# Date 2008-01-16 Time 01:46:59 PST -0800 (1200476819.30 s)
#phil __OFF__

Command line arguments: "../568.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 29353
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 568

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 47.3993, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.33, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.3993, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.979 1.99066
Completeness in resolution range: 0.958835
Completeness with d_max=infinity: 0.955841

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9790
                             d_min =   1.9907

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.3993, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.979 1.99066
Completeness in resolution range: 0.958835
Completeness with d_max=infinity: 0.955841

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9794 -  4.2590 [2156/2183]  1939   217  10.1%
  bin  2:  4.2590 -  3.3934 [2049/2065]  1846   203   9.9%
  bin  3:  3.3934 -  2.9682 [2044/2063]  1840   204  10.0%
  bin  4:  2.9682 -  2.6986 [2010/2040]  1810   200  10.0%
  bin  5:  2.6986 -  2.5061 [1999/2018]  1794   205  10.3%
  bin  6:  2.5061 -  2.3590 [2003/2039]  1807   196   9.8%
  bin  7:  2.3590 -  2.2412 [1980/2013]  1782   198  10.0%
  bin  8:  2.2412 -  2.1440 [1977/2012]  1776   201  10.2%
  bin  9:  2.1440 -  2.0616 [1956/1983]  1758   198  10.1%
  bin 10:  2.0616 -  1.9907 [1415/2014]  1278   137   9.7%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_568/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: 19
        2.42 -     3.04: 2173
        3.04 -     3.66: 4637
        3.66 -     4.28: 8945
        4.28 -     4.90: 12302
  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
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.012 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  2.047 3.040 -x+1,y-1/2,-z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 109 " - " O   HOH Z 417 "  2.238 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28071 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_568/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_568/model_refine_001.geo

CPU time processing inputs: 8.94


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 47.3993 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4471   r_free= 0.4307   ksol= 0.00   Bsol= 0.00   scale= 0.810    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.243411                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9794 -  4.7499 0.99   1395  154 0.3618 0.3397      6.5267      6.4904|
|  2:  4.7499 -  3.7903 0.99   1339  151 0.3477 0.3768       6.674      6.7681|
|  3:  3.7903 -  3.3171 0.99   1320  148 0.3994 0.3629      6.6037      6.5611|
|  4:  3.3171 -  3.0165 0.99   1300  135 0.4263 0.3876      6.4674      6.3875|
|  5:  3.0165 -  2.8018 0.99   1300  149 0.4724 0.4652      6.3361      6.3477|
|  6:  2.8018 -  2.6376 0.99   1298  147 0.4719 0.5226      6.2514      6.2051|
|  7:  2.6376 -  2.5061 0.99   1277  145 0.4816 0.4468      6.2097      6.1196|
|  8:  2.5061 -  2.3975 0.98   1303  138 0.4932 0.4337      6.1694      6.1254|
|  9:  2.3975 -  2.3055 0.98   1270  146 0.4983 0.4953      6.0948      6.1044|
| 10:  2.3055 -  2.2262 0.98   1257  135 0.5229 0.4453      6.1274      6.0367|
| 11:  2.2262 -  2.1568 1.00   1282  147 0.5007 0.4653      6.0147      6.0476|
| 12:  2.1568 -  2.0953 0.97   1273  137 0.5135 0.5022      5.9583      5.9971|
| 13:  2.0953 -  2.0403 0.98   1258  141 0.5041 0.5251      5.8856      5.8307|
| 14:  2.0403 -  1.9907 0.60    758   86 0.5287 0.4397      5.8619      5.7267|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9794 -  4.7499  1395   154  0.73  31.50   0.81     0.74      60119.46|
|  2:  4.7499 -  3.7903  1339   151  0.76  30.29   0.90     0.80      81707.56|
|  3:  3.7903 -  3.3171  1320   148  0.68  36.84   0.85     0.76      84786.33|
|  4:  3.3171 -  3.0165  1300   135  0.62  41.90   0.82     0.68      73322.97|
|  5:  3.0165 -  2.8018  1300   149  0.53  49.23   0.76     0.60      63626.99|
|  6:  2.8018 -  2.6376  1298   147  0.51  51.43   0.75     0.57      58109.69|
|  7:  2.6376 -  2.5061  1277   145  0.49  53.03   0.76     0.55      53333.86|
|  8:  2.5061 -  2.3975  1303   138  0.50  51.97   0.75     0.57      46574.91|
|  9:  2.3975 -  2.3055  1270   146  0.51  51.50   0.73     0.58      41735.13|
| 10:  2.3055 -  2.2262  1257   135  0.50  52.18   0.75     0.58      38854.65|
| 11:  2.2262 -  2.1568  1282   147  0.47  54.89   0.74     0.55      38024.39|
| 12:  2.1568 -  2.0953  1273   137  0.42  58.32   0.77     0.52      36895.98|
| 13:  2.0953 -  2.0403  1258   141  0.41  59.41   0.74     0.48      32810.71|
| 14:  2.0403 -  1.9907   758    86  0.42  58.72   0.72     0.45      26645.88|
|alpha:            min =        0.45 max =            0.80 mean =         0.61|
|beta:             min =    26645.88 max =        84786.33 mean =     53685.76|
|figures of merit: min =        0.00 max =            1.00 mean =         0.55|
|phase err.(work): min =        0.00 max =           89.98 mean =        48.14|
|phase err.(test): min =        0.00 max =           89.92 mean =        48.33|
|-----------------------------------------------------------------------------|

============================== 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 = 8.518273              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.463   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.737257              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.016   (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:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       22 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      167 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      676 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1492 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2608 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3877 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5036 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6544 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7692 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.029 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.093    4.900  1.196 |       1.702 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.053)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.053)------------------------------------------|
|    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: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4544   r_free= 0.4325   ksol= 0.00   Bsol= 0.00   scale= 0.780    |
|                                                                             |
| 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: 6.249199                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4393   r_free= 0.4198   ksol= 0.33   Bsol= 20.00   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.89,9.48,9.44,0.00,0.00,0.00); trace/3= 8.60                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.236458                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.914334              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.049   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.687582              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 75.516   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4393      final r-factor (work) = 0.3297          |
| start r-factor (free) = 0.4198      final r-factor (free) = 0.3471          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 78.7739 = 7.91 * 0.50 * 6.2532 + 1.00 * 54.0290                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.2181 = 7.91 * 0.50 * 6.0883 + 1.00 * 0.1258                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3297      final r-factor (work) = 0.2709          |
| start r-factor (free) = 0.3471      final r-factor (free) = 0.3087          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2005 = 0.69 * 1.00 * 6.0883 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0874 = 0.69 * 1.00 * 5.9262 + 1.00 * 0.0126                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.053)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.77   11.16    None  None   None       |
|    all(noH): 2823   0      0.00    78.77   11.16    None  None   None       |
|    Sol.    : 438    0      0.00    78.77   27.39    None  None   None       |
|    Mac.    : 2385   0      0.00    60.28   8.17     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 -   7.877: 1489   |   5:    39.383 -  47.259:   65        |
|      1:     7.877 -  15.753:  709   |   6:    47.259 -  55.136:   39        |
|      2:    15.753 -  23.630:  259   |   7:    55.136 -  63.013:    9        |
|      3:    23.630 -  31.506:  149   |   8:    63.013 -  70.889:    0        |
|      4:    31.506 -  39.383:  103   |   9:    70.889 -  78.766:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2709 r_free = 0.3087             target_work(ml) = 5.879         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2703 r_free = 0.3094             target_work(ml) = 5.878         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2703   r_free= 0.3094   ksol= 0.33   Bsol= 20.00   scale= 1.091   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.89,9.48,9.44,0.00,0.00,0.00); trace/3= 8.60                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.878245                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2655   r_free= 0.3052   ksol= 0.33   Bsol= 44.65   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.38,5.54,5.70,0.00,0.00,0.00); trace/3= 4.87                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.878742                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.327731              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.751   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.309713              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.684  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2655      final r-factor (work) = 0.1843          |
| start r-factor (free) = 0.3052      final r-factor (free) = 0.2213          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0010 = 3.33 * 0.50 * 5.9351 + 1.00 * 0.1258                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5653 = 3.33 * 0.50 * 5.7105 + 1.00 * 0.0638                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1843      final r-factor (work) = 0.1684          |
| start r-factor (free) = 0.2213      final r-factor (free) = 0.2056          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7872 = 0.31 * 1.00 * 5.7105 + 1.00 * 0.0186                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7455 = 0.31 * 1.00 * 5.5044 + 1.00 * 0.0407                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.053)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.59   11.31    None  None   None       |
|    all(noH): 2823   0      0.00    75.59   11.31    None  None   None       |
|    Sol.    : 438    0      1.15    75.59   31.52    None  None   None       |
|    Mac.    : 2385   0      0.00    68.37   7.60     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 -   7.559: 1573   |   5:    37.794 -  45.353:   98        |
|      1:     7.559 -  15.118:  644   |   6:    45.353 -  52.911:   62        |
|      2:    15.118 -  22.676:  179   |   7:    52.911 -  60.470:   24        |
|      3:    22.676 -  30.235:  127   |   8:    60.470 -  68.029:    4        |
|      4:    30.235 -  37.794:  110   |   9:    68.029 -  75.587:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1684 r_free = 0.2056             target_work(ml) = 5.474         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1682 r_free = 0.2057             target_work(ml) = 5.474         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1682   r_free= 0.2057   ksol= 0.33   Bsol= 44.65   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.38,5.54,5.70,0.00,0.00,0.00); trace/3= 4.87                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.473753                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1678   r_free= 0.2056   ksol= 0.32   Bsol= 55.03   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.57,3.96,4.54,0.00,0.00,0.00); trace/3= 3.69                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.474311                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.077033              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.648  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.698654              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.769   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1678      final r-factor (work) = 0.1278          |
| start r-factor (free) = 0.2056      final r-factor (free) = 0.1664          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.2961 = 4.08 * 0.50 * 5.5100 + 1.00 * 0.0638                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.9877 = 4.08 * 0.50 * 5.3537 + 1.00 * 0.0741                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1278      final r-factor (work) = 0.1204          |
| start r-factor (free) = 0.1664      final r-factor (free) = 0.1624          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7534 = 0.70 * 1.00 * 5.3537 + 1.00 * 0.0130                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6549 = 0.70 * 1.00 * 5.2111 + 1.00 * 0.0142                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.053)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.08   11.88    None  None   None       |
|    all(noH): 2823   0      0.00    77.08   11.88    None  None   None       |
|    Sol.    : 438    0      0.00    72.49   35.12    None  None   None       |
|    Mac.    : 2385   0      0.00    77.08   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 -   7.708: 1640   |   5:    38.538 -  46.246:   86        |
|      1:     7.708 -  15.415:  579   |   6:    46.246 -  53.954:   81        |
|      2:    15.415 -  23.123:  167   |   7:    53.954 -  61.661:   43        |
|      3:    23.123 -  30.831:  106   |   8:    61.661 -  69.369:   20        |
|      4:    30.831 -  38.538:   97   |   9:    69.369 -  77.077:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1204 r_free = 0.1624             target_work(ml) = 5.199         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1203 r_free = 0.1624             target_work(ml) = 5.198         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1203   r_free= 0.1624   ksol= 0.32   Bsol= 55.03   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.57,3.96,4.54,0.00,0.00,0.00); trace/3= 3.69                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.198256                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1205   r_free= 0.1624   ksol= 0.33   Bsol= 55.03   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.52,3.49,4.36,0.00,0.00,0.00); trace/3= 3.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.199145                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.402929              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 131.728  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.383155              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 98.697   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1205      final r-factor (work) = 0.1151          |
| start r-factor (free) = 0.1624      final r-factor (free) = 0.1593          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3355 = 2.40 * 0.50 * 5.2115 + 1.00 * 0.0741                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.2934 = 2.40 * 0.50 * 5.1812 + 1.00 * 0.0684                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1151      final r-factor (work) = 0.1148          |
| start r-factor (free) = 0.1593      final r-factor (free) = 0.1586          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9991 = 0.38 * 1.00 * 5.1812 + 1.00 * 0.0139                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0198 = 0.38 * 1.00 * 5.1690 + 1.00 * 0.0393                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.053)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.56   11.64    None  None   None       |
|    all(noH): 2823   0      0.00    79.56   11.64    None  None   None       |
|    Sol.    : 438    0      0.49    70.46   34.17    None  None   None       |
|    Mac.    : 2385   0      0.00    79.56   7.50     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 -   7.956: 1701   |   5:    39.780 -  47.736:   84        |
|      1:     7.956 -  15.912:  543   |   6:    47.736 -  55.692:   64        |
|      2:    15.912 -  23.868:  156   |   7:    55.692 -  63.649:   30        |
|      3:    23.868 -  31.824:  110   |   8:    63.649 -  71.605:   17        |
|      4:    31.824 -  39.780:  116   |   9:    71.605 -  79.561:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1148 r_free = 0.1586             target_work(ml) = 5.167         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1146 r_free = 0.1586             target_work(ml) = 5.167         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1146   r_free= 0.1586   ksol= 0.33   Bsol= 55.03   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.52,3.49,4.36,0.00,0.00,0.00); trace/3= 3.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.166574                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1146   r_free= 0.1586   ksol= 0.33   Bsol= 55.03   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.58,3.42,4.40,0.00,0.00,0.00); trace/3= 3.47                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.166494                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.950454              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 152.897  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.328978              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.586   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1146      final r-factor (work) = 0.1110          |
| start r-factor (free) = 0.1586      final r-factor (free) = 0.1571          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6930 = 2.95 * 0.50 * 5.1684 + 1.00 * 0.0684                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6793 = 2.95 * 0.50 * 5.1519 + 1.00 * 0.0791                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1110      final r-factor (work) = 0.1102          |
| start r-factor (free) = 0.1571      final r-factor (free) = 0.1579          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8654 = 1.33 * 1.00 * 5.1519 + 1.00 * 0.0186                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.8481 = 1.33 * 1.00 * 5.1428 + 1.00 * 0.0134                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.053)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.87   11.68    None  None   None       |
|    all(noH): 2823   0      0.00    82.87   11.68    None  None   None       |
|    Sol.    : 438    0      0.47    71.80   34.61    None  None   None       |
|    Mac.    : 2385   0      0.00    82.87   7.47     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.287: 1731   |   5:    41.433 -  49.720:   86        |
|      1:     8.287 -  16.573:  528   |   6:    49.720 -  58.006:   62        |
|      2:    16.573 -  24.860:  154   |   7:    58.006 -  66.293:   24        |
|      3:    24.860 -  33.146:  110   |   8:    66.293 -  74.580:   15        |
|      4:    33.146 -  41.433:  111   |   9:    74.580 -  82.866:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1102 r_free = 0.1579             target_work(ml) = 5.147         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1102 r_free = 0.1579             target_work(ml) = 5.147         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1102   r_free= 0.1579   ksol= 0.33   Bsol= 55.03   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.58,3.42,4.40,0.00,0.00,0.00); trace/3= 3.47                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.146698                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9794 -  4.7499 0.99   1395  154 0.0994 0.1279      5.3873      5.5321|
|  2:  4.7499 -  3.7903 0.99   1339  151 0.0841 0.1107        5.43      5.6459|
|  3:  3.7903 -  3.3171 0.99   1320  148 0.1031 0.1498      5.4547      5.8453|
|  4:  3.3171 -  3.0165 0.99   1300  135 0.1170 0.1472      5.4266       5.567|
|  5:  3.0165 -  2.8018 0.99   1300  149 0.1307 0.1702      5.3215      5.5174|
|  6:  2.8018 -  2.6376 0.99   1298  147 0.1208 0.2029      5.2127      5.5233|
|  7:  2.6376 -  2.5061 0.99   1277  145 0.1234 0.1642      5.1693      5.3382|
|  8:  2.5061 -  2.3975 0.98   1303  138 0.1133 0.1674      5.0766      5.3554|
|  9:  2.3975 -  2.3055 0.98   1270  146 0.1176 0.1952      5.0416      5.3349|
| 10:  2.3055 -  2.2262 0.98   1257  135 0.1128 0.1593       4.991      5.2006|
| 11:  2.2262 -  2.1568 1.00   1282  147 0.1125 0.1866      4.9467      5.2904|
| 12:  2.1568 -  2.0953 0.97   1273  137 0.1115 0.1681      4.8825      5.1884|
| 13:  2.0953 -  2.0403 0.98   1258  141 0.1094 0.1743      4.7838       5.026|
| 14:  2.0403 -  1.9907 0.60    758   86 0.1031 0.1778      4.6756      4.9826|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9794 -  4.7499  1395   154  0.94   9.20   0.97     0.95       7349.75|
|  2:  4.7499 -  3.7903  1339   151  0.95   7.92   1.01     0.99       9025.08|
|  3:  3.7903 -  3.3171  1320   148  0.94  11.11   1.02     1.01      10172.87|
|  4:  3.3171 -  3.0165  1300   135  0.92  13.08   1.00     0.99       9933.11|
|  5:  3.0165 -  2.8018  1300   149  0.90  15.95   0.99     0.96       8298.14|
|  6:  2.8018 -  2.6376  1298   147  0.90  16.50   0.98     0.95       7256.68|
|  7:  2.6376 -  2.5061  1277   145  0.90  15.63   0.98     0.95       6312.02|
|  8:  2.5061 -  2.3975  1303   138  0.91  15.20   0.99     0.96       5538.64|
|  9:  2.3975 -  2.3055  1270   146  0.90  16.19   1.00     0.96       5284.79|
| 10:  2.3055 -  2.2262  1257   135  0.89  16.67   0.99     0.95       4799.42|
| 11:  2.2262 -  2.1568  1282   147  0.90  16.51   0.98     0.95       4589.39|
| 12:  2.1568 -  2.0953  1273   137  0.91  15.69   1.00     0.99       4080.35|
| 13:  2.0953 -  2.0403  1258   141  0.90  16.14   0.99     0.97       3399.97|
| 14:  2.0403 -  1.9907   758    86  0.91  14.78   0.96     0.92       2623.28|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2623.28 max =        10172.87 mean =      6480.48|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.25|
|phase err.(test): min =        0.00 max =           87.98 mean =        13.77|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1102   r_free= 0.1578   ksol= 0.32   Bsol= 56.86   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.86,-0.08,0.94,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.146691                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1102   r_free= 0.1578   ksol= 0.32   Bsol= 56.86   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.86,-0.08,0.94,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.146691                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9794 -  4.7499 0.99   1395  154 0.0993 0.1280      5.3862      5.5317|
|  2:  4.7499 -  3.7903 0.99   1339  151 0.0841 0.1105      5.4294      5.6449|
|  3:  3.7903 -  3.3171 0.99   1320  148 0.1031 0.1499      5.4545      5.8459|
|  4:  3.3171 -  3.0165 0.99   1300  135 0.1170 0.1473      5.4268      5.5673|
|  5:  3.0165 -  2.8018 0.99   1300  149 0.1308 0.1702       5.322      5.5177|
|  6:  2.8018 -  2.6376 0.99   1298  147 0.1208 0.2030       5.213      5.5234|
|  7:  2.6376 -  2.5061 0.99   1277  145 0.1235 0.1643      5.1696      5.3386|
|  8:  2.5061 -  2.3975 0.98   1303  138 0.1133 0.1674      5.0767      5.3554|
|  9:  2.3975 -  2.3055 0.98   1270  146 0.1176 0.1950      5.0417      5.3347|
| 10:  2.3055 -  2.2262 0.98   1257  135 0.1127 0.1593      4.9911      5.2013|
| 11:  2.2262 -  2.1568 1.00   1282  147 0.1125 0.1865      4.9468      5.2903|
| 12:  2.1568 -  2.0953 0.97   1273  137 0.1115 0.1681      4.8826      5.1886|
| 13:  2.0953 -  2.0403 0.98   1258  141 0.1094 0.1742      4.7837      5.0255|
| 14:  2.0403 -  1.9907 0.60    758   86 0.1031 0.1778      4.6756      4.9824|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9794 -  4.7499  1395   154  0.94   9.18   0.97     0.95       7331.61|
|  2:  4.7499 -  3.7903  1339   151  0.95   7.91   1.01     0.99       9012.10|
|  3:  3.7903 -  3.3171  1320   148  0.94  11.11   1.02     1.02      10168.77|
|  4:  3.3171 -  3.0165  1300   135  0.92  13.09   1.00     0.99       9940.60|
|  5:  3.0165 -  2.8018  1300   149  0.90  15.96   1.00     0.96       8303.99|
|  6:  2.8018 -  2.6376  1298   147  0.90  16.50   0.98     0.95       7260.81|
|  7:  2.6376 -  2.5061  1277   145  0.90  15.63   0.98     0.95       6315.46|
|  8:  2.5061 -  2.3975  1303   138  0.91  15.21   0.99     0.97       5539.76|
|  9:  2.3975 -  2.3055  1270   146  0.90  16.20   1.00     0.97       5286.84|
| 10:  2.3055 -  2.2262  1257   135  0.89  16.67   0.99     0.95       4800.24|
| 11:  2.2262 -  2.1568  1282   147  0.90  16.51   0.99     0.95       4590.80|
| 12:  2.1568 -  2.0953  1273   137  0.91  15.70   1.01     0.99       4081.38|
| 13:  2.0953 -  2.0403  1258   141  0.90  16.14   1.00     0.98       3399.08|
| 14:  2.0403 -  1.9907   758    86  0.91  14.77   0.97     0.93       2621.55|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2621.55 max =        10168.77 mean =      6479.61|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        14.25|
|phase err.(test): min =        0.00 max =           87.97 mean =        13.77|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.053)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.61    86.48   15.29    None  None   None       |
|    all(noH): 2823   0      3.61    86.48   15.29    None  None   None       |
|    Sol.    : 438    0      4.08    75.41   38.22    None  None   None       |
|    Mac.    : 2385   0      3.61    86.48   11.08    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:     3.610 -  11.897: 1731   |   5:    45.043 -  53.330:   86        |
|      1:    11.897 -  20.183:  528   |   6:    53.330 -  61.616:   62        |
|      2:    20.183 -  28.470:  154   |   7:    61.616 -  69.903:   24        |
|      3:    28.470 -  36.756:  110   |   8:    69.903 -  78.189:   15        |
|      4:    36.756 -  45.043:  111   |   9:    78.189 -  86.476:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 313         
Filter by distance & map next to the model:
   mapped sites are within: 0.235 - 5.741
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 305 from: 313
   mapped sites are within: 0.701 - 5.741

peak=   10.435 closest distance to " CG2 VAL A 230 " =    1.365
peak=    6.405 closest distance to " CG  LEU A   5 " =    1.164
peak=    6.071 closest distance to " NH2 ARG A  56 " =    2.285
peak=    5.938 closest distance to " CB  VAL A 296 " =    1.114
peak=    5.873 closest distance to " CG  LEU A 228 " =    1.169
peak=    5.297 closest distance to " CG  PRO A  54 " =    1.236
peak=    5.193 closest distance to " CB  VAL A 230 " =    1.187
peak=    5.143 closest distance to " CB  GLN A 223 " =    1.457
peak=    4.980 closest distance to " NE2 GLN A  11 " =    1.117
peak=    4.936 closest distance to " CD2 LEU A   5 " =    1.148
peak=    4.912 closest distance to " CB  ARG A 275 " =    0.927
peak=    4.899 closest distance to " CB  GLN A 183 " =    1.310
peak=    4.694 closest distance to " O   HOH Z 232 " =    2.356
peak=    4.670 closest distance to " CB  SER A  63 " =    1.213
peak=    4.666 closest distance to " O   HOH Z 142 " =    1.630
peak=    4.605 closest distance to " CG2 VAL A 296 " =    0.991
peak=    4.505 closest distance to " CZ  PHE A 218 " =    1.181
peak=    4.474 closest distance to " O   HOH Z 209 " =    2.278
peak=    4.467 closest distance to " C   PRO A 198 " =    1.496
peak=    4.438 closest distance to " CA  TYR A  30 " =    0.920
peak=    4.433 closest distance to " O   SER A  87 " =    2.243
peak=    4.413 closest distance to " CB  ARG A 190 " =    1.671
peak=    4.385 closest distance to " O   HOH Z 126 " =    1.924
peak=    4.345 closest distance to " O   HOH Z 403 " =    1.732
peak=    4.324 closest distance to " CB  GLU A 152 " =    1.161
peak=    4.304 closest distance to " CB  PRO A  54 " =    0.904
peak=    4.301 closest distance to " CG  PRO A 213 " =    1.184
peak=    4.293 closest distance to " O   HOH Z  43 " =    2.032
peak=    4.288 closest distance to " CB  ASN A 148 " =    1.417
peak=    4.271 closest distance to " O   HOH Z 280 " =    2.895
peak=    4.268 closest distance to " CB  ARG A  79 " =    1.442
peak=    4.252 closest distance to " O   HOH Z 369 " =    2.301
peak=    4.237 closest distance to " O   HOH Z 265 " =    2.151
peak=    4.224 closest distance to " O   HOH Z 346 " =    1.560
peak=    4.197 closest distance to " O   HOH Z 423 " =    1.864
peak=    4.185 closest distance to " CG1 VAL A 296 " =    1.173
peak=    4.170 closest distance to " O   HOH Z 427 " =    2.988
peak=    4.159 closest distance to " O   HOH Z 236 " =    1.984
peak=    4.156 closest distance to " O   HOH Z 272 " =    1.890
peak=    4.143 closest distance to " O   HOH Z 248 " =    1.569
peak=    4.121 closest distance to " O   HOH Z 298 " =    1.800
peak=    4.118 closest distance to " O   HOH Z 368 " =    2.357
peak=    4.118 closest distance to " O   HOH Z 193 " =    1.817
peak=    4.100 closest distance to " O   HOH Z  61 " =    1.587
peak=    4.076 closest distance to " OD1 ASN A  69 " =    2.562
peak=    4.072 closest distance to " O   HOH Z 234 " =    3.644
peak=    4.067 closest distance to " O   HOH Z 189 " =    2.757
peak=    4.064 closest distance to " O   HOH Z 158 " =    3.179
peak=    4.058 closest distance to " O   HOH Z 316 " =    3.032
peak=    4.047 closest distance to " CG  PRO A 243 " =    1.122
peak=    4.031 closest distance to " OG BSER A 164 " =    2.209
peak=    4.024 closest distance to " CB  GLU A 277 " =    3.630
peak=    4.000 closest distance to " O   HOH Z 303 " =    2.096
peak=    3.976 closest distance to " CB  VAL A 265 " =    1.318
peak=    3.968 closest distance to " O   HOH Z  63 " =    1.987
peak=    3.961 closest distance to " O   HOH Z  59 " =    2.331
peak=    3.945 closest distance to " CB  TRP A 266 " =    0.986
peak=    3.918 closest distance to " CB  ASP A 140 " =    1.102
peak=    3.915 closest distance to " O   HOH Z 412 " =    3.865
peak=    3.906 closest distance to " O   HOH Z 147 " =    1.819
peak=    3.897 closest distance to " ND2 ASN A 187 " =    1.498
peak=    3.890 closest distance to " O   HOH Z  78 " =    1.631
peak=    3.880 closest distance to " O   HOH Z 402 " =    1.431
peak=    3.876 closest distance to " CB  VAL A 202 " =    1.495
peak=    3.874 closest distance to " O   HOH Z 389 " =    1.924
peak=    3.871 closest distance to " O   HOH Z 261 " =    1.993
peak=    3.870 closest distance to " CG1 ILE A  49 " =    1.526
peak=    3.868 closest distance to " CB  GLU A 128 " =    1.033
peak=    3.863 closest distance to " O   HOH Z 193 " =    2.072
peak=    3.853 closest distance to " O   HOH Z 214 " =    2.320
peak=    3.850 closest distance to " O   HOH Z 126 " =    1.577
peak=    3.830 closest distance to " O   HOH Z 197 " =    2.861
peak=    3.817 closest distance to " CD2 TRP A 179 " =    1.349
peak=    3.816 closest distance to " CB  TRP A 179 " =    1.420
peak=    3.804 closest distance to " O   HOH Z  80 " =    1.807
peak=    3.802 closest distance to " O   HOH Z 422 " =    2.664
peak=    3.794 closest distance to " O   HOH Z 250 " =    1.305
peak=    3.793 closest distance to " CB  ASN A  39 " =    0.873
peak=    3.788 closest distance to " CA  ALA A  51 " =    0.948
peak=    3.779 closest distance to " O   HOH Z  97 " =    2.367
peak=    3.777 closest distance to " CG  ARG A  66 " =    2.521
peak=    3.772 closest distance to " O   HOH Z 313 " =    1.798
peak=    3.768 closest distance to " O   HOH Z 203 " =    1.739
peak=    3.766 closest distance to " CD2 LEU A 228 " =    1.183
peak=    3.757 closest distance to " CA  ARG A 195 " =    1.219
peak=    3.752 closest distance to " N   ASN A  39 " =    1.310
peak=    3.750 closest distance to " O   HOH Z  97 " =    1.978
peak=    3.743 closest distance to " O   HOH Z 426 " =    1.556
peak=    3.724 closest distance to " CG  PRO A 198 " =    1.238
peak=    3.721 closest distance to " O   HOH Z  15 " =    2.132
peak=    3.708 closest distance to " CB  ALA A   9 " =    1.640
peak=    3.706 closest distance to " O   HOH Z 251 " =    1.493
peak=    3.704 closest distance to " NE2 GLN A  77 " =    3.347
peak=    3.701 closest distance to " O   HOH Z  19 " =    1.887
peak=    3.698 closest distance to " O   HOH Z 273 " =    2.919
peak=    3.682 closest distance to " CA  ARG A  36 " =    1.046
peak=    3.680 closest distance to " O   HOH Z 285 " =    2.733
peak=    3.679 closest distance to " CG  MET A 185 " =    1.135
peak=    3.677 closest distance to " CB  THR A  31 " =    1.563
peak=    3.676 closest distance to " CD  LYS A 166 " =    1.330
peak=    3.673 closest distance to " CE  LYS A  76 " =    0.855
peak=    3.658 closest distance to " O   HOH Z 299 " =    4.240
peak=    3.658 closest distance to " O   HOH Z 371 " =    3.126
peak=    3.650 closest distance to " CB  SER A  26 " =    1.830
peak=    3.644 closest distance to " CB  ASN A 142 " =    1.180
peak=    3.643 closest distance to " CD1 LEU A  96 " =    0.701
peak=    3.636 closest distance to " CB  GLN A  88 " =    1.191
peak=    3.631 closest distance to " CA  ALA A  21 " =    1.147
peak=    3.622 closest distance to " CG1BVAL A  72 " =    1.727
peak=    3.619 closest distance to " CB  THR A  52 " =    0.881
peak=    3.619 closest distance to " CB  ARG A  79 " =    0.916
peak=    3.608 closest distance to " CB  GLU A  46 " =    1.024
peak=    3.586 closest distance to " CE1 TYR A 186 " =    1.308
peak=    3.585 closest distance to " O   HOH Z 145 " =    2.338
peak=    3.585 closest distance to " O   HOH Z  21 " =    1.783
peak=    3.583 closest distance to " CB  SER A   3 " =    1.234
peak=    3.578 closest distance to " O   ARG A  56 " =    2.922
peak=    3.573 closest distance to " O   HOH Z  40 " =    1.825
peak=    3.572 closest distance to " CA  LYS A 117 " =    1.294
peak=    3.569 closest distance to " CA  ASN A 215 " =    1.142
peak=    3.557 closest distance to " NZ  LYS A  48 " =    1.258
peak=    3.554 closest distance to " C   ILE A 106 " =    1.894
peak=    3.553 closest distance to " O   HOH Z  66 " =    2.218
peak=    3.550 closest distance to " NH2 ARG A 156 " =    1.099
peak=    3.546 closest distance to " CG2 ILE A  20 " =    1.428
peak=    3.542 closest distance to " O   HOH Z 365 " =    2.902
peak=    3.534 closest distance to " O  BHOH Z 338 " =    2.394
peak=    3.533 closest distance to " CB  ARG A 139 " =    0.929
peak=    3.528 closest distance to " O   HOH Z 172 " =    3.823
peak=    3.526 closest distance to " O   HOH Z 425 " =    2.008
peak=    3.517 closest distance to " O   HOH Z 359 " =    1.425
peak=    3.515 closest distance to " O   HOH Z 180 " =    2.158
peak=    3.507 closest distance to " O   HOH Z 407 " =    2.522
peak=    3.505 closest distance to " O   HOH Z 128 " =    2.056
peak=    3.497 closest distance to " O   HOH Z 437 " =    1.762
peak=    3.495 closest distance to " N   ASP A 162 " =    1.226
peak=    3.491 closest distance to " CD  ARG A 159 " =    0.755
peak=    3.486 closest distance to " CG1 ILE A  33 " =    1.220
peak=    3.479 closest distance to " CA  THR A 264 " =    0.742
peak=    3.478 closest distance to " NZ  LYS A 117 " =    3.194
peak=    3.477 closest distance to " CB  ASN A 110 " =    1.180
peak=    3.474 closest distance to " O   HOH Z 417 " =    3.153
peak=    3.473 closest distance to " O   LYS A 290 " =    2.420
peak=    3.471 closest distance to " O   HOH Z  35 " =    2.378
peak=    3.471 closest distance to " CG  MET A 185 " =    1.036
peak=    3.469 closest distance to " CG1 VAL A 153 " =    0.959
peak=    3.468 closest distance to " CB AVAL A  41 " =    1.090
peak=    3.468 closest distance to " CB  TRP A 150 " =    1.431
peak=    3.467 closest distance to " CG  LEU A 167 " =    1.227
peak=    3.459 closest distance to " CA  ALA A 291 " =    0.866
peak=    3.456 closest distance to " O   HOH Z 171 " =    2.250
peak=    3.449 closest distance to " O   HOH Z 383 " =    2.010
peak=    3.441 closest distance to " O   ASP A 124 " =    1.226
peak=    3.436 closest distance to " CZ3 TRP A  85 " =    0.944
peak=    3.436 closest distance to " O   HOH Z 403 " =    1.410
peak=    3.435 closest distance to " CD1 LEU A 300 " =    1.223
peak=    3.431 closest distance to " O   TRP A 274 " =    1.897
peak=    3.430 closest distance to " O   HOH Z  85 " =    1.441
peak=    3.421 closest distance to " O   HOH Z  48 " =    1.587
peak=    3.419 closest distance to " OE1 GLU A   2 " =    2.037
peak=    3.415 closest distance to " O   HOH Z  54 " =    1.592
peak=    3.414 closest distance to " O   HOH Z 112 " =    1.688
peak=    3.413 closest distance to " O   HOH Z 353 " =    2.680
peak=    3.411 closest distance to " CA  VAL A 125 " =    1.156
peak=    3.410 closest distance to " CB  ALA A 248 " =    1.393
peak=    3.409 closest distance to " CD  ARG A 269 " =    0.992
peak=    3.400 closest distance to " O   HOH Z 187 " =    2.331
peak=    3.397 closest distance to " CD  LYS A  76 " =    1.866
peak=    3.396 closest distance to " CB  THR A 157 " =    1.196
peak=    3.392 closest distance to " O   GLN A 278 " =    1.208
peak=    3.388 closest distance to " CA  ALA A 158 " =    1.324
peak=    3.383 closest distance to " O   HOH Z 325 " =    2.180
peak=    3.383 closest distance to " N   PHE A 130 " =    1.270
peak=    3.382 closest distance to " O   HOH Z 344 " =    2.948
peak=    3.381 closest distance to " CG2 THR A 221 " =    1.257
peak=    3.369 closest distance to " CE1 HIS A 108 " =    1.121
peak=    3.365 closest distance to " O   HOH Z 357 " =    2.004
peak=    3.364 closest distance to " CB  GLN A  89 " =    1.258
peak=    3.363 closest distance to " O   HOH Z 130 " =    2.312
peak=    3.356 closest distance to " CD BLYS A 290 " =    1.019
peak=    3.355 closest distance to " CA  ALA A 295 " =    1.057
peak=    3.345 closest distance to " O   HOH Z 171 " =    3.888
peak=    3.345 closest distance to " N   VAL A 126 " =    1.468
peak=    3.341 closest distance to " O   HOH Z 245 " =    1.350
peak=    3.339 closest distance to " CB  GLN A 103 " =    1.050
peak=    3.335 closest distance to " O   HOH Z 128 " =    2.454
peak=    3.332 closest distance to " O   HOH Z 291 " =    1.464
peak=    3.325 closest distance to " CB  SER A 212 " =    1.148
peak=    3.324 closest distance to " O   HOH Z 154 " =    1.343
peak=    3.322 closest distance to " CZ  PHE A  38 " =    1.207
peak=    3.320 closest distance to " CA  VAL A  41 " =    0.842
peak=    3.317 closest distance to " O   ALA A 165 " =    1.487
peak=    3.312 closest distance to " O   HOH Z 102 " =    1.269
peak=    3.311 closest distance to " OG BSER A 134 " =    2.917
peak=    3.304 closest distance to " CB  ASN A 215 " =    1.202
peak=    3.302 closest distance to " CA  ASN A 217 " =    1.172
peak=    3.301 closest distance to " OD1 ASN A 217 " =    1.727
peak=    3.300 closest distance to " NH1AARG A 145 " =    1.232
peak=    3.295 closest distance to " O   HOH Z 345 " =    3.185
peak=    3.294 closest distance to " O   HOH Z 384 " =    3.208
peak=    3.289 closest distance to " CG BARG A 275 " =    1.308
peak=    3.287 closest distance to " O   HOH Z 271 " =    2.570
peak=    3.283 closest distance to " O   HOH Z 133 " =    2.531
peak=    3.279 closest distance to " O   HOH Z 305 " =    3.656
peak=    3.277 closest distance to " O   HOH Z 420 " =    5.741
peak=    3.272 closest distance to " CA  ILE A 106 " =    0.759
peak=    3.271 closest distance to " CA  THR A 221 " =    0.935
peak=    3.271 closest distance to " O   HOH Z 406 " =    1.501
peak=    3.270 closest distance to " O   HOH Z 250 " =    1.407
peak=    3.269 closest distance to " O   HOH Z 435 " =    1.954
peak=    3.268 closest distance to " CB  ALA A 291 " =    1.356
peak=    3.267 closest distance to " CB  ALA A 295 " =    1.153
peak=    3.260 closest distance to " CA  LYS A 181 " =    1.088
peak=    3.259 closest distance to " CG2 ILE A 120 " =    1.054
peak=    3.256 closest distance to " CA  LEU A 282 " =    1.100
peak=    3.255 closest distance to " O   ASN A  74 " =    1.587
peak=    3.255 closest distance to " O   HOH Z 411 " =    1.773
peak=    3.249 closest distance to " CG1 ILE A 151 " =    1.101
peak=    3.246 closest distance to " O   GLN A  88 " =    1.674
peak=    3.246 closest distance to " O   HOH Z 258 " =    2.130
peak=    3.245 closest distance to " NH2AARG A 275 " =    3.542
peak=    3.245 closest distance to " O   HOH Z 189 " =    2.694
peak=    3.243 closest distance to " O   HOH Z 368 " =    3.628
peak=    3.239 closest distance to " OG  SER A  22 " =    2.735
peak=    3.237 closest distance to " CA  ASP A 191 " =    1.143
peak=    3.232 closest distance to " CB  ALA A 100 " =    1.211
peak=    3.231 closest distance to " ND1 HIS A  81 " =    1.684
peak=    3.230 closest distance to " CG2 VAL A 257 " =    0.813
peak=    3.228 closest distance to " O   HOH Z 279 " =    2.168
peak=    3.228 closest distance to " O   HOH Z 227 " =    1.516
peak=    3.227 closest distance to " CA  TYR A 116 " =    1.431
peak=    3.225 closest distance to " O   HOH Z 380 " =    1.868
peak=    3.222 closest distance to " O   HOH Z  88 " =    3.108
peak=    3.219 closest distance to " OD2 ASP A 286 " =    2.870
peak=    3.218 closest distance to " O   HOH Z  66 " =    2.348
peak=    3.217 closest distance to " O   HOH Z 116 " =    1.789
peak=    3.217 closest distance to " CD1 LEU A   5 " =    1.288
peak=    3.215 closest distance to " O   HOH Z 294 " =    1.507
peak=    3.214 closest distance to " CB  PRO A  90 " =    1.166
peak=    3.210 closest distance to " O   HOH Z 361 " =    3.671
peak=    3.210 closest distance to " O   SER A 164 " =    1.100
peak=    3.206 closest distance to " NH2 ARG A  79 " =    1.360
peak=    3.205 closest distance to " CD  ARG A  79 " =    1.909
peak=    3.204 closest distance to " O   HOH Z 329 " =    4.100
peak=    3.198 closest distance to " CB  ALA A 248 " =    0.981
peak=    3.196 closest distance to " CB  ALA A 104 " =    0.710
peak=    3.190 closest distance to " O   HOH Z  88 " =    2.548
peak=    3.190 closest distance to " N   SER A 135 " =    1.443
peak=    3.190 closest distance to " OE2 GLU A  53 " =    2.015
peak=    3.190 closest distance to " O   HOH Z 134 " =    1.254
peak=    3.183 closest distance to " O   HOH Z 109 " =    2.598
peak=    3.180 closest distance to " CA  ASN A 176 " =    1.187
peak=    3.180 closest distance to " CB  MET A  40 " =    0.806
peak=    3.179 closest distance to " O   HOH Z 302 " =    2.011
peak=    3.179 closest distance to " CG  GLN A  88 " =    1.031
peak=    3.177 closest distance to " CG  GLN A  77 " =    2.225
peak=    3.176 closest distance to " CG2 ILE A 234 " =    0.862
peak=    3.173 closest distance to " CB  MET A  47 " =    1.001
peak=    3.173 closest distance to " CB  GLN A 205 " =    1.110
peak=    3.173 closest distance to " CB  GLN A 278 " =    0.935
peak=    3.172 closest distance to " CA  ALA A 248 " =    1.228
peak=    3.169 closest distance to " NE2 HIS A 207 " =    1.302
peak=    3.168 closest distance to " CD  LYS A 119 " =    1.808
peak=    3.164 closest distance to " CA  MET A 105 " =    0.961
peak=    3.163 closest distance to " CG BARG A 102 " =    1.765
peak=    3.160 closest distance to " O   HOH Z 227 " =    2.059
peak=    3.158 closest distance to " CA  ALA A 160 " =    0.883
peak=    3.156 closest distance to " CG2 VAL A 197 " =    1.075
peak=    3.156 closest distance to " CD1 ILE A 199 " =    0.864
peak=    3.155 closest distance to " CG  PHE A 204 " =    0.859
peak=    3.155 closest distance to " O   HOH Z  85 " =    2.096
peak=    3.153 closest distance to " O   HOH Z  90 " =    3.359
peak=    3.153 closest distance to " OG  SER A 245 " =    1.570
peak=    3.152 closest distance to " O   HOH Z 419 " =    1.560
peak=    3.151 closest distance to " NH2BARG A 190 " =    1.789
peak=    3.151 closest distance to " CB  PHE A 204 " =    0.883
peak=    3.149 closest distance to " CA  SER A 146 " =    1.793
peak=    3.148 closest distance to " CD2 TYR A 186 " =    1.082
peak=    3.147 closest distance to " O   HOH Z 391 " =    2.951
peak=    3.142 closest distance to " O   HOH Z 420 " =    2.121
peak=    3.142 closest distance to " O   HOH Z 292 " =    1.590
peak=    3.137 closest distance to " O   HOH Z 213 " =    1.748
peak=    3.134 closest distance to " O   THR A  31 " =    1.608
peak=    3.127 closest distance to " O   ALA A 158 " =    1.326
peak=    3.125 closest distance to " O   HOH Z  63 " =    2.126
peak=    3.124 closest distance to " O   HOH Z 148 " =    3.298
peak=    3.124 closest distance to " O   HOH Z 417 " =    2.269
peak=    3.122 closest distance to " CA  GLY A 211 " =    1.329
peak=    3.119 closest distance to " CA  ASP A 162 " =    1.079
peak=    3.116 closest distance to " CB  ASN A 187 " =    1.062
peak=    3.112 closest distance to " CH2 TRP A 266 " =    1.082
peak=    3.106 closest distance to " O   ILE A  20 " =    2.205
peak=    3.106 closest distance to " O   HOH Z 425 " =    1.283
peak=    3.104 closest distance to " C   ALA A 299 " =    0.928
peak=    3.098 closest distance to " O   HOH Z 193 " =    1.607
peak=    3.095 closest distance to " CB  TYR A 116 " =    0.854
peak=    3.079 closest distance to " CB  LEU A  96 " =    1.262
peak=    3.076 closest distance to " CA  ARG A 102 " =    1.133
peak=    3.073 closest distance to " CB  ALA A   1 " =    4.872
peak=    3.053 closest distance to " CA  ALA A 233 " =    1.505
peak=    3.036 closest distance to " O   ASP A 124 " =    1.763
peak=    3.031 closest distance to " N   ASN A 127 " =    1.272
peak=    3.018 closest distance to " O   HOH Z 357 " =    2.498
peak=    3.017 closest distance to " O   HOH Z 124 " =    2.246
peak=    3.008 closest distance to " O   HOH Z  94 " =    2.335

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 218         
Filter by distance & map next to the model:
   mapped sites are within: 0.814 - 5.619
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 217 from: 218
   mapped sites are within: 0.814 - 5.619

peak=   -5.416 closest distance to " CG2 VAL A 230 " =    0.814
peak=   -4.912 closest distance to " SG  CYS A 254 " =    3.366
peak=   -4.567 closest distance to " CD  GLN A  58 " =    1.060
peak=   -4.540 closest distance to " O   HOH Z 266 " =    5.246
peak=   -4.496 closest distance to " CD  ARG A 156 " =    2.038
peak=   -4.432 closest distance to " CB  PRO A 243 " =    2.650
peak=   -4.330 closest distance to " O   HOH Z 196 " =    2.068
peak=   -4.175 closest distance to " OG BSER A 134 " =    1.267
peak=   -4.163 closest distance to " OE1 GLN A 223 " =    2.184
peak=   -4.140 closest distance to " CG2BVAL A  41 " =    2.728
peak=   -4.079 closest distance to " CB  PHE A 192 " =    2.017
peak=   -4.072 closest distance to " C   HIS A 108 " =    1.206
peak=   -4.071 closest distance to " OXT GLY A 302 " =    2.805
peak=   -4.060 closest distance to " O   HOH Z 166 " =    1.839
peak=   -4.034 closest distance to " OG  SER A  97 " =    2.293
peak=   -3.982 closest distance to " CZ3 TRP A 179 " =    1.235
peak=   -3.980 closest distance to " O   HOH Z 231 " =    2.242
peak=   -3.956 closest distance to " CB  ALA A 161 " =    2.474
peak=   -3.938 closest distance to " CA  ASP A 298 " =    1.060
peak=   -3.922 closest distance to " CG1 VAL A 250 " =    2.783
peak=   -3.897 closest distance to " CA  VAL A  67 " =    2.933
peak=   -3.895 closest distance to " O   PRO A 163 " =    2.192
peak=   -3.828 closest distance to " CB  ALA A 248 " =    2.296
peak=   -3.827 closest distance to " NE2 GLN A  88 " =    1.891
peak=   -3.825 closest distance to " ND2 ASN A 187 " =    1.574
peak=   -3.809 closest distance to " O   HOH Z 114 " =    3.142
peak=   -3.803 closest distance to " CD1 LEU A 101 " =    2.366
peak=   -3.793 closest distance to " O   HOH Z 283 " =    2.238
peak=   -3.782 closest distance to " O   HOH Z  37 " =    1.899
peak=   -3.767 closest distance to " CE2 TYR A  30 " =    2.712
peak=   -3.755 closest distance to " O   HOH Z 394 " =    1.565
peak=   -3.740 closest distance to " O   HOH Z 290 " =    1.233
peak=   -3.739 closest distance to " CB  ASP A 171 " =    2.266
peak=   -3.713 closest distance to " O   HOH Z 351 " =    1.536
peak=   -3.682 closest distance to " CE3 TRP A 150 " =    2.206
peak=   -3.679 closest distance to " CZ  TYR A 169 " =    1.763
peak=   -3.679 closest distance to " CB  ALA A 291 " =    2.282
peak=   -3.669 closest distance to " NH2AARG A 275 " =    5.081
peak=   -3.668 closest distance to " CB  ASP A 132 " =    2.330
peak=   -3.643 closest distance to " CG1 VAL A 112 " =    2.703
peak=   -3.637 closest distance to " CG1 VAL A 296 " =    1.152
peak=   -3.632 closest distance to " O   HOH Z 166 " =    1.509
peak=   -3.625 closest distance to " CD  ARG A 139 " =    1.653
peak=   -3.611 closest distance to " CD  LYS A 289 " =    2.456
peak=   -3.604 closest distance to " O   HOH Z  52 " =    1.572
peak=   -3.603 closest distance to " O   SER A 271 " =    2.058
peak=   -3.601 closest distance to " ND2 ASN A  45 " =    1.179
peak=   -3.601 closest distance to " O   VAL A  67 " =    2.208
peak=   -3.598 closest distance to " OD1 ASN A 148 " =    1.469
peak=   -3.595 closest distance to " CD2 TYR A 293 " =    2.005
peak=   -3.588 closest distance to " CB  ALA A 248 " =    2.147
peak=   -3.583 closest distance to " CB  PRO A 163 " =    2.504
peak=   -3.579 closest distance to " CG1 VAL A 112 " =    2.583
peak=   -3.573 closest distance to " CG2 ILE A 263 " =    2.318
peak=   -3.568 closest distance to " O   ARG A  24 " =    2.056
peak=   -3.563 closest distance to " CD1 PHE A  59 " =    2.009
peak=   -3.557 closest distance to " O   HOH Z  13 " =    1.706
peak=   -3.557 closest distance to " O   HOH Z  44 " =    2.189
peak=   -3.555 closest distance to " O   HOH Z 185 " =    2.557
peak=   -3.548 closest distance to " CG1 VAL A 112 " =    2.877
peak=   -3.542 closest distance to " N   ALA A  43 " =    2.630
peak=   -3.534 closest distance to " O   HOH Z 113 " =    2.424
peak=   -3.533 closest distance to " C   ILE A 239 " =    2.101
peak=   -3.532 closest distance to " O   HOH Z 389 " =    1.884
peak=   -3.528 closest distance to " O   HOH Z 435 " =    2.748
peak=   -3.522 closest distance to " O   PRO A 198 " =    1.254
peak=   -3.515 closest distance to " O   HOH Z  11 " =    1.871
peak=   -3.509 closest distance to " O   HOH Z 211 " =    1.640
peak=   -3.506 closest distance to " O   HOH Z 177 " =    1.743
peak=   -3.496 closest distance to " O   SER A 210 " =    1.810
peak=   -3.494 closest distance to " ND2 ASN A  45 " =    1.862
peak=   -3.492 closest distance to " N   ALA A 226 " =    2.039
peak=   -3.488 closest distance to " NE2 GLN A 194 " =    1.842
peak=   -3.487 closest distance to " N   SER A 276 " =    1.406
peak=   -3.477 closest distance to " ND2 ASN A  45 " =    1.353
peak=   -3.473 closest distance to " O   VAL A 189 " =    2.684
peak=   -3.472 closest distance to " CG  ASP A 231 " =    0.818
peak=   -3.468 closest distance to " CG1 VAL A 230 " =    1.912
peak=   -3.465 closest distance to " CA  GLY A 241 " =    3.089
peak=   -3.457 closest distance to " CD2 LEU A 167 " =    1.796
peak=   -3.455 closest distance to " O   HOH Z  88 " =    4.454
peak=   -3.454 closest distance to " CE BMET A  47 " =    2.001
peak=   -3.453 closest distance to " N   THR A 235 " =    1.350
peak=   -3.453 closest distance to " CG2 ILE A  49 " =    2.726
peak=   -3.452 closest distance to " O   HOH Z   6 " =    1.661
peak=   -3.448 closest distance to " NE2 GLN A 103 " =    1.751
peak=   -3.440 closest distance to " O   HOH Z 407 " =    2.953
peak=   -3.433 closest distance to " O   HOH Z 198 " =    2.330
peak=   -3.428 closest distance to " C   LEU A 143 " =    1.020
peak=   -3.423 closest distance to " O   PHE A 218 " =    1.641
peak=   -3.421 closest distance to " N   ASP A 171 " =    2.244
peak=   -3.409 closest distance to " CG2 VAL A 296 " =    1.336
peak=   -3.401 closest distance to " CG  ARG A 269 " =    2.327
peak=   -3.400 closest distance to " O   HOH Z 193 " =    1.718
peak=   -3.400 closest distance to " CE  MET A 105 " =    2.224
peak=   -3.399 closest distance to " N   ALA A 248 " =    1.916
peak=   -3.394 closest distance to " O   HOH Z  10 " =    1.529
peak=   -3.374 closest distance to " NE2 GLN A  88 " =    1.083
peak=   -3.363 closest distance to " O   ILE A 234 " =    1.187
peak=   -3.363 closest distance to " CD  PRO A 213 " =    2.164
peak=   -3.363 closest distance to " CG2 VAL A 189 " =    2.050
peak=   -3.362 closest distance to " CD2 TYR A 247 " =    2.268
peak=   -3.361 closest distance to " CD2 LEU A 300 " =    2.599
peak=   -3.360 closest distance to " CB  ALA A  43 " =    2.548
peak=   -3.355 closest distance to " O   HOH Z  38 " =    1.669
peak=   -3.353 closest distance to " O   HOH Z 123 " =    2.464
peak=   -3.352 closest distance to " CG  GLU A 277 " =    1.148
peak=   -3.350 closest distance to " CA  GLY A 133 " =    2.332
peak=   -3.349 closest distance to " C   MET A 188 " =    1.447
peak=   -3.345 closest distance to " O   HOH Z 234 " =    4.179
peak=   -3.343 closest distance to " NH2 ARG A  79 " =    2.009
peak=   -3.338 closest distance to " N   ALA A 248 " =    2.339
peak=   -3.334 closest distance to " NE  ARG A  66 " =    4.163
peak=   -3.330 closest distance to " OH  TYR A 247 " =    2.075
peak=   -3.325 closest distance to " O   HOH Z 350 " =    2.111
peak=   -3.324 closest distance to " ND2 ASN A  69 " =    1.852
peak=   -3.321 closest distance to " CG  TRP A 266 " =    1.876
peak=   -3.314 closest distance to " O   HOH Z 253 " =    3.955
peak=   -3.312 closest distance to " CD1 ILE A 199 " =    2.448
peak=   -3.305 closest distance to " O   GLY A 196 " =    1.190
peak=   -3.302 closest distance to " O   HOH Z  19 " =    2.275
peak=   -3.297 closest distance to " O   HOH Z 264 " =    1.757
peak=   -3.296 closest distance to " O   HOH Z 426 " =    1.688
peak=   -3.295 closest distance to " O   HOH Z 285 " =    1.648
peak=   -3.294 closest distance to " OG ASER A 134 " =    1.299
peak=   -3.292 closest distance to " O   HOH Z 136 " =    2.403
peak=   -3.287 closest distance to " OD1 ASN A 249 " =    2.274
peak=   -3.285 closest distance to " O   HOH Z  71 " =    1.683
peak=   -3.285 closest distance to " CB  VAL A 230 " =    1.014
peak=   -3.282 closest distance to " OD2 ASP A  50 " =    2.226
peak=   -3.281 closest distance to " O   HOH Z 139 " =    3.144
peak=   -3.281 closest distance to " N   PHE A  59 " =    2.225
peak=   -3.280 closest distance to " O   HOH Z 252 " =    3.900
peak=   -3.274 closest distance to " O   PRO A 198 " =    1.374
peak=   -3.267 closest distance to " CB  ALA A 291 " =    2.209
peak=   -3.260 closest distance to " N   MET A 105 " =    2.618
peak=   -3.259 closest distance to " CB  TRP A  85 " =    2.602
peak=   -3.256 closest distance to " C   SER A 206 " =    1.492
peak=   -3.253 closest distance to " CB  LEU A  83 " =    2.343
peak=   -3.253 closest distance to " O   HOH Z 165 " =    1.914
peak=   -3.245 closest distance to " CG  GLU A  53 " =    1.641
peak=   -3.244 closest distance to " O   HOH Z 102 " =    1.581
peak=   -3.243 closest distance to " O   HOH Z 392 " =    1.880
peak=   -3.242 closest distance to " O   HOH Z 311 " =    3.743
peak=   -3.241 closest distance to " O   ASN A  45 " =    1.913
peak=   -3.239 closest distance to " CZ2 TRP A 274 " =    1.063
peak=   -3.237 closest distance to " O   ALA A  51 " =    1.354
peak=   -3.235 closest distance to " OG  SER A 206 " =    1.679
peak=   -3.235 closest distance to " C   ALA A 158 " =    1.287
peak=   -3.234 closest distance to " OD1 ASN A 187 " =    1.690
peak=   -3.233 closest distance to " CG1 VAL A  67 " =    3.034
peak=   -3.232 closest distance to " O   HOH Z 222 " =    1.571
peak=   -3.230 closest distance to " C   ASN A 187 " =    1.916
peak=   -3.229 closest distance to " O   HOH Z 295 " =    1.499
peak=   -3.228 closest distance to " O   ALA A 161 " =    1.768
peak=   -3.225 closest distance to " CD  GLN A 223 " =    0.845
peak=   -3.223 closest distance to " O   HOH Z 131 " =    4.022
peak=   -3.221 closest distance to " O   HOH Z 191 " =    5.619
peak=   -3.220 closest distance to " CA  SER A  62 " =    2.607
peak=   -3.214 closest distance to " N   GLN A  58 " =    1.631
peak=   -3.212 closest distance to " OD1 ASN A 301 " =    2.007
peak=   -3.212 closest distance to " ND2 ASN A  39 " =    1.210
peak=   -3.211 closest distance to " OG  SER A  62 " =    1.697
peak=   -3.206 closest distance to " O   HOH Z 369 " =    2.299
peak=   -3.205 closest distance to " CD1 ILE A 151 " =    2.390
peak=   -3.203 closest distance to " O   HOH Z 348 " =    2.322
peak=   -3.201 closest distance to " CE2 PHE A 218 " =    2.578
peak=   -3.196 closest distance to " N   THR A  52 " =    1.710
peak=   -3.193 closest distance to " O   HOH Z 313 " =    1.154
peak=   -3.192 closest distance to " O   HOH Z 216 " =    1.690
peak=   -3.190 closest distance to " CB  ASN A  39 " =    2.301
peak=   -3.184 closest distance to " O   HOH Z 353 " =    2.121
peak=   -3.172 closest distance to " O   ASP A 171 " =    1.989
peak=   -3.172 closest distance to " CD  ARG A 195 " =    5.185
peak=   -3.165 closest distance to " O   HOH Z 380 " =    1.535
peak=   -3.165 closest distance to " O   HOH Z 116 " =    1.461
peak=   -3.164 closest distance to " O   ALA A  10 " =    1.757
peak=   -3.160 closest distance to " O   HOH Z 174 " =    2.445
peak=   -3.159 closest distance to " N   SER A   3 " =    2.113
peak=   -3.159 closest distance to " ND2 ASN A  60 " =    1.315
peak=   -3.156 closest distance to " O   GLN A 240 " =    2.135
peak=   -3.151 closest distance to " CB  ASN A  69 " =    1.221
peak=   -3.151 closest distance to " O   HOH Z 339 " =    1.789
peak=   -3.146 closest distance to " CE1 HIS A  81 " =    1.459
peak=   -3.146 closest distance to " CG1 VAL A 197 " =    2.172
peak=   -3.142 closest distance to " CA  GLY A 133 " =    1.953
peak=   -3.140 closest distance to " O   GLY A  75 " =    1.841
peak=   -3.139 closest distance to " O   HOH Z 422 " =    1.621
peak=   -3.135 closest distance to " NH2 ARG A  79 " =    1.618
peak=   -3.133 closest distance to " O   HOH Z 313 " =    1.878
peak=   -3.127 closest distance to " O   HOH Z 292 " =    1.934
peak=   -3.125 closest distance to " O   HOH Z 431 " =    1.901
peak=   -3.122 closest distance to " O   HOH Z  60 " =    1.956
peak=   -3.120 closest distance to " CD2 PHE A  61 " =    2.514
peak=   -3.118 closest distance to " O   ALA A   1 " =    1.720
peak=   -3.117 closest distance to " CD1 LEU A 228 " =    2.185
peak=   -3.103 closest distance to " O   HOH Z 177 " =    1.397
peak=   -3.101 closest distance to " O   ASN A 301 " =    1.446
peak=   -3.093 closest distance to " OD1 ASN A  39 " =    2.173
peak=   -3.092 closest distance to " OG BSER A 134 " =    1.877
peak=   -3.091 closest distance to " O   MET A  40 " =    2.807
peak=   -3.090 closest distance to " CB  ASP A 132 " =    2.392
peak=   -3.085 closest distance to " O   HOH Z 174 " =    4.153
peak=   -3.084 closest distance to " O   HOH Z 251 " =    5.230
peak=   -3.076 closest distance to " CG  LEU A 228 " =    1.046
peak=   -3.074 closest distance to " O   HOH Z 241 " =    1.587
peak=   -3.070 closest distance to " CG2 THR A 178 " =    2.235
peak=   -3.063 closest distance to " N   GLY A  23 " =    2.344
peak=   -3.063 closest distance to " NH2 ARG A  66 " =    1.857
peak=   -3.062 closest distance to " CE1 TYR A 247 " =    2.635
peak=   -3.057 closest distance to " CB  GLN A  11 " =    1.900
peak=   -3.051 closest distance to " CG  PHE A 283 " =    2.671
peak=   -3.049 closest distance to " CG  PRO A 163 " =    2.646
peak=   -3.042 closest distance to " O   VAL A 174 " =    2.108
peak=   -3.030 closest distance to " O   HOH Z 236 " =    1.474
peak=   -3.030 closest distance to " OD1 ASN A 173 " =    1.451
peak=   -3.007 closest distance to " C   ASP A 270 " =    1.252

================= 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    :  0.4471 0.4307   6.243411e+00   6.215877e+00
   1_bss:  0.4393 0.4198   6.236458e+00   6.203691e+00
   1_xyz:  0.3297 0.3471   6.039668e+00   6.070752e+00
   1_adp:  0.2709 0.3087   5.879241e+00   5.976838e+00
   1_occ:  0.2703 0.3094   5.878245e+00   5.978038e+00
   2_bss:  0.2655 0.3052   5.878742e+00   5.975284e+00
   2_xyz:  0.1843 0.2213   5.550503e+00   5.709726e+00
   2_adp:  0.1684 0.2056   5.474067e+00   5.640162e+00
   2_occ:  0.1682 0.2057   5.473753e+00   5.640851e+00
   3_bss:  0.1678 0.2056   5.474311e+00   5.640142e+00
   3_xyz:  0.1278 0.1664   5.238735e+00   5.448138e+00
   3_adp:  0.1204 0.1624   5.198808e+00   5.423502e+00
   3_occ:  0.1203 0.1624   5.198256e+00   5.423097e+00
   4_bss:  0.1205 0.1624   5.199145e+00   5.422712e+00
   4_xyz:  0.1151 0.1593   5.170472e+00   5.404017e+00
   4_adp:  0.1148 0.1586   5.167283e+00   5.400999e+00
   4_occ:  0.1146 0.1586   5.166574e+00   5.400913e+00
   5_bss:  0.1146 0.1586   5.166494e+00   5.400870e+00
   5_xyz:  0.1110 0.1571   5.146715e+00   5.392908e+00
   5_adp:  0.1102 0.1579   5.146816e+00   5.398088e+00
   5_occ:  0.1102 0.1579   5.146698e+00   5.398088e+00
   5_bss:  0.1102 0.1578   5.146691e+00   5.398113e+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:  0.331  20.000   6.889   9.480   9.442   0.000   0.000   0.000
   1_xyz:  0.331  20.000   6.889   9.480   9.442   0.000   0.000   0.000
   1_adp:  0.331  20.000   6.889   9.480   9.442   0.000   0.000   0.000
   1_occ:  0.331  20.000   6.889   9.480   9.442   0.000   0.000   0.000
   2_bss:  0.327  44.646   3.377   5.539   5.697   0.000   0.000   0.000
   2_xyz:  0.327  44.646   3.377   5.539   5.697   0.000   0.000   0.000
   2_adp:  0.327  44.646   3.377   5.539   5.697   0.000   0.000   0.000
   2_occ:  0.327  44.646   3.377   5.539   5.697   0.000   0.000   0.000
   3_bss:  0.317  55.030   2.567   3.958   4.543   0.000   0.000   0.000
   3_xyz:  0.317  55.030   2.567   3.958   4.543   0.000   0.000   0.000
   3_adp:  0.317  55.030   2.567   3.958   4.543   0.000   0.000   0.000
   3_occ:  0.317  55.030   2.567   3.958   4.543   0.000   0.000   0.000
   4_bss:  0.328  55.030   2.517   3.492   4.363   0.000   0.000   0.000
   4_xyz:  0.328  55.030   2.517   3.492   4.363   0.000   0.000   0.000
   4_adp:  0.328  55.030   2.517   3.492   4.363   0.000   0.000   0.000
   4_occ:  0.328  55.030   2.517   3.492   4.363   0.000   0.000   0.000
   5_bss:  0.328  55.030   2.582   3.422   4.397   0.000   0.000   0.000
   5_xyz:  0.328  55.030   2.582   3.422   4.397   0.000   0.000   0.000
   5_adp:  0.328  55.030   2.582   3.422   4.397   0.000   0.000   0.000
   5_occ:  0.328  55.030   2.582   3.422   4.397   0.000   0.000   0.000
   5_bss:  0.324  56.863  -0.863  -0.082   0.945   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  48.156 0.5451  0.6092    53683.568
   1_bss:  47.287 0.5546  0.8032    51160.982
   1_xyz:  37.541 0.6709  0.9389    32857.928
   1_adp:  31.634 0.7399  1.0218    24950.114
   1_occ:  31.689 0.7393  1.0204    25034.770
   2_bss:  31.509 0.7413  0.8964    24825.080
   2_xyz:  22.088 0.8407  0.9830    12763.031
   2_adp:  19.995 0.8619  0.9972    10998.392
   2_occ:  20.007 0.8618  0.9971    11005.191
   3_bss:  19.944 0.8625  0.9559    10987.525
   3_xyz:  15.507 0.9021  0.9779     7200.846
   3_adp:  14.929 0.9072  0.9773     6867.104
   3_occ:  14.918 0.9073  0.9774     6863.397
   4_bss:  14.919 0.9073  0.9693     6865.271
   4_xyz:  14.385 0.9121  0.9708     6596.234
   4_adp:  14.271 0.9132  0.9678     6552.480
   4_occ:  14.265 0.9133  0.9677     6551.375
   5_bss:  14.262 0.9133  0.9681     6551.396
   5_xyz:  14.120 0.9143  0.9690     6442.089
   5_adp:  14.201 0.9137  0.9643     6479.605
   5_occ:  14.199 0.9137  0.9643     6479.805
   5_bss:  14.201 0.9137  0.9692     6478.939
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.093   5.4029e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.093   5.4029e+01
   1_xyz:   1.591  0.012  0.105 17.790  0.006  4.113   1.2582e-01
   1_adp:   1.591  0.012  0.105 17.790  0.006  4.113   1.2582e-01
   1_occ:   1.591  0.012  0.105 17.790  0.006  4.113   1.2582e-01
   2_bss:   1.591  0.012  0.105 17.790  0.006  4.113   1.2582e-01
   2_xyz:   1.021  0.007  0.071 16.065  0.004  4.127   6.3771e-02
   2_adp:   1.021  0.007  0.071 16.065  0.004  4.127   6.3771e-02
   2_occ:   1.021  0.007  0.071 16.065  0.004  4.127   6.3771e-02
   3_bss:   1.021  0.007  0.071 16.065  0.004  4.127   6.3771e-02
   3_xyz:   1.105  0.009  0.087 15.852  0.004  4.114   7.4094e-02
   3_adp:   1.105  0.009  0.087 15.852  0.004  4.114   7.4094e-02
   3_occ:   1.105  0.009  0.087 15.852  0.004  4.114   7.4094e-02
   4_bss:   1.105  0.009  0.087 15.852  0.004  4.114   7.4094e-02
   4_xyz:   1.058  0.009  0.086 15.541  0.004  4.119   6.8424e-02
   4_adp:   1.058  0.009  0.086 15.541  0.004  4.119   6.8424e-02
   4_occ:   1.058  0.009  0.086 15.541  0.004  4.119   6.8424e-02
   5_bss:   1.058  0.009  0.086 15.541  0.004  4.119   6.8424e-02
   5_xyz:   1.143  0.010  0.093 15.634  0.004  4.122   7.9079e-02
   5_adp:   1.143  0.010  0.093 15.634  0.004  4.122   7.9079e-02
   5_occ:   1.143  0.010  0.093 15.634  0.004  4.122   7.9079e-02
   5_bss:   1.143  0.010  0.093 15.634  0.004  4.122   7.9079e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0051e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0051e+00
   1_xyz:  14.285  0.147  0.468 86.440  0.037  2.318   9.5708e-02
   1_adp:  14.285  0.147  0.468 86.440  0.037  2.318   9.5708e-02
   1_occ:  14.285  0.147  0.468 86.440  0.037  2.318   9.5708e-02
   2_bss:  14.285  0.147  0.468 86.440  0.037  2.318   9.5708e-02
   2_xyz:   6.503  0.078  0.259 83.642  0.029  2.187   4.9888e-02
   2_adp:   6.503  0.078  0.259 83.642  0.029  2.187   4.9888e-02
   2_occ:   6.503  0.078  0.259 83.642  0.029  2.187   4.9888e-02
   3_bss:   6.503  0.078  0.259 83.642  0.029  2.187   4.9888e-02
   3_xyz:   7.475  0.052  0.506 83.451  0.041  2.296   5.8367e-02
   3_adp:   7.475  0.052  0.506 83.451  0.041  2.296   5.8367e-02
   3_occ:   7.475  0.052  0.506 83.451  0.041  2.296   5.8367e-02
   4_bss:   7.475  0.052  0.506 83.451  0.041  2.296   5.8367e-02
   4_xyz:   7.530  0.052  0.485 82.119  0.042  2.296   4.8126e-02
   4_adp:   7.530  0.052  0.485 82.119  0.042  2.296   4.8126e-02
   4_occ:   7.530  0.052  0.485 82.119  0.042  2.296   4.8126e-02
   5_bss:   7.530  0.052  0.485 82.119  0.042  2.296   4.8126e-02
   5_xyz:   7.880  0.055  0.579 82.021  0.039  2.284   5.6439e-02
   5_adp:   7.880  0.055  0.579 82.021  0.039  2.284   5.6439e-02
   5_occ:   7.880  0.055  0.579 82.021  0.039  2.284   5.6439e-02
   5_bss:   7.880  0.055  0.579 82.021  0.039  2.284   5.6439e-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:  78.77   0.00  11.16  60.28   0.00   8.17  78.77   0.00  27.39
   1_occ:  78.77   0.00  11.16  60.28   0.00   8.17  78.77   0.00  27.39
   2_bss:  78.77   0.00  11.16  60.28   0.00   8.17  78.77   0.00  27.39
   2_xyz:  78.77   0.00  11.16  60.28   0.00   8.17  78.77   0.00  27.39
   2_adp:  75.59   0.00  11.31  68.37   0.00   7.60  75.59   1.15  31.52
   2_occ:  75.59   0.00  11.31  68.37   0.00   7.60  75.59   1.15  31.52
   3_bss:  75.59   0.00  11.31  68.37   0.00   7.60  75.59   1.15  31.52
   3_xyz:  75.59   0.00  11.31  68.37   0.00   7.60  75.59   1.15  31.52
   3_adp:  77.08   0.00  11.88  77.08   0.00   7.61  72.49   0.00  35.12
   3_occ:  77.08   0.00  11.88  77.08   0.00   7.61  72.49   0.00  35.12
   4_bss:  77.08   0.00  11.88  77.08   0.00   7.61  72.49   0.00  35.12
   4_xyz:  77.08   0.00  11.88  77.08   0.00   7.61  72.49   0.00  35.12
   4_adp:  79.56   0.00  11.64  79.56   0.00   7.50  70.46   0.49  34.17
   4_occ:  79.56   0.00  11.64  79.56   0.00   7.50  70.46   0.49  34.17
   5_bss:  79.56   0.00  11.64  79.56   0.00   7.50  70.46   0.49  34.17
   5_xyz:  79.56   0.00  11.64  79.56   0.00   7.50  70.46   0.49  34.17
   5_adp:  82.87   0.00  11.68  82.87   0.00   7.47  71.80   0.47  34.61
   5_occ:  82.87   0.00  11.68  82.87   0.00   7.47  71.80   0.47  34.61
   5_bss:  86.48   3.61  15.29  86.48   3.61  11.08  75.41   4.08  38.22
------------------------------------------------------------------------
 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:    1.229    0.023    0.408
   1_adp:    1.229    0.023    0.408
   1_occ:    1.229    0.023    0.408
   2_bss:    1.229    0.023    0.408
   2_xyz:    1.635    0.037    0.523
   2_adp:    1.635    0.037    0.523
   2_occ:    1.635    0.037    0.523
   3_bss:    1.635    0.037    0.523
   3_xyz:    1.523    0.057    0.577
   3_adp:    1.523    0.057    0.577
   3_occ:    1.523    0.057    0.577
   4_bss:    1.523    0.057    0.577
   4_xyz:    1.618    0.044    0.592
   4_adp:    1.618    0.044    0.592
   4_occ:    1.618    0.044    0.592
   5_bss:    1.618    0.044    0.592
   5_xyz:    1.617    0.061    0.605
   5_adp:    1.617    0.061    0.605
   5_occ:    1.617    0.061    0.605
   5_bss:    1.617    0.061    0.605
------------------------------------------------------------------------

CPU time actual refinement: 328.13


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_568/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_568/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_568/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_568/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_568/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 327.99 
  Macro-tasks:
    bulk solvent and scale       = 47.16  
    individual site refinement   = 125.06 
    weights calculation          = 32.07  
    collect and process          = 6.69   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 211.07 
  Micro-tasks:
    mask                            = 1.67   
    f_calc                          = 99.27  
    alpha_beta                      = 8.27   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 103.88 
    fmodel                         = 7.69   
    r_factors                      = 0.18   
    phase_errors                   = 11.61  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 234.03 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.684 micro seconds
Total CPU time: 5.69 minutes
from_scatterers_fft:    641 calls, 98.82 s
gradients_fft:          585 calls, 93.16 s

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

# Date 2008-01-16 Time 01:52:40 PST -0800 (1200477160.75 s)
Start R-work = 0.4471, R-free = 0.4307 (no bulk solvent and anisotropic scale)
Final R-work = 0.1275, R-free = 0.1736 (no bulk solvent and anisotropic scale)

Start R-work = 0.4393, R-free = 0.4198
Final R-work = 0.1102, R-free = 0.1578