# Date 2008-01-16 Time 01:14:23 PST -0800 (1200474863.25 s)
#phil __OFF__

Command line arguments: "../329.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 = 20285
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 329

-------------------------------------------------------------------------------
  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, 47.3993, 88.5498, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.3993, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.959 1.97091
Completeness in resolution range: 0.926676
Completeness with d_max=infinity: 0.923879

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9590
                             d_min =   1.9709

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, 47.3993, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.959 1.97091
Completeness in resolution range: 0.926676
Completeness with d_max=infinity: 0.923879

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9594 -  4.2175 [2219/2247]  1994   225  10.1%
  bin  2:  4.2175 -  3.3600 [2126/2149]  1911   215  10.1%
  bin  3:  3.3600 -  2.9389 [2112/2134]  1909   203   9.6%
  bin  4:  2.9389 -  2.6719 [2089/2108]  1874   215  10.3%
  bin  5:  2.6719 -  2.4813 [2062/2091]  1850   212  10.3%
  bin  6:  2.4813 -  2.3356 [2052/2094]  1853   199   9.7%
  bin  7:  2.3356 -  2.2190 [2050/2086]  1849   201   9.8%
  bin  8:  2.2190 -  2.1227 [2058/2098]  1849   209  10.2%
  bin  9:  2.1227 -  2.0412 [2019/2060]  1826   193   9.6%
  bin 10:  2.0412 -  1.9709 [ 802/2072]   715    87  10.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_329/model_refine_data.mtz


========================== Anomalous scatterer groups =========================

All atoms refined with f_prime=0 and f_double_prime=0.

========================== Set up restraints manager ==========================

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.42 -     2.12: 17
        2.12 -     2.81: 813
        2.81 -     3.51: 4435
        3.51 -     4.20: 9216
        4.20 -     4.90: 13589
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.423 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.460 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.533 3.040 -x+1,y+1/2,-z+1/2
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.647 3.120 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.690 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28065 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_329/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_329/model_refine_001.geo

CPU time processing inputs: 9.08


============================ 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 47.3993 88.54975 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 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4968   r_free= 0.4818   ksol= 0.00   Bsol= 0.00   scale= 0.777    |
|                                                                             |
| 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:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.295294                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9594 -  4.7040 0.99   1443  159 0.3968 0.3868      6.6165      6.6189|
|  2:  4.7040 -  3.7531 0.99   1396  154 0.4193 0.4788       6.802      6.9405|
|  3:  3.7531 -  3.2844 0.99   1354  156 0.4739 0.4310       6.697      6.6697|
|  4:  3.2844 -  2.9867 0.99   1354  139 0.4942 0.4617      6.5258      6.5015|
|  5:  2.9867 -  2.7741 0.99   1338  155 0.5230 0.4932      6.3686      6.3998|
|  6:  2.7741 -  2.6115 0.98   1329  148 0.5262 0.5543      6.2894       6.203|
|  7:  2.6115 -  2.4813 0.99   1324  159 0.5342 0.4593      6.2353      6.1538|
|  8:  2.4813 -  2.3737 0.99   1344  139 0.5411 0.4653      6.1844      6.1331|
|  9:  2.3737 -  2.2827 0.98   1319  144 0.5425 0.5491      6.1338      6.1982|
| 10:  2.2827 -  2.2042 0.98   1314  143 0.5526 0.5199      6.0962      6.0877|
| 11:  2.2042 -  2.1354 0.98   1302  159 0.5261 0.5551      6.0151      6.0335|
| 12:  2.1354 -  2.0746 0.99   1339  141 0.5473 0.5047      5.9566      5.9364|
| 13:  2.0746 -  2.0201 0.87   1160  118 0.5421 0.5388      5.8841      5.8569|
| 14:  2.0201 -  1.9709 0.24    314   45 0.5142 0.4073      5.9174      5.7089|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9594 -  4.7040  1443   159  0.69  35.30   0.79     0.70      73965.29|
|  2:  4.7040 -  3.7531  1396   154  0.66  38.28   0.87     0.72     120829.86|
|  3:  3.7531 -  3.2844  1354   156  0.56  47.37   0.80     0.67     126905.66|
|  4:  3.2844 -  2.9867  1354   139  0.45  55.83   0.78     0.55     111578.50|
|  5:  2.9867 -  2.7741  1338   155  0.37  62.28   0.72     0.44      87983.96|
|  6:  2.7741 -  2.6115  1329   148  0.31  66.43   0.71     0.37      79328.59|
|  7:  2.6115 -  2.4813  1324   159  0.35  63.98   0.72     0.40      66910.63|
|  8:  2.4813 -  2.3737  1344   139  0.38  61.29   0.70     0.45      56538.36|
|  9:  2.3737 -  2.2827  1319   144  0.39  60.51   0.71     0.48      52241.22|
| 10:  2.2827 -  2.2042  1314   143  0.33  65.18   0.72     0.40      48728.88|
| 11:  2.2042 -  2.1354  1302   159  0.26  70.39   0.73     0.33      51137.10|
| 12:  2.1354 -  2.0746  1339   141  0.24  71.96   0.72     0.32      46465.21|
| 13:  2.0746 -  2.0201  1160   118  0.27  70.03   0.71     0.35      40388.77|
| 14:  2.0201 -  1.9709   314    45  0.37  62.26   0.79     0.38      29042.15|
|alpha:            min =        0.32 max =            0.72 mean =         0.48|
|beta:             min =    29042.15 max =       126905.66 mean =     73950.59|
|figures of merit: min =        0.00 max =            1.00 mean =         0.41|
|phase err.(work): min =        0.00 max =           89.99 mean =        58.82|
|phase err.(test): min =        0.00 max =           89.83 mean =        59.09|
|-----------------------------------------------------------------------------|

============================== 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 = 16.830540             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.783   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.576518              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.519   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        7 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       26 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      172 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      698 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1499 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2602 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3877 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5033 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6524 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7675 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.065 |
| 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  1.196 |       2.133 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.997)------------------------------------------|
|    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 = 11.997)------------------------------------------|
|    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 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5013   r_free= 0.4849   ksol= 0.00   Bsol= 0.00   scale= 0.748    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.296766                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4876   r_free= 0.4751   ksol= 0.34   Bsol= 20.00   scale= 0.980   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.69,8.32,11.55,0.00,0.00,0.00); trace/3= 8.85                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.289529                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.588174             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.688   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.391983              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.713   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4876      final r-factor (work) = 0.4114          |
| start r-factor (free) = 0.4751      final r-factor (free) = 0.4354          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 99.9619 = 14.59 * 0.50 * 6.2924 + 1.00 * 54.0647                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 45.5060 = 14.59 * 0.50 * 6.2180 + 1.00 * 0.1515                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4114      final r-factor (work) = 0.3682          |
| start r-factor (free) = 0.4354      final r-factor (free) = 0.4219          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.6698 = 1.39 * 1.00 * 6.2180 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.5722 = 1.39 * 1.00 * 6.1449 + 1.00 * 0.0186                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.997)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.08   14.65    None  None   None       |
|    all(noH): 2823   0      0.00    88.08   14.65    None  None   None       |
|    Sol.    : 438    0      0.00    88.08   26.80    None  None   None       |
|    Mac.    : 2385   0      0.00    68.70   12.42    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.808: 1129   |   5:    44.039 -  52.847:   53        |
|      1:     8.808 -  17.616:  794   |   6:    52.847 -  61.655:   30        |
|      2:    17.616 -  26.424:  472   |   7:    61.655 -  70.463:   14        |
|      3:    26.424 -  35.232:  222   |   8:    70.463 -  79.271:    5        |
|      4:    35.232 -  44.039:  103   |   9:    79.271 -  88.079:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3682 r_free = 0.4219             target_work(ml) = 6.127         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3681 r_free = 0.4229             target_work(ml) = 6.127         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3681   r_free= 0.4229   ksol= 0.34   Bsol= 20.00   scale= 1.107   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.69,8.32,11.55,0.00,0.00,0.00); trace/3= 8.85                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.126939                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3652   r_free= 0.4198   ksol= 0.33   Bsol= 41.78   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.80,4.49,7.44,0.00,0.00,0.00); trace/3= 4.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.128683                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.342364              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.574  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.582858              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.263  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3652      final r-factor (work) = 0.2811          |
| start r-factor (free) = 0.4198      final r-factor (free) = 0.3369          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.8349 = 9.34 * 0.50 * 6.1405 + 1.00 * 0.1515                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.2314 = 9.34 * 0.50 * 6.0234 + 1.00 * 0.0948                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2811      final r-factor (work) = 0.2577          |
| start r-factor (free) = 0.3369      final r-factor (free) = 0.3166          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5296 = 0.58 * 1.00 * 6.0234 + 1.00 * 0.0188                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4379 = 0.58 * 1.00 * 5.8769 + 1.00 * 0.0125                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.997)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.46   14.37    None  None   None       |
|    all(noH): 2823   0      0.00    87.46   14.37    None  None   None       |
|    Sol.    : 438    0      0.00    87.46   32.41    None  None   None       |
|    Mac.    : 2385   0      0.00    70.07   11.06    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.746: 1244   |   5:    43.729 -  52.475:   61        |
|      1:     8.746 -  17.492:  792   |   6:    52.475 -  61.221:   34        |
|      2:    17.492 -  26.238:  348   |   7:    61.221 -  69.967:   12        |
|      3:    26.238 -  34.984:  192   |   8:    69.967 -  78.713:    5        |
|      4:    34.984 -  43.729:  134   |   9:    78.713 -  87.459:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2577 r_free = 0.3166             target_work(ml) = 5.856         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2574 r_free = 0.3163             target_work(ml) = 5.855         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2574   r_free= 0.3163   ksol= 0.33   Bsol= 41.78   scale= 1.058   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.80,4.49,7.44,0.00,0.00,0.00); trace/3= 4.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.855319                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2556   r_free= 0.3158   ksol= 0.31   Bsol= 41.78   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.11,2.64,4.67,0.00,0.00,0.00); trace/3= 2.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.855608                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.307128              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.827  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.469078              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.761  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2556      final r-factor (work) = 0.2035          |
| start r-factor (free) = 0.3158      final r-factor (free) = 0.2564          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8182 = 3.31 * 0.50 * 5.8802 + 1.00 * 0.0948                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5940 = 3.31 * 0.50 * 5.7635 + 1.00 * 0.0637                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2035      final r-factor (work) = 0.1849          |
| start r-factor (free) = 0.2564      final r-factor (free) = 0.2447          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 20.0067 = 3.47 * 1.00 * 5.7635 + 1.00 * 0.0126                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 19.4816 = 3.47 * 1.00 * 5.6102 + 1.00 * 0.0195                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.997)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.87   15.76    None  None   None       |
|    all(noH): 2823   0      0.00    97.87   15.76    None  None   None       |
|    Sol.    : 438    0      1.34    97.87   42.67    None  None   None       |
|    Mac.    : 2385   0      0.00    81.01   10.82    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:     0.000 -   9.788: 1450   |   5:    48.937 -  58.725:   98        |
|      1:     9.788 -  19.575:  690   |   6:    58.725 -  68.512:   58        |
|      2:    19.575 -  29.363:  241   |   7:    68.512 -  78.300:   37        |
|      3:    29.363 -  39.150:  123   |   8:    78.300 -  88.087:   20        |
|      4:    39.150 -  48.937:  101   |   9:    88.087 -  97.875:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1849 r_free = 0.2447             target_work(ml) = 5.590         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1848 r_free = 0.2449             target_work(ml) = 5.590         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1848   r_free= 0.2449   ksol= 0.31   Bsol= 41.78   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.11,2.64,4.67,0.00,0.00,0.00); trace/3= 2.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.590013                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1844   r_free= 0.2441   ksol= 0.33   Bsol= 65.75   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.47,1.88,3.66,0.00,0.00,0.00); trace/3= 2.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.587629                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.620774              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.654  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.929063              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.491  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1844      final r-factor (work) = 0.1534          |
| start r-factor (free) = 0.2441      final r-factor (free) = 0.2099          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4185 = 2.62 * 0.50 * 5.6127 + 1.00 * 0.0637                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2877 = 2.62 * 0.50 * 5.5131 + 1.00 * 0.0634                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1534      final r-factor (work) = 0.1451          |
| start r-factor (free) = 0.2099      final r-factor (free) = 0.1998          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.6544 = 1.93 * 1.00 * 5.5131 + 1.00 * 0.0193                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.4425 = 1.93 * 1.00 * 5.4033 + 1.00 * 0.0193                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.997)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.14  15.43    None  None   None       |
|    all(noH): 2823   0      0.00    106.14  15.43    None  None   None       |
|    Sol.    : 438    0      1.18    106.14  43.76    None  None   None       |
|    Mac.    : 2385   0      0.00    87.78   10.23    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 -  10.614: 1638   |   5:    53.072 -  63.686:   90        |
|      1:    10.614 -  21.229:  625   |   6:    63.686 -  74.300:   44        |
|      2:    21.229 -  31.843:  163   |   7:    74.300 -  84.914:   29        |
|      3:    31.843 -  42.457:  106   |   8:    84.914 -  95.529:   12        |
|      4:    42.457 -  53.072:  113   |   9:    95.529 - 106.143:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1451 r_free = 0.1998             target_work(ml) = 5.378         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1450 r_free = 0.1998             target_work(ml) = 5.378         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1450   r_free= 0.1998   ksol= 0.33   Bsol= 65.75   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.47,1.88,3.66,0.00,0.00,0.00); trace/3= 2.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.377650                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1452   r_free= 0.2003   ksol= 0.33   Bsol= 68.83   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.46,1.64,3.24,0.00,0.00,0.00); trace/3= 1.78                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.379182                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.839256              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.224  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.993649              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 101.857  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1452      final r-factor (work) = 0.1356          |
| start r-factor (free) = 0.2003      final r-factor (free) = 0.1859          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0329 = 1.84 * 0.50 * 5.4038 + 1.00 * 0.0634                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9792 = 1.84 * 0.50 * 5.3516 + 1.00 * 0.0578                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1356      final r-factor (work) = 0.1329          |
| start r-factor (free) = 0.1859      final r-factor (free) = 0.1825          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 21.3932 = 3.99 * 1.00 * 5.3516 + 1.00 * 0.0210                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 21.2273 = 3.99 * 1.00 * 5.3107 + 1.00 * 0.0182                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.997)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    111.50  15.25    None  None   None       |
|    all(noH): 2823   0      0.00    111.50  15.25    None  None   None       |
|    Sol.    : 438    0      1.01    111.50  43.95    None  None   None       |
|    Mac.    : 2385   0      0.00    94.87   9.98     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 -  11.151: 1741   |   5:    55.752 -  66.903:   71        |
|      1:    11.151 -  22.301:  554   |   6:    66.903 -  78.053:   48        |
|      2:    22.301 -  33.451:  160   |   7:    78.053 -  89.204:   25        |
|      3:    33.451 -  44.602:  104   |   8:    89.204 - 100.354:   10        |
|      4:    44.602 -  55.752:  107   |   9:   100.354 - 111.505:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1329 r_free = 0.1825             target_work(ml) = 5.303         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1328 r_free = 0.1825             target_work(ml) = 5.303         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1328   r_free= 0.1825   ksol= 0.33   Bsol= 68.83   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.46,1.64,3.24,0.00,0.00,0.00); trace/3= 1.78                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.302742                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9594 -  4.7040 0.99   1443  159 0.1026 0.1420       5.451      5.6579|
|  2:  4.7040 -  3.7531 0.99   1396  154 0.0939 0.1170      5.5213      5.7167|
|  3:  3.7531 -  3.2844 0.99   1354  156 0.1234 0.1659      5.6081      5.9064|
|  4:  3.2844 -  2.9867 0.99   1354  139 0.1478 0.1964      5.5884      5.8039|
|  5:  2.9867 -  2.7741 0.99   1338  155 0.1636 0.1854      5.5222      5.6534|
|  6:  2.7741 -  2.6115 0.98   1329  148 0.1523 0.2562      5.3848      5.6911|
|  7:  2.6115 -  2.4813 0.99   1324  159 0.1549 0.1806      5.3435      5.4518|
|  8:  2.4813 -  2.3737 0.99   1344  139 0.1468 0.2155      5.2652      5.4891|
|  9:  2.3737 -  2.2827 0.98   1319  144 0.1408 0.2119      5.1795      5.4948|
| 10:  2.2827 -  2.2042 0.98   1314  143 0.1377 0.1875       5.109      5.2572|
| 11:  2.2042 -  2.1354 0.98   1302  159 0.1336 0.2174      5.0412      5.4228|
| 12:  2.1354 -  2.0746 0.99   1339  141 0.1369 0.1806      5.0193      5.2283|
| 13:  2.0746 -  2.0201 0.87   1160  118 0.1323 0.1965       4.924      5.1298|
| 14:  2.0201 -  1.9709 0.24    314   45 0.1139 0.1961      4.8278      5.0693|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9594 -  4.7040  1443   159  0.93  10.48   0.96     0.93       8863.06|
|  2:  4.7040 -  3.7531  1396   154  0.94   9.31   1.01     0.99      10807.17|
|  3:  3.7531 -  3.2844  1354   156  0.92  13.37   1.04     1.03      13386.56|
|  4:  3.2844 -  2.9867  1354   139  0.90  16.54   1.02     1.00      13321.74|
|  5:  2.9867 -  2.7741  1338   155  0.86  20.06   1.01     0.98      12842.94|
|  6:  2.7741 -  2.6115  1329   148  0.86  20.26   0.98     0.93      10212.46|
|  7:  2.6115 -  2.4813  1324   159  0.87  19.80   0.99     0.95       9126.07|
|  8:  2.4813 -  2.3737  1344   139  0.87  19.83   1.00     0.95       8103.88|
|  9:  2.3737 -  2.2827  1319   144  0.87  19.33   0.99     0.94       6830.48|
| 10:  2.2827 -  2.2042  1314   143  0.88  18.77   0.99     0.95       5922.06|
| 11:  2.2042 -  2.1354  1302   159  0.88  19.00   0.99     0.93       5389.06|
| 12:  2.1354 -  2.0746  1339   141  0.88  19.20   0.99     0.98       5294.15|
| 13:  2.0746 -  2.0201  1160   118  0.87  19.64   0.97     0.94       4524.91|
| 14:  2.0201 -  1.9709   314    45  0.90  16.67   0.96     0.91       3537.12|
|alpha:            min =        0.91 max =            1.03 mean =         0.96|
|beta:             min =     3537.12 max =        13386.56 mean =      8793.30|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.95 mean =        17.24|
|phase err.(test): min =        0.00 max =           88.89 mean =        16.61|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1328   r_free= 0.1825   ksol= 0.33   Bsol= 68.57   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.24,-0.17,1.41,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.302874                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1328   r_free= 0.1825   ksol= 0.33   Bsol= 68.57   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.24,-0.17,1.41,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.302874                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9594 -  4.7040 0.99   1443  159 0.1026 0.1421      5.4506      5.6581|
|  2:  4.7040 -  3.7531 0.99   1396  154 0.0938 0.1169      5.5211      5.7158|
|  3:  3.7531 -  3.2844 0.99   1354  156 0.1234 0.1660      5.6083      5.9073|
|  4:  3.2844 -  2.9867 0.99   1354  139 0.1478 0.1966      5.5887      5.8045|
|  5:  2.9867 -  2.7741 0.99   1338  155 0.1636 0.1854      5.5226      5.6539|
|  6:  2.7741 -  2.6115 0.98   1329  148 0.1523 0.2562       5.385      5.6913|
|  7:  2.6115 -  2.4813 0.99   1324  159 0.1550 0.1808      5.3438      5.4521|
|  8:  2.4813 -  2.3737 0.99   1344  139 0.1468 0.2156      5.2656      5.4897|
|  9:  2.3737 -  2.2827 0.98   1319  144 0.1407 0.2121      5.1798      5.4958|
| 10:  2.2827 -  2.2042 0.98   1314  143 0.1377 0.1876      5.1091      5.2567|
| 11:  2.2042 -  2.1354 0.98   1302  159 0.1336 0.2173      5.0412      5.4224|
| 12:  2.1354 -  2.0746 0.99   1339  141 0.1370 0.1809      5.0196       5.229|
| 13:  2.0746 -  2.0201 0.87   1160  118 0.1323 0.1963      4.9239      5.1287|
| 14:  2.0201 -  1.9709 0.24    314   45 0.1139 0.1961      4.8288      5.0698|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9594 -  4.7040  1443   159  0.93  10.49   0.96     0.93       8862.23|
|  2:  4.7040 -  3.7531  1396   154  0.94   9.31   1.02     1.00      10803.97|
|  3:  3.7531 -  3.2844  1354   156  0.92  13.37   1.04     1.03      13389.07|
|  4:  3.2844 -  2.9867  1354   139  0.90  16.56   1.02     1.00      13330.53|
|  5:  2.9867 -  2.7741  1338   155  0.86  20.07   1.01     0.98      12858.91|
|  6:  2.7741 -  2.6115  1329   148  0.86  20.27   0.98     0.93      10217.22|
|  7:  2.6115 -  2.4813  1324   159  0.87  19.82   0.99     0.95       9136.55|
|  8:  2.4813 -  2.3737  1344   139  0.87  19.85   1.00     0.96       8112.50|
|  9:  2.3737 -  2.2827  1319   144  0.87  19.34   1.00     0.94       6838.69|
| 10:  2.2827 -  2.2042  1314   143  0.88  18.77   0.99     0.95       5922.13|
| 11:  2.2042 -  2.1354  1302   159  0.88  19.00   0.99     0.93       5386.19|
| 12:  2.1354 -  2.0746  1339   141  0.88  19.20   0.99     0.99       5294.67|
| 13:  2.0746 -  2.0201  1160   118  0.87  19.64   0.98     0.95       4521.21|
| 14:  2.0201 -  1.9709   314    45  0.90  16.67   0.97     0.92       3533.14|
|alpha:            min =        0.92 max =            1.03 mean =         0.96|
|beta:             min =     3533.14 max =        13389.07 mean =      8797.00|
|figures of merit: min =        0.00 max =            1.00 mean =         0.89|
|phase err.(work): min =        0.00 max =           89.95 mean =        17.24|
|phase err.(test): min =        0.00 max =           88.90 mean =        16.62|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.997)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.85    113.36  17.10    None  None   None       |
|    all(noH): 2823   0      1.85    113.36  17.10    None  None   None       |
|    Sol.    : 438    0      2.86    113.36  45.81    None  None   None       |
|    Mac.    : 2385   0      1.85    96.72   11.83    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.853 -  13.003: 1741   |   5:    57.605 -  68.756:   71        |
|      1:    13.003 -  24.154:  554   |   6:    68.756 -  79.906:   48        |
|      2:    24.154 -  35.304:  160   |   7:    79.906 -  91.057:   25        |
|      3:    35.304 -  46.455:  104   |   8:    91.057 - 102.207:   10        |
|      4:    46.455 -  57.605:  107   |   9:   102.207 - 113.358:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 319         
Filter by distance & map next to the model:
   mapped sites are within: 0.549 - 5.131
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 312 from: 319
   mapped sites are within: 0.723 - 5.131

peak=    9.336 closest distance to " CB  VAL A 230 " =    1.364
peak=    8.097 closest distance to " CG1 VAL A 296 " =    1.286
peak=    6.351 closest distance to " CG  ARG A 138 " =    1.217
peak=    6.108 closest distance to " CD1AILE A 234 " =    1.123
peak=    6.055 closest distance to " CD2 LEU A   5 " =    1.208
peak=    5.850 closest distance to " O   HOH Z 248 " =    1.411
peak=    5.790 closest distance to " NH1 ARG A 138 " =    1.000
peak=    5.602 closest distance to " O   HOH Z 255 " =    0.977
peak=    5.174 closest distance to " O   HOH Z 210 " =    1.271
peak=    5.088 closest distance to " O   HOH Z 403 " =    1.878
peak=    5.022 closest distance to " O   HOH Z 203 " =    0.897
peak=    4.957 closest distance to " CB  GLN A 223 " =    1.497
peak=    4.807 closest distance to " CG  PRO A  54 " =    1.468
peak=    4.805 closest distance to " O  BHOH Z  74 " =    1.126
peak=    4.798 closest distance to " CZ3 TRP A 266 " =    1.154
peak=    4.796 closest distance to " O   HOH Z 107 " =    1.226
peak=    4.742 closest distance to " O   HOH Z 394 " =    1.547
peak=    4.702 closest distance to " O   HOH Z 425 " =    1.630
peak=    4.687 closest distance to " CZ  PHE A 218 " =    1.188
peak=    4.684 closest distance to " O   HOH Z 214 " =    1.543
peak=    4.679 closest distance to " O   HOH Z 404 " =    1.080
peak=    4.614 closest distance to " O   HOH Z 127 " =    0.941
peak=    4.595 closest distance to " CB  VAL A 230 " =    1.307
peak=    4.591 closest distance to " CA  TYR A  30 " =    0.999
peak=    4.582 closest distance to " NH2 ARG A  56 " =    2.039
peak=    4.569 closest distance to " CD2 LEU A 228 " =    1.260
peak=    4.534 closest distance to " O   HOH Z  69 " =    0.889
peak=    4.509 closest distance to " NE2 GLN A  11 " =    1.085
peak=    4.467 closest distance to " CB  ARG A 275 " =    1.033
peak=    4.458 closest distance to " CB  GLN A  58 " =    1.012
peak=    4.455 closest distance to " CG  PRO A 243 " =    1.136
peak=    4.441 closest distance to " O   HOH Z 258 " =    1.279
peak=    4.433 closest distance to " O   HOH Z  76 " =    1.450
peak=    4.420 closest distance to " O   HOH Z 188 " =    1.320
peak=    4.409 closest distance to " O   HOH Z 128 " =    1.548
peak=    4.394 closest distance to " CB  ASN A 148 " =    1.392
peak=    4.344 closest distance to " O   HOH Z 402 " =    1.519
peak=    4.334 closest distance to " CD2 TRP A 179 " =    1.289
peak=    4.310 closest distance to " O   HOH Z  65 " =    0.813
peak=    4.260 closest distance to " O   HOH Z 232 " =    2.254
peak=    4.254 closest distance to " O   PRO A 198 " =    1.621
peak=    4.250 closest distance to " O   HOH Z 251 " =    1.848
peak=    4.250 closest distance to " O   HOH Z 117 " =    1.172
peak=    4.235 closest distance to " NH2AARG A 145 " =    1.143
peak=    4.201 closest distance to " O   HOH Z 124 " =    1.335
peak=    4.194 closest distance to " O   HOH Z 246 " =    1.153
peak=    4.190 closest distance to " O   HOH Z 126 " =    1.618
peak=    4.174 closest distance to " O   HOH Z 369 " =    2.129
peak=    4.153 closest distance to " CB  SER A  26 " =    1.745
peak=    4.121 closest distance to " N   SER A 164 " =    0.883
peak=    4.116 closest distance to " CG  LEU A   5 " =    1.247
peak=    4.102 closest distance to " O   HOH Z 372 " =    1.036
peak=    4.096 closest distance to " O   HOH Z 411 " =    3.894
peak=    4.075 closest distance to " O   HOH Z 422 " =    2.576
peak=    4.072 closest distance to " CG  PRO A 198 " =    1.222
peak=    4.072 closest distance to " O   SER A  87 " =    2.326
peak=    4.046 closest distance to " CB  TRP A 179 " =    1.404
peak=    4.046 closest distance to " O   HOH Z 365 " =    2.712
peak=    4.025 closest distance to " O   HOH Z 331 " =    0.942
peak=    4.012 closest distance to " O   HOH Z 287 " =    1.616
peak=    4.002 closest distance to " CB  VAL A 265 " =    1.213
peak=    4.002 closest distance to " O   HOH Z   4 " =    1.684
peak=    3.989 closest distance to " CE3 TRP A 274 " =    1.147
peak=    3.976 closest distance to " CE  LYS A  76 " =    0.888
peak=    3.968 closest distance to " CG2 VAL A 296 " =    1.013
peak=    3.967 closest distance to " O   HOH Z 207 " =    1.301
peak=    3.953 closest distance to " CB  ARG A 138 " =    1.113
peak=    3.948 closest distance to " CA  ARG A  36 " =    0.975
peak=    3.934 closest distance to " CG  LEU A 228 " =    1.290
peak=    3.929 closest distance to " CA  GLN A  58 " =    0.825
peak=    3.922 closest distance to " O   HOH Z 303 " =    2.188
peak=    3.917 closest distance to " O   HOH Z 103 " =    0.951
peak=    3.911 closest distance to " O   HOH Z 142 " =    1.683
peak=    3.901 closest distance to " CG  GLN A  58 " =    1.069
peak=    3.894 closest distance to " O   HOH Z 154 " =    1.747
peak=    3.892 closest distance to " CG  ARG A  66 " =    2.638
peak=    3.884 closest distance to " CG2 VAL A 197 " =    1.159
peak=    3.867 closest distance to " CD  LYS A 119 " =    1.910
peak=    3.860 closest distance to " CD  LYS A  76 " =    1.814
peak=    3.852 closest distance to " CD2 LEU A 297 " =    0.802
peak=    3.850 closest distance to " O   HOH Z 357 " =    2.133
peak=    3.835 closest distance to " CG  PHE A 204 " =    0.931
peak=    3.826 closest distance to " CZ  PHE A  38 " =    1.050
peak=    3.824 closest distance to " CA  ARG A 195 " =    1.227
peak=    3.810 closest distance to " CA  ALA A 100 " =    0.944
peak=    3.807 closest distance to " O   HOH Z 258 " =    1.477
peak=    3.800 closest distance to " CG2AVAL A 121 " =    2.124
peak=    3.800 closest distance to " O   HOH Z  85 " =    1.332
peak=    3.798 closest distance to " O   HOH Z 154 " =    2.130
peak=    3.792 closest distance to " O   HOH Z 316 " =    3.115
peak=    3.784 closest distance to " CB  SER A 273 " =    0.968
peak=    3.783 closest distance to " CG2 ILE A 234 " =    1.185
peak=    3.779 closest distance to " O   HOH Z 112 " =    1.009
peak=    3.776 closest distance to " CB  THR A  52 " =    0.840
peak=    3.768 closest distance to " CA  ASP A 162 " =    1.155
peak=    3.756 closest distance to " CB  ARG A 190 " =    1.680
peak=    3.754 closest distance to " CG1 ILE A 120 " =    0.908
peak=    3.752 closest distance to " ND2BASN A 224 " =    0.832
peak=    3.749 closest distance to " CB  GLN A  89 " =    1.378
peak=    3.744 closest distance to " CA  GLU A 152 " =    0.736
peak=    3.743 closest distance to " CB  GLU A 277 " =    3.749
peak=    3.743 closest distance to " O   HOH Z 193 " =    1.907
peak=    3.738 closest distance to " CD  LYS A 166 " =    1.486
peak=    3.737 closest distance to " CD  PRO A  54 " =    0.986
peak=    3.730 closest distance to " CA  ALA A  51 " =    1.117
peak=    3.728 closest distance to " CB  GLN A 183 " =    1.227
peak=    3.720 closest distance to " O   HOH Z 132 " =    2.873
peak=    3.714 closest distance to " CA  VAL A 125 " =    1.211
peak=    3.709 closest distance to " CG  MET A 185 " =    1.189
peak=    3.708 closest distance to " O   HOH Z 188 " =    2.597
peak=    3.708 closest distance to " O   HOH Z 261 " =    2.438
peak=    3.708 closest distance to " O   HOH Z 365 " =    2.370
peak=    3.703 closest distance to " CA  ALA A 160 " =    0.942
peak=    3.693 closest distance to " O   HOH Z 371 " =    2.569
peak=    3.689 closest distance to " O   HOH Z  49 " =    1.274
peak=    3.682 closest distance to " NH2 ARG A  56 " =    1.147
peak=    3.677 closest distance to " O   HOH Z 238 " =    1.483
peak=    3.673 closest distance to " O   HOH Z   9 " =    1.159
peak=    3.673 closest distance to " CB  ASN A 142 " =    1.196
peak=    3.670 closest distance to " O   HOH Z 193 " =    2.057
peak=    3.653 closest distance to " CD  ARG A 269 " =    1.101
peak=    3.651 closest distance to " CB  PRO A  54 " =    0.972
peak=    3.651 closest distance to " O   HOH Z  40 " =    1.648
peak=    3.646 closest distance to " CB  ALA A 248 " =    1.479
peak=    3.646 closest distance to " CB  PRO A  90 " =    1.087
peak=    3.640 closest distance to " CD1 LEU A  96 " =    0.847
peak=    3.631 closest distance to " O   HOH Z  88 " =    3.505
peak=    3.629 closest distance to " CB  ARG A  79 " =    1.198
peak=    3.622 closest distance to " CB  ASN A 187 " =    1.504
peak=    3.610 closest distance to " CB  ASP A 107 " =    1.232
peak=    3.609 closest distance to " CB  ALA A 114 " =    0.859
peak=    3.608 closest distance to " O   HOH Z 130 " =    0.999
peak=    3.606 closest distance to " O   HOH Z 359 " =    1.972
peak=    3.601 closest distance to " CD  ARG A 159 " =    0.737
peak=    3.599 closest distance to " CB  SER A  63 " =    1.201
peak=    3.595 closest distance to " NE2 GLN A  77 " =    3.232
peak=    3.580 closest distance to " CE3 TRP A  85 " =    1.269
peak=    3.574 closest distance to " O   HOH Z 433 " =    1.497
peak=    3.573 closest distance to " O   HOH Z 126 " =    1.765
peak=    3.563 closest distance to " O   HOH Z 214 " =    3.236
peak=    3.562 closest distance to " CD  ARG A 138 " =    1.212
peak=    3.553 closest distance to " O   HOH Z 162 " =    1.667
peak=    3.549 closest distance to " O   HOH Z 406 " =    1.608
peak=    3.549 closest distance to " O   THR A 220 " =    1.316
peak=    3.544 closest distance to " CB  ASN A 110 " =    1.106
peak=    3.544 closest distance to " CA  TYR A 116 " =    1.462
peak=    3.540 closest distance to " N   ALA A 256 " =    1.171
peak=    3.539 closest distance to " CB BVAL A  41 " =    1.337
peak=    3.529 closest distance to " O   HOH Z  85 " =    1.737
peak=    3.519 closest distance to " N   ASP A 231 " =    1.537
peak=    3.515 closest distance to " CA  ARG A 156 " =    1.122
peak=    3.514 closest distance to " CB  THR A 235 " =    1.484
peak=    3.514 closest distance to " CE1 TYR A 186 " =    1.231
peak=    3.512 closest distance to " O   HOH Z 427 " =    3.023
peak=    3.512 closest distance to " O   HOH Z  63 " =    1.725
peak=    3.511 closest distance to " CG AARG A 275 " =    1.345
peak=    3.510 closest distance to " CB  ASN A  39 " =    0.865
peak=    3.505 closest distance to " CG  LEU A 167 " =    1.135
peak=    3.505 closest distance to " O   HOH Z 329 " =    4.120
peak=    3.503 closest distance to " O   HOH Z 368 " =    3.351
peak=    3.500 closest distance to " CB  VAL A 202 " =    1.435
peak=    3.496 closest distance to " CB  PRO A 198 " =    1.199
peak=    3.492 closest distance to " O  BHOH Z 338 " =    2.186
peak=    3.486 closest distance to " CB  GLN A  55 " =    0.910
peak=    3.484 closest distance to " CB  GLU A 175 " =    1.320
peak=    3.481 closest distance to " NZ  LYS A 117 " =    2.956
peak=    3.475 closest distance to " O   HOH Z 421 " =    1.881
peak=    3.473 closest distance to " O   HOH Z 234 " =    3.536
peak=    3.466 closest distance to " O   HOH Z 236 " =    1.583
peak=    3.460 closest distance to " O   HOH Z 116 " =    1.118
peak=    3.458 closest distance to " O   HOH Z 298 " =    2.194
peak=    3.453 closest distance to " CB  ASP A 124 " =    0.940
peak=    3.451 closest distance to " CB  VAL A 296 " =    1.124
peak=    3.451 closest distance to " O   HOH Z 265 " =    2.069
peak=    3.449 closest distance to " N   ASP A 162 " =    1.345
peak=    3.433 closest distance to " O   HOH Z  80 " =    2.081
peak=    3.431 closest distance to " CB  LYS A 117 " =    1.179
peak=    3.428 closest distance to " O   HOH Z 393 " =    3.226
peak=    3.426 closest distance to " CB  SER A  95 " =    1.119
peak=    3.424 closest distance to " NH1AARG A 102 " =    1.002
peak=    3.423 closest distance to " CA  ALA A 295 " =    0.936
peak=    3.423 closest distance to " O   HOH Z 284 " =    3.041
peak=    3.421 closest distance to " CB  MET A  40 " =    0.790
peak=    3.421 closest distance to " O   HOH Z 343 " =    2.828
peak=    3.420 closest distance to " O   HOH Z 151 " =    1.690
peak=    3.419 closest distance to " CG1 VAL A 257 " =    1.394
peak=    3.413 closest distance to " CD  ARG A 139 " =    0.995
peak=    3.410 closest distance to " CB  PRO A 243 " =    1.180
peak=    3.405 closest distance to " CG2 VAL A 257 " =    0.794
peak=    3.403 closest distance to " ND2 ASN A 249 " =    0.881
peak=    3.396 closest distance to " O   HOH Z 129 " =    1.119
peak=    3.392 closest distance to " N   TYR A 247 " =    1.287
peak=    3.390 closest distance to " O   HOH Z 221 " =    1.067
peak=    3.385 closest distance to " O   HOH Z 133 " =    1.346
peak=    3.385 closest distance to " CB  SER A  62 " =    1.122
peak=    3.378 closest distance to " NE1 TRP A  92 " =    1.788
peak=    3.374 closest distance to " CA  ALA A 154 " =    1.107
peak=    3.365 closest distance to " OG BSER A  99 " =    3.001
peak=    3.362 closest distance to " N   TYR A  15 " =    1.138
peak=    3.362 closest distance to " OG BSER A 212 " =    2.578
peak=    3.362 closest distance to " O   HOH Z 227 " =    1.425
peak=    3.361 closest distance to " CA  ILE A 239 " =    0.950
peak=    3.360 closest distance to " CB  TRP A 150 " =    1.303
peak=    3.360 closest distance to " CG2 ILE A  20 " =    1.536
peak=    3.359 closest distance to " O   HOH Z 313 " =    1.943
peak=    3.350 closest distance to " NH1AARG A 145 " =    1.305
peak=    3.348 closest distance to " CA  ASN A 217 " =    1.182
peak=    3.345 closest distance to " O   HOH Z 134 " =    1.015
peak=    3.344 closest distance to " O   ASP A 124 " =    1.173
peak=    3.344 closest distance to " CB  ASN A 215 " =    1.172
peak=    3.343 closest distance to " CB  ARG A 275 " =    0.979
peak=    3.342 closest distance to " O   HOH Z 415 " =    3.161
peak=    3.341 closest distance to " O   HOH Z 361 " =    2.546
peak=    3.338 closest distance to " O   THR A 251 " =    1.093
peak=    3.337 closest distance to " O   HOH Z   1 " =    2.179
peak=    3.334 closest distance to " O   HOH Z 337 " =    1.722
peak=    3.326 closest distance to " O   HOH Z 371 " =    1.496
peak=    3.321 closest distance to " O   HOH Z 215 " =    1.266
peak=    3.319 closest distance to " O   HOH Z 353 " =    2.746
peak=    3.318 closest distance to " CG1 ILE A  33 " =    1.290
peak=    3.317 closest distance to " O   HOH Z  19 " =    1.901
peak=    3.315 closest distance to " CB  GLU A 128 " =    1.148
peak=    3.311 closest distance to " CB  GLU A 152 " =    1.476
peak=    3.309 closest distance to " O   HOH Z   3 " =    1.548
peak=    3.305 closest distance to " O   HOH Z 346 " =    1.558
peak=    3.298 closest distance to " CB  ASP A 191 " =    1.338
peak=    3.297 closest distance to " O   HOH Z  43 " =    2.173
peak=    3.292 closest distance to " O   HOH Z 389 " =    1.991
peak=    3.291 closest distance to " CD1 ILE A  33 " =    1.658
peak=    3.289 closest distance to " OG BSER A 258 " =    2.777
peak=    3.288 closest distance to " CB  ASP A 171 " =    0.723
peak=    3.288 closest distance to " O   HOH Z 174 " =    2.295
peak=    3.284 closest distance to " CB  GLU A  46 " =    1.018
peak=    3.284 closest distance to " O   GLN A  88 " =    1.593
peak=    3.282 closest distance to " CB  TRP A 266 " =    1.075
peak=    3.282 closest distance to " O   HOH Z 213 " =    1.791
peak=    3.276 closest distance to " O   HOH Z 272 " =    1.792
peak=    3.271 closest distance to " O   HOH Z  30 " =    1.157
peak=    3.270 closest distance to " O   HOH Z 438 " =    2.732
peak=    3.267 closest distance to " NE  ARG A 138 " =    1.190
peak=    3.266 closest distance to " CA  ILE A 234 " =    0.950
peak=    3.262 closest distance to " O   HOH Z 200 " =    2.689
peak=    3.260 closest distance to " OG  SER A 135 " =    1.345
peak=    3.260 closest distance to " O   GLY A  91 " =    1.207
peak=    3.257 closest distance to " O   HOH Z  26 " =    1.108
peak=    3.249 closest distance to " OG  SER A  22 " =    2.541
peak=    3.249 closest distance to " CE  MET A  93 " =    1.374
peak=    3.246 closest distance to " O   HOH Z 293 " =    2.157
peak=    3.245 closest distance to " O   HOH Z 141 " =    1.535
peak=    3.242 closest distance to " OG  SER A 146 " =    0.758
peak=    3.239 closest distance to " CB  ASN A  45 " =    1.158
peak=    3.238 closest distance to " CG AARG A 102 " =    1.298
peak=    3.232 closest distance to " O   HOH Z 189 " =    2.827
peak=    3.229 closest distance to " N   PHE A 130 " =    1.452
peak=    3.228 closest distance to " O   HOH Z 209 " =    2.232
peak=    3.228 closest distance to " O   HOH Z 290 " =    1.328
peak=    3.227 closest distance to " CG  GLN A  11 " =    1.552
peak=    3.220 closest distance to " O   HOH Z 380 " =    2.104
peak=    3.218 closest distance to " OE1 GLU A   2 " =    1.394
peak=    3.217 closest distance to " O   HOH Z 298 " =    4.385
peak=    3.213 closest distance to " N   ASN A  39 " =    1.275
peak=    3.211 closest distance to " CA  LYS A 117 " =    1.311
peak=    3.209 closest distance to " O   HOH Z 263 " =    1.537
peak=    3.209 closest distance to " CG2 THR A 220 " =    0.867
peak=    3.205 closest distance to " N   THR A  52 " =    1.231
peak=    3.203 closest distance to " O   HOH Z 146 " =    1.414
peak=    3.202 closest distance to " O   HOH Z 192 " =    1.173
peak=    3.202 closest distance to " O   HOH Z 252 " =    2.601
peak=    3.196 closest distance to " CG2 ILE A 120 " =    1.401
peak=    3.193 closest distance to " O   HOH Z 314 " =    1.785
peak=    3.188 closest distance to " O   THR A 294 " =    1.739
peak=    3.185 closest distance to " CB  ASP A 298 " =    1.156
peak=    3.185 closest distance to " CD  ARG A 195 " =    0.975
peak=    3.184 closest distance to " CG1 ILE A  20 " =    1.168
peak=    3.175 closest distance to " O   HOH Z 327 " =    2.081
peak=    3.169 closest distance to " C   PHE A 208 " =    1.038
peak=    3.168 closest distance to " CB  ILE A 199 " =    1.101
peak=    3.168 closest distance to " CG1 VAL A 153 " =    1.014
peak=    3.167 closest distance to " O   HOH Z  29 " =    1.179
peak=    3.165 closest distance to " OE2 GLU A  53 " =    1.063
peak=    3.163 closest distance to " CA  TYR A 214 " =    1.228
peak=    3.163 closest distance to " CG  ARG A  56 " =    1.265
peak=    3.163 closest distance to " O   HOH Z 285 " =    2.213
peak=    3.160 closest distance to " O   HOH Z 111 " =    1.297
peak=    3.159 closest distance to " O   ALA A 292 " =    1.102
peak=    3.158 closest distance to " O   GLU A   2 " =    1.638
peak=    3.156 closest distance to " CA  ASN A 215 " =    1.128
peak=    3.150 closest distance to " O   THR A 157 " =    1.100
peak=    3.134 closest distance to " O   HOH Z 344 " =    2.823
peak=    3.129 closest distance to " O   HOH Z 368 " =    4.082
peak=    3.124 closest distance to " CB  ALA A 292 " =    0.856
peak=    3.124 closest distance to " O   HOH Z 171 " =    3.590
peak=    3.122 closest distance to " CE1 HIS A  81 " =    1.584
peak=    3.116 closest distance to " O   HOH Z 279 " =    2.332
peak=    3.112 closest distance to " CA  ASP A 124 " =    0.776
peak=    3.106 closest distance to " O   HOH Z 420 " =    5.131
peak=    3.106 closest distance to " NE2 GLN A 103 " =    0.977
peak=    3.104 closest distance to " O   HOH Z 172 " =    3.609
peak=    3.095 closest distance to " O   HOH Z 143 " =    1.355
peak=    3.095 closest distance to " NE2 GLN A  58 " =    2.953
peak=    3.088 closest distance to " O   HOH Z 222 " =    1.145
peak=    3.086 closest distance to " NH1 ARG A  14 " =    1.431
peak=    3.073 closest distance to " CA  ASP A 149 " =    1.099
peak=    3.071 closest distance to " O   HOH Z 423 " =    2.893
peak=    3.070 closest distance to " O   HOH Z  63 " =    1.805
peak=    3.061 closest distance to " NE  ARG A  24 " =    0.957
peak=    3.060 closest distance to " CE1 HIS A 115 " =    1.071
peak=    3.058 closest distance to " O   HOH Z 403 " =    1.335
peak=    3.056 closest distance to " O   HOH Z 361 " =    2.966
peak=    3.047 closest distance to " CB  ASN A  74 " =    1.462
peak=    3.037 closest distance to " CZ  PHE A 155 " =    0.825
peak=    3.036 closest distance to " O   ASN A 187 " =    1.425

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.428 - 5.929
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 202 from: 204
   mapped sites are within: 0.748 - 5.929

peak=   -5.788 closest distance to " O   HOH Z 203 " =    0.970
peak=   -4.964 closest distance to " CD  ARG A 138 " =    1.184
peak=   -4.676 closest distance to " OG BSER A 134 " =    1.449
peak=   -4.652 closest distance to " CG2 VAL A 230 " =    0.830
peak=   -4.515 closest distance to " CG1 VAL A 296 " =    1.013
peak=   -4.492 closest distance to " O   PRO A 198 " =    1.330
peak=   -4.457 closest distance to " O   HOH Z 166 " =    1.505
peak=   -4.354 closest distance to " CD1 PHE A  59 " =    2.090
peak=   -4.346 closest distance to " CG  GLN A  58 " =    0.933
peak=   -4.176 closest distance to " O   HOH Z 411 " =    5.637
peak=   -4.144 closest distance to " CZ2 TRP A  92 " =    2.807
peak=   -4.093 closest distance to " CD2 TYR A 293 " =    1.897
peak=   -4.073 closest distance to " CG2BVAL A  41 " =    2.253
peak=   -4.045 closest distance to " CA  GLN A  58 " =    1.005
peak=   -4.027 closest distance to " CE2 TYR A  30 " =    2.733
peak=   -3.971 closest distance to " CG1 VAL A  78 " =    2.389
peak=   -3.967 closest distance to " O   HOH Z 131 " =    4.058
peak=   -3.938 closest distance to " CD  ARG A  14 " =    3.264
peak=   -3.928 closest distance to " CD2 LEU A 237 " =    2.729
peak=   -3.920 closest distance to " O   HOH Z 214 " =    2.511
peak=   -3.905 closest distance to " CE3 TRP A 150 " =    2.235
peak=   -3.896 closest distance to " CD2 HIS A 207 " =    2.159
peak=   -3.879 closest distance to " O   HOH Z 221 " =    1.192
peak=   -3.861 closest distance to " CG  ARG A 138 " =    1.027
peak=   -3.850 closest distance to " O   PRO A 163 " =    2.021
peak=   -3.796 closest distance to " CE1 PHE A 218 " =    1.382
peak=   -3.790 closest distance to " CE2 TRP A  70 " =    2.265
peak=   -3.788 closest distance to " O   HOH Z 119 " =    2.073
peak=   -3.781 closest distance to " O   HOH Z 165 " =    2.059
peak=   -3.762 closest distance to " O   HOH Z 359 " =    2.651
peak=   -3.757 closest distance to " C   HIS A 108 " =    1.136
peak=   -3.756 closest distance to " O   SER A 271 " =    2.059
peak=   -3.754 closest distance to " O   HOH Z 216 " =    1.111
peak=   -3.747 closest distance to " NE2 GLN A  11 " =    1.612
peak=   -3.732 closest distance to " O   HOH Z 388 " =    2.110
peak=   -3.719 closest distance to " CD1 LEU A 101 " =    2.394
peak=   -3.715 closest distance to " CG2 VAL A 189 " =    2.064
peak=   -3.700 closest distance to " CG2 ILE A  20 " =    2.726
peak=   -3.698 closest distance to " CD  ARG A 156 " =    2.134
peak=   -3.695 closest distance to " O   HOH Z 348 " =    2.295
peak=   -3.688 closest distance to " CE  LYS A  76 " =    0.813
peak=   -3.684 closest distance to " OE1 GLN A 223 " =    2.478
peak=   -3.683 closest distance to " O   HOH Z 116 " =    1.359
peak=   -3.675 closest distance to " O   HOH Z 275 " =    1.832
peak=   -3.647 closest distance to " O   HOH Z 278 " =    1.121
peak=   -3.634 closest distance to " O   HOH Z 423 " =    2.913
peak=   -3.625 closest distance to " CB  HIS A  86 " =    1.217
peak=   -3.620 closest distance to " CG  TRP A 266 " =    1.864
peak=   -3.614 closest distance to " O   HOH Z  64 " =    1.794
peak=   -3.613 closest distance to " O   HOH Z 111 " =    1.415
peak=   -3.588 closest distance to " CZ  PHE A  38 " =    2.494
peak=   -3.584 closest distance to " O   HOH Z 431 " =    2.046
peak=   -3.564 closest distance to " CB  VAL A 230 " =    1.008
peak=   -3.564 closest distance to " O   HOH Z  19 " =    2.293
peak=   -3.555 closest distance to " CB  ASP A 286 " =    1.788
peak=   -3.552 closest distance to " CG1 VAL A 112 " =    2.533
peak=   -3.547 closest distance to " O   HOH Z 285 " =    1.941
peak=   -3.546 closest distance to " CG  LEU A 281 " =    2.166
peak=   -3.544 closest distance to " OXT GLY A 302 " =    3.048
peak=   -3.535 closest distance to " O   HOH Z 154 " =    1.223
peak=   -3.528 closest distance to " O   HOH Z  30 " =    1.675
peak=   -3.528 closest distance to " CG  PRO A 243 " =    1.656
peak=   -3.528 closest distance to " O   VAL A 174 " =    2.270
peak=   -3.508 closest distance to " O   HOH Z 136 " =    1.443
peak=   -3.500 closest distance to " O   HOH Z  68 " =    1.384
peak=   -3.499 closest distance to " CG  ARG A 269 " =    2.273
peak=   -3.492 closest distance to " CD2 LEU A 237 " =    2.194
peak=   -3.485 closest distance to " CE  MET A 105 " =    2.898
peak=   -3.481 closest distance to " NE2 GLN A 194 " =    2.105
peak=   -3.472 closest distance to " OG  SER A  97 " =    2.184
peak=   -3.468 closest distance to " O   HOH Z 106 " =    1.859
peak=   -3.465 closest distance to " CD1 ILE A 239 " =    2.302
peak=   -3.459 closest distance to " O   HOH Z 340 " =    1.797
peak=   -3.457 closest distance to " CB  ALA A 248 " =    2.225
peak=   -3.448 closest distance to " CD1 ILE A 263 " =    2.320
peak=   -3.446 closest distance to " CB  ASN A  39 " =    2.302
peak=   -3.440 closest distance to " CZ  TYR A 169 " =    1.911
peak=   -3.432 closest distance to " O   HOH Z 387 " =    3.092
peak=   -3.432 closest distance to " CA  ASP A 298 " =    1.060
peak=   -3.426 closest distance to " NZ  LYS A 119 " =    1.154
peak=   -3.425 closest distance to " NE  ARG A  66 " =    4.466
peak=   -3.424 closest distance to " CE1 PHE A 192 " =    1.948
peak=   -3.421 closest distance to " O   HOH Z 231 " =    2.365
peak=   -3.420 closest distance to " O   HOH Z 109 " =    1.102
peak=   -3.410 closest distance to " CB  PRO A 243 " =    2.844
peak=   -3.407 closest distance to " CB  ALA A  43 " =    2.596
peak=   -3.403 closest distance to " SG BCYS A 201 " =    2.517
peak=   -3.391 closest distance to " O   SER A 273 " =    1.123
peak=   -3.391 closest distance to " O   HOH Z 411 " =    1.497
peak=   -3.390 closest distance to " CE BMET A  47 " =    1.285
peak=   -3.390 closest distance to " CG  GLN A  55 " =    1.140
peak=   -3.389 closest distance to " O   HOH Z 283 " =    2.526
peak=   -3.382 closest distance to " CD2 HIS A 115 " =    0.832
peak=   -3.378 closest distance to " O   HOH Z  10 " =    1.482
peak=   -3.377 closest distance to " O   HOH Z 166 " =    2.292
peak=   -3.376 closest distance to " NE2 GLN A  88 " =    1.138
peak=   -3.374 closest distance to " CG2 THR A 178 " =    2.436
peak=   -3.373 closest distance to " O   HOH Z  13 " =    1.956
peak=   -3.371 closest distance to " O   HOH Z  69 " =    1.567
peak=   -3.370 closest distance to " O   ASP A 253 " =    1.959
peak=   -3.364 closest distance to " CA  GLY A 241 " =    2.236
peak=   -3.361 closest distance to " O   HOH Z 133 " =    0.748
peak=   -3.356 closest distance to " CB  SER A 245 " =    2.191
peak=   -3.348 closest distance to " CG  ARG A 259 " =    2.461
peak=   -3.347 closest distance to " CD  GLN A 223 " =    1.810
peak=   -3.346 closest distance to " O   HOH Z 103 " =    1.350
peak=   -3.342 closest distance to " O   LEU A 282 " =    2.246
peak=   -3.337 closest distance to " N   ILE A 120 " =    1.026
peak=   -3.334 closest distance to " O   GLY A  17 " =    1.146
peak=   -3.332 closest distance to " CB  ALA A 248 " =    2.075
peak=   -3.331 closest distance to " NH2 ARG A 156 " =    1.115
peak=   -3.329 closest distance to " O   GLY A 203 " =    2.508
peak=   -3.324 closest distance to " O   HOH Z  43 " =    1.852
peak=   -3.323 closest distance to " CG  GLN A 103 " =    2.389
peak=   -3.315 closest distance to " O   HOH Z 137 " =    1.611
peak=   -3.310 closest distance to " O   HOH Z 147 " =    2.216
peak=   -3.310 closest distance to " O   HOH Z 128 " =    2.267
peak=   -3.308 closest distance to " CD  PRO A 243 " =    1.776
peak=   -3.307 closest distance to " ND2 ASN A  60 " =    1.389
peak=   -3.305 closest distance to " N   ALA A  43 " =    2.763
peak=   -3.300 closest distance to " C   ASN A 285 " =    2.177
peak=   -3.297 closest distance to " O   GLY A  80 " =    2.617
peak=   -3.289 closest distance to " O   HOH Z 145 " =    2.893
peak=   -3.288 closest distance to " O   HOH Z 352 " =    1.610
peak=   -3.279 closest distance to " O   HOH Z  54 " =    1.898
peak=   -3.276 closest distance to " O   ASN A 252 " =    1.363
peak=   -3.272 closest distance to " CG2 VAL A 202 " =    2.704
peak=   -3.270 closest distance to " CE3 TRP A  70 " =    1.625
peak=   -3.265 closest distance to " CE1 TYR A 247 " =    2.581
peak=   -3.251 closest distance to " O   ALA A  21 " =    1.954
peak=   -3.245 closest distance to " N   ASN A 215 " =    1.700
peak=   -3.243 closest distance to " O   HOH Z 128 " =    1.064
peak=   -3.241 closest distance to " CG  MET A 105 " =    0.974
peak=   -3.235 closest distance to " CZ3 TRP A 274 " =    2.042
peak=   -3.233 closest distance to " CD  GLN A  73 " =    0.785
peak=   -3.233 closest distance to " O   HOH Z 421 " =    3.726
peak=   -3.231 closest distance to " O   HOH Z 211 " =    1.228
peak=   -3.228 closest distance to " CD1 TYR A 169 " =    2.326
peak=   -3.228 closest distance to " OE2 GLU A 128 " =    2.037
peak=   -3.227 closest distance to " O   TRP A  92 " =    2.044
peak=   -3.226 closest distance to " CG  GLU A  53 " =    1.366
peak=   -3.223 closest distance to " CG1BVAL A  41 " =    2.288
peak=   -3.223 closest distance to " ND2 ASN A  69 " =    2.043
peak=   -3.219 closest distance to " O   HOH Z  28 " =    2.201
peak=   -3.218 closest distance to " CH2 TRP A 150 " =    1.112
peak=   -3.217 closest distance to " CB  TRP A  85 " =    2.618
peak=   -3.215 closest distance to " O   ALA A 227 " =    1.316
peak=   -3.210 closest distance to " O   HOH Z 183 " =    1.632
peak=   -3.209 closest distance to " O   HOH Z 252 " =    3.641
peak=   -3.207 closest distance to " O   HOH Z  67 " =    1.936
peak=   -3.206 closest distance to " O   HOH Z 345 " =    2.722
peak=   -3.205 closest distance to " O   HOH Z 307 " =    1.948
peak=   -3.189 closest distance to " N   ASP A 191 " =    1.402
peak=   -3.189 closest distance to " O   HOH Z 392 " =    1.785
peak=   -3.181 closest distance to " CA  GLY A 203 " =    2.340
peak=   -3.178 closest distance to " O   THR A 220 " =    1.682
peak=   -3.174 closest distance to " O   ILE A 263 " =    2.187
peak=   -3.171 closest distance to " O   HOH Z 260 " =    1.602
peak=   -3.162 closest distance to " CB  ALA A  10 " =    2.273
peak=   -3.162 closest distance to " O  BHOH Z  74 " =    0.985
peak=   -3.160 closest distance to " O   ALA A 256 " =    1.895
peak=   -3.159 closest distance to " O   HOH Z  63 " =    1.216
peak=   -3.157 closest distance to " ND2 ASN A 285 " =    1.968
peak=   -3.154 closest distance to " O   HOH Z 429 " =    1.440
peak=   -3.154 closest distance to " NH2 ARG A  66 " =    5.929
peak=   -3.141 closest distance to " CD  LYS A 289 " =    2.367
peak=   -3.141 closest distance to " O   HOH Z 210 " =    2.355
peak=   -3.140 closest distance to " O   GLU A 152 " =    1.545
peak=   -3.138 closest distance to " O   HOH Z 328 " =    1.596
peak=   -3.134 closest distance to " CD2 LEU A  96 " =    1.966
peak=   -3.131 closest distance to " CB  SER A  62 " =    5.889
peak=   -3.129 closest distance to " NH2 ARG A  79 " =    1.400
peak=   -3.128 closest distance to " CG  PHE A 283 " =    2.721
peak=   -3.127 closest distance to " SD  MET A 105 " =    2.613
peak=   -3.119 closest distance to " O   HOH Z 139 " =    5.381
peak=   -3.119 closest distance to " CB  ASN A  45 " =    2.083
peak=   -3.114 closest distance to " O   HOH Z 287 " =    1.824
peak=   -3.114 closest distance to " NH2 ARG A 159 " =    2.353
peak=   -3.114 closest distance to " CG  GLN A  58 " =    1.549
peak=   -3.114 closest distance to " O   HOH Z 107 " =    0.987
peak=   -3.112 closest distance to " CD2 PHE A 225 " =    1.111
peak=   -3.111 closest distance to " O   HOH Z   2 " =    1.432
peak=   -3.106 closest distance to " O   HOH Z 100 " =    0.932
peak=   -3.100 closest distance to " OD2 ASP A  50 " =    1.490
peak=   -3.100 closest distance to " O   HOH Z 329 " =    0.781
peak=   -3.099 closest distance to " CD  ARG A  79 " =    1.146
peak=   -3.099 closest distance to " CD1 LEU A   5 " =    2.104
peak=   -3.093 closest distance to " CD  ARG A  36 " =    0.978
peak=   -3.093 closest distance to " CD2 LEU A 237 " =    2.506
peak=   -3.092 closest distance to " O   SER A 210 " =    1.828
peak=   -3.090 closest distance to " CZ  ARG A 259 " =    0.968
peak=   -3.086 closest distance to " CD1 ILE A 151 " =    2.052
peak=   -3.084 closest distance to " O   HOH Z   6 " =    1.801
peak=   -3.082 closest distance to " O   HOH Z 166 " =    1.768
peak=   -3.079 closest distance to " CG  PRO A 163 " =    2.087
peak=   -3.076 closest distance to " N   ALA A 226 " =    1.976
peak=   -3.069 closest distance to " O   HOH Z 377 " =    2.008
peak=   -3.060 closest distance to " OG  SER A  32 " =    1.420
peak=   -3.050 closest distance to " O   HOH Z 103 " =    1.150
peak=   -3.026 closest distance to " O   HOH Z 150 " =    1.759
peak=   -3.012 closest distance to " CE  MET A 105 " =    2.379
peak=   -2.999 closest distance to " CD2 LEU A 237 " =    2.265

================= 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    :  0.4968 0.4818   6.295294e+00   6.285773e+00
   1_bss:  0.4876 0.4751   6.289529e+00   6.281512e+00
   1_xyz:  0.4114 0.4354   6.195699e+00   6.229559e+00
   1_adp:  0.3682 0.4219   6.127468e+00   6.204383e+00
   1_occ:  0.3681 0.4229   6.126939e+00   6.205495e+00
   2_bss:  0.3652 0.4198   6.128683e+00   6.206008e+00
   2_xyz:  0.2811 0.3369   5.914478e+00   6.059144e+00
   2_adp:  0.2577 0.3166   5.856018e+00   6.019503e+00
   2_occ:  0.2574 0.3163   5.855319e+00   6.019195e+00
   3_bss:  0.2556 0.3158   5.855608e+00   6.019649e+00
   3_xyz:  0.2035 0.2564   5.653091e+00   5.841376e+00
   3_adp:  0.1849 0.2447   5.589693e+00   5.799462e+00
   3_occ:  0.1848 0.2449   5.590013e+00   5.800352e+00
   4_bss:  0.1844 0.2441   5.587629e+00   5.797261e+00
   4_xyz:  0.1534 0.2099   5.426718e+00   5.651988e+00
   4_adp:  0.1451 0.1998   5.377987e+00   5.603998e+00
   4_occ:  0.1450 0.1998   5.377650e+00   5.603737e+00
   5_bss:  0.1452 0.2003   5.379182e+00   5.604560e+00
   5_xyz:  0.1356 0.1859   5.318419e+00   5.545419e+00
   5_adp:  0.1329 0.1825   5.302868e+00   5.529409e+00
   5_occ:  0.1328 0.1825   5.302742e+00   5.529544e+00
   5_bss:  0.1328 0.1825   5.302874e+00   5.529744e+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:  0.336  20.000   6.687   8.316  11.549   0.000   0.000   0.000
   1_xyz:  0.336  20.000   6.687   8.316  11.549   0.000   0.000   0.000
   1_adp:  0.336  20.000   6.687   8.316  11.549   0.000   0.000   0.000
   1_occ:  0.336  20.000   6.687   8.316  11.549   0.000   0.000   0.000
   2_bss:  0.328  41.779   2.804   4.487   7.443   0.000   0.000   0.000
   2_xyz:  0.328  41.779   2.804   4.487   7.443   0.000   0.000   0.000
   2_adp:  0.328  41.779   2.804   4.487   7.443   0.000   0.000   0.000
   2_occ:  0.328  41.779   2.804   4.487   7.443   0.000   0.000   0.000
   3_bss:  0.311  41.779   1.108   2.643   4.671   0.000   0.000   0.000
   3_xyz:  0.311  41.779   1.108   2.643   4.671   0.000   0.000   0.000
   3_adp:  0.311  41.779   1.108   2.643   4.671   0.000   0.000   0.000
   3_occ:  0.311  41.779   1.108   2.643   4.671   0.000   0.000   0.000
   4_bss:  0.329  65.749   0.465   1.879   3.658   0.000   0.000   0.000
   4_xyz:  0.329  65.749   0.465   1.879   3.658   0.000   0.000   0.000
   4_adp:  0.329  65.749   0.465   1.879   3.658   0.000   0.000   0.000
   4_occ:  0.329  65.749   0.465   1.879   3.658   0.000   0.000   0.000
   5_bss:  0.331  68.828   0.462   1.639   3.237   0.000   0.000   0.000
   5_xyz:  0.331  68.828   0.462   1.639   3.237   0.000   0.000   0.000
   5_adp:  0.331  68.828   0.462   1.639   3.237   0.000   0.000   0.000
   5_occ:  0.331  68.828   0.462   1.639   3.237   0.000   0.000   0.000
   5_bss:  0.328  68.568  -1.237  -0.171   1.408  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  58.850 0.4088  0.4784    73946.900
   1_bss:  58.301 0.4150  0.6319    72520.700
   1_xyz:  50.565 0.5124  0.7609    56214.359
   1_adp:  47.191 0.5550  0.8832    51617.247
   1_occ:  47.263 0.5541  0.8804    51739.623
   2_bss:  47.037 0.5571  0.7741    51728.980
   2_xyz:  35.783 0.6917  0.9381    30917.164
   2_adp:  33.303 0.7208  0.9698    27913.307
   2_occ:  33.276 0.7211  0.9699    27882.390
   3_bss:  33.139 0.7226  0.9024    27793.497
   3_xyz:  25.794 0.8029  0.9694    17303.269
   3_adp:  24.276 0.8190  0.9722    15809.048
   3_occ:  24.304 0.8187  0.9720    15831.372
   4_bss:  24.155 0.8201  0.9465    15643.116
   4_xyz:  20.281 0.8584  0.9723    11265.110
   4_adp:  19.010 0.8710  0.9703    10301.335
   4_occ:  19.004 0.8710  0.9705    10300.752
   5_bss:  19.030 0.8709  0.9628    10346.986
   5_xyz:  17.617 0.8840  0.9686     9080.900
   5_adp:  17.176 0.8883  0.9616     8795.510
   5_occ:  17.175 0.8883  0.9615     8792.995
   5_bss:  17.180 0.8883  0.9640     8796.689
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.4065e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.4065e+01
   1_xyz:   1.759  0.014  0.108 18.319  0.007  4.110   1.5149e-01
   1_adp:   1.759  0.014  0.108 18.319  0.007  4.110   1.5149e-01
   1_occ:   1.759  0.014  0.108 18.319  0.007  4.110   1.5149e-01
   2_bss:   1.759  0.014  0.108 18.319  0.007  4.110   1.5149e-01
   2_xyz:   1.291  0.009  0.084 16.513  0.005  4.110   9.4837e-02
   2_adp:   1.291  0.009  0.084 16.513  0.005  4.110   9.4837e-02
   2_occ:   1.291  0.009  0.084 16.513  0.005  4.110   9.4837e-02
   3_bss:   1.291  0.009  0.084 16.513  0.005  4.110   9.4837e-02
   3_xyz:   1.020  0.007  0.074 15.783  0.004  4.129   6.3679e-02
   3_adp:   1.020  0.007  0.074 15.783  0.004  4.129   6.3679e-02
   3_occ:   1.020  0.007  0.074 15.783  0.004  4.129   6.3679e-02
   4_bss:   1.020  0.007  0.074 15.783  0.004  4.129   6.3679e-02
   4_xyz:   1.022  0.007  0.075 15.554  0.004  4.115   6.3449e-02
   4_adp:   1.022  0.007  0.075 15.554  0.004  4.115   6.3449e-02
   4_occ:   1.022  0.007  0.075 15.554  0.004  4.115   6.3449e-02
   5_bss:   1.022  0.007  0.075 15.554  0.004  4.115   6.3449e-02
   5_xyz:   0.966  0.007  0.074 15.450  0.003  4.120   5.7783e-02
   5_adp:   0.966  0.007  0.074 15.450  0.003  4.120   5.7783e-02
   5_occ:   0.966  0.007  0.074 15.450  0.003  4.120   5.7783e-02
   5_bss:   0.966  0.007  0.074 15.450  0.003  4.120   5.7783e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0061e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0061e+00
   1_xyz:  14.964  0.177  0.478 86.197  0.061  2.139   1.0854e-01
   1_adp:  14.964  0.177  0.478 86.197  0.061  2.139   1.0854e-01
   1_occ:  14.964  0.177  0.478 86.197  0.061  2.139   1.0854e-01
   2_bss:  14.964  0.177  0.478 86.197  0.061  2.139   1.0854e-01
   2_xyz:   8.892  0.093  0.297 87.291  0.042  2.128   7.8272e-02
   2_adp:   8.892  0.093  0.297 87.291  0.042  2.128   7.8272e-02
   2_occ:   8.892  0.093  0.297 87.291  0.042  2.128   7.8272e-02
   3_bss:   8.892  0.093  0.297 87.291  0.042  2.128   7.8272e-02
   3_xyz:   6.644  0.054  0.254 79.405  0.050  2.261   4.5520e-02
   3_adp:   6.644  0.054  0.254 79.405  0.050  2.261   4.5520e-02
   3_occ:   6.644  0.054  0.254 79.405  0.050  2.261   4.5520e-02
   4_bss:   6.644  0.054  0.254 79.405  0.050  2.261   4.5520e-02
   4_xyz:   7.133  0.049  0.256 81.251  0.040  2.336   6.2017e-02
   4_adp:   7.133  0.049  0.256 81.251  0.040  2.336   6.2017e-02
   4_occ:   7.133  0.049  0.256 81.251  0.040  2.336   6.2017e-02
   5_bss:   7.133  0.049  0.256 81.251  0.040  2.336   6.2017e-02
   5_xyz:   6.322  0.050  0.268 84.226  0.042  2.325   3.0445e-02
   5_adp:   6.322  0.050  0.268 84.226  0.042  2.325   3.0445e-02
   5_occ:   6.322  0.050  0.268 84.226  0.042  2.325   3.0445e-02
   5_bss:   6.322  0.050  0.268 84.226  0.042  2.325   3.0445e-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:  88.08   0.00  14.65  68.70   0.00  12.42  88.08   0.00  26.80
   1_occ:  88.08   0.00  14.65  68.70   0.00  12.42  88.08   0.00  26.80
   2_bss:  88.08   0.00  14.65  68.70   0.00  12.42  88.08   0.00  26.80
   2_xyz:  88.08   0.00  14.65  68.70   0.00  12.42  88.08   0.00  26.80
   2_adp:  87.46   0.00  14.37  70.07   0.00  11.06  87.46   0.00  32.41
   2_occ:  87.46   0.00  14.37  70.07   0.00  11.06  87.46   0.00  32.41
   3_bss:  87.46   0.00  14.37  70.07   0.00  11.06  87.46   0.00  32.41
   3_xyz:  87.46   0.00  14.37  70.07   0.00  11.06  87.46   0.00  32.41
   3_adp:  97.87   0.00  15.76  81.01   0.00  10.82  97.87   1.34  42.67
   3_occ:  97.87   0.00  15.76  81.01   0.00  10.82  97.87   1.34  42.67
   4_bss:  97.87   0.00  15.76  81.01   0.00  10.82  97.87   1.34  42.67
   4_xyz:  97.87   0.00  15.76  81.01   0.00  10.82  97.87   1.34  42.67
   4_adp: 106.14   0.00  15.43  87.78   0.00  10.23 106.14   1.18  43.76
   4_occ: 106.14   0.00  15.43  87.78   0.00  10.23 106.14   1.18  43.76
   5_bss: 106.14   0.00  15.43  87.78   0.00  10.23 106.14   1.18  43.76
   5_xyz: 106.14   0.00  15.43  87.78   0.00  10.23 106.14   1.18  43.76
   5_adp: 111.50   0.00  15.25  94.87   0.00   9.98 111.50   1.01  43.95
   5_occ: 111.50   0.00  15.25  94.87   0.00   9.98 111.50   1.01  43.95
   5_bss: 113.36   1.85  17.10  96.72   1.85  11.83 113.36   2.86  45.81
------------------------------------------------------------------------
 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:    1.301    0.020    0.415
   1_adp:    1.301    0.020    0.415
   1_occ:    1.301    0.020    0.415
   2_bss:    1.301    0.020    0.415
   2_xyz:    1.963    0.048    0.596
   2_adp:    1.963    0.048    0.596
   2_occ:    1.963    0.048    0.596
   3_bss:    1.963    0.048    0.596
   3_xyz:    1.837    0.063    0.672
   3_adp:    1.837    0.063    0.672
   3_occ:    1.837    0.063    0.672
   4_bss:    1.837    0.063    0.672
   4_xyz:    2.046    0.040    0.743
   4_adp:    2.046    0.040    0.743
   4_occ:    2.046    0.040    0.743
   5_bss:    2.046    0.040    0.743
   5_xyz:    2.071    0.035    0.759
   5_adp:    2.071    0.035    0.759
   5_occ:    2.071    0.035    0.759
   5_bss:    2.071    0.035    0.759
------------------------------------------------------------------------

CPU time actual refinement: 339.25


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_329/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_329/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_329/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_329/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_329/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 339.09 
  Macro-tasks:
    bulk solvent and scale       = 40.77  
    individual site refinement   = 133.67 
    weights calculation          = 31.92  
    collect and process          = 6.57   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 213.04 
  Micro-tasks:
    mask                            = 2.40   
    f_calc                          = 106.54 
    alpha_beta                      = 8.38   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 114.98 
    fmodel                         = 7.50   
    r_factors                      = 0.21   
    phase_errors                   = 10.50  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 251.97 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.829 micro seconds
Total CPU time: 5.88 minutes
from_scatterers_fft:    652 calls, 106.20 s
gradients_fft:          596 calls, 102.21 s

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

# Date 2008-01-16 Time 01:20:17 PST -0800 (1200475217.20 s)
Start R-work = 0.4968, R-free = 0.4818 (no bulk solvent and anisotropic scale)
Final R-work = 0.1495, R-free = 0.1972 (no bulk solvent and anisotropic scale)

Start R-work = 0.4876, R-free = 0.4751
Final R-work = 0.1328, R-free = 0.1825