# Date 2008-01-16 Time 02:33:42 PST -0800 (1200479622.92 s)
#phil __OFF__

Command line arguments: "../884.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 24912
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 884

-------------------------------------------------------------------------------
  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: (70.9525, 46.4607, 85.9581, 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: 3.29, 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: (70.9525, 46.4607, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0819 1.98157
Completeness in resolution range: 0.964595
Completeness with d_max=infinity: 0.961659

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0819
                             d_min =   1.9816

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: (70.9525, 46.4607, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0819 1.98157
Completeness in resolution range: 0.964595
Completeness with d_max=infinity: 0.961659

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0824 -  4.2405 [2126/2151]  1916   210   9.9%
  bin  2:  4.2405 -  3.3783 [2050/2070]  1844   206  10.0%
  bin  3:  3.3783 -  2.9549 [2029/2048]  1824   205  10.1%
  bin  4:  2.9549 -  2.6864 [2006/2036]  1810   196   9.8%
  bin  5:  2.6864 -  2.4947 [2000/2019]  1801   199   9.9%
  bin  6:  2.4947 -  2.3482 [1985/2010]  1780   205  10.3%
  bin  7:  2.3482 -  2.2310 [1947/1975]  1753   194  10.0%
  bin  8:  2.2310 -  2.1342 [1987/2023]  1786   201  10.1%
  bin  9:  2.1342 -  2.0522 [1957/1999]  1764   193   9.9%
  bin 10:  2.0522 -  1.9816 [1502/1977]  1352   150  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_884/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:
        1.81 -     2.42: 16
        2.42 -     3.04: 2195
        3.04 -     3.66: 4711
        3.66 -     4.28: 9087
        4.28 -     4.90: 12323
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 204 " - " O   HOH Z 296 "  2.224 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 201 " - " O   HOH Z 349 "  2.275 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.305 3.040 x,y+1,z
  ... (remaining 28327 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_884/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_884/model_refine_001.geo

CPU time processing inputs: 9.69


============================ 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 = 70.9525 46.4607 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4421   r_free= 0.4260   ksol= 0.00   Bsol= 0.00   scale= 0.819    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.237397                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0824 -  4.7298 0.99   1390  155 0.3762 0.3695      6.5377      6.5172|
|  2:  4.7298 -  3.7736 0.99   1332  147 0.3389 0.3417      6.6823      6.6468|
|  3:  3.7736 -  3.3023 0.99   1304  142 0.3797 0.3479      6.5672      6.6005|
|  4:  3.3023 -  3.0029 0.99   1303  153 0.4193 0.3750       6.478      6.3895|
|  5:  3.0029 -  2.7892 0.99   1294  142 0.4669 0.4597      6.3254      6.3427|
|  6:  2.7892 -  2.6256 0.99   1282  137 0.4634 0.4743      6.2416      6.1854|
|  7:  2.6256 -  2.4947 0.99   1290  140 0.4915 0.4715      6.2241      6.2272|
|  8:  2.4947 -  2.3866 0.98   1261  148 0.4903 0.4327      6.1579      6.1273|
|  9:  2.3866 -  2.2950 0.98   1266  141 0.4724 0.4665      6.0906       6.063|
| 10:  2.2950 -  2.2161 1.00   1279  139 0.4983 0.4820      6.0954      6.0951|
| 11:  2.2161 -  2.1470 0.97   1257  140 0.5056 0.4698      6.0275      6.0061|
| 12:  2.1470 -  2.0858 0.98   1250  139 0.4889 0.5310      5.9676      6.0234|
| 13:  2.0858 -  2.0310 0.99   1287  142 0.5176 0.4981      5.8788      5.8129|
| 14:  2.0310 -  1.9816 0.66    835   94 0.5252 0.4910      5.8477      5.7766|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0824 -  4.7298  1390   155  0.72  32.81   0.81     0.76      64976.24|
|  2:  4.7298 -  3.7736  1332   147  0.77  29.05   0.90     0.83      78367.06|
|  3:  3.7736 -  3.3023  1304   142  0.70  35.55   0.88     0.81      80219.31|
|  4:  3.3023 -  3.0029  1303   153  0.65  40.14   0.83     0.73      71805.17|
|  5:  3.0029 -  2.7892  1294   142  0.54  49.03   0.76     0.62      63999.76|
|  6:  2.7892 -  2.6256  1282   137  0.51  51.58   0.76     0.56      58350.05|
|  7:  2.6256 -  2.4947  1290   140  0.48  53.70   0.76     0.54      55121.59|
|  8:  2.4947 -  2.3866  1261   148  0.48  53.74   0.75     0.55      49569.51|
|  9:  2.3866 -  2.2950  1266   141  0.50  51.79   0.75     0.56      43147.74|
| 10:  2.2950 -  2.2161  1279   139  0.48  53.58   0.78     0.56      38847.71|
| 11:  2.2161 -  2.1470  1257   140  0.46  55.11   0.77     0.54      37827.83|
| 12:  2.1470 -  2.0858  1250   139  0.42  58.26   0.79     0.51      38197.67|
| 13:  2.0858 -  2.0310  1287   142  0.37  62.07   0.74     0.46      34423.95|
| 14:  2.0310 -  1.9816   835    94  0.39  61.19   0.72     0.41      27809.78|
|alpha:            min =        0.41 max =            0.83 mean =         0.61|
|beta:             min =    27809.78 max =        80219.31 mean =     53955.60|
|figures of merit: min =        0.00 max =            1.00 mean =         0.54|
|phase err.(work): min =        0.00 max =           90.00 mean =        48.60|
|phase err.(test): min =        0.00 max =           89.90 mean =        48.71|
|-----------------------------------------------------------------------------|

============================== 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 = 8.766428              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 75.673   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.742832              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.829   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      171 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      682 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1509 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2654 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3929 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5086 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6563 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7746 |
|-----------------------------------------------------------------------------|
|-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 |       53.657 |
| 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  1.196 |       1.701 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.866)------------------------------------------|
|    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 = 11.866)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4492   r_free= 0.4335   ksol= 0.00   Bsol= 0.00   scale= 0.787    |
|                                                                             |
| 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:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.242195                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4330   r_free= 0.4158   ksol= 0.35   Bsol= 12.48   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.14,9.25,7.88,0.00,0.00,0.00); trace/3= 8.42                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.231594                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.072977              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.435   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.737803              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.088   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4330      final r-factor (work) = 0.3292          |
| start r-factor (free) = 0.4158      final r-factor (free) = 0.3523          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 78.8666 = 8.07 * 0.50 * 6.2454 + 1.00 * 53.6572                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.7251 = 8.07 * 0.50 * 6.0951 + 1.00 * 0.1221                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3292      final r-factor (work) = 0.2709          |
| start r-factor (free) = 0.3523      final r-factor (free) = 0.3140          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5117 = 0.74 * 1.00 * 6.0951 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3938 = 0.74 * 1.00 * 5.9379 + 1.00 * 0.0129                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.866)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    67.21   11.09    None  None   None       |
|    all(noH): 2823   0      0.00    67.21   11.09    None  None   None       |
|    Sol.    : 438    0      0.00    67.21   27.29    None  None   None       |
|    Mac.    : 2385   0      0.00    66.69   8.12     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.721: 1285   |   5:    33.605 -  40.326:   82        |
|      1:     6.721 -  13.442:  768   |   6:    40.326 -  47.047:   49        |
|      2:    13.442 -  20.163:  294   |   7:    47.047 -  53.768:   17        |
|      3:    20.163 -  26.884:  189   |   8:    53.768 -  60.489:   11        |
|      4:    26.884 -  33.605:  124   |   9:    60.489 -  67.210:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2709 r_free = 0.3140             target_work(ml) = 5.887         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2704 r_free = 0.3145             target_work(ml) = 5.886         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2704   r_free= 0.3145   ksol= 0.35   Bsol= 12.48   scale= 1.099   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.14,9.25,7.88,0.00,0.00,0.00); trace/3= 8.42                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.885739                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2650   r_free= 0.3069   ksol= 0.35   Bsol= 41.63   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.60,5.19,4.94,0.00,0.00,0.00); trace/3= 4.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.881424                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.261935              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.622   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.352570              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.664  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2650      final r-factor (work) = 0.1834          |
| start r-factor (free) = 0.3069      final r-factor (free) = 0.2288          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8108 = 3.26 * 0.50 * 5.9407 + 1.00 * 0.1217                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3783 = 3.26 * 0.50 * 5.7126 + 1.00 * 0.0613                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1834      final r-factor (work) = 0.1656          |
| start r-factor (free) = 0.2288      final r-factor (free) = 0.2121          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0268 = 0.35 * 1.00 * 5.7126 + 1.00 * 0.0127                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9507 = 0.35 * 1.00 * 5.5025 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.866)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    70.26   11.36    None  None   None       |
|    all(noH): 2823   0      0.00    70.26   11.36    None  None   None       |
|    Sol.    : 438    0      0.00    70.26   31.78    None  None   None       |
|    Mac.    : 2385   0      0.00    69.23   7.61     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.026: 1491   |   5:    35.128 -  42.153:  117        |
|      1:     7.026 -  14.051:  665   |   6:    42.153 -  49.179:   76        |
|      2:    14.051 -  21.077:  201   |   7:    49.179 -  56.205:   19        |
|      3:    21.077 -  28.102:  122   |   8:    56.205 -  63.230:   11        |
|      4:    28.102 -  35.128:  117   |   9:    63.230 -  70.256:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1656 r_free = 0.2121             target_work(ml) = 5.467         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1656 r_free = 0.2120             target_work(ml) = 5.466         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1656   r_free= 0.2120   ksol= 0.35   Bsol= 41.63   scale= 1.038   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.60,5.19,4.94,0.00,0.00,0.00); trace/3= 4.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.466321                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1646   r_free= 0.2105   ksol= 0.33   Bsol= 41.63   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.35,3.23,4.13,0.00,0.00,0.00); trace/3= 3.57                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.464774                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.711899              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.599  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.246465              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.697  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1646      final r-factor (work) = 0.1342          |
| start r-factor (free) = 0.2105      final r-factor (free) = 0.1777          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7780 = 1.71 * 0.50 * 5.5106 + 1.00 * 0.0613                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6521 = 1.71 * 0.50 * 5.3731 + 1.00 * 0.0530                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1342      final r-factor (work) = 0.1277          |
| start r-factor (free) = 0.1777      final r-factor (free) = 0.1730          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.7080 = 1.25 * 1.00 * 5.3731 + 1.00 * 0.0106                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.5761 = 1.25 * 1.00 * 5.2647 + 1.00 * 0.0138                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.866)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.70   12.30    None  None   None       |
|    all(noH): 2823   0      0.00    80.70   12.30    None  None   None       |
|    Sol.    : 438    0      0.87    79.81   36.31    None  None   None       |
|    Mac.    : 2385   0      0.00    80.70   7.89     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 -   8.070: 1644   |   5:    40.351 -  48.422:   85        |
|      1:     8.070 -  16.141:  574   |   6:    48.422 -  56.492:   82        |
|      2:    16.141 -  24.211:  173   |   7:    56.492 -  64.562:   32        |
|      3:    24.211 -  32.281:   99   |   8:    64.562 -  72.632:   17        |
|      4:    32.281 -  40.351:  109   |   9:    72.632 -  80.703:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1277 r_free = 0.1730             target_work(ml) = 5.249         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1277 r_free = 0.1729             target_work(ml) = 5.249         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1277   r_free= 0.1729   ksol= 0.33   Bsol= 41.63   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.35,3.23,4.13,0.00,0.00,0.00); trace/3= 3.57                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.248875                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1279   r_free= 0.1726   ksol= 0.33   Bsol= 47.54   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.05,2.84,3.91,0.00,0.00,0.00); trace/3= 3.27                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.248863                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.207880              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 116.994  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.203450              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.454  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1279      final r-factor (work) = 0.1165          |
| start r-factor (free) = 0.1726      final r-factor (free) = 0.1632          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8655 = 2.21 * 0.50 * 5.2652 + 1.00 * 0.0530                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8109 = 2.21 * 0.50 * 5.2081 + 1.00 * 0.0615                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1165      final r-factor (work) = 0.1165          |
| start r-factor (free) = 0.1632      final r-factor (free) = 0.1598          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0734 = 0.20 * 1.00 * 5.2081 + 1.00 * 0.0138                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0648 = 0.20 * 1.00 * 5.1832 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.866)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.56   11.72    None  None   None       |
|    all(noH): 2823   0      0.00    80.56   11.72    None  None   None       |
|    Sol.    : 438    0      1.57    74.97   33.81    None  None   None       |
|    Mac.    : 2385   0      0.00    80.56   7.67     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 -   8.056: 1689   |   5:    40.279 -  48.335:   90        |
|      1:     8.056 -  16.112:  574   |   6:    48.335 -  56.391:   57        |
|      2:    16.112 -  24.167:  143   |   7:    56.391 -  64.446:   26        |
|      3:    24.167 -  32.223:  130   |   8:    64.446 -  72.502:    7        |
|      4:    32.223 -  40.279:   99   |   9:    72.502 -  80.558:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1165 r_free = 0.1598             target_work(ml) = 5.171         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1165 r_free = 0.1597             target_work(ml) = 5.170         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1165   r_free= 0.1597   ksol= 0.33   Bsol= 47.54   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.05,2.84,3.91,0.00,0.00,0.00); trace/3= 3.27                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.170043                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1165   r_free= 0.1596   ksol= 0.33   Bsol= 47.54   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.92,2.70,3.84,0.00,0.00,0.00); trace/3= 3.15                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.170046                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.476464              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 145.391  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.365501              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 155.406  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1165      final r-factor (work) = 0.1165          |
| start r-factor (free) = 0.1596      final r-factor (free) = 0.1592          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8875 = 1.48 * 0.50 * 5.1827 + 1.00 * 0.0615                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8706 = 1.48 * 0.50 * 5.1704 + 1.00 * 0.0536                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1165      final r-factor (work) = 0.1157          |
| start r-factor (free) = 0.1592      final r-factor (free) = 0.1592          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9001 = 0.37 * 1.00 * 5.1704 + 1.00 * 0.0103                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8997 = 0.37 * 1.00 * 5.1674 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.866)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.94   11.70    None  None   None       |
|    all(noH): 2823   0      0.00    80.94   11.70    None  None   None       |
|    Sol.    : 438    0      1.69    74.84   33.85    None  None   None       |
|    Mac.    : 2385   0      0.00    80.94   7.63     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 -   8.094: 1689   |   5:    40.469 -  48.562:   91        |
|      1:     8.094 -  16.188:  572   |   6:    48.562 -  56.656:   57        |
|      2:    16.188 -  24.281:  146   |   7:    56.656 -  64.750:   25        |
|      3:    24.281 -  32.375:  129   |   8:    64.750 -  72.843:    8        |
|      4:    32.375 -  40.469:  100   |   9:    72.843 -  80.937:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1157 r_free = 0.1592             target_work(ml) = 5.169         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1156 r_free = 0.1591             target_work(ml) = 5.168         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1156   r_free= 0.1591   ksol= 0.33   Bsol= 47.54   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.92,2.70,3.84,0.00,0.00,0.00); trace/3= 3.15                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.168464                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0824 -  4.7298 0.99   1390  155 0.1030 0.1277       5.404      5.5238|
|  2:  4.7298 -  3.7736 0.99   1332  147 0.0898 0.1152      5.4666      5.6415|
|  3:  3.7736 -  3.3023 0.99   1304  142 0.1092 0.1506      5.5004      5.8578|
|  4:  3.3023 -  3.0029 0.99   1303  153 0.1237 0.1605      5.4751       5.603|
|  5:  3.0029 -  2.7892 0.99   1294  142 0.1377 0.1838      5.3612      5.5938|
|  6:  2.7892 -  2.6256 0.99   1282  137 0.1231 0.1874      5.2221      5.4865|
|  7:  2.6256 -  2.4947 0.99   1290  140 0.1329 0.1567      5.2086      5.3491|
|  8:  2.4947 -  2.3866 0.98   1261  148 0.1207 0.1823      5.0895       5.395|
|  9:  2.3866 -  2.2950 0.98   1266  141 0.1212 0.1831      5.0703      5.2979|
| 10:  2.2950 -  2.2161 1.00   1279  139 0.1167 0.1721      4.9775      5.2598|
| 11:  2.2161 -  2.1470 0.97   1257  140 0.1184 0.1769      4.9724      5.2717|
| 12:  2.1470 -  2.0858 0.98   1250  139 0.1147 0.1750      4.8936      5.2082|
| 13:  2.0858 -  2.0310 0.99   1287  142 0.1182 0.1724      4.8124      5.0798|
| 14:  2.0310 -  1.9816 0.66    835   94 0.1068 0.1580      4.6767      4.8747|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0824 -  4.7298  1390   155  0.94   9.13   0.98     0.96       7211.92|
|  2:  4.7298 -  3.7736  1332   147  0.95   7.98   1.01     1.00       9149.47|
|  3:  3.7736 -  3.3023  1304   142  0.93  11.51   1.02     1.02      10769.73|
|  4:  3.3023 -  3.0029  1303   153  0.92  13.83   1.01     0.98      10625.20|
|  5:  3.0029 -  2.7892  1294   142  0.90  16.41   0.99     0.97       8786.31|
|  6:  2.7892 -  2.6256  1282   137  0.90  16.20   0.98     0.96       7276.35|
|  7:  2.6256 -  2.4947  1290   140  0.90  16.01   0.99     0.96       6497.05|
|  8:  2.4947 -  2.3866  1261   148  0.91  15.53   0.99     0.97       5431.12|
|  9:  2.3866 -  2.2950  1266   141  0.90  15.82   1.00     0.98       5334.25|
| 10:  2.2950 -  2.2161  1279   139  0.90  15.46   1.00     0.96       4401.20|
| 11:  2.2161 -  2.1470  1257   140  0.90  16.29   1.00     0.95       4447.12|
| 12:  2.1470 -  2.0858  1250   139  0.91  15.10   1.02     1.01       4020.91|
| 13:  2.0858 -  2.0310  1287   142  0.90  16.60   1.00     0.99       3468.44|
| 14:  2.0310 -  1.9816   835    94  0.92  14.43   0.98     0.95       2572.09|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2572.09 max =        10769.73 mean =      6559.14|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.25|
|phase err.(test): min =        0.00 max =           89.81 mean =        13.72|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1156   r_free= 0.1591   ksol= 0.33   Bsol= 50.71   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.25,-0.46,0.70,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.168480                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.08 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1156   r_free= 0.1591   ksol= 0.33   Bsol= 50.71   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.25,-0.46,0.70,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.168480                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0824 -  4.7298 0.99   1390  155 0.1030 0.1278      5.4041      5.5239|
|  2:  4.7298 -  3.7736 0.99   1332  147 0.0898 0.1152      5.4666      5.6415|
|  3:  3.7736 -  3.3023 0.99   1304  142 0.1092 0.1506      5.5004      5.8577|
|  4:  3.3023 -  3.0029 0.99   1303  153 0.1237 0.1605      5.4751       5.603|
|  5:  3.0029 -  2.7892 0.99   1294  142 0.1377 0.1838      5.3613      5.5939|
|  6:  2.7892 -  2.6256 0.99   1282  137 0.1231 0.1873      5.2221      5.4863|
|  7:  2.6256 -  2.4947 0.99   1290  140 0.1329 0.1567      5.2086      5.3491|
|  8:  2.4947 -  2.3866 0.98   1261  148 0.1207 0.1822      5.0895       5.395|
|  9:  2.3866 -  2.2950 0.98   1266  141 0.1212 0.1831      5.0703      5.2978|
| 10:  2.2950 -  2.2161 1.00   1279  139 0.1167 0.1720      4.9775      5.2599|
| 11:  2.2161 -  2.1470 0.97   1257  140 0.1184 0.1769      4.9724      5.2719|
| 12:  2.1470 -  2.0858 0.98   1250  139 0.1147 0.1750      4.8937      5.2083|
| 13:  2.0858 -  2.0310 0.99   1287  142 0.1182 0.1724      4.8125      5.0798|
| 14:  2.0310 -  1.9816 0.66    835   94 0.1069 0.1580      4.6766      4.8746|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0824 -  4.7298  1390   155  0.94   9.13   0.98     0.96       7213.40|
|  2:  4.7298 -  3.7736  1332   147  0.95   7.98   1.01     1.00       9149.76|
|  3:  3.7736 -  3.3023  1304   142  0.93  11.51   1.02     1.02      10768.25|
|  4:  3.3023 -  3.0029  1303   153  0.92  13.83   1.01     0.99      10625.22|
|  5:  3.0029 -  2.7892  1294   142  0.90  16.41   0.99     0.97       8785.27|
|  6:  2.7892 -  2.6256  1282   137  0.90  16.19   0.98     0.96       7276.22|
|  7:  2.6256 -  2.4947  1290   140  0.90  16.01   0.99     0.96       6496.13|
|  8:  2.4947 -  2.3866  1261   148  0.91  15.53   0.99     0.97       5430.81|
|  9:  2.3866 -  2.2950  1266   141  0.90  15.82   1.00     0.98       5333.69|
| 10:  2.2950 -  2.2161  1279   139  0.90  15.46   1.00     0.97       4401.91|
| 11:  2.2161 -  2.1470  1257   140  0.90  16.29   1.00     0.95       4448.07|
| 12:  2.1470 -  2.0858  1250   139  0.91  15.10   1.02     1.01       4022.22|
| 13:  2.0858 -  2.0310  1287   142  0.90  16.60   1.01     0.99       3468.70|
| 14:  2.0310 -  1.9816   835    94  0.92  14.43   0.98     0.95       2571.65|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2571.65 max =        10768.25 mean =      6559.17|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.25|
|phase err.(test): min =        0.00 max =           89.81 mean =        13.72|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.866)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.18    84.11   14.87    None  None   None       |
|    all(noH): 2823   0      3.18    84.11   14.87    None  None   None       |
|    Sol.    : 438    0      4.87    78.01   37.03    None  None   None       |
|    Mac.    : 2385   0      3.18    84.11   10.80    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.176 -  11.269: 1689   |   5:    43.644 -  51.738:   91        |
|      1:    11.269 -  19.363:  572   |   6:    51.738 -  59.832:   57        |
|      2:    19.363 -  27.457:  146   |   7:    59.832 -  67.925:   25        |
|      3:    27.457 -  35.550:  129   |   8:    67.925 -  76.019:    8        |
|      4:    35.550 -  43.644:  100   |   9:    76.019 -  84.113:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 306         
Filter by distance & map next to the model:
   mapped sites are within: 0.376 - 3.920
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 301 from: 306
   mapped sites are within: 0.724 - 3.920

peak=   11.145 closest distance to " CB  VAL A 230 " =    1.485
peak=    8.131 closest distance to " CG2 VAL A 296 " =    1.198
peak=    7.282 closest distance to " CG  ARG A 138 " =    1.144
peak=    6.229 closest distance to " CD2 LEU A   5 " =    1.263
peak=    6.061 closest distance to " CG  LEU A   5 " =    1.292
peak=    5.877 closest distance to " NH2 ARG A  56 " =    2.170
peak=    5.756 closest distance to " NH1 ARG A 138 " =    0.979
peak=    5.716 closest distance to " CG  PRO A  54 " =    1.370
peak=    5.670 closest distance to " CD1AILE A 234 " =    1.069
peak=    5.530 closest distance to " NE2 GLN A  11 " =    1.147
peak=    5.283 closest distance to " O   HOH Z 232 " =    2.325
peak=    5.256 closest distance to " CB  GLN A 223 " =    1.400
peak=    5.162 closest distance to " O   HOH Z 144 " =    1.954
peak=    5.087 closest distance to " CG  LEU A 228 " =    1.188
peak=    5.074 closest distance to " CB  PRO A  54 " =    1.051
peak=    5.014 closest distance to " CB  GLN A 183 " =    1.189
peak=    4.925 closest distance to " CG  PRO A 198 " =    1.239
peak=    4.901 closest distance to " O   HOH Z 126 " =    1.976
peak=    4.823 closest distance to " CD2 LEU A 228 " =    1.194
peak=    4.753 closest distance to " CG  PRO A 213 " =    1.255
peak=    4.708 closest distance to " CB  ASN A 148 " =    1.364
peak=    4.667 closest distance to " CD  ARG A 138 " =    1.086
peak=    4.633 closest distance to " O   HOH Z 427 " =    2.781
peak=    4.626 closest distance to " CB  ARG A 275 " =    0.887
peak=    4.614 closest distance to " CG  PRO A 243 " =    1.151
peak=    4.611 closest distance to " O   HOH Z 425 " =    1.491
peak=    4.573 closest distance to " C   PRO A 198 " =    1.567
peak=    4.573 closest distance to " O   HOH Z 272 " =    1.861
peak=    4.506 closest distance to " O   HOH Z 369 " =    2.030
peak=    4.489 closest distance to " CB  VAL A 296 " =    1.137
peak=    4.469 closest distance to " CB  VAL A 230 " =    1.180
peak=    4.464 closest distance to " O   HOH Z 316 " =    2.979
peak=    4.419 closest distance to " CB  SER A  63 " =    1.281
peak=    4.364 closest distance to " CB  SER A   3 " =    1.380
peak=    4.363 closest distance to " O   HOH Z 298 " =    1.826
peak=    4.328 closest distance to " CB  TRP A 266 " =    0.987
peak=    4.318 closest distance to " CB  GLU A 152 " =    1.289
peak=    4.299 closest distance to " CB  SER A 216 " =    0.842
peak=    4.251 closest distance to " CB  VAL A 265 " =    1.291
peak=    4.240 closest distance to " O   HOH Z 236 " =    2.006
peak=    4.155 closest distance to " CG  LEU A 167 " =    1.187
peak=    4.139 closest distance to " O   HOH Z 368 " =    2.021
peak=    4.135 closest distance to " CB  ASN A  39 " =    0.919
peak=    4.126 closest distance to " ND2 ASN A 187 " =    1.541
peak=    4.112 closest distance to " CG2 VAL A 257 " =    0.916
peak=    4.106 closest distance to " CB  GLU A 128 " =    1.022
peak=    4.085 closest distance to " O   HOH Z  78 " =    1.744
peak=    4.083 closest distance to " O   HOH Z 193 " =    1.845
peak=    4.023 closest distance to " O   HOH Z 263 " =    1.584
peak=    4.014 closest distance to " O   HOH Z 209 " =    2.335
peak=    3.987 closest distance to " O   HOH Z  55 " =    2.328
peak=    3.987 closest distance to " OD2 ASP A 286 " =    2.788
peak=    3.981 closest distance to " O   HOH Z 303 " =    2.158
peak=    3.976 closest distance to " N   PHE A 130 " =    1.247
peak=    3.960 closest distance to " O   HOH Z   7 " =    1.169
peak=    3.951 closest distance to " O   HOH Z 234 " =    3.602
peak=    3.950 closest distance to " O   HOH Z   2 " =    1.698
peak=    3.947 closest distance to " O   HOH Z  78 " =    2.315
peak=    3.946 closest distance to " O   HOH Z 346 " =    1.584
peak=    3.942 closest distance to " CA  ASN A 215 " =    1.146
peak=    3.938 closest distance to " OD1 ASN A  69 " =    2.624
peak=    3.920 closest distance to " CD  ARG A  66 " =    2.557
peak=    3.909 closest distance to " O   HOH Z 193 " =    1.704
peak=    3.906 closest distance to " O   SER A  87 " =    2.355
peak=    3.893 closest distance to " CA  THR A 264 " =    0.767
peak=    3.883 closest distance to " O   HOH Z 411 " =    3.676
peak=    3.878 closest distance to " CB  LEU A 143 " =    1.143
peak=    3.856 closest distance to " O   HOH Z 344 " =    2.866
peak=    3.854 closest distance to " CB  ASN A 187 " =    1.135
peak=    3.853 closest distance to " CA  ALA A  21 " =    1.142
peak=    3.850 closest distance to " O   HOH Z 189 " =    2.862
peak=    3.850 closest distance to " O   HOH Z 273 " =    2.694
peak=    3.844 closest distance to " CA  TYR A  30 " =    0.944
peak=    3.837 closest distance to " CD  ARG A 159 " =    0.747
peak=    3.832 closest distance to " CA  ALA A  51 " =    1.015
peak=    3.828 closest distance to " O   HOH Z   9 " =    1.987
peak=    3.814 closest distance to " O   HOH Z  61 " =    1.621
peak=    3.807 closest distance to " O   HOH Z  88 " =    3.193
peak=    3.776 closest distance to " NH1AARG A 145 " =    1.109
peak=    3.776 closest distance to " O   HOH Z  30 " =    1.493
peak=    3.766 closest distance to " O   HOH Z 389 " =    1.973
peak=    3.743 closest distance to " O   HOH Z 352 " =    1.809
peak=    3.734 closest distance to " O   HOH Z 437 " =    2.053
peak=    3.728 closest distance to " C   ALA A 299 " =    0.984
peak=    3.722 closest distance to " CB  MET A  40 " =    0.824
peak=    3.720 closest distance to " O   HOH Z 158 " =    3.028
peak=    3.720 closest distance to " CZ  PHE A 218 " =    1.088
peak=    3.718 closest distance to " CA  SER A  87 " =    0.953
peak=    3.702 closest distance to " O   HOH Z 222 " =    2.378
peak=    3.699 closest distance to " NH2AARG A 190 " =    1.831
peak=    3.698 closest distance to " O   HOH Z  68 " =    2.093
peak=    3.698 closest distance to " NZ  LYS A 117 " =    3.162
peak=    3.696 closest distance to " CG1BVAL A  72 " =    1.604
peak=    3.694 closest distance to " CB  TRP A 179 " =    1.397
peak=    3.689 closest distance to " CA  ILE A 234 " =    0.932
peak=    3.689 closest distance to " CD BLYS A 290 " =    1.100
peak=    3.686 closest distance to " O   HOH Z 435 " =    2.121
peak=    3.684 closest distance to " O   HOH Z 128 " =    2.037
peak=    3.681 closest distance to " O   HOH Z 403 " =    1.703
peak=    3.678 closest distance to " CD1 LEU A 300 " =    1.155
peak=    3.676 closest distance to " CB  LEU A 228 " =    1.230
peak=    3.666 closest distance to " CB  ARG A  79 " =    1.438
peak=    3.665 closest distance to " CG BARG A 102 " =    1.842
peak=    3.657 closest distance to " CB  VAL A 202 " =    1.604
peak=    3.656 closest distance to " CG1 ILE A  33 " =    1.361
peak=    3.644 closest distance to " CB  SER A 212 " =    1.176
peak=    3.638 closest distance to " O   HOH Z 130 " =    2.171
peak=    3.634 closest distance to " CG  GLN A  88 " =    1.102
peak=    3.605 closest distance to " O   HOH Z 214 " =    2.022
peak=    3.601 closest distance to " CB  ASN A 142 " =    0.967
peak=    3.582 closest distance to " CB  ALA A 291 " =    1.354
peak=    3.575 closest distance to " CB  ARG A 139 " =    0.960
peak=    3.575 closest distance to " CB BVAL A  41 " =    1.275
peak=    3.571 closest distance to " O   HOH Z 280 " =    2.951
peak=    3.570 closest distance to " CZ  PHE A 192 " =    0.946
peak=    3.570 closest distance to " CB  THR A 157 " =    1.124
peak=    3.570 closest distance to " O   HOH Z   1 " =    1.846
peak=    3.569 closest distance to " CB  GLN A  88 " =    1.260
peak=    3.562 closest distance to " CE  LYS A  76 " =    0.918
peak=    3.558 closest distance to " O   HOH Z 368 " =    3.596
peak=    3.557 closest distance to " CB  HIS A 108 " =    0.839
peak=    3.553 closest distance to " O   HOH Z  97 " =    1.996
peak=    3.552 closest distance to " CB  GLU A 277 " =    3.562
peak=    3.544 closest distance to " O   HOH Z   3 " =    1.918
peak=    3.536 closest distance to " CD1 ILE A  33 " =    1.675
peak=    3.525 closest distance to " O   HOH Z 261 " =    2.173
peak=    3.525 closest distance to " CD  ARG A 269 " =    1.037
peak=    3.522 closest distance to " CG1 ILE A 151 " =    1.140
peak=    3.511 closest distance to " O   HOH Z 419 " =    1.897
peak=    3.506 closest distance to " CB  VAL A 250 " =    1.097
peak=    3.506 closest distance to " CG2 THR A 221 " =    1.062
peak=    3.504 closest distance to " CG1 VAL A 153 " =    0.926
peak=    3.501 closest distance to " O   HOH Z 132 " =    2.525
peak=    3.501 closest distance to " CB  LYS A 117 " =    1.220
peak=    3.501 closest distance to " CA  LYS A 117 " =    1.216
peak=    3.496 closest distance to " O   HOH Z 197 " =    3.333
peak=    3.492 closest distance to " O   HOH Z 133 " =    1.705
peak=    3.476 closest distance to " O   GLN A 278 " =    1.339
peak=    3.473 closest distance to " CB  ASP A 140 " =    0.850
peak=    3.466 closest distance to " O   HOH Z 227 " =    1.690
peak=    3.466 closest distance to " O   HOH Z  43 " =    1.918
peak=    3.465 closest distance to " CA  LEU A 282 " =    1.118
peak=    3.464 closest distance to " O   HOH Z 135 " =    1.969
peak=    3.462 closest distance to " CD2 LEU A 255 " =    1.612
peak=    3.461 closest distance to " O   HOH Z   9 " =    1.168
peak=    3.458 closest distance to " OG BSER A 164 " =    2.277
peak=    3.457 closest distance to " O   HOH Z 371 " =    1.703
peak=    3.448 closest distance to " O   HOH Z  58 " =    1.640
peak=    3.442 closest distance to " CB  THR A  82 " =    1.323
peak=    3.441 closest distance to " NH2BARG A 145 " =    1.976
peak=    3.440 closest distance to " O   HOH Z 371 " =    2.818
peak=    3.439 closest distance to " ND1 HIS A  86 " =    1.697
peak=    3.437 closest distance to " CB  SER A 210 " =    0.741
peak=    3.436 closest distance to " O   HOH Z 250 " =    1.352
peak=    3.431 closest distance to " OG  SER A 206 " =    1.155
peak=    3.430 closest distance to " CA  ALA A 154 " =    1.043
peak=    3.429 closest distance to " NH1 ARG A  14 " =    0.893
peak=    3.423 closest distance to " N   VAL A 126 " =    1.291
peak=    3.422 closest distance to " O   HOH Z 180 " =    2.118
peak=    3.419 closest distance to " CA  LYS A 290 " =    1.279
peak=    3.418 closest distance to " O   HOH Z  40 " =    2.034
peak=    3.412 closest distance to " O   HOH Z 193 " =    1.866
peak=    3.412 closest distance to " O   HOH Z  10 " =    1.767
peak=    3.410 closest distance to " O   TRP A 274 " =    1.825
peak=    3.409 closest distance to " O   HOH Z  59 " =    1.819
peak=    3.408 closest distance to " CB  ARG A 190 " =    1.684
peak=    3.405 closest distance to " CD  LYS A 166 " =    1.336
peak=    3.403 closest distance to " CB  ILE A 234 " =    0.966
peak=    3.398 closest distance to " O   HOH Z 175 " =    2.149
peak=    3.393 closest distance to " O   HOH Z 124 " =    1.296
peak=    3.385 closest distance to " CB  GLU A 236 " =    1.158
peak=    3.378 closest distance to " O   HOH Z 145 " =    1.749
peak=    3.376 closest distance to " CA  ALA A 158 " =    1.168
peak=    3.367 closest distance to " O   HOH Z 184 " =    1.385
peak=    3.362 closest distance to " N   ASN A  39 " =    1.077
peak=    3.358 closest distance to " CG  MET A 185 " =    1.106
peak=    3.353 closest distance to " N   ARG A 156 " =    1.303
peak=    3.352 closest distance to " O   HOH Z 147 " =    1.681
peak=    3.351 closest distance to " O   HOH Z 423 " =    1.524
peak=    3.351 closest distance to " CD1 LEU A  96 " =    0.781
peak=    3.350 closest distance to " O   HOH Z 313 " =    1.697
peak=    3.349 closest distance to " CE1 TYR A 186 " =    1.366
peak=    3.348 closest distance to " ND2 ASN A 110 " =    1.788
peak=    3.346 closest distance to " CZ3 TRP A 123 " =    1.376
peak=    3.342 closest distance to " CB  ILE A 120 " =    1.321
peak=    3.342 closest distance to " O   HOH Z 303 " =    1.809
peak=    3.342 closest distance to " CA  VAL A  41 " =    0.870
peak=    3.342 closest distance to " O   MET A 105 " =    1.760
peak=    3.338 closest distance to " O   HOH Z 282 " =    1.931
peak=    3.338 closest distance to " O   HOH Z 108 " =    2.419
peak=    3.335 closest distance to " O  BHOH Z 338 " =    2.489
peak=    3.334 closest distance to " O   HOH Z 290 " =    1.137
peak=    3.332 closest distance to " O   HOH Z 271 " =    2.033
peak=    3.329 closest distance to " O   HOH Z 248 " =    1.684
peak=    3.328 closest distance to " O   HOH Z 353 " =    2.640
peak=    3.326 closest distance to " O   HOH Z 422 " =    2.643
peak=    3.323 closest distance to " CA  GLY A 267 " =    0.987
peak=    3.321 closest distance to " CA  ARG A  36 " =    1.089
peak=    3.320 closest distance to " O   HOH Z 227 " =    2.004
peak=    3.313 closest distance to " CA  ASP A 162 " =    1.048
peak=    3.311 closest distance to " O   HOH Z 112 " =    1.608
peak=    3.308 closest distance to " CA  THR A 221 " =    0.889
peak=    3.307 closest distance to " CB  SER A  62 " =    1.144
peak=    3.306 closest distance to " CA  ARG A 195 " =    1.214
peak=    3.306 closest distance to " CG1 VAL A 174 " =    1.073
peak=    3.305 closest distance to " CA  VAL A 126 " =    1.007
peak=    3.303 closest distance to " NE AARG A 275 " =    1.303
peak=    3.302 closest distance to " N   SER A 271 " =    0.989
peak=    3.298 closest distance to " O   HOH Z   1 " =    1.817
peak=    3.297 closest distance to " CB  PRO A 198 " =    0.961
peak=    3.296 closest distance to " CB  ALA A 104 " =    0.727
peak=    3.296 closest distance to " CB  ASN A 110 " =    1.169
peak=    3.290 closest distance to " NZ BLYS A 290 " =    1.076
peak=    3.289 closest distance to " CB  SER A  26 " =    1.640
peak=    3.284 closest distance to " O   HOH Z 366 " =    2.819
peak=    3.280 closest distance to " CG2 ILE A 106 " =    0.980
peak=    3.277 closest distance to " CB  LEU A 255 " =    0.827
peak=    3.276 closest distance to " O   HOH Z 407 " =    2.227
peak=    3.276 closest distance to " CB  TYR A  30 " =    1.552
peak=    3.276 closest distance to " O   HOH Z  63 " =    1.284
peak=    3.274 closest distance to " O   HOH Z 409 " =    2.971
peak=    3.273 closest distance to " O   HOH Z 145 " =    3.514
peak=    3.272 closest distance to " O   HOH Z 392 " =    1.256
peak=    3.263 closest distance to " CG  MET A 185 " =    1.013
peak=    3.261 closest distance to " O   HOH Z 305 " =    3.467
peak=    3.259 closest distance to " CB  LEU A 237 " =    0.868
peak=    3.259 closest distance to " N   SER A  12 " =    1.640
peak=    3.256 closest distance to " O   HOH Z 213 " =    2.449
peak=    3.255 closest distance to " NH1 ARG A  56 " =    0.884
peak=    3.253 closest distance to " NH2BARG A 190 " =    1.591
peak=    3.250 closest distance to " OG  SER A  62 " =    2.861
peak=    3.250 closest distance to " O   HOH Z 402 " =    1.414
peak=    3.243 closest distance to " O   HOH Z  61 " =    1.587
peak=    3.239 closest distance to " N   ALA A 256 " =    1.096
peak=    3.239 closest distance to " CD1 ILE A 106 " =    0.877
peak=    3.237 closest distance to " O   HOH Z 329 " =    3.787
peak=    3.230 closest distance to " CB  ALA A 248 " =    1.421
peak=    3.229 closest distance to " O   ALA A 158 " =    1.391
peak=    3.226 closest distance to " CB  VAL A 268 " =    0.852
peak=    3.224 closest distance to " O   PRO A  90 " =    1.467
peak=    3.223 closest distance to " O   HOH Z 172 " =    3.322
peak=    3.221 closest distance to " CB  SER A 273 " =    0.878
peak=    3.218 closest distance to " OG  SER A  62 " =    3.025
peak=    3.215 closest distance to " N   SER A 135 " =    1.253
peak=    3.208 closest distance to " CD2 TRP A 179 " =    1.344
peak=    3.204 closest distance to " N   GLN A 278 " =    1.053
peak=    3.204 closest distance to " CG  ARG A 159 " =    0.978
peak=    3.203 closest distance to " CD2 TYR A 186 " =    1.058
peak=    3.202 closest distance to " OG BSER A 134 " =    3.080
peak=    3.201 closest distance to " O   HOH Z 128 " =    1.958
peak=    3.201 closest distance to " O   HOH Z 285 " =    2.147
peak=    3.196 closest distance to " O   HOH Z 359 " =    3.920
peak=    3.194 closest distance to " N   ASN A 127 " =    1.277
peak=    3.193 closest distance to " O  BHOH Z  74 " =    1.307
peak=    3.191 closest distance to " CB  GLU A  46 " =    1.048
peak=    3.187 closest distance to " CA  ASN A 127 " =    1.096
peak=    3.181 closest distance to " CB  GLN A 103 " =    1.023
peak=    3.179 closest distance to " CA  ILE A 106 " =    0.769
peak=    3.178 closest distance to " O   HOH Z 285 " =    2.946
peak=    3.171 closest distance to " ND2 ASN A 249 " =    0.873
peak=    3.169 closest distance to " O   HOH Z 216 " =    2.722
peak=    3.168 closest distance to " O   HOH Z  21 " =    1.743
peak=    3.167 closest distance to " O   HOH Z 424 " =    2.635
peak=    3.165 closest distance to " O   HOH Z 334 " =    1.563
peak=    3.164 closest distance to " CB  ALA A   9 " =    1.581
peak=    3.159 closest distance to " O   HOH Z 423 " =    2.712
peak=    3.159 closest distance to " CD1 LEU A 101 " =    1.201
peak=    3.156 closest distance to " OG BSER A 212 " =    2.780
peak=    3.156 closest distance to " O   HOH Z 345 " =    3.548
peak=    3.155 closest distance to " OD1BASN A 224 " =    2.363
peak=    3.146 closest distance to " O   HOH Z 148 " =    3.404
peak=    3.144 closest distance to " NZ  LYS A  48 " =    2.178
peak=    3.141 closest distance to " O   HOH Z 425 " =    2.018
peak=    3.140 closest distance to " O   HOH Z 302 " =    1.821
peak=    3.136 closest distance to " O   GLY A 203 " =    1.517
peak=    3.135 closest distance to " O   HOH Z 426 " =    1.716
peak=    3.131 closest distance to " O   HOH Z 126 " =    1.562
peak=    3.130 closest distance to " CG1 ILE A  49 " =    1.439
peak=    3.129 closest distance to " OE2 GLU A  53 " =    2.049
peak=    3.128 closest distance to " NE2 HIS A 207 " =    1.354
peak=    3.128 closest distance to " OG  SER A  22 " =    2.853
peak=    3.123 closest distance to " CE  MET A  93 " =    1.503
peak=    3.123 closest distance to " O   HOH Z 109 " =    2.512
peak=    3.122 closest distance to " O   HOH Z 380 " =    1.662
peak=    3.118 closest distance to " O   HOH Z 148 " =    2.254
peak=    3.118 closest distance to " CB  TRP A 150 " =    1.488
peak=    3.117 closest distance to " CA  ARG A 102 " =    1.172
peak=    3.115 closest distance to " ND1 HIS A  81 " =    1.680
peak=    3.109 closest distance to " O   HOH Z 238 " =    3.669
peak=    3.103 closest distance to " O   HOH Z 339 " =    2.161
peak=    3.100 closest distance to " O   HOH Z 105 " =    1.527
peak=    3.092 closest distance to " CG2 ILE A  20 " =    1.571
peak=    3.088 closest distance to " N   TYR A  15 " =    0.810
peak=    3.088 closest distance to " O   HOH Z  49 " =    2.328
peak=    3.087 closest distance to " CB  PRO A 243 " =    1.373
peak=    3.086 closest distance to " CB  GLN A 278 " =    0.858
peak=    3.084 closest distance to " O   TYR A 116 " =    1.247
peak=    3.084 closest distance to " CB  ALA A 114 " =    1.210
peak=    3.051 closest distance to " CB  ALA A  34 " =    0.724
peak=    3.050 closest distance to " O   HOH Z 116 " =    1.689
peak=    3.006 closest distance to " O   HOH Z 213 " =    1.978

                           ----------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: 0.754 - 5.459
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 201 from: 202
   mapped sites are within: 0.754 - 5.459

peak=   -5.339 closest distance to " CG2 VAL A 230 " =    0.754
peak=   -4.657 closest distance to " CD  ARG A 138 " =    1.145
peak=   -4.603 closest distance to " CG  ARG A 138 " =    0.909
peak=   -4.483 closest distance to " CD  ARG A 156 " =    2.015
peak=   -4.228 closest distance to " O   HOH Z 290 " =    1.109
peak=   -4.119 closest distance to " CD  ARG A  14 " =    3.173
peak=   -4.107 closest distance to " O   HOH Z 231 " =    1.651
peak=   -4.071 closest distance to " O   HOH Z 435 " =    2.840
peak=   -4.067 closest distance to " CB  PRO A 243 " =    2.631
peak=   -4.065 closest distance to " O   HOH Z 266 " =    4.991
peak=   -4.034 closest distance to " O   HOH Z  52 " =    1.414
peak=   -3.993 closest distance to " CG  GLN A 223 " =    2.009
peak=   -3.970 closest distance to " OG BSER A 134 " =    1.192
peak=   -3.943 closest distance to " CB  PRO A 163 " =    2.565
peak=   -3.926 closest distance to " CG  ASP A 231 " =    0.754
peak=   -3.915 closest distance to " O   PRO A 198 " =    1.182
peak=   -3.888 closest distance to " CG1 VAL A 296 " =    1.281
peak=   -3.871 closest distance to " CZ3 TRP A 179 " =    1.185
peak=   -3.864 closest distance to " O   HOH Z 351 " =    1.387
peak=   -3.842 closest distance to " CG2 VAL A 296 " =    1.117
peak=   -3.766 closest distance to " N   ALA A  43 " =    2.372
peak=   -3.760 closest distance to " CB  PHE A 192 " =    1.816
peak=   -3.752 closest distance to " CE2 TYR A  30 " =    2.814
peak=   -3.747 closest distance to " C   ALA A 158 " =    1.381
peak=   -3.747 closest distance to " N   THR A 157 " =    1.442
peak=   -3.744 closest distance to " O   HOH Z 389 " =    1.948
peak=   -3.719 closest distance to " O   ARG A 145 " =    1.582
peak=   -3.719 closest distance to " NH2 ARG A  79 " =    1.948
peak=   -3.713 closest distance to " CB  ALA A 248 " =    2.042
peak=   -3.700 closest distance to " CG  PHE A 283 " =    2.654
peak=   -3.690 closest distance to " C   ASP A 231 " =    2.418
peak=   -3.676 closest distance to " CA  GLY A 241 " =    2.259
peak=   -3.675 closest distance to " O   HOH Z 185 " =    2.195
peak=   -3.673 closest distance to " O   ILE A 109 " =    2.639
peak=   -3.669 closest distance to " CE2 PHE A 218 " =    2.566
peak=   -3.669 closest distance to " CB  ALA A  43 " =    2.472
peak=   -3.667 closest distance to " C   HIS A 108 " =    1.129
peak=   -3.651 closest distance to " ND2 ASN A  45 " =    1.100
peak=   -3.647 closest distance to " CG2 THR A   4 " =    1.919
peak=   -3.633 closest distance to " CG2 THR A 178 " =    2.221
peak=   -3.623 closest distance to " O   HOH Z 377 " =    1.985
peak=   -3.617 closest distance to " O   HOH Z  43 " =    1.782
peak=   -3.613 closest distance to " O   PRO A 163 " =    1.862
peak=   -3.609 closest distance to " OG  SER A  87 " =    1.417
peak=   -3.608 closest distance to " CD1 LEU A 228 " =    2.301
peak=   -3.607 closest distance to " CG1 VAL A 112 " =    3.049
peak=   -3.603 closest distance to " C   LEU A 222 " =    0.826
peak=   -3.599 closest distance to " N   GLN A  58 " =    1.901
peak=   -3.597 closest distance to " CA  ASP A  27 " =    2.398
peak=   -3.586 closest distance to " CD1 LEU A 101 " =    2.342
peak=   -3.585 closest distance to " O   HOH Z 211 " =    1.529
peak=   -3.579 closest distance to " O   TYR A 247 " =    2.853
peak=   -3.570 closest distance to " O   HOH Z 295 " =    1.539
peak=   -3.559 closest distance to " CG  TRP A 266 " =    1.867
peak=   -3.551 closest distance to " O   HOH Z 166 " =    2.079
peak=   -3.551 closest distance to " O   HOH Z 437 " =    1.828
peak=   -3.544 closest distance to " C   MET A 188 " =    1.560
peak=   -3.528 closest distance to " CG1 VAL A 197 " =    2.354
peak=   -3.527 closest distance to " NH2AARG A 275 " =    5.262
peak=   -3.527 closest distance to " O   HOH Z 241 " =    1.293
peak=   -3.522 closest distance to " OD1 ASN A 187 " =    1.532
peak=   -3.520 closest distance to " ND2 ASN A  45 " =    1.447
peak=   -3.518 closest distance to " O   VAL A  67 " =    2.593
peak=   -3.506 closest distance to " O   SER A  22 " =    2.188
peak=   -3.506 closest distance to " O   HOH Z 309 " =    2.338
peak=   -3.505 closest distance to " O   HOH Z 231 " =    1.183
peak=   -3.502 closest distance to " CE  MET A 105 " =    2.349
peak=   -3.496 closest distance to " NZ  LYS A 119 " =    3.344
peak=   -3.495 closest distance to " O   HOH Z 359 " =    3.373
peak=   -3.481 closest distance to " O   HOH Z 359 " =    1.578
peak=   -3.468 closest distance to " O   HOH Z 394 " =    1.491
peak=   -3.466 closest distance to " CA  SER A 271 " =    2.285
peak=   -3.462 closest distance to " CG  MET A 105 " =    0.937
peak=   -3.459 closest distance to " O   VAL A  67 " =    2.642
peak=   -3.457 closest distance to " O   HOH Z 140 " =    1.442
peak=   -3.453 closest distance to " O   HOH Z 417 " =    2.812
peak=   -3.452 closest distance to " OG  SER A 206 " =    1.689
peak=   -3.448 closest distance to " CD  GLN A  58 " =    1.014
peak=   -3.448 closest distance to " O   HOH Z  38 " =    1.822
peak=   -3.446 closest distance to " O   HOH Z 423 " =    2.148
peak=   -3.446 closest distance to " O   HOH Z 102 " =    1.615
peak=   -3.444 closest distance to " OG  SER A  97 " =    2.197
peak=   -3.444 closest distance to " O   HOH Z 114 " =    3.055
peak=   -3.427 closest distance to " CB  ALA A 248 " =    2.470
peak=   -3.423 closest distance to " CE BMET A  47 " =    1.623
peak=   -3.422 closest distance to " O   HOH Z 407 " =    3.107
peak=   -3.412 closest distance to " O   HOH Z 166 " =    1.470
peak=   -3.411 closest distance to " O   HOH Z 134 " =    2.743
peak=   -3.409 closest distance to " O   HOH Z 377 " =    0.866
peak=   -3.409 closest distance to " O   HOH Z 350 " =    1.833
peak=   -3.408 closest distance to " CE3 TRP A 150 " =    2.141
peak=   -3.408 closest distance to " C   ASN A 285 " =    2.439
peak=   -3.403 closest distance to " O   GLY A  17 " =    1.340
peak=   -3.402 closest distance to " O   HOH Z  60 " =    2.211
peak=   -3.401 closest distance to " CD2 LEU A   5 " =    1.023
peak=   -3.398 closest distance to " CD1 ILE A 199 " =    2.571
peak=   -3.397 closest distance to " CG1 VAL A 112 " =    2.621
peak=   -3.397 closest distance to " O   SER A 135 " =    1.426
peak=   -3.381 closest distance to " CD  LYS A 289 " =    2.551
peak=   -3.379 closest distance to " O   HOH Z   9 " =    1.550
peak=   -3.378 closest distance to " CB  TYR A  15 " =    2.099
peak=   -3.377 closest distance to " O   GLY A 203 " =    2.400
peak=   -3.377 closest distance to " O   HOH Z 281 " =    2.762
peak=   -3.376 closest distance to " O   HOH Z 388 " =    2.210
peak=   -3.371 closest distance to " CZ  PHE A  59 " =    1.435
peak=   -3.367 closest distance to " OE1 GLN A  88 " =    1.146
peak=   -3.362 closest distance to " CA  GLY A  98 " =    1.945
peak=   -3.359 closest distance to " CB  ALA A 291 " =    2.234
peak=   -3.355 closest distance to " CD1 PHE A  59 " =    1.959
peak=   -3.354 closest distance to " N   ALA A 248 " =    1.586
peak=   -3.352 closest distance to " O   GLY A  80 " =    2.416
peak=   -3.349 closest distance to " O   HOH Z 275 " =    1.457
peak=   -3.345 closest distance to " O   HOH Z 166 " =    2.149
peak=   -3.343 closest distance to " O   HOH Z 345 " =    2.112
peak=   -3.340 closest distance to " O   GLY A 211 " =    1.285
peak=   -3.333 closest distance to " OG ASER A 134 " =    1.383
peak=   -3.332 closest distance to " CD  ARG A 139 " =    1.634
peak=   -3.322 closest distance to " CB  VAL A 296 " =    1.120
peak=   -3.319 closest distance to " OG BSER A 134 " =    1.714
peak=   -3.318 closest distance to " CD1 LEU A 101 " =    2.647
peak=   -3.312 closest distance to " CZ  TYR A 172 " =    1.777
peak=   -3.309 closest distance to " N   ALA A 226 " =    2.156
peak=   -3.307 closest distance to " N   SER A 212 " =    1.888
peak=   -3.305 closest distance to " N   PHE A  59 " =    2.213
peak=   -3.304 closest distance to " CD  PRO A 243 " =    2.118
peak=   -3.299 closest distance to " O   ALA A 161 " =    1.563
peak=   -3.298 closest distance to " O   VAL A 189 " =    2.591
peak=   -3.296 closest distance to " CG  PRO A 163 " =    2.535
peak=   -3.289 closest distance to " CG  LEU A 101 " =    2.539
peak=   -3.282 closest distance to " O   HOH Z 298 " =    1.213
peak=   -3.280 closest distance to " C   GLY A 229 " =    1.181
peak=   -3.277 closest distance to " O   HOH Z 111 " =    4.309
peak=   -3.276 closest distance to " O   HOH Z 256 " =    1.299
peak=   -3.270 closest distance to " OXT GLY A 302 " =    2.997
peak=   -3.266 closest distance to " CD2 LEU A 237 " =    2.660
peak=   -3.265 closest distance to " O   HOH Z  51 " =    1.082
peak=   -3.264 closest distance to " O   HOH Z 372 " =    2.437
peak=   -3.258 closest distance to " O   HOH Z 103 " =    1.775
peak=   -3.253 closest distance to " O   HOH Z  98 " =    2.171
peak=   -3.250 closest distance to " CA  ARG A 139 " =    1.011
peak=   -3.248 closest distance to " C   PHE A  59 " =    1.316
peak=   -3.242 closest distance to " ND2 ASN A  60 " =    1.831
peak=   -3.235 closest distance to " O   HOH Z 313 " =    1.568
peak=   -3.230 closest distance to " CE  LYS A 166 " =    1.228
peak=   -3.229 closest distance to " CG2AVAL A  72 " =    4.385
peak=   -3.226 closest distance to " O   HOH Z  13 " =    1.442
peak=   -3.214 closest distance to " CB  ASN A  39 " =    2.142
peak=   -3.213 closest distance to " O   HOH Z 423 " =    1.179
peak=   -3.210 closest distance to " N   ASP A 270 " =    1.470
peak=   -3.209 closest distance to " CB  ALA A 291 " =    2.162
peak=   -3.204 closest distance to " O   HOH Z 417 " =    2.716
peak=   -3.199 closest distance to " O   HOH Z 165 " =    2.045
peak=   -3.197 closest distance to " CG1 VAL A 265 " =    2.437
peak=   -3.197 closest distance to " CZ  PHE A  38 " =    2.642
peak=   -3.191 closest distance to " N   THR A 235 " =    1.212
peak=   -3.190 closest distance to " CA  SER A 135 " =    1.386
peak=   -3.190 closest distance to " CD2 TYR A 293 " =    2.004
peak=   -3.187 closest distance to " CD2 TYR A 247 " =    2.552
peak=   -3.186 closest distance to " OD2 ASP A 191 " =    1.382
peak=   -3.184 closest distance to " O   HOH Z   2 " =    1.796
peak=   -3.183 closest distance to " CB  TRP A  85 " =    2.463
peak=   -3.181 closest distance to " O   HOH Z 198 " =    1.530
peak=   -3.180 closest distance to " OXT GLY A 302 " =    3.507
peak=   -3.178 closest distance to " CA  GLY A 241 " =    3.034
peak=   -3.176 closest distance to " O   HOH Z 357 " =    1.870
peak=   -3.175 closest distance to " O   TYR A  30 " =    2.821
peak=   -3.175 closest distance to " CD1 TRP A 179 " =    0.854
peak=   -3.171 closest distance to " O   HOH Z 171 " =    2.015
peak=   -3.170 closest distance to " C   LEU A 143 " =    1.194
peak=   -3.167 closest distance to " O   HOH Z  65 " =    1.200
peak=   -3.166 closest distance to " NH2BARG A 275 " =    1.673
peak=   -3.163 closest distance to " O   MET A  40 " =    2.724
peak=   -3.161 closest distance to " O   HOH Z 371 " =    2.355
peak=   -3.161 closest distance to " O   HOH Z 111 " =    1.123
peak=   -3.158 closest distance to " CG1 VAL A 296 " =    1.270
peak=   -3.156 closest distance to " O   HOH Z 168 " =    1.954
peak=   -3.149 closest distance to " CH2 TRP A 179 " =    1.773
peak=   -3.135 closest distance to " CZ  TYR A 169 " =    1.519
peak=   -3.135 closest distance to " CG  ASP A  50 " =    2.313
peak=   -3.123 closest distance to " CA  VAL A 296 " =    1.039
peak=   -3.119 closest distance to " CD2 PHE A  61 " =    1.854
peak=   -3.119 closest distance to " NH1 ARG A  56 " =    2.450
peak=   -3.115 closest distance to " CB  CYS A 201 " =    2.327
peak=   -3.113 closest distance to " O   ALA A  51 " =    1.464
peak=   -3.111 closest distance to " CB  ASP A 132 " =    2.353
peak=   -3.107 closest distance to " OD1 ASP A 191 " =    1.499
peak=   -3.107 closest distance to " CD2 LEU A 300 " =    3.379
peak=   -3.103 closest distance to " O   SER A  62 " =    2.299
peak=   -3.093 closest distance to " O   HOH Z 134 " =    3.493
peak=   -3.091 closest distance to " CG2 VAL A 202 " =    2.635
peak=   -3.089 closest distance to " CD1 TYR A 247 " =    2.627
peak=   -3.087 closest distance to " CG  ARG A 269 " =    2.371
peak=   -3.072 closest distance to " CD1 LEU A 297 " =    2.493
peak=   -3.067 closest distance to " O   HOH Z  71 " =    1.078
peak=   -3.056 closest distance to " NE2 GLN A  88 " =    1.106
peak=   -3.048 closest distance to " O   TRP A  70 " =    1.427
peak=   -3.048 closest distance to " O   ILE A  49 " =    1.771
peak=   -3.045 closest distance to " O   HOH Z 336 " =    5.459
peak=   -3.039 closest distance to " O   HOH Z 250 " =    1.407
peak=   -3.035 closest distance to " O   HOH Z 410 " =    2.075
peak=   -3.029 closest distance to " CE BMET A  47 " =    1.166

================= 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    :  0.4421 0.4260   6.237397e+00   6.216179e+00
   1_bss:  0.4330 0.4158   6.231594e+00   6.206998e+00
   1_xyz:  0.3292 0.3523   6.042998e+00   6.088641e+00
   1_adp:  0.2709 0.3140   5.886649e+00   5.996937e+00
   1_occ:  0.2704 0.3145   5.885739e+00   5.998277e+00
   2_bss:  0.2650 0.3069   5.881424e+00   5.991830e+00
   2_xyz:  0.1834 0.2288   5.556177e+00   5.729378e+00
   2_adp:  0.1656 0.2121   5.466678e+00   5.656932e+00
   2_occ:  0.1656 0.2120   5.466321e+00   5.656611e+00
   3_bss:  0.1646 0.2105   5.464774e+00   5.654802e+00
   3_xyz:  0.1342 0.1777   5.288590e+00   5.503846e+00
   3_adp:  0.1277 0.1730   5.249038e+00   5.472053e+00
   3_occ:  0.1277 0.1729   5.248875e+00   5.471897e+00
   4_bss:  0.1279 0.1726   5.248863e+00   5.470987e+00
   4_xyz:  0.1165 0.1632   5.179951e+00   5.422239e+00
   4_adp:  0.1165 0.1598   5.170787e+00   5.402546e+00
   4_occ:  0.1165 0.1597   5.170043e+00   5.401416e+00
   5_bss:  0.1165 0.1596   5.170046e+00   5.401391e+00
   5_xyz:  0.1165 0.1592   5.170966e+00   5.402776e+00
   5_adp:  0.1157 0.1592   5.168823e+00   5.405016e+00
   5_occ:  0.1156 0.1591   5.168464e+00   5.404550e+00
   5_bss:  0.1156 0.1591   5.168480e+00   5.404548e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.355  12.478   8.139   9.250   7.881   0.000   0.000   0.000
   1_xyz:  0.355  12.478   8.139   9.250   7.881   0.000   0.000   0.000
   1_adp:  0.355  12.478   8.139   9.250   7.881   0.000   0.000   0.000
   1_occ:  0.355  12.478   8.139   9.250   7.881   0.000   0.000   0.000
   2_bss:  0.347  41.631   4.604   5.191   4.937   0.000   0.000   0.000
   2_xyz:  0.347  41.631   4.604   5.191   4.937   0.000   0.000   0.000
   2_adp:  0.347  41.631   4.604   5.191   4.937   0.000   0.000   0.000
   2_occ:  0.347  41.631   4.604   5.191   4.937   0.000   0.000   0.000
   3_bss:  0.330  41.631   3.351   3.228   4.126   0.000   0.000   0.000
   3_xyz:  0.330  41.631   3.351   3.228   4.126   0.000   0.000   0.000
   3_adp:  0.330  41.631   3.351   3.228   4.126   0.000   0.000   0.000
   3_occ:  0.330  41.631   3.351   3.228   4.126   0.000   0.000   0.000
   4_bss:  0.328  47.538   3.051   2.838   3.911   0.000   0.000   0.000
   4_xyz:  0.328  47.538   3.051   2.838   3.911   0.000   0.000   0.000
   4_adp:  0.328  47.538   3.051   2.838   3.911   0.000   0.000   0.000
   4_occ:  0.328  47.538   3.051   2.838   3.911   0.000   0.000   0.000
   5_bss:  0.331  47.538   2.918   2.699   3.843   0.000   0.000   0.000
   5_xyz:  0.331  47.538   2.918   2.699   3.843   0.000   0.000   0.000
   5_adp:  0.331  47.538   2.918   2.699   3.843   0.000   0.000   0.000
   5_occ:  0.331  47.538   2.918   2.699   3.843   0.000   0.000   0.000
   5_bss:  0.331  50.713  -0.245  -0.458   0.703   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  48.607 0.5391  0.6107    53955.401
   1_bss:  48.820 0.5344  0.7748    51837.044
   1_xyz:  38.459 0.6603  0.9336    34765.484
   1_adp:  31.647 0.7405  1.0409    26107.658
   1_occ:  31.720 0.7396  1.0385    26156.291
   2_bss:  31.280 0.7443  0.9211    25503.336
   2_xyz:  22.161 0.8403  0.9998    13065.402
   2_adp:  20.009 0.8620  1.0146    11224.677
   2_occ:  20.002 0.8620  1.0144    11211.270
   3_bss:  19.920 0.8627  0.9666    11123.846
   3_xyz:  16.401 0.8947  0.9870     8013.018
   3_adp:  15.686 0.9012  0.9893     7568.538
   3_occ:  15.682 0.9013  0.9893     7564.339
   4_bss:  15.660 0.9015  0.9783     7555.010
   4_xyz:  14.658 0.9097  0.9813     6777.335
   4_adp:  14.195 0.9137  0.9828     6557.541
   4_occ:  14.176 0.9138  0.9828     6540.648
   5_bss:  14.174 0.9138  0.9789     6540.858
   5_xyz:  14.163 0.9140  0.9783     6544.346
   5_adp:  14.200 0.9137  0.9755     6564.520
   5_occ:  14.193 0.9138  0.9755     6559.449
   5_bss:  14.193 0.9138  0.9763     6559.475
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.3657e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.3657e+01
   1_xyz:   1.548  0.012  0.101 17.924  0.006  4.121   1.2212e-01
   1_adp:   1.548  0.012  0.101 17.924  0.006  4.121   1.2212e-01
   1_occ:   1.548  0.012  0.101 17.924  0.006  4.121   1.2212e-01
   2_bss:   1.548  0.012  0.101 17.924  0.006  4.121   1.2212e-01
   2_xyz:   0.971  0.007  0.070 15.941  0.004  4.120   6.1289e-02
   2_adp:   0.971  0.007  0.070 15.941  0.004  4.120   6.1289e-02
   2_occ:   0.971  0.007  0.070 15.941  0.004  4.120   6.1289e-02
   3_bss:   0.971  0.007  0.070 15.941  0.004  4.120   6.1289e-02
   3_xyz:   0.911  0.005  0.072 15.543  0.003  4.123   5.2971e-02
   3_adp:   0.911  0.005  0.072 15.543  0.003  4.123   5.2971e-02
   3_occ:   0.911  0.005  0.072 15.543  0.003  4.123   5.2971e-02
   4_bss:   0.911  0.005  0.072 15.543  0.003  4.123   5.2971e-02
   4_xyz:   1.004  0.007  0.080 15.743  0.003  4.128   6.1528e-02
   4_adp:   1.004  0.007  0.080 15.743  0.003  4.128   6.1528e-02
   4_occ:   1.004  0.007  0.080 15.743  0.003  4.128   6.1528e-02
   5_bss:   1.004  0.007  0.080 15.743  0.003  4.128   6.1528e-02
   5_xyz:   0.911  0.006  0.073 15.510  0.003  4.119   5.3648e-02
   5_adp:   0.911  0.006  0.073 15.510  0.003  4.119   5.3648e-02
   5_occ:   0.911  0.006  0.073 15.510  0.003  4.119   5.3648e-02
   5_bss:   0.911  0.006  0.073 15.510  0.003  4.119   5.3648e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9570e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9570e+00
   1_xyz:  13.267  0.149  0.428 88.613  0.035  2.247   9.1020e-02
   1_adp:  13.267  0.149  0.428 88.613  0.035  2.247   9.1020e-02
   1_occ:  13.267  0.149  0.428 88.613  0.035  2.247   9.1020e-02
   2_bss:  13.267  0.149  0.428 88.613  0.035  2.247   9.1020e-02
   2_xyz:   6.560  0.080  0.285 87.847  0.045  2.343   5.4049e-02
   2_adp:   6.560  0.080  0.285 87.847  0.045  2.343   5.4049e-02
   2_occ:   6.560  0.080  0.285 87.847  0.045  2.343   5.4049e-02
   3_bss:   6.560  0.080  0.285 87.847  0.045  2.343   5.4049e-02
   3_xyz:   7.652  0.046  0.378 82.804  0.026  2.348   3.8630e-02
   3_adp:   7.652  0.046  0.378 82.804  0.026  2.348   3.8630e-02
   3_occ:   7.652  0.046  0.378 82.804  0.026  2.348   3.8630e-02
   4_bss:   7.652  0.046  0.378 82.804  0.026  2.348   3.8630e-02
   4_xyz:   8.031  0.059  0.501 83.824  0.037  2.342   3.8673e-02
   4_adp:   8.031  0.059  0.501 83.824  0.037  2.342   3.8673e-02
   4_occ:   8.031  0.059  0.501 83.824  0.037  2.342   3.8673e-02
   5_bss:   8.031  0.059  0.501 83.824  0.037  2.342   3.8673e-02
   5_xyz:   7.369  0.043  0.421 83.382  0.033  2.349   2.9837e-02
   5_adp:   7.369  0.043  0.421 83.382  0.033  2.349   2.9837e-02
   5_occ:   7.369  0.043  0.421 83.382  0.033  2.349   2.9837e-02
   5_bss:   7.369  0.043  0.421 83.382  0.033  2.349   2.9837e-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:  67.21   0.00  11.09  66.69   0.00   8.12  67.21   0.00  27.29
   1_occ:  67.21   0.00  11.09  66.69   0.00   8.12  67.21   0.00  27.29
   2_bss:  67.21   0.00  11.09  66.69   0.00   8.12  67.21   0.00  27.29
   2_xyz:  67.21   0.00  11.09  66.69   0.00   8.12  67.21   0.00  27.29
   2_adp:  70.26   0.00  11.36  69.23   0.00   7.61  70.26   0.00  31.78
   2_occ:  70.26   0.00  11.36  69.23   0.00   7.61  70.26   0.00  31.78
   3_bss:  70.26   0.00  11.36  69.23   0.00   7.61  70.26   0.00  31.78
   3_xyz:  70.26   0.00  11.36  69.23   0.00   7.61  70.26   0.00  31.78
   3_adp:  80.70   0.00  12.30  80.70   0.00   7.89  79.81   0.87  36.31
   3_occ:  80.70   0.00  12.30  80.70   0.00   7.89  79.81   0.87  36.31
   4_bss:  80.70   0.00  12.30  80.70   0.00   7.89  79.81   0.87  36.31
   4_xyz:  80.70   0.00  12.30  80.70   0.00   7.89  79.81   0.87  36.31
   4_adp:  80.56   0.00  11.72  80.56   0.00   7.67  74.97   1.57  33.81
   4_occ:  80.56   0.00  11.72  80.56   0.00   7.67  74.97   1.57  33.81
   5_bss:  80.56   0.00  11.72  80.56   0.00   7.67  74.97   1.57  33.81
   5_xyz:  80.56   0.00  11.72  80.56   0.00   7.67  74.97   1.57  33.81
   5_adp:  80.94   0.00  11.70  80.94   0.00   7.63  74.84   1.69  33.85
   5_occ:  80.94   0.00  11.70  80.94   0.00   7.63  74.84   1.69  33.85
   5_bss:  84.11   3.18  14.87  84.11   3.18  10.80  78.01   4.87  37.03
------------------------------------------------------------------------
 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:    1.178    0.007    0.405
   1_adp:    1.178    0.007    0.405
   1_occ:    1.178    0.007    0.405
   2_bss:    1.178    0.007    0.405
   2_xyz:    1.398    0.048    0.521
   2_adp:    1.398    0.048    0.521
   2_occ:    1.398    0.048    0.521
   3_bss:    1.398    0.048    0.521
   3_xyz:    1.505    0.041    0.551
   3_adp:    1.505    0.041    0.551
   3_occ:    1.505    0.041    0.551
   4_bss:    1.505    0.041    0.551
   4_xyz:    1.691    0.038    0.579
   4_adp:    1.691    0.038    0.579
   4_occ:    1.691    0.038    0.579
   5_bss:    1.691    0.038    0.579
   5_xyz:    1.781    0.050    0.586
   5_adp:    1.781    0.050    0.586
   5_occ:    1.781    0.050    0.586
   5_bss:    1.781    0.050    0.586
------------------------------------------------------------------------

CPU time actual refinement: 334.13


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_884/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_884/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_884/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_884/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_884/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 333.96 
  Macro-tasks:
    bulk solvent and scale       = 41.08  
    individual site refinement   = 137.20 
    weights calculation          = 32.93  
    collect and process          = 6.59   
    model show statistics        = 0.15   
    TOTAL for macro-tasks        = 217.95 
  Micro-tasks:
    mask                            = 1.81   
    f_calc                          = 102.25 
    alpha_beta                      = 8.18   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 113.67 
    fmodel                         = 7.21   
    r_factors                      = 0.29   
    phase_errors                   = 10.65  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 245.47 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.662 micro seconds
Total CPU time: 5.80 minutes
from_scatterers_fft:    660 calls, 102.05 s
gradients_fft:          605 calls,  99.71 s

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

# Date 2008-01-16 Time 02:39:29 PST -0800 (1200479969.95 s)
Start R-work = 0.4421, R-free = 0.4260 (no bulk solvent and anisotropic scale)
Final R-work = 0.1327, R-free = 0.1762 (no bulk solvent and anisotropic scale)

Start R-work = 0.4330, R-free = 0.4158
Final R-work = 0.1156, R-free = 0.1591