# Date 2008-01-16 Time 01:26:32 PST -0800 (1200475592.21 s)
#phil __OFF__

Command line arguments: "../410.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 26332
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 410

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.5475, 46.6953, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 46.6953, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.844 1.98044
Completeness in resolution range: 0.98156
Completeness with d_max=infinity: 0.978423

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8440
                             d_min =   1.9804

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 46.6953, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.844 1.98044
Completeness in resolution range: 0.98156
Completeness with d_max=infinity: 0.978423

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8444 -  4.2367 [2093/2118]  1884   209  10.0%
  bin  2:  4.2367 -  3.3758 [2024/2042]  1822   202  10.0%
  bin  3:  3.3758 -  2.9529 [1983/2002]  1784   199  10.0%
  bin  4:  2.9529 -  2.6847 [1956/1986]  1761   195  10.0%
  bin  5:  2.6847 -  2.4932 [1960/1979]  1764   196  10.0%
  bin  6:  2.4932 -  2.3468 [1949/1974]  1751   198  10.2%
  bin  7:  2.3468 -  2.2297 [1944/1972]  1755   189   9.7%
  bin  8:  2.2297 -  2.1329 [1941/1977]  1744   197  10.1%
  bin  9:  2.1329 -  2.0510 [1902/1944]  1711   191  10.0%
  bin 10:  2.0510 -  1.9804 [1837/1963]  1654   183  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_410/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:
        1.75 -     2.38: 18
        2.38 -     3.01: 2018
        3.01 -     3.64: 4668
        3.64 -     4.27: 9247
        4.27 -     4.90: 12700
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.748 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  37 " - " O   HOH Z 416 "  2.016 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  2.024 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  2.070 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28646 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_410/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_410/model_refine_001.geo

CPU time processing inputs: 9.14


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.5475 46.69535 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4348   r_free= 0.4227   ksol= 0.00   Bsol= 0.00   scale= 0.830    |
|                                                                             |
| 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:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.228712                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8444 -  4.7250 0.99   1370  153 0.3624 0.3559       6.514      6.5101|
|  2:  4.7250 -  3.7706 0.99   1303  145 0.3392 0.3361       6.652      6.6524|
|  3:  3.7706 -  3.3000 0.99   1281  142 0.3734 0.3538      6.5649      6.5984|
|  4:  3.3000 -  3.0010 0.99   1280  140 0.4065 0.3889      6.4548       6.393|
|  5:  3.0010 -  2.7874 0.99   1257  142 0.4478 0.4762      6.3189       6.322|
|  6:  2.7874 -  2.6240 0.99   1274  140 0.4586 0.5145      6.2505      6.2753|
|  7:  2.6240 -  2.4932 0.99   1250  139 0.4688 0.4445      6.2102      6.1213|
|  8:  2.4932 -  2.3851 0.98   1254  140 0.4805 0.4529      6.1622      6.1805|
|  9:  2.3851 -  2.2937 0.98   1241  140 0.4892 0.4713       6.097      6.0814|
| 10:  2.2937 -  2.2148 0.99   1237  137 0.4912 0.4736      6.1139      6.0577|
| 11:  2.2148 -  2.1457 0.98   1252  137 0.4913 0.4273      6.0466      5.9818|
| 12:  2.1457 -  2.0846 0.97   1236  138 0.4941 0.4529      5.9905      5.9933|
| 13:  2.0846 -  2.0298 1.00   1230  134 0.5090 0.5171      5.8958      5.8966|
| 14:  2.0298 -  1.9804 0.91   1165  132 0.5081 0.4722      5.8341      5.7609|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8444 -  4.7250  1370   153  0.71  33.49   0.82     0.74      66427.37|
|  2:  4.7250 -  3.7706  1303   145  0.76  30.06   0.92     0.82      80670.88|
|  3:  3.7706 -  3.3000  1281   142  0.70  35.59   0.89     0.80      81850.82|
|  4:  3.3000 -  3.0010  1280   140  0.63  41.20   0.85     0.71      73532.91|
|  5:  3.0010 -  2.7874  1257   142  0.53  49.21   0.78     0.61      65465.49|
|  6:  2.7874 -  2.6240  1274   140  0.50  51.87   0.76     0.57      60195.71|
|  7:  2.6240 -  2.4932  1250   139  0.49  53.13   0.76     0.55      55565.36|
|  8:  2.4932 -  2.3851  1254   140  0.49  52.72   0.78     0.57      49112.67|
|  9:  2.3851 -  2.2937  1241   140  0.51  51.14   0.75     0.58      41517.72|
| 10:  2.2937 -  2.2148  1237   137  0.54  48.76   0.79     0.62      35377.60|
| 11:  2.2148 -  2.1457  1252   137  0.54  49.40   0.78     0.62      33271.91|
| 12:  2.1457 -  2.0846  1236   138  0.49  52.92   0.79     0.58      34039.35|
| 13:  2.0846 -  2.0298  1230   134  0.42  58.16   0.78     0.51      32082.88|
| 14:  2.0298 -  1.9804  1165   132  0.40  59.72   0.75     0.44      26920.12|
|alpha:            min =        0.44 max =            0.82 mean =         0.63|
|beta:             min =    26920.12 max =        81850.82 mean =     53032.03|
|figures of merit: min =        0.00 max =            1.00 mean =         0.55|
|phase err.(work): min =        0.00 max =           89.98 mean =        47.42|
|phase err.(test): min =        0.00 max =           89.84 mean =        47.53|
|-----------------------------------------------------------------------------|

============================== 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 = 7.717977              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 75.828   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.651695              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.236   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      171 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      701 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1546 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2674 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3958 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5154 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6629 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7814 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.208 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.894 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.609)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.609)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4433   r_free= 0.4313   ksol= 0.00   Bsol= 0.00   scale= 0.797    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.233509                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4263   r_free= 0.4155   ksol= 0.36   Bsol= 11.14   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.64,8.52,8.46,0.00,0.00,0.00); trace/3= 8.21                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.221735                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.046321              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.315   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.654018              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.895   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4263      final r-factor (work) = 0.3221          |
| start r-factor (free) = 0.4155      final r-factor (free) = 0.3436          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 75.1998 = 7.05 * 0.50 * 6.2422 + 1.00 * 53.2076                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.5347 = 7.05 * 0.50 * 6.0788 + 1.00 * 0.1183                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3221      final r-factor (work) = 0.2590          |
| start r-factor (free) = 0.3436      final r-factor (free) = 0.2944          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9903 = 0.65 * 1.00 * 6.0788 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8684 = 0.65 * 1.00 * 5.8960 + 1.00 * 0.0123                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.609)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    69.77   10.79    None  None   None       |
|    all(noH): 2823   0      0.00    69.77   10.79    None  None   None       |
|    Sol.    : 438    0      0.00    61.88   27.46    None  None   None       |
|    Mac.    : 2385   0      0.00    69.77   7.73     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 -   6.977: 1419   |   5:    34.883 -  41.860:   94        |
|      1:     6.977 -  13.953:  702   |   6:    41.860 -  48.836:   40        |
|      2:    13.953 -  20.930:  247   |   7:    48.836 -  55.813:   19        |
|      3:    20.930 -  27.907:  168   |   8:    55.813 -  62.790:    4        |
|      4:    27.907 -  34.883:  129   |   9:    62.790 -  69.766:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2590 r_free = 0.2944             target_work(ml) = 5.834         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2585 r_free = 0.2941             target_work(ml) = 5.833         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2585   r_free= 0.2941   ksol= 0.36   Bsol= 11.14   scale= 1.100   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.64,8.52,8.46,0.00,0.00,0.00); trace/3= 8.21                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.832693                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2532   r_free= 0.2878   ksol= 0.33   Bsol= 27.78   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.89,4.55,5.38,0.00,0.00,0.00); trace/3= 4.61                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.830099                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.619290              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.338   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.330492              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.752  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2532      final r-factor (work) = 0.1721          |
| start r-factor (free) = 0.2878      final r-factor (free) = 0.2106          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8519 = 2.62 * 0.50 * 5.9057 + 1.00 * 0.1176                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4603 = 2.62 * 0.50 * 5.6544 + 1.00 * 0.0550                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1721      final r-factor (work) = 0.1545          |
| start r-factor (free) = 0.2106      final r-factor (free) = 0.1943          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8840 = 0.33 * 1.00 * 5.6544 + 1.00 * 0.0153                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8207 = 0.33 * 1.00 * 5.4341 + 1.00 * 0.0248                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.609)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.47   11.39    None  None   None       |
|    all(noH): 2823   0      0.00    76.47   11.39    None  None   None       |
|    Sol.    : 438    0      1.39    63.57   32.43    None  None   None       |
|    Mac.    : 2385   0      0.00    76.47   7.53     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 -   7.647: 1647   |   5:    38.237 -  45.884:  112        |
|      1:     7.647 -  15.295:  565   |   6:    45.884 -  53.532:   56        |
|      2:    15.295 -  22.942:  176   |   7:    53.532 -  61.179:   25        |
|      3:    22.942 -  30.590:  105   |   8:    61.179 -  68.827:    4        |
|      4:    30.590 -  38.237:  131   |   9:    68.827 -  76.474:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1545 r_free = 0.1943             target_work(ml) = 5.396         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1542 r_free = 0.1938             target_work(ml) = 5.395         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1542   r_free= 0.1938   ksol= 0.33   Bsol= 27.78   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.89,4.55,5.38,0.00,0.00,0.00); trace/3= 4.61                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.394910                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1537   r_free= 0.1938   ksol= 0.33   Bsol= 33.87   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.86,3.39,4.32,0.00,0.00,0.00); trace/3= 3.52                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.394436                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.913200              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.244  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.308647              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.563   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1537      final r-factor (work) = 0.1252          |
| start r-factor (free) = 0.1938      final r-factor (free) = 0.1636          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2590 = 1.91 * 0.50 * 5.4401 + 1.00 * 0.0550                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1251 = 1.91 * 0.50 * 5.2993 + 1.00 * 0.0558                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1252      final r-factor (work) = 0.1210          |
| start r-factor (free) = 0.1636      final r-factor (free) = 0.1596          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6872 = 0.31 * 1.00 * 5.2993 + 1.00 * 0.0516                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6140 = 0.31 * 1.00 * 5.1947 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.609)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.08   11.53    None  None   None       |
|    all(noH): 2823   0      0.00    81.08   11.53    None  None   None       |
|    Sol.    : 438    0      1.01    67.61   33.60    None  None   None       |
|    Mac.    : 2385   0      0.00    81.08   7.48     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 -   8.108: 1735   |   5:    40.540 -  48.647:   91        |
|      1:     8.108 -  16.216:  534   |   6:    48.647 -  56.755:   64        |
|      2:    16.216 -  24.324:  133   |   7:    56.755 -  64.863:   17        |
|      3:    24.324 -  32.432:  123   |   8:    64.863 -  72.971:    3        |
|      4:    32.432 -  40.540:  120   |   9:    72.971 -  81.079:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1210 r_free = 0.1596             target_work(ml) = 5.183         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1210 r_free = 0.1594             target_work(ml) = 5.182         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1210   r_free= 0.1594   ksol= 0.33   Bsol= 33.87   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.86,3.39,4.32,0.00,0.00,0.00); trace/3= 3.52                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.182281                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1213   r_free= 0.1599   ksol= 0.32   Bsol= 35.06   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.70,3.15,4.04,0.00,0.00,0.00); trace/3= 3.30                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.184038                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.120307              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 133.199  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.449093              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.253  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1213      final r-factor (work) = 0.1099          |
| start r-factor (free) = 0.1599      final r-factor (free) = 0.1537          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1612 = 3.12 * 0.50 * 5.1953 + 1.00 * 0.0558                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0872 = 3.12 * 0.50 * 5.1388 + 1.00 * 0.0699                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1099      final r-factor (work) = 0.1085          |
| start r-factor (free) = 0.1537      final r-factor (free) = 0.1541          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3184 = 0.45 * 1.00 * 5.1388 + 1.00 * 0.0106                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3063 = 0.45 * 1.00 * 5.1108 + 1.00 * 0.0111                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.609)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.39   11.44    None  None   None       |
|    all(noH): 2823   0      0.00    82.39   11.44    None  None   None       |
|    Sol.    : 438    0      1.07    68.25   33.41    None  None   None       |
|    Mac.    : 2385   0      0.00    82.39   7.41     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.240: 1744   |   5:    41.197 -  49.437:   87        |
|      1:     8.240 -  16.479:  531   |   6:    49.437 -  57.676:   55        |
|      2:    16.479 -  24.719:  141   |   7:    57.676 -  65.916:   18        |
|      3:    24.719 -  32.958:  123   |   8:    65.916 -  74.155:    3        |
|      4:    32.958 -  41.197:  118   |   9:    74.155 -  82.395:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1085 r_free = 0.1541             target_work(ml) = 5.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1085 r_free = 0.1540             target_work(ml) = 5.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1085   r_free= 0.1540   ksol= 0.32   Bsol= 35.06   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.70,3.15,4.04,0.00,0.00,0.00); trace/3= 3.30                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.111550                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1085   r_free= 0.1540   ksol= 0.32   Bsol= 35.06   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.70,3.12,4.05,0.00,0.00,0.00); trace/3= 3.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.111538                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.906858              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 159.917  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.666536              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.558  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1085      final r-factor (work) = 0.1070          |
| start r-factor (free) = 0.1540      final r-factor (free) = 0.1539          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4979 = 2.91 * 0.50 * 5.1107 + 1.00 * 0.0699                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4899 = 2.91 * 0.50 * 5.1066 + 1.00 * 0.0679                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1070      final r-factor (work) = 0.1065          |
| start r-factor (free) = 0.1539      final r-factor (free) = 0.1545          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4148 = 0.67 * 1.00 * 5.1066 + 1.00 * 0.0111                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4135 = 0.67 * 1.00 * 5.1035 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.609)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.42   11.40    None  None   None       |
|    all(noH): 2823   0      0.00    84.42   11.40    None  None   None       |
|    Sol.    : 438    0      1.05    68.15   33.38    None  None   None       |
|    Mac.    : 2385   0      0.00    84.42   7.37     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 -   8.442: 1771   |   5:    42.208 -  50.649:   94        |
|      1:     8.442 -  16.883:  507   |   6:    50.649 -  59.091:   39        |
|      2:    16.883 -  25.325:  150   |   7:    59.091 -  67.532:   18        |
|      3:    25.325 -  33.766:  128   |   8:    67.532 -  75.974:    2        |
|      4:    33.766 -  42.208:  111   |   9:    75.974 -  84.415:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1065 r_free = 0.1545             target_work(ml) = 5.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1065 r_free = 0.1546             target_work(ml) = 5.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1065   r_free= 0.1546   ksol= 0.32   Bsol= 35.06   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.70,3.12,4.05,0.00,0.00,0.00); trace/3= 3.29                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.107199                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8444 -  4.7250 0.99   1370  153 0.0987 0.1254      5.3726      5.5087|
|  2:  4.7250 -  3.7706 0.99   1303  145 0.0836 0.1118      5.4222      5.6264|
|  3:  3.7706 -  3.3000 0.99   1281  142 0.1010 0.1510      5.4479       5.858|
|  4:  3.3000 -  3.0010 0.99   1280  140 0.1155 0.1483      5.4258      5.5649|
|  5:  3.0010 -  2.7874 0.99   1257  142 0.1204 0.1705      5.2801      5.5134|
|  6:  2.7874 -  2.6240 0.99   1274  140 0.1131 0.1710      5.1688      5.4134|
|  7:  2.6240 -  2.4932 0.99   1250  139 0.1185 0.1616      5.1223      5.3544|
|  8:  2.4932 -  2.3851 0.98   1254  140 0.1095 0.1737      5.0412      5.3615|
|  9:  2.3851 -  2.2937 0.98   1241  140 0.1115 0.1667      5.0057      5.2336|
| 10:  2.2937 -  2.2148 0.99   1237  137 0.1051 0.1818      4.9333      5.2386|
| 11:  2.2148 -  2.1457 0.98   1252  137 0.1067 0.1613      4.9022       5.203|
| 12:  2.1457 -  2.0846 0.97   1236  138 0.1061 0.1681      4.8511      5.2093|
| 13:  2.0846 -  2.0298 1.00   1230  134 0.1063 0.1622       4.775      5.0228|
| 14:  2.0298 -  1.9804 0.91   1165  132 0.1009 0.1768      4.6545       4.956|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8444 -  4.7250  1370   153  0.94   8.98   0.98     0.96       6948.50|
|  2:  4.7250 -  3.7706  1303   145  0.95   7.77   1.03     1.01       8873.47|
|  3:  3.7706 -  3.3000  1281   142  0.94  10.73   1.03     1.02       9937.64|
|  4:  3.3000 -  3.0010  1280   140  0.93  12.87   1.01     1.00       9832.16|
|  5:  3.0010 -  2.7874  1257   142  0.91  14.81   1.00     0.96       7693.35|
|  6:  2.7874 -  2.6240  1274   140  0.91  15.11   0.99     0.96       6613.51|
|  7:  2.6240 -  2.4932  1250   139  0.91  15.03   0.99     0.96       5782.18|
|  8:  2.4932 -  2.3851  1254   140  0.92  14.11   0.99     0.97       5002.97|
|  9:  2.3851 -  2.2937  1241   140  0.91  14.93   1.01     0.99       4821.20|
| 10:  2.2937 -  2.2148  1237   137  0.91  14.85   1.00     0.96       4176.50|
| 11:  2.2148 -  2.1457  1252   137  0.90  15.60   1.00     0.97       4163.72|
| 12:  2.1457 -  2.0846  1236   138  0.92  14.59   1.02     1.00       3744.53|
| 13:  2.0846 -  2.0298  1230   134  0.91  15.10   1.01     1.01       3273.19|
| 14:  2.0298 -  1.9804  1165   132  0.92  14.49   0.99     0.96       2543.16|
|alpha:            min =        0.96 max =            1.02 mean =         0.98|
|beta:             min =     2543.16 max =         9937.64 mean =      6011.00|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.93 mean =        13.44|
|phase err.(test): min =        0.00 max =           89.93 mean =        13.02|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1065   r_free= 0.1545   ksol= 0.33   Bsol= 41.55   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.59,-0.18,0.77,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.106972                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1065   r_free= 0.1545   ksol= 0.33   Bsol= 41.55   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.59,-0.18,0.77,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.106972                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8444 -  4.7250 0.99   1370  153 0.0989 0.1257      5.3741      5.5107|
|  2:  4.7250 -  3.7706 0.99   1303  145 0.0838 0.1121      5.4248      5.6287|
|  3:  3.7706 -  3.3000 0.99   1281  142 0.1011 0.1510      5.4491      5.8585|
|  4:  3.3000 -  3.0010 0.99   1280  140 0.1155 0.1481      5.4253      5.5639|
|  5:  3.0010 -  2.7874 0.99   1257  142 0.1203 0.1703      5.2789      5.5121|
|  6:  2.7874 -  2.6240 0.99   1274  140 0.1129 0.1708      5.1673      5.4121|
|  7:  2.6240 -  2.4932 0.99   1250  139 0.1184 0.1614      5.1209      5.3532|
|  8:  2.4932 -  2.3851 0.98   1254  140 0.1094 0.1735      5.0402        5.36|
|  9:  2.3851 -  2.2937 0.98   1241  140 0.1114 0.1668      5.0052      5.2339|
| 10:  2.2937 -  2.2148 0.99   1237  137 0.1051 0.1818      4.9332      5.2381|
| 11:  2.2148 -  2.1457 0.98   1252  137 0.1066 0.1612      4.9018      5.2027|
| 12:  2.1457 -  2.0846 0.97   1236  138 0.1061 0.1681      4.8507      5.2091|
| 13:  2.0846 -  2.0298 1.00   1230  134 0.1063 0.1622      4.7743      5.0224|
| 14:  2.0298 -  1.9804 0.91   1165  132 0.1009 0.1765      4.6533      4.9542|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8444 -  4.7250  1370   153  0.94   9.01   0.99     0.96       6981.26|
|  2:  4.7250 -  3.7706  1303   145  0.95   7.78   1.03     1.01       8909.41|
|  3:  3.7706 -  3.3000  1281   142  0.94  10.74   1.03     1.03       9959.04|
|  4:  3.3000 -  3.0010  1280   140  0.93  12.86   1.01     1.00       9818.81|
|  5:  3.0010 -  2.7874  1257   142  0.91  14.79   1.00     0.97       7675.29|
|  6:  2.7874 -  2.6240  1274   140  0.91  15.08   0.99     0.96       6592.52|
|  7:  2.6240 -  2.4932  1250   139  0.91  15.01   0.99     0.96       5763.73|
|  8:  2.4932 -  2.3851  1254   140  0.92  14.08   1.00     0.98       4991.64|
|  9:  2.3851 -  2.2937  1241   140  0.91  14.92   1.01     0.99       4817.17|
| 10:  2.2937 -  2.2148  1237   137  0.91  14.85   1.01     0.97       4176.10|
| 11:  2.2148 -  2.1457  1252   137  0.90  15.59   1.01     0.98       4161.53|
| 12:  2.1457 -  2.0846  1236   138  0.92  14.58   1.02     1.01       3740.02|
| 13:  2.0846 -  2.0298  1230   134  0.91  15.08   1.02     1.01       3265.16|
| 14:  2.0298 -  1.9804  1165   132  0.92  14.47   1.00     0.96       2534.19|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2534.19 max =         9959.04 mean =      6009.93|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.69 mean =        13.43|
|phase err.(test): min =        0.00 max =           87.17 mean =        13.00|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.609)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.39    87.80   14.79    None  None   None       |
|    all(noH): 2823   0      3.39    87.80   14.79    None  None   None       |
|    Sol.    : 438    0      4.44    71.54   36.77    None  None   None       |
|    Mac.    : 2385   0      3.39    87.80   10.76    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.389 -  11.831: 1771   |   5:    45.597 -  54.038:   94        |
|      1:    11.831 -  20.272:  507   |   6:    54.038 -  62.480:   39        |
|      2:    20.272 -  28.714:  150   |   7:    62.480 -  70.921:   18        |
|      3:    28.714 -  37.155:  128   |   8:    70.921 -  79.363:    2        |
|      4:    37.155 -  45.597:  111   |   9:    79.363 -  87.805:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 294         
Filter by distance & map next to the model:
   mapped sites are within: 0.322 - 5.509
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 291 from: 294
   mapped sites are within: 0.714 - 5.509

peak=   11.539 closest distance to " CB  VAL A 230 " =    1.457
peak=    6.650 closest distance to " CG2 VAL A 296 " =    1.106
peak=    6.559 closest distance to " CG  LEU A   5 " =    1.179
peak=    5.778 closest distance to " CB  VAL A 296 " =    1.091
peak=    5.711 closest distance to " NE2 GLN A  11 " =    1.144
peak=    5.589 closest distance to " CG  LEU A 228 " =    1.159
peak=    5.455 closest distance to " O   HOH Z 142 " =    1.842
peak=    5.181 closest distance to " O   HOH Z 193 " =    1.736
peak=    5.180 closest distance to " CD2 LEU A   5 " =    1.158
peak=    5.146 closest distance to " NH2 ARG A  56 " =    2.131
peak=    5.135 closest distance to " CG  PRO A  54 " =    1.220
peak=    5.065 closest distance to " CB  ARG A 275 " =    0.938
peak=    5.054 closest distance to " O   HOH Z 126 " =    1.901
peak=    5.043 closest distance to " CB  GLN A 183 " =    1.265
peak=    4.911 closest distance to " O   HOH Z 232 " =    2.380
peak=    4.821 closest distance to " CB  GLN A 223 " =    1.479
peak=    4.797 closest distance to " O   HOH Z 209 " =    2.295
peak=    4.764 closest distance to " CB  GLU A 152 " =    1.202
peak=    4.721 closest distance to " O   HOH Z 427 " =    2.846
peak=    4.651 closest distance to " CB  SER A  63 " =    1.213
peak=    4.635 closest distance to " O   HOH Z 236 " =    1.948
peak=    4.563 closest distance to " C   PRO A 198 " =    1.480
peak=    4.562 closest distance to " O   HOH Z 272 " =    1.851
peak=    4.533 closest distance to " O   SER A  87 " =    2.308
peak=    4.511 closest distance to " CB  VAL A 230 " =    1.132
peak=    4.507 closest distance to " CG  PRO A 213 " =    1.210
peak=    4.458 closest distance to " CB  ARG A  79 " =    1.433
peak=    4.429 closest distance to " O   HOH Z 316 " =    2.964
peak=    4.360 closest distance to " CB  PRO A  54 " =    0.952
peak=    4.330 closest distance to " O   HOH Z  78 " =    1.834
peak=    4.296 closest distance to " O   HOH Z   9 " =    2.271
peak=    4.293 closest distance to " OD1 ASN A  69 " =    2.594
peak=    4.268 closest distance to " O   HOH Z 203 " =    1.635
peak=    4.259 closest distance to " CB  SER A   3 " =    1.307
peak=    4.254 closest distance to " O   HOH Z 402 " =    1.429
peak=    4.248 closest distance to " ND2 ASN A 187 " =    1.469
peak=    4.232 closest distance to " O   HOH Z 124 " =    1.412
peak=    4.185 closest distance to " O   HOH Z 346 " =    1.592
peak=    4.178 closest distance to " CB  ASN A 148 " =    1.409
peak=    4.174 closest distance to " CB  ARG A 139 " =    0.966
peak=    4.174 closest distance to " O   HOH Z  61 " =    1.620
peak=    4.166 closest distance to " O   HOH Z 298 " =    1.786
peak=    4.162 closest distance to " O   HOH Z 371 " =    3.017
peak=    4.160 closest distance to " O   HOH Z  59 " =    1.896
peak=    4.147 closest distance to " CG1BVAL A  72 " =    1.524
peak=    4.137 closest distance to " O   HOH Z 130 " =    2.340
peak=    4.121 closest distance to " CB  VAL A 265 " =    1.298
peak=    4.109 closest distance to " O   HOH Z 303 " =    2.066
peak=    4.090 closest distance to " O   HOH Z 369 " =    2.142
peak=    4.076 closest distance to " CB  TYR A 169 " =    0.714
peak=    4.075 closest distance to " O   HOH Z 368 " =    2.055
peak=    4.066 closest distance to " O   HOH Z 234 " =    3.436
peak=    4.060 closest distance to " O   HOH Z 126 " =    2.034
peak=    4.055 closest distance to " OG BSER A 164 " =    2.157
peak=    4.055 closest distance to " O   HOH Z 250 " =    1.352
peak=    4.042 closest distance to " O   HOH Z 403 " =    1.700
peak=    4.031 closest distance to " O   HOH Z 265 " =    2.438
peak=    4.006 closest distance to " O   HOH Z 392 " =    3.093
peak=    3.997 closest distance to " CB  TRP A 179 " =    1.295
peak=    3.994 closest distance to " O   HOH Z 158 " =    3.040
peak=    3.988 closest distance to " CA  ASN A 215 " =    1.177
peak=    3.987 closest distance to " O   HOH Z  66 " =    2.146
peak=    3.968 closest distance to " O   HOH Z  44 " =    1.781
peak=    3.963 closest distance to " OD2 ASP A 286 " =    2.689
peak=    3.959 closest distance to " O   HOH Z 245 " =    1.362
peak=    3.923 closest distance to " O   HOH Z 248 " =    1.601
peak=    3.922 closest distance to " O   HOH Z  85 " =    1.343
peak=    3.897 closest distance to " CB  TRP A 266 " =    1.017
peak=    3.889 closest distance to " O   HOH Z 144 " =    2.216
peak=    3.883 closest distance to " CB  SER A  26 " =    1.648
peak=    3.880 closest distance to " O   HOH Z 425 " =    2.178
peak=    3.868 closest distance to " O   HOH Z  54 " =    1.658
peak=    3.864 closest distance to " O   HOH Z 128 " =    2.072
peak=    3.855 closest distance to " O   HOH Z  97 " =    2.557
peak=    3.854 closest distance to " O   HOH Z 407 " =    2.479
peak=    3.822 closest distance to " O   HOH Z 411 " =    3.799
peak=    3.809 closest distance to " O   HOH Z   9 " =    1.990
peak=    3.806 closest distance to " O   HOH Z 322 " =    2.028
peak=    3.799 closest distance to " O   HOH Z 389 " =    1.840
peak=    3.784 closest distance to " O   HOH Z 145 " =    2.079
peak=    3.782 closest distance to " O   HOH Z 189 " =    2.715
peak=    3.779 closest distance to " O   HOH Z  97 " =    1.917
peak=    3.775 closest distance to " O   HOH Z 280 " =    2.936
peak=    3.770 closest distance to " O   HOH Z 227 " =    2.165
peak=    3.769 closest distance to " O   HOH Z 423 " =    1.817
peak=    3.764 closest distance to " CB  ASN A  39 " =    0.869
peak=    3.753 closest distance to " CD2 LEU A 228 " =    1.122
peak=    3.748 closest distance to " CA  TYR A  30 " =    0.950
peak=    3.743 closest distance to " CD2 TRP A 179 " =    1.445
peak=    3.732 closest distance to " CB  ALA A   9 " =    1.625
peak=    3.717 closest distance to " O   HOH Z 344 " =    2.886
peak=    3.693 closest distance to " O   HOH Z 345 " =    3.249
peak=    3.690 closest distance to " O   HOH Z 130 " =    2.859
peak=    3.687 closest distance to " CG  GLN A  77 " =    2.211
peak=    3.684 closest distance to " O   HOH Z 273 " =    2.681
peak=    3.683 closest distance to " O   HOH Z 263 " =    1.575
peak=    3.682 closest distance to " CB  GLU A 277 " =    3.487
peak=    3.681 closest distance to " O   HOH Z 426 " =    1.515
peak=    3.668 closest distance to " CB  ASP A 140 " =    0.948
peak=    3.665 closest distance to " CG  PRO A 243 " =    1.145
peak=    3.645 closest distance to " CB  VAL A 202 " =    1.587
peak=    3.644 closest distance to " O   HOH Z 327 " =    1.553
peak=    3.634 closest distance to " CA  PHE A 283 " =    1.166
peak=    3.632 closest distance to " O   HOH Z 366 " =    2.909
peak=    3.625 closest distance to " CB  GLU A 128 " =    0.974
peak=    3.614 closest distance to " O   HOH Z 112 " =    1.620
peak=    3.610 closest distance to " CD BLYS A 290 " =    1.222
peak=    3.608 closest distance to " O   HOH Z 128 " =    2.113
peak=    3.608 closest distance to " O   HOH Z 193 " =    1.822
peak=    3.607 closest distance to " NZ  LYS A 117 " =    3.052
peak=    3.606 closest distance to " CG2 ILE A  20 " =    1.519
peak=    3.599 closest distance to " CG2 ILE A 120 " =    1.220
peak=    3.591 closest distance to " CA  ALA A  21 " =    1.153
peak=    3.588 closest distance to " CG2 VAL A 257 " =    0.803
peak=    3.588 closest distance to " CG1 ILE A  33 " =    1.304
peak=    3.585 closest distance to " O   HOH Z  43 " =    2.208
peak=    3.579 closest distance to " OE1 GLU A   2 " =    2.137
peak=    3.577 closest distance to " O   TRP A 274 " =    1.857
peak=    3.577 closest distance to " O   HOH Z 417 " =    3.284
peak=    3.570 closest distance to " O   HOH Z 222 " =    2.452
peak=    3.567 closest distance to " N   ASN A  39 " =    1.158
peak=    3.565 closest distance to " CZ  PHE A 218 " =    1.092
peak=    3.564 closest distance to " O   HOH Z 299 " =    4.231
peak=    3.563 closest distance to " O   HOH Z 329 " =    3.816
peak=    3.562 closest distance to " CA  VAL A  41 " =    0.790
peak=    3.559 closest distance to " O   HOH Z  10 " =    1.821
peak=    3.555 closest distance to " O   HOH Z 251 " =    1.605
peak=    3.554 closest distance to " CA  ALA A 158 " =    1.276
peak=    3.531 closest distance to " O   HOH Z   1 " =    1.816
peak=    3.520 closest distance to " O   HOH Z 180 " =    2.147
peak=    3.520 closest distance to " CB  ARG A 190 " =    1.672
peak=    3.514 closest distance to " CA  LYS A 117 " =    1.257
peak=    3.513 closest distance to " O   HOH Z 132 " =    2.484
peak=    3.509 closest distance to " N   PHE A 130 " =    1.285
peak=    3.499 closest distance to " O   HOH Z  61 " =    1.543
peak=    3.497 closest distance to " O   HOH Z 286 " =    2.313
peak=    3.491 closest distance to " CB  GLN A  88 " =    1.231
peak=    3.489 closest distance to " O   HOH Z  43 " =    2.813
peak=    3.484 closest distance to " CD1 ILE A 106 " =    1.119
peak=    3.464 closest distance to " CB  SER A 216 " =    0.738
peak=    3.463 closest distance to " O   HOH Z 147 " =    1.722
peak=    3.463 closest distance to " CG  MET A 185 " =    1.167
peak=    3.457 closest distance to " CB  GLN A 278 " =    0.845
peak=    3.455 closest distance to " O   HOH Z   3 " =    1.865
peak=    3.449 closest distance to " OE2 GLU A  53 " =    1.990
peak=    3.447 closest distance to " O   HOH Z 234 " =    1.890
peak=    3.447 closest distance to " O   HOH Z 218 " =    2.447
peak=    3.444 closest distance to " O   HOH Z 425 " =    1.306
peak=    3.438 closest distance to " CD  ARG A 269 " =    1.009
peak=    3.435 closest distance to " CA  ASP A 162 " =    1.066
peak=    3.435 closest distance to " CB BVAL A  41 " =    1.243
peak=    3.434 closest distance to " O  BHOH Z 338 " =    2.424
peak=    3.433 closest distance to " O   HOH Z 435 " =    1.904
peak=    3.432 closest distance to " O   HOH Z 118 " =    1.407
peak=    3.430 closest distance to " CB  LEU A 255 " =    0.752
peak=    3.429 closest distance to " CB  LEU A 143 " =    1.157
peak=    3.424 closest distance to " O   HOH Z 214 " =    2.252
peak=    3.414 closest distance to " CD2 HIS A  81 " =    1.009
peak=    3.410 closest distance to " CB  THR A  31 " =    1.678
peak=    3.403 closest distance to " O   HOH Z 423 " =    2.892
peak=    3.403 closest distance to " O   HOH Z  89 " =    2.353
peak=    3.402 closest distance to " O   HOH Z  71 " =    2.087
peak=    3.397 closest distance to " O   HOH Z 250 " =    1.782
peak=    3.389 closest distance to " O   ASP A 124 " =    1.146
peak=    3.389 closest distance to " CA  ALA A 233 " =    1.076
peak=    3.388 closest distance to " ND2 ASN A 110 " =    1.730
peak=    3.386 closest distance to " CB  ASN A 142 " =    1.111
peak=    3.384 closest distance to " O   HOH Z 291 " =    1.478
peak=    3.377 closest distance to " O   HOH Z 374 " =    2.527
peak=    3.377 closest distance to " CG  LEU A 167 " =    1.184
peak=    3.376 closest distance to " CG2 THR A 221 " =    1.276
peak=    3.375 closest distance to " N   ARG A 156 " =    1.333
peak=    3.373 closest distance to " CD  LYS A 119 " =    1.452
peak=    3.370 closest distance to " CB  THR A 157 " =    1.083
peak=    3.366 closest distance to " CG  PRO A 198 " =    1.183
peak=    3.362 closest distance to " CB  ALA A 248 " =    1.379
peak=    3.361 closest distance to " O   HOH Z 187 " =    2.198
peak=    3.360 closest distance to " O   HOH Z 422 " =    2.593
peak=    3.358 closest distance to " CG1 ILE A 151 " =    1.077
peak=    3.358 closest distance to " CE1 TYR A 186 " =    1.332
peak=    3.355 closest distance to " CB  ASN A 110 " =    1.073
peak=    3.354 closest distance to " CA  ARG A  36 " =    1.006
peak=    3.352 closest distance to " OD1 ASN A 148 " =    1.682
peak=    3.352 closest distance to " O   ALA A   1 " =    1.747
peak=    3.351 closest distance to " O   HOH Z 438 " =    1.862
peak=    3.342 closest distance to " O   GLN A 278 " =    1.224
peak=    3.340 closest distance to " CD  GLN A 194 " =    1.357
peak=    3.337 closest distance to " CA  ALA A  51 " =    0.976
peak=    3.335 closest distance to " CD1 LEU A 300 " =    1.323
peak=    3.333 closest distance to " O   HOH Z 368 " =    3.629
peak=    3.331 closest distance to " O   HOH Z  48 " =    1.394
peak=    3.327 closest distance to " CA  ASP A 140 " =    1.212
peak=    3.326 closest distance to " O   HOH Z 313 " =    1.858
peak=    3.318 closest distance to " O   HOH Z 337 " =    3.449
peak=    3.316 closest distance to " CG  ARG A  66 " =    2.473
peak=    3.316 closest distance to " O   HOH Z 172 " =    3.636
peak=    3.316 closest distance to " CB  ILE A  20 " =    1.447
peak=    3.316 closest distance to " O   HOH Z  88 " =    2.860
peak=    3.314 closest distance to " O   LYS A 290 " =    2.384
peak=    3.308 closest distance to " CB  ALA A  71 " =    1.399
peak=    3.307 closest distance to " NH2 ARG A 156 " =    1.075
peak=    3.307 closest distance to " O   MET A 105 " =    1.861
peak=    3.303 closest distance to " O   HOH Z 193 " =    1.620
peak=    3.303 closest distance to " CB  HIS A 108 " =    0.832
peak=    3.303 closest distance to " CB  LYS A 290 " =    1.095
peak=    3.292 closest distance to " O   HOH Z  21 " =    1.738
peak=    3.287 closest distance to " O   HOH Z 412 " =    2.029
peak=    3.285 closest distance to " O   HOH Z 148 " =    3.325
peak=    3.284 closest distance to " O   HOH Z 227 " =    1.680
peak=    3.278 closest distance to " O   HOH Z  40 " =    1.920
peak=    3.278 closest distance to " CD1 LEU A 228 " =    1.969
peak=    3.277 closest distance to " CD2 LEU A 297 " =    0.978
peak=    3.275 closest distance to " O   HOH Z 233 " =    1.747
peak=    3.269 closest distance to " O   HOH Z 437 " =    1.979
peak=    3.268 closest distance to " O   HOH Z 189 " =    2.591
peak=    3.264 closest distance to " O   HOH Z 118 " =    1.121
peak=    3.262 closest distance to " CB  ALA A 291 " =    1.391
peak=    3.262 closest distance to " O   HOH Z 367 " =    3.515
peak=    3.258 closest distance to " O   HOH Z 368 " =    2.594
peak=    3.252 closest distance to " OG  SER A  22 " =    2.715
peak=    3.252 closest distance to " CD  LYS A 166 " =    1.265
peak=    3.251 closest distance to " O   HOH Z 433 " =    1.819
peak=    3.248 closest distance to " CA  VAL A 126 " =    0.903
peak=    3.246 closest distance to " NH1AARG A 145 " =    1.063
peak=    3.245 closest distance to " CB  GLN A 205 " =    1.202
peak=    3.244 closest distance to " CG  MET A 185 " =    1.078
peak=    3.242 closest distance to " O   HOH Z  89 " =    1.773
peak=    3.241 closest distance to " O   HOH Z 421 " =    1.646
peak=    3.240 closest distance to " CA  ASN A 176 " =    1.108
peak=    3.240 closest distance to " O   HOH Z 336 " =    1.765
peak=    3.239 closest distance to " O   HOH Z 298 " =    4.637
peak=    3.239 closest distance to " CB  GLU A  46 " =    1.107
peak=    3.233 closest distance to " CB  ASN A 224 " =    1.008
peak=    3.233 closest distance to " CE  LYS A  48 " =    1.120
peak=    3.230 closest distance to " O   HOH Z 227 " =    1.510
peak=    3.230 closest distance to " O   HOH Z 175 " =    2.053
peak=    3.227 closest distance to " CD1 ILE A  33 " =    1.590
peak=    3.225 closest distance to " O   HOH Z 388 " =    2.015
peak=    3.225 closest distance to " O   HOH Z  85 " =    2.139
peak=    3.225 closest distance to " CZ2 TRP A 179 " =    1.702
peak=    3.222 closest distance to " CG BARG A 102 " =    1.771
peak=    3.219 closest distance to " CG2 THR A 294 " =    1.570
peak=    3.218 closest distance to " CB  TRP A 150 " =    1.462
peak=    3.212 closest distance to " N   SER A 135 " =    1.259
peak=    3.212 closest distance to " NH2BARG A 145 " =    2.019
peak=    3.205 closest distance to " CD1 ILE A 263 " =    1.317
peak=    3.203 closest distance to " CB  SER A  62 " =    1.289
peak=    3.202 closest distance to " CG1 ILE A 120 " =    1.202
peak=    3.202 closest distance to " O   HOH Z 430 " =    5.509
peak=    3.200 closest distance to " O   HOH Z 250 " =    1.363
peak=    3.200 closest distance to " O   HOH Z 128 " =    1.946
peak=    3.198 closest distance to " CA  LYS A 290 " =    1.358
peak=    3.196 closest distance to " O   HOH Z 357 " =    1.818
peak=    3.196 closest distance to " O   HOH Z 257 " =    2.235
peak=    3.194 closest distance to " CB  LYS A 117 " =    1.179
peak=    3.186 closest distance to " O   HOH Z 173 " =    2.208
peak=    3.185 closest distance to " CA  ASN A 127 " =    1.051
peak=    3.182 closest distance to " CA  GLN A 194 " =    1.238
peak=    3.181 closest distance to " CB  VAL A 268 " =    0.831
peak=    3.171 closest distance to " O   HOH Z 432 " =    1.469
peak=    3.169 closest distance to " O   HOH Z  62 " =    2.250
peak=    3.168 closest distance to " CA  THR A 221 " =    0.975
peak=    3.165 closest distance to " CA  THR A 264 " =    0.801
peak=    3.163 closest distance to " O   HOH Z 188 " =    1.999
peak=    3.163 closest distance to " CA  SER A 146 " =    1.782
peak=    3.162 closest distance to " O   HOH Z 383 " =    1.818
peak=    3.160 closest distance to " O   HOH Z 261 " =    1.525
peak=    3.157 closest distance to " CB  ASN A 215 " =    1.119
peak=    3.151 closest distance to " N   ASP A 162 " =    1.275
peak=    3.145 closest distance to " CG2 VAL A 202 " =    1.154
peak=    3.145 closest distance to " CD1 LEU A 261 " =    1.129
peak=    3.142 closest distance to " O   HOH Z 305 " =    3.525
peak=    3.140 closest distance to " O   HOH Z 419 " =    1.915
peak=    3.140 closest distance to " CB  SER A 212 " =    1.157
peak=    3.139 closest distance to " NZ  LYS A  76 " =    1.397
peak=    3.129 closest distance to " NH1 ARG A 138 " =    1.154
peak=    3.119 closest distance to " O   SER A 164 " =    1.171
peak=    3.116 closest distance to " O   HOH Z 302 " =    1.880
peak=    3.112 closest distance to " O   HOH Z 151 " =    1.714
peak=    3.111 closest distance to " O   HOH Z  49 " =    2.261
peak=    3.110 closest distance to " O   HOH Z 285 " =    3.028
peak=    3.099 closest distance to " O   HOH Z 353 " =    2.622
peak=    3.092 closest distance to " CG  LYS A  76 " =    0.999
peak=    3.092 closest distance to " C   ALA A 299 " =    0.942
peak=    3.087 closest distance to " CD2 LEU A 255 " =    1.444
peak=    3.076 closest distance to " CZ3 TRP A  85 " =    0.928
peak=    3.051 closest distance to " O   HOH Z  46 " =    1.505
peak=    3.050 closest distance to " ND1 HIS A  81 " =    1.650
peak=    3.042 closest distance to " O   HOH Z 303 " =    1.586
peak=    3.040 closest distance to " O   HOH Z  47 " =    1.695
peak=    3.027 closest distance to " O   HOH Z 151 " =    1.544

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 203         
Filter by distance & map next to the model:
   mapped sites are within: 0.629 - 5.435
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 201 from: 203
   mapped sites are within: 0.742 - 5.435

peak=   -5.160 closest distance to " CG2 VAL A 230 " =    0.742
peak=   -4.649 closest distance to " CD  ARG A 156 " =    2.034
peak=   -4.509 closest distance to " O   HOH Z 266 " =    4.779
peak=   -4.501 closest distance to " SG  CYS A 254 " =    3.247
peak=   -4.442 closest distance to " OG BSER A 134 " =    1.181
peak=   -4.266 closest distance to " O   VAL A  67 " =    2.667
peak=   -4.188 closest distance to " C   HIS A 108 " =    1.198
peak=   -4.150 closest distance to " CG  GLN A 223 " =    1.980
peak=   -4.143 closest distance to " O   HOH Z 435 " =    2.798
peak=   -4.121 closest distance to " O   HOH Z 290 " =    1.132
peak=   -4.096 closest distance to " CG2 VAL A 296 " =    1.189
peak=   -4.059 closest distance to " O   HOH Z 429 " =    1.935
peak=   -4.013 closest distance to " CB  PRO A 243 " =    2.642
peak=   -4.012 closest distance to " O   PRO A 163 " =    2.097
peak=   -4.012 closest distance to " CA  VAL A  67 " =    2.765
peak=   -3.965 closest distance to " CB  PHE A 192 " =    1.886
peak=   -3.953 closest distance to " OXT GLY A 302 " =    2.741
peak=   -3.950 closest distance to " O   HOH Z  11 " =    1.874
peak=   -3.950 closest distance to " NE2 GLN A  88 " =    1.976
peak=   -3.879 closest distance to " O   HOH Z 211 " =    1.665
peak=   -3.877 closest distance to " N   GLN A  58 " =    1.751
peak=   -3.868 closest distance to " CB  ALA A 161 " =    2.496
peak=   -3.866 closest distance to " CE2 PHE A 218 " =    2.549
peak=   -3.865 closest distance to " CG  ASP A 231 " =    0.803
peak=   -3.854 closest distance to " O   PRO A 198 " =    1.241
peak=   -3.840 closest distance to " CB  ASP A 132 " =    2.350
peak=   -3.818 closest distance to " N   THR A 157 " =    1.519
peak=   -3.810 closest distance to " N   HIS A 115 " =    2.031
peak=   -3.801 closest distance to " CE2 TYR A  30 " =    2.770
peak=   -3.800 closest distance to " O   HOH Z 114 " =    3.063
peak=   -3.790 closest distance to " O   HOH Z 389 " =    1.818
peak=   -3.785 closest distance to " O   HOH Z 166 " =    1.511
peak=   -3.781 closest distance to " CE  MET A 105 " =    2.173
peak=   -3.763 closest distance to " CD2 LEU A 300 " =    2.884
peak=   -3.762 closest distance to " CZ  PHE A  59 " =    1.481
peak=   -3.759 closest distance to " CZ  TYR A 169 " =    1.733
peak=   -3.744 closest distance to " O   HOH Z 351 " =    1.442
peak=   -3.716 closest distance to " O   HOH Z 407 " =    2.983
peak=   -3.715 closest distance to " CB  ASP A 132 " =    2.284
peak=   -3.702 closest distance to " ND2 ASN A  45 " =    1.181
peak=   -3.700 closest distance to " ND2 ASN A 187 " =    1.517
peak=   -3.692 closest distance to " O   HOH Z 231 " =    2.099
peak=   -3.689 closest distance to " OG  SER A   3 " =    1.674
peak=   -3.676 closest distance to " CG1 VAL A 112 " =    2.668
peak=   -3.668 closest distance to " O   SER A  22 " =    2.277
peak=   -3.668 closest distance to " CB  PRO A 280 " =    2.124
peak=   -3.665 closest distance to " O   HOH Z 185 " =    2.316
peak=   -3.655 closest distance to " N   ALA A 248 " =    1.586
peak=   -3.646 closest distance to " CZ3 TRP A 179 " =    1.224
peak=   -3.633 closest distance to " CB  PRO A 163 " =    2.523
peak=   -3.631 closest distance to " O   ALA A 161 " =    1.667
peak=   -3.630 closest distance to " CB  ALA A 291 " =    2.348
peak=   -3.626 closest distance to " CD1 PHE A  59 " =    1.905
peak=   -3.623 closest distance to " CD  GLN A  58 " =    1.166
peak=   -3.601 closest distance to " CG  LEU A 228 " =    1.057
peak=   -3.590 closest distance to " CD  ARG A 139 " =    1.592
peak=   -3.577 closest distance to " O   HOH Z 102 " =    1.633
peak=   -3.571 closest distance to " CB  ALA A 248 " =    2.337
peak=   -3.564 closest distance to " O   ALA A   8 " =    1.916
peak=   -3.562 closest distance to " O   HOH Z 166 " =    1.965
peak=   -3.561 closest distance to " CD1 LEU A 101 " =    2.389
peak=   -3.555 closest distance to " CD  LYS A 289 " =    2.463
peak=   -3.554 closest distance to " O   PHE A 218 " =    1.660
peak=   -3.551 closest distance to " C   MET A 188 " =    1.477
peak=   -3.548 closest distance to " NH2AARG A 275 " =    5.010
peak=   -3.538 closest distance to " OD1 ASN A  39 " =    2.185
peak=   -3.531 closest distance to " CB  ALA A  43 " =    2.271
peak=   -3.525 closest distance to " OG  SER A  97 " =    2.200
peak=   -3.522 closest distance to " O   HOH Z 103 " =    1.785
peak=   -3.517 closest distance to " CB  ASN A  39 " =    2.251
peak=   -3.511 closest distance to " O   HOH Z  13 " =    1.564
peak=   -3.508 closest distance to " N   ALA A 226 " =    1.964
peak=   -3.496 closest distance to " ND2 ASN A  45 " =    1.604
peak=   -3.495 closest distance to " O   HOH Z  47 " =    1.552
peak=   -3.486 closest distance to " NH2 ARG A  79 " =    1.909
peak=   -3.474 closest distance to " CG  GLU A   2 " =    1.973
peak=   -3.458 closest distance to " O   HOH Z 385 " =    1.983
peak=   -3.447 closest distance to " N   PHE A  59 " =    2.187
peak=   -3.446 closest distance to " C   GLN A 205 " =    1.946
peak=   -3.444 closest distance to " CG2 THR A 178 " =    2.230
peak=   -3.438 closest distance to " NZ  LYS A 119 " =    3.441
peak=   -3.437 closest distance to " O   HOH Z 198 " =    2.133
peak=   -3.434 closest distance to " O   ALA A  51 " =    1.301
peak=   -3.432 closest distance to " OG  SER A  87 " =    1.320
peak=   -3.431 closest distance to " N   SER A 276 " =    1.305
peak=   -3.430 closest distance to " CA  GLY A  98 " =    1.847
peak=   -3.424 closest distance to " O   HOH Z  43 " =    1.923
peak=   -3.423 closest distance to " CG  TRP A 266 " =    1.944
peak=   -3.422 closest distance to " N   MET A 188 " =    1.911
peak=   -3.421 closest distance to " O   HOH Z 166 " =    2.193
peak=   -3.420 closest distance to " O   SER A  95 " =    1.535
peak=   -3.399 closest distance to " C   ALA A 158 " =    1.288
peak=   -3.399 closest distance to " CG1 VAL A 230 " =    1.806
peak=   -3.397 closest distance to " O   HOH Z 423 " =    2.158
peak=   -3.395 closest distance to " O   MET A  40 " =    2.650
peak=   -3.395 closest distance to " OXT GLY A 302 " =    3.614
peak=   -3.394 closest distance to " CB  VAL A 296 " =    1.101
peak=   -3.394 closest distance to " CG  PHE A 283 " =    2.629
peak=   -3.393 closest distance to " CA  GLY A 133 " =    1.982
peak=   -3.391 closest distance to " CD1 LEU A 228 " =    2.019
peak=   -3.389 closest distance to " CB  ASP A 132 " =    2.218
peak=   -3.377 closest distance to " OD1 ASN A 148 " =    1.495
peak=   -3.377 closest distance to " O   HOH Z 348 " =    1.831
peak=   -3.374 closest distance to " O   PRO A 198 " =    1.282
peak=   -3.373 closest distance to " O   HOH Z 191 " =    5.435
peak=   -3.366 closest distance to " O   HOH Z 313 " =    1.731
peak=   -3.361 closest distance to " OG  SER A 206 " =    1.603
peak=   -3.340 closest distance to " CG1 VAL A 112 " =    2.926
peak=   -3.332 closest distance to " O   HOH Z  90 " =    2.645
peak=   -3.325 closest distance to " O   HOH Z 174 " =    4.351
peak=   -3.317 closest distance to " O   HOH Z 295 " =    1.592
peak=   -3.310 closest distance to " C   LEU A 143 " =    0.991
peak=   -3.307 closest distance to " N   GLN A  77 " =    1.709
peak=   -3.306 closest distance to " O   HOH Z 148 " =    1.819
peak=   -3.296 closest distance to " OG BSER A 134 " =    1.639
peak=   -3.293 closest distance to " O   SER A 135 " =    1.450
peak=   -3.291 closest distance to " CG  ASP A  50 " =    2.293
peak=   -3.289 closest distance to " CD2 TYR A 293 " =    2.086
peak=   -3.285 closest distance to " CA  GLY A 203 " =    2.194
peak=   -3.284 closest distance to " O   HOH Z 389 " =    4.760
peak=   -3.284 closest distance to " CA  GLY A 241 " =    3.029
peak=   -3.283 closest distance to " O   HOH Z 394 " =    1.551
peak=   -3.282 closest distance to " OD1 ASP A 191 " =    1.501
peak=   -3.281 closest distance to " O   HOH Z  38 " =    1.782
peak=   -3.280 closest distance to " CG1 VAL A 197 " =    2.174
peak=   -3.276 closest distance to " O   HOH Z  63 " =    1.289
peak=   -3.272 closest distance to " NE2 GLN A 278 " =    1.868
peak=   -3.269 closest distance to " O   HOH Z 131 " =    4.039
peak=   -3.267 closest distance to " C   ASP A 231 " =    2.443
peak=   -3.266 closest distance to " O   VAL A 174 " =    2.000
peak=   -3.264 closest distance to " O   HOH Z 417 " =    2.579
peak=   -3.262 closest distance to " CG1 VAL A 250 " =    2.676
peak=   -3.261 closest distance to " N   THR A 235 " =    1.345
peak=   -3.254 closest distance to " OG  SER A  62 " =    1.526
peak=   -3.253 closest distance to " O   HOH Z 385 " =    1.939
peak=   -3.248 closest distance to " O   HOH Z 427 " =    1.405
peak=   -3.245 closest distance to " CG2 ILE A 263 " =    2.236
peak=   -3.242 closest distance to " O   HOH Z 139 " =    3.131
peak=   -3.240 closest distance to " OD2 ASP A 191 " =    1.407
peak=   -3.240 closest distance to " O   HOH Z 210 " =    1.202
peak=   -3.235 closest distance to " O   HOH Z  11 " =    2.018
peak=   -3.233 closest distance to " O   GLY A  75 " =    1.859
peak=   -3.232 closest distance to " O   TRP A  70 " =    1.464
peak=   -3.228 closest distance to " O   HOH Z 193 " =    1.577
peak=   -3.228 closest distance to " O   HOH Z 165 " =    1.956
peak=   -3.227 closest distance to " CD2 LEU A 237 " =    2.780
peak=   -3.226 closest distance to " O   HOH Z 359 " =    3.241
peak=   -3.223 closest distance to " CD1 TYR A 247 " =    2.413
peak=   -3.223 closest distance to " O   HOH Z 372 " =    2.327
peak=   -3.220 closest distance to " OD2 ASP A 171 " =    2.270
peak=   -3.217 closest distance to " CA  ASP A 298 " =    1.064
peak=   -3.214 closest distance to " CB  ALA A 291 " =    2.120
peak=   -3.205 closest distance to " O   HOH Z 265 " =    1.831
peak=   -3.200 closest distance to " CD1 ILE A 239 " =    2.523
peak=   -3.199 closest distance to " O   HOH Z 234 " =    3.908
peak=   -3.195 closest distance to " CB  ASN A  69 " =    1.114
peak=   -3.195 closest distance to " O   HOH Z 353 " =    2.116
peak=   -3.191 closest distance to " O   GLY A  80 " =    2.553
peak=   -3.190 closest distance to " CG1 VAL A 296 " =    1.344
peak=   -3.187 closest distance to " CG2BVAL A  72 " =    2.184
peak=   -3.184 closest distance to " O   HOH Z 250 " =    1.420
peak=   -3.182 closest distance to " O   VAL A 189 " =    2.603
peak=   -3.181 closest distance to " O   SER A 210 " =    1.890
peak=   -3.180 closest distance to " O   HOH Z 313 " =    1.060
peak=   -3.179 closest distance to " O   HOH Z 411 " =    3.907
peak=   -3.175 closest distance to " ND2 ASN A 252 " =    1.770
peak=   -3.175 closest distance to " O   VAL A 125 " =    2.295
peak=   -3.175 closest distance to " CG  PRO A 163 " =    2.725
peak=   -3.173 closest distance to " O   HOH Z 405 " =    2.636
peak=   -3.168 closest distance to " OH  TYR A 214 " =    1.252
peak=   -3.167 closest distance to " OG1 THR A 178 " =    1.233
peak=   -3.165 closest distance to " O   HOH Z  52 " =    1.486
peak=   -3.160 closest distance to " O   HOH Z 139 " =    5.083
peak=   -3.159 closest distance to " O   HOH Z 243 " =    1.955
peak=   -3.159 closest distance to " N   ALA A  43 " =    2.422
peak=   -3.155 closest distance to " CD  GLN A  88 " =    1.121
peak=   -3.153 closest distance to " CA  TYR A  30 " =    2.869
peak=   -3.151 closest distance to " ND2 ASN A 249 " =    2.282
peak=   -3.147 closest distance to " CG  GLU A 277 " =    1.151
peak=   -3.146 closest distance to " O   HOH Z 200 " =    4.528
peak=   -3.140 closest distance to " CA  GLY A 133 " =    2.201
peak=   -3.139 closest distance to " O   HOH Z 407 " =    3.130
peak=   -3.133 closest distance to " O   HOH Z 421 " =    3.058
peak=   -3.131 closest distance to " OD1 ASN A 301 " =    2.068
peak=   -3.130 closest distance to " O   HOH Z 311 " =    3.615
peak=   -3.125 closest distance to " OE1 GLN A  73 " =    2.464
peak=   -3.122 closest distance to " O   HOH Z 281 " =    2.829
peak=   -3.120 closest distance to " O   ASN A 170 " =    1.912
peak=   -3.120 closest distance to " OG  SER A  26 " =    1.180
peak=   -3.110 closest distance to " CE1 HIS A  81 " =    1.510
peak=   -3.110 closest distance to " CZ2 TRP A 274 " =    0.925
peak=   -3.108 closest distance to " O   LYS A 117 " =    1.638
peak=   -3.103 closest distance to " N   VAL A  72 " =    1.613
peak=   -3.100 closest distance to " O   HOH Z 123 " =    2.328
peak=   -3.079 closest distance to " NH2 ARG A  79 " =    1.599
peak=   -3.073 closest distance to " C   LEU A 222 " =    0.788
peak=   -3.052 closest distance to " N   LYS A 289 " =    1.493
peak=   -3.050 closest distance to " O   HOH Z 417 " =    2.621
peak=   -3.044 closest distance to " CG2 VAL A 189 " =    1.989
peak=   -3.043 closest distance to " CG  GLU A 152 " =    1.512
peak=   -3.013 closest distance to " O   HOH Z 244 " =    2.071

================= 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    :  0.4348 0.4227   6.228712e+00   6.209028e+00
   1_bss:  0.4263 0.4155   6.221735e+00   6.193053e+00
   1_xyz:  0.3221 0.3436   6.021065e+00   6.059569e+00
   1_adp:  0.2590 0.2944   5.834014e+00   5.942789e+00
   1_occ:  0.2585 0.2941   5.832693e+00   5.942865e+00
   2_bss:  0.2532 0.2878   5.830099e+00   5.936794e+00
   2_xyz:  0.1721 0.2106   5.491065e+00   5.664931e+00
   2_adp:  0.1545 0.1943   5.396302e+00   5.584639e+00
   2_occ:  0.1542 0.1938   5.394910e+00   5.582783e+00
   3_bss:  0.1537 0.1938   5.394436e+00   5.581249e+00
   3_xyz:  0.1252 0.1636   5.211194e+00   5.421435e+00
   3_adp:  0.1210 0.1596   5.182755e+00   5.395068e+00
   3_occ:  0.1210 0.1594   5.182281e+00   5.394509e+00
   4_bss:  0.1213 0.1599   5.184038e+00   5.395650e+00
   4_xyz:  0.1099 0.1537   5.116917e+00   5.361233e+00
   4_adp:  0.1085 0.1541   5.111752e+00   5.361703e+00
   4_occ:  0.1085 0.1540   5.111550e+00   5.361429e+00
   5_bss:  0.1085 0.1540   5.111538e+00   5.361442e+00
   5_xyz:  0.1070 0.1539   5.106194e+00   5.362339e+00
   5_adp:  0.1065 0.1545   5.107278e+00   5.367400e+00
   5_occ:  0.1065 0.1546   5.107199e+00   5.367318e+00
   5_bss:  0.1065 0.1545   5.106972e+00   5.367037e+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:  0.355  11.143   7.641   8.515   8.465   0.000   0.000   0.000
   1_xyz:  0.355  11.143   7.641   8.515   8.465   0.000   0.000   0.000
   1_adp:  0.355  11.143   7.641   8.515   8.465   0.000   0.000   0.000
   1_occ:  0.355  11.143   7.641   8.515   8.465   0.000   0.000   0.000
   2_bss:  0.326  27.782   3.891   4.546   5.380   0.000   0.000   0.000
   2_xyz:  0.326  27.782   3.891   4.546   5.380   0.000   0.000   0.000
   2_adp:  0.326  27.782   3.891   4.546   5.380   0.000   0.000   0.000
   2_occ:  0.326  27.782   3.891   4.546   5.380   0.000   0.000   0.000
   3_bss:  0.325  33.869   2.861   3.393   4.317   0.000   0.000   0.000
   3_xyz:  0.325  33.869   2.861   3.393   4.317   0.000   0.000   0.000
   3_adp:  0.325  33.869   2.861   3.393   4.317   0.000   0.000   0.000
   3_occ:  0.325  33.869   2.861   3.393   4.317   0.000   0.000   0.000
   4_bss:  0.322  35.057   2.695   3.151   4.042   0.000   0.000   0.000
   4_xyz:  0.322  35.057   2.695   3.151   4.042   0.000   0.000   0.000
   4_adp:  0.322  35.057   2.695   3.151   4.042   0.000   0.000   0.000
   4_occ:  0.322  35.057   2.695   3.151   4.042   0.000   0.000   0.000
   5_bss:  0.322  35.057   2.704   3.125   4.054   0.000   0.000   0.000
   5_xyz:  0.322  35.057   2.704   3.125   4.054   0.000   0.000   0.000
   5_adp:  0.322  35.057   2.704   3.125   4.054   0.000   0.000   0.000
   5_occ:  0.322  35.057   2.704   3.125   4.054   0.000   0.000   0.000
   5_bss:  0.325  41.550  -0.590  -0.176   0.765   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  47.430 0.5545  0.6261    53030.939
   1_bss:  48.151 0.5425  0.7795    50372.487
   1_xyz:  36.520 0.6831  0.9609    31693.967
   1_adp:  29.518 0.7639  1.0534    22441.952
   1_occ:  29.502 0.7641  1.0527    22364.727
   2_bss:  29.193 0.7672  0.9263    21910.554
   2_xyz:  20.217 0.8595  1.0023    11171.540
   2_adp:  18.065 0.8805  1.0176     9543.300
   2_occ:  18.021 0.8809  1.0176     9496.174
   3_bss:  17.989 0.8811  0.9783     9486.834
   3_xyz:  14.627 0.9096  0.9921     6721.854
   3_adp:  14.062 0.9146  0.9945     6415.776
   3_occ:  14.051 0.9147  0.9945     6405.863
   4_bss:  14.074 0.9145  0.9856     6434.034
   4_xyz:  13.362 0.9200  0.9879     5936.253
   4_adp:  13.358 0.9202  0.9856     5947.868
   4_occ:  13.355 0.9202  0.9855     5945.117
   5_bss:  13.354 0.9202  0.9854     5945.123
   5_xyz:  13.309 0.9207  0.9852     5968.046
   5_adp:  13.395 0.9201  0.9817     6010.389
   5_occ:  13.396 0.9201  0.9816     6010.641
   5_bss:  13.386 0.9201  0.9852     6009.577
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3208e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3208e+01
   1_xyz:   1.527  0.011  0.101 17.855  0.006  4.117   1.1826e-01
   1_adp:   1.527  0.011  0.101 17.855  0.006  4.117   1.1826e-01
   1_occ:   1.527  0.011  0.101 17.855  0.006  4.117   1.1826e-01
   2_bss:   1.527  0.011  0.101 17.855  0.006  4.117   1.1826e-01
   2_xyz:   0.916  0.005  0.069 15.660  0.003  4.115   5.5035e-02
   2_adp:   0.916  0.005  0.069 15.660  0.003  4.115   5.5035e-02
   2_occ:   0.916  0.005  0.069 15.660  0.003  4.115   5.5035e-02
   3_bss:   0.916  0.005  0.069 15.660  0.003  4.115   5.5035e-02
   3_xyz:   0.947  0.005  0.074 15.670  0.003  4.117   5.5782e-02
   3_adp:   0.947  0.005  0.074 15.670  0.003  4.117   5.5782e-02
   3_occ:   0.947  0.005  0.074 15.670  0.003  4.117   5.5782e-02
   4_bss:   0.947  0.005  0.074 15.670  0.003  4.117   5.5782e-02
   4_xyz:   1.083  0.008  0.088 15.839  0.004  4.108   6.9878e-02
   4_adp:   1.083  0.008  0.088 15.839  0.004  4.108   6.9878e-02
   4_occ:   1.083  0.008  0.088 15.839  0.004  4.108   6.9878e-02
   5_bss:   1.083  0.008  0.088 15.839  0.004  4.108   6.9878e-02
   5_xyz:   1.064  0.008  0.087 15.634  0.004  4.108   6.7864e-02
   5_adp:   1.064  0.008  0.087 15.634  0.004  4.108   6.7864e-02
   5_occ:   1.064  0.008  0.087 15.634  0.004  4.108   6.7864e-02
   5_bss:   1.064  0.008  0.087 15.634  0.004  4.108   6.7864e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.8972e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.8972e+00
   1_xyz:  12.951  0.142  0.433 89.548  0.039  2.282   8.6582e-02
   1_adp:  12.951  0.142  0.433 89.548  0.039  2.282   8.6582e-02
   1_occ:  12.951  0.142  0.433 89.548  0.039  2.282   8.6582e-02
   2_bss:  12.951  0.142  0.433 89.548  0.039  2.282   8.6582e-02
   2_xyz:   6.168  0.047  0.290 85.310  0.031  2.380   4.2554e-02
   2_adp:   6.168  0.047  0.290 85.310  0.031  2.380   4.2554e-02
   2_occ:   6.168  0.047  0.290 85.310  0.031  2.380   4.2554e-02
   3_bss:   6.168  0.047  0.290 85.310  0.031  2.380   4.2554e-02
   3_xyz:   7.694  0.044  0.435 83.400  0.028  2.323   3.3421e-02
   3_adp:   7.694  0.044  0.435 83.400  0.028  2.323   3.3421e-02
   3_occ:   7.694  0.044  0.435 83.400  0.028  2.323   3.3421e-02
   4_bss:   7.694  0.044  0.435 83.400  0.028  2.323   3.3421e-02
   4_xyz:   6.632  0.046  0.639 83.452  0.036  2.249   5.4467e-02
   4_adp:   6.632  0.046  0.639 83.452  0.036  2.249   5.4467e-02
   4_occ:   6.632  0.046  0.639 83.452  0.036  2.249   5.4467e-02
   5_bss:   6.632  0.046  0.639 83.452  0.036  2.249   5.4467e-02
   5_xyz:   6.457  0.047  0.654 82.537  0.036  2.288   5.3603e-02
   5_adp:   6.457  0.047  0.654 82.537  0.036  2.288   5.3603e-02
   5_occ:   6.457  0.047  0.654 82.537  0.036  2.288   5.3603e-02
   5_bss:   6.457  0.047  0.654 82.537  0.036  2.288   5.3603e-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:  69.77   0.00  10.79  69.77   0.00   7.73  61.88   0.00  27.46
   1_occ:  69.77   0.00  10.79  69.77   0.00   7.73  61.88   0.00  27.46
   2_bss:  69.77   0.00  10.79  69.77   0.00   7.73  61.88   0.00  27.46
   2_xyz:  69.77   0.00  10.79  69.77   0.00   7.73  61.88   0.00  27.46
   2_adp:  76.47   0.00  11.39  76.47   0.00   7.53  63.57   1.39  32.43
   2_occ:  76.47   0.00  11.39  76.47   0.00   7.53  63.57   1.39  32.43
   3_bss:  76.47   0.00  11.39  76.47   0.00   7.53  63.57   1.39  32.43
   3_xyz:  76.47   0.00  11.39  76.47   0.00   7.53  63.57   1.39  32.43
   3_adp:  81.08   0.00  11.53  81.08   0.00   7.48  67.61   1.01  33.60
   3_occ:  81.08   0.00  11.53  81.08   0.00   7.48  67.61   1.01  33.60
   4_bss:  81.08   0.00  11.53  81.08   0.00   7.48  67.61   1.01  33.60
   4_xyz:  81.08   0.00  11.53  81.08   0.00   7.48  67.61   1.01  33.60
   4_adp:  82.39   0.00  11.44  82.39   0.00   7.41  68.25   1.07  33.41
   4_occ:  82.39   0.00  11.44  82.39   0.00   7.41  68.25   1.07  33.41
   5_bss:  82.39   0.00  11.44  82.39   0.00   7.41  68.25   1.07  33.41
   5_xyz:  82.39   0.00  11.44  82.39   0.00   7.41  68.25   1.07  33.41
   5_adp:  84.42   0.00  11.40  84.42   0.00   7.37  68.15   1.05  33.38
   5_occ:  84.42   0.00  11.40  84.42   0.00   7.37  68.15   1.05  33.38
   5_bss:  87.80   3.39  14.79  87.80   3.39  10.76  71.54   4.44  36.77
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.181    0.020    0.402
   1_adp:    1.181    0.020    0.402
   1_occ:    1.181    0.020    0.402
   2_bss:    1.181    0.020    0.402
   2_xyz:    1.439    0.031    0.506
   2_adp:    1.439    0.031    0.506
   2_occ:    1.439    0.031    0.506
   3_bss:    1.439    0.031    0.506
   3_xyz:    1.455    0.020    0.535
   3_adp:    1.455    0.020    0.535
   3_occ:    1.455    0.020    0.535
   4_bss:    1.455    0.020    0.535
   4_xyz:    1.515    0.041    0.559
   4_adp:    1.515    0.041    0.559
   4_occ:    1.515    0.041    0.559
   5_bss:    1.515    0.041    0.559
   5_xyz:    1.502    0.028    0.566
   5_adp:    1.502    0.028    0.566
   5_occ:    1.502    0.028    0.566
   5_bss:    1.502    0.028    0.566
------------------------------------------------------------------------

CPU time actual refinement: 339.90


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_410/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_410/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_410/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_410/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_410/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 339.75 
  Macro-tasks:
    bulk solvent and scale       = 41.54  
    individual site refinement   = 144.32 
    weights calculation          = 31.81  
    collect and process          = 6.52   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 224.29 
  Micro-tasks:
    mask                            = 1.73   
    f_calc                          = 105.06 
    alpha_beta                      = 8.09   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 117.03 
    fmodel                         = 7.13   
    r_factors                      = 0.20   
    phase_errors                   = 10.76  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 251.42 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.676 micro seconds
Total CPU time: 5.89 minutes
from_scatterers_fft:    674 calls, 104.68 s
gradients_fft:          618 calls, 102.69 s

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

# Date 2008-01-16 Time 01:32:24 PST -0800 (1200475944.54 s)
Start R-work = 0.4348, R-free = 0.4227 (no bulk solvent and anisotropic scale)
Final R-work = 0.1244, R-free = 0.1707 (no bulk solvent and anisotropic scale)

Start R-work = 0.4263, R-free = 0.4155
Final R-work = 0.1065, R-free = 0.1545