# Date 2008-01-16 Time 01:45:26 PST -0800 (1200476726.50 s)
#phil __OFF__

Command line arguments: "../549.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 17580
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 549

-------------------------------------------------------------------------------
  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, 46.93, 88.5498, 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: 3.27, per 1000 atoms: 1.16


================================== 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, 46.93, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.037 1.99076
Completeness in resolution range: 0.95319
Completeness with d_max=infinity: 0.95023

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0370
                             d_min =   1.9908

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, 46.93, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.037 1.99076
Completeness in resolution range: 0.95319
Completeness with d_max=infinity: 0.95023

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0375 -  4.2595 [2165/2189]  1946   219  10.1%
  bin  2:  4.2595 -  3.3937 [2061/2080]  1856   205   9.9%
  bin  3:  3.3937 -  2.9684 [2048/2067]  1847   201   9.8%
  bin  4:  2.9684 -  2.6987 [2032/2062]  1821   211  10.4%
  bin  5:  2.6987 -  2.5063 [2002/2021]  1805   197   9.8%
  bin  6:  2.5063 -  2.3591 [2012/2037]  1810   202  10.0%
  bin  7:  2.3591 -  2.2413 [2011/2039]  1813   198   9.8%
  bin  8:  2.2413 -  2.1441 [1974/2010]  1771   203  10.3%
  bin  9:  2.1441 -  2.0617 [1983/2025]  1790   193   9.7%
  bin 10:  2.0617 -  1.9908 [1301/2021]  1171   130  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_549/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:
        1.38 -     2.09: 11
        2.09 -     2.79: 639
        2.79 -     3.49: 4418
        3.49 -     4.20: 9237
        4.20 -     4.90: 13727
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.384 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.488 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.564 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.700 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.700 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28027 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_549/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_549/model_refine_001.geo

CPU time processing inputs: 9.13


============================ 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 46.93 88.54975 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: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4643   r_free= 0.4529   ksol= 0.00   Bsol= 0.00   scale= 0.795    |
|                                                                             |
| 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:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.268318                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0375 -  4.7507 0.99   1405  155 0.3842 0.3496      6.5922      6.5104|
|  2:  4.7507 -  3.7907 0.99   1352  151 0.3692 0.4207      6.7304      6.8676|
|  3:  3.7907 -  3.3174 0.99   1310  148 0.4221 0.3999      6.6583      6.6187|
|  4:  3.3174 -  3.0167 0.99   1324  140 0.4584 0.4358      6.5129      6.4484|
|  5:  3.0167 -  2.8020 0.99   1298  149 0.4883 0.4544      6.3478      6.3594|
|  6:  2.8020 -  2.6377 0.99   1304  143 0.4850 0.5701      6.2697       6.231|
|  7:  2.6377 -  2.5063 0.99   1282  147 0.4954 0.4706      6.2187      6.1512|
|  8:  2.5063 -  2.3976 0.98   1292  142 0.5246 0.4436      6.1956      6.1387|
|  9:  2.3976 -  2.3057 0.98   1284  139 0.5029 0.5289      6.0984      6.1585|
| 10:  2.3057 -  2.2263 0.99   1293  143 0.5252 0.4415      6.1112      6.0297|
| 11:  2.2263 -  2.1569 0.98   1273  144 0.5070 0.5510      6.0271       6.067|
| 12:  2.1569 -  2.0955 0.97   1261  139 0.5191 0.4571      5.9535      6.0086|
| 13:  2.0955 -  2.0404 0.99   1272  138 0.5144 0.5191      5.8904      5.8233|
| 14:  2.0404 -  1.9908 0.52    680   81 0.5114 0.4507      5.8921      5.7347|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0375 -  4.7507  1405   155  0.73  31.78   0.80     0.75      62073.72|
|  2:  4.7507 -  3.7907  1352   151  0.73  32.50   0.88     0.79      93704.67|
|  3:  3.7907 -  3.3174  1310   148  0.65  39.92   0.83     0.75      99387.33|
|  4:  3.3174 -  3.0167  1324   140  0.56  47.44   0.80     0.63      89542.79|
|  5:  3.0167 -  2.8020  1298   149  0.45  55.68   0.75     0.52      76581.72|
|  6:  2.8020 -  2.6377  1304   143  0.40  59.99   0.73     0.45      71628.16|
|  7:  2.6377 -  2.5063  1282   147  0.40  60.09   0.74     0.45      63254.87|
|  8:  2.5063 -  2.3976  1292   142  0.43  57.66   0.72     0.50      53606.48|
|  9:  2.3976 -  2.3057  1284   139  0.45  56.05   0.73     0.52      47452.41|
| 10:  2.3057 -  2.2263  1293   143  0.44  57.17   0.73     0.50      43143.95|
| 11:  2.2263 -  2.1569  1273   144  0.39  60.56   0.76     0.48      43784.29|
| 12:  2.1569 -  2.0955  1261   139  0.39  60.92   0.74     0.48      39321.69|
| 13:  2.0955 -  2.0404  1272   138  0.41  59.66   0.73     0.50      33539.72|
| 14:  2.0404 -  1.9908   680    81  0.49  53.36   0.75     0.51      23810.32|
|alpha:            min =        0.45 max =            0.79 mean =         0.56|
|beta:             min =    23810.32 max =        99387.33 mean =     61639.39|
|figures of merit: min =        0.00 max =            1.00 mean =         0.50|
|phase err.(work): min =        0.00 max =           89.98 mean =        52.05|
|phase err.(test): min =        0.00 max =           89.97 mean =        52.38|
|-----------------------------------------------------------------------------|

============================== 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 = 11.307077             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.149   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.888369              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.050   (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 |  1.165 -  1.538:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.538 -  1.912:       20 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.912 -  2.285:      157 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.285 -  2.659:      656 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.659 -  3.032:     1447 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.032 -  3.406:     2541 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.406 -  3.779:     3905 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.779 -  4.153:     5057 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.153 -  4.526:     6572 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.526 -  4.900:     7687 |
|-----------------------------------------------------------------------------|
|-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 |       54.150 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.165 |       1.888 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.056)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.056)------------------------------------------|
|    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: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4716   r_free= 0.4558   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:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.272647                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4548   r_free= 0.4418   ksol= 0.33   Bsol= 16.55   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.65,7.29,12.57,0.00,0.00,0.00); trace/3= 8.84                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.259895                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.969914              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.094   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.867186              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.279   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4548      final r-factor (work) = 0.3656          |
| start r-factor (free) = 0.4418      final r-factor (free) = 0.3861          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 85.3996 = 9.97 * 0.50 * 6.2688 + 1.00 * 54.1501                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.8189 = 9.97 * 0.50 * 6.1557 + 1.00 * 0.1330                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3656      final r-factor (work) = 0.3156          |
| start r-factor (free) = 0.3861      final r-factor (free) = 0.3615          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3525 = 0.87 * 1.00 * 6.1557 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2577 = 0.87 * 1.00 * 6.0467 + 1.00 * 0.0141                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.056)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    70.06   12.56    None  None   None       |
|    all(noH): 2823   0      0.00    70.06   12.56    None  None   None       |
|    Sol.    : 438    0      0.00    70.06   26.86    None  None   None       |
|    Mac.    : 2385   0      0.00    55.02   9.93     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 -   7.006: 1136   |   5:    35.031 -  42.037:   86        |
|      1:     7.006 -  14.012:  773   |   6:    42.037 -  49.043:   48        |
|      2:    14.012 -  21.019:  376   |   7:    49.043 -  56.050:   31        |
|      3:    21.019 -  28.025:  228   |   8:    56.050 -  63.056:    7        |
|      4:    28.025 -  35.031:  135   |   9:    63.056 -  70.062:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3156 r_free = 0.3615             target_work(ml) = 6.019         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3148 r_free = 0.3623             target_work(ml) = 6.018         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3148   r_free= 0.3623   ksol= 0.33   Bsol= 16.55   scale= 1.099   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.65,7.29,12.57,0.00,0.00,0.00); trace/3= 8.84                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 6.018475                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3114   r_free= 0.3586   ksol= 0.33   Bsol= 46.40   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.29,3.82,8.91,0.00,0.00,0.00); trace/3= 5.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 6.018775                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.074940              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.914   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.420715              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.124  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3114      final r-factor (work) = 0.2434          |
| start r-factor (free) = 0.3586      final r-factor (free) = 0.2932          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.4474 = 4.07 * 0.50 * 6.0440 + 1.00 * 0.1330                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.0919 = 4.07 * 0.50 * 5.8996 + 1.00 * 0.0716                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2434      final r-factor (work) = 0.2268          |
| start r-factor (free) = 0.2932      final r-factor (free) = 0.2771          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4964 = 0.42 * 1.00 * 5.8996 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4397 = 0.42 * 1.00 * 5.7726 + 1.00 * 0.0111                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.056)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    68.64   12.54    None  None   None       |
|    all(noH): 2823   0      0.00    68.64   12.54    None  None   None       |
|    Sol.    : 438    0      0.00    68.64   31.57    None  None   None       |
|    Mac.    : 2385   0      0.00    62.09   9.04     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 -   6.864: 1222   |   5:    34.319 -  41.183:  108        |
|      1:     6.864 -  13.728:  755   |   6:    41.183 -  48.046:   64        |
|      2:    13.728 -  20.591:  326   |   7:    48.046 -  54.910:   40        |
|      3:    20.591 -  27.455:  162   |   8:    54.910 -  61.774:   17        |
|      4:    27.455 -  34.319:  123   |   9:    61.774 -  68.638:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2268 r_free = 0.2771             target_work(ml) = 5.752         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2268 r_free = 0.2771             target_work(ml) = 5.752         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2268   r_free= 0.2771   ksol= 0.33   Bsol= 46.40   scale= 1.045   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.29,3.82,8.91,0.00,0.00,0.00); trace/3= 5.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.752256                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2255   r_free= 0.2778   ksol= 0.32   Bsol= 56.32   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.89,2.62,5.88,0.00,0.00,0.00); trace/3= 3.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.753287                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.481458              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.667   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.415366              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.085  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2255      final r-factor (work) = 0.1745          |
| start r-factor (free) = 0.2778      final r-factor (free) = 0.2272          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2406 = 2.48 * 0.50 * 5.7781 + 1.00 * 0.0716                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0552 = 2.48 * 0.50 * 5.6372 + 1.00 * 0.0610                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1745      final r-factor (work) = 0.1627          |
| start r-factor (free) = 0.2272      final r-factor (free) = 0.2137          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3526 = 0.42 * 1.00 * 5.6372 + 1.00 * 0.0111                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2925 = 0.42 * 1.00 * 5.4916 + 1.00 * 0.0115                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.056)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    69.75   12.63    None  None   None       |
|    all(noH): 2823   0      0.00    69.75   12.63    None  None   None       |
|    Sol.    : 438    0      1.21    69.75   34.57    None  None   None       |
|    Mac.    : 2385   0      0.00    67.88   8.60     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 -   6.975: 1315   |   5:    34.873 -  41.847:  114        |
|      1:     6.975 -  13.949:  758   |   6:    41.847 -  48.822:   95        |
|      2:    13.949 -  20.924:  247   |   7:    48.822 -  55.796:   40        |
|      3:    20.924 -  27.898:  114   |   8:    55.796 -  62.771:   20        |
|      4:    27.898 -  34.873:  109   |   9:    62.771 -  69.745:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1627 r_free = 0.2137             target_work(ml) = 5.464         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1626 r_free = 0.2135             target_work(ml) = 5.464         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1626   r_free= 0.2135   ksol= 0.32   Bsol= 56.32   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.89,2.62,5.88,0.00,0.00,0.00); trace/3= 3.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.463660                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1622   r_free= 0.2132   ksol= 0.33   Bsol= 60.40   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.57,2.22,4.65,0.00,0.00,0.00); trace/3= 2.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.463557                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.253678              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.010  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.481186              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.586  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1622      final r-factor (work) = 0.1326          |
| start r-factor (free) = 0.2132      final r-factor (free) = 0.1785          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9972 = 3.25 * 0.50 * 5.4930 + 1.00 * 0.0610                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8222 = 3.25 * 0.50 * 5.3775 + 1.00 * 0.0739                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1326      final r-factor (work) = 0.1257          |
| start r-factor (free) = 0.1785      final r-factor (free) = 0.1746          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.9765 = 1.48 * 1.00 * 5.3775 + 1.00 * 0.0114                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.8145 = 1.48 * 1.00 * 5.2633 + 1.00 * 0.0185                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.056)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.29   13.14    None  None   None       |
|    all(noH): 2823   0      0.00    85.29   13.14    None  None   None       |
|    Sol.    : 438    0      1.26    85.29   38.12    None  None   None       |
|    Mac.    : 2385   0      0.00    77.24   8.55     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 -   8.529: 1593   |   5:    42.646 -  51.176:   92        |
|      1:     8.529 -  17.059:  628   |   6:    51.176 -  59.705:   79        |
|      2:    17.059 -  25.588:  178   |   7:    59.705 -  68.234:   36        |
|      3:    25.588 -  34.117:   95   |   8:    68.234 -  76.763:   13        |
|      4:    34.117 -  42.646:  104   |   9:    76.763 -  85.292:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1257 r_free = 0.1746             target_work(ml) = 5.251         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1256 r_free = 0.1746             target_work(ml) = 5.251         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1256   r_free= 0.1746   ksol= 0.33   Bsol= 60.40   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.57,2.22,4.65,0.00,0.00,0.00); trace/3= 2.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.251248                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1254   r_free= 0.1745   ksol= 0.33   Bsol= 60.40   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.79,2.33,4.35,0.00,0.00,0.00); trace/3= 2.83                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.249995                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.011892              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 141.837  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.446383              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 98.148   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1254      final r-factor (work) = 0.1215          |
| start r-factor (free) = 0.1745      final r-factor (free) = 0.1691          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3680 = 2.01 * 0.50 * 5.2628 + 1.00 * 0.0739                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3303 = 2.01 * 0.50 * 5.2383 + 1.00 * 0.0609                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1215      final r-factor (work) = 0.1204          |
| start r-factor (free) = 0.1691      final r-factor (free) = 0.1689          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.8306 = 2.45 * 1.00 * 5.2383 + 1.00 * 0.0157                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.7865 = 2.45 * 1.00 * 5.2202 + 1.00 * 0.0158                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.056)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.45   13.15    None  None   None       |
|    all(noH): 2823   0      0.00    99.45   13.15    None  None   None       |
|    Sol.    : 438    0      0.85    99.45   38.49    None  None   None       |
|    Mac.    : 2385   0      0.00    85.60   8.49     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 -   9.945: 1798   |   5:    49.723 -  59.668:   87        |
|      1:     9.945 -  19.889:  496   |   6:    59.668 -  69.613:   43        |
|      2:    19.889 -  29.834:  160   |   7:    69.613 -  79.557:   20        |
|      3:    29.834 -  39.779:  122   |   8:    79.557 -  89.502:    8        |
|      4:    39.779 -  49.723:   88   |   9:    89.502 -  99.447:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1204 r_free = 0.1689             target_work(ml) = 5.220         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1203 r_free = 0.1688             target_work(ml) = 5.220         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1203   r_free= 0.1688   ksol= 0.33   Bsol= 60.40   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.79,2.33,4.35,0.00,0.00,0.00); trace/3= 2.83                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.220085                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0375 -  4.7507 0.99   1405  155 0.1006 0.1321      5.4184      5.5689|
|  2:  4.7507 -  3.7907 0.99   1352  151 0.0872 0.1171      5.4685      5.6799|
|  3:  3.7907 -  3.3174 0.99   1310  148 0.1116 0.1577      5.5288      5.8768|
|  4:  3.3174 -  3.0167 0.99   1324  140 0.1295 0.1772       5.505      5.6952|
|  5:  3.0167 -  2.8020 0.99   1298  149 0.1448 0.1657       5.408      5.5671|
|  6:  2.8020 -  2.6377 0.99   1304  143 0.1339 0.2260      5.2894      5.6105|
|  7:  2.6377 -  2.5063 0.99   1282  147 0.1394 0.1752      5.2676      5.4034|
|  8:  2.5063 -  2.3976 0.98   1292  142 0.1269 0.1800      5.1768       5.423|
|  9:  2.3976 -  2.3057 0.98   1284  139 0.1307 0.2123      5.1205      5.4567|
| 10:  2.3057 -  2.2263 0.99   1293  143 0.1257 0.1664      5.0444      5.2109|
| 11:  2.2263 -  2.1569 0.98   1273  144 0.1257 0.1991      5.0237      5.3285|
| 12:  2.1569 -  2.0955 0.97   1261  139 0.1294 0.1792      4.9862      5.2995|
| 13:  2.0955 -  2.0404 0.99   1272  138 0.1187 0.1862      4.8491       5.072|
| 14:  2.0404 -  1.9908 0.52    680   81 0.1011 0.1722      4.6852      4.9769|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0375 -  4.7507  1405   155  0.93   9.90   0.97     0.94       8136.77|
|  2:  4.7507 -  3.7907  1352   151  0.95   8.54   1.01     0.99       9866.04|
|  3:  3.7907 -  3.3174  1310   148  0.93  11.96   1.02     1.02      11429.61|
|  4:  3.3174 -  3.0167  1324   140  0.91  14.48   1.01     1.00      11339.30|
|  5:  3.0167 -  2.8020  1298   149  0.89  17.10   1.00     0.97       9609.89|
|  6:  2.8020 -  2.6377  1304   143  0.88  17.88   0.97     0.94       8422.27|
|  7:  2.6377 -  2.5063  1282   147  0.89  17.52   0.99     0.94       7621.53|
|  8:  2.5063 -  2.3976  1292   142  0.89  17.20   0.99     0.95       6779.56|
|  9:  2.3976 -  2.3057  1284   139  0.89  17.49   0.99     0.95       6080.84|
| 10:  2.3057 -  2.2263  1293   143  0.89  17.56   0.99     0.94       5216.88|
| 11:  2.2263 -  2.1569  1273   144  0.88  18.02   0.99     0.94       5229.44|
| 12:  2.1569 -  2.0955  1261   139  0.89  17.78   0.99     0.98       4892.55|
| 13:  2.0955 -  2.0404  1272   138  0.89  17.49   0.98     0.95       3846.49|
| 14:  2.0404 -  1.9908   680    81  0.92  14.11   0.96     0.93       2646.84|
|alpha:            min =        0.93 max =            1.02 mean =         0.96|
|beta:             min =     2646.84 max =        11429.61 mean =      7420.06|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.94 mean =        15.48|
|phase err.(test): min =        0.00 max =           87.77 mean =        14.95|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1202   r_free= 0.1687   ksol= 0.33   Bsol= 63.39   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.96,-0.48,1.44,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.220257                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.04 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1202   r_free= 0.1687   ksol= 0.33   Bsol= 63.39   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.96,-0.48,1.44,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.220257                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0375 -  4.7507 0.99   1405  155 0.1006 0.1322      5.4191        5.57|
|  2:  4.7507 -  3.7907 0.99   1352  151 0.0873 0.1171      5.4692      5.6801|
|  3:  3.7907 -  3.3174 0.99   1310  148 0.1116 0.1578      5.5292      5.8777|
|  4:  3.3174 -  3.0167 0.99   1324  140 0.1295 0.1772      5.5051      5.6955|
|  5:  3.0167 -  2.8020 0.99   1298  149 0.1447 0.1655      5.4079      5.5668|
|  6:  2.8020 -  2.6377 0.99   1304  143 0.1339 0.2261      5.2895      5.6107|
|  7:  2.6377 -  2.5063 0.99   1282  147 0.1393 0.1754      5.2677      5.4039|
|  8:  2.5063 -  2.3976 0.98   1292  142 0.1269 0.1802      5.1775      5.4235|
|  9:  2.3976 -  2.3057 0.98   1284  139 0.1307 0.2123      5.1208      5.4571|
| 10:  2.3057 -  2.2263 0.99   1293  143 0.1257 0.1666      5.0444      5.2109|
| 11:  2.2263 -  2.1569 0.98   1273  144 0.1257 0.1986      5.0231      5.3268|
| 12:  2.1569 -  2.0955 0.97   1261  139 0.1294 0.1792       4.986      5.2993|
| 13:  2.0955 -  2.0404 0.99   1272  138 0.1187 0.1866      4.8491      5.0732|
| 14:  2.0404 -  1.9908 0.52    680   81 0.1012 0.1718      4.6857      4.9761|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0375 -  4.7507  1405   155  0.93   9.91   0.97     0.94       8151.50|
|  2:  4.7507 -  3.7907  1352   151  0.95   8.55   1.01     0.99       9880.20|
|  3:  3.7907 -  3.3174  1310   148  0.93  11.97   1.03     1.02      11445.61|
|  4:  3.3174 -  3.0167  1324   140  0.91  14.50   1.01     1.00      11345.33|
|  5:  3.0167 -  2.8020  1298   149  0.89  17.10   1.00     0.97       9615.35|
|  6:  2.8020 -  2.6377  1304   143  0.88  17.88   0.98     0.95       8420.71|
|  7:  2.6377 -  2.5063  1282   147  0.89  17.53   0.99     0.95       7626.50|
|  8:  2.5063 -  2.3976  1292   142  0.89  17.22   0.99     0.96       6792.62|
|  9:  2.3976 -  2.3057  1284   139  0.89  17.51   1.00     0.95       6088.01|
| 10:  2.3057 -  2.2263  1293   143  0.89  17.55   1.00     0.95       5214.00|
| 11:  2.2263 -  2.1569  1273   144  0.88  18.00   1.00     0.95       5219.26|
| 12:  2.1569 -  2.0955  1261   139  0.89  17.77   1.00     0.99       4888.30|
| 13:  2.0955 -  2.0404  1272   138  0.89  17.49   0.99     0.95       3845.50|
| 14:  2.0404 -  1.9908   680    81  0.92  14.11   0.97     0.94       2646.72|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2646.72 max =        11445.61 mean =      7424.77|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.94 mean =        15.48|
|phase err.(test): min =        0.00 max =           87.77 mean =        14.95|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.056)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.99    102.44  16.14    None  None   None       |
|    all(noH): 2823   0      2.99    102.44  16.14    None  None   None       |
|    Sol.    : 438    0      3.85    102.44  41.49    None  None   None       |
|    Mac.    : 2385   0      2.99    88.59   11.49    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:     2.994 -  12.939: 1798   |   5:    52.717 -  62.662:   87        |
|      1:    12.939 -  22.883:  496   |   6:    62.662 -  72.607:   43        |
|      2:    22.883 -  32.828:  160   |   7:    72.607 -  82.551:   20        |
|      3:    32.828 -  42.773:  122   |   8:    82.551 -  92.496:    8        |
|      4:    42.773 -  52.717:   88   |   9:    92.496 - 102.441:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 320         
Filter by distance & map next to the model:
   mapped sites are within: 0.157 - 5.622
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 309 from: 320
   mapped sites are within: 0.713 - 5.622

peak=   10.358 closest distance to " CB  VAL A 230 " =    1.440
peak=    5.770 closest distance to " CD2 LEU A   5 " =    1.171
peak=    5.457 closest distance to " CG  PRO A  54 " =    1.385
peak=    5.440 closest distance to " NE2 GLN A  11 " =    1.105
peak=    5.379 closest distance to " CG2 VAL A 296 " =    1.078
peak=    5.235 closest distance to " CB  GLN A 223 " =    1.522
peak=    5.205 closest distance to " CG  LEU A   5 " =    1.239
peak=    5.196 closest distance to " CG  LEU A 228 " =    1.185
peak=    5.194 closest distance to " CG1 VAL A 296 " =    1.202
peak=    5.183 closest distance to " O   HOH Z 142 " =    1.917
peak=    5.177 closest distance to " CB  VAL A 296 " =    1.101
peak=    5.145 closest distance to " NH2 ARG A  56 " =    2.075
peak=    4.969 closest distance to " O   HOH Z 248 " =    1.312
peak=    4.936 closest distance to " CD1AILE A 234 " =    1.029
peak=    4.721 closest distance to " CB  ASN A 148 " =    1.459
peak=    4.705 closest distance to " CZ  PHE A 218 " =    1.147
peak=    4.646 closest distance to " O   HOH Z 265 " =    2.068
peak=    4.616 closest distance to " NH1 ARG A 138 " =    0.968
peak=    4.590 closest distance to " CB  PRO A  54 " =    1.012
peak=    4.583 closest distance to " NH2AARG A 145 " =    1.168
peak=    4.555 closest distance to " CB  ASN A 142 " =    1.163
peak=    4.525 closest distance to " CZ3 TRP A 266 " =    1.154
peak=    4.512 closest distance to " O   SER A  87 " =    2.424
peak=    4.497 closest distance to " CB  GLN A 183 " =    1.231
peak=    4.496 closest distance to " O   HOH Z 313 " =    1.993
peak=    4.450 closest distance to " CG  PRO A 198 " =    1.275
peak=    4.414 closest distance to " CG  PRO A 243 " =    1.128
peak=    4.412 closest distance to " O   HOH Z 232 " =    2.256
peak=    4.338 closest distance to " O   HOH Z 369 " =    2.300
peak=    4.320 closest distance to " O   HOH Z 425 " =    1.510
peak=    4.267 closest distance to " CA  TYR A  30 " =    0.975
peak=    4.250 closest distance to " O   PRO A 198 " =    1.552
peak=    4.246 closest distance to " CB  TYR A 169 " =    0.745
peak=    4.215 closest distance to " CB  ARG A 275 " =    0.947
peak=    4.208 closest distance to " CD2 LEU A 228 " =    1.208
peak=    4.204 closest distance to " O   HOH Z 251 " =    1.669
peak=    4.192 closest distance to " CB  ARG A 190 " =    1.640
peak=    4.190 closest distance to " O   HOH Z   9 " =    1.485
peak=    4.181 closest distance to " O   HOH Z 261 " =    2.166
peak=    4.168 closest distance to " O   HOH Z 126 " =    1.549
peak=    4.155 closest distance to " O   HOH Z 427 " =    2.980
peak=    4.147 closest distance to " O   HOH Z  78 " =    1.629
peak=    4.121 closest distance to " CD2 TRP A 179 " =    1.267
peak=    4.110 closest distance to " CE  LYS A  76 " =    0.907
peak=    4.084 closest distance to " CB  GLU A 277 " =    3.724
peak=    4.056 closest distance to " O  BHOH Z 338 " =    2.283
peak=    4.054 closest distance to " CB  VAL A 265 " =    1.203
peak=    4.039 closest distance to " O   HOH Z  43 " =    2.055
peak=    4.022 closest distance to " O   HOH Z 402 " =    1.363
peak=    4.006 closest distance to " CA  ARG A 195 " =    1.217
peak=    3.988 closest distance to " CB  ASP A 124 " =    0.825
peak=    3.984 closest distance to " CB  VAL A 230 " =    1.232
peak=    3.984 closest distance to " CG  GLN A  58 " =    0.965
peak=    3.973 closest distance to " ND2 ASN A 249 " =    0.911
peak=    3.964 closest distance to " CA  ALA A  51 " =    0.960
peak=    3.950 closest distance to " O   HOH Z 353 " =    2.671
peak=    3.940 closest distance to " O   HOH Z 290 " =    1.100
peak=    3.937 closest distance to " CB  SER A  63 " =    1.182
peak=    3.936 closest distance to " O   HOH Z 411 " =    3.922
peak=    3.930 closest distance to " O   HOH Z 303 " =    2.106
peak=    3.917 closest distance to " NH1AARG A 145 " =    1.211
peak=    3.914 closest distance to " O   HOH Z 346 " =    1.506
peak=    3.912 closest distance to " O   HOH Z 188 " =    2.762
peak=    3.884 closest distance to " O   HOH Z 287 " =    2.006
peak=    3.877 closest distance to " CB  ASN A  39 " =    0.939
peak=    3.873 closest distance to " O   HOH Z 406 " =    1.591
peak=    3.859 closest distance to " CG  MET A 185 " =    1.310
peak=    3.854 closest distance to " CG  PRO A 213 " =    1.135
peak=    3.839 closest distance to " O   HOH Z 207 " =    1.125
peak=    3.832 closest distance to " O   HOH Z 214 " =    2.746
peak=    3.832 closest distance to " CG2 VAL A 257 " =    0.823
peak=    3.826 closest distance to " CB  TRP A 266 " =    1.059
peak=    3.816 closest distance to " CB  PRO A  90 " =    1.068
peak=    3.809 closest distance to " O   HOH Z   4 " =    1.544
peak=    3.806 closest distance to " CB  VAL A 202 " =    1.575
peak=    3.800 closest distance to " CB  GLN A  89 " =    1.227
peak=    3.796 closest distance to " O   HOH Z 368 " =    2.458
peak=    3.794 closest distance to " O   HOH Z 298 " =    1.801
peak=    3.789 closest distance to " CB  SER A  26 " =    1.812
peak=    3.781 closest distance to " CG2 ILE A 234 " =    0.999
peak=    3.780 closest distance to " CA  VAL A 125 " =    1.265
peak=    3.767 closest distance to " CB  ASN A 110 " =    1.132
peak=    3.762 closest distance to " CD  LYS A 166 " =    1.332
peak=    3.762 closest distance to " CB  SER A   3 " =    1.332
peak=    3.761 closest distance to " O   HOH Z  92 " =    2.113
peak=    3.756 closest distance to " ND2 ASN A 187 " =    1.654
peak=    3.748 closest distance to " CB  ARG A  79 " =    1.392
peak=    3.747 closest distance to " OE1 GLN A  55 " =    1.549
peak=    3.740 closest distance to " CG  GLU A  37 " =    0.937
peak=    3.735 closest distance to " CZ  PHE A  38 " =    1.151
peak=    3.724 closest distance to " O   HOH Z  80 " =    1.815
peak=    3.717 closest distance to " O   HOH Z   3 " =    2.023
peak=    3.711 closest distance to " O   ASP A 124 " =    1.128
peak=    3.708 closest distance to " CD1 LEU A  96 " =    0.780
peak=    3.706 closest distance to " N   ASN A  39 " =    1.259
peak=    3.700 closest distance to " CG  LEU A 167 " =    1.208
peak=    3.700 closest distance to " N   ALA A 256 " =    1.110
peak=    3.698 closest distance to " CB  GLU A 128 " =    1.015
peak=    3.696 closest distance to " O  BHOH Z  74 " =    1.199
peak=    3.695 closest distance to " O   HOH Z 214 " =    1.322
peak=    3.692 closest distance to " O   HOH Z 258 " =    1.837
peak=    3.689 closest distance to " O   HOH Z 126 " =    2.013
peak=    3.684 closest distance to " O   HOH Z 422 " =    2.670
peak=    3.683 closest distance to " CD1 ILE A  33 " =    1.800
peak=    3.678 closest distance to " CG AARG A 275 " =    1.299
peak=    3.677 closest distance to " O   HOH Z 359 " =    1.708
peak=    3.671 closest distance to " O   HOH Z 203 " =    1.680
peak=    3.667 closest distance to " O   HOH Z 222 " =    2.370
peak=    3.667 closest distance to " O   HOH Z  88 " =    3.675
peak=    3.666 closest distance to " CD1 ILE A 199 " =    1.146
peak=    3.665 closest distance to " CD  ARG A 269 " =    0.990
peak=    3.664 closest distance to " CG  ARG A  66 " =    2.711
peak=    3.659 closest distance to " CA  ARG A  36 " =    1.064
peak=    3.657 closest distance to " CB  SER A 273 " =    0.968
peak=    3.650 closest distance to " O   HOH Z 365 " =    2.805
peak=    3.642 closest distance to " CD  ARG A 159 " =    0.713
peak=    3.633 closest distance to " O   HOH Z 273 " =    2.977
peak=    3.619 closest distance to " O   HOH Z 193 " =    1.376
peak=    3.616 closest distance to " O   HOH Z 371 " =    2.701
peak=    3.609 closest distance to " NE2 HIS A 207 " =    1.099
peak=    3.605 closest distance to " O   HOH Z  76 " =    1.156
peak=    3.596 closest distance to " O   HOH Z 258 " =    1.233
peak=    3.594 closest distance to " CB  THR A  52 " =    0.795
peak=    3.575 closest distance to " O   HOH Z  59 " =    2.170
peak=    3.570 closest distance to " CD BLYS A 290 " =    1.151
peak=    3.566 closest distance to " OG BSER A 164 " =    2.309
peak=    3.561 closest distance to " O   HOH Z 127 " =    1.083
peak=    3.558 closest distance to " CB  ASP A 140 " =    1.151
peak=    3.550 closest distance to " CD  LYS A  76 " =    1.945
peak=    3.546 closest distance to " O   THR A 182 " =    1.413
peak=    3.544 closest distance to " CA  LEU A 282 " =    1.168
peak=    3.537 closest distance to " O   HOH Z  61 " =    1.808
peak=    3.536 closest distance to " CB  LYS A 117 " =    1.243
peak=    3.534 closest distance to " CA  ALA A 160 " =    1.020
peak=    3.523 closest distance to " CA  ASN A 127 " =    1.094
peak=    3.523 closest distance to " CG1 VAL A 153 " =    0.952
peak=    3.521 closest distance to " CA  ALA A 154 " =    1.073
peak=    3.493 closest distance to " O   HOH Z 316 " =    3.120
peak=    3.489 closest distance to " O   HOH Z 280 " =    2.963
peak=    3.485 closest distance to " O   HOH Z 162 " =    1.239
peak=    3.479 closest distance to " CA  TYR A 116 " =    1.431
peak=    3.479 closest distance to " CB  TRP A 179 " =    1.457
peak=    3.475 closest distance to " CA  PHE A 283 " =    1.185
peak=    3.472 closest distance to " CA  ALA A 295 " =    1.093
peak=    3.463 closest distance to " CE  LYS A  48 " =    1.180
peak=    3.460 closest distance to " CA  ILE A 234 " =    1.042
peak=    3.459 closest distance to " CB  ARG A 145 " =    0.911
peak=    3.459 closest distance to " O   HOH Z 128 " =    1.153
peak=    3.456 closest distance to " O   PHE A 192 " =    1.365
peak=    3.456 closest distance to " O   HOH Z 263 " =    1.674
peak=    3.455 closest distance to " CB  SER A 212 " =    1.314
peak=    3.448 closest distance to " O   HOH Z 337 " =    1.896
peak=    3.445 closest distance to " O   ASN A  74 " =    1.385
peak=    3.445 closest distance to " CB  ALA A 248 " =    1.398
peak=    3.445 closest distance to " CB  GLU A 152 " =    1.189
peak=    3.444 closest distance to " O   HOH Z 193 " =    1.757
peak=    3.439 closest distance to " CB  ARG A 102 " =    0.948
peak=    3.432 closest distance to " NZ  LYS A 117 " =    3.113
peak=    3.426 closest distance to " CA  MET A 105 " =    1.035
peak=    3.425 closest distance to " CG2AVAL A  72 " =    1.749
peak=    3.424 closest distance to " NH2 ARG A  56 " =    1.156
peak=    3.423 closest distance to " CB  MET A  40 " =    0.780
peak=    3.420 closest distance to " OD1 ASN A  69 " =    2.469
peak=    3.419 closest distance to " CB  SER A  62 " =    1.013
peak=    3.417 closest distance to " CE1 TYR A 186 " =    1.260
peak=    3.414 closest distance to " CB  THR A  31 " =    1.541
peak=    3.413 closest distance to " O   HOH Z 112 " =    0.944
peak=    3.412 closest distance to " CB BVAL A  41 " =    1.269
peak=    3.401 closest distance to " CB  PHE A 204 " =    0.923
peak=    3.400 closest distance to " N   PHE A 130 " =    1.280
peak=    3.399 closest distance to " CG  LEU A   5 " =    0.747
peak=    3.393 closest distance to " CB  ASN A 215 " =    1.162
peak=    3.393 closest distance to " CA  SER A  87 " =    1.064
peak=    3.390 closest distance to " O   HOH Z 423 " =    1.758
peak=    3.388 closest distance to " CD1BILE A 234 " =    0.930
peak=    3.384 closest distance to " O   HOH Z  66 " =    2.279
peak=    3.382 closest distance to " O   HOH Z 329 " =    4.250
peak=    3.382 closest distance to " CG2 ILE A 120 " =    1.283
peak=    3.377 closest distance to " CB  GLN A  88 " =    1.268
peak=    3.375 closest distance to " O   HOH Z 272 " =    1.778
peak=    3.375 closest distance to " CA  ASP A 162 " =    1.008
peak=    3.371 closest distance to " NZ  LYS A 117 " =    1.207
peak=    3.371 closest distance to " O   HOH Z 172 " =    3.628
peak=    3.370 closest distance to " O   HOH Z 368 " =    3.292
peak=    3.370 closest distance to " CB  ASP A 191 " =    1.326
peak=    3.369 closest distance to " ND2BASN A 224 " =    0.795
peak=    3.368 closest distance to " N   ASP A 162 " =    1.226
peak=    3.368 closest distance to " O   HOH Z 213 " =    1.891
peak=    3.367 closest distance to " OG  SER A 276 " =    1.250
peak=    3.366 closest distance to " CA  VAL A 153 " =    0.967
peak=    3.362 closest distance to " CB  SER A 210 " =    0.776
peak=    3.359 closest distance to " CA  ALA A 158 " =    1.405
peak=    3.354 closest distance to " NZ  LYS A  48 " =    1.143
peak=    3.351 closest distance to " CG  PHE A 204 " =    0.918
peak=    3.350 closest distance to " CA  ALA A 129 " =    1.395
peak=    3.346 closest distance to " CG  LEU A 281 " =    1.050
peak=    3.338 closest distance to " CA  ASN A 215 " =    1.063
peak=    3.337 closest distance to " O   HOH Z 299 " =    4.302
peak=    3.336 closest distance to " CD2 LEU A 297 " =    0.903
peak=    3.335 closest distance to " O   ILE A  49 " =    1.158
peak=    3.334 closest distance to " OE2 GLU A  53 " =    1.906
peak=    3.331 closest distance to " CA  GLY A 267 " =    0.951
peak=    3.329 closest distance to " CA  ALA A 291 " =    0.854
peak=    3.327 closest distance to " CB  ASN A 173 " =    1.052
peak=    3.327 closest distance to " CA  ALA A 100 " =    0.836
peak=    3.326 closest distance to " O   GLN A  88 " =    1.618
peak=    3.326 closest distance to " O   HOH Z 193 " =    1.734
peak=    3.324 closest distance to " CA  ARG A 139 " =    1.075
peak=    3.323 closest distance to " CD1 LEU A 300 " =    1.143
peak=    3.323 closest distance to " CB  GLN A 205 " =    1.083
peak=    3.322 closest distance to " CG2BVAL A 121 " =    0.761
peak=    3.321 closest distance to " O   HOH Z  30 " =    1.399
peak=    3.311 closest distance to " O   HOH Z 244 " =    1.733
peak=    3.310 closest distance to " C   ALA A 299 " =    0.861
peak=    3.308 closest distance to " O   HOH Z 385 " =    3.878
peak=    3.305 closest distance to " CG2 ILE A  20 " =    1.527
peak=    3.301 closest distance to " CD  LYS A 119 " =    2.050
peak=    3.299 closest distance to " NE2 GLN A  73 " =    1.428
peak=    3.299 closest distance to " NE2 GLN A  77 " =    3.240
peak=    3.297 closest distance to " CB  LEU A 143 " =    1.245
peak=    3.292 closest distance to " CA  ASN A 217 " =    1.141
peak=    3.291 closest distance to " O   HOH Z 234 " =    3.572
peak=    3.283 closest distance to " O   HOH Z 158 " =    3.106
peak=    3.281 closest distance to " OG  SER A 245 " =    1.555
peak=    3.279 closest distance to " N   ASP A 231 " =    1.696
peak=    3.278 closest distance to " O   PHE A  61 " =    1.424
peak=    3.277 closest distance to " CB  GLU A  46 " =    0.939
peak=    3.275 closest distance to " O   HOH Z  40 " =    1.861
peak=    3.274 closest distance to " O   HOH Z  63 " =    1.719
peak=    3.271 closest distance to " O   HOH Z 345 " =    3.428
peak=    3.269 closest distance to " CG  ARG A 138 " =    1.332
peak=    3.265 closest distance to " CG BARG A 102 " =    1.881
peak=    3.261 closest distance to " OG1 THR A 279 " =    1.480
peak=    3.260 closest distance to " CE3 TRP A  85 " =    1.253
peak=    3.257 closest distance to " OG1 THR A  82 " =    0.895
peak=    3.256 closest distance to " O   HOH Z 189 " =    3.035
peak=    3.255 closest distance to " CA  THR A 264 " =    0.821
peak=    3.251 closest distance to " O   HOH Z 133 " =    2.768
peak=    3.248 closest distance to " O   HOH Z 124 " =    1.934
peak=    3.247 closest distance to " CB  ALA A   9 " =    1.626
peak=    3.246 closest distance to " O   SER A 164 " =    1.392
peak=    3.244 closest distance to " O   HOH Z 293 " =    1.946
peak=    3.244 closest distance to " O   HOH Z 171 " =    4.070
peak=    3.243 closest distance to " O   HOH Z  78 " =    2.345
peak=    3.242 closest distance to " O   HOH Z  35 " =    4.463
peak=    3.241 closest distance to " CA  ASN A  74 " =    1.180
peak=    3.240 closest distance to " CZ3 TRP A  92 " =    1.249
peak=    3.240 closest distance to " O   HOH Z 261 " =    1.427
peak=    3.236 closest distance to " CB  ASP A 298 " =    1.164
peak=    3.232 closest distance to " CE3 TRP A 150 " =    1.137
peak=    3.228 closest distance to " O   HOH Z 281 " =    2.584
peak=    3.228 closest distance to " CB  SER A 216 " =    0.943
peak=    3.227 closest distance to " CB  ARG A 156 " =    1.262
peak=    3.221 closest distance to " O   HOH Z 180 " =    2.201
peak=    3.211 closest distance to " O   HOH Z  32 " =    1.924
peak=    3.206 closest distance to " O   HOH Z 357 " =    2.574
peak=    3.205 closest distance to " O   HOH Z 246 " =    1.331
peak=    3.201 closest distance to " CB  ALA A 114 " =    0.776
peak=    3.197 closest distance to " CA  LYS A 117 " =    1.312
peak=    3.197 closest distance to " CG1 ILE A  20 " =    1.292
peak=    3.196 closest distance to " O   HOH Z 236 " =    1.573
peak=    3.195 closest distance to " O   HOH Z 148 " =    3.533
peak=    3.194 closest distance to " CA  ALA A  21 " =    1.058
peak=    3.194 closest distance to " O   HOH Z 430 " =    5.622
peak=    3.192 closest distance to " O   HOH Z 421 " =    2.961
peak=    3.192 closest distance to " CG1 ILE A 151 " =    1.037
peak=    3.187 closest distance to " CB  PRO A 243 " =    1.478
peak=    3.187 closest distance to " O   HOH Z 187 " =    2.287
peak=    3.186 closest distance to " O   HOH Z 128 " =    1.900
peak=    3.185 closest distance to " CB  LEU A 300 " =    0.918
peak=    3.181 closest distance to " CA  ASP A 140 " =    1.536
peak=    3.180 closest distance to " O   HOH Z 394 " =    3.676
peak=    3.178 closest distance to " N   GLN A 278 " =    1.551
peak=    3.177 closest distance to " O   MET A 105 " =    1.871
peak=    3.175 closest distance to " CE3 TRP A 274 " =    1.305
peak=    3.172 closest distance to " CG2 VAL A 197 " =    1.044
peak=    3.169 closest distance to " O   ASN A 284 " =    1.753
peak=    3.168 closest distance to " O   HOH Z 305 " =    3.417
peak=    3.167 closest distance to " OE2 GLU A   2 " =    1.909
peak=    3.157 closest distance to " CA  LEU A  83 " =    1.139
peak=    3.157 closest distance to " O   HOH Z  80 " =    2.059
peak=    3.155 closest distance to " O   HOH Z 290 " =    1.274
peak=    3.154 closest distance to " CA  GLY A 133 " =    3.842
peak=    3.150 closest distance to " O   HOH Z 403 " =    1.544
peak=    3.148 closest distance to " NE1 TRP A  85 " =    1.188
peak=    3.141 closest distance to " O   HOH Z 112 " =    1.514
peak=    3.140 closest distance to " O   HOH Z 337 " =    3.596
peak=    3.134 closest distance to " O   HOH Z 117 " =    2.099
peak=    3.133 closest distance to " O   ALA A 158 " =    1.256
peak=    3.128 closest distance to " O   LEU A 228 " =    1.818
peak=    3.127 closest distance to " O   HOH Z 357 " =    2.221
peak=    3.125 closest distance to " N   TYR A 247 " =    1.286
peak=    3.123 closest distance to " O   HOH Z  85 " =    1.377
peak=    3.109 closest distance to " O   HOH Z 188 " =    1.360
peak=    3.107 closest distance to " O   GLY A  91 " =    1.281
peak=    3.103 closest distance to " O   CYS A 168 " =    1.110
peak=    3.095 closest distance to " O   HOH Z 393 " =    3.081
peak=    3.091 closest distance to " O   HOH Z 303 " =    2.999
peak=    3.084 closest distance to " CB  ASN A 187 " =    1.444
peak=    3.080 closest distance to " CB  THR A 235 " =    1.457
peak=    3.076 closest distance to " O   HOH Z 383 " =    1.862
peak=    3.073 closest distance to " CG2 VAL A 126 " =    0.887
peak=    3.066 closest distance to " CD  GLU A 236 " =    0.945
peak=    3.065 closest distance to " CD  ARG A  66 " =    2.437
peak=    3.041 closest distance to " CA  LYS A 290 " =    1.147
peak=    3.030 closest distance to " CG  GLN A  55 " =    2.507
peak=    3.025 closest distance to " CB  ALA A 227 " =    0.991
peak=    3.002 closest distance to " CB  PRO A 198 " =    1.008
peak=    2.945 closest distance to " O   HOH Z 371 " =    1.657

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 209         
Filter by distance & map next to the model:
   mapped sites are within: 0.786 - 5.674
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 209 from: 209
   mapped sites are within: 0.786 - 5.674

peak=   -4.837 closest distance to " CD  ARG A  14 " =    3.280
peak=   -4.507 closest distance to " O   HOH Z 127 " =    0.933
peak=   -4.403 closest distance to " CG2 VAL A 230 " =    0.786
peak=   -4.397 closest distance to " CG1 VAL A 296 " =    1.045
peak=   -4.358 closest distance to " O   HOH Z 211 " =    0.984
peak=   -4.327 closest distance to " CB  PRO A 243 " =    2.759
peak=   -4.313 closest distance to " O   PRO A 198 " =    1.234
peak=   -4.210 closest distance to " C   HIS A 108 " =    1.189
peak=   -4.169 closest distance to " O   HOH Z 193 " =    0.873
peak=   -4.142 closest distance to " OG BSER A 134 " =    1.421
peak=   -4.132 closest distance to " CE3 TRP A 150 " =    2.309
peak=   -4.128 closest distance to " O   VAL A  67 " =    2.597
peak=   -4.110 closest distance to " CG  GLN A  58 " =    1.011
peak=   -4.065 closest distance to " O   HOH Z 100 " =    0.913
peak=   -4.061 closest distance to " CZ2 TRP A  92 " =    2.866
peak=   -4.047 closest distance to " CA  ASP A 298 " =    1.101
peak=   -3.994 closest distance to " CD  ARG A 156 " =    2.150
peak=   -3.972 closest distance to " O   HOH Z 394 " =    1.615
peak=   -3.970 closest distance to " OE1 GLN A 223 " =    2.335
peak=   -3.962 closest distance to " O   HOH Z 411 " =    5.674
peak=   -3.937 closest distance to " NE2 GLN A  11 " =    1.760
peak=   -3.935 closest distance to " O   HOH Z 359 " =    2.868
peak=   -3.912 closest distance to " CG1 VAL A 112 " =    2.785
peak=   -3.907 closest distance to " O   HOH Z 166 " =    2.274
peak=   -3.898 closest distance to " O   HOH Z 133 " =    1.130
peak=   -3.883 closest distance to " O   HOH Z 166 " =    1.925
peak=   -3.879 closest distance to " CB  PHE A 192 " =    1.988
peak=   -3.875 closest distance to " CG1 VAL A 112 " =    2.682
peak=   -3.855 closest distance to " O   HOH Z 231 " =    2.079
peak=   -3.854 closest distance to " O   HOH Z 106 " =    1.755
peak=   -3.851 closest distance to " CB  ALA A  43 " =    2.648
peak=   -3.827 closest distance to " CA  VAL A  67 " =    3.070
peak=   -3.798 closest distance to " O   HOH Z 295 " =    1.523
peak=   -3.776 closest distance to " CG1 VAL A 250 " =    2.697
peak=   -3.773 closest distance to " O   PRO A 163 " =    2.129
peak=   -3.772 closest distance to " CE2 TRP A  70 " =    2.158
peak=   -3.756 closest distance to " CE2 TYR A  30 " =    2.629
peak=   -3.734 closest distance to " CB  VAL A 230 " =    1.188
peak=   -3.733 closest distance to " O   HOH Z  69 " =    1.653
peak=   -3.722 closest distance to " CD2 TYR A 293 " =    1.998
peak=   -3.715 closest distance to " CG2 THR A 178 " =    2.415
peak=   -3.697 closest distance to " O   HOH Z 216 " =    1.131
peak=   -3.679 closest distance to " O   SER A 271 " =    2.090
peak=   -3.679 closest distance to " O   HOH Z 238 " =    0.885
peak=   -3.669 closest distance to " OE1 GLN A  88 " =    1.021
peak=   -3.663 closest distance to " O   HOH Z 131 " =    4.008
peak=   -3.661 closest distance to " CG2 VAL A 296 " =    1.191
peak=   -3.659 closest distance to " N   THR A  52 " =    1.640
peak=   -3.657 closest distance to " O   HOH Z 149 " =    1.956
peak=   -3.656 closest distance to " O   HOH Z 377 " =    2.094
peak=   -3.648 closest distance to " OG  SER A  97 " =    2.361
peak=   -3.639 closest distance to " O   HOH Z 198 " =    1.852
peak=   -3.635 closest distance to " CG  TRP A 266 " =    1.762
peak=   -3.624 closest distance to " CD1 LEU A 101 " =    2.380
peak=   -3.621 closest distance to " O   HOH Z 128 " =    1.013
peak=   -3.616 closest distance to " O   HOH Z  73 " =    2.418
peak=   -3.609 closest distance to " CG  GLU A 277 " =    1.260
peak=   -3.607 closest distance to " CE2 PHE A  61 " =    2.691
peak=   -3.602 closest distance to " CE BMET A  47 " =    1.275
peak=   -3.599 closest distance to " ND2 ASN A  45 " =    1.176
peak=   -3.584 closest distance to " O   HOH Z 252 " =    3.802
peak=   -3.579 closest distance to " O   HOH Z 371 " =    2.438
peak=   -3.579 closest distance to " CG  ARG A 269 " =    2.283
peak=   -3.568 closest distance to " O   HOH Z 110 " =    1.328
peak=   -3.565 closest distance to " CG2AVAL A  41 " =    2.856
peak=   -3.550 closest distance to " CG2 VAL A 189 " =    2.031
peak=   -3.528 closest distance to " C   ALA A 158 " =    1.222
peak=   -3.525 closest distance to " CD2 PHE A 225 " =    1.082
peak=   -3.521 closest distance to " CB  HIS A  86 " =    1.122
peak=   -3.521 closest distance to " O   HOH Z 236 " =    1.424
peak=   -3.515 closest distance to " CB  ALA A 161 " =    2.522
peak=   -3.509 closest distance to " O   TRP A  70 " =    1.553
peak=   -3.503 closest distance to " CA  GLY A 241 " =    2.367
peak=   -3.499 closest distance to " OXT GLY A 302 " =    3.051
peak=   -3.498 closest distance to " O   ALA A 227 " =    1.339
peak=   -3.494 closest distance to " CB  GLN A  55 " =    1.216
peak=   -3.493 closest distance to " O   HOH Z 115 " =    1.694
peak=   -3.491 closest distance to " O   HOH Z  68 " =    1.307
peak=   -3.483 closest distance to " OD1 ASN A 148 " =    1.384
peak=   -3.482 closest distance to " O   HOH Z 103 " =    1.731
peak=   -3.481 closest distance to " O   HOH Z  11 " =    2.222
peak=   -3.476 closest distance to " O   HOH Z 128 " =    2.286
peak=   -3.464 closest distance to " O   HOH Z 351 " =    1.641
peak=   -3.464 closest distance to " CD1 LEU A 255 " =    2.895
peak=   -3.462 closest distance to " CG1 VAL A 125 " =    1.879
peak=   -3.457 closest distance to " CD2 HIS A 207 " =    2.137
peak=   -3.444 closest distance to " CG  GLN A 103 " =    2.501
peak=   -3.442 closest distance to " O   HOH Z 111 " =    1.586
peak=   -3.432 closest distance to " O   HOH Z   9 " =    1.588
peak=   -3.429 closest distance to " O   HOH Z 174 " =    2.425
peak=   -3.428 closest distance to " O   HOH Z 275 " =    1.773
peak=   -3.425 closest distance to " O   HOH Z 191 " =    5.636
peak=   -3.423 closest distance to " O   HOH Z 201 " =    2.205
peak=   -3.417 closest distance to " CZ3 TRP A 179 " =    1.297
peak=   -3.415 closest distance to " CG2 VAL A 202 " =    2.722
peak=   -3.410 closest distance to " O   SER A 276 " =    1.710
peak=   -3.408 closest distance to " O   GLY A  17 " =    1.136
peak=   -3.404 closest distance to " O   HOH Z  64 " =    1.548
peak=   -3.402 closest distance to " O   HOH Z 154 " =    1.677
peak=   -3.402 closest distance to " NE  ARG A  66 " =    4.259
peak=   -3.392 closest distance to " O   HOH Z 286 " =    1.853
peak=   -3.382 closest distance to " O   HOH Z 285 " =    2.009
peak=   -3.382 closest distance to " CE3 TRP A  70 " =    1.767
peak=   -3.381 closest distance to " OH  TYR A 172 " =    1.873
peak=   -3.376 closest distance to " CD  PRO A 243 " =    1.882
peak=   -3.374 closest distance to " O   HOH Z  52 " =    1.727
peak=   -3.372 closest distance to " O   HOH Z  11 " =    1.723
peak=   -3.371 closest distance to " CB  ALA A  10 " =    2.275
peak=   -3.362 closest distance to " CD1 ILE A 199 " =    2.437
peak=   -3.359 closest distance to " CE  MET A 105 " =    2.485
peak=   -3.357 closest distance to " O   ASN A 252 " =    1.372
peak=   -3.348 closest distance to " O   HOH Z 102 " =    1.657
peak=   -3.346 closest distance to " O   HOH Z 429 " =    1.745
peak=   -3.337 closest distance to " CA  ASP A  27 " =    2.468
peak=   -3.334 closest distance to " CA  GLY A 203 " =    2.559
peak=   -3.333 closest distance to " NE2 GLN A  88 " =    1.128
peak=   -3.328 closest distance to " O   SER A 210 " =    1.759
peak=   -3.324 closest distance to " O   HOH Z 275 " =    1.530
peak=   -3.323 closest distance to " CD2 LEU A 237 " =    2.818
peak=   -3.322 closest distance to " O   HOH Z 185 " =    2.304
peak=   -3.321 closest distance to " O   TYR A 186 " =    1.730
peak=   -3.318 closest distance to " OD2 ASP A  50 " =    2.420
peak=   -3.316 closest distance to " O   HOH Z 256 " =    1.406
peak=   -3.314 closest distance to " O   ILE A 106 " =    1.844
peak=   -3.312 closest distance to " C   MET A 188 " =    1.464
peak=   -3.311 closest distance to " NH2 ARG A  79 " =    1.542
peak=   -3.305 closest distance to " O   HOH Z 147 " =    2.044
peak=   -3.302 closest distance to " O   HOH Z  20 " =    1.195
peak=   -3.298 closest distance to " CB  ALA A 248 " =    2.331
peak=   -3.297 closest distance to " O   HOH Z 389 " =    1.482
peak=   -3.294 closest distance to " CA  GLY A 133 " =    2.295
peak=   -3.292 closest distance to " CG  ASP A 231 " =    0.947
peak=   -3.292 closest distance to " CD  GLN A 223 " =    1.672
peak=   -3.290 closest distance to " O   HOH Z 119 " =    2.139
peak=   -3.287 closest distance to " O   HOH Z 251 " =    4.978
peak=   -3.285 closest distance to " CZ  PHE A  38 " =    2.465
peak=   -3.284 closest distance to " ND2 ASN A 249 " =    2.402
peak=   -3.284 closest distance to " CG  PRO A 243 " =    1.635
peak=   -3.270 closest distance to " O   HOH Z  44 " =    0.891
peak=   -3.258 closest distance to " O   HOH Z 345 " =    2.167
peak=   -3.257 closest distance to " O   HOH Z 262 " =    2.372
peak=   -3.248 closest distance to " CG1 VAL A  67 " =    2.900
peak=   -3.246 closest distance to " CB  ALA A 248 " =    2.186
peak=   -3.245 closest distance to " CB  TRP A  85 " =    2.632
peak=   -3.242 closest distance to " CB  ALA A 114 " =    2.547
peak=   -3.240 closest distance to " O   ALA A 180 " =    1.413
peak=   -3.232 closest distance to " CA  HIS A 207 " =    1.169
peak=   -3.230 closest distance to " NH1 ARG A  66 " =    3.716
peak=   -3.221 closest distance to " CZ2 TRP A 274 " =    1.033
peak=   -3.211 closest distance to " N   TRP A 274 " =    0.980
peak=   -3.210 closest distance to " O   HOH Z  65 " =    1.341
peak=   -3.203 closest distance to " ND2 ASN A  45 " =    1.860
peak=   -3.200 closest distance to " OD1 ASN A 173 " =    1.401
peak=   -3.198 closest distance to " N   SER A 276 " =    1.362
peak=   -3.193 closest distance to " N   ALA A 248 " =    1.893
peak=   -3.191 closest distance to " O   HOH Z 139 " =    5.342
peak=   -3.190 closest distance to " OG1 THR A  82 " =    1.316
peak=   -3.189 closest distance to " O   ASP A  27 " =    1.965
peak=   -3.186 closest distance to " NE  ARG A  79 " =    1.153
peak=   -3.181 closest distance to " CA  GLY A 241 " =    3.208
peak=   -3.180 closest distance to " O   HOH Z 431 " =    1.978
peak=   -3.179 closest distance to " CD  LYS A 289 " =    2.411
peak=   -3.174 closest distance to " O   HOH Z 357 " =    2.279
peak=   -3.173 closest distance to " CD  GLU A 236 " =    1.174
peak=   -3.172 closest distance to " OE1 GLN A 223 " =    2.946
peak=   -3.171 closest distance to " O   HOH Z 352 " =    1.430
peak=   -3.170 closest distance to " CD1 PHE A  59 " =    2.278
peak=   -3.166 closest distance to " N   ALA A  43 " =    2.744
peak=   -3.164 closest distance to " CZ  ARG A 259 " =    0.941
peak=   -3.162 closest distance to " O   HOH Z 265 " =    1.580
peak=   -3.162 closest distance to " O   HOH Z 165 " =    1.934
peak=   -3.161 closest distance to " O   HOH Z 368 " =    1.438
peak=   -3.160 closest distance to " CB  ALA A   9 " =    2.452
peak=   -3.160 closest distance to " OD2 ASP A 191 " =    1.460
peak=   -3.154 closest distance to " CB  ASP A 171 " =    2.196
peak=   -3.150 closest distance to " CD1 ILE A 239 " =    2.205
peak=   -3.148 closest distance to " O   HOH Z 171 " =    2.056
peak=   -3.147 closest distance to " N   ASP A 286 " =    2.323
peak=   -3.143 closest distance to " NE2 GLN A 278 " =    1.834
peak=   -3.143 closest distance to " O   HOH Z 290 " =    1.166
peak=   -3.137 closest distance to " CB  PRO A 163 " =    2.453
peak=   -3.132 closest distance to " CG  LYS A 193 " =    2.716
peak=   -3.132 closest distance to " O   HOH Z  78 " =    1.946
peak=   -3.125 closest distance to " CG2 THR A  29 " =    2.561
peak=   -3.123 closest distance to " N   HIS A 115 " =    2.276
peak=   -3.122 closest distance to " O   HOH Z   9 " =    3.026
peak=   -3.121 closest distance to " O   HOH Z 244 " =    2.076
peak=   -3.119 closest distance to " CB  VAL A 296 " =    1.362
peak=   -3.118 closest distance to " OG ASER A 212 " =    1.609
peak=   -3.115 closest distance to " OH  TYR A 247 " =    1.849
peak=   -3.114 closest distance to " CG1BVAL A  72 " =    2.446
peak=   -3.111 closest distance to " O   GLU A 152 " =    1.336
peak=   -3.110 closest distance to " O   HOH Z 423 " =    2.214
peak=   -3.110 closest distance to " NH2 ARG A 159 " =    2.292
peak=   -3.108 closest distance to " N   ALA A 226 " =    2.033
peak=   -3.102 closest distance to " CB  LYS A 289 " =    3.035
peak=   -3.097 closest distance to " CG2 ILE A 151 " =    2.606
peak=   -3.085 closest distance to " O   ARG A 145 " =    1.713
peak=   -3.079 closest distance to " ND2 ASN A  69 " =    2.061
peak=   -3.077 closest distance to " O   HOH Z   6 " =    1.669
peak=   -3.076 closest distance to " C   ASP A 270 " =    1.348
peak=   -3.074 closest distance to " N   ALA A 248 " =    2.282
peak=   -3.073 closest distance to " O   ALA A  51 " =    1.347
peak=   -3.070 closest distance to " OD1 ASP A 171 " =    1.604
peak=   -3.068 closest distance to " O   GLY A 203 " =    2.557
peak=   -3.067 closest distance to " CD1 LEU A 228 " =    2.279
peak=   -3.060 closest distance to " O   HOH Z  89 " =    2.735
peak=   -3.058 closest distance to " O   HOH Z 407 " =    2.833
peak=   -3.021 closest distance to " O   GLY A  80 " =    2.629

================= 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    :  0.4643 0.4529   6.268318e+00   6.247169e+00
   1_bss:  0.4548 0.4418   6.259895e+00   6.233429e+00
   1_xyz:  0.3656 0.3861   6.126111e+00   6.157743e+00
   1_adp:  0.3156 0.3615   6.019409e+00   6.105689e+00
   1_occ:  0.3148 0.3623   6.018475e+00   6.107792e+00
   2_bss:  0.3114 0.3586   6.018775e+00   6.107245e+00
   2_xyz:  0.2434 0.2932   5.806188e+00   5.949172e+00
   2_adp:  0.2268 0.2771   5.752309e+00   5.910720e+00
   2_occ:  0.2268 0.2771   5.752256e+00   5.911217e+00
   3_bss:  0.2255 0.2778   5.753287e+00   5.912316e+00
   3_xyz:  0.1745 0.2272   5.525487e+00   5.717414e+00
   3_adp:  0.1627 0.2137   5.463793e+00   5.661791e+00
   3_occ:  0.1626 0.2135   5.463660e+00   5.662207e+00
   4_bss:  0.1622 0.2132   5.463557e+00   5.662198e+00
   4_xyz:  0.1326 0.1785   5.287473e+00   5.510404e+00
   4_adp:  0.1257 0.1746   5.251330e+00   5.485562e+00
   4_occ:  0.1256 0.1746   5.251248e+00   5.486000e+00
   5_bss:  0.1254 0.1745   5.249995e+00   5.484067e+00
   5_xyz:  0.1215 0.1691   5.225595e+00   5.462213e+00
   5_adp:  0.1204 0.1689   5.220267e+00   5.459430e+00
   5_occ:  0.1203 0.1688   5.220085e+00   5.459288e+00
   5_bss:  0.1202 0.1687   5.220257e+00   5.459480e+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:  0.335  16.553   6.651   7.292  12.570   0.000   0.000   0.000
   1_xyz:  0.335  16.553   6.651   7.292  12.570   0.000   0.000   0.000
   1_adp:  0.335  16.553   6.651   7.292  12.570   0.000   0.000   0.000
   1_occ:  0.335  16.553   6.651   7.292  12.570   0.000   0.000   0.000
   2_bss:  0.334  46.397   3.291   3.823   8.906   0.000   0.000   0.000
   2_xyz:  0.334  46.397   3.291   3.823   8.906   0.000   0.000   0.000
   2_adp:  0.334  46.397   3.291   3.823   8.906   0.000   0.000   0.000
   2_occ:  0.334  46.397   3.291   3.823   8.906   0.000   0.000   0.000
   3_bss:  0.316  56.319   1.888   2.617   5.880   0.000   0.000   0.000
   3_xyz:  0.316  56.319   1.888   2.617   5.880   0.000   0.000   0.000
   3_adp:  0.316  56.319   1.888   2.617   5.880   0.000   0.000   0.000
   3_occ:  0.316  56.319   1.888   2.617   5.880   0.000   0.000   0.000
   4_bss:  0.329  60.399   1.566   2.223   4.652   0.000   0.000   0.000
   4_xyz:  0.329  60.399   1.566   2.223   4.652   0.000   0.000   0.000
   4_adp:  0.329  60.399   1.566   2.223   4.652   0.000   0.000   0.000
   4_occ:  0.329  60.399   1.566   2.223   4.652   0.000   0.000   0.000
   5_bss:  0.329  60.399   1.794   2.330   4.353   0.000   0.000   0.000
   5_xyz:  0.329  60.399   1.794   2.330   4.353   0.000   0.000   0.000
   5_adp:  0.329  60.399   1.794   2.330   4.353   0.000   0.000   0.000
   5_occ:  0.329  60.399   1.794   2.330   4.353   0.000   0.000   0.000
   5_bss:  0.329  63.393  -0.963  -0.479   1.442   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  52.086 0.4955  0.5637    61635.406
   1_bss:  51.329 0.5041  0.7470    59309.077
   1_xyz:  42.943 0.6071  0.8715    42810.693
   1_adp:  38.616 0.6596  0.9692    36435.334
   1_occ:  38.698 0.6586  0.9665    36563.348
   2_bss:  38.464 0.6614  0.8587    36311.821
   2_xyz:  30.179 0.7559  0.9622    23095.487
   2_adp:  28.059 0.7796  0.9845    20791.393
   2_occ:  28.080 0.7794  0.9841    20810.475
   3_bss:  28.002 0.7804  0.9217    20864.808
   3_xyz:  21.967 0.8427  0.9689    13124.506
   3_adp:  20.296 0.8595  0.9752    11664.733
   3_occ:  20.310 0.8593  0.9751    11659.344
   4_bss:  20.261 0.8599  0.9540    11660.646
   4_xyz:  16.745 0.8917  0.9707     8317.015
   4_adp:  16.155 0.8971  0.9645     7923.805
   4_occ:  16.163 0.8970  0.9644     7930.005
   5_bss:  16.123 0.8973  0.9650     7888.945
   5_xyz:  15.505 0.9029  0.9687     7465.359
   5_adp:  15.427 0.9037  0.9617     7423.758
   5_occ:  15.423 0.9037  0.9617     7419.197
   5_bss:  15.427 0.9037  0.9675     7423.899
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.4150e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.4150e+01
   1_xyz:   1.637  0.013  0.105 18.095  0.006  4.111   1.3296e-01
   1_adp:   1.637  0.013  0.105 18.095  0.006  4.111   1.3296e-01
   1_occ:   1.637  0.013  0.105 18.095  0.006  4.111   1.3296e-01
   2_bss:   1.637  0.013  0.105 18.095  0.006  4.111   1.3296e-01
   2_xyz:   1.096  0.008  0.075 16.037  0.004  4.125   7.1621e-02
   2_adp:   1.096  0.008  0.075 16.037  0.004  4.125   7.1621e-02
   2_occ:   1.096  0.008  0.075 16.037  0.004  4.125   7.1621e-02
   3_bss:   1.096  0.008  0.075 16.037  0.004  4.125   7.1621e-02
   3_xyz:   1.009  0.007  0.075 15.756  0.004  4.127   6.0995e-02
   3_adp:   1.009  0.007  0.075 15.756  0.004  4.127   6.0995e-02
   3_occ:   1.009  0.007  0.075 15.756  0.004  4.127   6.0995e-02
   4_bss:   1.009  0.007  0.075 15.756  0.004  4.127   6.0995e-02
   4_xyz:   1.099  0.009  0.084 16.012  0.004  4.115   7.3927e-02
   4_adp:   1.099  0.009  0.084 16.012  0.004  4.115   7.3927e-02
   4_occ:   1.099  0.009  0.084 16.012  0.004  4.115   7.3927e-02
   5_bss:   1.099  0.009  0.084 16.012  0.004  4.115   7.3927e-02
   5_xyz:   0.990  0.007  0.078 15.447  0.003  4.118   6.0870e-02
   5_adp:   0.990  0.007  0.078 15.447  0.003  4.118   6.0870e-02
   5_occ:   0.990  0.007  0.078 15.447  0.003  4.118   6.0870e-02
   5_bss:   0.990  0.007  0.078 15.447  0.003  4.118   6.0870e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.165   7.0192e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.165   7.0192e+00
   1_xyz:  13.461  0.159  0.408 88.993  0.043  2.162   9.8448e-02
   1_adp:  13.461  0.159  0.408 88.993  0.043  2.162   9.8448e-02
   1_occ:  13.461  0.159  0.408 88.993  0.043  2.162   9.8448e-02
   2_bss:  13.461  0.159  0.408 88.993  0.043  2.162   9.8448e-02
   2_xyz:   6.639  0.059  0.245 86.098  0.034  2.300   7.2367e-02
   2_adp:   6.639  0.059  0.245 86.098  0.034  2.300   7.2367e-02
   2_occ:   6.639  0.059  0.245 86.098  0.034  2.300   7.2367e-02
   3_bss:   6.639  0.059  0.245 86.098  0.034  2.300   7.2367e-02
   3_xyz:   6.076  0.046  0.249 83.781  0.039  2.333   4.7329e-02
   3_adp:   6.076  0.046  0.249 83.781  0.039  2.333   4.7329e-02
   3_occ:   6.076  0.046  0.249 83.781  0.039  2.333   4.7329e-02
   4_bss:   6.076  0.046  0.249 83.781  0.039  2.333   4.7329e-02
   4_xyz:   9.180  0.059  0.407 83.972  0.039  2.347   4.5302e-02
   4_adp:   9.180  0.059  0.407 83.972  0.039  2.347   4.5302e-02
   4_occ:   9.180  0.059  0.407 83.972  0.039  2.347   4.5302e-02
   5_bss:   9.180  0.059  0.407 83.972  0.039  2.347   4.5302e-02
   5_xyz:   6.474  0.048  0.370 81.013  0.037  2.388   3.7070e-02
   5_adp:   6.474  0.048  0.370 81.013  0.037  2.388   3.7070e-02
   5_occ:   6.474  0.048  0.370 81.013  0.037  2.388   3.7070e-02
   5_bss:   6.474  0.048  0.370 81.013  0.037  2.388   3.7070e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  70.06   0.00  12.56  55.02   0.00   9.93  70.06   0.00  26.86
   1_occ:  70.06   0.00  12.56  55.02   0.00   9.93  70.06   0.00  26.86
   2_bss:  70.06   0.00  12.56  55.02   0.00   9.93  70.06   0.00  26.86
   2_xyz:  70.06   0.00  12.56  55.02   0.00   9.93  70.06   0.00  26.86
   2_adp:  68.64   0.00  12.54  62.09   0.00   9.04  68.64   0.00  31.57
   2_occ:  68.64   0.00  12.54  62.09   0.00   9.04  68.64   0.00  31.57
   3_bss:  68.64   0.00  12.54  62.09   0.00   9.04  68.64   0.00  31.57
   3_xyz:  68.64   0.00  12.54  62.09   0.00   9.04  68.64   0.00  31.57
   3_adp:  69.75   0.00  12.63  67.88   0.00   8.60  69.75   1.21  34.57
   3_occ:  69.75   0.00  12.63  67.88   0.00   8.60  69.75   1.21  34.57
   4_bss:  69.75   0.00  12.63  67.88   0.00   8.60  69.75   1.21  34.57
   4_xyz:  69.75   0.00  12.63  67.88   0.00   8.60  69.75   1.21  34.57
   4_adp:  85.29   0.00  13.14  77.24   0.00   8.55  85.29   1.26  38.12
   4_occ:  85.29   0.00  13.14  77.24   0.00   8.55  85.29   1.26  38.12
   5_bss:  85.29   0.00  13.14  77.24   0.00   8.55  85.29   1.26  38.12
   5_xyz:  85.29   0.00  13.14  77.24   0.00   8.55  85.29   1.26  38.12
   5_adp:  99.45   0.00  13.15  85.60   0.00   8.49  99.45   0.85  38.49
   5_occ:  99.45   0.00  13.15  85.60   0.00   8.49  99.45   0.85  38.49
   5_bss: 102.44   2.99  16.14  88.59   2.99  11.49 102.44   3.85  41.49
------------------------------------------------------------------------
 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:    1.252    0.020    0.408
   1_adp:    1.252    0.020    0.408
   1_occ:    1.252    0.020    0.408
   2_bss:    1.252    0.020    0.408
   2_xyz:    1.853    0.044    0.531
   2_adp:    1.853    0.044    0.531
   2_occ:    1.853    0.044    0.531
   3_bss:    1.853    0.044    0.531
   3_xyz:    1.714    0.041    0.599
   3_adp:    1.714    0.041    0.599
   3_occ:    1.714    0.041    0.599
   4_bss:    1.714    0.041    0.599
   4_xyz:    1.907    0.053    0.658
   4_adp:    1.907    0.053    0.658
   4_occ:    1.907    0.053    0.658
   5_bss:    1.907    0.053    0.658
   5_xyz:    1.960    0.043    0.667
   5_adp:    1.960    0.043    0.667
   5_occ:    1.960    0.043    0.667
   5_bss:    1.960    0.043    0.667
------------------------------------------------------------------------

CPU time actual refinement: 345.59


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_549/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_549/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_549/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_549/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_549/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 345.43 
  Macro-tasks:
    bulk solvent and scale       = 41.16  
    individual site refinement   = 133.50 
    weights calculation          = 33.11  
    collect and process          = 6.80   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 214.71 
  Micro-tasks:
    mask                            = 2.27   
    f_calc                          = 108.37 
    alpha_beta                      = 8.54   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 116.77 
    fmodel                         = 7.64   
    r_factors                      = 0.27   
    phase_errors                   = 10.72  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 256.00 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.926 micro seconds
Total CPU time: 5.98 minutes
from_scatterers_fft:    664 calls, 108.01 s
gradients_fft:          609 calls, 104.03 s

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

# Date 2008-01-16 Time 01:51:24 PST -0800 (1200477084.98 s)
Start R-work = 0.4643, R-free = 0.4529 (no bulk solvent and anisotropic scale)
Final R-work = 0.1378, R-free = 0.1847 (no bulk solvent and anisotropic scale)

Start R-work = 0.4548, R-free = 0.4418
Final R-work = 0.1202, R-free = 0.1687