0.0100                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1668 = 0.42 * 1.00 * 5.1654 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 35     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.373)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.46   13.64    None  None   None       |
|    all(noH): 2823   0      0.00    92.46   13.64    None  None   None       |
|    Sol.    : 438    0      2.90    88.38   37.40    None  None   None       |
|    Mac.    : 2385   0      0.00    92.46   9.27     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.246: 1647   |   5:    46.232 -  55.478:   88        |
|      1:     9.246 -  18.493:  626   |   6:    55.478 -  64.724:   47        |
|      2:    18.493 -  27.739:  148   |   7:    64.724 -  73.971:   17        |
|      3:    27.739 -  36.985:  127   |   8:    73.971 -  83.217:    8        |
|      4:    36.985 -  46.232:  110   |   9:    83.217 -  92.463:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1155 r_free = 0.1623             target_work(ml) = 5.164         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1154 r_free = 0.1622             target_work(ml) = 5.163         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1154   r_free= 0.1622   ksol= 0.32   Bsol= 33.39   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.05,1.38,2.01,0.00,0.00,0.00); trace/3= 1.48                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.163286                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7824 -  4.6566 0.99   1387  154 0.1021 0.1249      5.3974      5.5076|
|  2:  4.6566 -  3.7154 0.99   1354  147 0.0895 0.1221      5.4573      5.6991|
|  3:  3.7154 -  3.2514 0.99   1307  150 0.1117 0.1486      5.5086      5.8095|
|  4:  3.2514 -  2.9568 0.99   1310  146 0.1274 0.1725      5.4841      5.6586|
|  5:  2.9568 -  2.7463 0.99   1304  142 0.1297 0.1624      5.3129      5.4476|
|  6:  2.7463 -  2.5853 0.99   1286  145 0.1238 0.1882      5.2117      5.4887|
|  7:  2.5853 -  2.4564 0.99   1295  139 0.1254 0.1721      5.1743      5.3952|
|  8:  2.4564 -  2.3499 0.98   1273  149 0.1197 0.1724      5.0834      5.3282|
|  9:  2.3499 -  2.2598 0.98   1281  142 0.1193 0.1910      5.0408      5.3198|
| 10:  2.2598 -  2.1821 0.98   1275  134 0.1169 0.1693       4.972      5.1832|
| 11:  2.1821 -  2.1140 1.00   1265  147 0.1157 0.1827       4.961      5.3406|
| 12:  2.1140 -  2.0538 0.97   1261  134 0.1132 0.1661      4.8951      5.1297|
| 13:  2.0538 -  1.9998 0.98   1268  145 0.1195 0.1895       4.831      5.1079|
| 14:  1.9998 -  1.9511 0.59    764   85 0.1100 0.1659      4.7078      4.9054|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7824 -  4.6566  1387   154  0.94   8.72   0.99     0.97       6843.35|
|  2:  4.6566 -  3.7154  1354   147  0.95   7.85   1.03     1.02       8853.78|
|  3:  3.7154 -  3.2514  1307   150  0.93  11.97   1.05     1.04      10875.90|
|  4:  3.2514 -  2.9568  1310   146  0.92  13.79   1.03     1.01      10523.29|
|  5:  2.9568 -  2.7463  1304   142  0.90  15.66   1.00     0.96       7911.67|
|  6:  2.7463 -  2.5853  1286   145  0.90  15.94   0.99     0.97       7100.41|
|  7:  2.5853 -  2.4564  1295   139  0.90  15.64   1.00     0.96       6296.24|
|  8:  2.4564 -  2.3499  1273   149  0.90  15.78   1.00     0.97       5450.83|
|  9:  2.3499 -  2.2598  1281   142  0.91  15.15   1.02     1.01       5021.17|
| 10:  2.2598 -  2.1821  1275   134  0.90  15.75   1.01     0.98       4443.47|
| 11:  2.1821 -  2.1140  1265   147  0.90  16.72   1.02     0.99       4573.87|
| 12:  2.1140 -  2.0538  1261   134  0.91  15.61   1.02     1.00       4147.14|
| 13:  2.0538 -  1.9998  1268   145  0.89  16.93   1.03     1.02       3625.61|
| 14:  1.9998 -  1.9511   764    85  0.91  15.45   1.01     0.99       2775.46|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     2775.46 max =        10875.90 mean =      6457.82|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.92 mean =        14.25|
|phase err.(test): min =        0.00 max =           89.22 mean =        13.77|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1154   r_free= 0.1622   ksol= 0.32   Bsol= 35.85   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.43,-0.10,0.53,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.163286                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.78 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1154   r_free= 0.1622   ksol= 0.32   Bsol= 35.85   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.43,-0.10,0.53,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.163286                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7824 -  4.6566 0.99   1387  154 0.1022 0.1249      5.3987      5.5088|
|  2:  4.6566 -  3.7154 0.99   1354  147 0.0895 0.1221      5.4576      5.6992|
|  3:  3.7154 -  3.2514 0.99   1307  150 0.1118 0.1487      5.5087      5.8097|
|  4:  3.2514 -  2.9568 0.99   1310  146 0.1274 0.1724      5.4842      5.6585|
|  5:  2.9568 -  2.7463 0.99   1304  142 0.1297 0.1623      5.3128      5.4473|
|  6:  2.7463 -  2.5853 0.99   1286  145 0.1237 0.1881      5.2115      5.4885|
|  7:  2.5853 -  2.4564 0.99   1295  139 0.1254 0.1721       5.174      5.3951|
|  8:  2.4564 -  2.3499 0.98   1273  149 0.1197 0.1724      5.0832      5.3279|
|  9:  2.3499 -  2.2598 0.98   1281  142 0.1193 0.1911      5.0406      5.3198|
| 10:  2.2598 -  2.1821 0.98   1275  134 0.1168 0.1692      4.9718      5.1829|
| 11:  2.1821 -  2.1140 1.00   1265  147 0.1157 0.1826      4.9608      5.3406|
| 12:  2.1140 -  2.0538 0.97   1261  134 0.1132 0.1661      4.8949      5.1295|
| 13:  2.0538 -  1.9998 0.98   1268  145 0.1195 0.1894      4.8307      5.1077|
| 14:  1.9998 -  1.9511 0.59    764   85 0.1100 0.1658      4.7074      4.9051|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.7824 -  4.6566  1387   154  0.94   8.72   0.99     0.97       6864.76|
|  2:  4.6566 -  3.7154  1354   147  0.95   7.86   1.03     1.02       8865.52|
|  3:  3.7154 -  3.2514  1307   150  0.93  11.97   1.05     1.04      10877.32|
|  4:  3.2514 -  2.9568  1310   146  0.92  13.79   1.03     1.01      10523.91|
|  5:  2.9568 -  2.7463  1304   142  0.90  15.66   1.00     0.96       7909.14|
|  6:  2.7463 -  2.5853  1286   145  0.90  15.94   0.99     0.97       7097.92|
|  7:  2.5853 -  2.4564  1295   139  0.90  15.64   1.00     0.96       6292.66|
|  8:  2.4564 -  2.3499  1273   149  0.90  15.78   1.00     0.97       5447.68|
|  9:  2.3499 -  2.2598  1281   142  0.91  15.15   1.02     1.01       5018.80|
| 10:  2.2598 -  2.1821  1275   134  0.90  15.74   1.01     0.98       4442.09|
| 11:  2.1821 -  2.1140  1265   147  0.90  16.72   1.02     0.99       4572.43|
| 12:  2.1140 -  2.0538  1261   134  0.91  15.61   1.02     1.00       4146.02|
| 13:  2.0538 -  1.9998  1268   145  0.89  16.92   1.03     1.02       3623.59|
| 14:  1.9998 -  1.9511   764    85  0.91  15.44   1.01     0.99       2773.02|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     2773.02 max =        10877.32 mean =      6458.99|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.90 mean =        14.25|
|phase err.(test): min =        0.00 max =           89.20 mean =        13.77|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.373)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.48    93.94   15.11    None  None   None       |
|    all(noH): 2823   0      1.48    93.94   15.11    None  None   None       |
|    Sol.    : 438    0      4.38    89.86   38.88    None  None   None       |
|    Mac.    : 2385   0      1.48    93.94   10.75    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.479 -  10.726: 1647   |   5:    47.711 -  56.957:   88        |
|      1:    10.726 -  19.972:  626   |   6:    56.957 -  66.204:   47        |
|      2:    19.972 -  29.218:  148   |   7:    66.204 -  75.450:   17        |
|      3:    29.218 -  38.465:  127   |   8:    75.450 -  84.696:    8        |
|      4:    38.465 -  47.711:  110   |   9:    84.696 -  93.943:    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)= 326         
Filter by distance & map next to the model:
   mapped sites are within: 0.400 - 5.744
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 325 from: 326
   mapped sites are within: 0.772 - 5.744

peak=   10.696 closest distance to " CB  VAL A 230 " =    1.430
peak=   10.651 closest distance to " CB  VAL A 296 " =    1.600
peak=    5.994 closest distance to " O   HOH Z 278 " =    1.922
peak=    5.881 closest distance to " NE2 GLN A  11 " =    1.179
peak=    5.865 closest distance to " O   HOH Z 236 " =    1.616
peak=    5.794 closest distance to " CG  LEU A   5 " =    1.245
peak=    5.658 closest distance to " O   HOH Z 124 " =    1.706
peak=    5.632 closest distance to " CD1AILE A 234 " =    0.980
peak=    5.541 closest distance to " O   HOH Z 142 " =    1.857
peak=    5.447 closest distance to " CD2 LEU A   5 " =    1.278
peak=    5.446 closest distance to " O   HOH Z 199 " =    1.111
peak=    5.240 closest distance to " O   HOH Z 132 " =    1.532
peak=    5.171 closest distance to " O   HOH Z 193 " =    1.688
peak=    5.089 closest distance to " CB  ARG A 275 " =    0.926
peak=    5.007 closest distance to " O   HOH Z 143 " =    1.331
peak=    4.980 closest distance to " CG  PRO A 213 " =    1.228
peak=    4.973 closest distance to " O   HOH Z 126 " =    2.053
peak=    4.901 closest distance to " O   HOH Z 202 " =    1.471
peak=    4.892 closest distance to " CB  VAL A 230 " =    1.138
peak=    4.886 closest distance to " CG  PRO A  54 " =    1.266
peak=    4.765 closest distance to " O   HOH Z 263 " =    1.477
peak=    4.749 closest distance to " CA  GLY A 241 " =    3.771
peak=    4.727 closest distance to " NH2 ARG A  56 " =    2.007
peak=    4.721 closest distance to " O   HOH Z 427 " =    2.645
peak=    4.716 closest distance to " CG  GLN A  11 " =    2.208
peak=    4.657 closest distance to " O   HOH Z 260 " =    1.420
peak=    4.647 closest distance to " CG  PRO A 198 " =    1.261
peak=    4.563 closest distance to " O   HOH Z 232 " =    2.192
peak=    4.515 closest distance to " O   HOH Z 272 " =    1.869
peak=    4.489 closest distance to " CG  LEU A 228 " =    1.149
peak=    4.462 closest distance to " CB  PRO A  54 " =    0.962
peak=    4.454 closest distance to " O   HOH Z  59 " =    1.674
peak=    4.446 closest distance to " CB  ASN A 148 " =    1.264
peak=    4.433 closest distance to " O   HOH Z 344 " =    1.303
peak=    4.428 closest distance to " O   HOH Z 108 " =    1.346
peak=    4.393 closest distance to " CB  GLN A 223 " =    1.500
peak=    4.390 closest distance to " CD2 LEU A 228 " =    1.212
peak=    4.371 closest distance to " O   HOH Z 326 " =    1.448
peak=    4.354 closest distance to " O   HOH Z 148 " =    1.705
peak=    4.350 closest distance to " O   HOH Z  78 " =    1.690
peak=    4.330 closest distance to " CB  GLN A 183 " =    1.300
peak=    4.314 closest distance to " CB  SER A  63 " =    1.237
peak=    4.306 closest distance to " O   HOH Z 192 " =    1.487
peak=    4.178 closest distance to " O   HOH Z 203 " =    1.627
peak=    4.178 closest distance to " O   HOH Z 316 " =    2.825
peak=    4.172 closest distance to " O   HOH Z 214 " =    1.255
peak=    4.168 closest distance to " CB  SER A   3 " =    1.343
peak=    4.159 closest distance to " CB  TRP A 179 " =    1.225
peak=    4.151 closest distance to " CB  GLN A  88 " =    1.286
peak=    4.139 closest distance to " CG1BVAL A  72 " =    1.315
peak=    4.110 closest distance to " O   HOH Z 134 " =    1.394
peak=    4.098 closest distance to " O   SER A  87 " =    2.372
peak=    4.081 closest distance to " NZ  LYS A 117 " =    3.230
peak=    4.072 closest distance to " O   HOH Z 227 " =    1.810
peak=    4.054 closest distance to " CB  VAL A 265 " =    1.255
peak=    4.049 closest distance to " O   HOH Z  85 " =    1.256
peak=    4.037 closest distance to " O   HOH Z 234 " =    3.538
peak=    4.030 closest distance to " O   PRO A 198 " =    1.550
peak=    4.014 closest distance to " O   HOH Z 289 " =    1.568
peak=    4.007 closest distance to " O   HOH Z  93 " =    2.282
peak=    4.002 closest distance to " NH1 ARG A  14 " =    1.040
peak=    4.001 closest distance to " O   HOH Z  44 " =    1.744
peak=    3.978 closest distance to " O   HOH Z  11 " =    1.432
peak=    3.976 closest distance to " CB  TYR A 169 " =    1.009
peak=    3.973 closest distance to " O   HOH Z  59 " =    2.159
peak=    3.964 closest distance to " OD2 ASP A 286 " =    2.556
peak=    3.959 closest distance to " CB  GLU A 152 " =    1.234
peak=    3.958 closest distance to " OD1 ASN A  69 " =    2.696
peak=    3.937 closest distance to " O   HOH Z 118 " =    1.657
peak=    3.926 closest distance to " O   HOH Z 284 " =    1.530
peak=    3.915 closest distance to " O   HOH Z 209 " =    2.276
peak=    3.907 closest distance to " CB BVAL A  41 " =    1.110
peak=    3.906 closest distance to " O   HOH Z 117 " =    2.064
peak=    3.902 closest distance to " CB  ARG A 102 " =    0.786
peak=    3.894 closest distance to " O   HOH Z 130 " =    2.665
peak=    3.892 closest distance to " CZ AARG A 102 " =    1.639
peak=    3.887 closest distance to " CA  TYR A  30 " =    1.090
peak=    3.884 closest distance to " CB  ARG A  79 " =    1.339
peak=    3.868 closest distance to " O   HOH Z   9 " =    2.179
peak=    3.855 closest distance to " O   HOH Z 123 " =    1.141
peak=    3.853 closest distance to " O   HOH Z  61 " =    1.600
peak=    3.852 closest distance to " O   HOH Z 345 " =    3.159
peak=    3.846 closest distance to " O   HOH Z 276 " =    1.388
peak=    3.846 closest distance to " CG2 THR A 221 " =    1.209
peak=    3.841 closest distance to " O   HOH Z 196 " =    3.231
peak=    3.840 closest distance to " CG2 VAL A 257 " =    0.816
peak=    3.835 closest distance to " CB  VAL A 202 " =    1.756
peak=    3.835 closest distance to " O   HOH Z 303 " =    2.230
peak=    3.829 closest distance to " O   HOH Z 136 " =    1.128
peak=    3.827 closest distance to " O   HOH Z 189 " =    2.311
peak=    3.821 closest distance to " O   HOH Z 423 " =    1.877
peak=    3.807 closest distance to " O   HOH Z 250 " =    1.435
peak=    3.771 closest distance to " O   HOH Z 425 " =    1.385
peak=    3.770 closest distance to " CA  VAL A 126 " =    1.051
peak=    3.765 closest distance to " O   HOH Z  48 " =    1.476
peak=    3.751 closest distance to " O   HOH Z 357 " =    1.908
peak=    3.746 closest distance to " O   HOH Z 284 " =    2.841
peak=    3.737 closest distance to " CG1 ILE A  33 " =    1.393
peak=    3.736 closest distance to " CG  LEU A 167 " =    1.139
peak=    3.726 closest distance to " O   HOH Z 214 " =    2.120
peak=    3.707 closest distance to " O   HOH Z 371 " =    3.143
peak=    3.705 closest distance to " CB  ARG A 139 " =    1.004
peak=    3.705 closest distance to " O   HOH Z 209 " =    2.354
peak=    3.702 closest distance to " O   HOH Z 389 " =    1.295
peak=    3.693 closest distance to " O   HOH Z 287 " =    1.553
peak=    3.693 closest distance to " O   HOH Z 145 " =    1.410
peak=    3.691 closest distance to " CB  LEU A 255 " =    0.836
peak=    3.682 closest distance to " O   HOH Z 133 " =    1.339
peak=    3.674 closest distance to " O   HOH Z   7 " =    1.533
peak=    3.662 closest distance to " CG1BVAL A 121 " =    1.080
peak=    3.657 closest distance to " CG  ASN A  60 " =    1.242
peak=    3.657 closest distance to " O   HOH Z 344 " =    2.681
peak=    3.653 closest distance to " O   SER A  26 " =    1.512
peak=    3.646 closest distance to " OE1 GLU A   2 " =    2.104
peak=    3.632 closest distance to " O   HOH Z   6 " =    2.202
peak=    3.629 closest distance to " O   HOH Z 279 " =    1.079
peak=    3.625 closest distance to " CA  VAL A  41 " =    0.832
peak=    3.618 closest distance to " O   HOH Z 193 " =    1.788
peak=    3.609 closest distance to " O   HOH Z 298 " =    1.764
peak=    3.609 closest distance to " O   HOH Z 280 " =    1.590
peak=    3.607 closest distance to " O   HOH Z  10 " =    1.746
peak=    3.601 closest distance to " CA  ALA A  21 " =    1.044
peak=    3.599 closest distance to " O   HOH Z 366 " =    2.930
peak=    3.596 closest distance to " CG AARG A 275 " =    1.145
peak=    3.592 closest distance to " O   HOH Z 128 " =    2.034
peak=    3.591 closest distance to " O   HOH Z 380 " =    1.709
peak=    3.590 closest distance to " O   HOH Z 369 " =    2.036
peak=    3.588 closest distance to " O   GLY A  57 " =    2.431
peak=    3.588 closest distance to " ND2 ASN A 187 " =    1.757
peak=    3.584 closest distance to " O   HOH Z 425 " =    2.062
peak=    3.568 closest distance to " O   HOH Z 303 " =    1.725
peak=    3.559 closest distance to " CG  GLN A  77 " =    0.962
peak=    3.559 closest distance to " O   HOH Z 368 " =    2.089
peak=    3.558 closest distance to " NH1BARG A 145 " =    1.421
peak=    3.558 closest distance to " O   HOH Z 261 " =    2.077
peak=    3.554 closest distance to " O   HOH Z  97 " =    1.298
peak=    3.550 closest distance to " O   HOH Z  43 " =    1.953
peak=    3.549 closest distance to " O   HOH Z 130 " =    1.022
peak=    3.544 closest distance to " CB  GLU A 277 " =    3.474
peak=    3.544 closest distance to " NH1 ARG A 138 " =    1.148
peak=    3.540 closest distance to " O   HOH Z 213 " =    1.781
peak=    3.537 closest distance to " O   HOH Z 389 " =    2.950
peak=    3.535 closest distance to " O   HOH Z  89 " =    2.213
peak=    3.533 closest distance to " C   ALA A 299 " =    0.941
peak=    3.529 closest distance to " O   HOH Z 130 " =    2.262
peak=    3.520 closest distance to " N   TRP A 177 " =    1.662
peak=    3.516 closest distance to " CD  GLN A 194 " =    1.474
peak=    3.516 closest distance to " O   HOH Z 193 " =    1.873
peak=    3.514 closest distance to " CA  PHE A 283 " =    1.300
peak=    3.514 closest distance to " O   HOH Z 153 " =    3.597
peak=    3.513 closest distance to " N   ARG A 156 " =    1.259
peak=    3.513 closest distance to " CB  SER A  62 " =    1.221
peak=    3.512 closest distance to " CB  SER A 216 " =    0.839
peak=    3.509 closest distance to " CG  MET A 188 " =    1.282
peak=    3.507 closest distance to " CG  GLN A  88 " =    1.066
peak=    3.507 closest distance to " NZ  LYS A  76 " =    1.341
peak=    3.500 closest distance to " CB  SER A  26 " =    1.547
peak=    3.492 closest distance to " O   HOH Z 152 " =    2.744
peak=    3.486 closest distance to " CB  GLU A 128 " =    1.097
peak=    3.484 closest distance to " O   HOH Z  63 " =    1.122
peak=    3.483 closest distance to " O   HOH Z 403 " =    1.613
peak=    3.482 closest distance to " O   HOH Z  61 " =    1.584
peak=    3.482 closest distance to " O   HOH Z  67 " =    1.687
peak=    3.479 closest distance to " CB  LEU A 228 " =    1.365
peak=    3.479 closest distance to " CD1 LEU A 228 " =    1.602
peak=    3.477 closest distance to " CB  ASN A 148 " =    1.859
peak=    3.468 closest distance to " OG BSER A 164 " =    2.274
peak=    3.468 closest distance to " O   HOH Z 249 " =    1.091
peak=    3.465 closest distance to " CA  LYS A 117 " =    1.200
peak=    3.462 closest distance to " O   HOH Z 196 " =    1.372
peak=    3.461 closest distance to " O   HOH Z 423 " =    1.433
peak=    3.457 closest distance to " OG  SER A  62 " =    3.030
peak=    3.455 closest distance to " NH2BARG A 190 " =    1.627
peak=    3.446 closest distance to " O   HOH Z 406 " =    1.588
peak=    3.439 closest distance to " CB  ALA A   1 " =    4.480
peak=    3.436 closest distance to " CG2 ILE A 120 " =    1.310
peak=    3.435 closest distance to " O   HOH Z 430 " =    1.749
peak=    3.432 closest distance to " O   HOH Z 247 " =    1.235
peak=    3.429 closest distance to " O   HOH Z 108 " =    1.747
peak=    3.428 closest distance to " CG  GLN A  77 " =    2.266
peak=    3.428 closest distance to " CB  TYR A  30 " =    1.670
peak=    3.427 closest distance to " O   HOH Z 411 " =    1.761
peak=    3.426 closest distance to " O   HOH Z 261 " =    1.623
peak=    3.424 closest distance to " O   HOH Z 222 " =    2.243
peak=    3.422 closest distance to " CB  SER A 273 " =    0.854
peak=    3.419 closest distance to " CD2 TRP A 179 " =    1.407
peak=    3.418 closest distance to " CA  LEU A 101 " =    1.484
peak=    3.417 closest distance to " O   HOH Z 422 " =    2.440
peak=    3.414 closest distance to " O   HOH Z  89 " =    1.653
peak=    3.409 closest distance to " CA  ALA A 248 " =    1.291
peak=    3.403 closest distance to " O   ALA A 165 " =    1.188
peak=    3.403 closest distance to " CB  THR A 157 " =    0.997
peak=    3.400 closest distance to " O   HOH Z  22 " =    2.143
peak=    3.398 closest distance to " O   PRO A 198 " =    1.223
peak=    3.392 closest distance to " NE2 GLN A  58 " =    5.640
peak=    3.390 closest distance to " O   HOH Z 374 " =    2.426
peak=    3.383 closest distance to " CG  PRO A 243 " =    1.255
peak=    3.381 closest distance to " CD1 ILE A  33 " =    1.621
peak=    3.380 closest distance to " CA  GLN A 194 " =    1.259
peak=    3.380 closest distance to " O   HOH Z  88 " =    3.151
peak=    3.374 closest distance to " O   HOH Z 180 " =    2.146
peak=    3.369 closest distance to " CG1 VAL A 153 " =    0.923
peak=    3.368 closest distance to " CB  PRO A 198 " =    0.945
peak=    3.368 closest distance to " O   SER A 164 " =    1.275
peak=    3.367 closest distance to " NZ  LYS A 117 " =    1.037
peak=    3.365 closest distance to " N   PHE A 130 " =    1.365
peak=    3.363 closest distance to " O   HOH Z 299 " =    4.013
peak=    3.362 closest distance to " O   HOH Z 194 " =    2.135
peak=    3.361 closest distance to " CB  ALA A  34 " =    0.964
peak=    3.359 closest distance to " O   HOH Z  54 " =    1.514
peak=    3.358 closest distance to " O   HOH Z 128 " =    1.946
peak=    3.358 closest distance to " O   HOH Z 172 " =    5.744
peak=    3.357 closest distance to " CG AARG A 275 " =    1.153
peak=    3.357 closest distance to " O   HOH Z  80 " =    1.689
peak=    3.353 closest distance to " CE1 TYR A 186 " =    1.211
peak=    3.351 closest distance to " O   HOH Z  68 " =    2.189
peak=    3.351 closest distance to " CA  THR A 221 " =    0.879
peak=    3.349 closest distance to " O   HOH Z 172 " =    3.606
peak=    3.345 closest distance to " O   HOH Z  15 " =    1.416
peak=    3.340 closest distance to " O   HOH Z 248 " =    1.821
peak=    3.340 closest distance to " O   HOH Z 405 " =    1.258
peak=    3.337 closest distance to " OG1 THR A 294 " =    2.386
peak=    3.335 closest distance to " CG  MET A 185 " =    1.242
peak=    3.330 closest distance to " O   HOH Z 148 " =    3.212
peak=    3.328 closest distance to " O   HOH Z 426 " =    2.935
peak=    3.326 closest distance to " O   HOH Z 352 " =    1.289
peak=    3.324 closest distance to " NH2BARG A 145 " =    1.288
peak=    3.323 closest distance to " CG  ARG A  66 " =    0.987
peak=    3.319 closest distance to " O   HOH Z 106 " =    2.236
peak=    3.319 closest distance to " O   HOH Z  50 " =    1.515
peak=    3.318 closest distance to " CB  ILE A 234 " =    0.934
peak=    3.317 closest distance to " CA  ASN A 127 " =    1.013
peak=    3.308 closest distance to " CA  LYS A 290 " =    1.265
peak=    3.307 closest distance to " O   MET A 105 " =    1.810
peak=    3.302 closest distance to " CB  TRP A 266 " =    1.062
peak=    3.302 closest distance to " O   GLN A  58 " =    1.445
peak=    3.298 closest distance to " O   HOH Z 313 " =    1.833
peak=    3.297 closest distance to " CA  ALA A  51 " =    0.993
peak=    3.295 closest distance to " CA  ASN A 284 " =    0.981
peak=    3.295 closest distance to " OD1 ASP A 286 " =    1.529
peak=    3.293 closest distance to " CD BLYS A 290 " =    1.177
peak=    3.292 closest distance to " O   HOH Z 285 " =    1.678
peak=    3.292 closest distance to " O   HOH Z 191 " =    1.453
peak=    3.290 closest distance to " O   HOH Z 302 " =    1.589
peak=    3.287 closest distance to " O   HOH Z  58 " =    1.781
peak=    3.281 closest distance to " O   HOH Z 356 " =    1.272
peak=    3.275 closest distance to " O   HOH Z 383 " =    1.795
peak=    3.274 closest distance to " OE2 GLU A  53 " =    1.989
peak=    3.273 closest distance to " ND1 HIS A  81 " =    1.468
peak=    3.272 closest distance to " O   HOH Z  59 " =    2.201
peak=    3.271 closest distance to " O   HOH Z  68 " =    2.776
peak=    3.271 closest distance to " CD2 HIS A  81 " =    1.116
peak=    3.268 closest distance to " O   HOH Z 217 " =    1.293
peak=    3.268 closest distance to " CD  LYS A 119 " =    1.618
peak=    3.267 closest distance to " O   HOH Z 403 " =    1.336
peak=    3.264 closest distance to " O   HOH Z 291 " =    1.601
peak=    3.263 closest distance to " CA  ASN A 215 " =    1.119
peak=    3.262 closest distance to " OG  SER A  97 " =    2.582
peak=    3.260 closest distance to " NH2BARG A 145 " =    2.174
peak=    3.255 closest distance to " O   HOH Z   1 " =    1.517
peak=    3.250 closest distance to " CB  CYS A 201 " =    0.930
peak=    3.250 closest distance to " N   ASN A  39 " =    1.124
peak=    3.241 closest distance to " O   HOH Z 280 " =    2.438
peak=    3.239 closest distance to " O   HOH Z 283 " =    1.630
peak=    3.239 closest distance to " CD2 TYR A  30 " =    0.953
peak=    3.236 closest distance to " CB  ALA A   9 " =    1.530
peak=    3.232 closest distance to " N   SER A 135 " =    1.328
peak=    3.232 closest distance to " CD  PRO A 243 " =    1.551
peak=    3.229 closest distance to " O   HOH Z 273 " =    3.068
peak=    3.228 closest distance to " CB  PRO A  90 " =    1.423
peak=    3.224 closest distance to " CB  THR A  31 " =    1.697
peak=    3.224 closest distance to " CB  ALA A   1 " =    1.132
peak=    3.215 closest distance to " N   ALA A 256 " =    0.908
peak=    3.214 closest distance to " O   HOH Z  43 " =    2.637
peak=    3.214 closest distance to " CZ2 TRP A 274 " =    1.747
peak=    3.211 closest distance to " CA  THR A 264 " =    0.772
peak=    3.210 closest distance to " O   ALA A 158 " =    1.283
peak=    3.206 closest distance to " CB  VAL A 296 " =    0.940
peak=    3.201 closest distance to " CB  GLN A 278 " =    0.773
peak=    3.200 closest distance to " CB  ALA A  84 " =    1.661
peak=    3.197 closest distance to " O   ASN A 217 " =    1.195
peak=    3.195 closest distance to " O   HOH Z 426 " =    1.450
peak=    3.194 closest distance to " N   VAL A 126 " =    1.125
peak=    3.192 closest distance to " C   GLU A 277 " =    1.367
peak=    3.188 closest distance to " CG  GLN A  89 " =    1.499
peak=    3.188 closest distance to " CA  ARG A  66 " =    0.901
peak=    3.186 closest distance to " CA  ARG A 275 " =    1.945
peak=    3.180 closest distance to " CG  ARG A 138 " =    0.909
peak=    3.170 closest distance to " CE  MET A  93 " =    1.518
peak=    3.166 closest distance to " O   HOH Z 151 " =    1.621
peak=    3.163 closest distance to " O  BHOH Z 338 " =    2.500
peak=    3.162 closest distance to " O   HOH Z 112 " =    1.701
peak=    3.158 closest distance to " NH1BARG A 190 " =    2.023
peak=    3.157 closest distance to " O   HOH Z 251 " =    1.522
peak=    3.154 closest distance to " O   HOH Z  88 " =    2.331
peak=    3.149 closest distance to " CA  ALA A 233 " =    1.104
peak=    3.149 closest distance to " O   HOH Z 303 " =    2.981
peak=    3.147 closest distance to " O   HOH Z 233 " =    1.536
peak=    3.134 closest distance to " NE1 TRP A 274 " =    0.928
peak=    3.134 closest distance to " O   HOH Z 368 " =    3.713
peak=    3.134 closest distance to " O   HOH Z 158 " =    2.826
peak=    3.133 closest distance to " N   GLN A 278 " =    0.996
peak=    3.132 closest distance to " CB  ALA A 114 " =    1.403
peak=    3.127 closest distance to " CG2 ILE A  20 " =    1.680
peak=    3.123 closest distance to " NE2 GLN A 223 " =    1.589
peak=    3.120 closest distance to " OG  SER A  95 " =    1.508
peak=    3.114 closest distance to " CB  ASN A 215 " =    0.933
peak=    3.108 closest distance to " O   HOH Z 265 " =    2.203
peak=    3.107 closest distance to " CA  ASN A 217 " =    1.229
peak=    3.104 closest distance to " O   HOH Z  30 " =    2.097
peak=    3.087 closest distance to " CA  ASN A 176 " =    1.077
peak=    3.087 closest distance to " CA  ASP A 191 " =    0.902
peak=    3.085 closest distance to " CD1 LEU A   5 " =    1.680
peak=    3.085 closest distance to " OG ASER A 134 " =    1.525
peak=    3.082 closest distance to " O   HOH Z 329 " =    3.173
peak=    3.082 closest distance to " OD1BASN A 224 " =    2.191
peak=    3.075 closest distance to " O   HOH Z 408 " =    1.453
peak=    3.069 closest distance to " O   HOH Z 125 " =    2.414
peak=    3.067 closest distance to " CG  LEU A 281 " =    0.974
peak=    3.061 closest distance to " O   HOH Z 423 " =    2.406
peak=    3.053 closest distance to " O   HOH Z 110 " =    1.553
peak=    3.047 closest distance to " CA  ALA A 158 " =    1.087
peak=    3.030 closest distance to " NZ  LYS A 119 " =    1.513
peak=    3.022 closest distance to " CE3 TRP A 274 " =    2.334
peak=    3.012 closest distance to " CB  TRP A 179 " =    1.788

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 175         
Filter by distance & map next to the model:
   mapped sites are within: 0.676 - 5.195
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 173 from: 175
   mapped sites are within: 0.726 - 5.195

peak=   -4.652 closest distance to " CG2 VAL A 230 " =    0.726
peak=   -4.637 closest distance to " O   HOH Z  43 " =    2.025
peak=   -4.497 closest distance to " CD  ARG A 156 " =    1.991
peak=   -4.441 closest distance to " SG  CYS A 254 " =    3.182
peak=   -4.387 closest distance to " CG2 THR A   4 " =    1.917
peak=   -4.338 closest distance to " N   GLN A  58 " =    1.808
peak=   -4.273 closest distance to " O   HOH Z 231 " =    1.533
peak=   -4.230 closest distance to " CB  TYR A  15 " =    2.095
peak=   -4.195 closest distance to " N   HIS A 115 " =    1.949
peak=   -4.139 closest distance to " NH2 ARG A  79 " =    1.934
peak=   -4.121 closest distance to " O   HOH Z  98 " =    1.621
peak=   -4.046 closest distance to " O   PRO A 163 " =    1.967
peak=   -4.043 closest distance to " C   HIS A 108 " =    1.157
peak=   -4.028 closest distance to " CD1 LEU A 101 " =    2.347
peak=   -3.996 closest distance to " CD1 LEU A 255 " =    2.754
peak=   -3.996 closest distance to " CE2 TYR A  30 " =    2.858
peak=   -3.964 closest distance to " O   PRO A 198 " =    1.322
peak=   -3.919 closest distance to " O   HOH Z 290 " =    0.988
peak=   -3.898 closest distance to " NH1 ARG A  56 " =    2.503
peak=   -3.891 closest distance to " O   ALA A 161 " =    1.586
peak=   -3.887 closest distance to " O   ASN A 187 " =    1.409
peak=   -3.861 closest distance to " CB  ALA A 248 " =    1.928
peak=   -3.850 closest distance to " O   HOH Z 166 " =    1.436
peak=   -3.840 closest distance to " N   ALA A 248 " =    1.654
peak=   -3.835 closest distance to " O   ILE A 109 " =    2.556
peak=   -3.806 closest distance to " O   HOH Z 266 " =    4.373
peak=   -3.804 closest distance to " C   ASP A 231 " =    2.484
peak=   -3.796 closest distance to " O   HOH Z  93 " =    1.494
peak=   -3.788 closest distance to " O   VAL A  67 " =    2.817
peak=   -3.785 closest distance to " OG ASER A 134 " =    1.166
peak=   -3.777 closest distance to " CD  GLU A 152 " =    2.514
peak=   -3.775 closest distance to " CG  PHE A 283 " =    2.601
peak=   -3.756 closest distance to " CD  GLN A  88 " =    0.911
peak=   -3.750 closest distance to " CG  LYS A 193 " =    2.284
peak=   -3.748 closest distance to " O   HOH Z 198 " =    2.068
peak=   -3.745 closest distance to " O   HOH Z 103 " =    1.666
peak=   -3.715 closest distance to " O   HOH Z 388 " =    2.022
peak=   -3.707 closest distance to " O   HOH Z 102 " =    1.711
peak=   -3.681 closest distance to " CA  GLY A  35 " =    2.055
peak=   -3.671 closest distance to " O   HOH Z 111 " =    4.451
peak=   -3.668 closest distance to " CE2 PHE A 218 " =    2.622
peak=   -3.665 closest distance to " O   VAL A  67 " =    2.630
peak=   -3.662 closest distance to " OG BSER A 134 " =    1.234
peak=   -3.648 closest distance to " C   ASN A 285 " =    2.121
peak=   -3.641 closest distance to " CG2 VAL A 296 " =    1.928
peak=   -3.637 closest distance to " CB  ALA A 244 " =    2.041
peak=   -3.632 closest distance to " O   HOH Z  11 " =    1.979
peak=   -3.630 closest distance to " OG  SER A   3 " =    1.344
peak=   -3.626 closest distance to " OD2 ASP A  50 " =    1.414
peak=   -3.605 closest distance to " O   PRO A 198 " =    1.301
peak=   -3.602 closest distance to " OD1 ASP A 191 " =    1.503
peak=   -3.601 closest distance to " N   SER A 276 " =    1.138
peak=   -3.599 closest distance to " CG  LEU A 228 " =    1.056
peak=   -3.597 closest distance to " O   HOH Z 191 " =    5.058
peak=   -3.592 closest distance to " CG2AVAL A  41 " =    2.973
peak=   -3.589 closest distance to " O   HOH Z 423 " =    2.139
peak=   -3.587 closest distance to " OXT GLY A 302 " =    2.795
peak=   -3.587 closest distance to " O   HOH Z 364 " =    2.733
peak=   -3.581 closest distance to " CG  ASP A 231 " =    0.754
peak=   -3.572 closest distance to " CB  PRO A 243 " =    2.557
peak=   -3.568 closest distance to " O   HOH Z 410 " =    2.124
peak=   -3.553 closest distance to " O   HOH Z 100 " =    1.099
peak=   -3.530 closest distance to " O   ALA A 158 " =    1.047
peak=   -3.527 closest distance to " CB  ALA A  51 " =    1.769
peak=   -3.527 closest distance to " O   HOH Z 426 " =    2.286
peak=   -3.524 closest distance to " OG  SER A 206 " =    1.514
peak=   -3.520 closest distance to " O   ILE A  49 " =    1.738
peak=   -3.520 closest distance to " NH2AARG A 275 " =    5.195
peak=   -3.507 closest distance to " C   LEU A 143 " =    1.142
peak=   -3.506 closest distance to " ND2 ASN A  39 " =    1.318
peak=   -3.496 closest distance to " O   HOH Z 377 " =    0.898
peak=   -3.491 closest distance to " O   HOH Z 407 " =    3.034
peak=   -3.489 closest distance to " CA  GLY A 133 " =    1.892
peak=   -3.487 closest distance to " CB  PRO A 280 " =    2.142
peak=   -3.485 closest distance to " O   ASP A 191 " =    1.680
peak=   -3.483 closest distance to " N   MET A 188 " =    1.817
peak=   -3.480 closest distance to " O   HOH Z 339 " =    1.712
peak=   -3.479 closest distance to " OD1 ASP A 200 " =    1.169
peak=   -3.472 closest distance to " O   HOH Z 165 " =    2.242
peak=   -3.467 closest distance to " CD  LYS A 289 " =    2.523
peak=   -3.466 closest distance to " CA  ASP A 298 " =    1.071
peak=   -3.460 closest distance to " OD2 ASP A 191 " =    1.426
peak=   -3.444 closest distance to " O   HOH Z  63 " =    0.986
peak=   -3.436 closest distance to " OG BSER A 134 " =    1.646
peak=   -3.434 closest distance to " O   HOH Z 250 " =    1.360
peak=   -3.425 closest distance to " O   HOH Z 427 " =    1.560
peak=   -3.423 closest distance to " O   ALA A  51 " =    1.256
peak=   -3.422 closest distance to " O   TRP A  70 " =    1.510
peak=   -3.398 closest distance to " O   HOH Z 308 " =    1.650
peak=   -3.396 closest distance to " CD1 LEU A 228 " =    2.041
peak=   -3.392 closest distance to " O   HOH Z 175 " =    4.412
peak=   -3.387 closest distance to " ND2 ASN A  45 " =    1.055
peak=   -3.382 closest distance to " O   SER A  22 " =    2.359
peak=   -3.381 closest distance to " OE1 GLN A  88 " =    1.160
peak=   -3.381 closest distance to " O   HOH Z 351 " =    1.434
peak=   -3.379 closest distance to " O   HOH Z 365 " =    1.302
peak=   -3.374 closest distance to " O   HOH Z 148 " =    2.039
peak=   -3.371 closest distance to " O   SER A 135 " =    1.565
peak=   -3.371 closest distance to " O   HOH Z 350 " =    2.044
peak=   -3.368 closest distance to " O   GLY A  57 " =    1.345
peak=   -3.367 closest distance to " O   HOH Z 389 " =    1.792
peak=   -3.364 closest distance to " O   HOH Z  56 " =    1.887
peak=   -3.357 closest distance to " CB  ASN A  39 " =    2.070
peak=   -3.353 closest distance to " O   HOH Z 134 " =    2.691
peak=   -3.352 closest distance to " O   HOH Z 385 " =    1.799
peak=   -3.350 closest distance to " CB  PRO A 163 " =    2.548
peak=   -3.348 closest distance to " O   MET A  40 " =    2.621
peak=   -3.325 closest distance to " O   SER A 146 " =    0.888
peak=   -3.324 closest distance to " O   HOH Z 231 " =    1.028
peak=   -3.324 closest distance to " O   HOH Z 143 " =    0.865
peak=   -3.324 closest distance to " O   HOH Z 184 " =    1.029
peak=   -3.316 closest distance to " CE3 TRP A 274 " =    2.341
peak=   -3.312 closest distance to " O   HOH Z  75 " =    1.849
peak=   -3.311 closest distance to " OD1 ASN A 249 " =    1.300
peak=   -3.310 closest distance to " O   HOH Z 385 " =    2.079
peak=   -3.295 closest distance to " OG1 THR A  82 " =    1.398
peak=   -3.287 closest distance to " OH  TYR A 214 " =    1.348
peak=   -3.282 closest distance to " O   HOH Z 352 " =    1.058
peak=   -3.268 closest distance to " O   HOH Z 193 " =    1.620
peak=   -3.266 closest distance to " CG  PRO A 163 " =    2.784
peak=   -3.265 closest distance to " C   ALA A 158 " =    1.202
peak=   -3.253 closest distance to " CB  ASP A 132 " =    2.207
peak=   -3.250 closest distance to " N   GLN A  77 " =    1.522
peak=   -3.248 closest distance to " O   ASP A 270 " =    1.834
peak=   -3.246 closest distance to " O   HOH Z  47 " =    1.466
peak=   -3.245 closest distance to " O   ASP A 231 " =    2.374
peak=   -3.242 closest distance to " O   HOH Z 368 " =    2.205
peak=   -3.242 closest distance to " O   HOH Z 436 " =    1.398
peak=   -3.239 closest distance to " O   HOH Z 392 " =    0.856
peak=   -3.237 closest distance to " CB  ILE A  33 " =    2.855
peak=   -3.231 closest distance to " O   HOH Z 211 " =    1.506
peak=   -3.226 closest distance to " O   HOH Z 402 " =    1.395
peak=   -3.225 closest distance to " CG  TRP A 266 " =    1.689
peak=   -3.223 closest distance to " CG  ASP A  50 " =    2.068
peak=   -3.223 closest distance to " O   HOH Z 417 " =    2.530
peak=   -3.222 closest distance to " O   HOH Z 281 " =    3.219
peak=   -3.221 closest distance to " O   HOH Z 344 " =    2.498
peak=   -3.209 closest distance to " O   ALA A   8 " =    1.721
peak=   -3.208 closest distance to " CB  ALA A  43 " =    2.283
peak=   -3.206 closest distance to " O   HOH Z 313 " =    1.642
peak=   -3.192 closest distance to " NE1 TRP A 274 " =    1.272
peak=   -3.188 closest distance to " O   TRP A  92 " =    1.764
peak=   -3.184 closest distance to " CG  MET A 105 " =    0.906
peak=   -3.181 closest distance to " OD2 ASP A 270 " =    1.287
peak=   -3.178 closest distance to " O   THR A 220 " =    1.700
peak=   -3.175 closest distance to " OG BSER A  99 " =    0.933
peak=   -3.168 closest distance to " CG  GLN A 223 " =    1.752
peak=   -3.168 closest distance to " O   HOH Z 137 " =    1.522
peak=   -3.162 closest distance to " CD2 TYR A 293 " =    2.091
peak=   -3.160 closest distance to " CD1 ILE A 239 " =    2.528
peak=   -3.159 closest distance to " CG2 VAL A 112 " =    2.501
peak=   -3.151 closest distance to " CZ  TYR A 169 " =    1.739
peak=   -3.151 closest distance to " CG  ASN A 217 " =    2.302
peak=   -3.143 closest distance to " N   PRO A 163 " =    1.588
peak=   -3.133 closest distance to " O   HOH Z 131 " =    3.904
peak=   -3.131 closest distance to " O   HOH Z 198 " =    1.471
peak=   -3.128 closest distance to " O   HOH Z 404 " =    1.479
peak=   -3.124 closest distance to " O   GLY A  80 " =    2.466
peak=   -3.116 closest distance to " O   HOH Z 193 " =    2.289
peak=   -3.104 closest distance to " CG  ARG A 219 " =    2.312
peak=   -3.100 closest distance to " CE  MET A 105 " =    1.940
peak=   -3.100 closest distance to " O   GLY A  98 " =    1.964
peak=   -3.092 closest distance to " O   HOH Z 137 " =    1.397
peak=   -3.090 closest distance to " O   HOH Z  88 " =    2.156
peak=   -3.088 closest distance to " O   HOH Z 211 " =    1.310
peak=   -3.088 closest distance to " CD  LYS A 166 " =    2.546
peak=   -3.087 closest distance to " OG  SER A  62 " =    1.618
peak=   -3.066 closest distance to " O   GLY A 118 " =    1.413
peak=   -3.043 closest distance to " O   HOH Z  13 " =    1.407
peak=   -3.040 closest distance to " CE BMET A  47 " =    1.375
peak=   -3.039 closest distance to " O   HOH Z 234 " =    3.937
peak=   -3.034 closest distance to " O   HOH Z 407 " =    3.417
peak=   -3.020 closest distance to " CD1 ILE A 151 " =    2.340

================= 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    :  0.4889 0.4801   6.287013e+00   6.279138e+00
   1_bss:  0.4806 0.4714   6.281564e+00   6.268112e+00
   1_xyz:  0.4119 0.4267   6.198239e+00   6.219020e+00
   1_adp:  0.3690 0.4209   6.134119e+00   6.205477e+00
   1_occ:  0.3683 0.4213   6.133806e+00   6.206083e+00
   2_bss:  0.3650 0.4171   6.133564e+00   6.203938e+00
   2_xyz:  0.2818 0.3378   5.927747e+00   6.064419e+00
   2_adp:  0.2584 0.3186   5.867392e+00   6.020138e+00
   2_occ:  0.2581 0.3192   5.867490e+00   6.020825e+00
   3_bss:  0.2568 0.3183   5.865996e+00   6.019055e+00
   3_xyz:  0.1834 0.2376   5.573882e+00   5.773782e+00
   3_adp:  0.1590 0.2131   5.447698e+00   5.670280e+00
   3_occ:  0.1587 0.2129   5.446865e+00   5.669295e+00
   4_bss:  0.1582 0.2111   5.440475e+00   5.662767e+00
   4_xyz:  0.1344 0.1823   5.293472e+00   5.521640e+00
   4_adp:  0.1288 0.1731   5.250775e+00   5.470911e+00
   4_occ:  0.1286 0.1729   5.249690e+00   5.469850e+00
   5_bss:  0.1287 0.1734   5.249710e+00   5.469581e+00
   5_xyz:  0.1174 0.1625   5.172898e+00   5.404987e+00
   5_adp:  0.1155 0.1623   5.163633e+00   5.399494e+00
   5_occ:  0.1154 0.1622   5.163286e+00   5.399083e+00
   5_bss:  0.1154 0.1622   5.163286e+00   5.399053e+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:  0.399  20.000   6.327   8.179   9.273   0.000   0.000   0.000
   1_xyz:  0.399  20.000   6.327   8.179   9.273   0.000   0.000   0.000
   1_adp:  0.399  20.000   6.327   8.179   9.273   0.000   0.000   0.000
   1_occ:  0.399  20.000   6.327   8.179   9.273   0.000   0.000   0.000
   2_bss:  0.356  29.668   2.994   4.005   5.841   0.000   0.000   0.000
   2_xyz:  0.356  29.668   2.994   4.005   5.841   0.000   0.000   0.000
   2_adp:  0.356  29.668   2.994   4.005   5.841   0.000   0.000   0.000
   2_occ:  0.356  29.668   2.994   4.005   5.841   0.000   0.000   0.000
   3_bss:  0.334  29.668   1.602   2.472   3.930   0.000   0.000   0.000
   3_xyz:  0.334  29.668   1.602   2.472   3.930   0.000   0.000   0.000
   3_adp:  0.334  29.668   1.602   2.472   3.930   0.000   0.000   0.000
   3_occ:  0.334  29.668   1.602   2.472   3.930   0.000   0.000   0.000
   4_bss:  0.309  32.694   1.105   1.518   2.414   0.000   0.000   0.000
   4_xyz:  0.309  32.694   1.105   1.518   2.414   0.000   0.000   0.000
   4_adp:  0.309  32.694   1.105   1.518   2.414   0.000   0.000   0.000
   4_occ:  0.309  32.694   1.105   1.518   2.414   0.000   0.000   0.000
   5_bss:  0.318  33.391   1.048   1.382   2.008   0.000   0.000   0.000
   5_xyz:  0.318  33.391   1.048   1.382   2.008   0.000   0.000   0.000
   5_adp:  0.318  33.391   1.048   1.382   2.008   0.000   0.000   0.000
   5_occ:  0.318  33.391   1.048   1.382   2.008   0.000   0.000   0.000
   5_bss:  0.322  35.850  -0.431  -0.098   0.529   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  58.520 0.4137  0.4967    73928.838
   1_bss:  59.034 0.4049  0.6073    70855.129
   1_xyz:  49.555 0.5256  0.7770    54820.070
   1_adp:  47.822 0.5476  0.8659    52903.463
   1_occ:  47.965 0.5457  0.8622    53018.052
   2_bss:  47.620 0.5498  0.7625    52414.667
   2_xyz:  36.475 0.6835  0.9300    31542.369
   2_adp:  33.279 0.7210  0.9744    27580.578
   2_occ:  33.315 0.7206  0.9737    27663.034
   3_bss:  33.161 0.7222  0.9201    27446.541
   3_xyz:  23.826 0.8233  1.0027    14775.989
   3_adp:  20.566 0.8566  1.0163    11784.180
   3_occ:  20.547 0.8568  1.0162    11751.852
   4_bss:  20.324 0.8586  0.9805    11460.009
   4_xyz:  16.896 0.8903  0.9952     8337.554
   4_adp:  15.658 0.9014  0.9967     7520.276
   4_occ:  15.628 0.9017  0.9968     7497.144
   5_bss:  15.626 0.9018  0.9895     7508.301
   5_xyz:  14.348 0.9120  0.9942     6524.836
   5_adp:  14.213 0.9133  0.9916     6467.145
   5_occ:  14.205 0.9134  0.9915     6458.367
   5_bss:  14.204 0.9134  0.9916     6459.538
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.087   5.2808e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.087   5.2808e+01
   1_xyz:   1.637  0.012  0.105 18.291  0.006  4.106   1.3580e-01
   1_adp:   1.637  0.012  0.105 18.291  0.006  4.106   1.3580e-01
   1_occ:   1.637  0.012  0.105 18.291  0.006  4.106   1.3580e-01
   2_bss:   1.637  0.012  0.105 18.291  0.006  4.106   1.3580e-01
   2_xyz:   1.200  0.009  0.084 16.416  0.005  4.106   8.8189e-02
   2_adp:   1.200  0.009  0.084 16.416  0.005  4.106   8.8189e-02
   2_occ:   1.200  0.009  0.084 16.416  0.005  4.106   8.8189e-02
   3_bss:   1.200  0.009  0.084 16.416  0.005  4.106   8.8189e-02
   3_xyz:   1.148  0.008  0.082 16.220  0.004  4.117   7.6631e-02
   3_adp:   1.148  0.008  0.082 16.220  0.004  4.117   7.6631e-02
   3_occ:   1.148  0.008  0.082 16.220  0.004  4.117   7.6631e-02
   4_bss:   1.148  0.008  0.082 16.220  0.004  4.117   7.6631e-02
   4_xyz:   0.944  0.005  0.068 15.714  0.003  4.106   5.6422e-02
   4_adp:   0.944  0.005  0.068 15.714  0.003  4.106   5.6422e-02
   4_occ:   0.944  0.005  0.068 15.714  0.003  4.106   5.6422e-02
   5_bss:   0.944  0.005  0.068 15.714  0.003  4.106   5.6422e-02
   5_xyz:   0.999  0.006  0.074 15.598  0.004  4.106   6.0035e-02
   5_adp:   0.999  0.006  0.074 15.598  0.004  4.106   6.0035e-02
   5_occ:   0.999  0.006  0.074 15.598  0.004  4.106   6.0035e-02
   5_bss:   0.999  0.006  0.074 15.598  0.004  4.106   6.0035e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.798   6.8416e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.798   6.8416e+00
   1_xyz:  13.196  0.163  0.424 84.392  0.052  2.200   9.2084e-02
   1_adp:  13.196  0.163  0.424 84.392  0.052  2.200   9.2084e-02
   1_occ:  13.196  0.163  0.424 84.392  0.052  2.200   9.2084e-02
   2_bss:  13.196  0.163  0.424 84.392  0.052  2.200   9.2084e-02
   2_xyz:   7.456  0.075  0.398 76.502  0.046  2.223   6.2300e-02
   2_adp:   7.456  0.075  0.398 76.502  0.046  2.223   6.2300e-02
   2_occ:   7.456  0.075  0.398 76.502  0.046  2.223   6.2300e-02
   3_bss:   7.456  0.075  0.398 76.502  0.046  2.223   6.2300e-02
   3_xyz:   6.958  0.056  0.395 83.661  0.026  2.290   7.3966e-02
   3_adp:   6.958  0.056  0.395 83.661  0.026  2.290   7.3966e-02
   3_occ:   6.958  0.056  0.395 83.661  0.026  2.290   7.3966e-02
   4_bss:   6.958  0.056  0.395 83.661  0.026  2.290   7.3966e-02
   4_xyz:   6.400  0.031  0.291 83.054  0.029  2.338   3.9371e-02
   4_adp:   6.400  0.031  0.291 83.054  0.029  2.338   3.9371e-02
   4_occ:   6.400  0.031  0.291 83.054  0.029  2.338   3.9371e-02
   5_bss:   6.400  0.031  0.291 83.054  0.029  2.338   3.9371e-02
   5_xyz:   6.602  0.042  0.366 85.009  0.034  2.271   4.1159e-02
   5_adp:   6.602  0.042  0.366 85.009  0.034  2.271   4.1159e-02
   5_occ:   6.602  0.042  0.366 85.009  0.034  2.271   4.1159e-02
   5_bss:   6.602  0.042  0.366 85.009  0.034  2.271   4.1159e-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:  78.38   0.00  14.04  78.38   0.00  11.85  75.98   0.00  25.94
   1_occ:  78.38   0.00  14.04  78.38   0.00  11.85  75.98   0.00  25.94
   2_bss:  78.38   0.00  14.04  78.38   0.00  11.85  75.98   0.00  25.94
   2_xyz:  78.38   0.00  14.04  78.38   0.00  11.85  75.98   0.00  25.94
   2_adp:  80.82   0.00  13.76  80.82   0.00  10.58  74.84   0.00  31.03
   2_occ:  80.82   0.00  13.76  80.82   0.00  10.58  74.84   0.00  31.03
   3_bss:  80.82   0.00  13.76  80.82   0.00  10.58  74.84   0.00  31.03
   3_xyz:  80.82   0.00  13.76  80.82   0.00  10.58  74.84   0.00  31.03
   3_adp:  89.76   0.00  14.25  89.76   0.00   9.77  81.18   1.87  38.67
   3_occ:  89.76   0.00  14.25  89.76   0.00   9.77  81.18   1.87  38.67
   4_bss:  89.76   0.00  14.25  89.76   0.00   9.77  81.18   1.87  38.67
   4_xyz:  89.76   0.00  14.25  89.76   0.00   9.77  81.18   1.87  38.67
   4_adp:  88.24   0.00  13.78  88.24   0.00   9.40  85.86   2.79  37.61
   4_occ:  88.24   0.00  13.78  88.24   0.00   9.40  85.86   2.79  37.61
   5_bss:  88.24   0.00  13.78  88.24   0.00   9.40  85.86   2.79  37.61
   5_xyz:  88.24   0.00  13.78  88.24   0.00   9.40  85.86   2.79  37.61
   5_adp:  92.46   0.00  13.64  92.46   0.00   9.27  88.38   2.90  37.40
   5_occ:  92.46   0.00  13.64  92.46   0.00   9.27  88.38   2.90  37.40
   5_bss:  93.94   1.48  15.11  93.94   1.48  10.75  89.86   4.38  38.88
------------------------------------------------------------------------
 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:    1.236    0.025    0.405
   1_adp:    1.236    0.025    0.405
   1_occ:    1.236    0.025    0.405
   2_bss:    1.236    0.025    0.405
   2_xyz:    1.661    0.033    0.578
   2_adp:    1.661    0.033    0.578
   2_occ:    1.661    0.033    0.578
   3_bss:    1.661    0.033    0.578
   3_xyz:    1.580    0.029    0.701
   3_adp:    1.580    0.029    0.701
   3_occ:    1.580    0.029    0.701
   4_bss:    1.580    0.029    0.701
   4_xyz:    1.686    0.064    0.739
   4_adp:    1.686    0.064    0.739
   4_occ:    1.686    0.064    0.739
   5_bss:    1.686    0.064    0.739
   5_xyz:    1.722    0.052    0.760
   5_adp:    1.722    0.052    0.760
   5_occ:    1.722    0.052    0.760
   5_bss:    1.722    0.052    0.760
------------------------------------------------------------------------

CPU time actual refinement: 286.13


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_396/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_396/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_396/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_396/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_396/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 286.00 
  Macro-tasks:
    bulk solvent and scale       = 33.95  
    individual site refinement   = 124.61 
    weights calculation          = 26.55  
    collect and process          = 5.35   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 190.56 
  Micro-tasks:
    mask                            = 1.99   
    f_calc                          = 88.79  
    alpha_beta                      = 6.98   
    target                          = 0.98   
    gradients_wrt_atomic_parameters = 99.05  
    fmodel                         = 5.91   
    r_factors                      = 0.26   
    phase_errors                   = 8.64   
    foms                           = 0.14   
    TOTAL for micro-tasks          = 212.74 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 3.963 micro seconds
Total CPU time: 4.97 minutes
from_scatterers_fft:    658 calls, 88.62 s
gradients_fft:          603 calls, 87.08 s

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

# Date 2008-01-16 Time 01:27:16 PST -0800 (1200475636.96 s)
Start R-work = 0.4889, R-free = 0.4801 (no bulk solvent and anisotropic scale)
Final R-work = 0.1325, R-free = 0.1787 (no bulk solvent and anisotropic scale)

Start R-work = 0.4806, R-free = 0.4714
Final R-work = 0.1154, R-free = 0.1622