# Date 2008-01-16 Time 02:02:12 PST -0800 (1200477732.98 s)
#phil __OFF__

Command line arguments: "../660.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 17773
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 660

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 46.93, 84.2302, 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: 2.79, per 1000 atoms: 0.99


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.93, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8895 1.9513
Completeness in resolution range: 0.940332
Completeness with d_max=infinity: 0.937497

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8895
                             d_min =   1.9513

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.93, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8895 1.9513
Completeness in resolution range: 0.940332
Completeness with d_max=infinity: 0.937497

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8899 -  4.1759 [2195/2224]  1977   218   9.9%
  bin  2:  4.1759 -  3.3267 [2089/2112]  1881   208  10.0%
  bin  3:  3.3267 -  2.9098 [2067/2089]  1856   211  10.2%
  bin  4:  2.9098 -  2.6453 [2065/2084]  1865   200   9.7%
  bin  5:  2.6453 -  2.4566 [2052/2081]  1842   210  10.2%
  bin  6:  2.4566 -  2.3124 [2028/2070]  1827   201   9.9%
  bin  7:  2.3124 -  2.1969 [2016/2052]  1815   201  10.0%
  bin  8:  2.1969 -  2.1016 [2003/2040]  1803   200  10.0%
  bin  9:  2.1016 -  2.0209 [2008/2040]  1802   206  10.3%
  bin 10:  2.0209 -  1.9513 [1066/2040]   962   104   9.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_660/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: 0.13 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:
        1.56 -     2.23: 26
        2.23 -     2.90: 1398
        2.90 -     3.57: 4508
        3.57 -     4.23: 9326
        4.23 -     4.90: 13439
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.563 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.579 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.773 3.120 -x,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.832 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28692 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_660/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_660/model_refine_001.geo

CPU time processing inputs: 8.00


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 46.93 84.23025 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: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4606   r_free= 0.4680   ksol= 0.00   Bsol= 0.00   scale= 0.812    |
|                                                                             |
| 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:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.263978                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8899 -  4.6579 0.99   1419  158 0.3844 0.3758      6.5702      6.5955|
|  2:  4.6579 -  3.7160 0.99   1366  147 0.3771 0.3709      6.7424      6.7243|
|  3:  3.7160 -  3.2519 0.99   1339  157 0.4188 0.4141      6.6411      6.7226|
|  4:  3.2519 -  2.9571 0.99   1339  145 0.4298 0.4684      6.4907      6.4977|
|  5:  2.9571 -  2.7466 0.99   1313  146 0.4792 0.4937      6.3549      6.3487|
|  6:  2.7466 -  2.5855 0.98   1319  145 0.4781 0.5267      6.2478      6.1983|
|  7:  2.5855 -  2.4566 0.99   1326  149 0.5053 0.4656      6.2478       6.168|
|  8:  2.4566 -  2.3501 0.99   1289  145 0.5126 0.5383      6.1406      6.1745|
|  9:  2.3501 -  2.2600 0.98   1322  149 0.5061 0.4915      6.1214      6.1093|
| 10:  2.2600 -  2.1822 0.98   1282  144 0.5241 0.5220      6.0902      6.0999|
| 11:  2.1822 -  2.1142 0.98   1285  137 0.5213 0.5146      6.0286      6.0256|
| 12:  2.1142 -  2.0539 0.99   1293  145 0.4999 0.5628      5.9506      5.9835|
| 13:  2.0539 -  2.0000 0.97   1288  144 0.5257 0.5100      5.8675       5.832|
| 14:  2.0000 -  1.9513 0.34    450   48 0.5431 0.5791      5.8537      5.7447|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8899 -  4.6579  1419   158  0.70  34.37   0.81     0.73      69983.84|
|  2:  4.6579 -  3.7160  1366   147  0.71  34.59   0.89     0.79     100782.92|
|  3:  3.7160 -  3.2519  1339   157  0.61  43.05   0.85     0.74     110584.24|
|  4:  3.2519 -  2.9571  1339   145  0.53  49.73   0.83     0.64      99066.78|
|  5:  2.9571 -  2.7466  1313   146  0.43  57.13   0.76     0.53      82520.27|
|  6:  2.7466 -  2.5855  1319   145  0.42  58.31   0.75     0.50      68416.96|
|  7:  2.5855 -  2.4566  1326   149  0.42  58.17   0.75     0.47      60269.11|
|  8:  2.4566 -  2.3501  1289   145  0.40  60.06   0.72     0.47      55402.81|
|  9:  2.3501 -  2.2600  1322   149  0.40  60.17   0.76     0.47      50643.87|
| 10:  2.2600 -  2.1822  1282   144  0.36  62.78   0.77     0.45      48850.70|
| 11:  2.1822 -  2.1142  1285   137  0.33  65.12   0.78     0.41      46273.38|
| 12:  2.1142 -  2.0539  1293   145  0.29  68.69   0.77     0.37      45782.33|
| 13:  2.0539 -  2.0000  1288   144  0.27  69.97   0.75     0.35      38959.64|
| 14:  2.0000 -  1.9513   450    48  0.32  66.53   0.71     0.36      30231.80|
|alpha:            min =        0.35 max =            0.79 mean =         0.53|
|beta:             min =    30231.80 max =       110584.24 mean =     66911.03|
|figures of merit: min =        0.00 max =            1.00 mean =         0.45|
|phase err.(work): min =        0.00 max =           90.00 mean =        55.55|
|phase err.(test): min =        0.00 max =           89.95 mean =        56.12|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.854768             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.348   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.120445              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.431   (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:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       28 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      174 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      716 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1528 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2678 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3977 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5101 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6661 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7796 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.231 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.196 |       2.005 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.612)------------------------------------------|
|    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 = 11.612)------------------------------------------|
|    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: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4686   r_free= 0.4760   ksol= 0.00   Bsol= 0.00   scale= 0.779    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.267417                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4525   r_free= 0.4571   ksol= 0.36   Bsol= 12.50   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.73,7.59,10.00,0.00,0.00,0.00); trace/3= 8.11                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.261519                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.751389              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.326   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.996761              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.823   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4525      final r-factor (work) = 0.3735          |
| start r-factor (free) = 0.4571      final r-factor (free) = 0.3978          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 83.7739 = 9.75 * 0.50 * 6.2643 + 1.00 * 53.2313                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.2101 = 9.75 * 0.50 * 6.1696 + 1.00 * 0.1289                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3735      final r-factor (work) = 0.3224          |
| start r-factor (free) = 0.3978      final r-factor (free) = 0.3743          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1640 = 1.00 * 1.00 * 6.1696 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0664 = 1.00 * 1.00 * 6.0707 + 1.00 * 0.0154                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.612)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    61.62   12.21    None  None   None       |
|    all(noH): 2823   0      0.00    61.62   12.21    None  None   None       |
|    Sol.    : 438    0      0.00    61.62   25.68    None  None   None       |
|    Mac.    : 2385   0      0.00    61.53   9.74     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.162: 1016   |   5:    30.810 -  36.971:  105        |
|      1:     6.162 -  12.324:  752   |   6:    36.971 -  43.133:   65        |
|      2:    12.324 -  18.486:  412   |   7:    43.133 -  49.295:   30        |
|      3:    18.486 -  24.648:  256   |   8:    49.295 -  55.457:   12        |
|      4:    24.648 -  30.810:  170   |   9:    55.457 -  61.619:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3224 r_free = 0.3743             target_work(ml) = 6.051         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3220 r_free = 0.3746             target_work(ml) = 6.051         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3220   r_free= 0.3746   ksol= 0.36   Bsol= 12.50   scale= 1.099   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.73,7.59,10.00,0.00,0.00,0.00); trace/3= 8.11                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.051042                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3185   r_free= 0.3715   ksol= 0.32   Bsol= 20.00   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.25,3.76,6.79,0.00,0.00,0.00); trace/3= 4.60                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.050706                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.294227              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.080   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.464546              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 120.938  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3185      final r-factor (work) = 0.2352          |
| start r-factor (free) = 0.3715      final r-factor (free) = 0.2929          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.2961 = 8.29 * 0.50 * 6.0686 + 1.00 * 0.1289                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.6519 = 8.29 * 0.50 * 5.9240 + 1.00 * 0.0842                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2352      final r-factor (work) = 0.2118          |
| start r-factor (free) = 0.2929      final r-factor (free) = 0.2702          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7714 = 0.46 * 1.00 * 5.9240 + 1.00 * 0.0194                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7127 = 0.46 * 1.00 * 5.7429 + 1.00 * 0.0449                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.612)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    128.88  12.44    None  None   None       |
|    all(noH): 2823   0      0.00    128.88  12.44    None  None   None       |
|    Sol.    : 438    0      1.15    59.55   30.33    None  None   None       |
|    Mac.    : 2385   0      0.00    128.88  9.15     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 -  12.888: 1918   |   5:    64.439 -  77.326:    0        |
|      1:    12.888 -  25.775:  502   |   6:    77.326 -  90.214:    0        |
|      2:    25.775 -  38.663:  256   |   7:    90.214 - 103.102:    0        |
|      3:    38.663 -  51.551:  131   |   8:   103.102 - 115.989:    0        |
|      4:    51.551 -  64.439:   15   |   9:   115.989 - 128.877:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2118 r_free = 0.2702             target_work(ml) = 5.704         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2117 r_free = 0.2703             target_work(ml) = 5.703         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2117   r_free= 0.2703   ksol= 0.32   Bsol= 20.00   scale= 1.052   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.25,3.76,6.79,0.00,0.00,0.00); trace/3= 4.60                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.703136                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2096   r_free= 0.2666   ksol= 0.33   Bsol= 32.50   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.11,2.51,3.82,0.00,0.00,0.00); trace/3= 2.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.696983                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.357857              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.657   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.471957              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.847   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2096      final r-factor (work) = 0.1536          |
| start r-factor (free) = 0.2666      final r-factor (free) = 0.2057          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.4815 = 5.36 * 0.50 * 5.7475 + 1.00 * 0.0842                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.0148 = 5.36 * 0.50 * 5.5785 + 1.00 * 0.0704                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1536      final r-factor (work) = 0.1379          |
| start r-factor (free) = 0.2057      final r-factor (free) = 0.1874          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6663 = 0.47 * 1.00 * 5.5785 + 1.00 * 0.0334                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5471 = 0.47 * 1.00 * 5.3748 + 1.00 * 0.0105                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.612)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.99   12.78    None  None   None       |
|    all(noH): 2823   0      0.00    72.99   12.78    None  None   None       |
|    Sol.    : 438    0      3.00    71.40   35.19    None  None   None       |
|    Mac.    : 2385   0      0.00    72.99   8.66     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.299: 1393   |   5:    36.496 -  43.795:  109        |
|      1:     7.299 -  14.598:  741   |   6:    43.795 -  51.094:   85        |
|      2:    14.598 -  21.898:  208   |   7:    51.094 -  58.393:   45        |
|      3:    21.898 -  29.197:  103   |   8:    58.393 -  65.692:   20        |
|      4:    29.197 -  36.496:  110   |   9:    65.692 -  72.992:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1379 r_free = 0.1874             target_work(ml) = 5.323         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1377 r_free = 0.1872             target_work(ml) = 5.322         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1377   r_free= 0.1872   ksol= 0.33   Bsol= 32.50   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.11,2.51,3.82,0.00,0.00,0.00); trace/3= 2.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.321761                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1375   r_free= 0.1860   ksol= 0.32   Bsol= 32.50   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.86,2.18,2.76,0.00,0.00,0.00); trace/3= 2.27                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.318644                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.652119              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.221  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.284514              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.546  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1375      final r-factor (work) = 0.1272          |
| start r-factor (free) = 0.1860      final r-factor (free) = 0.1721          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5111 = 1.65 * 0.50 * 5.3760 + 1.00 * 0.0702                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4220 = 1.65 * 0.50 * 5.2903 + 1.00 * 0.0519                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1272      final r-factor (work) = 0.1246          |
| start r-factor (free) = 0.1721      final r-factor (free) = 0.1683          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5156 = 0.28 * 1.00 * 5.2903 + 1.00 * 0.0104                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5017 = 0.28 * 1.00 * 5.2438 + 1.00 * 0.0098                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.612)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.18   12.76    None  None   None       |
|    all(noH): 2823   0      0.00    83.18   12.76    None  None   None       |
|    Sol.    : 438    0      2.16    82.94   35.35    None  None   None       |
|    Mac.    : 2385   0      0.00    83.18   8.61     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.318: 1579   |   5:    41.591 -  49.909:   89        |
|      1:     8.318 -  16.636:  656   |   6:    49.909 -  58.227:   61        |
|      2:    16.636 -  24.955:  159   |   7:    58.227 -  66.545:   19        |
|      3:    24.955 -  33.273:  121   |   8:    66.545 -  74.864:   10        |
|      4:    33.273 -  41.591:  124   |   9:    74.864 -  83.182:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1246 r_free = 0.1683             target_work(ml) = 5.231         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1245 r_free = 0.1681             target_work(ml) = 5.231         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1245   r_free= 0.1681   ksol= 0.32   Bsol= 32.50   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.86,2.18,2.76,0.00,0.00,0.00); trace/3= 2.27                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.230858                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1245   r_free= 0.1681   ksol= 0.31   Bsol= 34.06   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.76,2.08,2.43,0.00,0.00,0.00); trace/3= 2.09                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.230403                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.185390              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 133.960  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.234639              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 157.166  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1245      final r-factor (work) = 0.1133          |
| start r-factor (free) = 0.1681      final r-factor (free) = 0.1590          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4029 = 3.19 * 0.50 * 5.2433 + 1.00 * 0.0519                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3338 = 3.19 * 0.50 * 5.1889 + 1.00 * 0.0694                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1133      final r-factor (work) = 0.1126          |
| start r-factor (free) = 0.1590      final r-factor (free) = 0.1583          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2273 = 0.23 * 1.00 * 5.1889 + 1.00 * 0.0098                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2198 = 0.23 * 1.00 * 5.1556 + 1.00 * 0.0101                               |
|-----------------------------------------------------------------------------|
| number of iterations = 5       |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.612)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.25   12.71    None  None   None       |
|    all(noH): 2823   0      0.00    83.25   12.71    None  None   None       |
|    Sol.    : 438    0      1.97    83.09   35.17    None  None   None       |
|    Mac.    : 2385   0      0.00    83.25   8.59     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.325: 1587   |   5:    41.627 -  49.952:   87        |
|      1:     8.325 -  16.651:  654   |   6:    49.952 -  58.277:   59        |
|      2:    16.651 -  24.976:  155   |   7:    58.277 -  66.602:   19        |
|      3:    24.976 -  33.301:  127   |   8:    66.602 -  74.928:   10        |
|      4:    33.301 -  41.627:  120   |   9:    74.928 -  83.253:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1126 r_free = 0.1583             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1126 r_free = 0.1581             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1126   r_free= 0.1581   ksol= 0.31   Bsol= 34.06   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.76,2.08,2.43,0.00,0.00,0.00); trace/3= 2.09                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.152898                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8899 -  4.6579 0.99   1419  158 0.0996 0.1276      5.3841      5.5467|
|  2:  4.6579 -  3.7160 0.99   1366  147 0.0857 0.1146      5.4251      5.6344|
|  3:  3.7160 -  3.2519 0.99   1339  157 0.1063 0.1553      5.4616      5.8203|
|  4:  3.2519 -  2.9571 0.99   1339  145 0.1225 0.1471      5.4466      5.5754|
|  5:  2.9571 -  2.7466 0.99   1313  146 0.1283 0.1697      5.3131      5.4903|
|  6:  2.7466 -  2.5855 0.98   1319  145 0.1267 0.1991      5.2247      5.5086|
|  7:  2.5855 -  2.4566 0.99   1326  149 0.1265 0.1680      5.1869       5.407|
|  8:  2.4566 -  2.3501 0.99   1289  145 0.1174 0.1674      5.0627      5.2858|
|  9:  2.3501 -  2.2600 0.98   1322  149 0.1171 0.1748       5.024      5.2699|
| 10:  2.2600 -  2.1822 0.98   1282  144 0.1137 0.1759      4.9743       5.247|
| 11:  2.1822 -  2.1142 0.98   1285  137 0.1130 0.1818      4.9313       5.296|
| 12:  2.1142 -  2.0539 0.99   1293  145 0.1114 0.1682      4.8685      5.0749|
| 13:  2.0539 -  2.0000 0.97   1288  144 0.1180 0.1796      4.7889      5.0273|
| 14:  2.0000 -  1.9513 0.34    450   48 0.1082 0.1609      4.6646      4.8921|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8899 -  4.6579  1419   158  0.94   8.78   0.98     0.97       7093.12|
|  2:  4.6579 -  3.7160  1366   147  0.95   7.90   1.02     1.01       8661.63|
|  3:  3.7160 -  3.2519  1339   157  0.93  11.19   1.03     1.03      10047.34|
|  4:  3.2519 -  2.9571  1339   145  0.92  13.63   1.01     1.00      10089.54|
|  5:  2.9571 -  2.7466  1313   146  0.90  16.15   0.99     0.95       8193.23|
|  6:  2.7466 -  2.5855  1319   145  0.90  16.50   0.99     0.96       7282.69|
|  7:  2.5855 -  2.4566  1326   149  0.90  15.94   0.99     0.96       6496.47|
|  8:  2.4566 -  2.3501  1289   145  0.90  15.85   0.99     0.96       5402.06|
|  9:  2.3501 -  2.2600  1322   149  0.90  15.73   1.01     0.99       4976.36|
| 10:  2.2600 -  2.1822  1282   144  0.90  15.55   1.01     0.99       4566.79|
| 11:  2.1822 -  2.1142  1285   137  0.90  16.28   1.01     0.97       4339.19|
| 12:  2.1142 -  2.0539  1293   145  0.91  15.55   1.01     0.99       3969.02|
| 13:  2.0539 -  2.0000  1288   144  0.90  16.31   1.01     1.01       3302.64|
| 14:  2.0000 -  1.9513   450    48  0.90  15.74   1.00     0.98       2579.81|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2579.81 max =        10089.54 mean =      6429.79|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.23|
|phase err.(test): min =        0.00 max =           87.53 mean =        13.71|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1127   r_free= 0.1582   ksol= 0.32   Bsol= 37.54   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.33,-0.01,0.34,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.153610                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1127   r_free= 0.1582   ksol= 0.32   Bsol= 37.54   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.33,-0.01,0.34,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.153610                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8899 -  4.6579 0.99   1419  158 0.0975 0.1296      5.3755      5.5452|
|  2:  4.6579 -  3.7160 0.99   1366  147 0.0878 0.1142      5.4368      5.6392|
|  3:  3.7160 -  3.2519 0.99   1339  157 0.1067 0.1558      5.4656      5.8236|
|  4:  3.2519 -  2.9571 0.99   1339  145 0.1231 0.1480      5.4511      5.5796|
|  5:  2.9571 -  2.7466 0.99   1313  146 0.1287 0.1689      5.3161      5.4886|
|  6:  2.7466 -  2.5855 0.98   1319  145 0.1265 0.1998      5.2247      5.5095|
|  7:  2.5855 -  2.4566 0.99   1326  149 0.1266 0.1677      5.1866       5.408|
|  8:  2.4566 -  2.3501 0.99   1289  145 0.1172 0.1669      5.0632      5.2883|
|  9:  2.3501 -  2.2600 0.98   1322  149 0.1168 0.1752      5.0225      5.2695|
| 10:  2.2600 -  2.1822 0.98   1282  144 0.1130 0.1759      4.9732      5.2478|
| 11:  2.1822 -  2.1142 0.98   1285  137 0.1130 0.1817      4.9307       5.295|
| 12:  2.1142 -  2.0539 0.99   1293  145 0.1113 0.1686      4.8686      5.0775|
| 13:  2.0539 -  2.0000 0.97   1288  144 0.1180 0.1786      4.7876      5.0238|
| 14:  2.0000 -  1.9513 0.34    450   48 0.1083 0.1600      4.6617      4.8898|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8899 -  4.6579  1419   158  0.94   8.87   0.98     0.96       7114.76|
|  2:  4.6579 -  3.7160  1366   147  0.95   7.98   1.02     1.01       8730.83|
|  3:  3.7160 -  3.2519  1339   157  0.93  11.30   1.03     1.03      10188.01|
|  4:  3.2519 -  2.9571  1339   145  0.92  13.70   1.01     1.00      10169.11|
|  5:  2.9571 -  2.7466  1313   146  0.90  16.20   0.99     0.95       8217.72|
|  6:  2.7466 -  2.5855  1319   145  0.89  16.57   0.99     0.96       7323.57|
|  7:  2.5855 -  2.4566  1326   149  0.90  15.91   0.99     0.96       6483.65|
|  8:  2.4566 -  2.3501  1289   145  0.90  15.89   0.99     0.96       5431.42|
|  9:  2.3501 -  2.2600  1322   149  0.90  15.72   1.01     0.99       4974.56|
| 10:  2.2600 -  2.1822  1282   144  0.90  15.57   1.01     0.99       4578.51|
| 11:  2.1822 -  2.1142  1285   137  0.90  16.27   1.01     0.97       4334.66|
| 12:  2.1142 -  2.0539  1293   145  0.91  15.54   1.01     1.00       3972.82|
| 13:  2.0539 -  2.0000  1288   144  0.90  16.28   1.01     1.01       3291.75|
| 14:  2.0000 -  1.9513   450    48  0.90  15.66   1.00     0.98       2557.21|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2557.21 max =        10188.01 mean =      6458.98|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           90.00 mean =        14.26|
|phase err.(test): min =        0.00 max =           87.44 mean =        13.74|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.612)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.09    85.34   14.80    None  None   None       |
|    all(noH): 2823   0      2.09    85.34   14.80    None  None   None       |
|    Sol.    : 438    0      4.06    85.18   37.26    None  None   None       |
|    Mac.    : 2385   0      2.09    85.34   10.68    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.091 -  10.417: 1587   |   5:    43.718 -  52.043:   87        |
|      1:    10.417 -  18.742:  654   |   6:    52.043 -  60.368:   59        |
|      2:    18.742 -  27.067:  155   |   7:    60.368 -  68.694:   19        |
|      3:    27.067 -  35.392:  127   |   8:    68.694 -  77.019:   10        |
|      4:    35.392 -  43.718:  120   |   9:    77.019 -  85.344:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 336         
Filter by distance & map next to the model:
   mapped sites are within: 0.441 - 5.675
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 331 from: 336
   mapped sites are within: 0.740 - 5.675

peak=   10.487 closest distance to " CB  VAL A 230 " =    1.433
peak=    8.415 closest distance to " CG2 VAL A 296 " =    1.232
peak=    6.625 closest distance to " NH2 ARG A  56 " =    2.172
peak=    6.204 closest distance to " CG  LEU A   5 " =    1.286
peak=    5.970 closest distance to " O   HOH Z 278 " =    1.436
peak=    5.796 closest distance to " O   HOH Z 279 " =    1.062
peak=    5.511 closest distance to " CD2 LEU A   5 " =    1.196
peak=    5.474 closest distance to " NE2 GLN A  11 " =    1.150
peak=    5.454 closest distance to " O   HOH Z 132 " =    1.684
peak=    5.342 closest distance to " O   HOH Z 124 " =    1.473
peak=    4.960 closest distance to " O   HOH Z 202 " =    1.336
peak=    4.942 closest distance to " O   HOH Z 142 " =    1.763
peak=    4.866 closest distance to " O   HOH Z 126 " =    1.980
peak=    4.854 closest distance to " CB  SER A  63 " =    1.225
peak=    4.797 closest distance to " CB  GLN A 223 " =    1.445
peak=    4.791 closest distance to " O   HOH Z 193 " =    1.760
peak=    4.764 closest distance to " O   HOH Z 209 " =    2.489
peak=    4.755 closest distance to " CG  LEU A 228 " =    1.214
peak=    4.727 closest distance to " O   HOH Z  97 " =    1.899
peak=    4.721 closest distance to " CA  GLY A 241 " =    3.817
peak=    4.708 closest distance to " O   HOH Z 263 " =    1.429
peak=    4.707 closest distance to " O   HOH Z 427 " =    2.841
peak=    4.693 closest distance to " CB  GLN A 183 " =    1.250
peak=    4.677 closest distance to " CD1AILE A 234 " =    0.975
peak=    4.617 closest distance to " CB  SER A   3 " =    1.413
peak=    4.606 closest distance to " CD2 LEU A 228 " =    1.220
peak=    4.555 closest distance to " CG  PRO A  54 " =    1.194
peak=    4.538 closest distance to " O   HOH Z  48 " =    1.567
peak=    4.520 closest distance to " O   PRO A 198 " =    1.511
peak=    4.495 closest distance to " CB  ASN A 148 " =    1.432
peak=    4.474 closest distance to " CB  GLU A 152 " =    1.147
peak=    4.447 closest distance to " O   HOH Z 232 " =    2.194
peak=    4.403 closest distance to " CB  VAL A 296 " =    1.049
peak=    4.390 closest distance to " O   SER A  87 " =    2.307
peak=    4.384 closest distance to " CB  VAL A 230 " =    1.207
peak=    4.361 closest distance to " O   HOH Z  37 " =    1.148
peak=    4.326 closest distance to " O   HOH Z 108 " =    1.482
peak=    4.322 closest distance to " O   HOH Z 199 " =    0.831
peak=    4.322 closest distance to " O   HOH Z 272 " =    1.867
peak=    4.313 closest distance to " CB  ARG A 275 " =    0.858
peak=    4.309 closest distance to " O   HOH Z 303 " =    2.022
peak=    4.304 closest distance to " O   HOH Z 368 " =    2.038
peak=    4.292 closest distance to " O   HOH Z 371 " =    3.207
peak=    4.280 closest distance to " O   HOH Z 234 " =    3.762
peak=    4.261 closest distance to " CG  PRO A 213 " =    1.179
peak=    4.238 closest distance to " CB  TYR A 169 " =    0.959
peak=    4.231 closest distance to " CA  ALA A  21 " =    1.153
peak=    4.197 closest distance to " CB  PRO A  54 " =    0.821
peak=    4.174 closest distance to " OD1 ASN A  69 " =    2.621
peak=    4.164 closest distance to " O   HOH Z  93 " =    2.500
peak=    4.162 closest distance to " O   HOH Z 346 " =    1.546
peak=    4.132 closest distance to " O   HOH Z 326 " =    1.482
peak=    4.120 closest distance to " O   HOH Z 260 " =    1.221
peak=    4.108 closest distance to " CG1BVAL A  72 " =    1.492
peak=    4.105 closest distance to " O   HOH Z 276 " =    1.312
peak=    4.099 closest distance to " O   HOH Z 423 " =    1.943
peak=    4.093 closest distance to " O   HOH Z 133 " =    1.529
peak=    4.060 closest distance to " O   HOH Z 236 " =    1.482
peak=    4.050 closest distance to " OD2 ASP A 286 " =    2.675
peak=    4.034 closest distance to " O   HOH Z  59 " =    2.031
peak=    4.033 closest distance to " O   HOH Z 247 " =    1.203
peak=    4.029 closest distance to " O   HOH Z 126 " =    2.254
peak=    4.029 closest distance to " O   HOH Z 118 " =    1.493
peak=    4.027 closest distance to " CA  VAL A  41 " =    0.891
peak=    4.004 closest distance to " O   HOH Z 334 " =    2.936
peak=    3.996 closest distance to " O   HOH Z 316 " =    2.819
peak=    3.993 closest distance to " O   HOH Z  54 " =    1.549
peak=    3.991 closest distance to " O   HOH Z   3 " =    1.627
peak=    3.975 closest distance to " OE1 GLU A   2 " =    2.139
peak=    3.966 closest distance to " CG  ARG A  66 " =    2.739
peak=    3.961 closest distance to " O   HOH Z  15 " =    1.954
peak=    3.958 closest distance to " CB  ARG A  79 " =    1.362
peak=    3.945 closest distance to " O   HOH Z 369 " =    1.849
peak=    3.942 closest distance to " O   HOH Z 203 " =    1.605
peak=    3.940 closest distance to " O   HOH Z 345 " =    3.204
peak=    3.922 closest distance to " O   HOH Z  48 " =    1.625
peak=    3.920 closest distance to " O   HOH Z 116 " =    1.708
peak=    3.918 closest distance to " CB  GLN A  88 " =    1.258
peak=    3.917 closest distance to " O   HOH Z 214 " =    2.083
peak=    3.916 closest distance to " CG  PRO A 198 " =    1.318
peak=    3.903 closest distance to " CB  TRP A 179 " =    1.289
peak=    3.903 closest distance to " O   HOH Z 389 " =    1.760
peak=    3.902 closest distance to " CB  VAL A 202 " =    1.636
peak=    3.897 closest distance to " CB  VAL A 265 " =    1.207
peak=    3.895 closest distance to " O   HOH Z 334 " =    1.505
peak=    3.884 closest distance to " O   HOH Z 298 " =    1.880
peak=    3.883 closest distance to " O   HOH Z 128 " =    1.965
peak=    3.880 closest distance to " O   HOH Z 134 " =    1.506
peak=    3.868 closest distance to " O   HOH Z  44 " =    1.796
peak=    3.861 closest distance to " O   HOH Z 189 " =    2.672
peak=    3.860 closest distance to " O   TRP A 274 " =    1.866
peak=    3.822 closest distance to " O   HOH Z 322 " =    2.008
peak=    3.810 closest distance to " CB  GLU A 277 " =    3.524
peak=    3.805 closest distance to " O   HOH Z  88 " =    3.175
peak=    3.803 closest distance to " O   HOH Z 344 " =    2.719
peak=    3.798 closest distance to " O   HOH Z 213 " =    1.794
peak=    3.796 closest distance to " O   HOH Z 392 " =    2.877
peak=    3.795 closest distance to " O   HOH Z 426 " =    1.403
peak=    3.784 closest distance to " O   HOH Z 248 " =    1.793
peak=    3.783 closest distance to " CB  ASN A 148 " =    1.900
peak=    3.776 closest distance to " CB  GLU A 128 " =    1.130
peak=    3.774 closest distance to " CG2 THR A 221 " =    1.071
peak=    3.757 closest distance to " CA  THR A 221 " =    0.862
peak=    3.757 closest distance to " O   HOH Z  50 " =    1.652
peak=    3.757 closest distance to " O   HOH Z 273 " =    2.511
peak=    3.749 closest distance to " O   HOH Z 303 " =    1.745
peak=    3.744 closest distance to " CB  LEU A 228 " =    1.547
peak=    3.738 closest distance to " O   HOH Z  78 " =    1.708
peak=    3.738 closest distance to " O   HOH Z  68 " =    1.616
peak=    3.734 closest distance to " O   HOH Z 128 " =    2.064
peak=    3.731 closest distance to " O   MET A 105 " =    1.824
peak=    3.724 closest distance to " O   HOH Z 192 " =    1.367
peak=    3.720 closest distance to " O   HOH Z 236 " =    1.859
peak=    3.718 closest distance to " O   HOH Z 419 " =    1.757
peak=    3.698 closest distance to " CA  VAL A 126 " =    1.043
peak=    3.698 closest distance to " O   HOH Z 425 " =    1.410
peak=    3.693 closest distance to " NE2 GLN A  58 " =    5.675
peak=    3.668 closest distance to " O   HOH Z  68 " =    2.077
peak=    3.666 closest distance to " O   HOH Z 227 " =    1.730
peak=    3.646 closest distance to " CA  TYR A  30 " =    1.032
peak=    3.645 closest distance to " CA  LEU A 282 " =    1.038
peak=    3.641 closest distance to " O   HOH Z 374 " =    1.024
peak=    3.639 closest distance to " O   HOH Z 193 " =    1.979
peak=    3.639 closest distance to " CD1 ILE A  33 " =    1.651
peak=    3.630 closest distance to " NZ  LYS A 117 " =    3.132
peak=    3.629 closest distance to " O   HOH Z  40 " =    1.324
peak=    3.629 closest distance to " O   HOH Z  61 " =    1.581
peak=    3.621 closest distance to " O   HOH Z  49 " =    2.314
peak=    3.620 closest distance to " CD2 TRP A 179 " =    1.351
peak=    3.612 closest distance to " O   HOH Z  80 " =    1.678
peak=    3.604 closest distance to " CG  PRO A 243 " =    1.225
peak=    3.592 closest distance to " NE2 GLN A  58 " =    4.069
peak=    3.591 closest distance to " O   HOH Z 265 " =    2.131
peak=    3.587 closest distance to " O   HOH Z  20 " =    1.460
peak=    3.587 closest distance to " O   HOH Z  21 " =    1.827
peak=    3.586 closest distance to " O   HOH Z  10 " =    1.813
peak=    3.582 closest distance to " CB  ARG A 139 " =    0.980
peak=    3.581 closest distance to " O   HOH Z  43 " =    2.189
peak=    3.577 closest distance to " O   HOH Z 143 " =    1.001
peak=    3.576 closest distance to " O   ALA A 158 " =    1.313
peak=    3.562 closest distance to " OG  SER A  22 " =    2.741
peak=    3.553 closest distance to " O   HOH Z 261 " =    1.843
peak=    3.553 closest distance to " O   HOH Z 281 " =    4.405
peak=    3.550 closest distance to " O   ARG A  56 " =    2.706
peak=    3.540 closest distance to " O   HOH Z 283 " =    1.916
peak=    3.535 closest distance to " O   HOH Z 420 " =    1.911
peak=    3.529 closest distance to " O   HOH Z 280 " =    1.492
peak=    3.528 closest distance to " O   HOH Z 359 " =    1.980
peak=    3.523 closest distance to " CD  ARG A 269 " =    0.997
peak=    3.507 closest distance to " ND2 ASN A 187 " =    1.636
peak=    3.502 closest distance to " O   HOH Z 403 " =    1.697
peak=    3.499 closest distance to " O   HOH Z 130 " =    2.317
peak=    3.493 closest distance to " CD2 LEU A 255 " =    1.252
peak=    3.492 closest distance to " O   HOH Z 271 " =    1.874
peak=    3.489 closest distance to " O   HOH Z  40 " =    2.762
peak=    3.482 closest distance to " NH2BARG A 190 " =    1.948
peak=    3.482 closest distance to " CB BVAL A  41 " =    1.256
peak=    3.478 closest distance to " CA  ASP A 191 " =    0.871
peak=    3.477 closest distance to " O   HOH Z 407 " =    2.412
peak=    3.475 closest distance to " CZ AARG A 102 " =    1.859
peak=    3.472 closest distance to " O   HOH Z 403 " =    1.342
peak=    3.471 closest distance to " CG AARG A 275 " =    1.094
peak=    3.471 closest distance to " O   HOH Z  85 " =    1.361
peak=    3.464 closest distance to " O   HOH Z 284 " =    1.530
peak=    3.464 closest distance to " NH2 ARG A 156 " =    1.086
peak=    3.462 closest distance to " O   HOH Z 180 " =    2.157
peak=    3.455 closest distance to " CA  ALA A 295 " =    1.007
peak=    3.454 closest distance to " O   HOH Z 374 " =    2.414
peak=    3.450 closest distance to " C   ALA A 299 " =    0.970
peak=    3.447 closest distance to " CB  ILE A 234 " =    0.861
peak=    3.446 closest distance to " O   HOH Z 108 " =    1.823
peak=    3.446 closest distance to " O   HOH Z  61 " =    1.638
peak=    3.441 closest distance to " CA  ALA A 248 " =    1.386
peak=    3.434 closest distance to " OG  SER A  97 " =    2.520
peak=    3.434 closest distance to " OD1 ASP A 231 " =    1.854
peak=    3.432 closest distance to " CG1 ILE A  33 " =    1.343
peak=    3.432 closest distance to " NH2 ARG A 219 " =    1.764
peak=    3.430 closest distance to " O   HOH Z 344 " =    1.480
peak=    3.430 closest distance to " CD BLYS A 290 " =    1.201
peak=    3.425 closest distance to " O   HOH Z  19 " =    2.232
peak=    3.404 closest distance to " O   HOH Z 422 " =    2.582
peak=    3.404 closest distance to " O   HOH Z 394 " =    1.703
peak=    3.403 closest distance to " CB  GLN A  89 " =    1.103
peak=    3.403 closest distance to " O   HOH Z   4 " =    1.822
peak=    3.403 closest distance to " CG  LEU A 167 " =    1.172
peak=    3.400 closest distance to " O   HOH Z 329 " =    3.486
peak=    3.399 closest distance to " O   HOH Z 374 " =    3.013
peak=    3.398 closest distance to " O   HOH Z 217 " =    1.227
peak=    3.396 closest distance to " OE1 GLN A  11 " =    1.801
peak=    3.393 closest distance to " CA  LEU A 101 " =    1.588
peak=    3.389 closest distance to " O   HOH Z 409 " =    3.677
peak=    3.389 closest distance to " CG2 ILE A  20 " =    1.557
peak=    3.387 closest distance to " NZ  LYS A  76 " =    1.209
peak=    3.383 closest distance to " O   HOH Z 383 " =    2.059
peak=    3.381 closest distance to " CD2 HIS A  81 " =    1.212
peak=    3.380 closest distance to " O   HOH Z 148 " =    3.091
peak=    3.379 closest distance to " CD  LYS A 119 " =    1.825
peak=    3.379 closest distance to " O   ASN A 217 " =    1.240
peak=    3.376 closest distance to " C   LYS A 290 " =    1.348
peak=    3.376 closest distance to " O   HOH Z  14 " =    2.245
peak=    3.376 closest distance to " CB  LEU A 255 " =    0.782
peak=    3.372 closest distance to " CB  ALA A 248 " =    0.964
peak=    3.370 closest distance to " CB  TRP A 266 " =    0.981
peak=    3.366 closest distance to " CE1 TYR A 186 " =    1.253
peak=    3.364 closest distance to " O   HOH Z 132 " =    3.429
peak=    3.362 closest distance to " CB  ALA A   1 " =    1.299
peak=    3.358 closest distance to " OD1 ASN A 217 " =    1.755
peak=    3.356 closest distance to " O   HOH Z 171 " =    2.472
peak=    3.356 closest distance to " O   HOH Z 158 " =    2.943
peak=    3.351 closest distance to " N   ARG A 156 " =    1.262
peak=    3.350 closest distance to " CB  SER A 141 " =    1.048
peak=    3.348 closest distance to " O   HOH Z 112 " =    1.453
peak=    3.347 closest distance to " CB  ASN A  39 " =    0.782
peak=    3.344 closest distance to " O   HOH Z 193 " =    1.529
peak=    3.341 closest distance to " NH1 ARG A  14 " =    1.011
peak=    3.340 closest distance to " CG2 VAL A 257 " =    0.810
peak=    3.339 closest distance to " CG  GLN A  88 " =    1.039
peak=    3.337 closest distance to " CZ2 TRP A 179 " =    1.728
peak=    3.334 closest distance to " O   HOH Z 173 " =    2.151
peak=    3.330 closest distance to " O   HOH Z 215 " =    1.661
peak=    3.329 closest distance to " O   HOH Z 135 " =    1.842
peak=    3.328 closest distance to " O   HOH Z  59 " =    2.098
peak=    3.325 closest distance to " CG  MET A 185 " =    0.980
peak=    3.323 closest distance to " CA  ALA A 233 " =    1.377
peak=    3.320 closest distance to " O   GLN A  58 " =    1.531
peak=    3.317 closest distance to " O   HOH Z 266 " =    1.466
peak=    3.316 closest distance to " O   HOH Z 152 " =    1.632
peak=    3.315 closest distance to " O   HOH Z 352 " =    1.201
peak=    3.315 closest distance to " CA  PHE A 283 " =    1.290
peak=    3.313 closest distance to " O   HOH Z 172 " =    3.844
peak=    3.311 closest distance to " OG1 THR A 294 " =    2.319
peak=    3.309 closest distance to " CD  LYS A 166 " =    1.431
peak=    3.308 closest distance to " O   HOH Z 327 " =    1.575
peak=    3.299 closest distance to " CB  ALA A   9 " =    1.571
peak=    3.295 closest distance to " CE  MET A  93 " =    1.451
peak=    3.292 closest distance to " CD1 LEU A 300 " =    1.207
peak=    3.287 closest distance to " O   HOH Z 150 " =    1.708
peak=    3.283 closest distance to " CD2 TYR A 186 " =    0.990
peak=    3.283 closest distance to " CB  ALA A 291 " =    1.382
peak=    3.282 closest distance to " O   HOH Z 366 " =    2.865
peak=    3.282 closest distance to " CG2 ILE A 120 " =    1.265
peak=    3.282 closest distance to " O   HOH Z 355 " =    1.841
peak=    3.282 closest distance to " OD1 ASP A 286 " =    1.606
peak=    3.278 closest distance to " O   HOH Z 250 " =    1.317
peak=    3.276 closest distance to " O   HOH Z 155 " =    1.628
peak=    3.276 closest distance to " ND1 HIS A  81 " =    1.537
peak=    3.275 closest distance to " CB  ALA A 295 " =    1.395
peak=    3.274 closest distance to " O   THR A  31 " =    1.542
peak=    3.274 closest distance to " CA  ASN A 215 " =    1.200
peak=    3.270 closest distance to " O   HOH Z 364 " =    2.379
peak=    3.264 closest distance to " O   HOH Z 164 " =    1.958
peak=    3.262 closest distance to " CB  PRO A 198 " =    0.914
peak=    3.260 closest distance to " O   HOH Z 411 " =    1.827
peak=    3.258 closest distance to " CA  ALA A  51 " =    0.988
peak=    3.257 closest distance to " CA  ASN A 176 " =    1.081
peak=    3.257 closest distance to " O   HOH Z 261 " =    1.498
peak=    3.256 closest distance to " O   HOH Z 151 " =    1.492
peak=    3.255 closest distance to " CG1 VAL A 153 " =    0.932
peak=    3.255 closest distance to " CB  SER A  62 " =    1.219
peak=    3.249 closest distance to " O   HOH Z 406 " =    1.673
peak=    3.243 closest distance to " CA  LYS A 117 " =    1.215
peak=    3.241 closest distance to " CE BLYS A 290 " =    1.007
peak=    3.239 closest distance to " N   ASN A  39 " =    1.177
peak=    3.238 closest distance to " O   HOH Z 295 " =    1.545
peak=    3.238 closest distance to " O   HOH Z 136 " =    1.099
peak=    3.237 closest distance to " O   HOH Z 141 " =    1.552
peak=    3.232 closest distance to " O   HOH Z 255 " =    1.535
peak=    3.231 closest distance to " CG  MET A 188 " =    1.382
peak=    3.229 closest distance to " CG  MET A 185 " =    1.202
peak=    3.222 closest distance to " CB  ALA A 100 " =    1.246
peak=    3.219 closest distance to " CB  ARG A 102 " =    0.769
peak=    3.218 closest distance to " CA  ASP A 140 " =    1.186
peak=    3.215 closest distance to " CB  VAL A 268 " =    0.759
peak=    3.211 closest distance to " O   HOH Z 367 " =    3.482
peak=    3.201 closest distance to " CD  ARG A 159 " =    0.740
peak=    3.199 closest distance to " O   SER A  26 " =    1.589
peak=    3.197 closest distance to " CA  ALA A 291 " =    1.002
peak=    3.196 closest distance to " CA  GLN A 194 " =    1.256
peak=    3.193 closest distance to " O   HOH Z 291 " =    1.489
peak=    3.190 closest distance to " O   HOH Z 145 " =    2.012
peak=    3.189 closest distance to " CB  LEU A 143 " =    1.177
peak=    3.188 closest distance to " O   HOH Z 402 " =    1.389
peak=    3.185 closest distance to " CB  GLN A 278 " =    0.831
peak=    3.183 closest distance to " CG2AVAL A 121 " =    2.166
peak=    3.181 closest distance to " CD  ARG A 138 " =    0.830
peak=    3.179 closest distance to " O   HOH Z 423 " =    3.099
peak=    3.173 closest distance to " O   HOH Z 214 " =    1.033
peak=    3.172 closest distance to " CG  GLU A 277 " =    2.232
peak=    3.169 closest distance to " C   ALA A   1 " =    1.695
peak=    3.169 closest distance to " O   HOH Z   9 " =    1.632
peak=    3.163 closest distance to " O   HOH Z  30 " =    1.164
peak=    3.156 closest distance to " OG BSER A 164 " =    2.179
peak=    3.155 closest distance to " CA  THR A 264 " =    0.778
peak=    3.155 closest distance to " O   HOH Z 278 " =    1.285
peak=    3.155 closest distance to " CA  TYR A 116 " =    1.543
peak=    3.153 closest distance to " CG  GLN A  77 " =    2.165
peak=    3.153 closest distance to " O   HOH Z 334 " =    1.315
peak=    3.153 closest distance to " CA  MET A  40 " =    1.096
peak=    3.152 closest distance to " NH2 ARG A  79 " =    1.362
peak=    3.152 closest distance to " N   SER A  12 " =    1.559
peak=    3.147 closest distance to " NH2BARG A 145 " =    2.109
peak=    3.143 closest distance to " CB  ASN A 142 " =    1.083
peak=    3.140 closest distance to " O   HOH Z 359 " =    3.736
peak=    3.139 closest distance to " CZ2 TRP A 274 " =    1.587
peak=    3.138 closest distance to " O   HOH Z 380 " =    1.986
peak=    3.138 closest distance to " O   HOH Z 207 " =    2.057
peak=    3.134 closest distance to " CG2 VAL A 174 " =    1.330
peak=    3.133 closest distance to " CB  GLN A 205 " =    1.212
peak=    3.132 closest distance to " CA  SER A  87 " =    0.879
peak=    3.127 closest distance to " NH1BARG A 145 " =    1.795
peak=    3.118 closest distance to " O   HOH Z  11 " =    1.287
peak=    3.113 closest distance to " O   HOH Z 211 " =    2.191
peak=    3.109 closest distance to " NH2AARG A 190 " =    1.104
peak=    3.109 closest distance to " O   HOH Z 328 " =    1.780
peak=    3.105 closest distance to " O   HOH Z 280 " =    2.387
peak=    3.103 closest distance to " CD2 LEU A 282 " =    1.869
peak=    3.099 closest distance to " OG  SER A 206 " =    1.279
peak=    3.099 closest distance to " O   HOH Z  88 " =    2.410
peak=    3.095 closest distance to " CG1 ILE A  49 " =    1.427
peak=    3.090 closest distance to " O   PHE A  38 " =    1.899
peak=    3.088 closest distance to " O   HOH Z 152 " =    3.184
peak=    3.082 closest distance to " O   HOH Z 183 " =    1.329
peak=    3.082 closest distance to " CB  THR A  31 " =    1.617
peak=    3.075 closest distance to " O   HOH Z 381 " =    1.484
peak=    3.070 closest distance to " CA  ILE A 106 " =    0.841
peak=    3.067 closest distance to " NH1 ARG A  56 " =    1.112
peak=    3.048 closest distance to " CD1 LEU A  96 " =    0.832
peak=    3.046 closest distance to " O   HOH Z 409 " =    3.574
peak=    3.015 closest distance to " N   GLY A 241 " =    1.529
peak=    3.009 closest distance to " CD2 HIS A  81 " =    0.952
peak=    3.007 closest distance to " O   HOH Z 279 " =    2.208

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 194         
Filter by distance & map next to the model:
   mapped sites are within: 0.369 - 5.239
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 190 from: 194
   mapped sites are within: 0.797 - 5.239

peak=   -5.391 closest distance to " CG2 VAL A 230 " =    0.800
peak=   -4.452 closest distance to " O   HOH Z 290 " =    0.965
peak=   -4.408 closest distance to " CB  ALA A 161 " =    2.572
peak=   -4.300 closest distance to " SG  CYS A 254 " =    3.210
peak=   -4.295 closest distance to " OXT GLY A 302 " =    2.803
peak=   -4.267 closest distance to " CD  ARG A 156 " =    2.025
peak=   -4.213 closest distance to " CA  SER A 164 " =    2.040
peak=   -4.108 closest distance to " OG ASER A 134 " =    1.352
peak=   -4.102 closest distance to " O   HOH Z  92 " =    1.550
peak=   -4.097 closest distance to " O   HOH Z  11 " =    1.922
peak=   -4.086 closest distance to " O   HOH Z 266 " =    4.341
peak=   -4.029 closest distance to " O   HOH Z  13 " =    1.274
peak=   -3.989 closest distance to " N   GLN A  58 " =    1.800
peak=   -3.988 closest distance to " CG  LEU A 228 " =    0.945
peak=   -3.970 closest distance to " CG  LYS A 193 " =    2.288
peak=   -3.952 closest distance to " CE2 TYR A  30 " =    2.840
peak=   -3.946 closest distance to " OG BSER A 134 " =    1.672
peak=   -3.930 closest distance to " O   ALA A 161 " =    1.481
peak=   -3.905 closest distance to " CG  ASP A  50 " =    2.258
peak=   -3.904 closest distance to " CD  ARG A 139 " =    1.725
peak=   -3.878 closest distance to " C   ALA A 158 " =    1.203
peak=   -3.859 closest distance to " CD1 LEU A 101 " =    2.476
peak=   -3.858 closest distance to " O   HOH Z 166 " =    1.434
peak=   -3.844 closest distance to " C   HIS A 108 " =    1.149
peak=   -3.842 closest distance to " N   SER A 276 " =    1.275
peak=   -3.841 closest distance to " O   HOH Z 231 " =    1.761
peak=   -3.829 closest distance to " O   HOH Z  43 " =    1.756
peak=   -3.817 closest distance to " CG  GLN A 223 " =    2.228
peak=   -3.817 closest distance to " N   HIS A 115 " =    2.077
peak=   -3.815 closest distance to " O   HOH Z 377 " =    2.075
peak=   -3.813 closest distance to " O   HOH Z 198 " =    2.377
peak=   -3.810 closest distance to " CG2 VAL A 296 " =    1.444
peak=   -3.798 closest distance to " NH2 ARG A  79 " =    1.894
peak=   -3.777 closest distance to " O   PRO A 198 " =    1.285
peak=   -3.753 closest distance to " CB  ALA A 248 " =    1.957
peak=   -3.743 closest distance to " CZ  TYR A 169 " =    1.769
peak=   -3.711 closest distance to " N   ALA A 248 " =    1.660
peak=   -3.707 closest distance to " O   VAL A  67 " =    2.685
peak=   -3.707 closest distance to " OG BSER A 134 " =    1.226
peak=   -3.699 closest distance to " O   HOH Z  11 " =    1.762
peak=   -3.693 closest distance to " CB  TYR A  15 " =    2.145
peak=   -3.691 closest distance to " O   HOH Z  17 " =    1.474
peak=   -3.673 closest distance to " CD2 LEU A 300 " =    2.883
peak=   -3.666 closest distance to " O   HOH Z  98 " =    1.733
peak=   -3.659 closest distance to " CB  PRO A 243 " =    2.565
peak=   -3.646 closest distance to " N   THR A 157 " =    1.504
peak=   -3.643 closest distance to " O   HOH Z 166 " =    1.826
peak=   -3.626 closest distance to " O   HOH Z 165 " =    2.107
peak=   -3.620 closest distance to " OG  SER A  26 " =    1.024
peak=   -3.611 closest distance to " N   ALA A 226 " =    2.076
peak=   -3.599 closest distance to " C   ASN A 285 " =    2.420
peak=   -3.591 closest distance to " O   GLY A 196 " =    1.118
peak=   -3.585 closest distance to " CG  PHE A 283 " =    2.762
peak=   -3.577 closest distance to " CG  GLU A   2 " =    1.939
peak=   -3.575 closest distance to " CD2 LEU A 237 " =    2.764
peak=   -3.563 closest distance to " O   PRO A 198 " =    1.313
peak=   -3.561 closest distance to " C   ASN A 187 " =    1.812
peak=   -3.561 closest distance to " O   HOH Z  63 " =    0.935
peak=   -3.541 closest distance to " O   ALA A  51 " =    1.503
peak=   -3.539 closest distance to " ND2 ASN A 249 " =    2.317
peak=   -3.532 closest distance to " CG  ASP A 231 " =    0.797
peak=   -3.531 closest distance to " O   HOH Z 423 " =    2.225
peak=   -3.529 closest distance to " CG  MET A 105 " =    0.919
peak=   -3.528 closest distance to " O   ASN A 187 " =    1.511
peak=   -3.525 closest distance to " O   HOH Z 407 " =    3.112
peak=   -3.518 closest distance to " O   HOH Z 388 " =    1.961
peak=   -3.517 closest distance to " CB  CYS A 201 " =    2.560
peak=   -3.514 closest distance to " OE1 GLN A  73 " =    2.385
peak=   -3.512 closest distance to " O   HOH Z 435 " =    2.776
peak=   -3.507 closest distance to " O   HOH Z 389 " =    4.484
peak=   -3.505 closest distance to " OD1 ASN A 249 " =    1.298
peak=   -3.494 closest distance to " O   HOH Z 234 " =    4.129
peak=   -3.487 closest distance to " O   HOH Z  19 " =    2.164
peak=   -3.485 closest distance to " O   GLY A 211 " =    1.303
peak=   -3.484 closest distance to " ND2 ASN A  60 " =    1.380
peak=   -3.482 closest distance to " NH2AARG A 275 " =    5.178
peak=   -3.481 closest distance to " CB  PRO A 163 " =    2.689
peak=   -3.481 closest distance to " O   SER A 146 " =    1.023
peak=   -3.475 closest distance to " CD  LYS A 289 " =    2.538
peak=   -3.472 closest distance to " O   HOH Z  71 " =    1.184
peak=   -3.471 closest distance to " CA  GLY A  35 " =    2.073
peak=   -3.471 closest distance to " CA  ASP A 298 " =    1.072
peak=   -3.459 closest distance to " CE2 TRP A 179 " =    1.213
peak=   -3.448 closest distance to " CB  ALA A  51 " =    1.819
peak=   -3.425 closest distance to " O   HOH Z 426 " =    2.282
peak=   -3.420 closest distance to " OD2 ASP A  50 " =    1.380
peak=   -3.419 closest distance to " OXT GLY A 302 " =    3.453
peak=   -3.415 closest distance to " O   ALA A   8 " =    1.743
peak=   -3.409 closest distance to " O   HOH Z  15 " =    1.599
peak=   -3.405 closest distance to " CD1 PHE A  59 " =    1.864
peak=   -3.403 closest distance to " O   VAL A 153 " =    2.241
peak=   -3.402 closest distance to " CG  TRP A 266 " =    1.623
peak=   -3.393 closest distance to " O   HOH Z  52 " =    1.690
peak=   -3.389 closest distance to " N   GLN A  77 " =    1.600
peak=   -3.385 closest distance to " O   HOH Z 103 " =    1.771
peak=   -3.383 closest distance to " OG  SER A  97 " =    2.158
peak=   -3.380 closest distance to " CB  ASN A  39 " =    1.958
peak=   -3.377 closest distance to " O   SER A 135 " =    1.576
peak=   -3.377 closest distance to " CD1 LEU A  96 " =    2.327
peak=   -3.370 closest distance to " O   HOH Z  60 " =    2.360
peak=   -3.369 closest distance to " O   HOH Z  19 " =    2.226
peak=   -3.368 closest distance to " CD1 LEU A 228 " =    2.199
peak=   -3.360 closest distance to " CE2 PHE A 218 " =    2.630
peak=   -3.355 closest distance to " O   GLY A  80 " =    2.546
peak=   -3.353 closest distance to " O   HOH Z 310 " =    1.597
peak=   -3.350 closest distance to " OG1 THR A 178 " =    1.153
peak=   -3.349 closest distance to " CG  GLU A 152 " =    2.410
peak=   -3.348 closest distance to " O   HOH Z 151 " =    1.453
peak=   -3.346 closest distance to " CB  ALA A  43 " =    2.222
peak=   -3.345 closest distance to " CE BMET A  47 " =    1.478
peak=   -3.345 closest distance to " CG  PRO A 163 " =    2.681
peak=   -3.345 closest distance to " O   HOH Z 339 " =    1.699
peak=   -3.340 closest distance to " CB  ASP A 132 " =    2.248
peak=   -3.336 closest distance to " O   HOH Z 313 " =    1.852
peak=   -3.334 closest distance to " CG  GLU A  53 " =    1.528
peak=   -3.327 closest distance to " O   HOH Z 292 " =    2.851
peak=   -3.326 closest distance to " CD2 LEU A 167 " =    1.712
peak=   -3.323 closest distance to " OG1 THR A  82 " =    1.568
peak=   -3.321 closest distance to " O   HOH Z 385 " =    2.084
peak=   -3.317 closest distance to " C   ARG A 102 " =    1.423
peak=   -3.315 closest distance to " O   HOH Z 292 " =    4.340
peak=   -3.310 closest distance to " OD1 ASP A 200 " =    1.178
peak=   -3.309 closest distance to " CD  GLN A  88 " =    0.843
peak=   -3.309 closest distance to " O   HOH Z  10 " =    1.441
peak=   -3.306 closest distance to " CE  MET A 105 " =    1.971
peak=   -3.301 closest distance to " O   HOH Z 211 " =    1.191
peak=   -3.301 closest distance to " O   HOH Z  44 " =    2.088
peak=   -3.292 closest distance to " N   PHE A  59 " =    2.172
peak=   -3.292 closest distance to " CE  LYS A  76 " =    2.911
peak=   -3.291 closest distance to " CB  CYS A 254 " =    2.409
peak=   -3.288 closest distance to " O   HOH Z 148 " =    1.637
peak=   -3.284 closest distance to " SG ACYS A 201 " =    2.063
peak=   -3.279 closest distance to " O   GLU A  44 " =    1.816
peak=   -3.279 closest distance to " OG  SER A  87 " =    1.373
peak=   -3.278 closest distance to " O   HOH Z 211 " =    1.759
peak=   -3.273 closest distance to " ND2 ASN A  45 " =    1.112
peak=   -3.272 closest distance to " CG  GLU A 277 " =    1.141
peak=   -3.268 closest distance to " O   HOH Z 353 " =    2.321
peak=   -3.258 closest distance to " O   HOH Z  70 " =    1.444
peak=   -3.258 closest distance to " CA  TYR A  68 " =    2.713
peak=   -3.254 closest distance to " CD2 TYR A 293 " =    2.134
peak=   -3.250 closest distance to " O   HOH Z 410 " =    2.001
peak=   -3.243 closest distance to " O   HOH Z 134 " =    2.573
peak=   -3.242 closest distance to " NH1 ARG A  56 " =    2.533
peak=   -3.238 closest distance to " CB  GLN A  55 " =    1.570
peak=   -3.236 closest distance to " O   HOH Z 241 " =    1.374
peak=   -3.236 closest distance to " CD  GLN A  88 " =    2.198
peak=   -3.234 closest distance to " NH2 ARG A  66 " =    1.856
peak=   -3.230 closest distance to " O   HOH Z 189 " =    1.963
peak=   -3.217 closest distance to " C   LEU A 143 " =    1.199
peak=   -3.216 closest distance to " CA  GLY A 211 " =    1.859
peak=   -3.209 closest distance to " CZ3 TRP A 274 " =    1.095
peak=   -3.207 closest distance to " O   ALA A   1 " =    1.866
peak=   -3.202 closest distance to " OG  SER A 206 " =    1.719
peak=   -3.198 closest distance to " O   ASP A 231 " =    2.511
peak=   -3.192 closest distance to " O   HOH Z 191 " =    5.239
peak=   -3.192 closest distance to " O   VAL A 174 " =    2.002
peak=   -3.187 closest distance to " CB  ASP A 124 " =    2.081
peak=   -3.179 closest distance to " CE  MET A  93 " =    1.171
peak=   -3.177 closest distance to " CB  ALA A 291 " =    2.407
peak=   -3.162 closest distance to " ND2 ASN A 209 " =    1.746
peak=   -3.160 closest distance to " CD2 LEU A 237 " =    2.794
peak=   -3.158 closest distance to " O   HOH Z 427 " =    1.534
peak=   -3.148 closest distance to " O   HOH Z  97 " =    1.763
peak=   -3.145 closest distance to " O   HOH Z 297 " =    2.771
peak=   -3.144 closest distance to " CZ  PHE A  59 " =    1.611
peak=   -3.140 closest distance to " CA  GLY A 133 " =    1.850
peak=   -3.139 closest distance to " O   MET A  40 " =    2.655
peak=   -3.137 closest distance to " CA  ASN A 127 " =    1.166
peak=   -3.133 closest distance to " N   ARG A  66 " =    1.808
peak=   -3.124 closest distance to " OH  TYR A 214 " =    1.338
peak=   -3.121 closest distance to " O   TRP A  70 " =    1.637
peak=   -3.118 closest distance to " OD1 ASP A 191 " =    1.676
peak=   -3.118 closest distance to " O   HOH Z  47 " =    1.407
peak=   -3.112 closest distance to " ND2 ASN A 252 " =    1.625
peak=   -3.104 closest distance to " CG1 VAL A 112 " =    2.665
peak=   -3.103 closest distance to " ND2 ASN A  39 " =    1.337
peak=   -3.101 closest distance to " OE1 GLN A  88 " =    1.036
peak=   -3.091 closest distance to " O   HOH Z 407 " =    3.641
peak=   -3.088 closest distance to " C   MET A 188 " =    1.516
peak=   -3.084 closest distance to " O   HOH Z  78 " =    1.796
peak=   -3.077 closest distance to " O   HOH Z 150 " =    1.539
peak=   -3.059 closest distance to " O   HOH Z 309 " =    2.487
peak=   -3.053 closest distance to " O   HOH Z 108 " =    2.382
peak=   -3.049 closest distance to " OG  SER A   3 " =    1.611
peak=   -3.047 closest distance to " O   HOH Z 231 " =    0.966
peak=   -3.045 closest distance to " CE3 TRP A  70 " =    1.674
peak=   -3.040 closest distance to " O   ASP A 171 " =    2.037
peak=   -3.027 closest distance to " CB  ARG A  79 " =    2.481
peak=   -3.027 closest distance to " N   GLY A  23 " =    2.005

================= 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    :  0.4606 0.4680   6.263978e+00   6.261114e+00
   1_bss:  0.4525 0.4571   6.261519e+00   6.250292e+00
   1_xyz:  0.3735 0.3978   6.141251e+00   6.180390e+00
   1_adp:  0.3224 0.3743   6.051077e+00   6.146145e+00
   1_occ:  0.3220 0.3746   6.051042e+00   6.147079e+00
   2_bss:  0.3185 0.3715   6.050706e+00   6.144756e+00
   2_xyz:  0.2352 0.2929   5.787991e+00   5.950541e+00
   2_adp:  0.2118 0.2702   5.703698e+00   5.885753e+00
   2_occ:  0.2117 0.2703   5.703136e+00   5.885491e+00
   3_bss:  0.2096 0.2666   5.696983e+00   5.878045e+00
   3_xyz:  0.1536 0.2057   5.419816e+00   5.640469e+00
   3_adp:  0.1379 0.1874   5.322730e+00   5.548330e+00
   3_occ:  0.1377 0.1872   5.321761e+00   5.547253e+00
   4_bss:  0.1375 0.1860   5.318644e+00   5.543622e+00
   4_xyz:  0.1272 0.1721   5.251159e+00   5.471915e+00
   4_adp:  0.1246 0.1683   5.231426e+00   5.449796e+00
   4_occ:  0.1245 0.1681   5.230858e+00   5.449462e+00
   5_bss:  0.1245 0.1681   5.230403e+00   5.449381e+00
   5_xyz:  0.1133 0.1590   5.157705e+00   5.395537e+00
   5_adp:  0.1126 0.1583   5.153302e+00   5.391025e+00
   5_occ:  0.1126 0.1581   5.152898e+00   5.390620e+00
   5_bss:  0.1127 0.1582   5.153610e+00   5.391475e+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:  0.362  12.496   6.727   7.590  10.003   0.000   0.000   0.000
   1_xyz:  0.362  12.496   6.727   7.590  10.003   0.000   0.000   0.000
   1_adp:  0.362  12.496   6.727   7.590  10.003   0.000   0.000   0.000
   1_occ:  0.362  12.496   6.727   7.590  10.003   0.000   0.000   0.000
   2_bss:  0.320  20.000   3.252   3.764   6.794   0.000   0.000   0.000
   2_xyz:  0.320  20.000   3.252   3.764   6.794   0.000   0.000   0.000
   2_adp:  0.320  20.000   3.252   3.764   6.794   0.000   0.000   0.000
   2_occ:  0.320  20.000   3.252   3.764   6.794   0.000   0.000   0.000
   3_bss:  0.328  32.502   2.109   2.506   3.824   0.000   0.000   0.000
   3_xyz:  0.328  32.502   2.109   2.506   3.824   0.000   0.000   0.000
   3_adp:  0.328  32.502   2.109   2.506   3.824   0.000   0.000   0.000
   3_occ:  0.328  32.502   2.109   2.506   3.824   0.000   0.000   0.000
   4_bss:  0.317  32.502   1.864   2.184   2.763   0.000   0.000   0.000
   4_xyz:  0.317  32.502   1.864   2.184   2.763   0.000   0.000   0.000
   4_adp:  0.317  32.502   1.864   2.184   2.763   0.000   0.000   0.000
   4_occ:  0.317  32.502   1.864   2.184   2.763   0.000   0.000   0.000
   5_bss:  0.315  34.057   1.757   2.084   2.433   0.000   0.000   0.000
   5_xyz:  0.315  34.057   1.757   2.084   2.433   0.000   0.000   0.000
   5_adp:  0.315  34.057   1.757   2.084   2.433   0.000   0.000   0.000
   5_occ:  0.315  34.057   1.757   2.084   2.433   0.000   0.000   0.000
   5_bss:  0.317  37.541  -0.334  -0.007   0.342   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  55.605 0.4503  0.5315    66917.244
   1_bss:  55.273 0.4517  0.6685    62892.368
   1_xyz:  45.710 0.5719  0.8356    46490.391
   1_adp:  42.430 0.6125  0.9235    41608.148
   1_occ:  42.546 0.6111  0.9216    41836.710
   2_bss:  42.250 0.6146  0.8192    41419.859
   2_xyz:  31.004 0.7454  0.9675    23324.665
   2_adp:  27.740 0.7823  1.0036    19696.052
   2_occ:  27.734 0.7824  1.0032    19681.277
   3_bss:  27.354 0.7863  0.9440    19230.062
   3_xyz:  20.037 0.8609  0.9898    10909.169
   3_adp:  17.733 0.8830  0.9972     9110.683
   3_occ:  17.702 0.8832  0.9972     9084.890
   4_bss:  17.594 0.8841  0.9777     8983.834
   4_xyz:  15.899 0.8991  0.9858     7626.326
   4_adp:  15.323 0.9044  0.9877     7272.107
   4_occ:  15.307 0.9045  0.9876     7263.979
   5_bss:  15.301 0.9046  0.9812     7267.352
   5_xyz:  14.298 0.9125  0.9837     6476.882
   5_adp:  14.186 0.9136  0.9837     6432.813
   5_occ:  14.177 0.9136  0.9837     6430.323
   5_bss:  14.211 0.9134  0.9836     6459.542
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3231e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3231e+01
   1_xyz:   1.590  0.012  0.103 18.156  0.006  4.108   1.2888e-01
   1_adp:   1.590  0.012  0.103 18.156  0.006  4.108   1.2888e-01
   1_occ:   1.590  0.012  0.103 18.156  0.006  4.108   1.2888e-01
   2_bss:   1.590  0.012  0.103 18.156  0.006  4.108   1.2888e-01
   2_xyz:   1.158  0.009  0.087 16.423  0.005  4.113   8.4242e-02
   2_adp:   1.158  0.009  0.087 16.423  0.005  4.113   8.4242e-02
   2_occ:   1.158  0.009  0.087 16.423  0.005  4.113   8.4242e-02
   3_bss:   1.158  0.009  0.087 16.423  0.005  4.113   8.4242e-02
   3_xyz:   1.110  0.007  0.082 15.793  0.004  4.121   7.0400e-02
   3_adp:   1.110  0.007  0.082 15.793  0.004  4.121   7.0400e-02
   3_occ:   1.110  0.007  0.082 15.793  0.004  4.121   7.0400e-02
   4_bss:   1.110  0.007  0.082 15.793  0.004  4.121   7.0400e-02
   4_xyz:   0.899  0.005  0.069 15.389  0.003  4.115   5.1926e-02
   4_adp:   0.899  0.005  0.069 15.389  0.003  4.115   5.1926e-02
   4_occ:   0.899  0.005  0.069 15.389  0.003  4.115   5.1926e-02
   5_bss:   0.899  0.005  0.069 15.389  0.003  4.115   5.1926e-02
   5_xyz:   1.094  0.008  0.085 15.651  0.004  4.110   6.9424e-02
   5_adp:   1.094  0.008  0.085 15.651  0.004  4.110   6.9424e-02
   5_occ:   1.094  0.008  0.085 15.651  0.004  4.110   6.9424e-02
   5_bss:   1.094  0.008  0.085 15.651  0.004  4.110   6.9424e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.8994e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.8994e+00
   1_xyz:  13.490  0.153  0.435 86.070  0.052  2.222   8.9692e-02
   1_adp:  13.490  0.153  0.435 86.070  0.052  2.222   8.9692e-02
   1_occ:  13.490  0.153  0.435 86.070  0.052  2.222   8.9692e-02
   2_bss:  13.490  0.153  0.435 86.070  0.052  2.222   8.9692e-02
   2_xyz:   7.444  0.095  0.261 84.803  0.038  2.284   9.6612e-02
   2_adp:   7.444  0.095  0.261 84.803  0.038  2.284   9.6612e-02
   2_occ:   7.444  0.095  0.261 84.803  0.038  2.284   9.6612e-02
   3_bss:   7.444  0.095  0.261 84.803  0.038  2.284   9.6612e-02
   3_xyz:   7.098  0.042  0.513 82.860  0.020  2.337   6.8930e-02
   3_adp:   7.098  0.042  0.513 82.860  0.020  2.337   6.8930e-02
   3_occ:   7.098  0.042  0.513 82.860  0.020  2.337   6.8930e-02
   4_bss:   7.098  0.042  0.513 82.860  0.020  2.337   6.8930e-02
   4_xyz:   6.559  0.043  0.367 82.162  0.026  2.370   3.2669e-02
   4_adp:   6.559  0.043  0.367 82.162  0.026  2.370   3.2669e-02
   4_occ:   6.559  0.043  0.367 82.162  0.026  2.370   3.2669e-02
   5_bss:   6.559  0.043  0.367 82.162  0.026  2.370   3.2669e-02
   5_xyz:   6.920  0.043  0.593 82.984  0.027  2.235   6.5088e-02
   5_adp:   6.920  0.043  0.593 82.984  0.027  2.235   6.5088e-02
   5_occ:   6.920  0.043  0.593 82.984  0.027  2.235   6.5088e-02
   5_bss:   6.920  0.043  0.593 82.984  0.027  2.235   6.5088e-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:  61.62   0.00  12.21  61.53   0.00   9.74  61.62   0.00  25.68
   1_occ:  61.62   0.00  12.21  61.53   0.00   9.74  61.62   0.00  25.68
   2_bss:  61.62   0.00  12.21  61.53   0.00   9.74  61.62   0.00  25.68
   2_xyz:  61.62   0.00  12.21  61.53   0.00   9.74  61.62   0.00  25.68
   2_adp: 128.88   0.00  12.44 128.88   0.00   9.15  59.55   1.15  30.33
   2_occ: 128.88   0.00  12.44 128.88   0.00   9.15  59.55   1.15  30.33
   3_bss: 128.88   0.00  12.44 128.88   0.00   9.15  59.55   1.15  30.33
   3_xyz: 128.88   0.00  12.44 128.88   0.00   9.15  59.55   1.15  30.33
   3_adp:  72.99   0.00  12.78  72.99   0.00   8.66  71.40   3.00  35.19
   3_occ:  72.99   0.00  12.78  72.99   0.00   8.66  71.40   3.00  35.19
   4_bss:  72.99   0.00  12.78  72.99   0.00   8.66  71.40   3.00  35.19
   4_xyz:  72.99   0.00  12.78  72.99   0.00   8.66  71.40   3.00  35.19
   4_adp:  83.18   0.00  12.76  83.18   0.00   8.61  82.94   2.16  35.35
   4_occ:  83.18   0.00  12.76  83.18   0.00   8.61  82.94   2.16  35.35
   5_bss:  83.18   0.00  12.76  83.18   0.00   8.61  82.94   2.16  35.35
   5_xyz:  83.18   0.00  12.76  83.18   0.00   8.61  82.94   2.16  35.35
   5_adp:  83.25   0.00  12.71  83.25   0.00   8.59  83.09   1.97  35.17
   5_occ:  83.25   0.00  12.71  83.25   0.00   8.59  83.09   1.97  35.17
   5_bss:  85.34   2.09  14.80  85.34   2.09  10.68  85.18   4.06  37.26
------------------------------------------------------------------------
 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:    1.208    0.016    0.403
   1_adp:    1.208    0.016    0.403
   1_occ:    1.208    0.016    0.403
   2_bss:    1.208    0.016    0.403
   2_xyz:    1.531    0.018    0.580
   2_adp:    1.531    0.018    0.580
   2_occ:    1.531    0.018    0.580
   3_bss:    1.531    0.018    0.580
   3_xyz:    1.597    0.029    0.645
   3_adp:    1.597    0.029    0.645
   3_occ:    1.597    0.029    0.645
   4_bss:    1.597    0.029    0.645
   4_xyz:    1.634    0.004    0.664
   4_adp:    1.634    0.004    0.664
   4_occ:    1.634    0.004    0.664
   5_bss:    1.634    0.004    0.664
   5_xyz:    1.625    0.032    0.681
   5_adp:    1.625    0.032    0.681
   5_occ:    1.625    0.032    0.681
   5_bss:    1.625    0.032    0.681
------------------------------------------------------------------------

CPU time actual refinement: 300.68


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_660/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_660/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_660/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_660/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_660/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 300.55 
  Macro-tasks:
    bulk solvent and scale       = 39.46  
    individual site refinement   = 124.16 
    weights calculation          = 27.67  
    collect and process          = 5.36   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 196.75 
  Micro-tasks:
    mask                            = 2.13   
    f_calc                          = 94.26  
    alpha_beta                      = 6.79   
    target                          = 0.98   
    gradients_wrt_atomic_parameters = 102.54 
    fmodel                         = 6.47   
    r_factors                      = 0.18   
    phase_errors                   = 8.65   
    foms                           = 0.24   
    TOTAL for micro-tasks          = 222.24 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.218 micro seconds
Total CPU time: 5.21 minutes
from_scatterers_fft:    639 calls, 93.97 s
gradients_fft:          583 calls, 91.20 s

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

# Date 2008-01-16 Time 02:07:24 PST -0800 (1200478044.16 s)
Start R-work = 0.4606, R-free = 0.4680 (no bulk solvent and anisotropic scale)
Final R-work = 0.1299, R-free = 0.1747 (no bulk solvent and anisotropic scale)

Start R-work = 0.4525, R-free = 0.4571
Final R-work = 0.1127, R-free = 0.1582