# Date 2008-01-16 Time 03:24:08 PST -0800 (1200482648.34 s)
#phil __OFF__

Command line arguments: "../1224.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 = 22220
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1224

-------------------------------------------------------------------------------
  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: (72.0062, 45.9914, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (72.0062, 45.9914, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2211 1.96275
Completeness in resolution range: 0.937049
Completeness with d_max=infinity: 0.934367

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2211
                             d_min =   1.9628

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: (72.0062, 45.9914, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2211 1.96275
Completeness in resolution range: 0.937049
Completeness with d_max=infinity: 0.934367

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2215 -  4.2018 [2196/2223]  1979   217   9.9%
  bin  2:  4.2018 -  3.3467 [2100/2120]  1889   211  10.0%
  bin  3:  3.3467 -  2.9271 [2098/2117]  1882   216  10.3%
  bin  4:  2.9271 -  2.6610 [2040/2070]  1838   202   9.9%
  bin  5:  2.6610 -  2.4711 [2065/2084]  1863   202   9.8%
  bin  6:  2.4711 -  2.3260 [2027/2052]  1817   210  10.4%
  bin  7:  2.3260 -  2.2099 [2055/2083]  1848   207  10.1%
  bin  8:  2.2099 -  2.1139 [2008/2044]  1816   192   9.6%
  bin  9:  2.1139 -  2.0327 [1973/2056]  1776   197  10.0%
  bin 10:  2.0327 -  1.9628 [1027/2056]   922   105  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1224/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:
        1.65 -     2.30: 24
        2.30 -     2.95: 1683
        2.95 -     3.60: 4572
        3.60 -     4.25: 9265
        4.25 -     4.90: 12901
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.654 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 201 " - " O   HOH Z 349 "  1.744 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  " O   HOH Z 107 " - " O   HOH Z 340 "  1.887 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28440 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_1224/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1224/model_refine_001.geo

CPU time processing inputs: 9.19


============================ 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 = 72.00625 45.9914 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5092   r_free= 0.5012   ksol= 0.00   Bsol= 0.00   scale= 0.772    |
|                                                                             |
| 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:   0.84 A                  |
| x-ray target function (ml) for work reflections: 6.306025                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2215 -  4.6874 0.99   1422  162 0.4291 0.4555       6.641      6.6881|
|  2:  4.6874 -  3.7386 0.99   1372  150 0.4465 0.4403      6.8664      6.8552|
|  3:  3.7386 -  3.2714 0.99   1338  145 0.4827 0.4571      6.7133      6.7261|
|  4:  3.2714 -  2.9747 0.99   1345  158 0.5026 0.5048      6.5601      6.5217|
|  5:  2.9747 -  2.7629 0.99   1332  142 0.5303 0.5396      6.3907      6.4112|
|  6:  2.7629 -  2.6008 0.99   1327  148 0.5459 0.5243      6.2975      6.2362|
|  7:  2.6008 -  2.4711 0.99   1315  143 0.5557 0.4749      6.2618      6.1717|
|  8:  2.4711 -  2.3640 0.98   1295  149 0.5478 0.5013      6.1786      6.2079|
|  9:  2.3640 -  2.2733 0.98   1308  147 0.5399 0.5103      6.1445      6.1182|
| 10:  2.2733 -  2.1951 1.00   1287  150 0.5386 0.5368      6.0988      6.0722|
| 11:  2.1951 -  2.1266 0.98   1327  137 0.5370 0.5651      6.0356      6.0826|
| 12:  2.1266 -  2.0660 0.98   1279  151 0.5273 0.5845      5.9588      5.9781|
| 13:  2.0660 -  2.0117 0.89   1174  125 0.5641 0.4943      5.8794      5.8187|
| 14:  2.0117 -  1.9628 0.38    509   52 0.5739 0.5318      5.8572      5.8603|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2215 -  4.6874  1422   162  0.61  41.85   0.77     0.69     102847.62|
|  2:  4.6874 -  3.7386  1372   150  0.63  41.04   0.85     0.72     139771.70|
|  3:  3.7386 -  3.2714  1338   145  0.49  52.71   0.81     0.62     147694.78|
|  4:  3.2714 -  2.9747  1345   158  0.38  61.06   0.77     0.49     133210.25|
|  5:  2.9747 -  2.7629  1332   142  0.27  69.59   0.72     0.34     104380.99|
|  6:  2.7629 -  2.6008  1327   148  0.28  68.98   0.70     0.34      84854.15|
|  7:  2.6008 -  2.4711  1315   143  0.30  67.76   0.72     0.35      70519.66|
|  8:  2.4711 -  2.3640  1295   149  0.33  65.27   0.70     0.40      60598.67|
|  9:  2.3640 -  2.2733  1308   147  0.33  64.96   0.73     0.39      54886.19|
| 10:  2.2733 -  2.1951  1287   150  0.31  66.97   0.74     0.36      51521.98|
| 11:  2.1951 -  2.1266  1327   137  0.25  71.49   0.75     0.32      51825.11|
| 12:  2.1266 -  2.0660  1279   151  0.20  74.90   0.75     0.27      49007.20|
| 13:  2.0660 -  2.0117  1174   125  0.19  75.54   0.72     0.26      42023.65|
| 14:  2.0117 -  1.9628   509    52  0.26  70.42   0.68     0.30      32796.98|
|alpha:            min =        0.26 max =            0.72 mean =         0.43|
|beta:             min =    32796.98 max =       147694.78 mean =     83563.62|
|figures of merit: min =        0.00 max =            1.00 mean =         0.35|
|phase err.(work): min =        0.00 max =           89.99 mean =        63.11|
|phase err.(test): min =        0.00 max =           90.00 mean =        63.30|
|-----------------------------------------------------------------------------|

============================== 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 = 24.942743             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.792   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.007472              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.836   (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:       33 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      172 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      700 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1535 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2650 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3951 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5092 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6580 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7757 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.516 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.196 |       2.021 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.802)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.802)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5116   r_free= 0.5035   ksol= 0.00   Bsol= 0.00   scale= 0.744    |
|                                                                             |
| 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:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.306717                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5003   r_free= 0.4878   ksol= 0.37   Bsol= 20.00   scale= 0.958   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.96,8.55,6.62,0.00,0.00,0.00); trace/3= 8.04                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.86 A                  |
| x-ray target function (ml) for work reflections: 6.303197                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 20.226861             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.931   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.693787              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.405   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5003      final r-factor (work) = 0.4411          |
| start r-factor (free) = 0.4878      final r-factor (free) = 0.4681          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 117.2384 = 20.23 * 0.50 * 6.3008 + 1.00 * 53.5159                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 63.4012 = 20.23 * 0.50 * 6.2534 + 1.00 * 0.1577                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4411      final r-factor (work) = 0.4027          |
| start r-factor (free) = 0.4681      final r-factor (free) = 0.4613          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.6064 = 1.69 * 1.00 * 6.2534 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.5313 = 1.69 * 1.00 * 6.2060 + 1.00 * 0.0196                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.802)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.47   15.54    None  None   None       |
|    all(noH): 2823   0      0.00    91.47   15.54    None  None   None       |
|    Sol.    : 438    0      0.00    87.96   23.27    None  None   None       |
|    Mac.    : 2385   0      0.00    91.47   14.13    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 -   9.147: 1096   |   5:    45.735 -  54.882:   55        |
|      1:     9.147 -  18.294:  790   |   6:    54.882 -  64.029:   18        |
|      2:    18.294 -  27.441:  507   |   7:    64.029 -  73.176:   17        |
|      3:    27.441 -  36.588:  222   |   8:    73.176 -  82.323:    4        |
|      4:    36.588 -  45.735:  110   |   9:    82.323 -  91.470:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4027 r_free = 0.4613             target_work(ml) = 6.200         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4025 r_free = 0.4613             target_work(ml) = 6.199         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4025   r_free= 0.4613   ksol= 0.37   Bsol= 20.00   scale= 1.093   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.96,8.55,6.62,0.00,0.00,0.00); trace/3= 8.04                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.199250                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4016   r_free= 0.4591   ksol= 0.36   Bsol= 50.00   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.56,5.04,4.21,0.00,0.00,0.00); trace/3= 4.93                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.200140                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.375659              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.780  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.807583              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.357  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4016      final r-factor (work) = 0.3444          |
| start r-factor (free) = 0.4591      final r-factor (free) = 0.4124          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.2364 = 9.38 * 0.50 * 6.2030 + 1.00 * 0.1577                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.9092 = 9.38 * 0.50 * 6.1474 + 1.00 * 0.0911                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3444      final r-factor (work) = 0.3297          |
| start r-factor (free) = 0.4124      final r-factor (free) = 0.4026          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9841 = 0.81 * 1.00 * 6.1474 + 1.00 * 0.0195                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9216 = 0.81 * 1.00 * 6.0775 + 1.00 * 0.0135                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 42     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.802)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.05   15.74    None  None   None       |
|    all(noH): 2823   0      0.00    98.05   15.74    None  None   None       |
|    Sol.    : 438    0      0.00    85.25   28.08    None  None   None       |
|    Mac.    : 2385   0      0.00    98.05   13.48    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.805: 1127   |   5:    49.025 -  58.830:   43        |
|      1:     9.805 -  19.610:  846   |   6:    58.830 -  68.636:   12        |
|      2:    19.610 -  29.415:  488   |   7:    68.636 -  78.441:    7        |
|      3:    29.415 -  39.220:  189   |   8:    78.441 -  88.246:    4        |
|      4:    39.220 -  49.025:  105   |   9:    88.246 -  98.051:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3297 r_free = 0.4026             target_work(ml) = 6.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3295 r_free = 0.4029             target_work(ml) = 6.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3295   r_free= 0.4029   ksol= 0.36   Bsol= 50.00   scale= 1.069   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.56,5.04,4.21,0.00,0.00,0.00); trace/3= 4.93                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.065800                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3285   r_free= 0.4014   ksol= 0.36   Bsol= 69.30   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.28,2.55,2.60,0.00,0.00,0.00); trace/3= 2.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.066285                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.684482              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.616  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.388699              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.961  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3285      final r-factor (work) = 0.2718          |
| start r-factor (free) = 0.4014      final r-factor (free) = 0.3436          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.3626 = 5.68 * 0.50 * 6.0767 + 1.00 * 0.0912                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.1225 = 5.68 * 0.50 * 5.9960 + 1.00 * 0.0803                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2718      final r-factor (work) = 0.2584          |
| start r-factor (free) = 0.3436      final r-factor (free) = 0.3270          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3441 = 0.39 * 1.00 * 5.9960 + 1.00 * 0.0134                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3016 = 0.39 * 1.00 * 5.8967 + 1.00 * 0.0095                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.802)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.27   15.27    None  None   None       |
|    all(noH): 2823   0      0.00    95.27   15.27    None  None   None       |
|    Sol.    : 438    0      0.00    77.94   32.79    None  None   None       |
|    Mac.    : 2385   0      0.00    95.27   12.06    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 -   9.527: 1170   |   5:    47.633 -  57.160:   55        |
|      1:     9.527 -  19.053:  899   |   6:    57.160 -  66.686:   16        |
|      2:    19.053 -  28.580:  350   |   7:    66.686 -  76.213:    2        |
|      3:    28.580 -  38.106:  213   |   8:    76.213 -  85.739:    4        |
|      4:    38.106 -  47.633:  112   |   9:    85.739 -  95.266:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2584 r_free = 0.3270             target_work(ml) = 5.875         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2580 r_free = 0.3265             target_work(ml) = 5.874         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2580   r_free= 0.3265   ksol= 0.36   Bsol= 69.30   scale= 1.043   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.28,2.55,2.60,0.00,0.00,0.00); trace/3= 2.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.874095                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2573   r_free= 0.3259   ksol= 0.36   Bsol= 62.62   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.57,1.05,1.49,0.00,0.00,0.00); trace/3= 1.37                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.874628                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.140048              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.425  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.375474              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.836  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2573      final r-factor (work) = 0.1958          |
| start r-factor (free) = 0.3259      final r-factor (free) = 0.2509          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.2372 = 5.14 * 0.50 * 5.8976 + 1.00 * 0.0803                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.8913 = 5.14 * 0.50 * 5.7659 + 1.00 * 0.0728                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1958      final r-factor (work) = 0.1761          |
| start r-factor (free) = 0.2509      final r-factor (free) = 0.2320          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1745 = 0.38 * 1.00 * 5.7659 + 1.00 * 0.0095                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1087 = 0.38 * 1.00 * 5.5730 + 1.00 * 0.0161                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.802)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.37   15.55    None  None   None       |
|    all(noH): 2823   0      0.00    94.37   15.55    None  None   None       |
|    Sol.    : 438    0      3.04    82.06   39.00    None  None   None       |
|    Mac.    : 2385   0      0.00    94.37   11.25    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 -   9.437: 1306   |   5:    47.185 -  56.622:  108        |
|      1:     9.437 -  18.874:  842   |   6:    56.622 -  66.059:   46        |
|      2:    18.874 -  28.311:  243   |   7:    66.059 -  75.496:    9        |
|      3:    28.311 -  37.748:  127   |   8:    75.496 -  84.933:    4        |
|      4:    37.748 -  47.185:  135   |   9:    84.933 -  94.370:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1761 r_free = 0.2320             target_work(ml) = 5.536         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1758 r_free = 0.2311             target_work(ml) = 5.534         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1758   r_free= 0.2311   ksol= 0.36   Bsol= 62.62   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.57,1.05,1.49,0.00,0.00,0.00); trace/3= 1.37                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.534422                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1758   r_free= 0.2311   ksol= 0.34   Bsol= 54.46   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.55,-0.34,0.72,-0.00,0.00,0.00); trace/3= 0.31                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.534211                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.074072              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 111.255  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.306404              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.973   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1758      final r-factor (work) = 0.1494          |
| start r-factor (free) = 0.2311      final r-factor (free) = 0.2016          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8572 = 2.07 * 0.50 * 5.5779 + 1.00 * 0.0728                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7254 = 2.07 * 0.50 * 5.4683 + 1.00 * 0.0545                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1494      final r-factor (work) = 0.1470          |
| start r-factor (free) = 0.2016      final r-factor (free) = 0.1999          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6891 = 0.31 * 1.00 * 5.4683 + 1.00 * 0.0136                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6811 = 0.31 * 1.00 * 5.3859 + 1.00 * 0.0308                               |
|-----------------------------------------------------------------------------|
| number of iterations = 4       |    number of function evaluations = 7      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.802)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.37   15.59    None  None   None       |
|    all(noH): 2823   0      0.00    94.37   15.59    None  None   None       |
|    Sol.    : 438    0      4.12    82.06   39.07    None  None   None       |
|    Mac.    : 2385   0      0.00    94.37   11.28    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 -   9.437: 1328   |   5:    47.187 -  56.624:  106        |
|      1:     9.437 -  18.875:  823   |   6:    56.624 -  66.061:   47        |
|      2:    18.875 -  28.312:  241   |   7:    66.061 -  75.499:   10        |
|      3:    28.312 -  37.749:  126   |   8:    75.499 -  84.936:    5        |
|      4:    37.749 -  47.187:  134   |   9:    84.936 -  94.373:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1470 r_free = 0.1999             target_work(ml) = 5.380         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1469 r_free = 0.1997             target_work(ml) = 5.379         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1469   r_free= 0.1997   ksol= 0.34   Bsol= 54.46   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.55,-0.34,0.72,-0.00,0.00,0.00); trace/3= 0.31                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.379482                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2215 -  4.6874 0.99   1422  162 0.1070 0.1513      5.4579      5.6998|
|  2:  4.6874 -  3.7386 0.99   1372  150 0.1046 0.1454       5.616       5.902|
|  3:  3.7386 -  3.2714 0.99   1338  145 0.1402 0.1839      5.7042      5.9645|
|  4:  3.2714 -  2.9747 0.99   1345  158 0.1612 0.2090      5.6947      5.8336|
|  5:  2.9747 -  2.7629 0.99   1332  142 0.1772 0.2299      5.5713      5.8062|
|  6:  2.7629 -  2.6008 0.99   1327  148 0.1644 0.2298      5.4449      5.6342|
|  7:  2.6008 -  2.4711 0.99   1315  143 0.1743 0.2206      5.4093      5.5997|
|  8:  2.4711 -  2.3640 0.98   1295  149 0.1643 0.2193      5.3235      5.5322|
|  9:  2.3640 -  2.2733 0.98   1308  147 0.1627 0.2393      5.2897       5.533|
| 10:  2.2733 -  2.1951 1.00   1287  150 0.1535 0.2282      5.2087       5.433|
| 11:  2.1951 -  2.1266 0.98   1327  137 0.1535 0.2161      5.1882      5.5127|
| 12:  2.1266 -  2.0660 0.98   1279  151 0.1544 0.2223      5.1167      5.3363|
| 13:  2.0660 -  2.0117 0.89   1174  125 0.1616 0.2065       5.029      5.2142|
| 14:  2.0117 -  1.9628 0.38    509   52 0.1328 0.1698       4.859      5.0928|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2215 -  4.6874  1422   162  0.93  10.82   0.98     0.96       8903.32|
|  2:  4.6874 -  3.7386  1372   150  0.94  10.44   1.02     1.01      12960.23|
|  3:  3.7386 -  3.2714  1338   145  0.90  15.76   1.04     1.04      16628.35|
|  4:  3.2714 -  2.9747  1345   158  0.87  19.39   1.02     0.98      17258.80|
|  5:  2.9747 -  2.7629  1332   142  0.86  20.70   1.00     0.98      13497.22|
|  6:  2.7629 -  2.6008  1327   148  0.85  21.72   0.99     0.96      11719.53|
|  7:  2.6008 -  2.4711  1315   143  0.85  21.29   0.99     0.95       9947.29|
|  8:  2.4711 -  2.3640  1295   149  0.85  21.23   0.99     0.95       8806.76|
|  9:  2.3640 -  2.2733  1308   147  0.85  21.42   1.01     0.96       8407.46|
| 10:  2.2733 -  2.1951  1287   150  0.86  20.61   1.01     0.97       7298.00|
| 11:  2.1951 -  2.1266  1327   137  0.85  21.72   1.01     0.96       7374.09|
| 12:  2.1266 -  2.0660  1279   151  0.86  21.15   1.00     0.99       6429.19|
| 13:  2.0660 -  2.0117  1174   125  0.85  21.42   1.00     0.98       5222.72|
| 14:  2.0117 -  1.9628   509    52  0.88  18.81   1.00     0.96       3833.70|
|alpha:            min =        0.95 max =            1.04 mean =         0.98|
|beta:             min =     3833.70 max =        17258.80 mean =     10232.56|
|figures of merit: min =        0.00 max =            1.00 mean =         0.87|
|phase err.(work): min =        0.00 max =           89.95 mean =        18.94|
|phase err.(test): min =        0.00 max =           89.36 mean =        18.01|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1473   r_free= 0.2000   ksol= 0.34   Bsol= 54.63   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.21,-0.69,0.49,-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: 5.380706                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.22 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1473   r_free= 0.2000   ksol= 0.34   Bsol= 54.63   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.21,-0.69,0.49,-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: 5.380706                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2215 -  4.6874 0.99   1422  162 0.1085 0.1525      5.4665      5.7009|
|  2:  4.6874 -  3.7386 0.99   1372  150 0.1050 0.1461      5.6217      5.9083|
|  3:  3.7386 -  3.2714 0.99   1338  145 0.1402 0.1840       5.706      5.9644|
|  4:  3.2714 -  2.9747 0.99   1345  158 0.1619 0.2089      5.6965      5.8326|
|  5:  2.9747 -  2.7629 0.99   1332  142 0.1774 0.2294      5.5716      5.8047|
|  6:  2.7629 -  2.6008 0.99   1327  148 0.1643 0.2295      5.4438      5.6325|
|  7:  2.6008 -  2.4711 0.99   1315  143 0.1742 0.2205      5.4092      5.5981|
|  8:  2.4711 -  2.3640 0.98   1295  149 0.1640 0.2195      5.3224      5.5327|
|  9:  2.3640 -  2.2733 0.98   1308  147 0.1626 0.2388      5.2892       5.531|
| 10:  2.2733 -  2.1951 1.00   1287  150 0.1535 0.2283      5.2082      5.4342|
| 11:  2.1951 -  2.1266 0.98   1327  137 0.1534 0.2165      5.1883      5.5136|
| 12:  2.1266 -  2.0660 0.98   1279  151 0.1544 0.2225      5.1172      5.3375|
| 13:  2.0660 -  2.0117 0.89   1174  125 0.1616 0.2068      5.0292      5.2142|
| 14:  2.0117 -  1.9628 0.38    509   52 0.1327 0.1694      4.8584      5.0925|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2215 -  4.6874  1422   162  0.92  11.06   0.97     0.95       9056.66|
|  2:  4.6874 -  3.7386  1372   150  0.94  10.49   1.02     1.01      13066.45|
|  3:  3.7386 -  3.2714  1338   145  0.90  15.75   1.04     1.04      16663.82|
|  4:  3.2714 -  2.9747  1345   158  0.87  19.40   1.01     0.98      17277.14|
|  5:  2.9747 -  2.7629  1332   142  0.86  20.68   1.00     0.97      13477.46|
|  6:  2.7629 -  2.6008  1327   148  0.85  21.68   0.99     0.96      11677.48|
|  7:  2.6008 -  2.4711  1315   143  0.85  21.28   0.99     0.95       9939.09|
|  8:  2.4711 -  2.3640  1295   149  0.85  21.20   0.99     0.95       8788.39|
|  9:  2.3640 -  2.2733  1308   147  0.85  21.39   1.01     0.96       8394.02|
| 10:  2.2733 -  2.1951  1287   150  0.86  20.60   1.00     0.96       7290.78|
| 11:  2.1951 -  2.1266  1327   137  0.85  21.73   1.01     0.95       7385.01|
| 12:  2.1266 -  2.0660  1279   151  0.86  21.17   1.00     0.99       6440.64|
| 13:  2.0660 -  2.0117  1174   125  0.85  21.43   1.00     0.97       5228.94|
| 14:  2.0117 -  1.9628   509    52  0.88  18.79   0.99     0.96       3827.73|
|alpha:            min =        0.95 max =            1.04 mean =         0.97|
|beta:             min =     3827.73 max =        17277.14 mean =     10251.04|
|figures of merit: min =        0.00 max =            1.00 mean =         0.87|
|phase err.(work): min =        0.00 max =           89.98 mean =        18.96|
|phase err.(test): min =        0.00 max =           89.71 mean =        18.03|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.802)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.17    94.54   15.76    None  None   None       |
|    all(noH): 2823   0      0.17    94.54   15.76    None  None   None       |
|    Sol.    : 438    0      4.29    82.23   39.23    None  None   None       |
|    Mac.    : 2385   0      0.17    94.54   11.45    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:     0.167 -   9.604: 1328   |   5:    47.353 -  56.791:  106        |
|      1:     9.604 -  19.041:  823   |   6:    56.791 -  66.228:   47        |
|      2:    19.041 -  28.479:  241   |   7:    66.228 -  75.665:   10        |
|      3:    28.479 -  37.916:  126   |   8:    75.665 -  85.102:    5        |
|      4:    37.916 -  47.353:  134   |   9:    85.102 -  94.540:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 348         
Filter by distance & map next to the model:
   mapped sites are within: 0.301 - 5.312
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 343 from: 348
   mapped sites are within: 0.717 - 5.312

peak=    7.860 closest distance to " CB  VAL A 230 " =    1.443
peak=    6.582 closest distance to " CG2 VAL A 296 " =    1.306
peak=    6.413 closest distance to " O   HOH Z 130 " =    1.404
peak=    5.917 closest distance to " CD  ARG A 138 " =    1.140
peak=    5.605 closest distance to " CG  LEU A   5 " =    1.438
peak=    5.561 closest distance to " CB  PRO A  54 " =    1.231
peak=    5.557 closest distance to " NH1 ARG A 138 " =    1.081
peak=    5.418 closest distance to " O   HOH Z 178 " =    1.079
peak=    5.406 closest distance to " O   HOH Z 117 " =    1.278
peak=    5.336 closest distance to " O   HOH Z 255 " =    0.971
peak=    5.330 closest distance to " O   HOH Z 403 " =    1.645
peak=    5.298 closest distance to " CG  ARG A 138 " =    1.289
peak=    5.292 closest distance to " O   HOH Z  97 " =    1.535
peak=    5.288 closest distance to " O   HOH Z 183 " =    1.800
peak=    5.274 closest distance to " O   HOH Z 415 " =    1.235
peak=    5.241 closest distance to " NH1 ARG A  56 " =    1.467
peak=    5.232 closest distance to " O   HOH Z 111 " =    1.842
peak=    5.178 closest distance to " CD1AILE A 234 " =    1.132
peak=    5.158 closest distance to " O   HOH Z 268 " =    1.099
peak=    5.145 closest distance to " O   HOH Z 390 " =    1.076
peak=    5.109 closest distance to " OG  SER A 276 " =    0.938
peak=    5.095 closest distance to " O   HOH Z 126 " =    1.697
peak=    5.034 closest distance to " O   HOH Z 159 " =    1.008
peak=    5.030 closest distance to " O   HOH Z 102 " =    0.995
peak=    5.012 closest distance to " CA  SER A  87 " =    0.860
peak=    4.878 closest distance to " O   HOH Z 410 " =    1.962
peak=    4.873 closest distance to " NZ ALYS A 290 " =    1.239
peak=    4.868 closest distance to " O   HOH Z 401 " =    1.501
peak=    4.865 closest distance to " O   HOH Z  57 " =    1.641
peak=    4.843 closest distance to " O   HOH Z  15 " =    0.869
peak=    4.802 closest distance to " O   HOH Z 374 " =    1.227
peak=    4.800 closest distance to " O   HOH Z 182 " =    1.379
peak=    4.747 closest distance to " O   HOH Z  63 " =    1.521
peak=    4.736 closest distance to " O   HOH Z 350 " =    1.341
peak=    4.727 closest distance to " NE2 GLN A  11 " =    1.167
peak=    4.691 closest distance to " NH2AARG A 102 " =    1.152
peak=    4.685 closest distance to " O   HOH Z 222 " =    1.473
peak=    4.670 closest distance to " O   HOH Z  65 " =    1.597
peak=    4.661 closest distance to " O   HOH Z 147 " =    1.772
peak=    4.652 closest distance to " O   PRO A 198 " =    1.356
peak=    4.629 closest distance to " CB  VAL A 230 " =    1.326
peak=    4.608 closest distance to " CB  SER A 216 " =    1.046
peak=    4.601 closest distance to " O   HOH Z 144 " =    1.784
peak=    4.599 closest distance to " O   HOH Z   7 " =    1.851
peak=    4.564 closest distance to " CD ALYS A 290 " =    1.166
peak=    4.564 closest distance to " O   HOH Z  46 " =    1.255
peak=    4.537 closest distance to " CB  ASP A 124 " =    0.956
peak=    4.516 closest distance to " O   HOH Z  37 " =    1.340
peak=    4.504 closest distance to " CD2 LEU A 228 " =    1.295
peak=    4.435 closest distance to " O   HOH Z 385 " =    0.993
peak=    4.417 closest distance to " N   GLN A 278 " =    0.972
peak=    4.416 closest distance to " O   HOH Z 232 " =    2.161
peak=    4.366 closest distance to " O   HOH Z 120 " =    1.253
peak=    4.366 closest distance to " O   HOH Z 239 " =    1.667
peak=    4.359 closest distance to " O   HOH Z 133 " =    1.627
peak=    4.304 closest distance to " CB  ASN A 148 " =    1.269
peak=    4.300 closest distance to " NH2 ARG A 269 " =    0.933
peak=    4.268 closest distance to " CB  MET A  40 " =    0.815
peak=    4.256 closest distance to " O   HOH Z 184 " =    1.871
peak=    4.231 closest distance to " O   HOH Z 132 " =    1.397
peak=    4.222 closest distance to " CD2 TRP A 179 " =    1.965
peak=    4.196 closest distance to " CG  PRO A 198 " =    1.510
peak=    4.185 closest distance to " O   HOH Z 316 " =    3.080
peak=    4.167 closest distance to " CB  ARG A 275 " =    1.092
peak=    4.156 closest distance to " O   HOH Z  69 " =    2.294
peak=    4.154 closest distance to " CA  ALA A 295 " =    0.965
peak=    4.138 closest distance to " O   HOH Z 373 " =    1.900
peak=    4.114 closest distance to " O   HOH Z 170 " =    1.442
peak=    4.110 closest distance to " CB  SER A   3 " =    1.505
peak=    4.083 closest distance to " OD1 ASN A 217 " =    1.684
peak=    4.077 closest distance to " O   HOH Z 411 " =    3.333
peak=    4.060 closest distance to " O   HOH Z  48 " =    1.822
peak=    4.055 closest distance to " OE1 GLU A   2 " =    1.972
peak=    4.035 closest distance to " CB  PRO A  54 " =    1.342
peak=    4.030 closest distance to " O   HOH Z  51 " =    2.119
peak=    4.024 closest distance to " O   HOH Z 139 " =    1.705
peak=    4.012 closest distance to " CG2 THR A 279 " =    1.160
peak=    4.006 closest distance to " CZ3 TRP A 123 " =    1.434
peak=    4.002 closest distance to " CZ  PHE A 192 " =    1.096
peak=    3.988 closest distance to " CB  SER A  63 " =    1.402
peak=    3.987 closest distance to " CG  LEU A 167 " =    1.340
peak=    3.981 closest distance to " O   HOH Z  78 " =    1.689
peak=    3.957 closest distance to " O   HOH Z  41 " =    0.966
peak=    3.954 closest distance to " O   HOH Z 298 " =    2.174
peak=    3.941 closest distance to " CB  LYS A 290 " =    0.872
peak=    3.932 closest distance to " CA  MET A  47 " =    1.134
peak=    3.923 closest distance to " OG  SER A  26 " =    1.457
peak=    3.916 closest distance to " CA  LEU A 282 " =    0.982
peak=    3.906 closest distance to " N   CYS A 260 " =    1.128
peak=    3.905 closest distance to " O   HOH Z 357 " =    1.576
peak=    3.896 closest distance to " CE3 TRP A 274 " =    2.400
peak=    3.891 closest distance to " NE2 GLN A  58 " =    5.266
peak=    3.890 closest distance to " CD1 LEU A   5 " =    1.066
peak=    3.887 closest distance to " CB  MET A  47 " =    1.163
peak=    3.878 closest distance to " O   HOH Z 361 " =    1.577
peak=    3.865 closest distance to " CG  LEU A   5 " =    1.256
peak=    3.864 closest distance to " CA  ALA A  51 " =    1.046
peak=    3.864 closest distance to " CB  SER A 210 " =    0.979
peak=    3.864 closest distance to " CA  ILE A 234 " =    1.181
peak=    3.861 closest distance to " O   HOH Z 236 " =    1.862
peak=    3.854 closest distance to " CG  GLN A  88 " =    0.913
peak=    3.849 closest distance to " CA  GLU A 152 " =    1.134
peak=    3.843 closest distance to " O   HOH Z 186 " =    1.837
peak=    3.835 closest distance to " CG2 THR A 221 " =    1.352
peak=    3.834 closest distance to " N   GLY A  98 " =    1.080
peak=    3.830 closest distance to " O   HOH Z 427 " =    2.732
peak=    3.826 closest distance to " O   HOH Z 344 " =    1.203
peak=    3.825 closest distance to " NH2BARG A 190 " =    1.566
peak=    3.823 closest distance to " CA  VAL A 296 " =    1.122
peak=    3.822 closest distance to " CA  ASP A  50 " =    1.070
peak=    3.819 closest distance to " O   HOH Z 424 " =    1.275
peak=    3.818 closest distance to " CA  ASN A 284 " =    0.720
peak=    3.817 closest distance to " OE1 GLN A  88 " =    1.007
peak=    3.810 closest distance to " N   SER A 210 " =    0.871
peak=    3.808 closest distance to " O   HOH Z 127 " =    1.116
peak=    3.805 closest distance to " O   HOH Z 233 " =    1.380
peak=    3.804 closest distance to " O   GLU A 152 " =    1.476
peak=    3.803 closest distance to " NH2 ARG A  24 " =    0.723
peak=    3.797 closest distance to " O   HOH Z 226 " =    1.067
peak=    3.785 closest distance to " CE  MET A  93 " =    1.476
peak=    3.784 closest distance to " CG  PRO A 280 " =    1.031
peak=    3.762 closest distance to " O   HOH Z   9 " =    1.220
peak=    3.761 closest distance to " CB  GLN A 183 " =    1.151
peak=    3.760 closest distance to " CB  ALA A  10 " =    1.302
peak=    3.753 closest distance to " O   HOH Z 263 " =    1.602
peak=    3.751 closest distance to " CA  GLY A 136 " =    1.183
peak=    3.748 closest distance to " ND2 ASN A  60 " =    3.041
peak=    3.747 closest distance to " O   PRO A 198 " =    1.942
peak=    3.747 closest distance to " O   HOH Z 222 " =    1.942
peak=    3.745 closest distance to " CA  ASN A 127 " =    1.057
peak=    3.741 closest distance to " CG  LYS A  76 " =    1.699
peak=    3.734 closest distance to " O   HOH Z 236 " =    1.823
peak=    3.727 closest distance to " O   HOH Z 423 " =    1.763
peak=    3.723 closest distance to " CB  TYR A 169 " =    0.826
peak=    3.709 closest distance to " O   HOH Z 148 " =    2.191
peak=    3.707 closest distance to " NH2BARG A 145 " =    1.717
peak=    3.706 closest distance to " C   ASN A 209 " =    1.613
peak=    3.706 closest distance to " O   HOH Z 126 " =    2.286
peak=    3.704 closest distance to " O   HOH Z 214 " =    1.579
peak=    3.694 closest distance to " CG  LEU A 228 " =    1.167
peak=    3.693 closest distance to " OG ASER A 134 " =    1.297
peak=    3.686 closest distance to " O   HOH Z  44 " =    2.505
peak=    3.684 closest distance to " CG  GLU A   2 " =    1.280
peak=    3.684 closest distance to " O   HOH Z 112 " =    1.108
peak=    3.670 closest distance to " CH2 TRP A 150 " =    0.897
peak=    3.670 closest distance to " O   HOH Z 272 " =    1.994
peak=    3.667 closest distance to " O   HOH Z 217 " =    2.540
peak=    3.667 closest distance to " CB  TRP A 179 " =    1.450
peak=    3.667 closest distance to " O   HOH Z  59 " =    1.595
peak=    3.658 closest distance to " N   TYR A  15 " =    1.004
peak=    3.649 closest distance to " O   HOH Z 234 " =    3.624
peak=    3.645 closest distance to " O   HOH Z 282 " =    2.274
peak=    3.644 closest distance to " OD2 ASP A 286 " =    2.941
peak=    3.643 closest distance to " NH1AARG A 145 " =    1.113
peak=    3.636 closest distance to " O   HOH Z 371 " =    3.132
peak=    3.635 closest distance to " O   HOH Z 257 " =    2.401
peak=    3.633 closest distance to " O   HOH Z 193 " =    1.872
peak=    3.630 closest distance to " O   HOH Z 167 " =    1.700
peak=    3.626 closest distance to " NE AARG A 102 " =    1.297
peak=    3.624 closest distance to " O   HOH Z 116 " =    1.424
peak=    3.623 closest distance to " CG1 ILE A 120 " =    1.368
peak=    3.619 closest distance to " O   HOH Z 400 " =    0.921
peak=    3.617 closest distance to " CE3 TRP A 274 " =    1.433
peak=    3.607 closest distance to " CG2 ILE A 234 " =    0.934
peak=    3.607 closest distance to " CG1BVAL A 121 " =    2.088
peak=    3.601 closest distance to " CA  VAL A 153 " =    1.206
peak=    3.600 closest distance to " CG  PRO A 213 " =    1.364
peak=    3.590 closest distance to " N   GLN A  73 " =    1.175
peak=    3.582 closest distance to " O   HOH Z   1 " =    2.004
peak=    3.578 closest distance to " CB  GLN A 223 " =    1.310
peak=    3.576 closest distance to " CB  ALA A 100 " =    1.637
peak=    3.573 closest distance to " NH1BARG A 275 " =    1.538
peak=    3.572 closest distance to " CA  SER A  62 " =    0.794
peak=    3.563 closest distance to " CG  GLN A 144 " =    0.916
peak=    3.554 closest distance to " O   HOH Z 105 " =    1.392
peak=    3.553 closest distance to " CB  GLU A   2 " =    1.202
peak=    3.548 closest distance to " O   HOH Z 122 " =    2.108
peak=    3.548 closest distance to " O   HOH Z 192 " =    1.348
peak=    3.545 closest distance to " CG  PRO A 243 " =    1.129
peak=    3.535 closest distance to " O   HOH Z 225 " =    1.633
peak=    3.530 closest distance to " CB  PRO A 198 " =    1.138
peak=    3.530 closest distance to " O   HOH Z 416 " =    1.505
peak=    3.527 closest distance to " O   HOH Z 153 " =    3.953
peak=    3.517 closest distance to " O   HOH Z 325 " =    1.860
peak=    3.516 closest distance to " CB  TYR A  30 " =    1.488
peak=    3.514 closest distance to " O   HOH Z  11 " =    0.862
peak=    3.512 closest distance to " CB  VAL A 202 " =    1.568
peak=    3.508 closest distance to " CG2 VAL A 257 " =    1.258
peak=    3.507 closest distance to " O   HOH Z 155 " =    1.645
peak=    3.506 closest distance to " CB  TRP A 266 " =    0.967
peak=    3.505 closest distance to " O   HOH Z 207 " =    2.588
peak=    3.501 closest distance to " CB  ARG A 138 " =    0.828
peak=    3.500 closest distance to " CB  ASN A 187 " =    1.070
peak=    3.496 closest distance to " O   HOH Z 146 " =    1.689
peak=    3.488 closest distance to " O   HOH Z  30 " =    1.977
peak=    3.487 closest distance to " CG2 ILE A 109 " =    1.070
peak=    3.484 closest distance to " NZ  LYS A 117 " =    1.462
peak=    3.483 closest distance to " CB  GLU A 128 " =    1.064
peak=    3.479 closest distance to " N   PHE A 130 " =    1.300
peak=    3.476 closest distance to " O   HOH Z 108 " =    1.905
peak=    3.475 closest distance to " CE2 PHE A  16 " =    0.866
peak=    3.472 closest distance to " O   HOH Z 280 " =    2.892
peak=    3.471 closest distance to " OD1 ASN A  45 " =    1.555
peak=    3.470 closest distance to " CB  LEU A 300 " =    0.971
peak=    3.469 closest distance to " CD  ARG A  56 " =    0.947
peak=    3.459 closest distance to " CA  THR A 221 " =    0.844
peak=    3.448 closest distance to " O   HOH Z 104 " =    1.941
peak=    3.444 closest distance to " O   HOH Z  64 " =    2.020
peak=    3.441 closest distance to " O   HOH Z  33 " =    2.049
peak=    3.438 closest distance to " NE AARG A 275 " =    1.655
peak=    3.432 closest distance to " O   HOH Z 179 " =    0.831
peak=    3.432 closest distance to " O   HOH Z 271 " =    2.199
peak=    3.432 closest distance to " O   HOH Z 417 " =    1.201
peak=    3.431 closest distance to " CB  PHE A 225 " =    1.485
peak=    3.430 closest distance to " N   SER A  97 " =    0.763
peak=    3.427 closest distance to " NH2AARG A 145 " =    0.937
peak=    3.425 closest distance to " O   HOH Z 133 " =    2.412
peak=    3.420 closest distance to " O   HOH Z   9 " =    2.159
peak=    3.417 closest distance to " CA  VAL A  41 " =    0.978
peak=    3.416 closest distance to " CA  ALA A 180 " =    1.295
peak=    3.414 closest distance to " N   SER A  12 " =    1.581
peak=    3.412 closest distance to " N   ARG A  24 " =    0.949
peak=    3.406 closest distance to " OD1 ASN A 148 " =    2.166
peak=    3.406 closest distance to " N   GLU A   2 " =    1.331
peak=    3.405 closest distance to " O   HOH Z 368 " =    2.004
peak=    3.398 closest distance to " CA  TRP A  92 " =    1.314
peak=    3.398 closest distance to " CG2 THR A 251 " =    1.656
peak=    3.396 closest distance to " CD1 LEU A 300 " =    1.145
peak=    3.393 closest distance to " O   HOH Z 171 " =    1.798
peak=    3.390 closest distance to " O   HOH Z 369 " =    2.237
peak=    3.385 closest distance to " CD  LYS A 119 " =    1.239
peak=    3.384 closest distance to " CB  ALA A 104 " =    0.876
peak=    3.383 closest distance to " CG2 ILE A 151 " =    1.011
peak=    3.383 closest distance to " O   HOH Z 302 " =    1.670
peak=    3.380 closest distance to " NH1 ARG A  66 " =    1.814
peak=    3.375 closest distance to " CB  LYS A  48 " =    1.014
peak=    3.372 closest distance to " OE1 GLN A 240 " =    1.738
peak=    3.372 closest distance to " O   HOH Z 108 " =    1.699
peak=    3.362 closest distance to " ND2 ASN A 249 " =    1.991
peak=    3.357 closest distance to " O   HOH Z  94 " =    2.409
peak=    3.356 closest distance to " O   HOH Z 284 " =    1.490
peak=    3.351 closest distance to " O   HOH Z 177 " =    1.751
peak=    3.348 closest distance to " O   HOH Z 427 " =    1.543
peak=    3.344 closest distance to " O   HOH Z 409 " =    2.206
peak=    3.343 closest distance to " O   HOH Z 246 " =    1.533
peak=    3.335 closest distance to " O   HOH Z 311 " =    4.566
peak=    3.334 closest distance to " O   HOH Z 148 " =    2.471
peak=    3.327 closest distance to " O   HOH Z  85 " =    1.987
peak=    3.326 closest distance to " CA  ASP A 124 " =    0.854
peak=    3.326 closest distance to " CB  THR A  82 " =    1.113
peak=    3.320 closest distance to " O   HOH Z 418 " =    1.250
peak=    3.317 closest distance to " CB  ALA A  43 " =    0.919
peak=    3.312 closest distance to " O   HOH Z 204 " =    1.664
peak=    3.311 closest distance to " CB  ALA A 137 " =    0.947
peak=    3.308 closest distance to " O   HOH Z 380 " =    1.954
peak=    3.307 closest distance to " NE BARG A 275 " =    1.058
peak=    3.304 closest distance to " CG2 VAL A 202 " =    1.347
peak=    3.303 closest distance to " O   HOH Z 414 " =    1.689
peak=    3.303 closest distance to " CB  SER A 206 " =    1.071
peak=    3.300 closest distance to " O   HOH Z 153 " =    4.028
peak=    3.299 closest distance to " CB  GLN A 103 " =    1.322
peak=    3.290 closest distance to " NH2 ARG A 138 " =    1.413
peak=    3.289 closest distance to " O   HOH Z 124 " =    1.226
peak=    3.288 closest distance to " O   HOH Z  45 " =    0.796
peak=    3.286 closest distance to " N   ASP A 162 " =    1.275
peak=    3.284 closest distance to " OG BSER A 134 " =    2.689
peak=    3.282 closest distance to " NH2 ARG A  79 " =    1.679
peak=    3.281 closest distance to " O   GLY A 302 " =    2.215
peak=    3.279 closest distance to " CA  LEU A 101 " =    1.220
peak=    3.279 closest distance to " N   ALA A 292 " =    1.073
peak=    3.279 closest distance to " CA  ARG A 102 " =    1.149
peak=    3.275 closest distance to " O   HOH Z 164 " =    2.160
peak=    3.266 closest distance to " CG1 ILE A  33 " =    1.334
peak=    3.263 closest distance to " CA  ARG A  36 " =    1.249
peak=    3.262 closest distance to " CG  GLN A  89 " =    1.504
peak=    3.260 closest distance to " CB  GLU A 152 " =    1.374
peak=    3.258 closest distance to " O   ALA A  71 " =    1.025
peak=    3.257 closest distance to " N   ARG A  56 " =    0.795
peak=    3.256 closest distance to " O   HOH Z 253 " =    1.680
peak=    3.255 closest distance to " CG1AVAL A 121 " =    1.001
peak=    3.255 closest distance to " CB  SER A 273 " =    0.806
peak=    3.253 closest distance to " NH1 ARG A  79 " =    1.050
peak=    3.253 closest distance to " CB  ALA A 114 " =    1.022
peak=    3.252 closest distance to " N   GLN A  55 " =    0.852
peak=    3.251 closest distance to " CD  ARG A 269 " =    0.882
peak=    3.249 closest distance to " CB  SER A  62 " =    1.338
peak=    3.248 closest distance to " OG BSER A 258 " =    1.010
peak=    3.243 closest distance to " O   HOH Z 220 " =    1.479
peak=    3.239 closest distance to " CG  LYS A 166 " =    1.324
peak=    3.239 closest distance to " O   ALA A 291 " =    1.560
peak=    3.235 closest distance to " CA  GLY A 267 " =    1.335
peak=    3.232 closest distance to " SD  MET A 188 " =    1.559
peak=    3.227 closest distance to " O   HOH Z 419 " =    1.706
peak=    3.226 closest distance to " O   HOH Z 219 " =    2.139
peak=    3.223 closest distance to " O   HOH Z 287 " =    2.220
peak=    3.221 closest distance to " CB  GLU A 277 " =    3.634
peak=    3.213 closest distance to " CA  GLN A 223 " =    1.007
peak=    3.212 closest distance to " O   HOH Z 406 " =    1.700
peak=    3.209 closest distance to " CB  LEU A 228 " =    1.223
peak=    3.189 closest distance to " CB  ALA A 161 " =    1.108
peak=    3.184 closest distance to " O   HOH Z  51 " =    1.683
peak=    3.178 closest distance to " O   HOH Z 244 " =    1.716
peak=    3.177 closest distance to " CB  ASN A 285 " =    0.834
peak=    3.176 closest distance to " OD1 ASP A 231 " =    1.935
peak=    3.170 closest distance to " O   HOH Z  61 " =    1.917
peak=    3.166 closest distance to " O   HOH Z  59 " =    2.024
peak=    3.164 closest distance to " NE2 GLN A  58 " =    3.368
peak=    3.162 closest distance to " C   ALA A 299 " =    0.988
peak=    3.161 closest distance to " O   HOH Z 139 " =    1.920
peak=    3.159 closest distance to " CB  VAL A 265 " =    1.384
peak=    3.151 closest distance to " O   HOH Z 132 " =    2.101
peak=    3.143 closest distance to " CB  ILE A 120 " =    1.132
peak=    3.141 closest distance to " CG1 VAL A 296 " =    1.066
peak=    3.141 closest distance to " O   ALA A 233 " =    1.932
peak=    3.136 closest distance to " CB  ASP A 140 " =    0.923
peak=    3.129 closest distance to " CA  ALA A  21 " =    1.160
peak=    3.127 closest distance to " O   HOH Z  22 " =    1.896
peak=    3.125 closest distance to " CB  GLU A 236 " =    1.358
peak=    3.123 closest distance to " N   ILE A  33 " =    1.204
peak=    3.122 closest distance to " O   HOH Z 207 " =    1.653
peak=    3.119 closest distance to " O   HOH Z 217 " =    1.657
peak=    3.116 closest distance to " O   HOH Z 218 " =    2.175
peak=    3.113 closest distance to " O   ASN A 301 " =    2.157
peak=    3.113 closest distance to " CB  ARG A 138 " =    1.181
peak=    3.103 closest distance to " O   HOH Z 344 " =    3.072
peak=    3.098 closest distance to " CA  ARG A 159 " =    1.365
peak=    3.096 closest distance to " NH1BARG A 145 " =    1.064
peak=    3.096 closest distance to " CB  VAL A 250 " =    1.102
peak=    3.088 closest distance to " O   HOH Z 128 " =    2.183
peak=    3.087 closest distance to " O   HOH Z 172 " =    5.312
peak=    3.082 closest distance to " O   HOH Z 143 " =    1.195
peak=    3.082 closest distance to " O   HOH Z  43 " =    1.440
peak=    3.082 closest distance to " CB  ARG A  56 " =    0.972
peak=    3.080 closest distance to " CG  ARG A 159 " =    0.928
peak=    3.071 closest distance to " NZ  LYS A 193 " =    1.279
peak=    3.069 closest distance to " CB  ARG A 139 " =    0.717
peak=    3.062 closest distance to " CG2 VAL A 202 " =    1.597
peak=    3.056 closest distance to " CA  ILE A 263 " =    1.112
peak=    3.051 closest distance to " O   HOH Z 110 " =    1.616
peak=    3.049 closest distance to " O   ALA A 165 " =    1.297
peak=    3.043 closest distance to " O   ASN A 217 " =    1.500
peak=    3.020 closest distance to " CA  TYR A  30 " =    1.111
peak=    3.006 closest distance to " CA  TYR A 116 " =    1.500

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 208         
Filter by distance & map next to the model:
   mapped sites are within: 0.269 - 5.914
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 201 from: 208
   mapped sites are within: 0.708 - 5.914

peak=   -5.854 closest distance to " CD  ARG A 138 " =    1.004
peak=   -5.213 closest distance to " CG2 VAL A 230 " =    0.876
peak=   -4.578 closest distance to " C   ASN A 285 " =    2.401
peak=   -4.500 closest distance to " O   HOH Z 290 " =    1.129
peak=   -4.486 closest distance to " O   HOH Z 102 " =    0.834
peak=   -4.463 closest distance to " O   PRO A 198 " =    1.166
peak=   -4.286 closest distance to " CG  MET A 105 " =    0.859
peak=   -4.170 closest distance to " O   HOH Z 111 " =    2.335
peak=   -4.098 closest distance to " O   HOH Z  52 " =    1.566
peak=   -4.096 closest distance to " OE1 GLN A  88 " =    0.951
peak=   -4.078 closest distance to " O   HOH Z  97 " =    1.447
peak=   -4.045 closest distance to " O   HOH Z  71 " =    0.946
peak=   -4.040 closest distance to " CB  PRO A  54 " =    2.593
peak=   -4.000 closest distance to " C   PHE A 155 " =    0.790
peak=   -3.984 closest distance to " OG  SER A  97 " =    2.085
peak=   -3.925 closest distance to " O   HOH Z  97 " =    1.345
peak=   -3.923 closest distance to " CB  ALA A   9 " =    2.685
peak=   -3.920 closest distance to " CG  PRO A 163 " =    2.397
peak=   -3.916 closest distance to " O   HOH Z  51 " =    0.870
peak=   -3.879 closest distance to " OG ASER A 134 " =    1.019
peak=   -3.877 closest distance to " O   HOH Z 404 " =    1.149
peak=   -3.860 closest distance to " CD2 LEU A 143 " =    2.512
peak=   -3.831 closest distance to " CB  GLN A  55 " =    1.195
peak=   -3.810 closest distance to " NH1 ARG A 138 " =    1.009
peak=   -3.802 closest distance to " C   ASP A  50 " =    1.086
peak=   -3.768 closest distance to " CG  GLN A  88 " =    0.982
peak=   -3.759 closest distance to " ND2BASN A 224 " =    1.357
peak=   -3.758 closest distance to " O   GLY A 203 " =    2.404
peak=   -3.730 closest distance to " CD  ARG A  14 " =    2.998
peak=   -3.722 closest distance to " O   HOH Z  46 " =    0.743
peak=   -3.722 closest distance to " OG  SER A  87 " =    1.293
peak=   -3.717 closest distance to " NH2AARG A 275 " =    5.790
peak=   -3.666 closest distance to " O   ALA A 226 " =    1.424
peak=   -3.662 closest distance to " OE1 GLN A 278 " =    1.258
peak=   -3.646 closest distance to " O   HOH Z 377 " =    0.938
peak=   -3.637 closest distance to " CZ  ARG A  24 " =    2.011
peak=   -3.630 closest distance to " O   HOH Z  39 " =    1.216
peak=   -3.600 closest distance to " CA  GLY A 133 " =    2.027
peak=   -3.590 closest distance to " CD2 LEU A   5 " =    0.777
peak=   -3.586 closest distance to " CB  SER A 271 " =    1.218
peak=   -3.583 closest distance to " O   HOH Z 111 " =    0.869
peak=   -3.583 closest distance to " O   HOH Z 185 " =    2.643
peak=   -3.579 closest distance to " O   HOH Z 435 " =    2.302
peak=   -3.569 closest distance to " CB  ALA A  43 " =    2.277
peak=   -3.569 closest distance to " OG  SER A 245 " =    1.507
peak=   -3.565 closest distance to " OG  SER A  63 " =    1.224
peak=   -3.554 closest distance to " OG  SER A 206 " =    1.536
peak=   -3.553 closest distance to " O   HOH Z 359 " =    1.787
peak=   -3.552 closest distance to " O   HOH Z 266 " =    4.834
peak=   -3.549 closest distance to " O   GLY A  80 " =    2.390
peak=   -3.543 closest distance to " CD2 LEU A 237 " =    2.332
peak=   -3.543 closest distance to " O   HOH Z 103 " =    2.307
peak=   -3.542 closest distance to " CG BLYS A 290 " =    0.952
peak=   -3.534 closest distance to " O   HOH Z 389 " =    2.092
peak=   -3.527 closest distance to " CA  ARG A  56 " =    1.145
peak=   -3.525 closest distance to " O   HOH Z  90 " =    1.808
peak=   -3.521 closest distance to " OE1 GLU A 277 " =    2.486
peak=   -3.519 closest distance to " O   SER A 135 " =    1.499
peak=   -3.518 closest distance to " CD2 TRP A 150 " =    1.118
peak=   -3.516 closest distance to " CD  LYS A 289 " =    2.466
peak=   -3.513 closest distance to " O   HOH Z 298 " =    0.850
peak=   -3.510 closest distance to " O   GLY A  98 " =    2.119
peak=   -3.509 closest distance to " OE1 GLN A  11 " =    0.979
peak=   -3.506 closest distance to " O   HOH Z 255 " =    0.968
peak=   -3.484 closest distance to " O   HOH Z  95 " =    1.693
peak=   -3.483 closest distance to " O   HOH Z 407 " =    5.914
peak=   -3.479 closest distance to " O   HOH Z 407 " =    3.344
peak=   -3.479 closest distance to " O   HOH Z 191 " =    3.765
peak=   -3.476 closest distance to " CD  GLU A 277 " =    1.106
peak=   -3.474 closest distance to " CB  ASP A  27 " =    2.539
peak=   -3.473 closest distance to " O   HOH Z 125 " =    2.978
peak=   -3.461 closest distance to " CA  LEU A   5 " =    2.506
peak=   -3.461 closest distance to " CB  PHE A 130 " =    1.105
peak=   -3.445 closest distance to " CB  ALA A 227 " =    2.307
peak=   -3.441 closest distance to " CD  GLN A  58 " =    0.708
peak=   -3.437 closest distance to " CG  LEU A 282 " =    2.296
peak=   -3.431 closest distance to " N   VAL A 125 " =    1.101
peak=   -3.423 closest distance to " CG1BVAL A  72 " =    1.954
peak=   -3.414 closest distance to " O   HOH Z 134 " =    2.644
peak=   -3.410 closest distance to " O   LEU A 261 " =    1.042
peak=   -3.402 closest distance to " O   HOH Z 403 " =    1.217
peak=   -3.402 closest distance to " CG2 ILE A 151 " =    2.418
peak=   -3.401 closest distance to " CB  CYS A 254 " =    1.737
peak=   -3.388 closest distance to " CD1 TRP A 179 " =    0.956
peak=   -3.384 closest distance to " CD2 LEU A 282 " =    2.297
peak=   -3.382 closest distance to " O   HOH Z 313 " =    1.670
peak=   -3.381 closest distance to " OD1 ASN A 301 " =    2.011
peak=   -3.376 closest distance to " CG1 VAL A 296 " =    1.484
peak=   -3.372 closest distance to " CG  PRO A 213 " =    2.173
peak=   -3.368 closest distance to " CE2 TYR A  30 " =    2.850
peak=   -3.367 closest distance to " O   HOH Z  13 " =    1.582
peak=   -3.367 closest distance to " O   HOH Z 207 " =    1.936
peak=   -3.364 closest distance to " O   HOH Z 197 " =    3.266
peak=   -3.360 closest distance to " OG  SER A   3 " =    1.205
peak=   -3.358 closest distance to " O   HOH Z 192 " =    2.160
peak=   -3.355 closest distance to " O   PRO A 243 " =    2.359
peak=   -3.348 closest distance to " OG BSER A 134 " =    1.722
peak=   -3.342 closest distance to " O   ASN A 301 " =    1.487
peak=   -3.341 closest distance to " N   ALA A  43 " =    2.572
peak=   -3.340 closest distance to " CD1 PHE A  59 " =    1.881
peak=   -3.340 closest distance to " CE  MET A 188 " =    2.275
peak=   -3.339 closest distance to " O   HOH Z 124 " =    0.862
peak=   -3.338 closest distance to " O   HOH Z 350 " =    1.915
peak=   -3.337 closest distance to " CD1 TRP A 274 " =    1.028
peak=   -3.328 closest distance to " CB  SER A  63 " =    3.367
peak=   -3.320 closest distance to " O   HOH Z  60 " =    1.569
peak=   -3.318 closest distance to " O   GLN A 194 " =    1.260
peak=   -3.313 closest distance to " NE2 GLN A  58 " =    5.065
peak=   -3.311 closest distance to " O   HOH Z 163 " =    1.567
peak=   -3.303 closest distance to " O   HOH Z 112 " =    1.014
peak=   -3.297 closest distance to " N   THR A 157 " =    1.724
peak=   -3.291 closest distance to " O   GLY A 118 " =    1.452
peak=   -3.289 closest distance to " O   HOH Z  18 " =    0.759
peak=   -3.289 closest distance to " O   HOH Z 198 " =    0.798
peak=   -3.280 closest distance to " CB  TRP A  85 " =    2.528
peak=   -3.279 closest distance to " CG BMET A  47 " =    0.951
peak=   -3.272 closest distance to " NE2 GLN A 194 " =    0.808
peak=   -3.271 closest distance to " CA  GLY A 241 " =    2.156
peak=   -3.270 closest distance to " NH1 ARG A  66 " =    1.599
peak=   -3.267 closest distance to " CZ  PHE A 192 " =    2.202
peak=   -3.259 closest distance to " CD1 LEU A   5 " =    2.640
peak=   -3.256 closest distance to " O   HOH Z 118 " =    1.750
peak=   -3.255 closest distance to " O   HOH Z  61 " =    1.243
peak=   -3.252 closest distance to " O   HOH Z 231 " =    1.835
peak=   -3.251 closest distance to " CG1 VAL A 268 " =    2.405
peak=   -3.248 closest distance to " CB  VAL A 230 " =    1.001
peak=   -3.248 closest distance to " O   HOH Z 247 " =    0.856
peak=   -3.247 closest distance to " CB  ASN A 284 " =    1.417
peak=   -3.242 closest distance to " CD2 TYR A 169 " =    2.338
peak=   -3.241 closest distance to " O   HOH Z 377 " =    1.360
peak=   -3.241 closest distance to " CD2 TYR A 116 " =    2.210
peak=   -3.239 closest distance to " O   ALA A   1 " =    1.181
peak=   -3.237 closest distance to " O   HOH Z  76 " =    1.072
peak=   -3.227 closest distance to " O   ALA A 256 " =    2.633
peak=   -3.226 closest distance to " CB  PRO A 243 " =    2.449
peak=   -3.222 closest distance to " O   VAL A  67 " =    2.589
peak=   -3.217 closest distance to " OD1 ASN A  60 " =    1.075
peak=   -3.214 closest distance to " OH  TYR A 169 " =    0.990
peak=   -3.212 closest distance to " C   GLY A  23 " =    1.997
peak=   -3.210 closest distance to " CG1 VAL A 197 " =    2.702
peak=   -3.206 closest distance to " OE1 GLN A  88 " =    1.296
peak=   -3.202 closest distance to " CD1 LEU A 101 " =    2.742
peak=   -3.201 closest distance to " CB  PRO A 163 " =    2.401
peak=   -3.195 closest distance to " O   ASN A  60 " =    0.956
peak=   -3.191 closest distance to " N   PHE A 283 " =    1.751
peak=   -3.188 closest distance to " CD1 ILE A  33 " =    1.907
peak=   -3.186 closest distance to " CE2 TYR A 172 " =    1.734
peak=   -3.185 closest distance to " O   HOH Z 417 " =    2.783
peak=   -3.181 closest distance to " N   SER A  12 " =    1.146
peak=   -3.181 closest distance to " CA  GLY A 133 " =    2.220
peak=   -3.178 closest distance to " C   GLY A  13 " =    0.839
peak=   -3.177 closest distance to " O   HOH Z 331 " =    1.403
peak=   -3.177 closest distance to " O   SER A  97 " =    1.392
peak=   -3.171 closest distance to " O   HOH Z 130 " =    0.882
peak=   -3.171 closest distance to " CD2 LEU A 237 " =    2.146
peak=   -3.171 closest distance to " OG ASER A 210 " =    2.216
peak=   -3.170 closest distance to " O   HOH Z 139 " =    2.782
peak=   -3.169 closest distance to " O   HOH Z 174 " =    1.404
peak=   -3.167 closest distance to " O   HOH Z 297 " =    3.616
peak=   -3.163 closest distance to " N   ALA A 292 " =    2.398
peak=   -3.162 closest distance to " CB  ASP A  50 " =    2.180
peak=   -3.161 closest distance to " O   HOH Z 282 " =    1.086
peak=   -3.149 closest distance to " O   HOH Z 175 " =    4.109
peak=   -3.149 closest distance to " O   TRP A  70 " =    1.420
peak=   -3.149 closest distance to " CG1 VAL A 296 " =    2.332
peak=   -3.147 closest distance to " O   HOH Z 166 " =    1.606
peak=   -3.147 closest distance to " CB  ALA A 291 " =    1.821
peak=   -3.146 closest distance to " CG  TYR A 172 " =    2.214
peak=   -3.146 closest distance to " CB  ALA A 291 " =    2.271
peak=   -3.143 closest distance to " O   HOH Z 387 " =    0.721
peak=   -3.143 closest distance to " O   HOH Z 281 " =    4.081
peak=   -3.141 closest distance to " OD2 ASP A 298 " =    1.469
peak=   -3.139 closest distance to " CD1 PHE A 218 " =    0.994
peak=   -3.137 closest distance to " O   GLN A  11 " =    1.304
peak=   -3.136 closest distance to " O   HOH Z 380 " =    5.219
peak=   -3.134 closest distance to " O   SER A  32 " =    1.427
peak=   -3.129 closest distance to " O   HOH Z  88 " =    4.637
peak=   -3.126 closest distance to " NH2 ARG A  79 " =    1.868
peak=   -3.122 closest distance to " O   ASP A  65 " =    1.258
peak=   -3.116 closest distance to " O   HOH Z  43 " =    1.565
peak=   -3.111 closest distance to " O   ASP A 191 " =    2.039
peak=   -3.110 closest distance to " CG2 ILE A 120 " =    1.388
peak=   -3.109 closest distance to " CG  ASP A 231 " =    0.816
peak=   -3.108 closest distance to " CG2BVAL A  72 " =    2.019
peak=   -3.107 closest distance to " CA  GLY A  98 " =    1.896
peak=   -3.102 closest distance to " CB  ASN A  39 " =    2.101
peak=   -3.099 closest distance to " O   HOH Z 389 " =    4.652
peak=   -3.094 closest distance to " CZ3 TRP A 266 " =    1.540
peak=   -3.094 closest distance to " CD  GLN A  77 " =    1.260
peak=   -3.087 closest distance to " CB  ALA A 291 " =    2.064
peak=   -3.086 closest distance to " O   HOH Z  51 " =    1.758
peak=   -3.082 closest distance to " O   HOH Z 189 " =    3.122
peak=   -3.082 closest distance to " O   HOH Z  88 " =    2.161
peak=   -3.073 closest distance to " CD  ARG A 156 " =    1.868
peak=   -3.069 closest distance to " CZ  PHE A  16 " =    1.706
peak=   -3.068 closest distance to " O   HOH Z 166 " =    1.475
peak=   -3.065 closest distance to " NZ  LYS A 117 " =    1.022
peak=   -3.033 closest distance to " CD  LYS A 166 " =    2.552
peak=   -3.031 closest distance to " C   PHE A  59 " =    0.982
peak=   -3.025 closest distance to " O   HOH Z 285 " =    3.015
peak=   -3.010 closest distance to " CA  TYR A  68 " =    2.650

================= 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    :  0.5092 0.5012   6.306025e+00   6.297408e+00
   1_bss:  0.5003 0.4878   6.303197e+00   6.291651e+00
   1_xyz:  0.4411 0.4681   6.239802e+00   6.263028e+00
   1_adp:  0.4027 0.4613   6.199889e+00   6.261097e+00
   1_occ:  0.4025 0.4613   6.199250e+00   6.260970e+00
   2_bss:  0.4016 0.4591   6.200140e+00   6.260477e+00
   2_xyz:  0.3444 0.4124   6.089185e+00   6.194923e+00
   2_adp:  0.3297 0.4026   6.066122e+00   6.178469e+00
   2_occ:  0.3295 0.4029   6.065800e+00   6.178437e+00
   3_bss:  0.3285 0.4014   6.066285e+00   6.177804e+00
   3_xyz:  0.2718 0.3436   5.916477e+00   6.065495e+00
   3_adp:  0.2584 0.3270   5.874953e+00   6.028712e+00
   3_occ:  0.2580 0.3265   5.874095e+00   6.027729e+00
   4_bss:  0.2573 0.3259   5.874628e+00   6.026742e+00
   4_xyz:  0.1958 0.2509   5.624160e+00   5.814353e+00
   4_adp:  0.1761 0.2320   5.536466e+00   5.747166e+00
   4_occ:  0.1758 0.2311   5.534422e+00   5.744345e+00
   5_bss:  0.1758 0.2311   5.534211e+00   5.743459e+00
   5_xyz:  0.1494 0.2016   5.392594e+00   5.618287e+00
   5_adp:  0.1470 0.1999   5.380142e+00   5.607939e+00
   5_occ:  0.1469 0.1997   5.379482e+00   5.607231e+00
   5_bss:  0.1473 0.2000   5.380706e+00   5.607479e+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:  0.369  20.000   8.963   8.546   6.619   0.000   0.000   0.000
   1_xyz:  0.369  20.000   8.963   8.546   6.619   0.000   0.000   0.000
   1_adp:  0.369  20.000   8.963   8.546   6.619   0.000   0.000   0.000
   1_occ:  0.369  20.000   8.963   8.546   6.619   0.000   0.000   0.000
   2_bss:  0.358  50.000   5.556   5.036   4.208   0.000   0.000   0.000
   2_xyz:  0.358  50.000   5.556   5.036   4.208   0.000   0.000   0.000
   2_adp:  0.358  50.000   5.556   5.036   4.208   0.000   0.000   0.000
   2_occ:  0.358  50.000   5.556   5.036   4.208   0.000   0.000   0.000
   3_bss:  0.362  69.295   3.280   2.548   2.600   0.000   0.000   0.000
   3_xyz:  0.362  69.295   3.280   2.548   2.600   0.000   0.000   0.000
   3_adp:  0.362  69.295   3.280   2.548   2.600   0.000   0.000   0.000
   3_occ:  0.362  69.295   3.280   2.548   2.600   0.000   0.000   0.000
   4_bss:  0.355  62.623   1.567   1.048   1.494   0.000   0.000   0.000
   4_xyz:  0.355  62.623   1.567   1.048   1.494   0.000   0.000   0.000
   4_adp:  0.355  62.623   1.567   1.048   1.494   0.000   0.000   0.000
   4_occ:  0.355  62.623   1.567   1.048   1.494   0.000   0.000   0.000
   5_bss:  0.339  54.463   0.549  -0.344   0.721  -0.000   0.000   0.000
   5_xyz:  0.339  54.463   0.549  -0.344   0.721  -0.000   0.000   0.000
   5_adp:  0.339  54.463   0.549  -0.344   0.721  -0.000   0.000   0.000
   5_occ:  0.339  54.463   0.549  -0.344   0.721  -0.000   0.000   0.000
   5_bss:  0.339  54.630   0.208  -0.694   0.485  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  63.130 0.3539  0.4289    83570.662
   1_bss:  63.085 0.3534  0.5387    81559.094
   1_xyz:  57.654 0.4224  0.6322    69445.276
   1_adp:  56.610 0.4357  0.7106    68680.654
   1_occ:  56.660 0.4351  0.7086    68642.795
   2_bss:  56.465 0.4374  0.6425    68199.270
   2_xyz:  47.513 0.5497  0.8014    50978.454
   2_adp:  45.454 0.5756  0.8520    47988.235
   2_occ:  45.479 0.5753  0.8512    48000.540
   3_bss:  45.277 0.5776  0.7929    47687.860
   3_xyz:  36.378 0.6849  0.9152    32763.044
   3_adp:  33.878 0.7144  0.9448    29561.769
   3_occ:  33.864 0.7144  0.9441    29493.015
   4_bss:  33.795 0.7153  0.8981    29424.961
   4_xyz:  25.090 0.8098  0.9788    16426.615
   4_adp:  22.788 0.8340  0.9894    14072.363
   4_occ:  22.704 0.8348  0.9896    13959.079
   5_bss:  22.662 0.8352  0.9528    13923.231
   5_xyz:  19.170 0.8695  0.9720    10460.916
   5_adp:  18.864 0.8725  0.9766    10255.703
   5_occ:  18.844 0.8727  0.9767    10234.008
   5_bss:  18.863 0.8726  0.9715    10252.502
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3516e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3516e+01
   1_xyz:   1.769  0.014  0.110 18.685  0.007  4.107   1.5767e-01
   1_adp:   1.769  0.014  0.110 18.685  0.007  4.107   1.5767e-01
   1_occ:   1.769  0.014  0.110 18.685  0.007  4.107   1.5767e-01
   2_bss:   1.769  0.014  0.110 18.685  0.007  4.107   1.5767e-01
   2_xyz:   1.188  0.009  0.081 16.678  0.005  4.122   9.1054e-02
   2_adp:   1.188  0.009  0.081 16.678  0.005  4.122   9.1054e-02
   2_occ:   1.188  0.009  0.081 16.678  0.005  4.122   9.1054e-02
   3_bss:   1.188  0.009  0.081 16.678  0.005  4.122   9.1054e-02
   3_xyz:   1.146  0.008  0.079 16.134  0.005  4.115   8.0262e-02
   3_adp:   1.146  0.008  0.079 16.134  0.005  4.115   8.0262e-02
   3_occ:   1.146  0.008  0.079 16.134  0.005  4.115   8.0262e-02
   4_bss:   1.146  0.008  0.079 16.134  0.005  4.115   8.0262e-02
   4_xyz:   1.067  0.008  0.076 15.587  0.004  4.108   7.2759e-02
   4_adp:   1.067  0.008  0.076 15.587  0.004  4.108   7.2759e-02
   4_occ:   1.067  0.008  0.076 15.587  0.004  4.108   7.2759e-02
   5_bss:   1.067  0.008  0.076 15.587  0.004  4.108   7.2759e-02
   5_xyz:   0.932  0.006  0.068 14.893  0.003  4.116   5.4528e-02
   5_adp:   0.932  0.006  0.068 14.893  0.003  4.116   5.4528e-02
   5_occ:   0.932  0.006  0.068 14.893  0.003  4.116   5.4528e-02
   5_bss:   0.932  0.006  0.068 14.893  0.003  4.116   5.4528e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9364e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9364e+00
   1_xyz:  13.943  0.176  0.470 88.618  0.072  2.160   1.0762e-01
   1_adp:  13.943  0.176  0.470 88.618  0.072  2.160   1.0762e-01
   1_occ:  13.943  0.176  0.470 88.618  0.072  2.160   1.0762e-01
   2_bss:  13.943  0.176  0.470 88.618  0.072  2.160   1.0762e-01
   2_xyz:   8.739  0.087  0.283 83.937  0.035  2.196   6.3619e-02
   2_adp:   8.739  0.087  0.283 83.937  0.035  2.196   6.3619e-02
   2_occ:   8.739  0.087  0.283 83.937  0.035  2.196   6.3619e-02
   3_bss:   8.739  0.087  0.283 83.937  0.035  2.196   6.3619e-02
   3_xyz:   8.355  0.061  0.307 87.560  0.049  2.185   6.6792e-02
   3_adp:   8.355  0.061  0.307 87.560  0.049  2.185   6.6792e-02
   3_occ:   8.355  0.061  0.307 87.560  0.049  2.185   6.6792e-02
   4_bss:   8.355  0.061  0.307 87.560  0.049  2.185   6.6792e-02
   4_xyz:   7.847  0.055  0.329 86.132  0.036  2.241   5.7946e-02
   4_adp:   7.847  0.055  0.329 86.132  0.036  2.241   5.7946e-02
   4_occ:   7.847  0.055  0.329 86.132  0.036  2.241   5.7946e-02
   5_bss:   7.847  0.055  0.329 86.132  0.036  2.241   5.7946e-02
   5_xyz:   8.035  0.061  0.295 81.138  0.029  2.309   3.9638e-02
   5_adp:   8.035  0.061  0.295 81.138  0.029  2.309   3.9638e-02
   5_occ:   8.035  0.061  0.295 81.138  0.029  2.309   3.9638e-02
   5_bss:   8.035  0.061  0.295 81.138  0.029  2.309   3.9638e-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:  91.47   0.00  15.54  91.47   0.00  14.13  87.96   0.00  23.27
   1_occ:  91.47   0.00  15.54  91.47   0.00  14.13  87.96   0.00  23.27
   2_bss:  91.47   0.00  15.54  91.47   0.00  14.13  87.96   0.00  23.27
   2_xyz:  91.47   0.00  15.54  91.47   0.00  14.13  87.96   0.00  23.27
   2_adp:  98.05   0.00  15.74  98.05   0.00  13.48  85.25   0.00  28.08
   2_occ:  98.05   0.00  15.74  98.05   0.00  13.48  85.25   0.00  28.08
   3_bss:  98.05   0.00  15.74  98.05   0.00  13.48  85.25   0.00  28.08
   3_xyz:  98.05   0.00  15.74  98.05   0.00  13.48  85.25   0.00  28.08
   3_adp:  95.27   0.00  15.27  95.27   0.00  12.06  77.94   0.00  32.79
   3_occ:  95.27   0.00  15.27  95.27   0.00  12.06  77.94   0.00  32.79
   4_bss:  95.27   0.00  15.27  95.27   0.00  12.06  77.94   0.00  32.79
   4_xyz:  95.27   0.00  15.27  95.27   0.00  12.06  77.94   0.00  32.79
   4_adp:  94.37   0.00  15.55  94.37   0.00  11.25  82.06   3.04  39.00
   4_occ:  94.37   0.00  15.55  94.37   0.00  11.25  82.06   3.04  39.00
   5_bss:  94.37   0.00  15.55  94.37   0.00  11.25  82.06   3.04  39.00
   5_xyz:  94.37   0.00  15.55  94.37   0.00  11.25  82.06   3.04  39.00
   5_adp:  94.37   0.00  15.59  94.37   0.00  11.28  82.06   4.12  39.07
   5_occ:  94.37   0.00  15.59  94.37   0.00  11.28  82.06   4.12  39.07
   5_bss:  94.54   0.17  15.76  94.54   0.17  11.45  82.23   4.29  39.23
------------------------------------------------------------------------
 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:    1.262    0.015    0.416
   1_adp:    1.262    0.015    0.416
   1_occ:    1.262    0.015    0.416
   2_bss:    1.262    0.015    0.416
   2_xyz:    1.606    0.016    0.568
   2_adp:    1.606    0.016    0.568
   2_occ:    1.606    0.016    0.568
   3_bss:    1.606    0.016    0.568
   3_xyz:    1.674    0.071    0.673
   3_adp:    1.674    0.071    0.673
   3_occ:    1.674    0.071    0.673
   4_bss:    1.674    0.071    0.673
   4_xyz:    2.169    0.040    0.823
   4_adp:    2.169    0.040    0.823
   4_occ:    2.169    0.040    0.823
   5_bss:    2.169    0.040    0.823
   5_xyz:    2.301    0.066    0.857
   5_adp:    2.301    0.066    0.857
   5_occ:    2.301    0.066    0.857
   5_bss:    2.301    0.066    0.857
------------------------------------------------------------------------

CPU time actual refinement: 368.90


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1224/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_1224/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1224/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1224/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1224/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 368.74 
  Macro-tasks:
    bulk solvent and scale       = 39.74  
    individual site refinement   = 164.18 
    weights calculation          = 32.66  
    collect and process          = 6.41   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 243.12 
  Micro-tasks:
    mask                            = 3.02   
    f_calc                          = 120.14 
    alpha_beta                      = 8.42   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 131.40 
    fmodel                         = 7.21   
    r_factors                      = 0.27   
    phase_errors                   = 9.87   
    foms                           = 0.27   
    TOTAL for micro-tasks          = 281.77 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.106 micro seconds
Total CPU time: 6.38 minutes
from_scatterers_fft:    654 calls, 119.71 s
gradients_fft:          600 calls, 117.63 s

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

# Date 2008-01-16 Time 03:30:30 PST -0800 (1200483030.53 s)
Start R-work = 0.5092, R-free = 0.5012 (no bulk solvent and anisotropic scale)
Final R-work = 0.1624, R-free = 0.2155 (no bulk solvent and anisotropic scale)

Start R-work = 0.5003, R-free = 0.4878
Final R-work = 0.1473, R-free = 0.2000