# Date 2008-01-16 Time 03:01:16 PST -0800 (1200481276.24 s)
#phil __OFF__

Command line arguments: "../1063.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 = 10875
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1063

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.3037, 47.6339, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.6339, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1984 2.02102
Completeness in resolution range: 0.977885
Completeness with d_max=infinity: 0.974771

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1984
                             d_min =   2.0210

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.6339, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1984 2.02102
Completeness in resolution range: 0.977885
Completeness with d_max=infinity: 0.974771

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1989 -  4.3239 [2101/2125]  1892   209   9.9%
  bin  2:  4.3239 -  3.4451 [2029/2048]  1826   203  10.0%
  bin  3:  3.4451 -  3.0135 [1993/2012]  1790   203  10.2%
  bin  4:  3.0135 -  2.7397 [1966/1996]  1772   194   9.9%
  bin  5:  2.7397 -  2.5443 [1963/1982]  1767   196  10.0%
  bin  6:  2.5443 -  2.3949 [1952/1977]  1756   196  10.0%
  bin  7:  2.3949 -  2.2754 [1969/1997]  1772   197  10.0%
  bin  8:  2.2754 -  2.1767 [1927/1963]  1735   192  10.0%
  bin  9:  2.1767 -  2.0931 [1917/1959]  1728   189   9.9%
  bin 10:  2.0931 -  2.0210 [1772/1973]  1592   180  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1063/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:
        1.56 -     2.23: 5
        2.23 -     2.90: 1315
        2.90 -     3.56: 4368
        3.56 -     4.23: 8999
        4.23 -     4.90: 13074
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.561 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 343 " - " O   HOH Z 277 "  2.155 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 277 " - " O   HOH Z 343 "  2.155 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  ... (remaining 27756 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_1063/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1063/model_refine_001.geo

CPU time processing inputs: 9.18


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 47.63395 87.2539 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: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4788   r_free= 0.4627   ksol= 0.00   Bsol= 0.00   scale= 0.781    |
|                                                                             |
| 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:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.277674                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1989 -  4.8223 0.99   1372  153 0.3881 0.3657      6.5794      6.5021|
|  2:  4.8223 -  3.8481 0.99   1312  145 0.3913 0.4222      6.7792      6.8687|
|  3:  3.8481 -  3.3677 0.99   1288  144 0.4362 0.4094      6.6919      6.6426|
|  4:  3.3677 -  3.0625 0.99   1278  143 0.4696 0.4069      6.5457      6.4496|
|  5:  3.0625 -  2.8445 0.99   1270  140 0.4999 0.4835      6.3761      6.3878|
|  6:  2.8445 -  2.6778 0.99   1277  140 0.5110 0.5347      6.3004      6.2369|
|  7:  2.6778 -  2.5443 0.99   1250  140 0.5128 0.4724      6.2379       6.168|
|  8:  2.5443 -  2.4340 0.98   1263  140 0.5175 0.4498      6.1952      6.1744|
|  9:  2.4340 -  2.3407 0.98   1256  138 0.5220 0.5761      6.1227      6.1764|
| 10:  2.3407 -  2.2602 0.99   1237  138 0.5353 0.5108      6.1318      6.1288|
| 11:  2.2602 -  2.1897 0.98   1249  142 0.5131 0.4878      6.0431       6.089|
| 12:  2.1897 -  2.1273 0.97   1242  134 0.5486 0.4950      6.0057      6.0152|
| 13:  2.1273 -  2.0714 1.00   1233  141 0.5247 0.5117      5.8955      5.8778|
| 14:  2.0714 -  2.0210 0.86   1103  121 0.5493 0.5392      5.8506      5.7596|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1989 -  4.8223  1372   153  0.71  33.27   0.79     0.74      66815.00|
|  2:  4.8223 -  3.8481  1312   145  0.72  33.52   0.87     0.76      97296.08|
|  3:  3.8481 -  3.3677  1288   144  0.64  40.63   0.82     0.71     103416.59|
|  4:  3.3677 -  3.0625  1278   143  0.55  47.97   0.79     0.62      91148.88|
|  5:  3.0625 -  2.8445  1270   140  0.47  53.97   0.73     0.54      74608.76|
|  6:  2.8445 -  2.6778  1277   140  0.45  56.34   0.72     0.50      66190.08|
|  7:  2.6778 -  2.5443  1250   140  0.41  58.95   0.71     0.46      61548.97|
|  8:  2.5443 -  2.4340  1263   140  0.37  62.47   0.74     0.42      59812.91|
|  9:  2.4340 -  2.3407  1256   138  0.33  65.00   0.70     0.38      56316.71|
| 10:  2.3407 -  2.2602  1237   138  0.34  64.66   0.71     0.38      51807.16|
| 11:  2.2602 -  2.1897  1249   142  0.34  64.30   0.75     0.40      46032.17|
| 12:  2.1897 -  2.1273  1242   134  0.34  64.27   0.73     0.41      42307.90|
| 13:  2.1273 -  2.0714  1233   141  0.32  66.12   0.72     0.37      37217.59|
| 14:  2.0714 -  2.0210  1103   121  0.27  69.60   0.69     0.30      31844.88|
|alpha:            min =        0.30 max =            0.76 mean =         0.50|
|beta:             min =    31844.88 max =       103416.59 mean =     63904.89|
|figures of merit: min =        0.00 max =            1.00 mean =         0.45|
|phase err.(work): min =        0.00 max =           89.98 mean =        55.38|
|phase err.(test): min =        0.00 max =           89.97 mean =        55.26|
|-----------------------------------------------------------------------------|

============================== 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 = 13.019478             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.464   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.281209              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.635   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      160 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      676 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1472 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2573 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3828 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4972 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6458 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7631 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.520 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.094    4.900  1.196 |       1.652 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.378)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.378)------------------------------------------|
|    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: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4836   r_free= 0.4669   ksol= 0.00   Bsol= 0.00   scale= 0.754    |
|                                                                             |
| 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:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.279260                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4716   r_free= 0.4535   ksol= 0.31   Bsol= 33.91   scale= 0.971   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.16,9.60,8.33,0.00,0.00,0.00); trace/3= 8.36                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.273174                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.817256             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.588   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.098807              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.895   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4716      final r-factor (work) = 0.3805          |
| start r-factor (free) = 0.4535      final r-factor (free) = 0.4011          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 91.6264 = 11.82 * 0.50 * 6.2800 + 1.00 * 54.5199                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 36.6318 = 11.82 * 0.50 * 6.1750 + 1.00 * 0.1457                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3805      final r-factor (work) = 0.3353          |
| start r-factor (free) = 0.4011      final r-factor (free) = 0.3770          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.7996 = 1.10 * 1.00 * 6.1750 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.7002 = 1.10 * 1.00 * 6.0818 + 1.00 * 0.0174                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.378)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    114.16  12.66    None  None   None       |
|    all(noH): 2823   0      0.00    114.16  12.66    None  None   None       |
|    Sol.    : 438    0      0.00    114.16  27.88    None  None   None       |
|    Mac.    : 2385   0      0.00    76.86   9.87     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 -  11.416: 1709   |   5:    57.081 -  68.497:   18        |
|      1:    11.416 -  22.832:  668   |   6:    68.497 -  79.913:    8        |
|      2:    22.832 -  34.249:  261   |   7:    79.913 -  91.329:    1        |
|      3:    34.249 -  45.665:   90   |   8:    91.329 - 102.745:    2        |
|      4:    45.665 -  57.081:   65   |   9:   102.745 - 114.162:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3353 r_free = 0.3770             target_work(ml) = 6.059         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3346 r_free = 0.3771             target_work(ml) = 6.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3346   r_free= 0.3771   ksol= 0.31   Bsol= 33.91   scale= 1.063   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.16,9.60,8.33,0.00,0.00,0.00); trace/3= 8.36                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.057813                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3333   r_free= 0.3740   ksol= 0.28   Bsol= 33.91   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.54,6.64,5.51,0.00,0.00,0.00); trace/3= 5.56                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.53 A                  |
| x-ray target function (ml) for work reflections: 6.059271                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.409961              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.020   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.532556              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.068  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3333      final r-factor (work) = 0.2507          |
| start r-factor (free) = 0.3740      final r-factor (free) = 0.3005          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.5807 = 5.41 * 0.50 * 6.0758 + 1.00 * 0.1457                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.1286 = 5.41 * 0.50 * 5.9338 + 1.00 * 0.0779                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2507      final r-factor (work) = 0.2313          |
| start r-factor (free) = 0.3005      final r-factor (free) = 0.2793          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1784 = 0.53 * 1.00 * 5.9338 + 1.00 * 0.0184                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1013 = 0.53 * 1.00 * 5.7878 + 1.00 * 0.0190                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.378)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    114.53  12.54    None  None   None       |
|    all(noH): 2823   0      0.00    114.53  12.54    None  None   None       |
|    Sol.    : 438    0      0.00    114.53  32.81    None  None   None       |
|    Mac.    : 2385   0      0.00    78.74   8.82     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:     0.000 -  11.453: 1847   |   5:    57.267 -  68.720:   32        |
|      1:    11.453 -  22.907:  528   |   6:    68.720 -  80.173:   10        |
|      2:    22.907 -  34.360:  207   |   7:    80.173 -  91.626:    1        |
|      3:    34.360 -  45.813:  121   |   8:    91.626 - 103.080:    1        |
|      4:    45.813 -  57.267:   75   |   9:   103.080 - 114.533:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2313 r_free = 0.2793             target_work(ml) = 5.765         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2310 r_free = 0.2798             target_work(ml) = 5.764         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2310   r_free= 0.2798   ksol= 0.28   Bsol= 33.91   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.54,6.64,5.51,0.00,0.00,0.00); trace/3= 5.56                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.764381                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2297   r_free= 0.2787   ksol= 0.31   Bsol= 66.36   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.06,4.31,4.04,0.00,0.00,0.00); trace/3= 3.80                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.764180                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.573927              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.072  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.347093              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 107.849  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2297      final r-factor (work) = 0.1689          |
| start r-factor (free) = 0.2787      final r-factor (free) = 0.2108          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.4237 = 3.57 * 0.50 * 5.7896 + 1.00 * 0.0779                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1439 = 3.57 * 0.50 * 5.6356 + 1.00 * 0.0733                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1689      final r-factor (work) = 0.1544          |
| start r-factor (free) = 0.2108      final r-factor (free) = 0.1966          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9989 = 0.35 * 1.00 * 5.6356 + 1.00 * 0.0428                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8984 = 0.35 * 1.00 * 5.4349 + 1.00 * 0.0120                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.378)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    108.32  12.69    None  None   None       |
|    all(noH): 2823   0      0.00    108.32  12.69    None  None   None       |
|    Sol.    : 438    0      0.78    108.32  36.03    None  None   None       |
|    Mac.    : 2385   0      0.00    79.20   8.40     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.832: 1885   |   5:    54.162 -  64.995:   58        |
|      1:    10.832 -  21.665:  461   |   6:    64.995 -  75.827:   15        |
|      2:    21.665 -  32.497:  156   |   7:    75.827 -  86.659:    4        |
|      3:    32.497 -  43.330:  128   |   8:    86.659 -  97.492:    1        |
|      4:    43.330 -  54.162:  114   |   9:    97.492 - 108.324:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1544 r_free = 0.1966             target_work(ml) = 5.404         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1542 r_free = 0.1965             target_work(ml) = 5.403         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1542   r_free= 0.1965   ksol= 0.31   Bsol= 66.36   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.06,4.31,4.04,0.00,0.00,0.00); trace/3= 3.80                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.403449                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1542   r_free= 0.1964   ksol= 0.33   Bsol= 66.36   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.46,3.18,3.70,0.00,0.00,0.00); trace/3= 3.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.403443                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.801017              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.142  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.536214              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 156.437  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1542      final r-factor (work) = 0.1306          |
| start r-factor (free) = 0.1964      final r-factor (free) = 0.1763          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6872 = 2.80 * 0.50 * 5.4365 + 1.00 * 0.0733                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5421 = 2.80 * 0.50 * 5.3310 + 1.00 * 0.0761                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1306      final r-factor (work) = 0.1261          |
| start r-factor (free) = 0.1763      final r-factor (free) = 0.1746          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8704 = 0.54 * 1.00 * 5.3310 + 1.00 * 0.0119                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9742 = 0.54 * 1.00 * 5.2538 + 1.00 * 0.1570                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.378)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.78  12.66    None  None   None       |
|    all(noH): 2823   0      0.00    103.78  12.66    None  None   None       |
|    Sol.    : 438    0      1.36    103.78  36.87    None  None   None       |
|    Mac.    : 2385   0      0.00    80.34   8.22     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 -  10.378: 1854   |   5:    51.888 -  62.265:   73        |
|      1:    10.378 -  20.755:  473   |   6:    62.265 -  72.643:   20        |
|      2:    20.755 -  31.133:  154   |   7:    72.643 -  83.020:    8        |
|      3:    31.133 -  41.510:  117   |   8:    83.020 -  93.398:    1        |
|      4:    41.510 -  51.888:  122   |   9:    93.398 - 103.775:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1261 r_free = 0.1746             target_work(ml) = 5.247         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1260 r_free = 0.1744             target_work(ml) = 5.247         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1260   r_free= 0.1744   ksol= 0.33   Bsol= 66.36   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.46,3.18,3.70,0.00,0.00,0.00); trace/3= 3.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.246720                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1261   r_free= 0.1745   ksol= 0.33   Bsol= 64.15   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.47,3.00,3.75,0.00,0.00,0.00); trace/3= 3.07                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.247395                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.222899              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 139.964  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.603120              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.495   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1261      final r-factor (work) = 0.1179          |
| start r-factor (free) = 0.1745      final r-factor (free) = 0.1666          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.5419 = 3.22 * 0.50 * 5.2535 + 1.00 * 0.0762                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4946 = 3.22 * 0.50 * 5.2185 + 1.00 * 0.0853                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1179      final r-factor (work) = 0.1167          |
| start r-factor (free) = 0.1666      final r-factor (free) = 0.1674          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 18.8213 = 3.60 * 1.00 * 5.2185 + 1.00 * 0.0186                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 18.7719 = 3.60 * 1.00 * 5.1888 + 1.00 * 0.0760                              |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.378)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.41   12.79    None  None   None       |
|    all(noH): 2823   0      0.00    97.41   12.79    None  None   None       |
|    Sol.    : 438    0      1.13    97.41   37.84    None  None   None       |
|    Mac.    : 2385   0      0.00    87.49   8.19     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.741: 1798   |   5:    48.704 -  58.444:   96        |
|      1:     9.741 -  19.482:  500   |   6:    58.444 -  68.185:   42        |
|      2:    19.482 -  29.222:  148   |   7:    68.185 -  77.926:   19        |
|      3:    29.222 -  38.963:  114   |   8:    77.926 -  87.667:    7        |
|      4:    38.963 -  48.704:   98   |   9:    87.667 -  97.407:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1167 r_free = 0.1674             target_work(ml) = 5.194         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1166 r_free = 0.1674             target_work(ml) = 5.194         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1166   r_free= 0.1674   ksol= 0.33   Bsol= 64.15   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.47,3.00,3.75,0.00,0.00,0.00); trace/3= 3.07                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.194114                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1989 -  4.8223 0.99   1372  153 0.1014 0.1335      5.4126      5.5446|
|  2:  4.8223 -  3.8481 0.99   1312  145 0.0852 0.1093      5.4439      5.6344|
|  3:  3.8481 -  3.3677 0.99   1288  144 0.1066 0.1544      5.4976      5.8856|
|  4:  3.3677 -  3.0625 0.99   1278  143 0.1232 0.1604       5.483      5.6456|
|  5:  3.0625 -  2.8445 0.99   1270  140 0.1389 0.1833      5.3957      5.5747|
|  6:  2.8445 -  2.6778 0.99   1277  140 0.1290 0.2060      5.2901      5.5586|
|  7:  2.6778 -  2.5443 0.99   1250  140 0.1348 0.1872      5.2309      5.4675|
|  8:  2.5443 -  2.4340 0.98   1263  140 0.1269 0.1754      5.1523      5.4076|
|  9:  2.4340 -  2.3407 0.98   1256  138 0.1225 0.1905      5.0986      5.3509|
| 10:  2.3407 -  2.2602 0.99   1237  138 0.1214 0.2007      5.0586      5.3308|
| 11:  2.2602 -  2.1897 0.98   1249  142 0.1219 0.1805      5.0119      5.2953|
| 12:  2.1897 -  2.1273 0.97   1242  134 0.1196 0.1852      4.9491      5.2792|
| 13:  2.1273 -  2.0714 1.00   1233  141 0.1176 0.1757      4.8526      5.0974|
| 14:  2.0714 -  2.0210 0.86   1103  121 0.1108 0.1972       4.724       5.048|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1989 -  4.8223  1372   153  0.94   9.64   0.96     0.94       8005.89|
|  2:  4.8223 -  3.8481  1312   145  0.95   8.21   1.00     0.98       9343.20|
|  3:  3.8481 -  3.3677  1288   144  0.93  11.29   1.01     1.01      10877.10|
|  4:  3.3677 -  3.0625  1278   143  0.92  13.94   1.00     0.98      10889.36|
|  5:  3.0625 -  2.8445  1270   140  0.89  17.15   0.99     0.97       9692.94|
|  6:  2.8445 -  2.6778  1277   140  0.89  17.22   0.98     0.95       8391.90|
|  7:  2.6778 -  2.5443  1250   140  0.89  17.24   0.98     0.95       7248.20|
|  8:  2.5443 -  2.4340  1263   140  0.90  16.33   0.97     0.94       6237.37|
|  9:  2.4340 -  2.3407  1256   138  0.90  16.83   0.99     0.94       5829.65|
| 10:  2.3407 -  2.2602  1237   138  0.89  17.28   0.98     0.93       5368.98|
| 11:  2.2602 -  2.1897  1249   142  0.89  17.74   0.97     0.92       5016.25|
| 12:  2.1897 -  2.1273  1242   134  0.90  16.30   0.98     0.96       4557.00|
| 13:  2.1273 -  2.0714  1233   141  0.90  16.66   0.98     0.96       3834.71|
| 14:  2.0714 -  2.0210  1103   121  0.90  16.12   0.94     0.90       2891.81|
|alpha:            min =        0.90 max =            1.01 mean =         0.95|
|beta:             min =     2891.81 max =        10889.36 mean =      7086.76|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.91 mean =        15.06|
|phase err.(test): min =        0.00 max =           89.35 mean =        14.47|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1165   r_free= 0.1673   ksol= 0.32   Bsol= 64.64   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.56,-0.14,0.71,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.194070                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1165   r_free= 0.1673   ksol= 0.32   Bsol= 64.64   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.56,-0.14,0.71,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.194070                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1989 -  4.8223 0.99   1372  153 0.1012 0.1335      5.4109      5.5444|
|  2:  4.8223 -  3.8481 0.99   1312  145 0.0852 0.1091      5.4438      5.6333|
|  3:  3.8481 -  3.3677 0.99   1288  144 0.1066 0.1544      5.4975      5.8861|
|  4:  3.3677 -  3.0625 0.99   1278  143 0.1233 0.1604      5.4833      5.6459|
|  5:  3.0625 -  2.8445 0.99   1270  140 0.1391 0.1835      5.3961      5.5749|
|  6:  2.8445 -  2.6778 0.99   1277  140 0.1290 0.2059      5.2903      5.5581|
|  7:  2.6778 -  2.5443 0.99   1250  140 0.1349 0.1874      5.2311      5.4683|
|  8:  2.5443 -  2.4340 0.98   1263  140 0.1270 0.1754      5.1526      5.4076|
|  9:  2.4340 -  2.3407 0.98   1256  138 0.1225 0.1905      5.0985      5.3509|
| 10:  2.3407 -  2.2602 0.99   1237  138 0.1214 0.2007      5.0589      5.3311|
| 11:  2.2602 -  2.1897 0.98   1249  142 0.1219 0.1806       5.012      5.2955|
| 12:  2.1897 -  2.1273 0.97   1242  134 0.1196 0.1851      4.9492      5.2793|
| 13:  2.1273 -  2.0714 1.00   1233  141 0.1176 0.1756      4.8524      5.0977|
| 14:  2.0714 -  2.0210 0.86   1103  121 0.1109 0.1969      4.7237       5.047|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1989 -  4.8223  1372   153  0.94   9.65   0.96     0.94       8008.37|
|  2:  4.8223 -  3.8481  1312   145  0.95   8.22   1.00     0.98       9341.91|
|  3:  3.8481 -  3.3677  1288   144  0.93  11.29   1.02     1.01      10874.50|
|  4:  3.3677 -  3.0625  1278   143  0.92  13.95   1.01     0.98      10894.67|
|  5:  3.0625 -  2.8445  1270   140  0.89  17.15   1.00     0.97       9696.80|
|  6:  2.8445 -  2.6778  1277   140  0.89  17.23   0.98     0.95       8394.82|
|  7:  2.6778 -  2.5443  1250   140  0.89  17.24   0.98     0.96       7250.08|
|  8:  2.5443 -  2.4340  1263   140  0.90  16.33   0.98     0.95       6236.72|
|  9:  2.4340 -  2.3407  1256   138  0.90  16.83   1.00     0.95       5832.22|
| 10:  2.3407 -  2.2602  1237   138  0.89  17.28   0.99     0.94       5369.82|
| 11:  2.2602 -  2.1897  1249   142  0.89  17.74   0.98     0.93       5019.56|
| 12:  2.1897 -  2.1273  1242   134  0.90  16.31   0.99     0.97       4558.89|
| 13:  2.1273 -  2.0714  1233   141  0.90  16.65   0.99     0.97       3832.58|
| 14:  2.0714 -  2.0210  1103   121  0.90  16.11   0.96     0.91       2886.79|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     2886.79 max =        10894.67 mean =      7087.78|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        15.07|
|phase err.(test): min =        0.00 max =           89.35 mean =        14.49|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.378)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.28    100.69  16.07    None  None   None       |
|    all(noH): 2823   0      3.28    100.69  16.07    None  None   None       |
|    Sol.    : 438    0      4.42    100.69  41.12    None  None   None       |
|    Mac.    : 2385   0      3.28    90.77   11.47    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:     3.284 -  13.025: 1798   |   5:    51.988 -  61.729:   96        |
|      1:    13.025 -  22.766:  500   |   6:    61.729 -  71.470:   42        |
|      2:    22.766 -  32.507:  148   |   7:    71.470 -  81.210:   19        |
|      3:    32.507 -  42.247:  114   |   8:    81.210 -  90.951:    7        |
|      4:    42.247 -  51.988:   98   |   9:    90.951 - 100.692:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 336         
Filter by distance & map next to the model:
   mapped sites are within: 0.283 - 5.877
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 329 from: 336
   mapped sites are within: 0.729 - 5.877

peak=    9.660 closest distance to " CG2 VAL A 230 " =    1.381
peak=    6.132 closest distance to " CG2 VAL A 296 " =    1.050
peak=    6.099 closest distance to " O   HOH Z 111 " =    2.235
peak=    6.081 closest distance to " CG  LEU A   5 " =    1.129
peak=    5.557 closest distance to " CG  LEU A 228 " =    1.166
peak=    5.411 closest distance to " CD1AILE A 234 " =    1.131
peak=    5.394 closest distance to " CB  GLN A 223 " =    1.378
peak=    5.292 closest distance to " CB  VAL A 296 " =    1.081
peak=    5.185 closest distance to " CB  SER A  63 " =    1.282
peak=    4.868 closest distance to " CG  PRO A  54 " =    1.275
peak=    4.802 closest distance to " CB  VAL A 230 " =    1.230
peak=    4.790 closest distance to " CB  GLN A 183 " =    1.306
peak=    4.599 closest distance to " CG  PRO A 280 " =    0.893
peak=    4.597 closest distance to " O   HOH Z 232 " =    2.265
peak=    4.537 closest distance to " CB  GLU A 277 " =    3.764
peak=    4.508 closest distance to " CZ  PHE A 218 " =    1.108
peak=    4.460 closest distance to " NE2 GLN A  11 " =    1.115
peak=    4.443 closest distance to " O   HOH Z 369 " =    2.162
peak=    4.409 closest distance to " CB  PRO A  54 " =    0.868
peak=    4.387 closest distance to " O   HOH Z 433 " =    1.643
peak=    4.321 closest distance to " CG  PRO A 198 " =    1.194
peak=    4.306 closest distance to " CB  ARG A 190 " =    1.644
peak=    4.271 closest distance to " CA  TYR A  30 " =    0.952
peak=    4.258 closest distance to " CB  ARG A  79 " =    1.454
peak=    4.257 closest distance to " O   HOH Z 184 " =    1.560
peak=    4.257 closest distance to " O   HOH Z 403 " =    1.745
peak=    4.223 closest distance to " CD2 LEU A   5 " =    1.006
peak=    4.220 closest distance to " O   HOH Z 210 " =    1.040
peak=    4.194 closest distance to " O   HOH Z 425 " =    1.498
peak=    4.194 closest distance to " O   HOH Z 265 " =    2.131
peak=    4.191 closest distance to " CG  ARG A 138 " =    1.206
peak=    4.181 closest distance to " O   HOH Z  63 " =    1.942
peak=    4.168 closest distance to " CB  ARG A 275 " =    0.896
peak=    4.167 closest distance to " O   HOH Z 368 " =    2.385
peak=    4.159 closest distance to " CG  PRO A 213 " =    1.179
peak=    4.152 closest distance to " O   SER A  87 " =    2.287
peak=    4.149 closest distance to " CB  GLU A 128 " =    1.201
peak=    4.148 closest distance to " O   HOH Z 298 " =    1.961
peak=    4.143 closest distance to " CB  ASP A 140 " =    0.982
peak=    4.098 closest distance to " CB  TRP A 266 " =    1.017
peak=    4.080 closest distance to " CA  ALA A  51 " =    0.990
peak=    4.068 closest distance to " O   HOH Z 423 " =    1.779
peak=    4.065 closest distance to " CD  ARG A  66 " =    2.595
peak=    4.062 closest distance to " O   HOH Z 411 " =    3.762
peak=    4.060 closest distance to " O   PRO A 198 " =    1.543
peak=    4.011 closest distance to " O   HOH Z 131 " =    2.402
peak=    4.002 closest distance to " O   HOH Z 234 " =    3.720
peak=    3.986 closest distance to " OD1 ASN A  69 " =    2.584
peak=    3.982 closest distance to " O   HOH Z 280 " =    2.834
peak=    3.976 closest distance to " CB  TYR A 169 " =    0.759
peak=    3.958 closest distance to " OG BSER A 164 " =    2.058
peak=    3.957 closest distance to " O   HOH Z 247 " =    1.465
peak=    3.941 closest distance to " O   HOH Z 102 " =    1.399
peak=    3.929 closest distance to " O   HOH Z 134 " =    1.596
peak=    3.919 closest distance to " O   HOH Z 163 " =    1.702
peak=    3.918 closest distance to " CB  ASN A 148 " =    1.422
peak=    3.905 closest distance to " CG2 THR A 221 " =    1.111
peak=    3.905 closest distance to " CB  VAL A 202 " =    1.617
peak=    3.905 closest distance to " O   HOH Z 316 " =    3.149
peak=    3.891 closest distance to " CG1 ILE A  33 " =    1.219
peak=    3.889 closest distance to " O   HOH Z 427 " =    3.136
peak=    3.888 closest distance to " O   HOH Z  48 " =    1.843
peak=    3.878 closest distance to " CD  LYS A 166 " =    1.336
peak=    3.876 closest distance to " CA  ALA A 295 " =    1.090
peak=    3.866 closest distance to " O   HOH Z 303 " =    2.280
peak=    3.862 closest distance to " O   HOH Z 287 " =    1.922
peak=    3.849 closest distance to " O   HOH Z  49 " =    1.142
peak=    3.847 closest distance to " CG  PRO A 243 " =    1.155
peak=    3.846 closest distance to " O   HOH Z  44 " =    2.095
peak=    3.843 closest distance to " O   HOH Z 359 " =    1.583
peak=    3.837 closest distance to " O   HOH Z   9 " =    2.235
peak=    3.829 closest distance to " NH1AARG A 145 " =    1.232
peak=    3.829 closest distance to " CG1 VAL A 153 " =    1.062
peak=    3.825 closest distance to " O   HOH Z 285 " =    2.767
peak=    3.825 closest distance to " O   HOH Z  78 " =    1.777
peak=    3.821 closest distance to " O   HOH Z 126 " =    1.629
peak=    3.815 closest distance to " O   HOH Z 383 " =    2.236
peak=    3.802 closest distance to " O   HOH Z  61 " =    1.542
peak=    3.799 closest distance to " O   HOH Z  80 " =    1.841
peak=    3.788 closest distance to " CZ  PHE A 192 " =    0.988
peak=    3.776 closest distance to " CB  ALA A   9 " =    1.661
peak=    3.776 closest distance to " O   ASP A 124 " =    1.129
peak=    3.768 closest distance to " C   ILE A 106 " =    1.904
peak=    3.760 closest distance to " O   ALA A 158 " =    1.370
peak=    3.755 closest distance to " O   HOH Z 422 " =    2.699
peak=    3.746 closest distance to " NH2 ARG A 156 " =    1.095
peak=    3.745 closest distance to " O   HOH Z 368 " =    3.619
peak=    3.737 closest distance to " ND2 ASN A 249 " =    1.900
peak=    3.734 closest distance to " CA  GLY A 267 " =    0.729
peak=    3.729 closest distance to " O   HOH Z  43 " =    2.014
peak=    3.728 closest distance to " O   HOH Z 214 " =    2.457
peak=    3.726 closest distance to " O   HOH Z 128 " =    1.700
peak=    3.713 closest distance to " CD1 LEU A  96 " =    0.734
peak=    3.707 closest distance to " NZ  LYS A 117 " =    3.208
peak=    3.692 closest distance to " CD2 TRP A 179 " =    1.321
peak=    3.688 closest distance to " O   HOH Z 261 " =    1.763
peak=    3.687 closest distance to " OD1 ASN A 217 " =    1.632
peak=    3.682 closest distance to " O   HOH Z 371 " =    3.004
peak=    3.680 closest distance to " CB BVAL A  41 " =    1.231
peak=    3.678 closest distance to " O   HOH Z  56 " =    1.667
peak=    3.670 closest distance to " CB  GLU A 152 " =    1.182
peak=    3.669 closest distance to " CD  ARG A 269 " =    0.906
peak=    3.662 closest distance to " O   HOH Z 158 " =    3.053
peak=    3.654 closest distance to " CD1 LEU A   5 " =    1.359
peak=    3.648 closest distance to " CD2 LEU A 228 " =    1.082
peak=    3.648 closest distance to " CB  GLN A  89 " =    1.117
peak=    3.642 closest distance to " CB  TRP A 179 " =    1.416
peak=    3.640 closest distance to " O   HOH Z 346 " =    1.574
peak=    3.638 closest distance to " CA  ALA A 160 " =    0.910
peak=    3.637 closest distance to " CD ALYS A 290 " =    1.055
peak=    3.631 closest distance to " O   HOH Z 393 " =    3.851
peak=    3.623 closest distance to " CB  ASN A 142 " =    1.118
peak=    3.623 closest distance to " CB  ALA A 291 " =    1.391
peak=    3.619 closest distance to " O   HOH Z 126 " =    2.083
peak=    3.615 closest distance to " CB  ASN A  39 " =    0.850
peak=    3.613 closest distance to " CE  LYS A  76 " =    0.791
peak=    3.613 closest distance to " O   HOH Z  98 " =    1.794
peak=    3.611 closest distance to " ND2 ASN A 187 " =    1.529
peak=    3.601 closest distance to " O   HOH Z 189 " =    3.081
peak=    3.601 closest distance to " CB  SER A   3 " =    1.383
peak=    3.595 closest distance to " CD1 LEU A 300 " =    1.247
peak=    3.595 closest distance to " O   HOH Z  68 " =    1.811
peak=    3.593 closest distance to " CA  VAL A 125 " =    1.387
peak=    3.589 closest distance to " O   HOH Z  57 " =    1.448
peak=    3.587 closest distance to " OD2 ASP A 298 " =    3.847
peak=    3.585 closest distance to " O   ALA A 165 " =    1.405
peak=    3.583 closest distance to " O   HOH Z  19 " =    1.898
peak=    3.581 closest distance to " O   HOH Z 193 " =    1.936
peak=    3.580 closest distance to " CA  ASP A 191 " =    0.841
peak=    3.578 closest distance to " O   HOH Z 227 " =    1.736
peak=    3.577 closest distance to " O   HOH Z 117 " =    2.134
peak=    3.574 closest distance to " O   HOH Z 250 " =    1.384
peak=    3.571 closest distance to " O   HOH Z 193 " =    2.318
peak=    3.568 closest distance to " CB  GLU A  46 " =    0.971
peak=    3.563 closest distance to " O   HOH Z  88 " =    3.270
peak=    3.553 closest distance to " CB  VAL A 265 " =    1.258
peak=    3.553 closest distance to " CG  GLU A  37 " =    0.876
peak=    3.548 closest distance to " CA  ILE A 106 " =    0.751
peak=    3.547 closest distance to " CZ3 TRP A 266 " =    1.127
peak=    3.545 closest distance to " O   HOH Z 402 " =    1.492
peak=    3.543 closest distance to " CA  VAL A  41 " =    0.801
peak=    3.538 closest distance to " CG  MET A 185 " =    1.319
peak=    3.532 closest distance to " CD  ARG A  66 " =    2.459
peak=    3.531 closest distance to " CA  ALA A  21 " =    1.227
peak=    3.531 closest distance to " CD  ARG A 159 " =    0.765
peak=    3.530 closest distance to " O   HOH Z 437 " =    1.873
peak=    3.527 closest distance to " O   HOH Z  40 " =    1.721
peak=    3.524 closest distance to " CE1 TYR A 186 " =    1.279
peak=    3.521 closest distance to " O   HOH Z 313 " =    1.807
peak=    3.519 closest distance to " NH2 ARG A  79 " =    1.361
peak=    3.515 closest distance to " CA  ARG A 195 " =    1.171
peak=    3.509 closest distance to " O   HOH Z 133 " =    2.285
peak=    3.509 closest distance to " NE2 GLN A  77 " =    3.302
peak=    3.508 closest distance to " CB  MET A  40 " =    0.774
peak=    3.508 closest distance to " O   HOH Z 203 " =    1.905
peak=    3.505 closest distance to " O   HOH Z 271 " =    2.711
peak=    3.498 closest distance to " CA  THR A 264 " =    0.730
peak=    3.494 closest distance to " CG  LEU A 167 " =    1.155
peak=    3.493 closest distance to " CB  ALA A 248 " =    1.141
peak=    3.487 closest distance to " NZ  LYS A  48 " =    1.353
peak=    3.476 closest distance to " CB  PRO A  54 " =    1.380
peak=    3.472 closest distance to " O   HOH Z 147 " =    1.734
peak=    3.464 closest distance to " CB  LEU A 143 " =    1.248
peak=    3.455 closest distance to " O   HOH Z 142 " =    1.441
peak=    3.449 closest distance to " OE1 GLN A  11 " =    1.830
peak=    3.447 closest distance to " CB  TYR A 247 " =    0.987
peak=    3.447 closest distance to " CZ3 TRP A  85 " =    0.940
peak=    3.442 closest distance to " O   HOH Z 273 " =    3.113
peak=    3.441 closest distance to " CA  SER A  87 " =    1.044
peak=    3.436 closest distance to " CA  LEU A 282 " =    1.132
peak=    3.436 closest distance to " CA  THR A 221 " =    0.880
peak=    3.434 closest distance to " O   HOH Z   4 " =    1.765
peak=    3.433 closest distance to " OG BSER A 134 " =    2.830
peak=    3.432 closest distance to " CA  ARG A  36 " =    1.144
peak=    3.432 closest distance to " O   HOH Z 180 " =    2.148
peak=    3.428 closest distance to " O   HOH Z 326 " =    2.320
peak=    3.421 closest distance to " CA  TYR A 116 " =    1.335
peak=    3.417 closest distance to " CB  TRP A 150 " =    1.438
peak=    3.415 closest distance to " O   HOH Z 133 " =    1.715
peak=    3.410 closest distance to " CA  MET A 105 " =    1.003
peak=    3.409 closest distance to " O   HOH Z 124 " =    1.931
peak=    3.408 closest distance to " O   HOH Z 391 " =    2.990
peak=    3.403 closest distance to " O   HOH Z 248 " =    1.616
peak=    3.402 closest distance to " CB  ASN A 187 " =    1.045
peak=    3.401 closest distance to " O   HOH Z 141 " =    1.745
peak=    3.400 closest distance to " OE1 GLU A   2 " =    1.841
peak=    3.397 closest distance to " CB  THR A  31 " =    1.643
peak=    3.396 closest distance to " O   HOH Z 125 " =    4.019
peak=    3.393 closest distance to " CA  ASP A 140 " =    1.270
peak=    3.388 closest distance to " CB  LYS A 117 " =    1.164
peak=    3.386 closest distance to " CG AARG A 275 " =    1.218
peak=    3.384 closest distance to " CG2 ILE A 234 " =    0.878
peak=    3.377 closest distance to " CD  ARG A 195 " =    0.950
peak=    3.374 closest distance to " O   HOH Z 403 " =    1.387
peak=    3.372 closest distance to " O   HOH Z 112 " =    1.656
peak=    3.366 closest distance to " O   HOH Z 258 " =    2.062
peak=    3.364 closest distance to " O  BHOH Z 338 " =    2.354
peak=    3.364 closest distance to " N   ILE A  33 " =    1.037
peak=    3.360 closest distance to " O   PRO A 213 " =    1.612
peak=    3.357 closest distance to " O   HOH Z 199 " =    1.671
peak=    3.354 closest distance to " CG2 THR A  42 " =    0.792
peak=    3.350 closest distance to " O   HOH Z 245 " =    1.324
peak=    3.349 closest distance to " CB  LEU A  83 " =    0.810
peak=    3.346 closest distance to " O   HOH Z 193 " =    1.700
peak=    3.346 closest distance to " CB  SER A 273 " =    0.860
peak=    3.343 closest distance to " O   HOH Z 154 " =    1.325
peak=    3.340 closest distance to " O   HOH Z  21 " =    1.758
peak=    3.337 closest distance to " CB  THR A  82 " =    1.421
peak=    3.331 closest distance to " CA  LYS A 117 " =    1.224
peak=    3.331 closest distance to " CG2 ILE A  20 " =    1.439
peak=    3.331 closest distance to " CA  ALA A 100 " =    1.028
peak=    3.330 closest distance to " O   GLN A 278 " =    1.266
peak=    3.329 closest distance to " CD2 LEU A 297 " =    0.935
peak=    3.328 closest distance to " O   HOH Z 130 " =    2.306
peak=    3.310 closest distance to " N   ASN A  39 " =    1.296
peak=    3.310 closest distance to " O   HOH Z 392 " =    1.339
peak=    3.309 closest distance to " CB  LEU A 228 " =    1.223
peak=    3.306 closest distance to " CB  ALA A  43 " =    0.823
peak=    3.306 closest distance to " O   HOH Z 109 " =    2.400
peak=    3.306 closest distance to " O   THR A 220 " =    1.239
peak=    3.302 closest distance to " O   HOH Z 435 " =    1.874
peak=    3.298 closest distance to " CA  GLN A  88 " =    1.292
peak=    3.296 closest distance to " O   HOH Z  63 " =    1.055
peak=    3.293 closest distance to " CG1 ILE A  49 " =    1.610
peak=    3.290 closest distance to " CZ  PHE A  38 " =    1.263
peak=    3.287 closest distance to " O   HOH Z 327 " =    2.388
peak=    3.285 closest distance to " O   TRP A 274 " =    1.925
peak=    3.271 closest distance to " CB  ALA A 100 " =    1.367
peak=    3.266 closest distance to " CB  ALA A 242 " =    0.939
peak=    3.265 closest distance to " O   HOH Z 420 " =    5.877
peak=    3.265 closest distance to " OG  SER A 245 " =    1.583
peak=    3.264 closest distance to " CG1BVAL A  72 " =    1.726
peak=    3.261 closest distance to " CB  SER A 216 " =    0.881
peak=    3.257 closest distance to " O   HOH Z 116 " =    1.840
peak=    3.256 closest distance to " CZ3 TRP A  92 " =    1.304
peak=    3.256 closest distance to " CG ALYS A 290 " =    1.073
peak=    3.255 closest distance to " O   HOH Z 197 " =    1.974
peak=    3.253 closest distance to " O   HOH Z 301 " =    1.930
peak=    3.252 closest distance to " O   HOH Z 261 " =    1.751
peak=    3.251 closest distance to " CG BARG A 275 " =    1.383
peak=    3.251 closest distance to " O   HOH Z 139 " =    4.815
peak=    3.249 closest distance to " O   HOH Z 357 " =    2.609
peak=    3.244 closest distance to " O   HOH Z 295 " =    1.554
peak=    3.242 closest distance to " CB  THR A  52 " =    0.862
peak=    3.242 closest distance to " O   HOH Z 272 " =    1.902
peak=    3.240 closest distance to " ND2 ASN A 301 " =    1.730
peak=    3.239 closest distance to " CA  ALA A 158 " =    1.257
peak=    3.236 closest distance to " O   ASN A  74 " =    1.573
peak=    3.235 closest distance to " CB  ALA A 137 " =    1.157
peak=    3.232 closest distance to " CA  ASN A 217 " =    1.283
peak=    3.232 closest distance to " O   HOH Z 327 " =    1.730
peak=    3.228 closest distance to " CA  ALA A 291 " =    0.938
peak=    3.228 closest distance to " O   HOH Z 368 " =    4.237
peak=    3.227 closest distance to " CA  GLU A  46 " =    0.792
peak=    3.225 closest distance to " N   ASP A 162 " =    1.306
peak=    3.223 closest distance to " O   HOH Z 197 " =    2.497
peak=    3.217 closest distance to " OG  SER A  22 " =    2.918
peak=    3.211 closest distance to " O   HOH Z 281 " =    4.799
peak=    3.208 closest distance to " C   ALA A 299 " =    0.959
peak=    3.206 closest distance to " O   HOH Z 357 " =    2.135
peak=    3.206 closest distance to " O   HOH Z 213 " =    1.709
peak=    3.204 closest distance to " CD  PRO A  54 " =    1.151
peak=    3.204 closest distance to " O   HOH Z 329 " =    4.030
peak=    3.201 closest distance to " O   HOH Z 156 " =    2.610
peak=    3.200 closest distance to " CB  ARG A 139 " =    0.838
peak=    3.199 closest distance to " CB  ALA A 295 " =    1.402
peak=    3.199 closest distance to " CZ3 TRP A 274 " =    4.552
peak=    3.198 closest distance to " CA  ASP A 162 " =    1.113
peak=    3.197 closest distance to " O   HOH Z 196 " =    0.988
peak=    3.194 closest distance to " CB  SER A 212 " =    1.155
peak=    3.194 closest distance to " ND1 HIS A  81 " =    1.730
peak=    3.192 closest distance to " CG2 THR A 220 " =    0.887
peak=    3.188 closest distance to " O   HOH Z 201 " =    2.990
peak=    3.186 closest distance to " NH1 ARG A  14 " =    1.067
peak=    3.184 closest distance to " O   HOH Z 394 " =    1.691
peak=    3.183 closest distance to " O   HOH Z  47 " =    1.236
peak=    3.182 closest distance to " ND1 HIS A  86 " =    1.657
peak=    3.178 closest distance to " O   GLU A   2 " =    1.664
peak=    3.174 closest distance to " O   HOH Z 365 " =    2.916
peak=    3.174 closest distance to " N   SER A 135 " =    1.464
peak=    3.172 closest distance to " OE1 GLU A 152 " =    0.836
peak=    3.167 closest distance to " O   HOH Z 260 " =    1.466
peak=    3.166 closest distance to " O   HOH Z 417 " =    3.144
peak=    3.160 closest distance to " O   HOH Z 188 " =    1.927
peak=    3.159 closest distance to " O   HOH Z 162 " =    1.918
peak=    3.159 closest distance to " O   HOH Z  68 " =    1.866
peak=    3.159 closest distance to " CG2 VAL A 257 " =    0.829
peak=    3.159 closest distance to " CB  TYR A 116 " =    1.020
peak=    3.158 closest distance to " CB  THR A 157 " =    1.153
peak=    3.157 closest distance to " O   THR A  31 " =    1.629
peak=    3.157 closest distance to " O   HOH Z  46 " =    1.407
peak=    3.155 closest distance to " CB  GLN A 103 " =    1.041
peak=    3.153 closest distance to " CE2 TYR A  30 " =    0.774
peak=    3.153 closest distance to " O   HOH Z 374 " =    2.849
peak=    3.150 closest distance to " CB  ASN A 285 " =    0.920
peak=    3.147 closest distance to " CB  PRO A 243 " =    1.148
peak=    3.144 closest distance to " O   HOH Z 126 " =    1.724
peak=    3.143 closest distance to " CG2 VAL A 197 " =    1.131
peak=    3.142 closest distance to " O   HOH Z 344 " =    3.017
peak=    3.140 closest distance to " CB  ASN A 110 " =    1.276
peak=    3.137 closest distance to " CA  ARG A 102 " =    1.220
peak=    3.137 closest distance to " CB  ASN A 215 " =    1.224
peak=    3.136 closest distance to " O   HOH Z 294 " =    1.535
peak=    3.131 closest distance to " O   HOH Z 299 " =    4.387
peak=    3.130 closest distance to " O   HOH Z 271 " =    2.219
peak=    3.121 closest distance to " O   HOH Z 406 " =    1.500
peak=    3.117 closest distance to " O   HOH Z 423 " =    3.170
peak=    3.117 closest distance to " CA  ASN A 215 " =    1.204
peak=    3.115 closest distance to " CG2 THR A  29 " =    1.490
peak=    3.114 closest distance to " O   HOH Z 148 " =    1.991
peak=    3.111 closest distance to " CB  ASP A 298 " =    1.271
peak=    3.110 closest distance to " N   TYR A  15 " =    0.822
peak=    3.105 closest distance to " O   HOH Z 353 " =    2.776
peak=    3.104 closest distance to " O   ASP A 124 " =    1.799
peak=    3.100 closest distance to " O   HOH Z 345 " =    3.381
peak=    3.096 closest distance to " CE3 TRP A 150 " =    1.029
peak=    3.095 closest distance to " CD1 ILE A 199 " =    0.853
peak=    3.087 closest distance to " CA  LYS A 290 " =    1.233
peak=    3.086 closest distance to " O   HOH Z  89 " =    1.577
peak=    3.084 closest distance to " O   HOH Z 385 " =    2.780
peak=    3.083 closest distance to " O   ILE A  20 " =    2.246
peak=    3.081 closest distance to " NE2 HIS A 115 " =    0.980
peak=    3.067 closest distance to " CB  HIS A 108 " =    0.826
peak=    3.065 closest distance to " O   HOH Z  48 " =    3.034
peak=    3.063 closest distance to " O   HOH Z 134 " =    2.280
peak=    3.055 closest distance to " CA  ALA A 233 " =    1.712
peak=    3.051 closest distance to " O   HOH Z 305 " =    3.718
peak=    3.049 closest distance to " O   HOH Z 256 " =    2.106
peak=    3.024 closest distance to " O   HOH Z 371 " =    2.297

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 223         
Filter by distance & map next to the model:
   mapped sites are within: 0.779 - 5.743
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 222 from: 223
   mapped sites are within: 0.779 - 5.743

peak=   -5.006 closest distance to " CG2 VAL A 230 " =    0.880
peak=   -4.325 closest distance to " CG1 VAL A 250 " =    2.701
peak=   -4.292 closest distance to " CD  ARG A 156 " =    2.075
peak=   -4.263 closest distance to " O   HOH Z 266 " =    5.310
peak=   -4.187 closest distance to " CB  ALA A 291 " =    2.580
peak=   -4.115 closest distance to " CD  GLN A  58 " =    1.004
peak=   -4.069 closest distance to " CE2 TYR A  30 " =    2.769
peak=   -4.060 closest distance to " O   HOH Z 166 " =    1.683
peak=   -4.053 closest distance to " CA  ASP A 298 " =    1.061
peak=   -4.052 closest distance to " O   HOH Z  37 " =    1.928
peak=   -4.037 closest distance to " O   HOH Z  52 " =    1.627
peak=   -4.032 closest distance to " O   HOH Z 231 " =    2.255
peak=   -4.011 closest distance to " O   HOH Z 210 " =    0.914
peak=   -4.005 closest distance to " CB  ALA A 161 " =    2.720
peak=   -4.001 closest distance to " CG1 VAL A 112 " =    2.608
peak=   -3.980 closest distance to " O   HOH Z  10 " =    1.589
peak=   -3.974 closest distance to " CD  ARG A  14 " =    3.461
peak=   -3.959 closest distance to " OXT GLY A 302 " =    3.035
peak=   -3.951 closest distance to " CD1 PHE A  59 " =    1.996
peak=   -3.915 closest distance to " CB  PRO A 243 " =    2.717
peak=   -3.913 closest distance to " O   HOH Z  73 " =    2.241
peak=   -3.908 closest distance to " O   HOH Z 351 " =    1.537
peak=   -3.894 closest distance to " O   VAL A  67 " =    2.777
peak=   -3.877 closest distance to " N   ALA A  43 " =    2.700
peak=   -3.872 closest distance to " OE1 GLN A 223 " =    2.106
peak=   -3.860 closest distance to " OG  SER A  97 " =    2.312
peak=   -3.827 closest distance to " C   HIS A 108 " =    1.174
peak=   -3.821 closest distance to " CG  ARG A 269 " =    2.426
peak=   -3.815 closest distance to " CD  GLN A 223 " =    1.463
peak=   -3.806 closest distance to " C   ALA A 158 " =    1.232
peak=   -3.795 closest distance to " CZ3 TRP A 179 " =    1.164
peak=   -3.773 closest distance to " OG BSER A 134 " =    1.341
peak=   -3.770 closest distance to " OD1 ASN A 148 " =    1.451
peak=   -3.761 closest distance to " CA  GLY A 203 " =    2.342
peak=   -3.756 closest distance to " CE3 TRP A 150 " =    2.295
peak=   -3.740 closest distance to " CD2 LEU A 167 " =    1.706
peak=   -3.727 closest distance to " CG1 VAL A 112 " =    2.868
peak=   -3.698 closest distance to " CG  GLU A 277 " =    1.124
peak=   -3.697 closest distance to " O   HOH Z 185 " =    2.458
peak=   -3.691 closest distance to " CA  SER A 164 " =    2.223
peak=   -3.691 closest distance to " O   SER A 271 " =    2.034
peak=   -3.677 closest distance to " CA  GLY A 241 " =    3.155
peak=   -3.673 closest distance to " O   HOH Z 177 " =    1.764
peak=   -3.666 closest distance to " O   HOH Z 211 " =    1.360
peak=   -3.666 closest distance to " CD1 LEU A 101 " =    2.515
peak=   -3.660 closest distance to " O   HOH Z 426 " =    1.817
peak=   -3.657 closest distance to " CZ2 TRP A  92 " =    2.829
peak=   -3.656 closest distance to " C   LEU A 143 " =    1.171
peak=   -3.656 closest distance to " O   HOH Z 292 " =    4.627
peak=   -3.649 closest distance to " CG1 VAL A 296 " =    1.353
peak=   -3.635 closest distance to " O   HOH Z 150 " =    1.905
peak=   -3.631 closest distance to " O   SER A 276 " =    1.696
peak=   -3.612 closest distance to " CG  ASP A 231 " =    0.838
peak=   -3.598 closest distance to " O   GLY A 203 " =    2.379
peak=   -3.575 closest distance to " CE3 TRP A  70 " =    1.816
peak=   -3.574 closest distance to " O   HOH Z  19 " =    2.162
peak=   -3.560 closest distance to " O   HOH Z 407 " =    3.386
peak=   -3.560 closest distance to " CA  GLY A 133 " =    2.335
peak=   -3.555 closest distance to " OE1 GLN A  88 " =    0.893
peak=   -3.549 closest distance to " NH2 ARG A  66 " =    1.711
peak=   -3.547 closest distance to " O   HOH Z 234 " =    4.475
peak=   -3.523 closest distance to " O   HOH Z 394 " =    1.602
peak=   -3.520 closest distance to " CG2 VAL A 112 " =    2.561
peak=   -3.515 closest distance to " O   HOH Z  11 " =    1.879
peak=   -3.515 closest distance to " C   ASN A 285 " =    2.470
peak=   -3.512 closest distance to " O   HOH Z 350 " =    1.741
peak=   -3.506 closest distance to " O   HOH Z 166 " =    1.638
peak=   -3.505 closest distance to " O   HOH Z 236 " =    1.504
peak=   -3.502 closest distance to " CD2 TYR A 293 " =    1.807
peak=   -3.499 closest distance to " NH2AARG A 275 " =    5.315
peak=   -3.498 closest distance to " O   HOH Z 184 " =    1.419
peak=   -3.475 closest distance to " O   VAL A  67 " =    2.815
peak=   -3.473 closest distance to " O   HOH Z 174 " =    2.279
peak=   -3.472 closest distance to " O   HOH Z 252 " =    3.897
peak=   -3.459 closest distance to " CA  SER A  62 " =    2.624
peak=   -3.453 closest distance to " O   HOH Z 290 " =    1.257
peak=   -3.446 closest distance to " O   HOH Z  13 " =    1.630
peak=   -3.434 closest distance to " CD1 LEU A  25 " =    2.474
peak=   -3.433 closest distance to " O   HOH Z   6 " =    1.745
peak=   -3.430 closest distance to " O   HOH Z 308 " =    1.725
peak=   -3.429 closest distance to " CB  ALA A 248 " =    2.381
peak=   -3.429 closest distance to " CG  TRP A 266 " =    1.786
peak=   -3.427 closest distance to " O   ASP A  27 " =    2.114
peak=   -3.427 closest distance to " OG  SER A  26 " =    1.447
peak=   -3.422 closest distance to " CB  VAL A 230 " =    1.033
peak=   -3.419 closest distance to " N   ALA A 226 " =    2.142
peak=   -3.417 closest distance to " O   HOH Z  44 " =    2.151
peak=   -3.411 closest distance to " CD1 ILE A 151 " =    2.389
peak=   -3.410 closest distance to " O   HOH Z 111 " =    2.120
peak=   -3.410 closest distance to " CB  ALA A  10 " =    2.221
peak=   -3.404 closest distance to " O   HOH Z 396 " =    1.792
peak=   -3.389 closest distance to " CD1 TYR A 247 " =    2.372
peak=   -3.389 closest distance to " O   HOH Z 241 " =    1.257
peak=   -3.388 closest distance to " O   HOH Z 231 " =    1.869
peak=   -3.387 closest distance to " CD2 LEU A 300 " =    2.617
peak=   -3.380 closest distance to " O   HOH Z 368 " =    1.846
peak=   -3.380 closest distance to " ND2 ASN A  45 " =    1.150
peak=   -3.373 closest distance to " OD1 ASN A 173 " =    1.378
peak=   -3.372 closest distance to " O   SER A 210 " =    1.787
peak=   -3.369 closest distance to " OD1 ASN A 187 " =    1.508
peak=   -3.367 closest distance to " O   HOH Z 275 " =    1.499
peak=   -3.367 closest distance to " CA  GLY A 241 " =    2.273
peak=   -3.366 closest distance to " C   GLY A  17 " =    1.276
peak=   -3.362 closest distance to " O   HOH Z 106 " =    1.922
peak=   -3.359 closest distance to " O   HOH Z 114 " =    3.435
peak=   -3.359 closest distance to " O   HOH Z 165 " =    1.843
peak=   -3.356 closest distance to " C   GLN A 240 " =    2.295
peak=   -3.355 closest distance to " CD  LYS A 289 " =    2.429
peak=   -3.352 closest distance to " O   HOH Z 353 " =    2.267
peak=   -3.349 closest distance to " OG1 THR A  82 " =    1.400
peak=   -3.345 closest distance to " CD2 PHE A  61 " =    2.021
peak=   -3.342 closest distance to " O   HOH Z 264 " =    1.750
peak=   -3.341 closest distance to " CG  LYS A 166 " =    2.152
peak=   -3.338 closest distance to " CD  GLN A  88 " =    0.877
peak=   -3.337 closest distance to " O   HOH Z 200 " =    1.705
peak=   -3.335 closest distance to " O   VAL A 189 " =    2.628
peak=   -3.333 closest distance to " NE2 GLN A 194 " =    1.900
peak=   -3.331 closest distance to " N   TYR A  68 " =    2.953
peak=   -3.328 closest distance to " O   HOH Z 377 " =    1.831
peak=   -3.324 closest distance to " O   HOH Z 136 " =    2.409
peak=   -3.321 closest distance to " CG  GLU A  53 " =    1.661
peak=   -3.320 closest distance to " O   HOH Z  49 " =    0.977
peak=   -3.319 closest distance to " CG1 VAL A 197 " =    2.320
peak=   -3.318 closest distance to " N   THR A 235 " =    1.255
peak=   -3.316 closest distance to " CB  ALA A 248 " =    2.114
peak=   -3.316 closest distance to " CD1 LEU A 101 " =    2.642
peak=   -3.311 closest distance to " O   HOH Z  43 " =    1.619
peak=   -3.311 closest distance to " OD2 ASP A  50 " =    2.413
peak=   -3.309 closest distance to " CG2 VAL A 189 " =    2.122
peak=   -3.307 closest distance to " O   HOH Z  17 " =    1.396
peak=   -3.306 closest distance to " O   ALA A  10 " =    1.758
peak=   -3.306 closest distance to " O   HOH Z 193 " =    2.317
peak=   -3.303 closest distance to " O   HOH Z 431 " =    2.109
peak=   -3.302 closest distance to " NH2 ARG A  79 " =    1.633
peak=   -3.301 closest distance to " CG  MET A 105 " =    0.944
peak=   -3.293 closest distance to " CA  ASN A 127 " =    1.003
peak=   -3.292 closest distance to " O   HOH Z 171 " =    2.172
peak=   -3.290 closest distance to " NH2 ARG A 159 " =    2.439
peak=   -3.289 closest distance to " O   HOH Z 113 " =    2.000
peak=   -3.288 closest distance to " O   HOH Z  94 " =    2.082
peak=   -3.288 closest distance to " CZ2 TRP A 274 " =    1.054
peak=   -3.285 closest distance to " CG2 ILE A 263 " =    2.362
peak=   -3.284 closest distance to " O   PRO A 198 " =    1.262
peak=   -3.283 closest distance to " O   HOH Z  60 " =    2.104
peak=   -3.282 closest distance to " CG  HIS A  86 " =    1.053
peak=   -3.279 closest distance to " CD  ARG A 139 " =    1.629
peak=   -3.278 closest distance to " CZ  PHE A  38 " =    2.428
peak=   -3.274 closest distance to " O   HOH Z 251 " =    4.980
peak=   -3.273 closest distance to " CE2 PHE A  61 " =    2.529
peak=   -3.268 closest distance to " O   HOH Z 189 " =    2.246
peak=   -3.267 closest distance to " O   VAL A 125 " =    2.209
peak=   -3.258 closest distance to " CB  PRO A 163 " =    2.603
peak=   -3.256 closest distance to " CD1 LEU A   5 " =    2.552
peak=   -3.254 closest distance to " O   HOH Z  38 " =    1.447
peak=   -3.248 closest distance to " O   HOH Z 285 " =    1.599
peak=   -3.247 closest distance to " N   SER A   3 " =    2.148
peak=   -3.246 closest distance to " O   HOH Z  15 " =    1.582
peak=   -3.241 closest distance to " OG ASER A 134 " =    1.370
peak=   -3.238 closest distance to " CB  ASP A 132 " =    2.365
peak=   -3.231 closest distance to " CA  PRO A 243 " =    2.537
peak=   -3.230 closest distance to " N   SER A 276 " =    1.435
peak=   -3.230 closest distance to " CB  GLN A  11 " =    1.794
peak=   -3.230 closest distance to " O   HOH Z 378 " =    1.414
peak=   -3.229 closest distance to " O   HOH Z  71 " =    1.623
peak=   -3.228 closest distance to " ND2 ASN A  45 " =    2.098
peak=   -3.227 closest distance to " OG  SER A  87 " =    1.661
peak=   -3.226 closest distance to " CB  ALA A 291 " =    2.309
peak=   -3.226 closest distance to " O   HOH Z 292 " =    1.836
peak=   -3.224 closest distance to " O   HOH Z 111 " =    1.373
peak=   -3.222 closest distance to " C   SER A 206 " =    1.434
peak=   -3.217 closest distance to " O   HOH Z 253 " =    4.368
peak=   -3.214 closest distance to " O   HOH Z 105 " =    2.058
peak=   -3.213 closest distance to " O   HOH Z 377 " =    1.378
peak=   -3.212 closest distance to " CB  PHE A 208 " =    2.349
peak=   -3.212 closest distance to " O   ALA A  34 " =    2.634
peak=   -3.204 closest distance to " O   HOH Z 409 " =    4.913
peak=   -3.201 closest distance to " CB  ARG A  79 " =    2.686
peak=   -3.199 closest distance to " O   PHE A 218 " =    1.565
peak=   -3.195 closest distance to " CZ  TYR A 169 " =    1.753
peak=   -3.194 closest distance to " SG  CYS A 260 " =    2.359
peak=   -3.193 closest distance to " O   HOH Z  90 " =    1.624
peak=   -3.192 closest distance to " O   HOH Z 423 " =    2.159
peak=   -3.189 closest distance to " NE2 GLN A 103 " =    1.809
peak=   -3.187 closest distance to " OG1 THR A  82 " =    1.486
peak=   -3.183 closest distance to " SG ACYS A 201 " =    2.193
peak=   -3.182 closest distance to " O   HOH Z 232 " =    1.687
peak=   -3.175 closest distance to " O   HOH Z 191 " =    5.743
peak=   -3.169 closest distance to " O   HOH Z 114 " =    1.567
peak=   -3.164 closest distance to " O   HOH Z 109 " =    1.099
peak=   -3.158 closest distance to " OE1 GLN A  88 " =    0.779
peak=   -3.156 closest distance to " OD1 ASP A 191 " =    1.469
peak=   -3.154 closest distance to " CG  PRO A 163 " =    2.337
peak=   -3.148 closest distance to " O   HOH Z 222 " =    1.648
peak=   -3.139 closest distance to " CG  PRO A 243 " =    1.730
peak=   -3.139 closest distance to " OG BSER A 134 " =    1.994
peak=   -3.139 closest distance to " O   GLY A 211 " =    1.485
peak=   -3.134 closest distance to " O   HOH Z 216 " =    1.618
peak=   -3.132 closest distance to " C   ASP A 270 " =    1.290
peak=   -3.132 closest distance to " O   HOH Z  70 " =    2.241
peak=   -3.132 closest distance to " O   HOH Z 411 " =    1.829
peak=   -3.127 closest distance to " O   HOH Z  78 " =    1.882
peak=   -3.125 closest distance to " O   HOH Z 166 " =    1.830
peak=   -3.123 closest distance to " O   HOH Z 262 " =    2.810
peak=   -3.122 closest distance to " CG1 VAL A  78 " =    2.613
peak=   -3.119 closest distance to " NE  ARG A  66 " =    4.132
peak=   -3.118 closest distance to " NE2 GLN A  88 " =    1.077
peak=   -3.116 closest distance to " CA  VAL A 197 " =    1.080
peak=   -3.110 closest distance to " CD1 LEU A 228 " =    2.432
peak=   -3.106 closest distance to " O   HOH Z 139 " =    3.086
peak=   -3.104 closest distance to " O   HOH Z 198 " =    2.358
peak=   -3.103 closest distance to " NE2 GLN A 223 " =    1.459
peak=   -3.103 closest distance to " CG1 VAL A 112 " =    2.951
peak=   -3.101 closest distance to " O   HOH Z 246 " =    1.481
peak=   -3.097 closest distance to " ND2 ASN A  60 " =    1.923
peak=   -3.074 closest distance to " O   HOH Z 177 " =    1.395
peak=   -3.068 closest distance to " CE  MET A 105 " =    2.341
peak=   -3.068 closest distance to " C   THR A 279 " =    1.170
peak=   -3.061 closest distance to " CG1AVAL A  41 " =    2.965
peak=   -3.061 closest distance to " O   HOH Z 193 " =    1.831
peak=   -3.061 closest distance to " CG2 THR A 221 " =    2.317
peak=   -3.059 closest distance to " CD2 LEU A 237 " =    2.806
peak=   -3.038 closest distance to " OG  SER A  63 " =    1.234

================= 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    :  0.4788 0.4627   6.277674e+00   6.258039e+00
   1_bss:  0.4716 0.4535   6.273174e+00   6.249658e+00
   1_xyz:  0.3805 0.4011   6.146895e+00   6.174440e+00
   1_adp:  0.3353 0.3770   6.058752e+00   6.136830e+00
   1_occ:  0.3346 0.3771   6.057813e+00   6.138006e+00
   2_bss:  0.3333 0.3740   6.059271e+00   6.136966e+00
   2_xyz:  0.2507 0.3005   5.824936e+00   5.963906e+00
   2_adp:  0.2313 0.2793   5.764523e+00   5.913641e+00
   2_occ:  0.2310 0.2798   5.764381e+00   5.914164e+00
   3_bss:  0.2297 0.2787   5.764180e+00   5.912610e+00
   3_xyz:  0.1689 0.2108   5.478420e+00   5.664231e+00
   3_adp:  0.1544 0.1966   5.404354e+00   5.601517e+00
   3_occ:  0.1542 0.1965   5.403449e+00   5.601186e+00
   4_bss:  0.1542 0.1964   5.403443e+00   5.600053e+00
   4_xyz:  0.1306 0.1763   5.270527e+00   5.492277e+00
   4_adp:  0.1261 0.1746   5.247191e+00   5.478234e+00
   4_occ:  0.1260 0.1744   5.246720e+00   5.477677e+00
   5_bss:  0.1261 0.1745   5.247395e+00   5.478157e+00
   5_xyz:  0.1179 0.1666   5.195521e+00   5.437304e+00
   5_adp:  0.1167 0.1674   5.194251e+00   5.443666e+00
   5_occ:  0.1166 0.1674   5.194114e+00   5.443734e+00
   5_bss:  0.1165 0.1673   5.194070e+00   5.443748e+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:  0.314  33.909   7.164   9.601   8.328   0.000   0.000   0.000
   1_xyz:  0.314  33.909   7.164   9.601   8.328   0.000   0.000   0.000
   1_adp:  0.314  33.909   7.164   9.601   8.328   0.000   0.000   0.000
   1_occ:  0.314  33.909   7.164   9.601   8.328   0.000   0.000   0.000
   2_bss:  0.284  33.909   4.538   6.636   5.512   0.000   0.000   0.000
   2_xyz:  0.284  33.909   4.538   6.636   5.512   0.000   0.000   0.000
   2_adp:  0.284  33.909   4.538   6.636   5.512   0.000   0.000   0.000
   2_occ:  0.284  33.909   4.538   6.636   5.512   0.000   0.000   0.000
   3_bss:  0.307  66.363   3.056   4.313   4.045   0.000   0.000   0.000
   3_xyz:  0.307  66.363   3.056   4.313   4.045   0.000   0.000   0.000
   3_adp:  0.307  66.363   3.056   4.313   4.045   0.000   0.000   0.000
   3_occ:  0.307  66.363   3.056   4.313   4.045   0.000   0.000   0.000
   4_bss:  0.330  66.363   2.456   3.185   3.704   0.000   0.000   0.000
   4_xyz:  0.330  66.363   2.456   3.185   3.704   0.000   0.000   0.000
   4_adp:  0.330  66.363   2.456   3.185   3.704   0.000   0.000   0.000
   4_occ:  0.330  66.363   2.456   3.185   3.704   0.000   0.000   0.000
   5_bss:  0.325  64.145   2.466   3.003   3.753   0.000   0.000   0.000
   5_xyz:  0.325  64.145   2.466   3.003   3.753   0.000   0.000   0.000
   5_adp:  0.325  64.145   2.466   3.003   3.753   0.000   0.000   0.000
   5_occ:  0.325  64.145   2.466   3.003   3.753   0.000   0.000   0.000
   5_bss:  0.318  64.638  -0.562  -0.145   0.707  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  55.370 0.4531  0.5048    63904.768
   1_bss:  54.946 0.4575  0.6518    62706.564
   1_xyz:  46.090 0.5675  0.7863    45899.142
   1_adp:  41.547 0.6239  0.8853    39928.606
   1_occ:  41.574 0.6235  0.8839    40008.216
   2_bss:  41.515 0.6242  0.8024    39921.682
   2_xyz:  31.563 0.7396  0.9368    24098.064
   2_adp:  28.791 0.7713  0.9617    21121.418
   2_occ:  28.827 0.7709  0.9602    21160.152
   3_bss:  28.720 0.7721  0.9037    21054.237
   3_xyz:  20.398 0.8577  0.9688    11317.155
   3_adp:  18.580 0.8755  0.9725     9849.477
   3_occ:  18.564 0.8757  0.9726     9847.139
   4_bss:  18.530 0.8760  0.9494     9806.849
   4_xyz:  16.089 0.8978  0.9627     7796.460
   4_adp:  15.716 0.9012  0.9585     7614.149
   4_occ:  15.705 0.9013  0.9585     7607.057
   5_bss:  15.732 0.9011  0.9569     7632.909
   5_xyz:  14.884 0.9081  0.9607     7019.086
   5_adp:  14.998 0.9073  0.9524     7086.836
   5_occ:  15.003 0.9072  0.9522     7086.712
   5_bss:  15.007 0.9072  0.9593     7087.726
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.094   5.4520e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.094   5.4520e+01
   1_xyz:   1.723  0.014  0.110 17.989  0.007  4.112   1.4575e-01
   1_adp:   1.723  0.014  0.110 17.989  0.007  4.112   1.4575e-01
   1_occ:   1.723  0.014  0.110 17.989  0.007  4.112   1.4575e-01
   2_bss:   1.723  0.014  0.110 17.989  0.007  4.112   1.4575e-01
   2_xyz:   1.184  0.008  0.079 16.172  0.004  4.135   7.7861e-02
   2_adp:   1.184  0.008  0.079 16.172  0.004  4.135   7.7861e-02
   2_occ:   1.184  0.008  0.079 16.172  0.004  4.135   7.7861e-02
   3_bss:   1.184  0.008  0.079 16.172  0.004  4.135   7.7861e-02
   3_xyz:   1.088  0.009  0.083 15.771  0.004  4.119   7.3277e-02
   3_adp:   1.088  0.009  0.083 15.771  0.004  4.119   7.3277e-02
   3_occ:   1.088  0.009  0.083 15.771  0.004  4.119   7.3277e-02
   4_bss:   1.088  0.009  0.083 15.771  0.004  4.119   7.3277e-02
   4_xyz:   1.132  0.010  0.088 15.686  0.004  4.132   7.6055e-02
   4_adp:   1.132  0.010  0.088 15.686  0.004  4.132   7.6055e-02
   4_occ:   1.132  0.010  0.088 15.686  0.004  4.132   7.6055e-02
   5_bss:   1.132  0.010  0.088 15.686  0.004  4.132   7.6055e-02
   5_xyz:   1.182  0.012  0.095 15.511  0.004  4.133   8.5349e-02
   5_adp:   1.182  0.012  0.095 15.511  0.004  4.133   8.5349e-02
   5_occ:   1.182  0.012  0.095 15.511  0.004  4.133   8.5349e-02
   5_bss:   1.182  0.012  0.095 15.511  0.004  4.133   8.5349e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0692e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0692e+00
   1_xyz:  14.676  0.174  0.467 86.810  0.040  2.243   1.0804e-01
   1_adp:  14.676  0.174  0.467 86.810  0.040  2.243   1.0804e-01
   1_occ:  14.676  0.174  0.467 86.810  0.040  2.243   1.0804e-01
   2_bss:  14.676  0.174  0.467 86.810  0.040  2.243   1.0804e-01
   2_xyz:   9.171  0.070  0.291 88.605  0.032  2.132   5.4123e-02
   2_adp:   9.171  0.070  0.291 88.605  0.032  2.132   5.4123e-02
   2_occ:   9.171  0.070  0.291 88.605  0.032  2.132   5.4123e-02
   3_bss:   9.171  0.070  0.291 88.605  0.032  2.132   5.4123e-02
   3_xyz:   7.717  0.063  0.426 83.324  0.043  2.296   7.6117e-02
   3_adp:   7.717  0.063  0.426 83.324  0.043  2.296   7.6117e-02
   3_occ:   7.717  0.063  0.426 83.324  0.043  2.296   7.6117e-02
   4_bss:   7.717  0.063  0.426 83.324  0.043  2.296   7.6117e-02
   4_xyz:   9.251  0.058  0.562 82.645  0.031  2.324   4.8654e-02
   4_adp:   9.251  0.058  0.562 82.645  0.031  2.324   4.8654e-02
   4_occ:   9.251  0.058  0.562 82.645  0.031  2.324   4.8654e-02
   5_bss:   9.251  0.058  0.562 82.645  0.031  2.324   4.8654e-02
   5_xyz:   7.886  0.050  0.654 81.646  0.032  2.319   8.5542e-02
   5_adp:   7.886  0.050  0.654 81.646  0.032  2.319   8.5542e-02
   5_occ:   7.886  0.050  0.654 81.646  0.032  2.319   8.5542e-02
   5_bss:   7.886  0.050  0.654 81.646  0.032  2.319   8.5542e-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: 114.16   0.00  12.66  76.86   0.00   9.87 114.16   0.00  27.88
   1_occ: 114.16   0.00  12.66  76.86   0.00   9.87 114.16   0.00  27.88
   2_bss: 114.16   0.00  12.66  76.86   0.00   9.87 114.16   0.00  27.88
   2_xyz: 114.16   0.00  12.66  76.86   0.00   9.87 114.16   0.00  27.88
   2_adp: 114.53   0.00  12.54  78.74   0.00   8.82 114.53   0.00  32.81
   2_occ: 114.53   0.00  12.54  78.74   0.00   8.82 114.53   0.00  32.81
   3_bss: 114.53   0.00  12.54  78.74   0.00   8.82 114.53   0.00  32.81
   3_xyz: 114.53   0.00  12.54  78.74   0.00   8.82 114.53   0.00  32.81
   3_adp: 108.32   0.00  12.69  79.20   0.00   8.40 108.32   0.78  36.03
   3_occ: 108.32   0.00  12.69  79.20   0.00   8.40 108.32   0.78  36.03
   4_bss: 108.32   0.00  12.69  79.20   0.00   8.40 108.32   0.78  36.03
   4_xyz: 108.32   0.00  12.69  79.20   0.00   8.40 108.32   0.78  36.03
   4_adp: 103.78   0.00  12.66  80.34   0.00   8.22 103.78   1.36  36.87
   4_occ: 103.78   0.00  12.66  80.34   0.00   8.22 103.78   1.36  36.87
   5_bss: 103.78   0.00  12.66  80.34   0.00   8.22 103.78   1.36  36.87
   5_xyz: 103.78   0.00  12.66  80.34   0.00   8.22 103.78   1.36  36.87
   5_adp:  97.41   0.00  12.79  87.49   0.00   8.19  97.41   1.13  37.84
   5_occ:  97.41   0.00  12.79  87.49   0.00   8.19  97.41   1.13  37.84
   5_bss: 100.69   3.28  16.07  90.77   3.28  11.47 100.69   4.42  41.12
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.236    0.011    0.414
   1_adp:    1.236    0.011    0.414
   1_occ:    1.236    0.011    0.414
   2_bss:    1.236    0.011    0.414
   2_xyz:    1.748    0.045    0.570
   2_adp:    1.748    0.045    0.570
   2_occ:    1.748    0.045    0.570
   3_bss:    1.748    0.045    0.570
   3_xyz:    1.638    0.032    0.660
   3_adp:    1.638    0.032    0.660
   3_occ:    1.638    0.032    0.660
   4_bss:    1.638    0.032    0.660
   4_xyz:    1.746    0.048    0.710
   4_adp:    1.746    0.048    0.710
   4_occ:    1.746    0.048    0.710
   5_bss:    1.746    0.048    0.710
   5_xyz:    1.793    0.036    0.729
   5_adp:    1.793    0.036    0.729
   5_occ:    1.793    0.036    0.729
   5_bss:    1.793    0.036    0.729
------------------------------------------------------------------------

CPU time actual refinement: 322.49


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1063/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_1063/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1063/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1063/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1063/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 322.33 
  Macro-tasks:
    bulk solvent and scale       = 34.83  
    individual site refinement   = 138.03 
    weights calculation          = 31.50  
    collect and process          = 6.50   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 210.97 
  Micro-tasks:
    mask                            = 2.26   
    f_calc                          = 99.43  
    alpha_beta                      = 8.27   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 111.41 
    fmodel                         = 6.64   
    r_factors                      = 0.14   
    phase_errors                   = 10.63  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 240.24 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.499 micro seconds
Total CPU time: 5.60 minutes
from_scatterers_fft:    658 calls, 98.97 s
gradients_fft:          603 calls, 97.66 s

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

# Date 2008-01-16 Time 03:06:51 PST -0800 (1200481611.27 s)
Start R-work = 0.4788, R-free = 0.4627 (no bulk solvent and anisotropic scale)
Final R-work = 0.1323, R-free = 0.1814 (no bulk solvent and anisotropic scale)

Start R-work = 0.4716, R-free = 0.4535
Final R-work = 0.1165, R-free = 0.1673