# Date 2008-01-16 Time 01:40:57 PST -0800 (1200476457.27 s)
#phil __OFF__

Command line arguments: "../526.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 6096
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 526

-------------------------------------------------------------------------------
  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: (69.8988, 46.4607, 88.1178, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.24, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.4607, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0179 1.98226
Completeness in resolution range: 0.95463
Completeness with d_max=infinity: 0.951708

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0179
                             d_min =   1.9823

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: (69.8988, 46.4607, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0179 1.98226
Completeness in resolution range: 0.95463
Completeness with d_max=infinity: 0.951708

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0183 -  4.2416 [2156/2180]  1937   219  10.2%
  bin  2:  4.2416 -  3.3793 [2063/2083]  1858   205   9.9%
  bin  3:  3.3793 -  2.9558 [2047/2066]  1845   202   9.9%
  bin  4:  2.9558 -  2.6872 [2020/2050]  1817   203  10.0%
  bin  5:  2.6872 -  2.4956 [2000/2019]  1797   203  10.2%
  bin  6:  2.4956 -  2.3490 [2018/2043]  1814   204  10.1%
  bin  7:  2.3490 -  2.2318 [1992/2020]  1794   198   9.9%
  bin  8:  2.2318 -  2.1349 [1977/2013]  1781   196   9.9%
  bin  9:  2.1349 -  2.0529 [1967/2009]  1772   195   9.9%
  bin 10:  2.0529 -  1.9823 [1349/2037]  1215   134   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_526/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.50 -     2.18: 11
        2.18 -     2.86: 1151
        2.86 -     3.54: 4414
        3.54 -     4.22: 9216
        4.22 -     4.90: 13456
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.498 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.647 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.721 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.947 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28243 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_526/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_526/model_refine_001.geo

CPU time processing inputs: 9.08


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 46.4607 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


============================= ml refinement start =============================


   ----------structure factors based statistics (before refinement)----------  


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

|--(resolution: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4721   r_free= 0.4547   ksol= 0.00   Bsol= 0.00   scale= 0.797    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.272432                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.7308 0.99   1402  154 0.3905 0.3684      6.5865      6.5241|
|  2:  4.7308 -  3.7746 0.99   1349  152 0.3769 0.3842      6.7381      6.7849|
|  3:  3.7746 -  3.3033 0.99   1304  144 0.4214 0.3783      6.6538      6.6112|
|  4:  3.3033 -  3.0039 0.99   1321  149 0.4684 0.4480      6.5307      6.4725|
|  5:  3.0039 -  2.7901 0.99   1298  146 0.5025 0.4452      6.3575      6.3535|
|  6:  2.7901 -  2.6265 0.99   1304  139 0.4955 0.5515      6.2729      6.2291|
|  7:  2.6265 -  2.4956 0.99   1276  148 0.5111 0.4951      6.2285      6.1541|
|  8:  2.4956 -  2.3874 0.98   1297  142 0.5286 0.4737      6.1982      6.2005|
|  9:  2.3874 -  2.2958 0.98   1265  139 0.5026 0.5551      6.1022      6.1812|
| 10:  2.2958 -  2.2168 1.00   1309  145 0.5431 0.4600      6.1219      6.0595|
| 11:  2.2168 -  2.1477 0.97   1257  143 0.5148 0.5260      6.0318       6.048|
| 12:  2.1477 -  2.0865 0.98   1277  141 0.5302 0.4748      5.9803      6.0034|
| 13:  2.0865 -  2.0317 0.99   1268  134 0.5100 0.4876      5.8747      5.8081|
| 14:  2.0317 -  1.9823 0.54    703   83 0.5365 0.5306      5.8832      5.7898|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0183 -  4.7308  1402   154  0.71  33.03   0.80     0.75      67427.36|
|  2:  4.7308 -  3.7746  1349   152  0.73  32.31   0.88     0.80      93282.47|
|  3:  3.7746 -  3.3033  1304   144  0.65  39.80   0.85     0.76      98531.58|
|  4:  3.3033 -  3.0039  1321   149  0.56  47.13   0.79     0.64      89336.63|
|  5:  3.0039 -  2.7901  1298   146  0.45  55.51   0.75     0.53      76174.72|
|  6:  2.7901 -  2.6265  1304   139  0.41  59.32   0.72     0.47      70572.25|
|  7:  2.6265 -  2.4956  1276   148  0.37  62.14   0.74     0.43      65984.66|
|  8:  2.4956 -  2.3874  1297   142  0.38  61.83   0.71     0.44      58926.54|
|  9:  2.3874 -  2.2958  1265   139  0.38  61.18   0.74     0.45      52621.26|
| 10:  2.2958 -  2.2168  1309   145  0.39  60.74   0.73     0.46      46537.06|
| 11:  2.2168 -  2.1477  1257   143  0.37  61.92   0.76     0.47      45125.71|
| 12:  2.1477 -  2.0865  1277   141  0.37  62.14   0.75     0.46      40279.85|
| 13:  2.0865 -  2.0317  1268   134  0.36  63.08   0.73     0.44      35451.70|
| 14:  2.0317 -  1.9823   703    83  0.38  61.85   0.74     0.42      29843.01|
|alpha:            min =        0.42 max =            0.80 mean =         0.54|
|beta:             min =    29843.01 max =        98531.58 mean =     63526.43|
|figures of merit: min =        0.00 max =            1.00 mean =         0.47|
|phase err.(work): min =        0.00 max =           89.99 mean =        53.91|
|phase err.(test): min =        0.00 max =           89.92 mean =        54.18|
|-----------------------------------------------------------------------------|

============================== 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 = 11.910052             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.134   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.029872              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.381   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       26 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      176 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      687 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1497 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2628 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3905 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5070 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6568 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7693 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.833 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.870 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.891)------------------------------------------|
|    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 = 11.891)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4799   r_free= 0.4599   ksol= 0.00   Bsol= 0.00   scale= 0.766    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.275725                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4627   r_free= 0.4440   ksol= 0.34   Bsol= 10.88   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.87,8.56,11.51,0.00,0.00,0.00); trace/3= 8.98                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.264957                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.840298              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.454   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.950964              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.880   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4627      final r-factor (work) = 0.3747          |
| start r-factor (free) = 0.4440      final r-factor (free) = 0.3930          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 84.6870 = 9.84 * 0.50 * 6.2710 + 1.00 * 53.8328                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.4749 = 9.84 * 0.50 * 6.1665 + 1.00 * 0.1346                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3747      final r-factor (work) = 0.3264          |
| start r-factor (free) = 0.3930      final r-factor (free) = 0.3773          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8786 = 0.95 * 1.00 * 6.1665 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7780 = 0.95 * 1.00 * 6.0594 + 1.00 * 0.0158                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.891)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.99   12.95    None  None   None       |
|    all(noH): 2823   0      0.00    74.99   12.95    None  None   None       |
|    Sol.    : 438    0      0.00    74.99   26.52    None  None   None       |
|    Mac.    : 2385   0      0.00    58.61   10.46    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 -   7.499: 1116   |   5:    37.497 -  44.996:   66        |
|      1:     7.499 -  14.999:  796   |   6:    44.996 -  52.495:   43        |
|      2:    14.999 -  22.498:  453   |   7:    52.495 -  59.994:   23        |
|      3:    22.498 -  29.997:  205   |   8:    59.994 -  67.494:    2        |
|      4:    29.997 -  37.497:  118   |   9:    67.494 -  74.993:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3264 r_free = 0.3773             target_work(ml) = 6.039         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3257 r_free = 0.3772             target_work(ml) = 6.038         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3257   r_free= 0.3772   ksol= 0.34   Bsol= 10.88   scale= 1.119   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.87,8.56,11.51,0.00,0.00,0.00); trace/3= 8.98                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.038449                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3212   r_free= 0.3728   ksol= 0.33   Bsol= 38.01   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.25,4.26,7.41,0.00,0.00,0.00); trace/3= 4.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.038454                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.699848              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.119   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.462971              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.530  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3212      final r-factor (work) = 0.2251          |
| start r-factor (free) = 0.3728      final r-factor (free) = 0.2794          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.4240 = 6.70 * 0.50 * 6.0567 + 1.00 * 0.1346                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.8155 = 6.70 * 0.50 * 5.8911 + 1.00 * 0.0808                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2251      final r-factor (work) = 0.1982          |
| start r-factor (free) = 0.2794      final r-factor (free) = 0.2541          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7432 = 0.46 * 1.00 * 5.8911 + 1.00 * 0.0158                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6395 = 0.46 * 1.00 * 5.6757 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.891)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.87   12.60    None  None   None       |
|    all(noH): 2823   0      0.00    79.87   12.60    None  None   None       |
|    Sol.    : 438    0      0.00    79.87   32.65    None  None   None       |
|    Mac.    : 2385   0      0.00    58.23   8.92     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 -   7.987: 1402   |   5:    39.934 -  47.921:   95        |
|      1:     7.987 -  15.974:  744   |   6:    47.921 -  55.908:   41        |
|      2:    15.974 -  23.960:  242   |   7:    55.908 -  63.895:   19        |
|      3:    23.960 -  31.947:  140   |   8:    63.895 -  71.881:    1        |
|      4:    31.947 -  39.934:  138   |   9:    71.881 -  79.868:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1982 r_free = 0.2541             target_work(ml) = 5.627         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1981 r_free = 0.2540             target_work(ml) = 5.627         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1981   r_free= 0.2540   ksol= 0.33   Bsol= 38.01   scale= 1.055   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.25,4.26,7.41,0.00,0.00,0.00); trace/3= 4.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.627056                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1961   r_free= 0.2533   ksol= 0.32   Bsol= 50.05   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.04,2.58,4.84,0.00,0.00,0.00); trace/3= 3.15                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.627839                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.504507              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.301  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.263386              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 112.919  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1961      final r-factor (work) = 0.1539          |
| start r-factor (free) = 0.2533      final r-factor (free) = 0.2029          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1989 = 2.50 * 0.50 * 5.6843 + 1.00 * 0.0808                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9798 = 2.50 * 0.50 * 5.5261 + 1.00 * 0.0597                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1539      final r-factor (work) = 0.1422          |
| start r-factor (free) = 0.2029      final r-factor (free) = 0.1952          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.5196 = 2.26 * 1.00 * 5.5261 + 1.00 * 0.0119                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.1720 = 2.26 * 1.00 * 5.3708 + 1.00 * 0.0158                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.891)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.83   13.65    None  None   None       |
|    all(noH): 2823   0      0.00    86.83   13.65    None  None   None       |
|    Sol.    : 438    0      1.18    86.83   39.58    None  None   None       |
|    Mac.    : 2385   0      0.00    82.35   8.89     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 -   8.684: 1555   |   5:    43.417 -  52.101:   95        |
|      1:     8.684 -  17.367:  642   |   6:    52.101 -  60.784:   76        |
|      2:    17.367 -  26.050:  184   |   7:    60.784 -  69.468:   44        |
|      3:    26.050 -  34.734:  112   |   8:    69.468 -  78.151:   18        |
|      4:    34.734 -  43.417:   92   |   9:    78.151 -  86.834:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1422 r_free = 0.1952             target_work(ml) = 5.351         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1421 r_free = 0.1952             target_work(ml) = 5.351         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1421   r_free= 0.1952   ksol= 0.32   Bsol= 50.05   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.04,2.58,4.84,0.00,0.00,0.00); trace/3= 3.15                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.351084                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1419   r_free= 0.1952   ksol= 0.33   Bsol= 57.97   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.74,2.15,4.25,0.00,0.00,0.00); trace/3= 2.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.350605                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.824761              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 115.155  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.290801              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.123  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1419      final r-factor (work) = 0.1279          |
| start r-factor (free) = 0.1952      final r-factor (free) = 0.1797          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9607 = 1.82 * 0.50 * 5.3717 + 1.00 * 0.0597                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8996 = 1.82 * 0.50 * 5.3083 + 1.00 * 0.0564                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1279      final r-factor (work) = 0.1257          |
| start r-factor (free) = 0.1797      final r-factor (free) = 0.1759          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8677 = 1.29 * 1.00 * 5.3083 + 1.00 * 0.0158                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8037 = 1.29 * 1.00 * 5.2591 + 1.00 * 0.0152                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.891)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.50   13.39    None  None   None       |
|    all(noH): 2823   0      0.00    87.50   13.39    None  None   None       |
|    Sol.    : 438    0      1.26    87.50   39.30    None  None   None       |
|    Mac.    : 2385   0      0.00    84.50   8.63     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 -   8.750: 1618   |   5:    43.752 -  52.502:   94        |
|      1:     8.750 -  17.501:  599   |   6:    52.502 -  61.252:   69        |
|      2:    17.501 -  26.251:  175   |   7:    61.252 -  70.002:   43        |
|      3:    26.251 -  35.001:  108   |   8:    70.002 -  78.753:   18        |
|      4:    35.001 -  43.752:   93   |   9:    78.753 -  87.503:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1257 r_free = 0.1759             target_work(ml) = 5.249         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1256 r_free = 0.1758             target_work(ml) = 5.249         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1256   r_free= 0.1758   ksol= 0.33   Bsol= 57.97   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.74,2.15,4.25,0.00,0.00,0.00); trace/3= 2.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.248545                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1255   r_free= 0.1758   ksol= 0.33   Bsol= 56.44   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.96,2.27,4.24,0.00,0.00,0.00); trace/3= 2.82                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.248560                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.151593              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 139.979  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 8.454799              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.103  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1255      final r-factor (work) = 0.1187          |
| start r-factor (free) = 0.1758      final r-factor (free) = 0.1672          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7145 = 2.15 * 0.50 * 5.2594 + 1.00 * 0.0565                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6813 = 2.15 * 0.50 * 5.2249 + 1.00 * 0.0604                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1187      final r-factor (work) = 0.1172          |
| start r-factor (free) = 0.1672      final r-factor (free) = 0.1661          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 44.1904 = 8.45 * 1.00 * 5.2249 + 1.00 * 0.0151                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 43.9551 = 8.45 * 1.00 * 5.1969 + 1.00 * 0.0160                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.891)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.00   13.26    None  None   None       |
|    all(noH): 2823   0      0.00    93.00   13.26    None  None   None       |
|    Sol.    : 438    0      1.23    91.57   39.07    None  None   None       |
|    Mac.    : 2385   0      0.00    93.00   8.52     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.300: 1730   |   5:    46.498 -  55.798:   83        |
|      1:     9.300 -  18.599:  537   |   6:    55.798 -  65.098:   57        |
|      2:    18.599 -  27.899:  149   |   7:    65.098 -  74.398:   36        |
|      3:    27.899 -  37.199:  130   |   8:    74.398 -  83.697:   15        |
|      4:    37.199 -  46.498:   80   |   9:    83.697 -  92.997:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1172 r_free = 0.1661             target_work(ml) = 5.194         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1171 r_free = 0.1660             target_work(ml) = 5.194         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1171   r_free= 0.1660   ksol= 0.33   Bsol= 56.44   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.96,2.27,4.24,0.00,0.00,0.00); trace/3= 2.82                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.193900                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.7308 0.99   1402  154 0.1002 0.1288      5.4057      5.5553|
|  2:  4.7308 -  3.7746 0.99   1349  152 0.0863 0.1157      5.4533      5.6666|
|  3:  3.7746 -  3.3033 0.99   1304  144 0.1097 0.1518      5.5109      5.8543|
|  4:  3.3033 -  3.0039 0.99   1321  149 0.1264 0.1842      5.4832      5.6814|
|  5:  3.0039 -  2.7901 0.99   1298  146 0.1380 0.1620      5.3754      5.5581|
|  6:  2.7901 -  2.6265 0.99   1304  139 0.1285 0.2285      5.2558      5.5985|
|  7:  2.6265 -  2.4956 0.99   1276  148 0.1368 0.1729       5.245      5.3697|
|  8:  2.4956 -  2.3874 0.98   1297  142 0.1259 0.1702      5.1566      5.3897|
|  9:  2.3874 -  2.2958 0.98   1265  139 0.1259 0.2029      5.0969      5.4075|
| 10:  2.2958 -  2.2168 1.00   1309  145 0.1209 0.1677      5.0175      5.2109|
| 11:  2.2168 -  2.1477 0.97   1257  143 0.1196 0.2036      4.9959      5.3563|
| 12:  2.1477 -  2.0865 0.98   1277  141 0.1262 0.1767      4.9602      5.2643|
| 13:  2.0865 -  2.0317 0.99   1268  134 0.1134 0.1784      4.8055      5.0348|
| 14:  2.0317 -  1.9823 0.54    703   83 0.0960 0.1618      4.6502      4.8951|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0183 -  4.7308  1402   154  0.94   9.71   0.98     0.95       7850.75|
|  2:  4.7308 -  3.7746  1349   152  0.95   8.33   1.02     1.00       9558.30|
|  3:  3.7746 -  3.3033  1304   144  0.93  11.90   1.04     1.03      11146.37|
|  4:  3.3033 -  3.0039  1321   149  0.92  14.20   1.02     1.00      10912.28|
|  5:  3.0039 -  2.7901  1298   146  0.90  16.52   1.01     0.99       9252.89|
|  6:  2.7901 -  2.6265  1304   139  0.89  17.43   0.98     0.95       7916.47|
|  7:  2.6265 -  2.4956  1276   148  0.89  16.99   0.99     0.95       7205.84|
|  8:  2.4956 -  2.3874  1297   142  0.89  16.98   0.99     0.97       6463.10|
|  9:  2.3874 -  2.2958  1265   139  0.90  16.63   1.00     0.96       5749.72|
| 10:  2.2958 -  2.2168  1309   145  0.89  17.16   1.00     0.96       5049.62|
| 11:  2.2168 -  2.1477  1257   143  0.89  17.50   0.99     0.95       5010.76|
| 12:  2.1477 -  2.0865  1277   141  0.89  17.39   1.00     1.00       4623.01|
| 13:  2.0865 -  2.0317  1268   134  0.90  16.77   0.99     0.96       3542.52|
| 14:  2.0317 -  1.9823   703    83  0.93  13.41   0.98     0.95       2518.67|
|alpha:            min =        0.95 max =            1.03 mean =         0.97|
|beta:             min =     2518.67 max =        11146.37 mean =      7096.40|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        15.05|
|phase err.(test): min =        0.00 max =           89.09 mean =        14.51|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1172   r_free= 0.1661   ksol= 0.33   Bsol= 59.33   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.81,-0.58,1.39,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.193650                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1172   r_free= 0.1661   ksol= 0.33   Bsol= 59.33   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.81,-0.58,1.39,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.193650                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.7308 0.99   1402  154 0.0998 0.1288      5.4041      5.5473|
|  2:  4.7308 -  3.7746 0.99   1349  152 0.0865 0.1159      5.4543       5.662|
|  3:  3.7746 -  3.3033 0.99   1304  144 0.1103 0.1515      5.5126      5.8573|
|  4:  3.3033 -  3.0039 0.99   1321  149 0.1265 0.1855       5.484      5.6865|
|  5:  3.0039 -  2.7901 0.99   1298  146 0.1381 0.1609      5.3753      5.5544|
|  6:  2.7901 -  2.6265 0.99   1304  139 0.1285 0.2287      5.2548      5.5985|
|  7:  2.6265 -  2.4956 0.99   1276  148 0.1367 0.1731      5.2442      5.3694|
|  8:  2.4956 -  2.3874 0.98   1297  142 0.1259 0.1700      5.1564      5.3875|
|  9:  2.3874 -  2.2958 0.98   1265  139 0.1258 0.2026      5.0959      5.4069|
| 10:  2.2958 -  2.2168 1.00   1309  145 0.1208 0.1678      5.0171      5.2114|
| 11:  2.2168 -  2.1477 0.97   1257  143 0.1196 0.2036      4.9954      5.3558|
| 12:  2.1477 -  2.0865 0.98   1277  141 0.1261 0.1766      4.9599      5.2633|
| 13:  2.0865 -  2.0317 0.99   1268  134 0.1134 0.1783      4.8051      5.0349|
| 14:  2.0317 -  1.9823 0.54    703   83 0.0960 0.1614      4.6497       4.894|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0183 -  4.7308  1402   154  0.94   9.72   0.97     0.95       7883.91|
|  2:  4.7308 -  3.7746  1349   152  0.95   8.33   1.02     1.00       9519.03|
|  3:  3.7746 -  3.3033  1304   144  0.93  11.90   1.04     1.03      11094.01|
|  4:  3.3033 -  3.0039  1321   149  0.91  14.23   1.02     1.00      10951.73|
|  5:  3.0039 -  2.7901  1298   146  0.90  16.52   1.01     0.99       9254.51|
|  6:  2.7901 -  2.6265  1304   139  0.89  17.40   0.98     0.96       7889.31|
|  7:  2.6265 -  2.4956  1276   148  0.89  16.95   0.99     0.95       7181.04|
|  8:  2.4956 -  2.3874  1297   142  0.89  16.98   1.00     0.97       6454.71|
|  9:  2.3874 -  2.2958  1265   139  0.90  16.60   1.00     0.96       5737.70|
| 10:  2.2958 -  2.2168  1309   145  0.89  17.15   1.00     0.96       5046.68|
| 11:  2.2168 -  2.1477  1257   143  0.89  17.49   1.00     0.95       5003.50|
| 12:  2.1477 -  2.0865  1277   141  0.89  17.39   1.01     1.00       4622.10|
| 13:  2.0865 -  2.0317  1268   134  0.90  16.75   0.99     0.96       3537.15|
| 14:  2.0317 -  1.9823   703    83  0.93  13.39   0.99     0.96       2512.91|
|alpha:            min =        0.95 max =            1.03 mean =         0.97|
|beta:             min =     2512.91 max =        11094.01 mean =      7088.53|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.85 mean =        15.05|
|phase err.(test): min =        0.00 max =           87.26 mean =        14.51|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.891)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.90    95.89   16.16    None  None   None       |
|    all(noH): 2823   0      2.90    95.89   16.16    None  None   None       |
|    Sol.    : 438    0      4.12    94.46   41.97    None  None   None       |
|    Mac.    : 2385   0      2.90    95.89   11.41    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.896 -  12.196: 1730   |   5:    49.395 -  58.695:   83        |
|      1:    12.196 -  21.496:  537   |   6:    58.695 -  67.994:   57        |
|      2:    21.496 -  30.795:  149   |   7:    67.994 -  77.294:   36        |
|      3:    30.795 -  40.095:  130   |   8:    77.294 -  86.594:   15        |
|      4:    40.095 -  49.395:   80   |   9:    86.594 -  95.893:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 294         
Filter by distance & map next to the model:
   mapped sites are within: 0.208 - 4.842
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 291 from: 294
   mapped sites are within: 0.708 - 4.842

peak=   10.636 closest distance to " CB  VAL A 230 " =    1.435
peak=    9.324 closest distance to " CB  VAL A 296 " =    1.568
peak=    6.496 closest distance to " CD2 LEU A   5 " =    1.197
peak=    5.896 closest distance to " NE2 GLN A  11 " =    1.129
peak=    5.810 closest distance to " CG  PRO A  54 " =    1.383
peak=    5.513 closest distance to " CG  LEU A   5 " =    1.186
peak=    5.469 closest distance to " NH1 ARG A 138 " =    1.038
peak=    5.368 closest distance to " NH2 ARG A  56 " =    2.067
peak=    5.248 closest distance to " O   HOH Z 142 " =    2.050
peak=    5.194 closest distance to " CG  LEU A 228 " =    1.206
peak=    5.166 closest distance to " O   HOH Z   9 " =    2.011
peak=    4.997 closest distance to " CB  GLN A 223 " =    1.475
peak=    4.882 closest distance to " O   HOH Z 232 " =    2.262
peak=    4.858 closest distance to " CB  GLN A 183 " =    1.259
peak=    4.841 closest distance to " CB  PRO A  54 " =    1.015
peak=    4.826 closest distance to " O   HOH Z 427 " =    2.772
peak=    4.775 closest distance to " CB  ASN A 148 " =    1.355
peak=    4.727 closest distance to " O   HOH Z 369 " =    2.282
peak=    4.678 closest distance to " CD1AILE A 234 " =    0.921
peak=    4.589 closest distance to " CG  PRO A 198 " =    1.221
peak=    4.574 closest distance to " O   HOH Z 248 " =    1.297
peak=    4.512 closest distance to " O   HOH Z 425 " =    1.461
peak=    4.502 closest distance to " NH2AARG A 190 " =    1.995
peak=    4.486 closest distance to " CB  ASN A 142 " =    1.100
peak=    4.354 closest distance to " CB  ARG A 275 " =    1.023
peak=    4.339 closest distance to " O   HOH Z 287 " =    1.948
peak=    4.316 closest distance to " O   HOH Z 353 " =    2.573
peak=    4.310 closest distance to " O   HOH Z 346 " =    1.533
peak=    4.289 closest distance to " CG  PRO A 243 " =    1.151
peak=    4.253 closest distance to " O   SER A  87 " =    2.389
peak=    4.242 closest distance to " CB  VAL A 265 " =    1.340
peak=    4.240 closest distance to " O   HOH Z  78 " =    1.601
peak=    4.215 closest distance to " CB  VAL A 230 " =    1.224
peak=    4.183 closest distance to " ND2 ASN A 187 " =    1.652
peak=    4.120 closest distance to " O   PRO A 198 " =    1.568
peak=    4.119 closest distance to " CG  PRO A 213 " =    1.213
peak=    4.112 closest distance to " O   HOH Z 290 " =    1.075
peak=    4.104 closest distance to " CB  GLU A 277 " =    3.623
peak=    4.095 closest distance to " O   HOH Z 265 " =    1.949
peak=    4.069 closest distance to " CA  ALA A  51 " =    0.993
peak=    4.055 closest distance to " O   HOH Z 126 " =    2.092
peak=    4.051 closest distance to " O   HOH Z   3 " =    2.083
peak=    4.042 closest distance to " CD2 LEU A 228 " =    1.224
peak=    4.038 closest distance to " CB  VAL A 202 " =    1.655
peak=    4.036 closest distance to " CZ  PHE A 218 " =    1.105
peak=    4.035 closest distance to " CB  TRP A 266 " =    1.082
peak=    4.010 closest distance to " CG2 ILE A 234 " =    0.976
peak=    4.002 closest distance to " CG  LEU A 167 " =    1.255
peak=    3.978 closest distance to " CB  ARG A 190 " =    1.430
peak=    3.971 closest distance to " O   HOH Z 193 " =    1.652
peak=    3.966 closest distance to " CE  LYS A  76 " =    0.882
peak=    3.964 closest distance to " CB BVAL A  41 " =    1.218
peak=    3.956 closest distance to " O  BHOH Z 338 " =    2.388
peak=    3.954 closest distance to " O   HOH Z 303 " =    2.098
peak=    3.952 closest distance to " CB  TYR A 169 " =    0.794
peak=    3.950 closest distance to " CH2 TRP A 266 " =    1.125
peak=    3.950 closest distance to " O   HOH Z  59 " =    1.748
peak=    3.944 closest distance to " O   HOH Z 272 " =    1.783
peak=    3.930 closest distance to " O   HOH Z 214 " =    2.329
peak=    3.909 closest distance to " CG AARG A 275 " =    1.221
peak=    3.906 closest distance to " O   HOH Z 188 " =    2.927
peak=    3.889 closest distance to " CD  ARG A 269 " =    1.014
peak=    3.883 closest distance to " NH1AARG A 145 " =    1.185
peak=    3.880 closest distance to " O   HOH Z 423 " =    1.463
peak=    3.873 closest distance to " O   HOH Z 422 " =    2.651
peak=    3.871 closest distance to " O   HOH Z 359 " =    1.501
peak=    3.864 closest distance to " N   ALA A 256 " =    1.020
peak=    3.862 closest distance to " O   HOH Z 193 " =    1.522
peak=    3.862 closest distance to " CA  ARG A 195 " =    1.165
peak=    3.850 closest distance to " O   HOH Z  43 " =    1.837
peak=    3.846 closest distance to " CG2 VAL A 257 " =    0.859
peak=    3.835 closest distance to " O   HOH Z 380 " =    1.758
peak=    3.835 closest distance to " CD  LYS A  76 " =    1.812
peak=    3.820 closest distance to " O   HOH Z  40 " =    1.591
peak=    3.819 closest distance to " CB  SER A  63 " =    1.214
peak=    3.816 closest distance to " CA  TYR A  30 " =    0.958
peak=    3.814 closest distance to " O   HOH Z  61 " =    1.781
peak=    3.811 closest distance to " O   HOH Z 251 " =    1.500
peak=    3.806 closest distance to " CB  GLN A  89 " =    1.289
peak=    3.805 closest distance to " O   HOH Z 261 " =    1.818
peak=    3.805 closest distance to " CB  ASP A 124 " =    0.832
peak=    3.804 closest distance to " CB  ARG A  79 " =    1.477
peak=    3.804 closest distance to " N   ASN A  39 " =    1.227
peak=    3.784 closest distance to " O   HOH Z 258 " =    1.904
peak=    3.783 closest distance to " O   HOH Z 406 " =    1.406
peak=    3.783 closest distance to " CB  SER A   3 " =    1.410
peak=    3.780 closest distance to " O   HOH Z 203 " =    1.789
peak=    3.769 closest distance to " ND2 ASN A 249 " =    0.870
peak=    3.759 closest distance to " O   HOH Z 234 " =    3.577
peak=    3.759 closest distance to " O   HOH Z 419 " =    2.037
peak=    3.757 closest distance to " CB  ASN A  39 " =    0.991
peak=    3.756 closest distance to " CA  PHE A 283 " =    1.210
peak=    3.755 closest distance to " CA  VAL A 125 " =    1.209
peak=    3.745 closest distance to " CB  LYS A 117 " =    1.245
peak=    3.742 closest distance to " OG ASER A 258 " =    3.084
peak=    3.737 closest distance to " O   HOH Z 126 " =    1.586
peak=    3.713 closest distance to " O   HOH Z 389 " =    1.321
peak=    3.709 closest distance to " O   HOH Z 193 " =    1.371
peak=    3.708 closest distance to " O   HOH Z 298 " =    1.671
peak=    3.691 closest distance to " O   HOH Z 365 " =    2.922
peak=    3.689 closest distance to " CG  GLN A  58 " =    0.996
peak=    3.677 closest distance to " CB  GLN A  88 " =    1.301
peak=    3.670 closest distance to " O   HOH Z 112 " =    1.003
peak=    3.665 closest distance to " O   HOH Z 411 " =    3.680
peak=    3.665 closest distance to " O   HOH Z   7 " =    1.235
peak=    3.663 closest distance to " CD2 TRP A 179 " =    1.292
peak=    3.659 closest distance to " CA  ASN A 127 " =    1.036
peak=    3.658 closest distance to " CB  ALA A 114 " =    1.418
peak=    3.653 closest distance to " O   HOH Z 403 " =    1.527
peak=    3.650 closest distance to " CA  LYS A 117 " =    1.242
peak=    3.649 closest distance to " CD1 ILE A  33 " =    1.823
peak=    3.649 closest distance to " OE2 GLU A   2 " =    1.952
peak=    3.638 closest distance to " CB  PRO A  90 " =    1.095
peak=    3.638 closest distance to " O   HOH Z  10 " =    1.731
peak=    3.637 closest distance to " O   HOH Z 437 " =    1.501
peak=    3.629 closest distance to " CB  SER A 216 " =    0.897
peak=    3.629 closest distance to " N   PHE A 130 " =    1.326
peak=    3.628 closest distance to " CG2 ILE A  20 " =    1.563
peak=    3.627 closest distance to " O   HOH Z 368 " =    2.159
peak=    3.624 closest distance to " CA  ALA A 160 " =    0.951
peak=    3.611 closest distance to " CB  GLU A 128 " =    1.006
peak=    3.611 closest distance to " CB  ASN A 110 " =    1.121
peak=    3.611 closest distance to " O   HOH Z 368 " =    3.474
peak=    3.608 closest distance to " O   HOH Z  69 " =    2.218
peak=    3.585 closest distance to " CB  SER A 212 " =    1.306
peak=    3.580 closest distance to " O   HOH Z  88 " =    3.554
peak=    3.573 closest distance to " CG  ARG A  66 " =    2.867
peak=    3.568 closest distance to " O   ASP A 124 " =    1.110
peak=    3.549 closest distance to " CB  THR A  52 " =    0.861
peak=    3.541 closest distance to " O   HOH Z 143 " =    1.389
peak=    3.541 closest distance to " CA  SER A  87 " =    1.034
peak=    3.537 closest distance to " O   HOH Z   1 " =    1.706
peak=    3.532 closest distance to " O   HOH Z  80 " =    1.560
peak=    3.528 closest distance to " O   HOH Z 123 " =    0.980
peak=    3.524 closest distance to " CB  HIS A 108 " =    0.866
peak=    3.524 closest distance to " CZ  PHE A  38 " =    1.202
peak=    3.521 closest distance to " O   HOH Z  68 " =    2.215
peak=    3.519 closest distance to " O   THR A 182 " =    1.432
peak=    3.519 closest distance to " O   HOH Z 371 " =    2.859
peak=    3.516 closest distance to " O   HOH Z 222 " =    2.428
peak=    3.513 closest distance to " CE3 TRP A 150 " =    1.109
peak=    3.509 closest distance to " CE1 TYR A 186 " =    1.237
peak=    3.504 closest distance to " OG BSER A 164 " =    2.149
peak=    3.500 closest distance to " O   HOH Z  30 " =    1.588
peak=    3.484 closest distance to " N   GLN A 278 " =    1.417
peak=    3.483 closest distance to " O   HOH Z  92 " =    2.360
peak=    3.483 closest distance to " OE2 GLU A  53 " =    1.800
peak=    3.480 closest distance to " NZ  LYS A 117 " =    3.027
peak=    3.474 closest distance to " OD1 ASN A  69 " =    2.530
peak=    3.472 closest distance to " CG  MET A 185 " =    1.235
peak=    3.466 closest distance to " CA  ILE A 234 " =    0.982
peak=    3.463 closest distance to " CB  TRP A 179 " =    1.430
peak=    3.462 closest distance to " CG2 THR A 221 " =    1.148
peak=    3.455 closest distance to " O   HOH Z 423 " =    1.748
peak=    3.452 closest distance to " CA  GLY A 267 " =    0.904
peak=    3.450 closest distance to " O   HOH Z   4 " =    1.442
peak=    3.448 closest distance to " O   HOH Z 273 " =    3.036
peak=    3.443 closest distance to " CD  ARG A 159 " =    0.708
peak=    3.438 closest distance to " CB  SER A  26 " =    1.731
peak=    3.436 closest distance to " O   HOH Z 303 " =    2.699
peak=    3.435 closest distance to " O   HOH Z 261 " =    1.641
peak=    3.428 closest distance to " OG BSER A 164 " =    2.259
peak=    3.427 closest distance to " O   HOH Z 180 " =    2.172
peak=    3.424 closest distance to " O   HOH Z 405 " =    1.246
peak=    3.421 closest distance to " CB  SER A 273 " =    0.916
peak=    3.421 closest distance to " CG1 VAL A 153 " =    0.984
peak=    3.417 closest distance to " O   HOH Z 329 " =    4.243
peak=    3.414 closest distance to " CB  SER A  62 " =    1.061
peak=    3.414 closest distance to " O   HOH Z 133 " =    2.885
peak=    3.413 closest distance to " NH2AARG A 145 " =    1.087
peak=    3.408 closest distance to " CG1 ILE A 151 " =    1.121
peak=    3.402 closest distance to " N   ASP A 162 " =    1.106
peak=    3.398 closest distance to " CA  ASN A 215 " =    1.070
peak=    3.396 closest distance to " O   HOH Z 158 " =    3.276
peak=    3.395 closest distance to " O   PRO A 198 " =    1.246
peak=    3.389 closest distance to " O   ASN A  74 " =    1.568
peak=    3.385 closest distance to " CB  LEU A 300 " =    0.907
peak=    3.385 closest distance to " O   HOH Z 153 " =    3.769
peak=    3.375 closest distance to " O   HOH Z  69 " =    0.807
peak=    3.374 closest distance to " CG  GLU A  37 " =    0.894
peak=    3.373 closest distance to " CG2 ILE A 120 " =    1.370
peak=    3.370 closest distance to " O   HOH Z 305 " =    3.433
peak=    3.367 closest distance to " O   HOH Z 325 " =    2.109
peak=    3.365 closest distance to " O   HOH Z 207 " =    1.043
peak=    3.364 closest distance to " NE2 HIS A 207 " =    1.208
peak=    3.361 closest distance to " CA  ALA A 158 " =    1.359
peak=    3.358 closest distance to " O   HOH Z 116 " =    3.002
peak=    3.356 closest distance to " O   HOH Z 126 " =    1.758
peak=    3.356 closest distance to " CD  LYS A 166 " =    1.309
peak=    3.353 closest distance to " CA  MET A 105 " =    1.000
peak=    3.347 closest distance to " CD  ARG A 195 " =    3.498
peak=    3.343 closest distance to " O   HOH Z 211 " =    0.777
peak=    3.342 closest distance to " CA  ALA A  21 " =    1.194
peak=    3.342 closest distance to " O   ASP A 191 " =    1.566
peak=    3.342 closest distance to " CB  MET A  40 " =    0.785
peak=    3.340 closest distance to " O   HOH Z 357 " =    2.056
peak=    3.340 closest distance to " O   HOH Z 184 " =    1.361
peak=    3.340 closest distance to " CB  ASN A 215 " =    1.168
peak=    3.338 closest distance to " O   HOH Z   2 " =    1.562
peak=    3.331 closest distance to " CB  ALA A 248 " =    1.350
peak=    3.329 closest distance to " NE2 GLN A  73 " =    1.332
peak=    3.327 closest distance to " O   HOH Z 263 " =    1.669
peak=    3.326 closest distance to " O   HOH Z   1 " =    1.741
peak=    3.325 closest distance to " O   HOH Z 189 " =    2.827
peak=    3.323 closest distance to " CG BARG A 102 " =    1.879
peak=    3.320 closest distance to " CA  ARG A 139 " =    1.011
peak=    3.314 closest distance to " CA  ALA A 291 " =    0.855
peak=    3.310 closest distance to " CA  ALA A 129 " =    1.410
peak=    3.307 closest distance to " NZ  LYS A 117 " =    1.210
peak=    3.306 closest distance to " O   HOH Z  21 " =    1.739
peak=    3.303 closest distance to " CG  GLN A  88 " =    1.116
peak=    3.297 closest distance to " CA  LYS A 290 " =    1.247
peak=    3.292 closest distance to " N   SER A 135 " =    1.377
peak=    3.291 closest distance to " O   HOH Z  44 " =    1.541
peak=    3.290 closest distance to " CA  ARG A  36 " =    1.089
peak=    3.287 closest distance to " CD BLYS A 290 " =    1.100
peak=    3.287 closest distance to " CG1 ILE A  49 " =    1.518
peak=    3.286 closest distance to " CA  ASN A 217 " =    1.206
peak=    3.284 closest distance to " O   HOH Z 146 " =    1.372
peak=    3.280 closest distance to " O   HOH Z 148 " =    2.407
peak=    3.279 closest distance to " CB  GLU A  46 " =    0.931
peak=    3.272 closest distance to " N   SER A 271 " =    1.006
peak=    3.270 closest distance to " N   ASN A 127 " =    1.301
peak=    3.270 closest distance to " O   HOH Z 128 " =    2.140
peak=    3.262 closest distance to " O   HOH Z  20 " =    1.252
peak=    3.257 closest distance to " O   HOH Z 272 " =    2.331
peak=    3.257 closest distance to " O   HOH Z 389 " =    3.057
peak=    3.256 closest distance to " O   PHE A 192 " =    1.355
peak=    3.249 closest distance to " CB  ASP A 140 " =    0.996
peak=    3.249 closest distance to " O   HOH Z 172 " =    3.353
peak=    3.247 closest distance to " O   HOH Z 280 " =    3.042
peak=    3.247 closest distance to " OG BSER A  99 " =    2.172
peak=    3.245 closest distance to " O   HOH Z 299 " =    4.343
peak=    3.243 closest distance to " OG  SER A  62 " =    2.931
peak=    3.241 closest distance to " CG  LEU A 281 " =    1.021
peak=    3.240 closest distance to " CG  LYS A 119 " =    1.045
peak=    3.234 closest distance to " CB  GLU A 152 " =    1.205
peak=    3.228 closest distance to " CB  PHE A 204 " =    1.087
peak=    3.224 closest distance to " NE  ARG A  56 " =    3.539
peak=    3.222 closest distance to " O   HOH Z 227 " =    1.777
peak=    3.222 closest distance to " OG1 THR A 279 " =    1.382
peak=    3.219 closest distance to " CB  THR A 157 " =    1.109
peak=    3.215 closest distance to " O   HOH Z  40 " =    1.470
peak=    3.211 closest distance to " CG2AVAL A  72 " =    1.608
peak=    3.204 closest distance to " O   HOH Z  97 " =    2.493
peak=    3.203 closest distance to " O   HOH Z 196 " =    1.451
peak=    3.202 closest distance to " CG2 VAL A 197 " =    1.121
peak=    3.201 closest distance to " O   HOH Z 236 " =    1.491
peak=    3.197 closest distance to " CA  ASP A 162 " =    1.034
peak=    3.195 closest distance to " CD1 LEU A  96 " =    0.768
peak=    3.184 closest distance to " O   HOH Z  88 " =    2.676
peak=    3.182 closest distance to " CA  LEU A 282 " =    1.180
peak=    3.182 closest distance to " CZ3 TRP A  92 " =    1.181
peak=    3.182 closest distance to " CD1 LEU A 261 " =    1.141
peak=    3.175 closest distance to " CB  ASN A 176 " =    0.877
peak=    3.169 closest distance to " CB  SER A 210 " =    0.756
peak=    3.167 closest distance to " CG2BVAL A 121 " =    0.723
peak=    3.167 closest distance to " CG  MET A 113 " =    1.233
peak=    3.164 closest distance to " O   HOH Z 327 " =    1.879
peak=    3.163 closest distance to " OG  SER A  62 " =    2.717
peak=    3.163 closest distance to " O   HOH Z 218 " =    1.433
peak=    3.162 closest distance to " CD2 TYR A 186 " =    1.082
peak=    3.160 closest distance to " CB  LEU A  83 " =    0.773
peak=    3.155 closest distance to " CG  GLN A  55 " =    2.397
peak=    3.154 closest distance to " CD1 ILE A 106 " =    0.961
peak=    3.153 closest distance to " CA  ARG A 102 " =    1.153
peak=    3.150 closest distance to " O   HOH Z 281 " =    2.602
peak=    3.143 closest distance to " CD  GLN A 240 " =    1.479
peak=    3.135 closest distance to " O   HOH Z 117 " =    2.024
peak=    3.134 closest distance to " CA  TRP A 150 " =    1.095
peak=    3.128 closest distance to " CA  PHE A  59 " =    0.982
peak=    3.123 closest distance to " O   GLY A  57 " =    2.526
peak=    3.116 closest distance to " O   HOH Z 285 " =    2.102
peak=    3.112 closest distance to " CB  GLN A 278 " =    0.964
peak=    3.111 closest distance to " CG  ARG A 159 " =    0.878
peak=    3.109 closest distance to " CA  ALA A 295 " =    1.164
peak=    3.106 closest distance to " CA  VAL A 153 " =    1.082
peak=    3.090 closest distance to " O   HOH Z 371 " =    3.378
peak=    3.089 closest distance to " CB  ALA A 104 " =    0.750
peak=    3.087 closest distance to " O   HOH Z 403 " =    1.960
peak=    3.086 closest distance to " CA  ARG A 156 " =    1.062
peak=    3.082 closest distance to " O   HOH Z 128 " =    2.101
peak=    3.081 closest distance to " O   HOH Z 148 " =    1.397
peak=    3.078 closest distance to " CA  LEU A  83 " =    1.113
peak=    3.077 closest distance to " CB  ALA A   1 " =    4.842
peak=    3.073 closest distance to " O   HOH Z 109 " =    2.646
peak=    3.064 closest distance to " CB  ARG A 156 " =    1.137
peak=    3.063 closest distance to " O   HOH Z 425 " =    2.143
peak=    3.037 closest distance to " O   HOH Z 260 " =    1.542
peak=    3.027 closest distance to " O   HOH Z 394 " =    1.699
peak=    3.020 closest distance to " O   HOH Z 171 " =    4.143

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 202         
Filter by distance & map next to the model:
   mapped sites are within: 0.750 - 5.524
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 202 from: 202
   mapped sites are within: 0.750 - 5.524

peak=   -4.335 closest distance to " OG BSER A 134 " =    1.282
peak=   -4.325 closest distance to " CD  ARG A  14 " =    3.202
peak=   -4.310 closest distance to " CD  ARG A 156 " =    2.089
peak=   -4.300 closest distance to " CG2 VAL A 202 " =    2.714
peak=   -4.280 closest distance to " CG2 VAL A 230 " =    0.799
peak=   -4.217 closest distance to " C   HIS A 108 " =    1.176
peak=   -4.149 closest distance to " CZ2 TRP A  92 " =    2.872
peak=   -4.144 closest distance to " O   HOH Z 231 " =    2.045
peak=   -4.142 closest distance to " CB  PRO A 243 " =    2.724
peak=   -4.108 closest distance to " O   PRO A 198 " =    1.186
peak=   -4.058 closest distance to " O   HOH Z 411 " =    5.524
peak=   -4.053 closest distance to " O   HOH Z 211 " =    1.008
peak=   -4.052 closest distance to " CB  PHE A 192 " =    1.974
peak=   -4.051 closest distance to " CG  GLN A  58 " =    1.048
peak=   -4.015 closest distance to " CB  VAL A 230 " =    1.111
peak=   -4.002 closest distance to " CG  GLN A 223 " =    2.304
peak=   -3.994 closest distance to " O   HOH Z 100 " =    1.028
peak=   -3.973 closest distance to " O   VAL A  67 " =    2.617
peak=   -3.960 closest distance to " O   HOH Z 131 " =    4.068
peak=   -3.949 closest distance to " O   HOH Z 193 " =    1.161
peak=   -3.909 closest distance to " O   PRO A 163 " =    1.957
peak=   -3.855 closest distance to " CE BMET A  47 " =    1.163
peak=   -3.798 closest distance to " O   HOH Z 394 " =    1.558
peak=   -3.770 closest distance to " O   HOH Z  69 " =    1.762
peak=   -3.696 closest distance to " CD2 HIS A 207 " =    2.207
peak=   -3.686 closest distance to " CA  ASN A 127 " =    1.208
peak=   -3.680 closest distance to " CA  GLY A  35 " =    2.120
peak=   -3.671 closest distance to " CE2 TYR A  30 " =    2.696
peak=   -3.670 closest distance to " O   HOH Z 429 " =    1.973
peak=   -3.668 closest distance to " CB  ALA A 161 " =    2.485
peak=   -3.665 closest distance to " O   HOH Z 185 " =    2.269
peak=   -3.664 closest distance to " CB  ALA A  43 " =    2.728
peak=   -3.657 closest distance to " CA  GLY A 241 " =    2.300
peak=   -3.655 closest distance to " O   HOH Z 236 " =    1.402
peak=   -3.631 closest distance to " O   HOH Z 166 " =    2.050
peak=   -3.621 closest distance to " CG2 THR A 178 " =    2.346
peak=   -3.605 closest distance to " CD1 LEU A 101 " =    2.306
peak=   -3.587 closest distance to " N   THR A  52 " =    1.717
peak=   -3.586 closest distance to " CG  TRP A 266 " =    1.916
peak=   -3.574 closest distance to " CE  MET A 105 " =    2.393
peak=   -3.573 closest distance to " CB  ALA A 114 " =    2.567
peak=   -3.568 closest distance to " O   HOH Z 389 " =    1.470
peak=   -3.568 closest distance to " CA  ASP A 298 " =    1.070
peak=   -3.563 closest distance to " O   PHE A 218 " =    1.485
peak=   -3.558 closest distance to " O   HOH Z  73 " =    2.341
peak=   -3.555 closest distance to " CD1 LEU A 255 " =    2.795
peak=   -3.550 closest distance to " O   SER A  22 " =    2.347
peak=   -3.547 closest distance to " O   HOH Z  11 " =    1.773
peak=   -3.543 closest distance to " N   THR A 157 " =    1.509
peak=   -3.542 closest distance to " O   HOH Z 166 " =    2.046
peak=   -3.540 closest distance to " O   HOH Z 286 " =    1.714
peak=   -3.539 closest distance to " NE2 GLN A  11 " =    1.814
peak=   -3.537 closest distance to " O   HOH Z 276 " =    1.583
peak=   -3.531 closest distance to " OG  SER A  87 " =    1.403
peak=   -3.525 closest distance to " O   HOH Z 295 " =    1.602
peak=   -3.523 closest distance to " O   HOH Z 238 " =    0.976
peak=   -3.519 closest distance to " O   HOH Z 377 " =    2.109
peak=   -3.517 closest distance to " ND2 ASN A  45 " =    1.997
peak=   -3.516 closest distance to " OG  SER A  97 " =    2.252
peak=   -3.510 closest distance to " O   HOH Z 165 " =    2.113
peak=   -3.507 closest distance to " O   HOH Z 191 " =    5.475
peak=   -3.502 closest distance to " CZ2 TRP A 274 " =    0.969
peak=   -3.493 closest distance to " O   HOH Z 149 " =    2.115
peak=   -3.490 closest distance to " CB  ASP A  27 " =    2.435
peak=   -3.486 closest distance to " OG  SER A  62 " =    4.255
peak=   -3.485 closest distance to " O   HOH Z 243 " =    2.043
peak=   -3.483 closest distance to " O   HOH Z 351 " =    1.556
peak=   -3.474 closest distance to " O   HOH Z 111 " =    1.653
peak=   -3.472 closest distance to " CE3 TRP A 150 " =    2.307
peak=   -3.468 closest distance to " CA  VAL A  67 " =    3.003
peak=   -3.465 closest distance to " CD2 PHE A 225 " =    1.150
peak=   -3.460 closest distance to " NH2 ARG A  79 " =    2.124
peak=   -3.457 closest distance to " CG1 VAL A 125 " =    1.995
peak=   -3.455 closest distance to " C   MET A 188 " =    1.452
peak=   -3.454 closest distance to " CG2 VAL A 296 " =    1.872
peak=   -3.445 closest distance to " N   ALA A 226 " =    2.000
peak=   -3.444 closest distance to " CB  ASN A  39 " =    2.251
peak=   -3.431 closest distance to " CD  LYS A 289 " =    2.369
peak=   -3.430 closest distance to " OE1 GLN A  88 " =    1.068
peak=   -3.429 closest distance to " CB  TYR A  15 " =    2.241
peak=   -3.425 closest distance to " O   HOH Z 313 " =    1.616
peak=   -3.416 closest distance to " O   HOH Z 359 " =    3.027
peak=   -3.414 closest distance to " O   HOH Z 350 " =    1.805
peak=   -3.414 closest distance to " O   HOH Z  64 " =    1.447
peak=   -3.414 closest distance to " CG1 VAL A 112 " =    2.627
peak=   -3.413 closest distance to " OH  TYR A 172 " =    1.815
peak=   -3.408 closest distance to " O   HOH Z 201 " =    2.062
peak=   -3.406 closest distance to " ND2 ASN A 252 " =    1.986
peak=   -3.402 closest distance to " CD2 TYR A 293 " =    1.934
peak=   -3.395 closest distance to " O   HOH Z 102 " =    1.574
peak=   -3.392 closest distance to " CD2 LEU A   5 " =    1.119
peak=   -3.383 closest distance to " ND2 ASN A 249 " =    2.409
peak=   -3.374 closest distance to " N   ALA A 248 " =    1.656
peak=   -3.374 closest distance to " O   MET A  40 " =    2.851
peak=   -3.372 closest distance to " O   HOH Z 115 " =    1.884
peak=   -3.360 closest distance to " CD2 LEU A 237 " =    2.772
peak=   -3.360 closest distance to " O   HOH Z 198 " =    1.867
peak=   -3.354 closest distance to " CG1 VAL A 112 " =    2.901
peak=   -3.345 closest distance to " NH2 ARG A 219 " =    1.697
peak=   -3.344 closest distance to " ND2 ASN A  45 " =    1.290
peak=   -3.340 closest distance to " O   HOH Z  65 " =    1.300
peak=   -3.339 closest distance to " O   HOH Z 412 " =    4.172
peak=   -3.337 closest distance to " O   GLN A 144 " =    1.437
peak=   -3.335 closest distance to " O   HOH Z 231 " =    1.300
peak=   -3.330 closest distance to " O   SER A 271 " =    2.093
peak=   -3.329 closest distance to " CE2 TRP A  70 " =    2.250
peak=   -3.329 closest distance to " O   HOH Z  43 " =    1.781
peak=   -3.329 closest distance to " CB  ALA A 248 " =    2.272
peak=   -3.328 closest distance to " OD2 ASP A 191 " =    1.295
peak=   -3.318 closest distance to " O   HOH Z 292 " =    1.540
peak=   -3.318 closest distance to " ND2 ASN A 187 " =    1.525
peak=   -3.308 closest distance to " O   HOH Z 127 " =    1.130
peak=   -3.306 closest distance to " O   HOH Z 106 " =    1.726
peak=   -3.300 closest distance to " CG2 ILE A 151 " =    2.504
peak=   -3.296 closest distance to " ND2 ASN A  69 " =    1.807
peak=   -3.296 closest distance to " O   HOH Z 216 " =    1.425
peak=   -3.288 closest distance to " O   HOH Z 134 " =    4.141
peak=   -3.286 closest distance to " O   GLY A  17 " =    1.158
peak=   -3.286 closest distance to " O   HOH Z 318 " =    2.058
peak=   -3.276 closest distance to " O   GLY A  80 " =    2.474
peak=   -3.275 closest distance to " CD2 TYR A 247 " =    2.447
peak=   -3.274 closest distance to " O   HOH Z 389 " =    2.199
peak=   -3.273 closest distance to " O   HOH Z 116 " =    1.937
peak=   -3.273 closest distance to " O   TRP A  70 " =    1.485
peak=   -3.271 closest distance to " CG1 VAL A 250 " =    2.644
peak=   -3.271 closest distance to " O   HOH Z 250 " =    1.744
peak=   -3.271 closest distance to " O   SER A 135 " =    1.439
peak=   -3.264 closest distance to " O   VAL A 189 " =    2.608
peak=   -3.263 closest distance to " O   HOH Z 108 " =    1.386
peak=   -3.258 closest distance to " O   HOH Z 431 " =    1.841
peak=   -3.257 closest distance to " O   HOH Z 281 " =    2.751
peak=   -3.257 closest distance to " O   HOH Z  60 " =    1.823
peak=   -3.252 closest distance to " O   GLU A 152 " =    1.379
peak=   -3.244 closest distance to " O   HOH Z 231 " =    1.652
peak=   -3.241 closest distance to " CG  MET A 105 " =    1.002
peak=   -3.238 closest distance to " O   SER A 210 " =    1.822
peak=   -3.237 closest distance to " O   HOH Z 285 " =    2.153
peak=   -3.233 closest distance to " CE2 PHE A 218 " =    2.446
peak=   -3.220 closest distance to " CD  PRO A 243 " =    2.012
peak=   -3.217 closest distance to " CB  ASP A 171 " =    2.219
peak=   -3.217 closest distance to " CB  ALA A 291 " =    2.247
peak=   -3.215 closest distance to " O   HOH Z 103 " =    1.757
peak=   -3.214 closest distance to " CD1 ILE A 199 " =    2.449
peak=   -3.212 closest distance to " OE1 GLN A 183 " =    1.616
peak=   -3.210 closest distance to " CB  ALA A   7 " =    2.197
peak=   -3.209 closest distance to " O   HOH Z  68 " =    1.296
peak=   -3.206 closest distance to " CD2 PHE A  61 " =    1.978
peak=   -3.206 closest distance to " O   HOH Z 114 " =    2.917
peak=   -3.202 closest distance to " CZ  PHE A  38 " =    2.536
peak=   -3.195 closest distance to " OE1 GLU A 277 " =    2.163
peak=   -3.193 closest distance to " O   HOH Z 117 " =    1.890
peak=   -3.192 closest distance to " O   HOH Z 345 " =    2.118
peak=   -3.190 closest distance to " O   SER A 276 " =    1.611
peak=   -3.190 closest distance to " O   HOH Z 290 " =    1.210
peak=   -3.185 closest distance to " CD1 TRP A 274 " =    1.048
peak=   -3.183 closest distance to " N   ASP A 286 " =    2.320
peak=   -3.183 closest distance to " OE2 GLU A 152 " =    1.391
peak=   -3.175 closest distance to " CG  PHE A 283 " =    2.572
peak=   -3.173 closest distance to " O   HOH Z 357 " =    2.088
peak=   -3.172 closest distance to " CB  SER A 210 " =    1.076
peak=   -3.172 closest distance to " CB  HIS A  81 " =    0.949
peak=   -3.170 closest distance to " O   HOH Z 384 " =    2.112
peak=   -3.169 closest distance to " CZ3 TRP A 179 " =    1.276
peak=   -3.168 closest distance to " O   HOH Z 176 " =    0.750
peak=   -3.165 closest distance to " O   HOH Z 111 " =    4.430
peak=   -3.164 closest distance to " O   HOH Z 252 " =    3.893
peak=   -3.163 closest distance to " OG  SER A  63 " =    1.186
peak=   -3.163 closest distance to " O   HOH Z 140 " =    1.679
peak=   -3.156 closest distance to " O   HOH Z 427 " =    1.651
peak=   -3.156 closest distance to " O   HOH Z 138 " =    1.350
peak=   -3.156 closest distance to " O   HOH Z 359 " =    1.600
peak=   -3.155 closest distance to " O   HOH Z 390 " =    2.302
peak=   -3.154 closest distance to " CB  HIS A  86 " =    1.044
peak=   -3.153 closest distance to " O   ALA A 227 " =    1.514
peak=   -3.151 closest distance to " O   HOH Z 189 " =    2.283
peak=   -3.150 closest distance to " C   LYS A  76 " =    1.534
peak=   -3.144 closest distance to " C   LEU A 222 " =    0.899
peak=   -3.136 closest distance to " C   ARG A 269 " =    1.335
peak=   -3.133 closest distance to " OG ASER A 134 " =    1.287
peak=   -3.132 closest distance to " CD  GLN A  77 " =    1.426
peak=   -3.132 closest distance to " CZ  TYR A 169 " =    1.779
peak=   -3.129 closest distance to " OXT GLY A 302 " =    3.430
peak=   -3.126 closest distance to " NE2 GLN A 278 " =    1.806
peak=   -3.123 closest distance to " CB  PRO A 213 " =    2.190
peak=   -3.120 closest distance to " O   ALA A 180 " =    1.288
peak=   -3.119 closest distance to " CB  ALA A  10 " =    2.305
peak=   -3.116 closest distance to " CG2 ILE A 263 " =    2.345
peak=   -3.113 closest distance to " O   ASP A  27 " =    1.862
peak=   -3.110 closest distance to " CB  PRO A 163 " =    2.456
peak=   -3.105 closest distance to " O   HOH Z  39 " =    1.206
peak=   -3.093 closest distance to " CG  GLN A 103 " =    2.394
peak=   -3.091 closest distance to " CA  GLY A 203 " =    2.498
peak=   -3.082 closest distance to " N   SER A 276 " =    1.430
peak=   -3.072 closest distance to " O   HOH Z 139 " =    3.102
peak=   -3.072 closest distance to " CE1 HIS A  81 " =    1.617
peak=   -3.070 closest distance to " O   HOH Z 407 " =    2.896
peak=   -3.068 closest distance to " NE2 GLN A 240 " =    1.584
peak=   -3.061 closest distance to " OH  TYR A 247 " =    1.832
peak=   -3.051 closest distance to " CE BMET A  47 " =    1.668
peak=   -3.037 closest distance to " O   TYR A 186 " =    1.701
peak=   -3.037 closest distance to " OG BSER A 134 " =    1.822
peak=   -3.012 closest distance to " C   ASN A 148 " =    1.670

================= 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    :  0.4721 0.4547   6.272432e+00   6.250729e+00
   1_bss:  0.4627 0.4440   6.264957e+00   6.238303e+00
   1_xyz:  0.3747 0.3930   6.135119e+00   6.156248e+00
   1_adp:  0.3264 0.3773   6.039314e+00   6.125748e+00
   1_occ:  0.3257 0.3772   6.038449e+00   6.127067e+00
   2_bss:  0.3212 0.3728   6.038454e+00   6.126115e+00
   2_xyz:  0.2251 0.2794   5.734661e+00   5.902597e+00
   2_adp:  0.1982 0.2541   5.627169e+00   5.811630e+00
   2_occ:  0.1981 0.2540   5.627056e+00   5.811997e+00
   3_bss:  0.1961 0.2533   5.627839e+00   5.812516e+00
   3_xyz:  0.1539 0.2029   5.407954e+00   5.614764e+00
   3_adp:  0.1422 0.1952   5.351323e+00   5.573993e+00
   3_occ:  0.1421 0.1952   5.351084e+00   5.573877e+00
   4_bss:  0.1419 0.1952   5.350605e+00   5.573732e+00
   4_xyz:  0.1279 0.1797   5.266818e+00   5.502334e+00
   4_adp:  0.1257 0.1759   5.248780e+00   5.483111e+00
   4_occ:  0.1256 0.1758   5.248545e+00   5.483170e+00
   5_bss:  0.1255 0.1758   5.248560e+00   5.483332e+00
   5_xyz:  0.1187 0.1672   5.202731e+00   5.445045e+00
   5_adp:  0.1172 0.1661   5.194022e+00   5.437782e+00
   5_occ:  0.1171 0.1660   5.193900e+00   5.437726e+00
   5_bss:  0.1172 0.1661   5.193650e+00   5.436737e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.342  10.884   6.866   8.562  11.509   0.000   0.000   0.000
   1_xyz:  0.342  10.884   6.866   8.562  11.509   0.000   0.000   0.000
   1_adp:  0.342  10.884   6.866   8.562  11.509   0.000   0.000   0.000
   1_occ:  0.342  10.884   6.866   8.562  11.509   0.000   0.000   0.000
   2_bss:  0.334  38.007   3.250   4.260   7.414   0.000   0.000   0.000
   2_xyz:  0.334  38.007   3.250   4.260   7.414   0.000   0.000   0.000
   2_adp:  0.334  38.007   3.250   4.260   7.414   0.000   0.000   0.000
   2_occ:  0.334  38.007   3.250   4.260   7.414   0.000   0.000   0.000
   3_bss:  0.318  50.055   2.041   2.581   4.842   0.000   0.000   0.000
   3_xyz:  0.318  50.055   2.041   2.581   4.842   0.000   0.000   0.000
   3_adp:  0.318  50.055   2.041   2.581   4.842   0.000   0.000   0.000
   3_occ:  0.318  50.055   2.041   2.581   4.842   0.000   0.000   0.000
   4_bss:  0.328  57.975   1.737   2.153   4.253   0.000   0.000   0.000
   4_xyz:  0.328  57.975   1.737   2.153   4.253   0.000   0.000   0.000
   4_adp:  0.328  57.975   1.737   2.153   4.253   0.000   0.000   0.000
   4_occ:  0.328  57.975   1.737   2.153   4.253   0.000   0.000   0.000
   5_bss:  0.327  56.436   1.963   2.270   4.240   0.000   0.000   0.000
   5_xyz:  0.327  56.436   1.963   2.270   4.240   0.000   0.000   0.000
   5_adp:  0.327  56.436   1.963   2.270   4.240   0.000   0.000   0.000
   5_occ:  0.327  56.436   1.963   2.270   4.240   0.000   0.000   0.000
   5_bss:  0.326  59.332  -0.810  -0.575   1.385   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.940 0.4715  0.5443    63531.568
   1_bss:  53.568 0.4749  0.7127    61142.243
   1_xyz:  43.735 0.5968  0.8681    43110.571
   1_adp:  40.714 0.6335  0.9619    38912.402
   1_occ:  40.812 0.6322  0.9579    39027.945
   2_bss:  40.528 0.6356  0.8385    38693.477
   2_xyz:  28.466 0.7739  0.9863    20119.705
   2_adp:  24.745 0.8144  1.0114    16213.725
   2_occ:  24.771 0.8141  1.0109    16216.864
   3_bss:  24.739 0.8145  0.9475    16270.318
   3_xyz:  19.183 0.8695  0.9858    10367.121
   3_adp:  18.111 0.8799  0.9825     9588.835
   3_occ:  18.112 0.8799  0.9826     9587.120
   4_bss:  18.087 0.8801  0.9675     9578.039
   4_xyz:  16.536 0.8936  0.9739     8189.826
   4_adp:  16.017 0.8984  0.9696     7871.645
   4_occ:  16.013 0.8985  0.9696     7869.301
   5_bss:  16.013 0.8985  0.9736     7872.592
   5_xyz:  15.189 0.9053  0.9780     7217.496
   5_adp:  14.999 0.9071  0.9725     7099.426
   5_occ:  14.999 0.9071  0.9725     7096.913
   5_bss:  14.992 0.9072  0.9749     7089.049
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3833e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3833e+01
   1_xyz:   1.657  0.013  0.105 18.266  0.006  4.110   1.3460e-01
   1_adp:   1.657  0.013  0.105 18.266  0.006  4.110   1.3460e-01
   1_occ:   1.657  0.013  0.105 18.266  0.006  4.110   1.3460e-01
   2_bss:   1.657  0.013  0.105 18.266  0.006  4.110   1.3460e-01
   2_xyz:   1.155  0.009  0.083 16.370  0.005  4.111   8.0765e-02
   2_adp:   1.155  0.009  0.083 16.370  0.005  4.111   8.0765e-02
   2_occ:   1.155  0.009  0.083 16.370  0.005  4.111   8.0765e-02
   3_bss:   1.155  0.009  0.083 16.370  0.005  4.111   8.0765e-02
   3_xyz:   0.981  0.006  0.073 15.867  0.003  4.123   5.9704e-02
   3_adp:   0.981  0.006  0.073 15.867  0.003  4.123   5.9704e-02
   3_occ:   0.981  0.006  0.073 15.867  0.003  4.123   5.9704e-02
   4_bss:   0.981  0.006  0.073 15.867  0.003  4.123   5.9704e-02
   4_xyz:   0.935  0.006  0.072 15.696  0.003  4.128   5.6400e-02
   4_adp:   0.935  0.006  0.072 15.696  0.003  4.128   5.6400e-02
   4_occ:   0.935  0.006  0.072 15.696  0.003  4.128   5.6400e-02
   5_bss:   0.935  0.006  0.072 15.696  0.003  4.128   5.6400e-02
   5_xyz:   0.988  0.007  0.075 15.466  0.003  4.125   6.0356e-02
   5_adp:   0.988  0.007  0.075 15.466  0.003  4.125   6.0356e-02
   5_occ:   0.988  0.007  0.075 15.466  0.003  4.125   6.0356e-02
   5_bss:   0.988  0.007  0.075 15.466  0.003  4.125   6.0356e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9783e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9783e+00
   1_xyz:  13.490  0.165  0.405 84.957  0.032  2.132   9.7277e-02
   1_adp:  13.490  0.165  0.405 84.957  0.032  2.132   9.7277e-02
   1_occ:  13.490  0.165  0.405 84.957  0.032  2.132   9.7277e-02
   2_bss:  13.490  0.165  0.405 84.957  0.032  2.132   9.7277e-02
   2_xyz:   6.508  0.100  0.265 87.672  0.035  2.261   6.9919e-02
   2_adp:   6.508  0.100  0.265 87.672  0.035  2.261   6.9919e-02
   2_occ:   6.508  0.100  0.265 87.672  0.035  2.261   6.9919e-02
   3_bss:   6.508  0.100  0.265 87.672  0.035  2.261   6.9919e-02
   3_xyz:   6.826  0.042  0.327 88.824  0.031  2.327   3.8984e-02
   3_adp:   6.826  0.042  0.327 88.824  0.031  2.327   3.8984e-02
   3_occ:   6.826  0.042  0.327 88.824  0.031  2.327   3.8984e-02
   4_bss:   6.826  0.042  0.327 88.824  0.031  2.327   3.8984e-02
   4_xyz:   7.321  0.044  0.302 82.172  0.036  2.384   3.3061e-02
   4_adp:   7.321  0.044  0.302 82.172  0.036  2.384   3.3061e-02
   4_occ:   7.321  0.044  0.302 82.172  0.036  2.384   3.3061e-02
   5_bss:   7.321  0.044  0.302 82.172  0.036  2.384   3.3061e-02
   5_xyz:   6.314  0.049  0.293 85.669  0.038  2.326   4.5269e-02
   5_adp:   6.314  0.049  0.293 85.669  0.038  2.326   4.5269e-02
   5_occ:   6.314  0.049  0.293 85.669  0.038  2.326   4.5269e-02
   5_bss:   6.314  0.049  0.293 85.669  0.038  2.326   4.5269e-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:  74.99   0.00  12.95  58.61   0.00  10.46  74.99   0.00  26.52
   1_occ:  74.99   0.00  12.95  58.61   0.00  10.46  74.99   0.00  26.52
   2_bss:  74.99   0.00  12.95  58.61   0.00  10.46  74.99   0.00  26.52
   2_xyz:  74.99   0.00  12.95  58.61   0.00  10.46  74.99   0.00  26.52
   2_adp:  79.87   0.00  12.60  58.23   0.00   8.92  79.87   0.00  32.65
   2_occ:  79.87   0.00  12.60  58.23   0.00   8.92  79.87   0.00  32.65
   3_bss:  79.87   0.00  12.60  58.23   0.00   8.92  79.87   0.00  32.65
   3_xyz:  79.87   0.00  12.60  58.23   0.00   8.92  79.87   0.00  32.65
   3_adp:  86.83   0.00  13.65  82.35   0.00   8.89  86.83   1.18  39.58
   3_occ:  86.83   0.00  13.65  82.35   0.00   8.89  86.83   1.18  39.58
   4_bss:  86.83   0.00  13.65  82.35   0.00   8.89  86.83   1.18  39.58
   4_xyz:  86.83   0.00  13.65  82.35   0.00   8.89  86.83   1.18  39.58
   4_adp:  87.50   0.00  13.39  84.50   0.00   8.63  87.50   1.26  39.30
   4_occ:  87.50   0.00  13.39  84.50   0.00   8.63  87.50   1.26  39.30
   5_bss:  87.50   0.00  13.39  84.50   0.00   8.63  87.50   1.26  39.30
   5_xyz:  87.50   0.00  13.39  84.50   0.00   8.63  87.50   1.26  39.30
   5_adp:  93.00   0.00  13.26  93.00   0.00   8.52  91.57   1.23  39.07
   5_occ:  93.00   0.00  13.26  93.00   0.00   8.52  91.57   1.23  39.07
   5_bss:  95.89   2.90  16.16  95.89   2.90  11.41  94.46   4.12  41.97
------------------------------------------------------------------------
 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:    1.267    0.017    0.408
   1_adp:    1.267    0.017    0.408
   1_occ:    1.267    0.017    0.408
   2_bss:    1.267    0.017    0.408
   2_xyz:    1.642    0.022    0.573
   2_adp:    1.642    0.022    0.573
   2_occ:    1.642    0.022    0.573
   3_bss:    1.642    0.022    0.573
   3_xyz:    1.649    0.035    0.627
   3_adp:    1.649    0.035    0.627
   3_occ:    1.649    0.035    0.627
   4_bss:    1.649    0.035    0.627
   4_xyz:    1.741    0.034    0.657
   4_adp:    1.741    0.034    0.657
   4_occ:    1.741    0.034    0.657
   5_bss:    1.741    0.034    0.657
   5_xyz:    1.788    0.044    0.675
   5_adp:    1.788    0.044    0.675
   5_occ:    1.788    0.044    0.675
   5_bss:    1.788    0.044    0.675
------------------------------------------------------------------------

CPU time actual refinement: 322.47


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_526/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_526/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_526/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_526/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_526/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 322.32 
  Macro-tasks:
    bulk solvent and scale       = 42.63  
    individual site refinement   = 124.77 
    weights calculation          = 31.45  
    collect and process          = 6.46   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 205.42 
  Micro-tasks:
    mask                            = 2.34   
    f_calc                          = 97.87  
    alpha_beta                      = 8.11   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 106.43 
    fmodel                         = 6.99   
    r_factors                      = 0.15   
    phase_errors                   = 10.75  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 234.02 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.602 micro seconds
Total CPU time: 5.60 minutes
from_scatterers_fft:    639 calls, 97.45 s
gradients_fft:          584 calls, 93.87 s

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

# Date 2008-01-16 Time 01:46:33 PST -0800 (1200476793.01 s)
Start R-work = 0.4721, R-free = 0.4547 (no bulk solvent and anisotropic scale)
Final R-work = 0.1344, R-free = 0.1823 (no bulk solvent and anisotropic scale)

Start R-work = 0.4627, R-free = 0.4440
Final R-work = 0.1172, R-free = 0.1661