# Date 2008-01-16 Time 01:49:54 PST -0800 (1200476994.50 s)
#phil __OFF__

Command line arguments: "../573.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 = 6139
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 573

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 47.6339, 84.6622, 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: 3.30, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.6339, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8666 1.96142
Completeness in resolution range: 0.940784
Completeness with d_max=infinity: 0.937901

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8666
                             d_min =   1.9614

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.6339, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8666 1.96142
Completeness in resolution range: 0.940784
Completeness with d_max=infinity: 0.937901

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8670 -  4.1970 [2194/2222]  1975   219  10.0%
  bin  2:  4.1970 -  3.3438 [2089/2112]  1880   209  10.0%
  bin  3:  3.3438 -  2.9248 [2072/2097]  1862   210  10.1%
  bin  4:  2.9248 -  2.6590 [2054/2070]  1856   198   9.6%
  bin  5:  2.6590 -  2.4693 [2041/2085]  1830   211  10.3%
  bin  6:  2.4693 -  2.3243 [2028/2056]  1830   198   9.8%
  bin  7:  2.3243 -  2.2083 [2010/2046]  1807   203  10.1%
  bin  8:  2.2083 -  2.1125 [2004/2046]  1806   198   9.9%
  bin  9:  2.1125 -  2.0314 [2018/2064]  1816   202  10.0%
  bin 10:  2.0314 -  1.9614 [1079/2024]   968   111  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_573/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:
        1.67 -     2.32: 26
        2.32 -     2.96: 1750
        2.96 -     3.61: 4561
        3.61 -     4.25: 9235
        4.25 -     4.90: 12907
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.673 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.708 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.781 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.847 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28474 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_573/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_573/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 = 69.89875 47.63395 84.6622 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 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4831   r_free= 0.4838   ksol= 0.00   Bsol= 0.00   scale= 0.794    |
|                                                                             |
| 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:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.285023                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8670 -  4.6812 0.99   1421  158 0.3961 0.3943      6.5976      6.6107|
|  2:  4.6812 -  3.7350 0.99   1365  150 0.4055 0.4158      6.7943      6.8006|
|  3:  3.7350 -  3.2686 0.99   1337  153 0.4420 0.4209      6.6733      6.7023|
|  4:  3.2686 -  2.9723 0.99   1330  144 0.4577 0.4512      6.5053      6.4966|
|  5:  2.9723 -  2.7607 0.98   1333  148 0.5064 0.5365      6.3813      6.3771|
|  6:  2.7607 -  2.5989 0.99   1307  146 0.5088 0.5406      6.2716      6.1998|
|  7:  2.5989 -  2.4693 0.98   1310  148 0.5159 0.4350       6.261      6.1638|
|  8:  2.4693 -  2.3623 0.99   1293  140 0.5340 0.5235      6.1687      6.1908|
|  9:  2.3623 -  2.2717 0.99   1313  150 0.5455 0.5503      6.1317      6.1435|
| 10:  2.2717 -  2.1935 0.98   1298  137 0.5250 0.5685      6.1113      6.1429|
| 11:  2.1935 -  2.1252 0.97   1280  142 0.5377 0.5213      6.0433      6.0211|
| 12:  2.1252 -  2.0646 0.99   1282  149 0.5334 0.5990      5.9622      6.0037|
| 13:  2.0646 -  2.0104 0.94   1260  138 0.5479 0.5297      5.8744      5.8427|
| 14:  2.0104 -  1.9614 0.39    501   56 0.5669 0.5327      5.8602      5.7322|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8670 -  4.6812  1421   158  0.68  35.92   0.80     0.70      76198.87|
|  2:  4.6812 -  3.7350  1365   150  0.69  36.29   0.88     0.75     109323.21|
|  3:  3.7350 -  3.2686  1337   153  0.58  45.20   0.83     0.70     117779.97|
|  4:  3.2686 -  2.9723  1330   144  0.49  52.62   0.81     0.59     104200.00|
|  5:  2.9723 -  2.7607  1333   148  0.40  60.09   0.74     0.48      87314.97|
|  6:  2.7607 -  2.5989  1307   146  0.39  60.88   0.74     0.46      71797.74|
|  7:  2.5989 -  2.4693  1310   148  0.40  59.81   0.73     0.46      62691.21|
|  8:  2.4693 -  2.3623  1293   140  0.38  61.38   0.72     0.45      56942.84|
|  9:  2.3623 -  2.2717  1313   150  0.32  66.11   0.71     0.39      56157.54|
| 10:  2.2717 -  2.1935  1298   137  0.25  71.53   0.76     0.30      55784.38|
| 11:  2.1935 -  2.1252  1280   142  0.17  77.12   0.76     0.22      54463.71|
| 12:  2.1252 -  2.0646  1282   149  0.15  78.51   0.75     0.20      51323.28|
| 13:  2.0646 -  2.0104  1260   138  0.19  75.67   0.72     0.25      41443.84|
| 14:  2.0104 -  1.9614   501    56  0.33  65.36   0.71     0.38      29483.91|
|alpha:            min =        0.20 max =            0.75 mean =         0.46|
|beta:             min =    29483.91 max =       117779.97 mean =     71933.60|
|figures of merit: min =        0.00 max =            1.00 mean =         0.39|
|phase err.(work): min =        0.00 max =           90.00 mean =        59.87|
|phase err.(test): min =        0.00 max =           89.91 mean =        60.18|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.623090             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.613   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.432678              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 82.296   (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 |  1.042 -  1.428:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.428 -  1.814:       10 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.814 -  2.200:      105 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.200 -  2.585:      553 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.585 -  2.971:     1345 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.971 -  3.357:     2498 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.357 -  3.743:     3968 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.743 -  4.128:     5172 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.128 -  4.514:     6781 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.514 -  4.900:     8093 |
|-----------------------------------------------------------------------------|
|-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 |       53.434 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.042 |       2.068 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.761)------------------------------------------|
|    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 = 11.761)------------------------------------------|
|    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 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4889   r_free= 0.4916   ksol= 0.00   Bsol= 0.00   scale= 0.764    |
|                                                                             |
| 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:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.286438                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4760   r_free= 0.4747   ksol= 0.35   Bsol= 20.00   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.45,10.16,8.42,0.00,0.00,0.00); trace/3= 8.34                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.282887                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.560657             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.680   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.249151              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.731   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4760      final r-factor (work) = 0.4054          |
| start r-factor (free) = 0.4747      final r-factor (free) = 0.4215          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 92.9003 = 12.56 * 0.50 * 6.2841 + 1.00 * 53.4341                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 39.1148 = 12.56 * 0.50 * 6.2050 + 1.00 * 0.1451                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4054      final r-factor (work) = 0.3619          |
| start r-factor (free) = 0.4215      final r-factor (free) = 0.4032          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.7654 = 1.25 * 1.00 * 6.2050 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6783 = 1.25 * 1.00 * 6.1334 + 1.00 * 0.0168                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.761)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.53   13.76    None  None   None       |
|    all(noH): 2823   0      0.00    92.53   13.76    None  None   None       |
|    Sol.    : 438    0      0.00    92.53   26.61    None  None   None       |
|    Mac.    : 2385   0      0.00    70.74   11.40    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.253: 1299   |   5:    46.266 -  55.519:   42        |
|      1:     9.253 -  18.506:  792   |   6:    55.519 -  64.772:   13        |
|      2:    18.506 -  27.760:  372   |   7:    64.772 -  74.026:   14        |
|      3:    27.760 -  37.013:  188   |   8:    74.026 -  83.279:    2        |
|      4:    37.013 -  46.266:  100   |   9:    83.279 -  92.532:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3619 r_free = 0.4032             target_work(ml) = 6.118         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3612 r_free = 0.4035             target_work(ml) = 6.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3612   r_free= 0.4035   ksol= 0.35   Bsol= 20.00   scale= 1.102   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.45,10.16,8.42,0.00,0.00,0.00); trace/3= 8.34                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.117031                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3593   r_free= 0.3986   ksol= 0.35   Bsol= 50.00   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.16,6.52,5.71,0.00,0.00,0.00); trace/3= 5.13                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.117885                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.911853              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.187   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.577531              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.731  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3593      final r-factor (work) = 0.2636          |
| start r-factor (free) = 0.3986      final r-factor (free) = 0.3229          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.5246 = 9.91 * 0.50 * 6.1299 + 1.00 * 0.1451                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.8123 = 9.91 * 0.50 * 5.9966 + 1.00 * 0.0937                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2636      final r-factor (work) = 0.2368          |
| start r-factor (free) = 0.3229      final r-factor (free) = 0.2965          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4801 = 0.58 * 1.00 * 5.9966 + 1.00 * 0.0169                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3760 = 0.58 * 1.00 * 5.8252 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.761)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.25   13.87    None  None   None       |
|    all(noH): 2823   0      0.00    86.25   13.87    None  None   None       |
|    Sol.    : 438    0      1.30    86.25   33.19    None  None   None       |
|    Mac.    : 2385   0      0.00    71.97   10.32    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.625: 1319   |   5:    43.127 -  51.752:   84        |
|      1:     8.625 -  17.251:  787   |   6:    51.752 -  60.378:   39        |
|      2:    17.251 -  25.876:  279   |   7:    60.378 -  69.003:   15        |
|      3:    25.876 -  34.502:  167   |   8:    69.003 -  77.628:    5        |
|      4:    34.502 -  43.127:  126   |   9:    77.628 -  86.254:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2368 r_free = 0.2965             target_work(ml) = 5.787         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2365 r_free = 0.2967             target_work(ml) = 5.787         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2365   r_free= 0.2967   ksol= 0.35   Bsol= 50.00   scale= 1.074   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.16,6.52,5.71,0.00,0.00,0.00); trace/3= 5.13                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.786799                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2324   r_free= 0.2930   ksol= 0.33   Bsol= 45.09   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.36,3.22,2.74,0.00,0.00,0.00); trace/3= 2.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.783306                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.966816              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.326   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.361754              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.888  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2324      final r-factor (work) = 0.1795          |
| start r-factor (free) = 0.2930      final r-factor (free) = 0.2288          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7498 = 2.97 * 0.50 * 5.8353 + 1.00 * 0.0937                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4838 = 2.97 * 0.50 * 5.6816 + 1.00 * 0.0556                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1795      final r-factor (work) = 0.1678          |
| start r-factor (free) = 0.2288      final r-factor (free) = 0.2173          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0672 = 0.36 * 1.00 * 5.6816 + 1.00 * 0.0118                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0060 = 0.36 * 1.00 * 5.5167 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.761)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.32   13.97    None  None   None       |
|    all(noH): 2823   0      0.00    81.32   13.97    None  None   None       |
|    Sol.    : 438    0      3.72    81.32   36.15    None  None   None       |
|    Mac.    : 2385   0      0.00    77.09   9.89     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.133: 1308   |   5:    40.662 -  48.795:  115        |
|      1:     8.133 -  16.265:  826   |   6:    48.795 -  56.927:   65        |
|      2:    16.265 -  24.397:  213   |   7:    56.927 -  65.060:   22        |
|      3:    24.397 -  32.530:  127   |   8:    65.060 -  73.192:   16        |
|      4:    32.530 -  40.662:  127   |   9:    73.192 -  81.325:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1678 r_free = 0.2173             target_work(ml) = 5.489         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1675 r_free = 0.2173             target_work(ml) = 5.488         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1675   r_free= 0.2173   ksol= 0.33   Bsol= 45.09   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.36,3.22,2.74,0.00,0.00,0.00); trace/3= 2.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.488406                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1675   r_free= 0.2175   ksol= 0.32   Bsol= 45.09   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.66,2.23,1.86,0.00,0.00,0.00); trace/3= 1.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.488961                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.250314              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.448  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.870843              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.130  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1675      final r-factor (work) = 0.1325          |
| start r-factor (free) = 0.2175      final r-factor (free) = 0.1751          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0277 = 3.25 * 0.50 * 5.5207 + 1.00 * 0.0557                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8266 = 3.25 * 0.50 * 5.3910 + 1.00 * 0.0654                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1325      final r-factor (work) = 0.1252          |
| start r-factor (free) = 0.1751      final r-factor (free) = 0.1703          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7049 = 0.87 * 1.00 * 5.3910 + 1.00 * 0.0102                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5835 = 0.87 * 1.00 * 5.2498 + 1.00 * 0.0117                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 33     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.761)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.54   14.17    None  None   None       |
|    all(noH): 2823   0      0.00    84.54   14.17    None  None   None       |
|    Sol.    : 438    0      2.95    79.30   38.40    None  None   None       |
|    Mac.    : 2385   0      0.00    84.54   9.72     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.454: 1391   |   5:    42.270 -  50.724:  106        |
|      1:     8.454 -  16.908:  789   |   6:    50.724 -  59.178:   69        |
|      2:    16.908 -  25.362:  192   |   7:    59.178 -  67.632:   41        |
|      3:    25.362 -  33.816:  104   |   8:    67.632 -  76.086:   12        |
|      4:    33.816 -  42.270:  113   |   9:    76.086 -  84.540:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1252 r_free = 0.1703             target_work(ml) = 5.236         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1251 r_free = 0.1704             target_work(ml) = 5.236         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1251   r_free= 0.1704   ksol= 0.32   Bsol= 45.09   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.66,2.23,1.86,0.00,0.00,0.00); trace/3= 1.58                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.235885                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1254   r_free= 0.1710   ksol= 0.32   Bsol= 44.81   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.60,1.78,1.59,0.00,0.00,0.00); trace/3= 1.32                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.239489                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.659975              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 132.894  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.310544              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.311  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1254      final r-factor (work) = 0.1175          |
| start r-factor (free) = 0.1710      final r-factor (free) = 0.1648          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0500 = 2.66 * 0.50 * 5.2516 + 1.00 * 0.0654                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9981 = 2.66 * 0.50 * 5.2138 + 1.00 * 0.0638                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1175      final r-factor (work) = 0.1162          |
| start r-factor (free) = 0.1648      final r-factor (free) = 0.1649          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8446 = 1.31 * 1.00 * 5.2138 + 1.00 * 0.0117                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8135 = 1.31 * 1.00 * 5.1896 + 1.00 * 0.0123                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.761)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.58   14.11    None  None   None       |
|    all(noH): 2823   0      0.00    89.58   14.11    None  None   None       |
|    Sol.    : 438    0      2.14    79.48   38.51    None  None   None       |
|    Mac.    : 2385   0      0.00    89.58   9.63     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.958: 1515   |   5:    44.792 -  53.750:   92        |
|      1:     8.958 -  17.917:  712   |   6:    53.750 -  62.709:   68        |
|      2:    17.917 -  26.875:  181   |   7:    62.709 -  71.667:   28        |
|      3:    26.875 -  35.834:   98   |   8:    71.667 -  80.626:   10        |
|      4:    35.834 -  44.792:  114   |   9:    80.626 -  89.584:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1162 r_free = 0.1649             target_work(ml) = 5.188         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1161 r_free = 0.1649             target_work(ml) = 5.188         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1161   r_free= 0.1649   ksol= 0.32   Bsol= 44.81   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.60,1.78,1.59,0.00,0.00,0.00); trace/3= 1.32                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.188206                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8670 -  4.6812 0.99   1421  158 0.0971 0.1269      5.3748      5.5282|
|  2:  4.6812 -  3.7350 0.99   1365  150 0.0872 0.1146      5.4494      5.6748|
|  3:  3.7350 -  3.2686 0.99   1337  153 0.1082 0.1647      5.5012      5.8914|
|  4:  3.2686 -  2.9723 0.99   1330  144 0.1313 0.1591      5.4985      5.6671|
|  5:  2.9723 -  2.7607 0.98   1333  148 0.1384 0.1724      5.3633      5.5155|
|  6:  2.7607 -  2.5989 0.99   1307  146 0.1306 0.2159      5.2726      5.5555|
|  7:  2.5989 -  2.4693 0.98   1310  148 0.1278 0.1682      5.1941      5.4096|
|  8:  2.4693 -  2.3623 0.99   1293  140 0.1213 0.1699      5.1131      5.3225|
|  9:  2.3623 -  2.2717 0.99   1313  150 0.1206 0.1925      5.0635      5.3545|
| 10:  2.2717 -  2.1935 0.98   1298  137 0.1192 0.1936      5.0308      5.3461|
| 11:  2.1935 -  2.1252 0.97   1280  142 0.1202 0.1798      4.9738      5.2486|
| 12:  2.1252 -  2.0646 0.99   1282  149 0.1169 0.1779      4.9076       5.147|
| 13:  2.0646 -  2.0104 0.94   1260  138 0.1190 0.1909      4.8197      5.0936|
| 14:  2.0104 -  1.9614 0.39    501   56 0.1122 0.1780      4.7077      4.9737|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8670 -  4.6812  1421   158  0.94   9.13   0.98     0.96       7403.13|
|  2:  4.6812 -  3.7350  1365   150  0.95   8.39   1.02     1.00       9440.64|
|  3:  3.7350 -  3.2686  1337   153  0.93  12.15   1.03     1.03      11422.22|
|  4:  3.2686 -  2.9723  1330   144  0.91  15.07   1.01     0.99      11342.95|
|  5:  2.9723 -  2.7607  1333   148  0.89  17.07   1.00     0.97       9027.39|
|  6:  2.7607 -  2.5989  1307   146  0.89  17.03   0.99     0.96       8077.09|
|  7:  2.5989 -  2.4693  1310   148  0.90  16.15   0.99     0.96       6627.74|
|  8:  2.4693 -  2.3623  1293   140  0.90  16.81   1.00     0.97       6136.61|
|  9:  2.3623 -  2.2717  1313   150  0.89  17.01   1.00     0.97       5579.19|
| 10:  2.2717 -  2.1935  1298   137  0.89  16.74   0.99     0.96       5213.44|
| 11:  2.1935 -  2.1252  1280   142  0.89  17.64   1.00     0.96       4780.52|
| 12:  2.1252 -  2.0646  1282   149  0.91  16.04   0.99     0.98       4240.13|
| 13:  2.0646 -  2.0104  1260   138  0.89  17.41   1.00     0.99       3654.59|
| 14:  2.0104 -  1.9614   501    56  0.89  16.43   0.98     0.95       2854.09|
|alpha:            min =        0.95 max =            1.03 mean =         0.97|
|beta:             min =     2854.09 max =        11422.22 mean =      7070.52|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.93 mean =        15.09|
|phase err.(test): min =        0.00 max =           89.80 mean =        14.54|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1161   r_free= 0.1649   ksol= 0.32   Bsol= 47.93   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.66,0.38,0.28,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.188264                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1161   r_free= 0.1649   ksol= 0.32   Bsol= 47.93   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.66,0.38,0.28,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.188264                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8670 -  4.6812 0.99   1421  158 0.0971 0.1272      5.3759      5.5303|
|  2:  4.6812 -  3.7350 0.99   1365  150 0.0874 0.1149      5.4513      5.6773|
|  3:  3.7350 -  3.2686 0.99   1337  153 0.1082 0.1649      5.5025      5.8922|
|  4:  3.2686 -  2.9723 0.99   1330  144 0.1312 0.1592      5.4985      5.6672|
|  5:  2.9723 -  2.7607 0.98   1333  148 0.1383 0.1723      5.3626      5.5147|
|  6:  2.7607 -  2.5989 0.99   1307  146 0.1305 0.2156      5.2719       5.555|
|  7:  2.5989 -  2.4693 0.98   1310  148 0.1278 0.1683      5.1937      5.4102|
|  8:  2.4693 -  2.3623 0.99   1293  140 0.1212 0.1696      5.1129      5.3212|
|  9:  2.3623 -  2.2717 0.99   1313  150 0.1205 0.1926      5.0633      5.3551|
| 10:  2.2717 -  2.1935 0.98   1298  137 0.1192 0.1935      5.0306      5.3458|
| 11:  2.1935 -  2.1252 0.97   1280  142 0.1201 0.1795      4.9733      5.2474|
| 12:  2.1252 -  2.0646 0.99   1282  149 0.1169 0.1781      4.9073      5.1477|
| 13:  2.0646 -  2.0104 0.94   1260  138 0.1190 0.1906      4.8193      5.0923|
| 14:  2.0104 -  1.9614 0.39    501   56 0.1122 0.1777      4.7073      4.9735|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8670 -  4.6812  1421   158  0.94   9.15   0.98     0.96       7429.85|
|  2:  4.6812 -  3.7350  1365   150  0.95   8.41   1.02     1.00       9482.10|
|  3:  3.7350 -  3.2686  1337   153  0.93  12.18   1.03     1.03      11467.94|
|  4:  3.2686 -  2.9723  1330   144  0.91  15.08   1.01     0.99      11346.25|
|  5:  2.9723 -  2.7607  1333   148  0.89  17.05   1.00     0.97       9014.24|
|  6:  2.7607 -  2.5989  1307   146  0.89  17.02   0.99     0.97       8064.81|
|  7:  2.5989 -  2.4693  1310   148  0.90  16.15   0.99     0.96       6621.49|
|  8:  2.4693 -  2.3623  1293   140  0.90  16.81   1.00     0.97       6134.29|
|  9:  2.3623 -  2.2717  1313   150  0.89  17.01   1.01     0.98       5580.21|
| 10:  2.2717 -  2.1935  1298   137  0.89  16.73   1.00     0.96       5209.90|
| 11:  2.1935 -  2.1252  1280   142  0.89  17.63   1.00     0.96       4774.92|
| 12:  2.1252 -  2.0646  1282   149  0.91  16.03   1.00     0.98       4236.18|
| 13:  2.0646 -  2.0104  1260   138  0.89  17.40   1.00     1.00       3649.75|
| 14:  2.0104 -  1.9614   501    56  0.89  16.42   0.99     0.95       2848.98|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2848.98 max =        11467.94 mean =      7075.69|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           90.00 mean =        15.09|
|phase err.(test): min =        0.00 max =           89.79 mean =        14.55|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.761)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.42    91.00   15.53    None  None   None       |
|    all(noH): 2823   0      1.42    91.00   15.53    None  None   None       |
|    Sol.    : 438    0      3.57    80.90   39.93    None  None   None       |
|    Mac.    : 2385   0      1.42    91.00   11.05    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:     1.421 -  10.379: 1515   |   5:    46.213 -  55.171:   92        |
|      1:    10.379 -  19.337:  712   |   6:    55.171 -  64.129:   68        |
|      2:    19.337 -  28.296:  181   |   7:    64.129 -  73.088:   28        |
|      3:    28.296 -  37.254:   98   |   8:    73.088 -  82.046:   10        |
|      4:    37.254 -  46.213:  114   |   9:    82.046 -  91.005:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 338         
Filter by distance & map next to the model:
   mapped sites are within: 0.595 - 5.209
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 334 from: 338
   mapped sites are within: 0.763 - 5.209

peak=   10.006 closest distance to " CG2 VAL A 230 " =    1.404
peak=    8.005 closest distance to " O   HOH Z 120 " =    1.228
peak=    7.127 closest distance to " CG2 VAL A 296 " =    1.112
peak=    6.169 closest distance to " CG  LEU A   5 " =    1.247
peak=    5.914 closest distance to " O   HOH Z 279 " =    1.218
peak=    5.777 closest distance to " CD1AILE A 234 " =    1.093
peak=    5.722 closest distance to " NH2 ARG A  56 " =    2.253
peak=    5.582 closest distance to " O   HOH Z 278 " =    1.209
peak=    5.351 closest distance to " O   HOH Z 124 " =    1.646
peak=    5.181 closest distance to " CB  VAL A 296 " =    1.072
peak=    5.097 closest distance to " CG  PRO A  54 " =    1.187
peak=    5.076 closest distance to " O   HOH Z  48 " =    1.838
peak=    5.002 closest distance to " O   HOH Z 247 " =    1.388
peak=    4.995 closest distance to " CB  GLN A 223 " =    1.401
peak=    4.986 closest distance to " O   HOH Z 193 " =    1.727
peak=    4.814 closest distance to " CB  SER A  63 " =    1.233
peak=    4.775 closest distance to " O   HOH Z 210 " =    1.028
peak=    4.704 closest distance to " O   HOH Z  80 " =    1.792
peak=    4.679 closest distance to " CG  LEU A 228 " =    1.231
peak=    4.669 closest distance to " O   PRO A 198 " =    1.499
peak=    4.639 closest distance to " O   HOH Z 316 " =    2.658
peak=    4.638 closest distance to " O   HOH Z 402 " =    1.498
peak=    4.609 closest distance to " CB  ARG A 275 " =    0.875
peak=    4.556 closest distance to " CB  GLN A 183 " =    1.338
peak=    4.531 closest distance to " CD2 LEU A   5 " =    1.192
peak=    4.529 closest distance to " O   SER A  87 " =    2.334
peak=    4.528 closest distance to " O   HOH Z  11 " =    1.336
peak=    4.500 closest distance to " NE2 GLN A  11 " =    1.054
peak=    4.488 closest distance to " O   HOH Z 272 " =    1.898
peak=    4.477 closest distance to " CB  PRO A  54 " =    0.848
peak=    4.449 closest distance to " O   HOH Z 403 " =    1.790
peak=    4.448 closest distance to " CB  VAL A 230 " =    1.226
peak=    4.443 closest distance to " CG  PRO A 198 " =    1.248
peak=    4.429 closest distance to " CA  ALA A  21 " =    1.274
peak=    4.413 closest distance to " O   HOH Z 142 " =    1.622
peak=    4.411 closest distance to " O   HOH Z 232 " =    2.287
peak=    4.403 closest distance to " CG  PRO A 213 " =    1.192
peak=    4.401 closest distance to " O   HOH Z 371 " =    3.373
peak=    4.386 closest distance to " O   HOH Z 423 " =    1.834
peak=    4.379 closest distance to " O   HOH Z 132 " =    1.228
peak=    4.367 closest distance to " O   HOH Z 130 " =    2.643
peak=    4.358 closest distance to " O   HOH Z 234 " =    3.783
peak=    4.336 closest distance to " O   HOH Z 411 " =    3.572
peak=    4.335 closest distance to " CA  TYR A  30 " =    1.008
peak=    4.307 closest distance to " O   HOH Z  97 " =    1.864
peak=    4.279 closest distance to " O   HOH Z 394 " =    1.599
peak=    4.278 closest distance to " CB  SER A   3 " =    1.319
peak=    4.218 closest distance to " O   HOH Z 368 " =    2.280
peak=    4.209 closest distance to " O   HOH Z  85 " =    1.475
peak=    4.192 closest distance to " CD2 LEU A 228 " =    1.212
peak=    4.185 closest distance to " OD1 ASN A  69 " =    2.543
peak=    4.183 closest distance to " O   HOH Z 134 " =    1.803
peak=    4.154 closest distance to " O   HOH Z 112 " =    1.611
peak=    4.119 closest distance to " O   HOH Z  15 " =    2.334
peak=    4.119 closest distance to " O   HOH Z 389 " =    1.834
peak=    4.110 closest distance to " O   HOH Z  20 " =    1.563
peak=    4.099 closest distance to " CB  GLU A 152 " =    1.093
peak=    4.083 closest distance to " O   HOH Z  78 " =    1.726
peak=    4.075 closest distance to " O   HOH Z 260 " =    1.303
peak=    4.073 closest distance to " CG2 THR A 221 " =    1.159
peak=    4.065 closest distance to " CB  TRP A 179 " =    1.254
peak=    4.061 closest distance to " CB  SER A 141 " =    1.088
peak=    4.061 closest distance to " O   HOH Z 136 " =    1.421
peak=    4.054 closest distance to " O   HOH Z 426 " =    1.474
peak=    4.053 closest distance to " CB  GLU A 128 " =    1.162
peak=    4.047 closest distance to " NZ  LYS A 117 " =    3.188
peak=    4.018 closest distance to " O   HOH Z  44 " =    2.458
peak=    4.014 closest distance to " O   HOH Z 406 " =    1.702
peak=    4.013 closest distance to " O   HOH Z  43 " =    1.469
peak=    4.009 closest distance to " O   HOH Z 346 " =    1.477
peak=    4.007 closest distance to " O   HOH Z 189 " =    2.659
peak=    4.005 closest distance to " O   HOH Z 284 " =    3.023
peak=    4.001 closest distance to " O   HOH Z 126 " =    1.565
peak=    3.993 closest distance to " O   HOH Z  40 " =    1.714
peak=    3.984 closest distance to " O   HOH Z 344 " =    2.760
peak=    3.982 closest distance to " O   HOH Z 130 " =    1.135
peak=    3.975 closest distance to " CG1 ILE A  33 " =    1.278
peak=    3.968 closest distance to " CB  TYR A 169 " =    0.903
peak=    3.949 closest distance to " O   HOH Z 326 " =    1.502
peak=    3.936 closest distance to " CG AARG A 275 " =    1.067
peak=    3.932 closest distance to " O   HOH Z 126 " =    1.773
peak=    3.924 closest distance to " O   HOH Z 133 " =    1.652
peak=    3.924 closest distance to " NH2 ARG A 156 " =    1.101
peak=    3.924 closest distance to " O   HOH Z 357 " =    2.185
peak=    3.915 closest distance to " O   HOH Z 203 " =    1.624
peak=    3.913 closest distance to " O   HOH Z  61 " =    1.526
peak=    3.913 closest distance to " O   HOH Z 345 " =    2.877
peak=    3.912 closest distance to " O   HOH Z 128 " =    1.962
peak=    3.906 closest distance to " OD2 ASP A 286 " =    2.747
peak=    3.901 closest distance to " CG  ARG A  66 " =    1.015
peak=    3.898 closest distance to " O   HOH Z 131 " =    2.495
peak=    3.850 closest distance to " O   HOH Z  63 " =    2.032
peak=    3.843 closest distance to " OE1 GLU A   2 " =    2.151
peak=    3.843 closest distance to " O   HOH Z  97 " =    2.548
peak=    3.829 closest distance to " O   HOH Z 155 " =    1.555
peak=    3.825 closest distance to " O   HOH Z 227 " =    1.631
peak=    3.813 closest distance to " O   HOH Z 128 " =    1.972
peak=    3.813 closest distance to " CG1BVAL A  72 " =    1.579
peak=    3.804 closest distance to " CE  LYS A 119 " =    1.037
peak=    3.799 closest distance to " CD  ARG A 269 " =    1.121
peak=    3.797 closest distance to " CA  VAL A  41 " =    0.868
peak=    3.796 closest distance to " O   HOH Z 414 " =    1.644
peak=    3.795 closest distance to " O   HOH Z 193 " =    2.182
peak=    3.787 closest distance to " CB  VAL A 265 " =    1.194
peak=    3.777 closest distance to " CA  ASP A 191 " =    0.905
peak=    3.774 closest distance to " O   HOH Z  54 " =    1.508
peak=    3.767 closest distance to " O   HOH Z 265 " =    2.465
peak=    3.766 closest distance to " O   HOH Z 108 " =    2.430
peak=    3.764 closest distance to " O   HOH Z 102 " =    1.298
peak=    3.747 closest distance to " O   HOH Z 280 " =    1.572
peak=    3.742 closest distance to " O   HOH Z  67 " =    1.839
peak=    3.735 closest distance to " CD  LYS A 119 " =    1.751
peak=    3.731 closest distance to " CA  ALA A 295 " =    1.089
peak=    3.728 closest distance to " CB  GLU A 277 " =    3.616
peak=    3.726 closest distance to " CA  ASN A 176 " =    1.149
peak=    3.714 closest distance to " O   HOH Z 369 " =    2.169
peak=    3.712 closest distance to " O   GLY A  91 " =    1.438
peak=    3.691 closest distance to " O   HOH Z 303 " =    2.191
peak=    3.690 closest distance to " O   HOH Z   4 " =    1.517
peak=    3.685 closest distance to " O   HOH Z 263 " =    1.389
peak=    3.680 closest distance to " CB  ASN A 148 " =    1.314
peak=    3.667 closest distance to " O   HOH Z 245 " =    1.372
peak=    3.664 closest distance to " CG AARG A 275 " =    1.170
peak=    3.662 closest distance to " O   HOH Z 214 " =    2.483
peak=    3.657 closest distance to " OG1 THR A 294 " =    2.288
peak=    3.656 closest distance to " O   ALA A 158 " =    1.259
peak=    3.653 closest distance to " O   HOH Z 180 " =    2.189
peak=    3.650 closest distance to " O   HOH Z  48 " =    2.001
peak=    3.647 closest distance to " O   HOH Z 433 " =    1.489
peak=    3.641 closest distance to " CB  VAL A 202 " =    1.534
peak=    3.640 closest distance to " OE1 GLN A  11 " =    1.817
peak=    3.637 closest distance to " O   HOH Z 408 " =    1.549
peak=    3.634 closest distance to " O   HOH Z 163 " =    1.389
peak=    3.625 closest distance to " O   HOH Z 128 " =    1.684
peak=    3.613 closest distance to " O   HOH Z 301 " =    1.942
peak=    3.604 closest distance to " CA  ARG A 195 " =    1.165
peak=    3.603 closest distance to " CB  LEU A 228 " =    1.420
peak=    3.601 closest distance to " O   HOH Z 227 " =    1.800
peak=    3.599 closest distance to " CD  ARG A 195 " =    3.423
peak=    3.591 closest distance to " O   HOH Z 137 " =    2.034
peak=    3.586 closest distance to " O   MET A 105 " =    1.892
peak=    3.584 closest distance to " CB AVAL A  41 " =    1.158
peak=    3.581 closest distance to " O   HOH Z 419 " =    1.640
peak=    3.575 closest distance to " O   HOH Z 374 " =    2.519
peak=    3.573 closest distance to " O   HOH Z 132 " =    2.964
peak=    3.569 closest distance to " NH2BARG A 145 " =    2.187
peak=    3.566 closest distance to " O   HOH Z 298 " =    1.957
peak=    3.563 closest distance to " O   HOH Z 295 " =    1.586
peak=    3.560 closest distance to " CD2 LEU A 255 " =    1.158
peak=    3.559 closest distance to " O   HOH Z 344 " =    1.902
peak=    3.552 closest distance to " CA  ASP A 140 " =    1.224
peak=    3.542 closest distance to " O   HOH Z  88 " =    3.177
peak=    3.539 closest distance to " CB  ALA A   9 " =    1.536
peak=    3.539 closest distance to " CB  PRO A  54 " =    1.311
peak=    3.532 closest distance to " O   HOH Z 273 " =    2.707
peak=    3.529 closest distance to " O   TRP A 274 " =    1.845
peak=    3.528 closest distance to " O   HOH Z 261 " =    1.786
peak=    3.518 closest distance to " O   HOH Z 327 " =    1.618
peak=    3.512 closest distance to " CB  ASN A 187 " =    1.392
peak=    3.508 closest distance to " O   HOH Z 421 " =    1.665
peak=    3.507 closest distance to " CB  ARG A 190 " =    1.661
peak=    3.506 closest distance to " O   HOH Z 236 " =    1.686
peak=    3.499 closest distance to " CA  VAL A 126 " =    1.005
peak=    3.499 closest distance to " CD  ARG A 159 " =    0.785
peak=    3.494 closest distance to " CD2 TRP A 179 " =    1.391
peak=    3.494 closest distance to " O   HOH Z 427 " =    2.795
peak=    3.490 closest distance to " CB  ALA A 100 " =    1.276
peak=    3.485 closest distance to " O   ALA A 165 " =    1.252
peak=    3.484 closest distance to " O   HOH Z  69 " =    1.072
peak=    3.482 closest distance to " O   HOH Z 332 " =    1.588
peak=    3.482 closest distance to " O   HOH Z 261 " =    1.916
peak=    3.482 closest distance to " O   HOH Z 217 " =    1.382
peak=    3.477 closest distance to " O   HOH Z 411 " =    1.817
peak=    3.476 closest distance to " O   HOH Z 366 " =    2.850
peak=    3.473 closest distance to " O   HOH Z 334 " =    1.464
peak=    3.473 closest distance to " O   HOH Z 395 " =    1.421
peak=    3.470 closest distance to " O   HOH Z 431 " =    1.066
peak=    3.468 closest distance to " N   ASN A  39 " =    1.265
peak=    3.467 closest distance to " O   HOH Z 280 " =    2.293
peak=    3.467 closest distance to " CA  ALA A  51 " =    1.021
peak=    3.465 closest distance to " C   GLY A  80 " =    1.155
peak=    3.465 closest distance to " CA  ARG A  36 " =    1.068
peak=    3.461 closest distance to " C   SER A  32 " =    1.108
peak=    3.460 closest distance to " O   HOH Z 108 " =    1.065
peak=    3.459 closest distance to " O   HOH Z 123 " =    2.018
peak=    3.456 closest distance to " O   HOH Z 155 " =    2.753
peak=    3.452 closest distance to " CE1 TYR A 186 " =    1.217
peak=    3.449 closest distance to " O   HOH Z  47 " =    1.380
peak=    3.449 closest distance to " CA  LYS A 117 " =    1.265
peak=    3.441 closest distance to " O   ASP A 124 " =    1.242
peak=    3.425 closest distance to " O   HOH Z 345 " =    1.717
peak=    3.423 closest distance to " CD  LYS A 166 " =    1.393
peak=    3.416 closest distance to " O   HOH Z  44 " =    1.938
peak=    3.415 closest distance to " O   HOH Z  21 " =    1.920
peak=    3.414 closest distance to " OG BSER A 164 " =    2.224
peak=    3.414 closest distance to " O   HOH Z 403 " =    1.460
peak=    3.413 closest distance to " O   HOH Z  66 " =    2.153
peak=    3.412 closest distance to " CD2 HIS A  81 " =    1.176
peak=    3.409 closest distance to " NH1 ARG A  14 " =    1.176
peak=    3.408 closest distance to " ND2 ASN A 187 " =    1.589
peak=    3.405 closest distance to " CB  SER A  26 " =    1.711
peak=    3.401 closest distance to " O   HOH Z  35 " =    2.408
peak=    3.400 closest distance to " O   HOH Z 358 " =    2.229
peak=    3.390 closest distance to " CA  ALA A 160 " =    0.811
peak=    3.389 closest distance to " CG  PRO A 243 " =    1.247
peak=    3.386 closest distance to " CB  PRO A 198 " =    1.021
peak=    3.376 closest distance to " OD1 ASP A 286 " =    1.652
peak=    3.375 closest distance to " O   HOH Z 422 " =    2.518
peak=    3.366 closest distance to " O   HOH Z  43 " =    2.213
peak=    3.365 closest distance to " OG  SER A  97 " =    2.543
peak=    3.365 closest distance to " O   HOH Z 150 " =    1.823
peak=    3.364 closest distance to " CG2 ILE A 120 " =    1.314
peak=    3.363 closest distance to " CD BLYS A 290 " =    1.038
peak=    3.360 closest distance to " CB  SER A  62 " =    1.102
peak=    3.359 closest distance to " O   HOH Z 214 " =    1.159
peak=    3.350 closest distance to " NZ  LYS A 166 " =    2.909
peak=    3.348 closest distance to " O   HOH Z  85 " =    1.345
peak=    3.345 closest distance to " O   HOH Z  64 " =    1.846
peak=    3.344 closest distance to " O   HOH Z 192 " =    1.506
peak=    3.341 closest distance to " CB  ARG A  79 " =    1.458
peak=    3.340 closest distance to " O   THR A  31 " =    1.497
peak=    3.339 closest distance to " O   HOH Z  19 " =    1.897
peak=    3.335 closest distance to " CB  TRP A 266 " =    1.081
peak=    3.333 closest distance to " NH2AARG A 275 " =    3.809
peak=    3.330 closest distance to " CB  ASN A  39 " =    0.863
peak=    3.326 closest distance to " O   HOH Z 298 " =    4.994
peak=    3.325 closest distance to " O   HOH Z 118 " =    1.245
peak=    3.324 closest distance to " CG1 VAL A 153 " =    1.026
peak=    3.324 closest distance to " CD1 ILE A  33 " =    1.599
peak=    3.318 closest distance to " CB  SER A  62 " =    0.763
peak=    3.317 closest distance to " O   HOH Z 420 " =    2.097
peak=    3.315 closest distance to " O   HOH Z 284 " =    1.222
peak=    3.312 closest distance to " CD1 LEU A 300 " =    1.049
peak=    3.310 closest distance to " O   HOH Z 383 " =    1.852
peak=    3.310 closest distance to " O   HOH Z 236 " =    1.783
peak=    3.309 closest distance to " CA  LEU A 101 " =    1.441
peak=    3.307 closest distance to " O   HOH Z 329 " =    3.493
peak=    3.302 closest distance to " CA  THR A  52 " =    1.152
peak=    3.301 closest distance to " CB  ALA A 256 " =    0.991
peak=    3.299 closest distance to " O   HOH Z 194 " =    1.973
peak=    3.292 closest distance to " O   HOH Z 145 " =    2.432
peak=    3.290 closest distance to " CB  ALA A 137 " =    1.306
peak=    3.289 closest distance to " O   HOH Z 402 " =    2.829
peak=    3.288 closest distance to " O   HOH Z 197 " =    2.055
peak=    3.287 closest distance to " O   GLY A  57 " =    2.453
peak=    3.285 closest distance to " O   HOH Z 185 " =    1.623
peak=    3.284 closest distance to " O   HOH Z 154 " =    1.331
peak=    3.279 closest distance to " CB  SER A 273 " =    0.799
peak=    3.273 closest distance to " CA  THR A 246 " =    1.087
peak=    3.270 closest distance to " NE1 TRP A 274 " =    0.888
peak=    3.268 closest distance to " OG  SER A  22 " =    2.760
peak=    3.266 closest distance to " O   HOH Z 133 " =    2.149
peak=    3.266 closest distance to " O   HOH Z 248 " =    1.725
peak=    3.265 closest distance to " CB  ARG A 139 " =    0.814
peak=    3.264 closest distance to " CD  ARG A 195 " =    0.914
peak=    3.258 closest distance to " C   ALA A 299 " =    0.980
peak=    3.257 closest distance to " CG  GLN A  58 " =    2.502
peak=    3.255 closest distance to " O   HOH Z 147 " =    1.794
peak=    3.254 closest distance to " O   HOH Z 423 " =    3.135
peak=    3.253 closest distance to " O   HOH Z 279 " =    2.084
peak=    3.249 closest distance to " O   HOH Z 299 " =    4.285
peak=    3.248 closest distance to " O   HOH Z 114 " =    1.060
peak=    3.247 closest distance to " O   HOH Z 367 " =    3.476
peak=    3.244 closest distance to " O   SER A  26 " =    1.672
peak=    3.241 closest distance to " O   HOH Z 261 " =    2.051
peak=    3.239 closest distance to " O   HOH Z 368 " =    3.501
peak=    3.237 closest distance to " O   HOH Z 166 " =    1.735
peak=    3.235 closest distance to " OD1 ASN A  60 " =    1.467
peak=    3.234 closest distance to " O   HOH Z 284 " =    1.597
peak=    3.234 closest distance to " CZ AARG A 102 " =    1.846
peak=    3.227 closest distance to " O   HOH Z 355 " =    1.697
peak=    3.226 closest distance to " OD1 ASP A 231 " =    1.927
peak=    3.225 closest distance to " CA  ALA A 158 " =    1.155
peak=    3.217 closest distance to " O   HOH Z 276 " =    1.300
peak=    3.215 closest distance to " OD1 ASN A  45 " =    1.374
peak=    3.215 closest distance to " CA  LEU A  83 " =    1.365
peak=    3.215 closest distance to " CG1 VAL A 296 " =    1.132
peak=    3.208 closest distance to " O   HOH Z 435 " =    1.895
peak=    3.202 closest distance to " NH2 ARG A  79 " =    1.425
peak=    3.202 closest distance to " CD2 TYR A 186 " =    1.106
peak=    3.201 closest distance to " CB  TYR A 247 " =    1.006
peak=    3.193 closest distance to " OD2 ASP A 298 " =    3.974
peak=    3.191 closest distance to " O   HOH Z 251 " =    1.651
peak=    3.191 closest distance to " O   HOH Z 409 " =    3.852
peak=    3.190 closest distance to " CZ  PHE A  38 " =    1.428
peak=    3.188 closest distance to " CD1 LEU A 222 " =    0.801
peak=    3.187 closest distance to " CB  ALA A  71 " =    1.238
peak=    3.187 closest distance to " O   HOH Z 438 " =    2.385
peak=    3.185 closest distance to " CG  GLN A  88 " =    1.067
peak=    3.181 closest distance to " N   TYR A 247 " =    1.200
peak=    3.180 closest distance to " O   HOH Z 359 " =    1.836
peak=    3.177 closest distance to " O   HOH Z  90 " =    3.315
peak=    3.174 closest distance to " O   HOH Z 207 " =    2.344
peak=    3.173 closest distance to " O   HOH Z 250 " =    1.337
peak=    3.171 closest distance to " CA  THR A 221 " =    0.889
peak=    3.166 closest distance to " O   ALA A   1 " =    1.693
peak=    3.164 closest distance to " CA  ASN A 215 " =    1.153
peak=    3.163 closest distance to " NH1 ARG A 269 " =    0.854
peak=    3.152 closest distance to " NZ  LYS A  76 " =    1.455
peak=    3.149 closest distance to " CB  ASN A 215 " =    1.129
peak=    3.148 closest distance to " NH1BARG A 190 " =    2.190
peak=    3.142 closest distance to " O   THR A 251 " =    1.246
peak=    3.141 closest distance to " CB  THR A  31 " =    1.633
peak=    3.137 closest distance to " CD1 TRP A 266 " =    1.244
peak=    3.135 closest distance to " O   HOH Z 139 " =    5.209
peak=    3.128 closest distance to " O   HOH Z 221 " =    1.165
peak=    3.123 closest distance to " CG2 ILE A 106 " =    0.802
peak=    3.123 closest distance to " CA  THR A 264 " =    0.812
peak=    3.122 closest distance to " O   HOH Z  59 " =    2.360
peak=    3.120 closest distance to " O   HOH Z 116 " =    1.672
peak=    3.120 closest distance to " O   HOH Z 425 " =    1.286
peak=    3.113 closest distance to " CB  THR A 157 " =    1.025
peak=    3.110 closest distance to " CB  ALA A 291 " =    1.305
peak=    3.109 closest distance to " O   HOH Z 352 " =    1.284
peak=    3.108 closest distance to " O   HOH Z  20 " =    1.854
peak=    3.094 closest distance to " CH2 TRP A 274 " =    2.118
peak=    3.090 closest distance to " CD1 LEU A 228 " =    1.433
peak=    3.090 closest distance to " CG  MET A 188 " =    1.465
peak=    3.084 closest distance to " CG1BVAL A 121 " =    1.244
peak=    3.083 closest distance to " O   HOH Z 197 " =    2.482
peak=    3.082 closest distance to " O   HOH Z 211 " =    2.526
peak=    3.074 closest distance to " O   HOH Z  50 " =    2.207
peak=    3.073 closest distance to " O   HOH Z 109 " =    2.544
peak=    3.067 closest distance to " O   HOH Z 152 " =    1.521
peak=    3.065 closest distance to " CG2AVAL A 121 " =    2.070
peak=    3.059 closest distance to " O   HOH Z 173 " =    2.326
peak=    3.055 closest distance to " O   HOH Z 156 " =    2.446
peak=    3.046 closest distance to " CG  LEU A 167 " =    1.159
peak=    3.040 closest distance to " O   HOH Z   1 " =    2.276
peak=    3.040 closest distance to " CB  GLN A  58 " =    0.786
peak=    3.039 closest distance to " OG1 THR A 221 " =    1.290
peak=    3.036 closest distance to " CG  MET A  93 " =    1.082
peak=    3.011 closest distance to " O   HOH Z 192 " =    1.178
peak=    3.010 closest distance to " O   PHE A 155 " =    1.858

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 202         
Filter by distance & map next to the model:
   mapped sites are within: 0.845 - 5.476
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 201 from: 202
   mapped sites are within: 0.845 - 5.476

peak=   -5.051 closest distance to " CG2 VAL A 230 " =    0.863
peak=   -4.473 closest distance to " CD  ARG A 156 " =    2.008
peak=   -4.429 closest distance to " O   HOH Z 166 " =    1.757
peak=   -4.400 closest distance to " CG2BVAL A  41 " =    2.722
peak=   -4.369 closest distance to " O   HOH Z  13 " =    1.531
peak=   -4.339 closest distance to " CA  SER A 164 " =    2.079
peak=   -4.328 closest distance to " O   HOH Z 266 " =    4.391
peak=   -4.255 closest distance to " OG ASER A 134 " =    1.146
peak=   -4.188 closest distance to " NH2 ARG A  66 " =    1.314
peak=   -4.064 closest distance to " CD1 PHE A  59 " =    1.948
peak=   -4.059 closest distance to " OG1 THR A   4 " =    1.831
peak=   -4.033 closest distance to " CD1 LEU A 101 " =    2.539
peak=   -4.000 closest distance to " N   SER A 276 " =    1.419
peak=   -3.957 closest distance to " SG  CYS A 254 " =    3.171
peak=   -3.954 closest distance to " O   HOH Z 210 " =    0.900
peak=   -3.954 closest distance to " CB  ALA A 161 " =    2.564
peak=   -3.921 closest distance to " OXT GLY A 302 " =    2.782
peak=   -3.911 closest distance to " N   ALA A 226 " =    2.002
peak=   -3.902 closest distance to " CD2 LEU A 237 " =    2.674
peak=   -3.886 closest distance to " O   HOH Z 231 " =    2.109
peak=   -3.885 closest distance to " O   HOH Z 426 " =    1.809
peak=   -3.870 closest distance to " C   HIS A 108 " =    1.145
peak=   -3.859 closest distance to " CE2 TYR A  30 " =    2.766
peak=   -3.831 closest distance to " CD2 LEU A 300 " =    2.743
peak=   -3.830 closest distance to " O   HOH Z  71 " =    1.197
peak=   -3.807 closest distance to " O   HOH Z 266 " =    4.575
peak=   -3.798 closest distance to " OG BSER A 134 " =    1.331
peak=   -3.787 closest distance to " OG  SER A  97 " =    2.263
peak=   -3.765 closest distance to " O   HOH Z 103 " =    1.870
peak=   -3.755 closest distance to " O   HOH Z 407 " =    3.089
peak=   -3.731 closest distance to " CH2 TRP A 179 " =    1.264
peak=   -3.687 closest distance to " CG1 VAL A  78 " =    2.776
peak=   -3.683 closest distance to " CG  ASP A 231 " =    0.845
peak=   -3.683 closest distance to " O   HOH Z  92 " =    1.365
peak=   -3.680 closest distance to " CA  GLY A 203 " =    2.114
peak=   -3.680 closest distance to " O   HOH Z 126 " =    1.900
peak=   -3.676 closest distance to " O   VAL A  67 " =    2.612
peak=   -3.671 closest distance to " CB  LYS A 193 " =    2.367
peak=   -3.670 closest distance to " CB  TYR A  15 " =    2.230
peak=   -3.669 closest distance to " C   ALA A 158 " =    1.168
peak=   -3.669 closest distance to " O   HOH Z 423 " =    2.323
peak=   -3.653 closest distance to " O   HOH Z 377 " =    1.997
peak=   -3.651 closest distance to " C   THR A 279 " =    1.148
peak=   -3.648 closest distance to " CZ  TYR A 169 " =    1.899
peak=   -3.642 closest distance to " O   ASN A 187 " =    1.468
peak=   -3.636 closest distance to " N   GLN A  58 " =    1.705
peak=   -3.626 closest distance to " O   HOH Z 165 " =    2.051
peak=   -3.603 closest distance to " CB  CYS A 254 " =    2.489
peak=   -3.599 closest distance to " O   HOH Z 351 " =    1.423
peak=   -3.598 closest distance to " O   HOH Z  52 " =    1.869
peak=   -3.587 closest distance to " OG BSER A 134 " =    1.708
peak=   -3.584 closest distance to " NH2AARG A 275 " =    4.985
peak=   -3.581 closest distance to " CG  GLU A   2 " =    1.770
peak=   -3.576 closest distance to " CD  LYS A 289 " =    2.524
peak=   -3.571 closest distance to " CB  ALA A 248 " =    1.955
peak=   -3.569 closest distance to " CG  ARG A 219 " =    2.436
peak=   -3.555 closest distance to " O   HOH Z 234 " =    4.299
peak=   -3.532 closest distance to " O   HOH Z  48 " =    1.325
peak=   -3.529 closest distance to " O   ASP A 191 " =    1.338
peak=   -3.527 closest distance to " CA  ASP A 298 " =    1.044
peak=   -3.520 closest distance to " O   ALA A 161 " =    1.692
peak=   -3.516 closest distance to " CE BMET A  47 " =    1.517
peak=   -3.514 closest distance to " ND2 ASN A  60 " =    1.352
peak=   -3.504 closest distance to " O  BHOH Z 338 " =    1.537
peak=   -3.501 closest distance to " O   PHE A 218 " =    1.534
peak=   -3.498 closest distance to " O   HOH Z 196 " =    2.358
peak=   -3.489 closest distance to " O   HOH Z  11 " =    1.587
peak=   -3.487 closest distance to " CG2 VAL A 112 " =    2.527
peak=   -3.485 closest distance to " CD  GLN A  88 " =    2.202
peak=   -3.485 closest distance to " N   THR A 235 " =    1.277
peak=   -3.480 closest distance to " CG  GLU A  53 " =    1.452
peak=   -3.479 closest distance to " CD  ARG A 139 " =    1.608
peak=   -3.478 closest distance to " O   HOH Z 136 " =    2.136
peak=   -3.476 closest distance to " O   ALA A   1 " =    1.878
peak=   -3.474 closest distance to " O   HOH Z 150 " =    1.448
peak=   -3.465 closest distance to " OG  SER A  62 " =    1.443
peak=   -3.460 closest distance to " CG2 THR A 182 " =    2.278
peak=   -3.459 closest distance to " O   HOH Z 198 " =    2.164
peak=   -3.455 closest distance to " O   HOH Z 166 " =    2.178
peak=   -3.454 closest distance to " O   HOH Z 292 " =    4.348
peak=   -3.451 closest distance to " O   HOH Z  17 " =    1.267
peak=   -3.447 closest distance to " O   ALA A 256 " =    1.393
peak=   -3.432 closest distance to " O   HOH Z 311 " =    3.473
peak=   -3.430 closest distance to " OXT GLY A 302 " =    3.559
peak=   -3.429 closest distance to " O   HOH Z 396 " =    1.532
peak=   -3.428 closest distance to " CE  MET A 105 " =    2.040
peak=   -3.421 closest distance to " O   ALA A 160 " =    1.399
peak=   -3.419 closest distance to " O   HOH Z 151 " =    1.520
peak=   -3.413 closest distance to " O   HOH Z 290 " =    0.935
peak=   -3.405 closest distance to " CG2 VAL A 189 " =    1.971
peak=   -3.400 closest distance to " O   TRP A  92 " =    1.856
peak=   -3.399 closest distance to " O   SER A 271 " =    2.033
peak=   -3.397 closest distance to " O   SER A 146 " =    0.870
peak=   -3.395 closest distance to " O   HOH Z  43 " =    1.899
peak=   -3.394 closest distance to " CD2 TYR A 293 " =    2.088
peak=   -3.386 closest distance to " N   ALA A 248 " =    1.756
peak=   -3.383 closest distance to " CB  ASP A 162 " =    2.622
peak=   -3.378 closest distance to " O   LEU A 228 " =    2.347
peak=   -3.377 closest distance to " CA  GLY A 133 " =    1.950
peak=   -3.376 closest distance to " CB  ALA A  51 " =    1.865
peak=   -3.372 closest distance to " C   GLY A  91 " =    1.412
peak=   -3.371 closest distance to " ND2 ASN A  39 " =    1.210
peak=   -3.370 closest distance to " O   HOH Z 377 " =    1.327
peak=   -3.368 closest distance to " OD1 ASN A 148 " =    1.621
peak=   -3.366 closest distance to " O   HOH Z 313 " =    1.249
peak=   -3.360 closest distance to " CG2 ILE A 263 " =    2.278
peak=   -3.356 closest distance to " OG BSER A 210 " =    1.273
peak=   -3.349 closest distance to " CG  ASP A  50 " =    2.426
peak=   -3.348 closest distance to " CB  PHE A 208 " =    2.297
peak=   -3.342 closest distance to " O   HOH Z  38 " =    1.604
peak=   -3.342 closest distance to " O   HOH Z 171 " =    2.173
peak=   -3.341 closest distance to " CD  ARG A 195 " =    5.060
peak=   -3.338 closest distance to " CE3 TRP A 150 " =    2.220
peak=   -3.337 closest distance to " O   HOH Z 388 " =    2.059
peak=   -3.336 closest distance to " O   HOH Z 193 " =    1.754
peak=   -3.334 closest distance to " O   HOH Z 191 " =    5.476
peak=   -3.331 closest distance to " NH2 ARG A  79 " =    1.835
peak=   -3.327 closest distance to " O   HOH Z 435 " =    2.431
peak=   -3.319 closest distance to " O   HOH Z 426 " =    2.301
peak=   -3.319 closest distance to " O   HOH Z 431 " =    2.278
peak=   -3.315 closest distance to " O   HOH Z 208 " =    1.322
peak=   -3.309 closest distance to " CG2 VAL A 197 " =    2.259
peak=   -3.305 closest distance to " O   GLY A 196 " =    0.956
peak=   -3.304 closest distance to " CB  ALA A 248 " =    2.202
peak=   -3.301 closest distance to " OD1 ASP A 200 " =    1.217
peak=   -3.298 closest distance to " O   HOH Z  10 " =    1.488
peak=   -3.295 closest distance to " CD1 TRP A 179 " =    1.154
peak=   -3.287 closest distance to " O   ALA A  51 " =    1.469
peak=   -3.284 closest distance to " O   PRO A 198 " =    1.260
peak=   -3.279 closest distance to " CA  ASN A 127 " =    0.935
peak=   -3.279 closest distance to " O   HOH Z 283 " =    1.957
peak=   -3.277 closest distance to " OD1 ASN A 249 " =    1.179
peak=   -3.277 closest distance to " O   HOH Z 292 " =    2.672
peak=   -3.273 closest distance to " O   SER A  95 " =    1.626
peak=   -3.273 closest distance to " CA  VAL A 197 " =    0.988
peak=   -3.268 closest distance to " ND2 ASN A  45 " =    0.906
peak=   -3.267 closest distance to " OG  SER A 206 " =    1.645
peak=   -3.266 closest distance to " CD1 LEU A 228 " =    2.306
peak=   -3.261 closest distance to " O   HOH Z  97 " =    1.332
peak=   -3.253 closest distance to " O   ALA A   8 " =    1.946
peak=   -3.252 closest distance to " O   HOH Z 423 " =    1.069
peak=   -3.251 closest distance to " NE2 GLN A  88 " =    1.145
peak=   -3.248 closest distance to " CA  PRO A 243 " =    2.691
peak=   -3.246 closest distance to " CD1 TYR A 247 " =    2.273
peak=   -3.242 closest distance to " CB  ALA A  43 " =    2.504
peak=   -3.239 closest distance to " O   VAL A 197 " =    1.342
peak=   -3.230 closest distance to " O   HOH Z 411 " =    1.560
peak=   -3.230 closest distance to " O   HOH Z  19 " =    2.389
peak=   -3.229 closest distance to " C   VAL A 265 " =    0.850
peak=   -3.222 closest distance to " O   VAL A 125 " =    2.205
peak=   -3.219 closest distance to " N   THR A 157 " =    1.535
peak=   -3.217 closest distance to " ND2 ASN A  69 " =    1.560
peak=   -3.214 closest distance to " O   HOH Z 250 " =    1.413
peak=   -3.213 closest distance to " CB  PRO A 163 " =    2.781
peak=   -3.207 closest distance to " O   HOH Z 313 " =    2.137
peak=   -3.204 closest distance to " O   HOH Z  15 " =    1.558
peak=   -3.203 closest distance to " O   PRO A 198 " =    1.292
peak=   -3.201 closest distance to " CG1 VAL A 112 " =    2.338
peak=   -3.201 closest distance to " O   LEU A 300 " =    2.508
peak=   -3.193 closest distance to " O   HOH Z 297 " =    2.820
peak=   -3.193 closest distance to " O   HOH Z 353 " =    2.320
peak=   -3.186 closest distance to " O   HOH Z 412 " =    5.127
peak=   -3.185 closest distance to " O   HOH Z  60 " =    2.262
peak=   -3.181 closest distance to " CG  ARG A 269 " =    2.277
peak=   -3.181 closest distance to " O   HOH Z 418 " =    1.514
peak=   -3.180 closest distance to " CE  MET A  93 " =    1.247
peak=   -3.174 closest distance to " O   HOH Z 360 " =    2.570
peak=   -3.174 closest distance to " O   HOH Z 166 " =    1.417
peak=   -3.170 closest distance to " O   HOH Z 427 " =    1.370
peak=   -3.167 closest distance to " O   HOH Z 350 " =    1.949
peak=   -3.165 closest distance to " O   HOH Z 166 " =    1.504
peak=   -3.160 closest distance to " O   HOH Z 189 " =    1.691
peak=   -3.157 closest distance to " O   HOH Z 414 " =    2.046
peak=   -3.151 closest distance to " CG  GLU A   2 " =    1.574
peak=   -3.150 closest distance to " NE2 GLN A  58 " =    1.084
peak=   -3.150 closest distance to " CB  SER A 245 " =    2.414
peak=   -3.145 closest distance to " O   HOH Z 145 " =    1.651
peak=   -3.139 closest distance to " O   HOH Z 185 " =    2.141
peak=   -3.137 closest distance to " O   HOH Z   6 " =    2.043
peak=   -3.137 closest distance to " CG1 VAL A 296 " =    1.220
peak=   -3.135 closest distance to " CG  GLU A 277 " =    1.171
peak=   -3.135 closest distance to " O   HOH Z 301 " =    2.289
peak=   -3.133 closest distance to " C   LEU A 143 " =    1.130
peak=   -3.131 closest distance to " O   HOH Z  12 " =    3.671
peak=   -3.129 closest distance to " O   HOH Z  56 " =    2.222
peak=   -3.128 closest distance to " OG1 THR A  82 " =    1.441
peak=   -3.128 closest distance to " CG  TRP A 266 " =    1.708
peak=   -3.123 closest distance to " OD1 ASP A 191 " =    1.615
peak=   -3.122 closest distance to " O   GLY A  80 " =    2.417
peak=   -3.118 closest distance to " O   HOH Z 222 " =    1.428
peak=   -3.106 closest distance to " O   HOH Z 385 " =    3.770
peak=   -3.102 closest distance to " O   HOH Z 108 " =    2.071
peak=   -3.099 closest distance to " CD  GLN A 223 " =    1.808
peak=   -3.099 closest distance to " CE  LYS A 166 " =    2.913
peak=   -3.091 closest distance to " O   HOH Z 310 " =    1.617
peak=   -3.091 closest distance to " O   ALA A 100 " =    2.368
peak=   -3.083 closest distance to " O   HOH Z  55 " =    2.473
peak=   -3.064 closest distance to " ND2 ASN A 252 " =    1.691
peak=   -3.029 closest distance to " CA  ARG A  66 " =    1.839
peak=   -3.022 closest distance to " CA  GLY A 133 " =    2.101
peak=   -3.010 closest distance to " CG  PHE A  59 " =    2.110

================= 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    :  0.4831 0.4838   6.285023e+00   6.275362e+00
   1_bss:  0.4760 0.4747   6.282887e+00   6.266059e+00
   1_xyz:  0.4054 0.4215   6.184837e+00   6.214648e+00
   1_adp:  0.3619 0.4032   6.117598e+00   6.193633e+00
   1_occ:  0.3612 0.4035   6.117031e+00   6.193701e+00
   2_bss:  0.3593 0.3986   6.117885e+00   6.191940e+00
   2_xyz:  0.2636 0.3229   5.874709e+00   6.025356e+00
   2_adp:  0.2368 0.2965   5.787095e+00   5.954844e+00
   2_occ:  0.2365 0.2967   5.786799e+00   5.954934e+00
   3_bss:  0.2324 0.2930   5.783306e+00   5.950696e+00
   3_xyz:  0.1795 0.2288   5.548909e+00   5.743213e+00
   3_adp:  0.1678 0.2173   5.489104e+00   5.686406e+00
   3_occ:  0.1675 0.2173   5.488406e+00   5.685981e+00
   4_bss:  0.1675 0.2175   5.488961e+00   5.686476e+00
   4_xyz:  0.1325 0.1751   5.276989e+00   5.491962e+00
   4_adp:  0.1252 0.1703   5.235934e+00   5.463430e+00
   4_occ:  0.1251 0.1704   5.235885e+00   5.463863e+00
   5_bss:  0.1254 0.1710   5.239489e+00   5.467185e+00
   5_xyz:  0.1175 0.1648   5.194885e+00   5.435769e+00
   5_adp:  0.1162 0.1649   5.188482e+00   5.433823e+00
   5_occ:  0.1161 0.1649   5.188206e+00   5.433652e+00
   5_bss:  0.1161 0.1649   5.188264e+00   5.433834e+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:  0.353  20.000   6.451  10.156   8.425   0.000   0.000   0.000
   1_xyz:  0.353  20.000   6.451  10.156   8.425   0.000   0.000   0.000
   1_adp:  0.353  20.000   6.451  10.156   8.425   0.000   0.000   0.000
   1_occ:  0.353  20.000   6.451  10.156   8.425   0.000   0.000   0.000
   2_bss:  0.349  50.000   3.157   6.521   5.709   0.000   0.000   0.000
   2_xyz:  0.349  50.000   3.157   6.521   5.709   0.000   0.000   0.000
   2_adp:  0.349  50.000   3.157   6.521   5.709   0.000   0.000   0.000
   2_occ:  0.349  50.000   3.157   6.521   5.709   0.000   0.000   0.000
   3_bss:  0.326  45.094   1.365   3.222   2.745   0.000   0.000   0.000
   3_xyz:  0.326  45.094   1.365   3.222   2.745   0.000   0.000   0.000
   3_adp:  0.326  45.094   1.365   3.222   2.745   0.000   0.000   0.000
   3_occ:  0.326  45.094   1.365   3.222   2.745   0.000   0.000   0.000
   4_bss:  0.322  45.094   0.659   2.227   1.863   0.000   0.000   0.000
   4_xyz:  0.322  45.094   0.659   2.227   1.863   0.000   0.000   0.000
   4_adp:  0.322  45.094   0.659   2.227   1.863   0.000   0.000   0.000
   4_occ:  0.322  45.094   0.659   2.227   1.863   0.000   0.000   0.000
   5_bss:  0.322  44.811   0.599   1.776   1.591   0.000   0.000   0.000
   5_xyz:  0.322  44.811   0.599   1.776   1.591   0.000   0.000   0.000
   5_adp:  0.322  44.811   0.599   1.776   1.591   0.000   0.000   0.000
   5_occ:  0.322  44.811   0.599   1.776   1.591   0.000   0.000   0.000
   5_bss:  0.324  47.933  -0.659   0.383   0.276   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  59.900 0.3944  0.4603    71934.514
   1_bss:  59.753 0.3938  0.5761    68781.119
   1_xyz:  51.054 0.5045  0.7360    53777.171
   1_adp:  47.257 0.5529  0.8611    48744.886
   1_occ:  47.264 0.5527  0.8598    48727.467
   2_bss:  46.907 0.5571  0.7769    48208.042
   2_xyz:  34.242 0.7090  0.9736    28118.632
   2_adp:  30.625 0.7506  1.0140    23494.914
   2_occ:  30.640 0.7504  1.0134    23505.565
   3_bss:  30.386 0.7531  0.9230    23163.594
   3_xyz:  22.666 0.8350  0.9845    13747.499
   3_adp:  20.886 0.8533  0.9943    12149.130
   3_occ:  20.875 0.8535  0.9944    12147.825
   4_bss:  20.845 0.8537  0.9640    12120.347
   4_xyz:  16.437 0.8941  0.9873     7947.845
   4_adp:  15.806 0.8998  0.9869     7531.807
   4_occ:  15.812 0.8998  0.9867     7541.898
   5_bss:  15.866 0.8995  0.9772     7638.826
   5_xyz:  15.133 0.9058  0.9790     7115.198
   5_adp:  15.040 0.9067  0.9747     7070.776
   5_occ:  15.033 0.9067  0.9747     7070.362
   5_bss:  15.034 0.9067  0.9783     7075.539
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.3434e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.3434e+01
   1_xyz:   1.721  0.013  0.109 18.211  0.007  4.109   1.4511e-01
   1_adp:   1.721  0.013  0.109 18.211  0.007  4.109   1.4511e-01
   1_occ:   1.721  0.013  0.109 18.211  0.007  4.109   1.4511e-01
   2_bss:   1.721  0.013  0.109 18.211  0.007  4.109   1.4511e-01
   2_xyz:   1.253  0.010  0.085 16.414  0.005  4.116   9.3691e-02
   2_adp:   1.253  0.010  0.085 16.414  0.005  4.116   9.3691e-02
   2_occ:   1.253  0.010  0.085 16.414  0.005  4.116   9.3691e-02
   3_bss:   1.253  0.010  0.085 16.414  0.005  4.116   9.3691e-02
   3_xyz:   0.948  0.006  0.067 15.237  0.004  4.129   5.5615e-02
   3_adp:   0.948  0.006  0.067 15.237  0.004  4.129   5.5615e-02
   3_occ:   0.948  0.006  0.067 15.237  0.004  4.129   5.5615e-02
   4_bss:   0.948  0.006  0.067 15.237  0.004  4.129   5.5615e-02
   4_xyz:   1.049  0.007  0.081 15.481  0.004  4.124   6.5410e-02
   4_adp:   1.049  0.007  0.081 15.481  0.004  4.124   6.5410e-02
   4_occ:   1.049  0.007  0.081 15.481  0.004  4.124   6.5410e-02
   5_bss:   1.049  0.007  0.081 15.481  0.004  4.124   6.5410e-02
   5_xyz:   1.044  0.007  0.081 15.467  0.004  4.126   6.3769e-02
   5_adp:   1.044  0.007  0.081 15.467  0.004  4.126   6.3769e-02
   5_occ:   1.044  0.007  0.081 15.467  0.004  4.126   6.3769e-02
   5_bss:   1.044  0.007  0.081 15.467  0.004  4.126   6.3769e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.042   6.9252e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.042   6.9252e+00
   1_xyz:  15.157  0.170  0.504 87.578  0.056  2.181   1.0132e-01
   1_adp:  15.157  0.170  0.504 87.578  0.056  2.181   1.0132e-01
   1_occ:  15.157  0.170  0.504 87.578  0.056  2.181   1.0132e-01
   2_bss:  15.157  0.170  0.504 87.578  0.056  2.181   1.0132e-01
   2_xyz:   8.621  0.123  0.309 86.940  0.050  2.188   1.1019e-01
   2_adp:   8.621  0.123  0.309 86.940  0.050  2.188   1.1019e-01
   2_occ:   8.621  0.123  0.309 86.940  0.050  2.188   1.1019e-01
   3_bss:   8.621  0.123  0.309 86.940  0.050  2.188   1.1019e-01
   3_xyz:   6.988  0.043  0.304 86.737  0.047  2.307   4.4708e-02
   3_adp:   6.988  0.043  0.304 86.737  0.047  2.307   4.4708e-02
   3_occ:   6.988  0.043  0.304 86.737  0.047  2.307   4.4708e-02
   4_bss:   6.988  0.043  0.304 86.737  0.047  2.307   4.4708e-02
   4_xyz:   7.118  0.048  0.539 80.432  0.027  2.283   4.6262e-02
   4_adp:   7.118  0.048  0.539 80.432  0.027  2.283   4.6262e-02
   4_occ:   7.118  0.048  0.539 80.432  0.027  2.283   4.6262e-02
   5_bss:   7.118  0.048  0.539 80.432  0.027  2.283   4.6262e-02
   5_xyz:   7.107  0.039  0.577 81.556  0.029  2.332   4.4082e-02
   5_adp:   7.107  0.039  0.577 81.556  0.029  2.332   4.4082e-02
   5_occ:   7.107  0.039  0.577 81.556  0.029  2.332   4.4082e-02
   5_bss:   7.107  0.039  0.577 81.556  0.029  2.332   4.4082e-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:  92.53   0.00  13.76  70.74   0.00  11.40  92.53   0.00  26.61
   1_occ:  92.53   0.00  13.76  70.74   0.00  11.40  92.53   0.00  26.61
   2_bss:  92.53   0.00  13.76  70.74   0.00  11.40  92.53   0.00  26.61
   2_xyz:  92.53   0.00  13.76  70.74   0.00  11.40  92.53   0.00  26.61
   2_adp:  86.25   0.00  13.87  71.97   0.00  10.32  86.25   1.30  33.19
   2_occ:  86.25   0.00  13.87  71.97   0.00  10.32  86.25   1.30  33.19
   3_bss:  86.25   0.00  13.87  71.97   0.00  10.32  86.25   1.30  33.19
   3_xyz:  86.25   0.00  13.87  71.97   0.00  10.32  86.25   1.30  33.19
   3_adp:  81.32   0.00  13.97  77.09   0.00   9.89  81.32   3.72  36.15
   3_occ:  81.32   0.00  13.97  77.09   0.00   9.89  81.32   3.72  36.15
   4_bss:  81.32   0.00  13.97  77.09   0.00   9.89  81.32   3.72  36.15
   4_xyz:  81.32   0.00  13.97  77.09   0.00   9.89  81.32   3.72  36.15
   4_adp:  84.54   0.00  14.17  84.54   0.00   9.72  79.30   2.95  38.40
   4_occ:  84.54   0.00  14.17  84.54   0.00   9.72  79.30   2.95  38.40
   5_bss:  84.54   0.00  14.17  84.54   0.00   9.72  79.30   2.95  38.40
   5_xyz:  84.54   0.00  14.17  84.54   0.00   9.72  79.30   2.95  38.40
   5_adp:  89.58   0.00  14.11  89.58   0.00   9.63  79.48   2.14  38.51
   5_occ:  89.58   0.00  14.11  89.58   0.00   9.63  79.48   2.14  38.51
   5_bss:  91.00   1.42  15.53  91.00   1.42  11.05  80.90   3.57  39.93
------------------------------------------------------------------------
 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:    1.177    0.007    0.412
   1_adp:    1.177    0.007    0.412
   1_occ:    1.177    0.007    0.412
   2_bss:    1.177    0.007    0.412
   2_xyz:    1.876    0.038    0.622
   2_adp:    1.876    0.038    0.622
   2_occ:    1.876    0.038    0.622
   3_bss:    1.876    0.038    0.622
   3_xyz:    1.576    0.024    0.672
   3_adp:    1.576    0.024    0.672
   3_occ:    1.576    0.024    0.672
   4_bss:    1.576    0.024    0.672
   4_xyz:    1.739    0.059    0.754
   4_adp:    1.739    0.059    0.754
   4_occ:    1.739    0.059    0.754
   5_bss:    1.739    0.059    0.754
   5_xyz:    1.820    0.098    0.766
   5_adp:    1.820    0.098    0.766
   5_occ:    1.820    0.098    0.766
   5_bss:    1.820    0.098    0.766
------------------------------------------------------------------------

CPU time actual refinement: 336.95


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_573/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_573/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_573/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_573/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_573/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 336.78 
  Macro-tasks:
    bulk solvent and scale       = 40.03  
    individual site refinement   = 135.98 
    weights calculation          = 32.51  
    collect and process          = 6.44   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 215.09 
  Micro-tasks:
    mask                            = 2.48   
    f_calc                          = 105.79 
    alpha_beta                      = 8.06   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 114.61 
    fmodel                         = 7.10   
    r_factors                      = 0.28   
    phase_errors                   = 10.50  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 250.21 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.789 micro seconds
Total CPU time: 5.84 minutes
from_scatterers_fft:    631 calls, 105.48 s
gradients_fft:          576 calls, 101.73 s

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

# Date 2008-01-16 Time 01:55:46 PST -0800 (1200477346.32 s)
Start R-work = 0.4831, R-free = 0.4838 (no bulk solvent and anisotropic scale)
Final R-work = 0.1327, R-free = 0.1817 (no bulk solvent and anisotropic scale)

Start R-work = 0.4760, R-free = 0.4747
Final R-work = 0.1161, R-free = 0.1649