# Date 2008-01-16 Time 01:15:10 PST -0800 (1200474910.32 s)
#phil __OFF__

Command line arguments: "../335.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 21744
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 335

-------------------------------------------------------------------------------
  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: (69.1963, 47.6339, 86.39, 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: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.6339, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.903 1.9707
Completeness in resolution range: 0.94505
Completeness with d_max=infinity: 0.942141

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9030
                             d_min =   1.9707

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: (69.1963, 47.6339, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.903 1.9707
Completeness in resolution range: 0.94505
Completeness with d_max=infinity: 0.942141

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9034 -  4.2167 [2186/2214]  1964   222  10.2%
  bin  2:  4.2167 -  3.3595 [2084/2107]  1877   207   9.9%
  bin  3:  3.3595 -  2.9386 [2057/2082]  1851   206  10.0%
  bin  4:  2.9386 -  2.6716 [2054/2070]  1848   206  10.0%
  bin  5:  2.6716 -  2.4810 [2022/2061]  1817   205  10.1%
  bin  6:  2.4810 -  2.3353 [2031/2063]  1834   197   9.7%
  bin  7:  2.3353 -  2.2188 [2002/2039]  1800   202  10.1%
  bin  8:  2.2188 -  2.1225 [2007/2049]  1809   198   9.9%
  bin  9:  2.1225 -  2.0410 [1989/2028]  1791   198  10.0%
  bin 10:  2.0410 -  1.9707 [1157/2015]  1039   118  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_335/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: 0.15 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:
        1.59 -     2.25: 13
        2.25 -     2.91: 1462
        2.91 -     3.58: 4493
        3.58 -     4.24: 9178
        4.24 -     4.90: 13157
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.590 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.655 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.764 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  70 " - " O   HOH Z 296 "  1.898 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28298 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_335/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_335/model_refine_001.geo

CPU time processing inputs: 9.06


============================ 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 = 69.19625 47.63395 86.39 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: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4718   r_free= 0.4572   ksol= 0.00   Bsol= 0.00   scale= 0.800    |
|                                                                             |
| 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:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.272891                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9034 -  4.7030 0.99   1411  158 0.3816 0.3825      6.5629      6.6017|
|  2:  4.7030 -  3.7525 0.99   1363  151 0.3855 0.3872      6.7534      6.7832|
|  3:  3.7525 -  3.2840 0.99   1340  148 0.4294 0.3957       6.653      6.6575|
|  4:  3.2840 -  2.9864 0.99   1317  143 0.4569 0.4080      6.4987      6.4209|
|  5:  2.9864 -  2.7738 0.98   1321  148 0.5090 0.4968       6.366      6.3936|
|  6:  2.7738 -  2.6112 0.99   1302  148 0.4916 0.5145      6.2721      6.1733|
|  7:  2.6112 -  2.4810 0.99   1303  150 0.4952 0.4831      6.2348      6.1745|
|  8:  2.4810 -  2.3735 0.99   1319  136 0.5194 0.4638      6.1779      6.1409|
|  9:  2.3735 -  2.2824 0.99   1297  148 0.5230 0.5612       6.109      6.1886|
| 10:  2.2824 -  2.2039 0.98   1290  139 0.5279 0.4877      6.1162      6.0899|
| 11:  2.2039 -  2.1352 0.98   1274  148 0.5383 0.4908      6.0364      6.0205|
| 12:  2.1352 -  2.0743 1.00   1295  147 0.5219 0.5232      5.9591      5.9722|
| 13:  2.0743 -  2.0199 0.95   1264  131 0.5324 0.5348      5.8849      5.8405|
| 14:  2.0199 -  1.9707 0.42    534   64 0.5483 0.4943      5.8888      5.7356|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9034 -  4.7030  1411   158  0.68  35.92   0.81     0.69      74881.44|
|  2:  4.7030 -  3.7525  1363   151  0.71  34.58   0.90     0.76     100384.79|
|  3:  3.7525 -  3.2840  1340   148  0.63  41.29   0.85     0.73     102240.65|
|  4:  3.2840 -  2.9864  1317   143  0.57  46.38   0.80     0.65      84550.79|
|  5:  2.9864 -  2.7738  1321   148  0.47  54.67   0.73     0.55      73920.49|
|  6:  2.7738 -  2.6112  1302   148  0.44  56.73   0.73     0.50      66284.17|
|  7:  2.6112 -  2.4810  1303   150  0.41  59.35   0.76     0.46      62312.73|
|  8:  2.4810 -  2.3735  1319   136  0.42  58.54   0.73     0.49      53962.97|
|  9:  2.3735 -  2.2824  1297   148  0.41  59.40   0.72     0.49      49758.59|
| 10:  2.2824 -  2.2039  1290   139  0.42  58.79   0.74     0.49      45218.61|
| 11:  2.2039 -  2.1352  1274   148  0.37  62.01   0.73     0.46      44441.07|
| 12:  2.1352 -  2.0743  1295   147  0.34  64.47   0.76     0.44      42666.39|
| 13:  2.0743 -  2.0199  1264   131  0.32  66.37   0.72     0.40      37121.73|
| 14:  2.0199 -  1.9707   534    64  0.34  64.75   0.74     0.36      27944.23|
|alpha:            min =        0.36 max =            0.76 mean =         0.54|
|beta:             min =    27944.23 max =       102240.65 mean =     63740.42|
|figures of merit: min =        0.00 max =            1.00 mean =         0.47|
|phase err.(work): min =        0.00 max =           90.00 mean =        53.81|
|phase err.(test): min =        0.00 max =           89.86 mean =        53.96|
|-----------------------------------------------------------------------------|

============================== 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 = 11.896506             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.887   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.994739              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.141   (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 |  1.019 -  1.407:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.407 -  1.795:        9 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.795 -  2.183:       93 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.183 -  2.571:      527 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.571 -  2.959:     1319 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.959 -  3.348:     2455 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.348 -  3.736:     3947 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.736 -  4.124:     5197 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.124 -  4.512:     6749 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.512 -  4.900:     8071 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.671 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.019 |       2.062 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.838)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.838)------------------------------------------|
|    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: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4776   r_free= 0.4653   ksol= 0.00   Bsol= 0.00   scale= 0.770    |
|                                                                             |
| 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:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.274858                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4640   r_free= 0.4512   ksol= 0.34   Bsol= 20.00   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.32,10.74,7.65,0.00,0.00,0.00); trace/3= 8.57                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.264544                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.391811             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.255   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.998296              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.136   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4640      final r-factor (work) = 0.3697          |
| start r-factor (free) = 0.4512      final r-factor (free) = 0.3899          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 89.4173 = 11.39 * 0.50 * 6.2757 + 1.00 * 53.6713                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.2440 = 11.39 * 0.50 * 6.1623 + 1.00 * 0.1440                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3697      final r-factor (work) = 0.3181          |
| start r-factor (free) = 0.3899      final r-factor (free) = 0.3604          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1662 = 1.00 * 1.00 * 6.1623 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0554 = 1.00 * 1.00 * 6.0500 + 1.00 * 0.0157                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.838)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.68   12.58    None  None   None       |
|    all(noH): 2823   0      0.00    77.68   12.58    None  None   None       |
|    Sol.    : 438    0      0.00    77.68   26.64    None  None   None       |
|    Mac.    : 2385   0      0.00    69.45   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:     0.000 -   7.768: 1247   |   5:    38.842 -  46.610:   59        |
|      1:     7.768 -  15.537:  761   |   6:    46.610 -  54.378:   33        |
|      2:    15.537 -  23.305:  379   |   7:    54.378 -  62.147:   22        |
|      3:    23.305 -  31.073:  200   |   8:    62.147 -  69.915:    8        |
|      4:    31.073 -  38.842:  111   |   9:    69.915 -  77.683:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3181 r_free = 0.3604             target_work(ml) = 6.021         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3177 r_free = 0.3604             target_work(ml) = 6.020         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3177   r_free= 0.3604   ksol= 0.34   Bsol= 20.00   scale= 1.099   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.32,10.74,7.65,0.00,0.00,0.00); trace/3= 8.57                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 6.020149                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3148   r_free= 0.3558   ksol= 0.32   Bsol= 34.94   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.80,6.52,4.62,0.00,0.00,0.00); trace/3= 4.98                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 6.021171                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.219005              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.124   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.417391              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.140  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3148      final r-factor (work) = 0.2373          |
| start r-factor (free) = 0.3558      final r-factor (free) = 0.2845          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.9053 = 4.22 * 0.50 * 6.0495 + 1.00 * 0.1440                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.4948 = 4.22 * 0.50 * 5.8894 + 1.00 * 0.0712                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2373      final r-factor (work) = 0.2189          |
| start r-factor (free) = 0.2845      final r-factor (free) = 0.2690          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4739 = 0.42 * 1.00 * 5.8894 + 1.00 * 0.0157                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4092 = 0.42 * 1.00 * 5.7454 + 1.00 * 0.0111                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.838)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    73.91   12.50    None  None   None       |
|    all(noH): 2823   0      0.00    73.91   12.50    None  None   None       |
|    Sol.    : 438    0      1.02    73.91   31.05    None  None   None       |
|    Mac.    : 2385   0      0.00    71.63   9.10     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 -   7.391: 1308   |   5:    36.955 -  44.346:  106        |
|      1:     7.391 -  14.782:  777   |   6:    44.346 -  51.737:   52        |
|      2:    14.782 -  22.173:  264   |   7:    51.737 -  59.128:   31        |
|      3:    22.173 -  29.564:  171   |   8:    59.128 -  66.519:    7        |
|      4:    29.564 -  36.955:   98   |   9:    66.519 -  73.910:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2189 r_free = 0.2690             target_work(ml) = 5.721         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2187 r_free = 0.2692             target_work(ml) = 5.721         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2187   r_free= 0.2692   ksol= 0.32   Bsol= 34.94   scale= 1.045   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.80,6.52,4.62,0.00,0.00,0.00); trace/3= 4.98                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.720830                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2173   r_free= 0.2678   ksol= 0.31   Bsol= 45.39   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.99,4.23,3.53,0.00,0.00,0.00); trace/3= 3.25                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.719884                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.018192              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.680  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.209165              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 120.464  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2173      final r-factor (work) = 0.1543          |
| start r-factor (free) = 0.2678      final r-factor (free) = 0.1930          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.6240 = 4.02 * 0.50 * 5.7502 + 1.00 * 0.0712                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.2841 = 4.02 * 0.50 * 5.5815 + 1.00 * 0.0704                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1543      final r-factor (work) = 0.1410          |
| start r-factor (free) = 0.1930      final r-factor (free) = 0.1773          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1784 = 0.21 * 1.00 * 5.5815 + 1.00 * 0.0110                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1296 = 0.21 * 1.00 * 5.3548 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.838)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.74   12.44    None  None   None       |
|    all(noH): 2823   0      0.00    74.74   12.44    None  None   None       |
|    Sol.    : 438    0      1.81    69.59   33.45    None  None   None       |
|    Mac.    : 2385   0      0.00    74.74   8.59     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 -   7.474: 1396   |   5:    37.369 -  44.842:  101        |
|      1:     7.474 -  14.948:  790   |   6:    44.842 -  52.316:   70        |
|      2:    14.948 -  22.421:  182   |   7:    52.316 -  59.790:   32        |
|      3:    22.421 -  29.895:  113   |   8:    59.790 -  67.264:   12        |
|      4:    29.895 -  37.369:  122   |   9:    67.264 -  74.737:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1410 r_free = 0.1773             target_work(ml) = 5.315         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1407 r_free = 0.1770             target_work(ml) = 5.313         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1407   r_free= 0.1770   ksol= 0.31   Bsol= 45.39   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.99,4.23,3.53,0.00,0.00,0.00); trace/3= 3.25                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.313452                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1402   r_free= 0.1765   ksol= 0.32   Bsol= 45.39   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.30,2.85,3.05,0.00,0.00,0.00); trace/3= 2.40                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.312444                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.377004              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.220  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.320328              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 118.677  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1402      final r-factor (work) = 0.1234          |
| start r-factor (free) = 0.1765      final r-factor (free) = 0.1634          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4400 = 2.38 * 0.50 * 5.3594 + 1.00 * 0.0704                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3098 = 2.38 * 0.50 * 5.2550 + 1.00 * 0.0642                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1234      final r-factor (work) = 0.1200          |
| start r-factor (free) = 0.1634      final r-factor (free) = 0.1614          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6940 = 0.32 * 1.00 * 5.2550 + 1.00 * 0.0107                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6765 = 0.32 * 1.00 * 5.2022 + 1.00 * 0.0100                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.838)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.86   12.61    None  None   None       |
|    all(noH): 2823   0      0.00    75.86   12.61    None  None   None       |
|    Sol.    : 438    0      1.38    69.92   34.71    None  None   None       |
|    Mac.    : 2385   0      0.00    75.86   8.55     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 -   7.586: 1427   |   5:    37.929 -  45.515:   99        |
|      1:     7.586 -  15.172:  763   |   6:    45.515 -  53.100:   81        |
|      2:    15.172 -  22.757:  178   |   7:    53.100 -  60.686:   30        |
|      3:    22.757 -  30.343:  114   |   8:    60.686 -  68.272:   19        |
|      4:    30.343 -  37.929:  106   |   9:    68.272 -  75.858:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1200 r_free = 0.1614             target_work(ml) = 5.196         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1199 r_free = 0.1615             target_work(ml) = 5.196         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1199   r_free= 0.1615   ksol= 0.32   Bsol= 45.39   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.30,2.85,3.05,0.00,0.00,0.00); trace/3= 2.40                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.195580                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1199   r_free= 0.1615   ksol= 0.32   Bsol= 46.55   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.30,2.60,3.06,0.00,0.00,0.00); trace/3= 2.32                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.195515                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.182659              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 138.470  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.606730              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 159.732  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1199      final r-factor (work) = 0.1151          |
| start r-factor (free) = 0.1615      final r-factor (free) = 0.1583          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7411 = 2.18 * 0.50 * 5.2019 + 1.00 * 0.0642                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7168 = 2.18 * 0.50 * 5.1785 + 1.00 * 0.0653                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1151      final r-factor (work) = 0.1139          |
| start r-factor (free) = 0.1583      final r-factor (free) = 0.1590          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1519 = 0.61 * 1.00 * 5.1785 + 1.00 * 0.0100                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1436 = 0.61 * 1.00 * 5.1627 + 1.00 * 0.0112                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.838)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.24   12.61    None  None   None       |
|    all(noH): 2823   0      0.00    76.24   12.61    None  None   None       |
|    Sol.    : 438    0      1.54    69.96   35.07    None  None   None       |
|    Mac.    : 2385   0      0.00    76.24   8.49     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 -   7.624: 1472   |   5:    38.118 -  45.742:  100        |
|      1:     7.624 -  15.247:  705   |   6:    45.742 -  53.366:   84        |
|      2:    15.247 -  22.871:  194   |   7:    53.366 -  60.989:   31        |
|      3:    22.871 -  30.495:  108   |   8:    60.989 -  68.613:   18        |
|      4:    30.495 -  38.118:  103   |   9:    68.613 -  76.236:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1139 r_free = 0.1590             target_work(ml) = 5.166         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1139 r_free = 0.1590             target_work(ml) = 5.166         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1139   r_free= 0.1590   ksol= 0.32   Bsol= 46.55   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.30,2.60,3.06,0.00,0.00,0.00); trace/3= 2.32                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.165870                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9034 -  4.7030 0.99   1411  158 0.1014 0.1320      5.4015      5.5629|
|  2:  4.7030 -  3.7525 0.99   1363  151 0.0871 0.1091      5.4493      5.6435|
|  3:  3.7525 -  3.2840 0.99   1340  148 0.1070 0.1489      5.4787      5.8584|
|  4:  3.2840 -  2.9864 0.99   1317  143 0.1222 0.1554      5.4578      5.6149|
|  5:  2.9864 -  2.7738 0.98   1321  148 0.1373 0.1690      5.3509      5.5091|
|  6:  2.7738 -  2.6112 0.99   1302  148 0.1279 0.2165       5.244      5.5517|
|  7:  2.6112 -  2.4810 0.99   1303  150 0.1261 0.1591      5.1869      5.3702|
|  8:  2.4810 -  2.3735 0.99   1319  136 0.1179 0.1722      5.0956      5.3268|
|  9:  2.3735 -  2.2824 0.99   1297  148 0.1232 0.1967      5.0544      5.3685|
| 10:  2.2824 -  2.2039 0.98   1290  139 0.1134 0.1575      4.9703      5.1674|
| 11:  2.2039 -  2.1352 0.98   1274  148 0.1144 0.1782      4.9362       5.236|
| 12:  2.1352 -  2.0743 1.00   1295  147 0.1109 0.1632      4.8478      5.1278|
| 13:  2.0743 -  2.0199 0.95   1264  131 0.1145 0.1777      4.7986       5.063|
| 14:  2.0199 -  1.9707 0.42    534   64 0.1090 0.1848      4.7206      4.9469|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9034 -  4.7030  1411   158  0.94   9.15   0.98     0.96       7387.53|
|  2:  4.7030 -  3.7525  1363   151  0.95   8.26   1.01     1.00       9270.42|
|  3:  3.7525 -  3.2840  1340   148  0.93  11.48   1.02     1.01      10657.44|
|  4:  3.2840 -  2.9864  1317   143  0.92  14.08   1.01     1.00      10594.26|
|  5:  2.9864 -  2.7738  1321   148  0.89  16.66   0.99     0.96       8694.27|
|  6:  2.7738 -  2.6112  1302   148  0.89  16.88   0.97     0.94       7542.64|
|  7:  2.6112 -  2.4810  1303   150  0.90  15.85   0.98     0.95       6499.77|
|  8:  2.4810 -  2.3735  1319   136  0.90  15.78   0.99     0.96       5747.82|
|  9:  2.3735 -  2.2824  1297   148  0.90  16.52   1.00     0.97       5258.48|
| 10:  2.2824 -  2.2039  1290   139  0.90  16.10   0.99     0.96       4601.10|
| 11:  2.2039 -  2.1352  1274   148  0.90  16.23   1.00     0.96       4424.16|
| 12:  2.1352 -  2.0743  1295   147  0.91  15.24   1.00     0.98       3744.93|
| 13:  2.0743 -  2.0199  1264   131  0.90  16.38   0.99     0.98       3438.19|
| 14:  2.0199 -  1.9707   534    64  0.90  15.71   0.97     0.92       2874.45|
|alpha:            min =        0.92 max =            1.01 mean =         0.97|
|beta:             min =     2874.45 max =        10657.44 mean =      6680.19|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.91 mean =        14.48|
|phase err.(test): min =        0.00 max =           89.00 mean =        13.91|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1138   r_free= 0.1588   ksol= 0.32   Bsol= 48.96   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.99,0.22,0.77,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.166053                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.90 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1138   r_free= 0.1588   ksol= 0.32   Bsol= 48.96   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.99,0.22,0.77,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.166053                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9034 -  4.7030 0.99   1411  158 0.1005 0.1322      5.4021      5.5646|
|  2:  4.7030 -  3.7525 0.99   1363  151 0.0876 0.1063      5.4542      5.6366|
|  3:  3.7525 -  3.2840 0.99   1340  148 0.1069 0.1488      5.4773      5.8559|
|  4:  3.2840 -  2.9864 0.99   1317  143 0.1227 0.1549      5.4588      5.6138|
|  5:  2.9864 -  2.7738 0.98   1321  148 0.1374 0.1685      5.3513      5.5064|
|  6:  2.7738 -  2.6112 0.99   1302  148 0.1278 0.2174      5.2439      5.5536|
|  7:  2.6112 -  2.4810 0.99   1303  150 0.1257 0.1593      5.1862      5.3703|
|  8:  2.4810 -  2.3735 0.99   1319  136 0.1178 0.1720      5.0948       5.327|
|  9:  2.3735 -  2.2824 0.99   1297  148 0.1229 0.1963      5.0534       5.365|
| 10:  2.2824 -  2.2039 0.98   1290  139 0.1131 0.1578        4.97      5.1685|
| 11:  2.2039 -  2.1352 0.98   1274  148 0.1143 0.1781      4.9359      5.2355|
| 12:  2.1352 -  2.0743 1.00   1295  147 0.1106 0.1639       4.848      5.1305|
| 13:  2.0743 -  2.0199 0.95   1264  131 0.1146 0.1776      4.7988      5.0622|
| 14:  2.0199 -  1.9707 0.42    534   64 0.1088 0.1846      4.7195      4.9449|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9034 -  4.7030  1411   158  0.94   9.43   0.98     0.95       7520.49|
|  2:  4.7030 -  3.7525  1363   151  0.95   8.36   1.01     1.00       9294.59|
|  3:  3.7525 -  3.2840  1340   148  0.93  11.43   1.02     1.01      10591.66|
|  4:  3.2840 -  2.9864  1317   143  0.92  14.06   1.01     1.00      10549.90|
|  5:  2.9864 -  2.7738  1321   148  0.89  16.63   0.99     0.96       8678.38|
|  6:  2.7738 -  2.6112  1302   148  0.89  16.89   0.98     0.94       7545.46|
|  7:  2.6112 -  2.4810  1303   150  0.90  15.87   0.99     0.95       6507.57|
|  8:  2.4810 -  2.3735  1319   136  0.90  15.77   0.99     0.97       5738.93|
|  9:  2.3735 -  2.2824  1297   148  0.90  16.51   1.01     0.97       5248.95|
| 10:  2.2824 -  2.2039  1290   139  0.90  16.09   1.00     0.97       4593.74|
| 11:  2.2039 -  2.1352  1274   148  0.90  16.23   1.00     0.97       4425.44|
| 12:  2.1352 -  2.0743  1295   147  0.91  15.27   1.00     0.98       3754.23|
| 13:  2.0743 -  2.0199  1264   131  0.90  16.38   1.00     0.98       3439.54|
| 14:  2.0199 -  1.9707   534    64  0.90  15.68   0.97     0.93       2864.79|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2864.79 max =        10591.66 mean =      6682.66|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.92 mean =        14.50|
|phase err.(test): min =        0.00 max =           89.10 mean =        13.92|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.838)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.42    78.65   15.03    None  None   None       |
|    all(noH): 2823   0      2.42    78.65   15.03    None  None   None       |
|    Sol.    : 438    0      3.96    72.38   37.49    None  None   None       |
|    Mac.    : 2385   0      2.42    78.65   10.90    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:     2.416 -  10.039: 1472   |   5:    40.534 -  48.157:  100        |
|      1:    10.039 -  17.663:  705   |   6:    48.157 -  55.781:   84        |
|      2:    17.663 -  25.286:  194   |   7:    55.781 -  63.405:   31        |
|      3:    25.286 -  32.910:  108   |   8:    63.405 -  71.028:   18        |
|      4:    32.910 -  40.534:  103   |   9:    71.028 -  78.652:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 319         
Filter by distance & map next to the model:
   mapped sites are within: 0.325 - 4.722
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 313 from: 319
   mapped sites are within: 0.701 - 4.722

peak=   10.994 closest distance to " CB  VAL A 230 " =    1.439
peak=    6.943 closest distance to " CG2 VAL A 296 " =    1.108
peak=    6.289 closest distance to " CG  LEU A   5 " =    1.208
peak=    5.669 closest distance to " CB  VAL A 296 " =    1.035
peak=    5.581 closest distance to " NH2 ARG A  56 " =    2.220
peak=    5.448 closest distance to " CD1AILE A 234 " =    1.086
peak=    5.206 closest distance to " CG  LEU A 228 " =    1.153
peak=    5.146 closest distance to " CG  PRO A  54 " =    1.252
peak=    5.071 closest distance to " O   HOH Z 403 " =    1.827
peak=    5.047 closest distance to " CB  GLN A 223 " =    1.401
peak=    5.040 closest distance to " CB  ARG A 275 " =    0.958
peak=    5.015 closest distance to " CB  PRO A  54 " =    0.962
peak=    4.975 closest distance to " CB  SER A  63 " =    1.177
peak=    4.950 closest distance to " O   HOH Z 209 " =    2.303
peak=    4.890 closest distance to " O   HOH Z 124 " =    1.387
peak=    4.801 closest distance to " O   HOH Z 193 " =    1.788
peak=    4.773 closest distance to " CD2 LEU A   5 " =    1.082
peak=    4.753 closest distance to " CB  GLN A 183 " =    1.298
peak=    4.736 closest distance to " CG  PRO A 213 " =    1.264
peak=    4.676 closest distance to " O   HOH Z 402 " =    1.522
peak=    4.638 closest distance to " O   HOH Z  85 " =    1.605
peak=    4.613 closest distance to " O   HOH Z 232 " =    2.301
peak=    4.516 closest distance to " O   SER A  87 " =    2.235
peak=    4.484 closest distance to " O   HOH Z  63 " =    2.120
peak=    4.447 closest distance to " NE2 GLN A  11 " =    1.055
peak=    4.427 closest distance to " CA  TYR A  30 " =    0.916
peak=    4.422 closest distance to " O   HOH Z 272 " =    1.906
peak=    4.409 closest distance to " O   HOH Z 346 " =    1.538
peak=    4.384 closest distance to " CG  PRO A 198 " =    1.187
peak=    4.383 closest distance to " O   HOH Z 265 " =    2.316
peak=    4.382 closest distance to " CA  ALA A  51 " =    1.040
peak=    4.343 closest distance to " O   HOH Z 298 " =    1.835
peak=    4.330 closest distance to " O   HOH Z 327 " =    1.707
peak=    4.322 closest distance to " CB  GLU A 152 " =    1.153
peak=    4.322 closest distance to " CG  ARG A  66 " =    2.700
peak=    4.302 closest distance to " O   HOH Z 248 " =    1.541
peak=    4.301 closest distance to " O   HOH Z 142 " =    1.652
peak=    4.291 closest distance to " CD2 LEU A 228 " =    1.267
peak=    4.288 closest distance to " O   HOH Z 414 " =    1.785
peak=    4.251 closest distance to " O   HOH Z 102 " =    1.384
peak=    4.213 closest distance to " O   HOH Z 423 " =    1.790
peak=    4.207 closest distance to " O   HOH Z  43 " =    2.237
peak=    4.202 closest distance to " O   HOH Z 369 " =    2.350
peak=    4.201 closest distance to " O   HOH Z 126 " =    1.843
peak=    4.181 closest distance to " CB  TRP A 179 " =    1.211
peak=    4.175 closest distance to " O   HOH Z  80 " =    1.841
peak=    4.175 closest distance to " O   HOH Z 234 " =    3.610
peak=    4.170 closest distance to " CG  PRO A 243 " =    1.174
peak=    4.163 closest distance to " O   HOH Z 368 " =    2.262
peak=    4.156 closest distance to " CG1 ILE A  33 " =    1.268
peak=    4.151 closest distance to " CB  VAL A 230 " =    1.186
peak=    4.147 closest distance to " CB  GLU A 277 " =    3.599
peak=    4.146 closest distance to " CB  SER A   3 " =    1.238
peak=    4.145 closest distance to " O   HOH Z  59 " =    2.225
peak=    4.140 closest distance to " O   HOH Z  40 " =    1.897
peak=    4.139 closest distance to " O   HOH Z  97 " =    1.965
peak=    4.134 closest distance to " O   HOH Z  54 " =    1.623
peak=    4.096 closest distance to " O   HOH Z 426 " =    1.476
peak=    4.091 closest distance to " O   HOH Z 128 " =    1.542
peak=    4.074 closest distance to " C   PRO A 198 " =    1.473
peak=    4.029 closest distance to " ND2 ASN A 249 " =    1.957
peak=    4.023 closest distance to " O   HOH Z 154 " =    1.594
peak=    4.020 closest distance to " O   HOH Z 189 " =    2.497
peak=    4.000 closest distance to " CB  ARG A  79 " =    1.405
peak=    3.983 closest distance to " CD2 TRP A 179 " =    1.368
peak=    3.982 closest distance to " O   HOH Z 247 " =    1.325
peak=    3.972 closest distance to " O   HOH Z 214 " =    2.579
peak=    3.926 closest distance to " CD  ARG A 269 " =    1.042
peak=    3.913 closest distance to " CB  SER A  26 " =    1.736
peak=    3.905 closest distance to " O   HOH Z  49 " =    1.063
peak=    3.901 closest distance to " ND2 ASN A 187 " =    1.614
peak=    3.893 closest distance to " OE1 GLU A   2 " =    2.092
peak=    3.885 closest distance to " O   HOH Z 287 " =    1.818
peak=    3.877 closest distance to " O   HOH Z 203 " =    1.752
peak=    3.873 closest distance to " CD  LYS A 166 " =    1.397
peak=    3.868 closest distance to " N   ASN A  39 " =    1.252
peak=    3.863 closest distance to " CG1BVAL A  72 " =    1.762
peak=    3.858 closest distance to " O   HOH Z 134 " =    1.562
peak=    3.847 closest distance to " O   HOH Z  48 " =    1.693
peak=    3.843 closest distance to " O   HOH Z 245 " =    1.418
peak=    3.840 closest distance to " O   HOH Z 422 " =    2.595
peak=    3.838 closest distance to " CZ  PHE A 218 " =    1.148
peak=    3.835 closest distance to " O   HOH Z 284 " =    3.003
peak=    3.830 closest distance to " OG  SER A 276 " =    1.510
peak=    3.818 closest distance to " CA  ARG A 275 " =    1.876
peak=    3.815 closest distance to " O   HOH Z 412 " =    3.696
peak=    3.797 closest distance to " CB  ARG A 190 " =    1.758
peak=    3.780 closest distance to " CB  ASN A 148 " =    1.402
peak=    3.777 closest distance to " O   HOH Z 250 " =    1.380
peak=    3.775 closest distance to " NZ  LYS A 117 " =    2.926
peak=    3.770 closest distance to " O   HOH Z 128 " =    2.330
peak=    3.768 closest distance to " CB  VAL A 265 " =    1.227
peak=    3.760 closest distance to " O   HOH Z 345 " =    2.898
peak=    3.754 closest distance to " O   HOH Z 158 " =    2.994
peak=    3.744 closest distance to " O   HOH Z 261 " =    2.051
peak=    3.742 closest distance to " CB  TYR A 169 " =    0.708
peak=    3.742 closest distance to " CA  VAL A  41 " =    0.847
peak=    3.739 closest distance to " CB  ARG A  79 " =    0.899
peak=    3.727 closest distance to " OD1 ASN A  69 " =    2.448
peak=    3.726 closest distance to " CB  ALA A 248 " =    1.318
peak=    3.715 closest distance to " CG2 ILE A  20 " =    1.440
peak=    3.709 closest distance to " O   ASP A 124 " =    1.481
peak=    3.702 closest distance to " O   HOH Z  44 " =    1.968
peak=    3.696 closest distance to " CB BVAL A  41 " =    1.059
peak=    3.691 closest distance to " CB  ARG A 139 " =    0.860
peak=    3.683 closest distance to " O   HOH Z 227 " =    1.601
peak=    3.676 closest distance to " CB  GLU A 128 " =    1.115
peak=    3.673 closest distance to " O   HOH Z 417 " =    3.035
peak=    3.673 closest distance to " O   HOH Z   4 " =    1.718
peak=    3.659 closest distance to " O   HOH Z 345 " =    1.658
peak=    3.654 closest distance to " OD1 ASP A 286 " =    1.778
peak=    3.651 closest distance to " O   HOH Z  15 " =    2.072
peak=    3.646 closest distance to " CB  VAL A 202 " =    1.457
peak=    3.637 closest distance to " O   HOH Z 238 " =    0.860
peak=    3.635 closest distance to " O   HOH Z 371 " =    3.281
peak=    3.623 closest distance to " O   HOH Z 419 " =    1.816
peak=    3.622 closest distance to " O   HOH Z  48 " =    1.658
peak=    3.618 closest distance to " CB  ALA A   9 " =    1.617
peak=    3.614 closest distance to " CG1 VAL A 296 " =    1.177
peak=    3.613 closest distance to " O   HOH Z 303 " =    2.199
peak=    3.609 closest distance to " CD  LYS A  76 " =    1.943
peak=    3.602 closest distance to " O   HOH Z 193 " =    2.110
peak=    3.598 closest distance to " O   HOH Z 145 " =    2.330
peak=    3.596 closest distance to " O   HOH Z 316 " =    3.007
peak=    3.585 closest distance to " O   HOH Z 421 " =    1.804
peak=    3.582 closest distance to " CA  ARG A  36 " =    1.047
peak=    3.581 closest distance to " CZ  PHE A  38 " =    1.241
peak=    3.579 closest distance to " O   HOH Z 162 " =    1.713
peak=    3.577 closest distance to " CE1 HIS A 108 " =    1.135
peak=    3.575 closest distance to " CG  ARG A  66 " =    0.966
peak=    3.568 closest distance to " O   HOH Z 263 " =    1.670
peak=    3.568 closest distance to " CA  ALA A 295 " =    1.023
peak=    3.559 closest distance to " O   HOH Z  61 " =    1.532
peak=    3.558 closest distance to " O   HOH Z 126 " =    1.531
peak=    3.558 closest distance to " O   HOH Z 357 " =    1.941
peak=    3.557 closest distance to " O   GLY A  91 " =    1.396
peak=    3.553 closest distance to " O   HOH Z 366 " =    2.780
peak=    3.547 closest distance to " CB  THR A  52 " =    0.919
peak=    3.546 closest distance to " CD1 LEU A  96 " =    0.737
peak=    3.542 closest distance to " O   HOH Z 273 " =    2.845
peak=    3.541 closest distance to " O   HOH Z 433 " =    1.426
peak=    3.534 closest distance to " OG BSER A 164 " =    2.187
peak=    3.531 closest distance to " CB  ASN A  39 " =    0.789
peak=    3.527 closest distance to " N   SER A 135 " =    1.292
peak=    3.525 closest distance to " OE1 GLN A  11 " =    1.771
peak=    3.524 closest distance to " O   HOH Z 313 " =    1.694
peak=    3.519 closest distance to " O   HOH Z 257 " =    2.240
peak=    3.516 closest distance to " CB  TRP A 266 " =    1.031
peak=    3.513 closest distance to " CG1 VAL A 153 " =    1.001
peak=    3.511 closest distance to " CB  THR A  31 " =    1.509
peak=    3.511 closest distance to " O   HOH Z  97 " =    2.443
peak=    3.508 closest distance to " CA  ALA A  21 " =    1.237
peak=    3.508 closest distance to " O   HOH Z 359 " =    1.545
peak=    3.502 closest distance to " O   HOH Z 394 " =    1.485
peak=    3.502 closest distance to " O   HOH Z 427 " =    2.702
peak=    3.498 closest distance to " NH1BARG A 190 " =    2.140
peak=    3.490 closest distance to " NH2 ARG A 156 " =    1.079
peak=    3.477 closest distance to " NH2BARG A 145 " =    2.139
peak=    3.473 closest distance to " NE2 GLN A  77 " =    3.146
peak=    3.473 closest distance to " CG  MET A 185 " =    1.093
peak=    3.469 closest distance to " O   HOH Z 185 " =    1.676
peak=    3.459 closest distance to " CA  LYS A 117 " =    1.306
peak=    3.458 closest distance to " CB  SER A 141 " =    1.062
peak=    3.457 closest distance to " CD  LYS A 119 " =    1.964
peak=    3.453 closest distance to " CG  GLN A  58 " =    2.714
peak=    3.453 closest distance to " CB  ASN A  45 " =    1.065
peak=    3.452 closest distance to " OG1 THR A 294 " =    2.276
peak=    3.449 closest distance to " O   HOH Z 147 " =    1.794
peak=    3.447 closest distance to " CB  LEU A   5 " =    1.273
peak=    3.447 closest distance to " O   HOH Z 438 " =    2.061
peak=    3.441 closest distance to " CA  SER A  32 " =    1.642
peak=    3.440 closest distance to " CG2 ILE A 120 " =    1.200
peak=    3.438 closest distance to " O   HOH Z  67 " =    1.835
peak=    3.437 closest distance to " O   HOH Z 329 " =    4.001
peak=    3.424 closest distance to " O   HOH Z 112 " =    1.732
peak=    3.423 closest distance to " O   HOH Z 406 " =    1.272
peak=    3.422 closest distance to " CE  LYS A 119 " =    1.019
peak=    3.422 closest distance to " CG1 ILE A  49 " =    1.500
peak=    3.420 closest distance to " O   HOH Z 383 " =    1.978
peak=    3.419 closest distance to " O   HOH Z 189 " =    2.569
peak=    3.417 closest distance to " O   HOH Z 409 " =    3.881
peak=    3.412 closest distance to " C   ALA A 299 " =    0.864
peak=    3.406 closest distance to " NZ  LYS A  48 " =    1.302
peak=    3.402 closest distance to " O   HOH Z 301 " =    1.929
peak=    3.402 closest distance to " O   HOH Z 435 " =    1.872
peak=    3.401 closest distance to " O  BHOH Z  74 " =    1.487
peak=    3.398 closest distance to " CA  ASP A 191 " =    1.056
peak=    3.397 closest distance to " CB  ALA A 100 " =    1.209
peak=    3.393 closest distance to " O   HOH Z 416 " =    2.733
peak=    3.391 closest distance to " CB  TRP A 150 " =    1.449
peak=    3.388 closest distance to " O   HOH Z 130 " =    1.089
peak=    3.388 closest distance to " O   HOH Z 197 " =    2.607
peak=    3.387 closest distance to " CG2 THR A 221 " =    1.246
peak=    3.383 closest distance to " O   HOH Z  66 " =    2.233
peak=    3.381 closest distance to " O   HOH Z 271 " =    2.475
peak=    3.381 closest distance to " O   ALA A 165 " =    1.376
peak=    3.380 closest distance to " O   HOH Z 280 " =    2.585
peak=    3.371 closest distance to " O   HOH Z  88 " =    2.593
peak=    3.367 closest distance to " O   HOH Z 420 " =    1.856
peak=    3.366 closest distance to " CA  ARG A 195 " =    1.214
peak=    3.365 closest distance to " O   HOH Z  21 " =    1.850
peak=    3.364 closest distance to " O   HOH Z 406 " =    1.473
peak=    3.364 closest distance to " CB  TYR A 247 " =    0.996
peak=    3.363 closest distance to " O   HOH Z  78 " =    1.622
peak=    3.361 closest distance to " O   HOH Z 162 " =    1.993
peak=    3.360 closest distance to " O   HOH Z 253 " =    1.472
peak=    3.347 closest distance to " O   HOH Z 128 " =    1.827
peak=    3.342 closest distance to " CA  ASN A 176 " =    1.077
peak=    3.342 closest distance to " CB  ARG A 219 " =    1.344
peak=    3.341 closest distance to " CE1 TYR A 186 " =    1.288
peak=    3.341 closest distance to " CD  ARG A 159 " =    0.771
peak=    3.338 closest distance to " CB  PRO A 198 " =    1.011
peak=    3.336 closest distance to " CG  LEU A 167 " =    1.131
peak=    3.334 closest distance to " O   HOH Z 353 " =    2.713
peak=    3.332 closest distance to " CG2 ILE A 106 " =    0.821
peak=    3.329 closest distance to " O   HOH Z 344 " =    2.990
peak=    3.327 closest distance to " OD2 ASP A 286 " =    2.743
peak=    3.327 closest distance to " CA  ASP A 140 " =    1.133
peak=    3.326 closest distance to " O   HOH Z  63 " =    2.172
peak=    3.325 closest distance to " CA  LYS A 290 " =    1.139
peak=    3.317 closest distance to " O   HOH Z 427 " =    3.143
peak=    3.315 closest distance to " O   HOH Z 250 " =    1.467
peak=    3.312 closest distance to " CG AARG A 275 " =    1.252
peak=    3.308 closest distance to " CB  MET A  40 " =    0.865
peak=    3.307 closest distance to " O   HOH Z 227 " =    2.101
peak=    3.301 closest distance to " OH  TYR A 116 " =    1.190
peak=    3.300 closest distance to " NH1 ARG A  14 " =    1.162
peak=    3.298 closest distance to " NH1AARG A 145 " =    1.140
peak=    3.296 closest distance to " NH2AARG A 275 " =    3.678
peak=    3.292 closest distance to " CB  ASN A 142 " =    1.147
peak=    3.286 closest distance to " CG2 ILE A 234 " =    1.019
peak=    3.285 closest distance to " CG BARG A 102 " =    1.789
peak=    3.283 closest distance to " O   HOH Z 163 " =    1.364
peak=    3.274 closest distance to " O   HOH Z   1 " =    1.918
peak=    3.273 closest distance to " CA  TYR A 116 " =    1.411
peak=    3.273 closest distance to " CB  ALA A 295 " =    1.165
peak=    3.273 closest distance to " CD  ARG A  66 " =    2.807
peak=    3.271 closest distance to " O   HOH Z 367 " =    3.393
peak=    3.258 closest distance to " CB  ALA A 291 " =    1.332
peak=    3.254 closest distance to " OD2 ASP A 298 " =    3.885
peak=    3.252 closest distance to " CB  ASP A 140 " =    0.951
peak=    3.249 closest distance to " O   HOH Z 234 " =    1.834
peak=    3.247 closest distance to " N   ASP A 162 " =    1.279
peak=    3.247 closest distance to " CE  LYS A  76 " =    0.847
peak=    3.246 closest distance to " O   HOH Z  47 " =    1.591
peak=    3.245 closest distance to " CZ3 TRP A  85 " =    0.966
peak=    3.245 closest distance to " C   ILE A 106 " =    1.857
peak=    3.239 closest distance to " O   HOH Z 109 " =    2.145
peak=    3.235 closest distance to " CG  GLN A  77 " =    2.324
peak=    3.234 closest distance to " CB  GLN A 278 " =    0.895
peak=    3.230 closest distance to " CZ2 TRP A 150 " =    1.120
peak=    3.227 closest distance to " O   HOH Z 148 " =    3.235
peak=    3.227 closest distance to " O   HOH Z 437 " =    2.124
peak=    3.217 closest distance to " CB  ALA A  71 " =    1.303
peak=    3.214 closest distance to " CA  TRP A  85 " =    1.230
peak=    3.212 closest distance to " CG2 THR A  42 " =    0.836
peak=    3.212 closest distance to " CB  SER A  62 " =    0.836
peak=    3.210 closest distance to " CG2AVAL A 121 " =    2.134
peak=    3.206 closest distance to " CA  ASP A 162 " =    1.118
peak=    3.206 closest distance to " OG  SER A  62 " =    2.814
peak=    3.205 closest distance to " ND2 ASN A 249 " =    0.883
peak=    3.205 closest distance to " OG1 THR A 294 " =    1.609
peak=    3.202 closest distance to " O   HOH Z 299 " =    4.213
peak=    3.193 closest distance to " NZ  LYS A 166 " =    3.043
peak=    3.188 closest distance to " CB  MET A  47 " =    1.151
peak=    3.179 closest distance to " CD2 TYR A 186 " =    0.974
peak=    3.178 closest distance to " CD2 HIS A  81 " =    1.051
peak=    3.176 closest distance to " O   HOH Z 408 " =    1.645
peak=    3.173 closest distance to " CB  ARG A 259 " =    1.868
peak=    3.172 closest distance to " O   HOH Z 173 " =    2.466
peak=    3.172 closest distance to " O   HOH Z 403 " =    1.412
peak=    3.170 closest distance to " O   HOH Z  83 " =    1.533
peak=    3.168 closest distance to " O   HOH Z 362 " =    3.529
peak=    3.163 closest distance to " O   HOH Z 423 " =    3.242
peak=    3.162 closest distance to " CB  ASN A 215 " =    1.104
peak=    3.159 closest distance to " CD1 LEU A 222 " =    0.701
peak=    3.158 closest distance to " CB  GLN A  88 " =    1.137
peak=    3.158 closest distance to " N   PHE A 130 " =    1.306
peak=    3.155 closest distance to " CB  ASN A 285 " =    0.955
peak=    3.154 closest distance to " O   HOH Z 291 " =    1.560
peak=    3.153 closest distance to " O   HOH Z 387 " =    1.774
peak=    3.152 closest distance to " NH1 ARG A 138 " =    1.252
peak=    3.151 closest distance to " CB  ASN A 187 " =    1.031
peak=    3.150 closest distance to " CG2 ILE A 234 " =    2.107
peak=    3.150 closest distance to " CD1 ILE A 199 " =    0.986
peak=    3.150 closest distance to " O   HOH Z 197 " =    1.979
peak=    3.146 closest distance to " NH2 ARG A  79 " =    1.306
peak=    3.137 closest distance to " O   HOH Z   9 " =    2.359
peak=    3.135 closest distance to " CB  PRO A  90 " =    1.132
peak=    3.134 closest distance to " O   HOH Z 251 " =    1.774
peak=    3.133 closest distance to " O   ALA A   1 " =    1.728
peak=    3.130 closest distance to " CB  LYS A 290 " =    1.050
peak=    3.129 closest distance to " CG  MET A 185 " =    0.939
peak=    3.129 closest distance to " CG2 VAL A 197 " =    1.085
peak=    3.125 closest distance to " CB  PHE A  16 " =    1.034
peak=    3.118 closest distance to " O   HOH Z 281 " =    4.722
peak=    3.117 closest distance to " CA  ASN A 217 " =    1.244
peak=    3.116 closest distance to " CA  GLY A  80 " =    0.823
peak=    3.110 closest distance to " O   HOH Z 163 " =    2.023
peak=    3.110 closest distance to " O   HOH Z  46 " =    1.374
peak=    3.107 closest distance to " CG  GLU A  53 " =    1.741
peak=    3.097 closest distance to " O   HOH Z 417 " =    2.203
peak=    3.091 closest distance to " O   HOH Z 319 " =    2.356
peak=    3.087 closest distance to " OG  SER A 245 " =    1.504
peak=    3.084 closest distance to " O   ILE A  33 " =    1.232
peak=    3.080 closest distance to " CB  ALA A 104 " =    0.756
peak=    3.075 closest distance to " CG  GLU A  37 " =    0.844
peak=    3.070 closest distance to " CB  GLU A  46 " =    1.035
peak=    3.060 closest distance to " CA  SER A  87 " =    0.977
peak=    3.045 closest distance to " OG1 THR A 157 " =    1.198
peak=    3.034 closest distance to " O   HOH Z 305 " =    3.541
peak=    3.019 closest distance to " CB  THR A  52 " =    0.820
peak=    3.013 closest distance to " O   HOH Z  80 " =    2.043

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 198         
Filter by distance & map next to the model:
   mapped sites are within: 0.706 - 5.725
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 197 from: 198
   mapped sites are within: 0.706 - 5.725

peak=   -5.348 closest distance to " CG2 VAL A 230 " =    0.706
peak=   -4.626 closest distance to " CD  ARG A 156 " =    2.056
peak=   -4.498 closest distance to " CD  GLN A  58 " =    1.125
peak=   -4.435 closest distance to " O   HOH Z 266 " =    4.956
peak=   -4.404 closest distance to " SG  CYS A 254 " =    3.201
peak=   -4.264 closest distance to " O   HOH Z 290 " =    0.948
peak=   -4.244 closest distance to " O   PRO A 163 " =    2.133
peak=   -4.211 closest distance to " OXT GLY A 302 " =    2.871
peak=   -4.161 closest distance to " O   HOH Z 166 " =    1.669
peak=   -4.143 closest distance to " C   HIS A 108 " =    1.202
peak=   -4.139 closest distance to " CD1 LEU A 101 " =    2.425
peak=   -4.132 closest distance to " O   HOH Z 351 " =    1.590
peak=   -4.122 closest distance to " OG BSER A 134 " =    1.382
peak=   -4.114 closest distance to " CH2 TRP A 179 " =    1.259
peak=   -3.994 closest distance to " CB  ALA A 161 " =    2.525
peak=   -3.989 closest distance to " O   HOH Z  13 " =    1.714
peak=   -3.979 closest distance to " O   HOH Z 196 " =    2.141
peak=   -3.975 closest distance to " CD2 LEU A 237 " =    2.665
peak=   -3.966 closest distance to " CD2 TYR A  30 " =    2.753
peak=   -3.922 closest distance to " O   HOH Z 414 " =    1.856
peak=   -3.905 closest distance to " O   VAL A  67 " =    2.834
peak=   -3.868 closest distance to " CA  ASP A 298 " =    1.055
peak=   -3.839 closest distance to " CG2BVAL A  41 " =    2.675
peak=   -3.819 closest distance to " NE2 GLN A  88 " =    0.998
peak=   -3.818 closest distance to " CD1 LEU A  25 " =    2.509
peak=   -3.805 closest distance to " O   HOH Z 231 " =    2.242
peak=   -3.799 closest distance to " CD2 PHE A 192 " =    2.083
peak=   -3.790 closest distance to " O   HOH Z  60 " =    2.256
peak=   -3.790 closest distance to " CB  ALA A 248 " =    2.276
peak=   -3.784 closest distance to " O   HOH Z  37 " =    1.926
peak=   -3.773 closest distance to " OE1 GLN A 223 " =    2.365
peak=   -3.772 closest distance to " CG1 VAL A 112 " =    2.671
peak=   -3.772 closest distance to " CB  PHE A 208 " =    2.323
peak=   -3.767 closest distance to " C   THR A 279 " =    1.151
peak=   -3.762 closest distance to " CD1 PHE A  59 " =    2.046
peak=   -3.756 closest distance to " O   ASN A  45 " =    1.841
peak=   -3.740 closest distance to " CG  ASP A 231 " =    0.869
peak=   -3.738 closest distance to " O   HOH Z 165 " =    1.979
peak=   -3.735 closest distance to " ND2 ASN A 187 " =    1.590
peak=   -3.728 closest distance to " O   HOH Z 394 " =    1.622
peak=   -3.707 closest distance to " CB  PRO A 163 " =    2.546
peak=   -3.687 closest distance to " O   HOH Z  11 " =    1.872
peak=   -3.664 closest distance to " O   HOH Z 114 " =    3.343
peak=   -3.660 closest distance to " N   ALA A 248 " =    1.780
peak=   -3.657 closest distance to " N   ALA A 226 " =    1.975
peak=   -3.653 closest distance to " ND2 ASN A  69 " =    1.677
peak=   -3.650 closest distance to " OG  SER A  97 " =    2.308
peak=   -3.643 closest distance to " CD  LYS A 289 " =    2.493
peak=   -3.642 closest distance to " CZ  TYR A 169 " =    1.771
peak=   -3.633 closest distance to " O   PRO A 198 " =    1.278
peak=   -3.601 closest distance to " CD  GLN A 223 " =    0.779
peak=   -3.595 closest distance to " O   HOH Z 377 " =    1.961
peak=   -3.591 closest distance to " CB  ALA A 248 " =    2.001
peak=   -3.590 closest distance to " CB  PRO A 243 " =    2.657
peak=   -3.588 closest distance to " ND2 ASN A  45 " =    1.075
peak=   -3.575 closest distance to " N   THR A 235 " =    1.309
peak=   -3.565 closest distance to " O   HOH Z 377 " =    1.430
peak=   -3.561 closest distance to " CE3 TRP A 150 " =    2.260
peak=   -3.557 closest distance to " CD1 LEU A 255 " =    2.653
peak=   -3.556 closest distance to " CG  GLU A  53 " =    1.520
peak=   -3.553 closest distance to " O   HOH Z 423 " =    2.234
peak=   -3.550 closest distance to " O   HOH Z  92 " =    1.716
peak=   -3.548 closest distance to " CE  LYS A 166 " =    3.055
peak=   -3.547 closest distance to " O   HOH Z 377 " =    1.393
peak=   -3.546 closest distance to " O   HOH Z 136 " =    2.322
peak=   -3.517 closest distance to " CG2 VAL A 296 " =    1.371
peak=   -3.508 closest distance to " CD2 TYR A 293 " =    1.903
peak=   -3.504 closest distance to " O   HOH Z 193 " =    1.598
peak=   -3.494 closest distance to " CD  ARG A 139 " =    1.610
peak=   -3.478 closest distance to " ND2 ASN A  39 " =    1.095
peak=   -3.475 closest distance to " O   GLY A  80 " =    2.434
peak=   -3.468 closest distance to " O   HOH Z 191 " =    5.725
peak=   -3.460 closest distance to " O   HOH Z 301 " =    2.356
peak=   -3.457 closest distance to " O   HOH Z  44 " =    2.205
peak=   -3.455 closest distance to " O   GLY A 196 " =    1.067
peak=   -3.450 closest distance to " O   HOH Z 369 " =    2.218
peak=   -3.431 closest distance to " CD2 LEU A 300 " =    2.755
peak=   -3.429 closest distance to " OG1 THR A  82 " =    1.368
peak=   -3.429 closest distance to " O   SER A 210 " =    1.858
peak=   -3.427 closest distance to " CB  SER A 210 " =    1.195
peak=   -3.427 closest distance to " O   HOH Z 407 " =    2.917
peak=   -3.423 closest distance to " CE1 TYR A 247 " =    2.592
peak=   -3.422 closest distance to " O   TRP A  92 " =    2.029
peak=   -3.419 closest distance to " CB  GLN A  11 " =    1.900
peak=   -3.416 closest distance to " C   SER A 206 " =    1.565
peak=   -3.416 closest distance to " O   HOH Z 131 " =    4.073
peak=   -3.416 closest distance to " NH2 ARG A  66 " =    1.606
peak=   -3.415 closest distance to " O   HOH Z 177 " =    1.734
peak=   -3.414 closest distance to " O   HOH Z 283 " =    1.931
peak=   -3.409 closest distance to " OD1 ASN A  39 " =    2.143
peak=   -3.405 closest distance to " O   VAL A  67 " =    1.886
peak=   -3.398 closest distance to " O   SER A 271 " =    2.022
peak=   -3.397 closest distance to " CG  ASP A 132 " =    2.349
peak=   -3.397 closest distance to " O   HOH Z 174 " =    2.159
peak=   -3.396 closest distance to " OD1 ASN A 148 " =    1.472
peak=   -3.395 closest distance to " N   SER A 276 " =    1.367
peak=   -3.391 closest distance to " CG2 ILE A  49 " =    2.735
peak=   -3.389 closest distance to " NH2AARG A 275 " =    4.798
peak=   -3.389 closest distance to " CD2 LEU A 167 " =    1.756
peak=   -3.387 closest distance to " C   ALA A 158 " =    1.214
peak=   -3.386 closest distance to " CG  ASP A  50 " =    2.351
peak=   -3.383 closest distance to " O   HOH Z 193 " =    1.915
peak=   -3.377 closest distance to " CG2 ILE A 263 " =    2.311
peak=   -3.371 closest distance to " O   PHE A 218 " =    1.616
peak=   -3.364 closest distance to " O   HOH Z 150 " =    1.850
peak=   -3.362 closest distance to " CD1 PHE A  59 " =    2.122
peak=   -3.359 closest distance to " OXT GLY A 302 " =    3.388
peak=   -3.355 closest distance to " O   LYS A 117 " =    1.626
peak=   -3.353 closest distance to " CE  MET A 105 " =    2.312
peak=   -3.353 closest distance to " O   HOH Z 353 " =    2.161
peak=   -3.345 closest distance to " O   HOH Z 126 " =    1.883
peak=   -3.341 closest distance to " CG  ARG A 269 " =    2.205
peak=   -3.340 closest distance to " NE2 GLN A 103 " =    1.710
peak=   -3.332 closest distance to " O   HOH Z   6 " =    1.810
peak=   -3.327 closest distance to " CB  ALA A 291 " =    2.259
peak=   -3.326 closest distance to " N   THR A 157 " =    1.507
peak=   -3.325 closest distance to " OG ASER A 134 " =    1.297
peak=   -3.324 closest distance to " O   HOH Z 311 " =    3.653
peak=   -3.315 closest distance to " OG BSER A 210 " =    1.346
peak=   -3.308 closest distance to " OG  SER A   3 " =    1.540
peak=   -3.308 closest distance to " O   VAL A 174 " =    2.112
peak=   -3.304 closest distance to " O   HOH Z 234 " =    4.025
peak=   -3.297 closest distance to " NE2 GLN A 194 " =    1.694
peak=   -3.293 closest distance to " O   HOH Z 326 " =    5.129
peak=   -3.292 closest distance to " O   HOH Z 154 " =    1.514
peak=   -3.292 closest distance to " O   HOH Z 313 " =    1.233
peak=   -3.286 closest distance to " O   HOH Z 389 " =    1.784
peak=   -3.284 closest distance to " O   HOH Z 185 " =    2.449
peak=   -3.281 closest distance to " CE3 TRP A 274 " =    2.413
peak=   -3.278 closest distance to " O   HOH Z   5 " =    1.599
peak=   -3.274 closest distance to " CA  GLY A 203 " =    2.350
peak=   -3.274 closest distance to " O   VAL A 189 " =    2.667
peak=   -3.273 closest distance to " O   MET A  40 " =    2.773
peak=   -3.269 closest distance to " O   HOH Z 339 " =    1.820
peak=   -3.268 closest distance to " CG  TRP A 266 " =    1.986
peak=   -3.267 closest distance to " O   ALA A   1 " =    1.788
peak=   -3.264 closest distance to " O   SER A  95 " =    1.685
peak=   -3.264 closest distance to " CB  LEU A  83 " =    2.364
peak=   -3.261 closest distance to " NH1 ARG A  66 " =    1.118
peak=   -3.258 closest distance to " O   HOH Z  19 " =    2.311
peak=   -3.257 closest distance to " C   LEU A 143 " =    1.023
peak=   -3.254 closest distance to " OG  SER A  63 " =    1.135
peak=   -3.253 closest distance to " C   GLN A 205 " =    1.825
peak=   -3.252 closest distance to " O   HOH Z 252 " =    3.958
peak=   -3.252 closest distance to " O   HOH Z  15 " =    1.554
peak=   -3.251 closest distance to " CA  GLY A 241 " =    2.421
peak=   -3.246 closest distance to " OD2 ASP A 171 " =    2.354
peak=   -3.246 closest distance to " OG BSER A 134 " =    1.745
peak=   -3.245 closest distance to " C   MET A 188 " =    1.529
peak=   -3.245 closest distance to " O   HOH Z 422 " =    1.574
peak=   -3.236 closest distance to " CG  ARG A 219 " =    2.611
peak=   -3.228 closest distance to " CG2 THR A 182 " =    2.135
peak=   -3.228 closest distance to " O   HOH Z  71 " =    1.796
peak=   -3.216 closest distance to " N   GLN A  58 " =    2.061
peak=   -3.214 closest distance to " O   HOH Z 171 " =    2.106
peak=   -3.209 closest distance to " O   HOH Z 119 " =    2.126
peak=   -3.207 closest distance to " OD1 ASN A 301 " =    2.045
peak=   -3.207 closest distance to " CG1 VAL A 296 " =    1.311
peak=   -3.204 closest distance to " O   HOH Z  78 " =    1.750
peak=   -3.200 closest distance to " CG2 VAL A 189 " =    2.019
peak=   -3.195 closest distance to " O   ASP A 171 " =    1.923
peak=   -3.195 closest distance to " CG  LEU A  83 " =    1.958
peak=   -3.182 closest distance to " O   HOH Z 150 " =    2.086
peak=   -3.179 closest distance to " O   HOH Z 281 " =    2.551
peak=   -3.178 closest distance to " O   VAL A 189 " =    1.849
peak=   -3.175 closest distance to " O   HOH Z 265 " =    2.211
peak=   -3.173 closest distance to " O   ALA A 160 " =    1.399
peak=   -3.173 closest distance to " OD1 ASN A 249 " =    2.292
peak=   -3.172 closest distance to " CD2 LEU A 237 " =    2.730
peak=   -3.164 closest distance to " CB  TRP A  85 " =    2.578
peak=   -3.159 closest distance to " O   HOH Z 139 " =    3.251
peak=   -3.157 closest distance to " NE2 GLN A  58 " =    2.382
peak=   -3.151 closest distance to " NH2 ARG A  79 " =    2.027
peak=   -3.150 closest distance to " N   THR A  52 " =    1.634
peak=   -3.147 closest distance to " O   ALA A  10 " =    1.777
peak=   -3.138 closest distance to " O   HOH Z 166 " =    1.779
peak=   -3.137 closest distance to " O   HOH Z 174 " =    3.946
peak=   -3.133 closest distance to " O   HOH Z  17 " =    1.167
peak=   -3.130 closest distance to " CG  GLU A 277 " =    1.161
peak=   -3.126 closest distance to " C   ASN A 285 " =    2.254
peak=   -3.114 closest distance to " O   HOH Z 157 " =    3.518
peak=   -3.112 closest distance to " OD1 ASP A 191 " =    1.438
peak=   -3.108 closest distance to " CD  PRO A 243 " =    2.000
peak=   -3.107 closest distance to " O   ARG A  24 " =    1.990
peak=   -3.102 closest distance to " CH2 TRP A 150 " =    1.063
peak=   -3.086 closest distance to " N   ALA A 248 " =    2.265
peak=   -3.086 closest distance to " O   ALA A  34 " =    2.465
peak=   -3.086 closest distance to " OG  SER A  26 " =    1.226
peak=   -3.084 closest distance to " CD1 ILE A 109 " =    2.889
peak=   -3.078 closest distance to " O   HOH Z 429 " =    2.133
peak=   -3.070 closest distance to " O   HOH Z 151 " =    1.504
peak=   -3.067 closest distance to " O   PRO A 198 " =    1.239
peak=   -3.066 closest distance to " CZ  TYR A  68 " =    1.202
peak=   -3.062 closest distance to " O   HOH Z 407 " =    1.733
peak=   -3.030 closest distance to " CB  PHE A 208 " =    2.322
peak=   -3.029 closest distance to " O   SER A   3 " =    1.118
peak=   -3.027 closest distance to " N   SER A 271 " =    1.393

================= 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    :  0.4718 0.4572   6.272891e+00   6.256068e+00
   1_bss:  0.4640 0.4512   6.264544e+00   6.251302e+00
   1_xyz:  0.3697 0.3899   6.126017e+00   6.159552e+00
   1_adp:  0.3181 0.3604   6.021210e+00   6.112726e+00
   1_occ:  0.3177 0.3604   6.020149e+00   6.112621e+00
   2_bss:  0.3148 0.3558   6.021171e+00   6.111762e+00
   2_xyz:  0.2373 0.2845   5.781505e+00   5.930595e+00
   2_adp:  0.2189 0.2690   5.721024e+00   5.878014e+00
   2_occ:  0.2187 0.2692   5.720830e+00   5.878717e+00
   3_bss:  0.2173 0.2678   5.719884e+00   5.876215e+00
   3_xyz:  0.1543 0.1930   5.399997e+00   5.588000e+00
   3_adp:  0.1410 0.1773   5.314585e+00   5.505044e+00
   3_occ:  0.1407 0.1770   5.313452e+00   5.504251e+00
   4_bss:  0.1402 0.1765   5.312444e+00   5.502245e+00
   4_xyz:  0.1234 0.1634   5.215691e+00   5.430460e+00
   4_adp:  0.1200 0.1614   5.195806e+00   5.417757e+00
   4_occ:  0.1199 0.1615   5.195580e+00   5.417776e+00
   5_bss:  0.1199 0.1615   5.195515e+00   5.417864e+00
   5_xyz:  0.1151 0.1583   5.168598e+00   5.400646e+00
   5_adp:  0.1139 0.1590   5.165928e+00   5.405343e+00
   5_occ:  0.1139 0.1590   5.165870e+00   5.405528e+00
   5_bss:  0.1138 0.1588   5.166053e+00   5.404681e+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:  0.342  20.001   7.323  10.740   7.647   0.000   0.000   0.000
   1_xyz:  0.342  20.001   7.323  10.740   7.647   0.000   0.000   0.000
   1_adp:  0.342  20.001   7.323  10.740   7.647   0.000   0.000   0.000
   1_occ:  0.342  20.001   7.323  10.740   7.647   0.000   0.000   0.000
   2_bss:  0.319  34.936   3.798   6.517   4.615   0.000   0.000   0.000
   2_xyz:  0.319  34.936   3.798   6.517   4.615   0.000   0.000   0.000
   2_adp:  0.319  34.936   3.798   6.517   4.615   0.000   0.000   0.000
   2_occ:  0.319  34.936   3.798   6.517   4.615   0.000   0.000   0.000
   3_bss:  0.311  45.393   1.990   4.227   3.533   0.000   0.000   0.000
   3_xyz:  0.311  45.393   1.990   4.227   3.533   0.000   0.000   0.000
   3_adp:  0.311  45.393   1.990   4.227   3.533   0.000   0.000   0.000
   3_occ:  0.311  45.393   1.990   4.227   3.533   0.000   0.000   0.000
   4_bss:  0.323  45.393   1.300   2.853   3.051   0.000   0.000   0.000
   4_xyz:  0.323  45.393   1.300   2.853   3.051   0.000   0.000   0.000
   4_adp:  0.323  45.393   1.300   2.853   3.051   0.000   0.000   0.000
   4_occ:  0.323  45.393   1.300   2.853   3.051   0.000   0.000   0.000
   5_bss:  0.324  46.545   1.302   2.595   3.058   0.000   0.000   0.000
   5_xyz:  0.324  46.545   1.302   2.595   3.058   0.000   0.000   0.000
   5_adp:  0.324  46.545   1.302   2.595   3.058   0.000   0.000   0.000
   5_occ:  0.324  46.545   1.302   2.595   3.058   0.000   0.000   0.000
   5_bss:  0.323  48.961  -0.989   0.218   0.770   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.825 0.4738  0.5441    63736.878
   1_bss:  53.771 0.4729  0.7025    62050.883
   1_xyz:  44.027 0.5928  0.8586    43333.717
   1_adp:  38.974 0.6548  0.9755    36664.024
   1_occ:  38.957 0.6550  0.9747    36604.967
   2_bss:  38.652 0.6586  0.8635    36220.440
   2_xyz:  29.955 0.7573  0.9656    21949.966
   2_adp:  27.484 0.7851  0.9900    19210.920
   2_occ:  27.502 0.7849  0.9897    19224.203
   3_bss:  27.361 0.7864  0.9315    19058.955
   3_xyz:  18.712 0.8734  0.9928     9650.730
   3_adp:  16.727 0.8920  1.0022     8221.566
   3_occ:  16.704 0.8921  1.0023     8210.463
   4_bss:  16.656 0.8925  0.9733     8162.430
   4_xyz:  15.077 0.9061  0.9781     7015.830
   4_adp:  14.785 0.9087  0.9767     6867.769
   4_occ:  14.781 0.9088  0.9766     6869.883
   5_bss:  14.779 0.9088  0.9740     6872.413
   5_xyz:  14.352 0.9124  0.9747     6630.947
   5_adp:  14.423 0.9119  0.9694     6678.149
   5_occ:  14.422 0.9119  0.9694     6679.684
   5_bss:  14.443 0.9117  0.9724     6682.173
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3671e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3671e+01
   1_xyz:   1.721  0.014  0.111 17.964  0.007  4.108   1.4397e-01
   1_adp:   1.721  0.014  0.111 17.964  0.007  4.108   1.4397e-01
   1_occ:   1.721  0.014  0.111 17.964  0.007  4.108   1.4397e-01
   2_bss:   1.721  0.014  0.111 17.964  0.007  4.108   1.4397e-01
   2_xyz:   1.114  0.007  0.075 16.014  0.004  4.123   7.1158e-02
   2_adp:   1.114  0.007  0.075 16.014  0.004  4.123   7.1158e-02
   2_occ:   1.114  0.007  0.075 16.014  0.004  4.123   7.1158e-02
   3_bss:   1.114  0.007  0.075 16.014  0.004  4.123   7.1158e-02
   3_xyz:   1.091  0.007  0.082 15.835  0.004  4.111   7.0393e-02
   3_adp:   1.091  0.007  0.082 15.835  0.004  4.111   7.0393e-02
   3_occ:   1.091  0.007  0.082 15.835  0.004  4.111   7.0393e-02
   4_bss:   1.091  0.007  0.082 15.835  0.004  4.111   7.0393e-02
   4_xyz:   1.036  0.007  0.082 15.536  0.004  4.116   6.4152e-02
   4_adp:   1.036  0.007  0.082 15.536  0.004  4.116   6.4152e-02
   4_occ:   1.036  0.007  0.082 15.536  0.004  4.116   6.4152e-02
   5_bss:   1.036  0.007  0.082 15.536  0.004  4.116   6.4152e-02
   5_xyz:   1.045  0.008  0.084 15.453  0.004  4.120   6.5317e-02
   5_adp:   1.045  0.008  0.084 15.453  0.004  4.120   6.5317e-02
   5_occ:   1.045  0.008  0.084 15.453  0.004  4.120   6.5317e-02
   5_bss:   1.045  0.008  0.084 15.453  0.004  4.120   6.5317e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.019   6.9560e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.019   6.9560e+00
   1_xyz:  16.300  0.169  0.556 85.234  0.039  2.255   1.0602e-01
   1_adp:  16.300  0.169  0.556 85.234  0.039  2.255   1.0602e-01
   1_occ:  16.300  0.169  0.556 85.234  0.039  2.255   1.0602e-01
   2_bss:  16.300  0.169  0.556 85.234  0.039  2.255   1.0602e-01
   2_xyz:   7.184  0.079  0.246 83.104  0.028  2.164   5.8237e-02
   2_adp:   7.184  0.079  0.246 83.104  0.028  2.164   5.8237e-02
   2_occ:   7.184  0.079  0.246 83.104  0.028  2.164   5.8237e-02
   3_bss:   7.184  0.079  0.246 83.104  0.028  2.164   5.8237e-02
   3_xyz:   7.075  0.056  0.504 82.550  0.042  2.222   5.6527e-02
   3_adp:   7.075  0.056  0.504 82.550  0.042  2.222   5.6527e-02
   3_occ:   7.075  0.056  0.504 82.550  0.042  2.222   5.6527e-02
   4_bss:   7.075  0.056  0.504 82.550  0.042  2.222   5.6527e-02
   4_xyz:   7.255  0.044  0.571 83.584  0.038  2.266   4.4656e-02
   4_adp:   7.255  0.044  0.571 83.584  0.038  2.266   4.4656e-02
   4_occ:   7.255  0.044  0.571 83.584  0.038  2.266   4.4656e-02
   5_bss:   7.255  0.044  0.571 83.584  0.038  2.266   4.4656e-02
   5_xyz:   7.569  0.050  0.599 81.701  0.034  2.323   4.2886e-02
   5_adp:   7.569  0.050  0.599 81.701  0.034  2.323   4.2886e-02
   5_occ:   7.569  0.050  0.599 81.701  0.034  2.323   4.2886e-02
   5_bss:   7.569  0.050  0.599 81.701  0.034  2.323   4.2886e-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:  77.68   0.00  12.58  69.45   0.00  10.00  77.68   0.00  26.64
   1_occ:  77.68   0.00  12.58  69.45   0.00  10.00  77.68   0.00  26.64
   2_bss:  77.68   0.00  12.58  69.45   0.00  10.00  77.68   0.00  26.64
   2_xyz:  77.68   0.00  12.58  69.45   0.00  10.00  77.68   0.00  26.64
   2_adp:  73.91   0.00  12.50  71.63   0.00   9.10  73.91   1.02  31.05
   2_occ:  73.91   0.00  12.50  71.63   0.00   9.10  73.91   1.02  31.05
   3_bss:  73.91   0.00  12.50  71.63   0.00   9.10  73.91   1.02  31.05
   3_xyz:  73.91   0.00  12.50  71.63   0.00   9.10  73.91   1.02  31.05
   3_adp:  74.74   0.00  12.44  74.74   0.00   8.59  69.59   1.81  33.45
   3_occ:  74.74   0.00  12.44  74.74   0.00   8.59  69.59   1.81  33.45
   4_bss:  74.74   0.00  12.44  74.74   0.00   8.59  69.59   1.81  33.45
   4_xyz:  74.74   0.00  12.44  74.74   0.00   8.59  69.59   1.81  33.45
   4_adp:  75.86   0.00  12.61  75.86   0.00   8.55  69.92   1.38  34.71
   4_occ:  75.86   0.00  12.61  75.86   0.00   8.55  69.92   1.38  34.71
   5_bss:  75.86   0.00  12.61  75.86   0.00   8.55  69.92   1.38  34.71
   5_xyz:  75.86   0.00  12.61  75.86   0.00   8.55  69.92   1.38  34.71
   5_adp:  76.24   0.00  12.61  76.24   0.00   8.49  69.96   1.54  35.07
   5_occ:  76.24   0.00  12.61  76.24   0.00   8.49  69.96   1.54  35.07
   5_bss:  78.65   2.42  15.03  78.65   2.42  10.90  72.38   3.96  37.49
------------------------------------------------------------------------
 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:    1.203    0.022    0.416
   1_adp:    1.203    0.022    0.416
   1_occ:    1.203    0.022    0.416
   2_bss:    1.203    0.022    0.416
   2_xyz:    1.801    0.036    0.558
   2_adp:    1.801    0.036    0.558
   2_occ:    1.801    0.036    0.558
   3_bss:    1.801    0.036    0.558
   3_xyz:    1.739    0.036    0.654
   3_adp:    1.739    0.036    0.654
   3_occ:    1.739    0.036    0.654
   4_bss:    1.739    0.036    0.654
   4_xyz:    1.859    0.048    0.684
   4_adp:    1.859    0.048    0.684
   4_occ:    1.859    0.048    0.684
   5_bss:    1.859    0.048    0.684
   5_xyz:    1.988    0.046    0.703
   5_adp:    1.988    0.046    0.703
   5_occ:    1.988    0.046    0.703
   5_bss:    1.988    0.046    0.703
------------------------------------------------------------------------

CPU time actual refinement: 333.40


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_335/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_335/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_335/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_335/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_335/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 333.24 
  Macro-tasks:
    bulk solvent and scale       = 40.11  
    individual site refinement   = 135.78 
    weights calculation          = 31.73  
    collect and process          = 6.49   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 214.22 
  Micro-tasks:
    mask                            = 2.40   
    f_calc                          = 103.42 
    alpha_beta                      = 8.21   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 113.78 
    fmodel                         = 7.09   
    r_factors                      = 0.16   
    phase_errors                   = 10.72  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 247.20 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.695 micro seconds
Total CPU time: 5.78 minutes
from_scatterers_fft:    653 calls, 103.04 s
gradients_fft:          598 calls, 100.47 s

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

# Date 2008-01-16 Time 01:20:56 PST -0800 (1200475256.28 s)
Start R-work = 0.4718, R-free = 0.4572 (no bulk solvent and anisotropic scale)
Final R-work = 0.1314, R-free = 0.1739 (no bulk solvent and anisotropic scale)

Start R-work = 0.4640, R-free = 0.4512
Final R-work = 0.1138, R-free = 0.1588