# Date 2008-01-16 Time 01:28:34 PST -0800 (1200475714.34 s)
#phil __OFF__

Command line arguments: "../443.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 23887
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 443

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.5475, 47.3993, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.42, per 1000 atoms: 1.21


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 47.3993, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.844 1.98049
Completeness in resolution range: 0.967119
Completeness with d_max=infinity: 0.964073

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8440
                             d_min =   1.9805

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 47.3993, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.844 1.98049
Completeness in resolution range: 0.967119
Completeness with d_max=infinity: 0.964073

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8444 -  4.2369 [2122/2150]  1911   211   9.9%
  bin  2:  4.2369 -  3.3759 [2038/2057]  1832   206  10.1%
  bin  3:  3.3759 -  2.9530 [2026/2046]  1824   202  10.0%
  bin  4:  2.9530 -  2.6848 [1988/2013]  1792   196   9.9%
  bin  5:  2.6848 -  2.4933 [1987/2007]  1786   201  10.1%
  bin  6:  2.4933 -  2.3469 [1967/2013]  1774   193   9.8%
  bin  7:  2.3469 -  2.2298 [1962/1994]  1764   198  10.1%
  bin  8:  2.2298 -  2.1330 [1960/1996]  1760   200  10.2%
  bin  9:  2.1330 -  2.0511 [1944/1974]  1753   191   9.8%
  bin 10:  2.0511 -  1.9805 [1595/2005]  1434   161  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_443/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:
        1.81 -     2.42: 28
        2.42 -     3.04: 2203
        3.04 -     3.66: 4726
        3.66 -     4.28: 9053
        4.28 -     4.90: 12421
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.919 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.921 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  2.010 3.040 -x+1,y-1/2,-z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  2.053 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28426 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_443/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_443/model_refine_001.geo

CPU time processing inputs: 9.22


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.5475 47.3993 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4518   r_free= 0.4417   ksol= 0.00   Bsol= 0.00   scale= 0.816    |
|                                                                             |
| 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:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.248795                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8444 -  4.7251 0.99   1380  154 0.3706 0.3546      6.5334      6.5326|
|  2:  4.7251 -  3.7707 0.99   1329  146 0.3562 0.3653      6.6942      6.7176|
|  3:  3.7707 -  3.3000 0.99   1305  147 0.3953 0.3684      6.6084       6.629|
|  4:  3.3000 -  3.0010 0.99   1293  138 0.4274 0.3921      6.4753      6.3869|
|  5:  3.0010 -  2.7875 0.99   1283  146 0.4668 0.4908      6.3478      6.3849|
|  6:  2.7875 -  2.6241 0.98   1281  142 0.4755 0.5278      6.2516       6.219|
|  7:  2.6241 -  2.4933 0.99   1274  143 0.4930 0.4516      6.2343        6.12|
|  8:  2.4933 -  2.3852 0.98   1267  140 0.4935 0.4658      6.1695      6.1649|
|  9:  2.3852 -  2.2937 0.98   1276  146 0.5138 0.5267      6.1124      6.1402|
| 10:  2.2937 -  2.2148 0.97   1235  132 0.5060 0.5090      6.1114      6.0849|
| 11:  2.2148 -  2.1458 0.99   1273  144 0.5009 0.4575      6.0246      6.0543|
| 12:  2.1458 -  2.0846 0.98   1270  133 0.5266 0.5189      5.9842       6.009|
| 13:  2.0846 -  2.0299 0.97   1227  139 0.5166 0.5358      5.8905      5.8936|
| 14:  2.0299 -  1.9805 0.73    937  109 0.5328 0.4590      5.8713      5.7174|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8444 -  4.7251  1380   154  0.71  33.67   0.82     0.73      67045.93|
|  2:  4.7251 -  3.7707  1329   146  0.74  31.45   0.91     0.79      86139.93|
|  3:  3.7707 -  3.3000  1305   147  0.67  37.89   0.87     0.77      89428.41|
|  4:  3.3000 -  3.0010  1293   138  0.61  43.14   0.83     0.68      76923.89|
|  5:  3.0010 -  2.7875  1283   146  0.51  51.02   0.77     0.59      69202.65|
|  6:  2.7875 -  2.6241  1281   142  0.49  52.90   0.76     0.55      59954.37|
|  7:  2.6241 -  2.4933  1274   143  0.48  53.88   0.75     0.53      55786.96|
|  8:  2.4933 -  2.3852  1267   140  0.48  53.82   0.76     0.54      48748.19|
|  9:  2.3852 -  2.2937  1276   146  0.44  56.59   0.74     0.52      46665.55|
| 10:  2.2937 -  2.2148  1235   132  0.44  56.58   0.76     0.51      43726.49|
| 11:  2.2148 -  2.1458  1273   144  0.41  59.50   0.77     0.49      42653.53|
| 12:  2.1458 -  2.0846  1270   133  0.39  60.92   0.77     0.48      40340.16|
| 13:  2.0846 -  2.0299  1227   139  0.39  60.58   0.75     0.47      33555.98|
| 14:  2.0299 -  1.9805   937   109  0.47  54.35   0.73     0.51      23352.92|
|alpha:            min =        0.47 max =            0.79 mean =         0.59|
|beta:             min =    23352.92 max =        89428.41 mean =     56932.92|
|figures of merit: min =        0.00 max =            1.00 mean =         0.52|
|phase err.(work): min =        0.00 max =           89.99 mean =        50.14|
|phase err.(test): min =        0.00 max =           89.58 mean =        50.00|
|-----------------------------------------------------------------------------|

============================== 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 = 9.293698              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.343   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.774982              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.388   (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:        5 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      163 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      710 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1520 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2649 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3936 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5104 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6598 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7739 |
|-----------------------------------------------------------------------------|
|-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 |       53.544 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.893 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.765)------------------------------------------|
|    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 = 11.765)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4589   r_free= 0.4500   ksol= 0.00   Bsol= 0.00   scale= 0.785    |
|                                                                             |
| 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:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.251794                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4431   r_free= 0.4355   ksol= 0.35   Bsol= 17.11   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.31,9.58,8.13,0.00,0.00,0.00); trace/3= 8.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.241570                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.910616              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.079   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.819863              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.452   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4431      final r-factor (work) = 0.3408          |
| start r-factor (free) = 0.4355      final r-factor (free) = 0.3638          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 81.4255 = 8.91 * 0.50 * 6.2579 + 1.00 * 53.5445                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.3622 = 8.91 * 0.50 * 6.1120 + 1.00 * 0.1313                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3408      final r-factor (work) = 0.2853          |
| start r-factor (free) = 0.3638      final r-factor (free) = 0.3219          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0253 = 0.82 * 1.00 * 6.1120 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9055 = 0.82 * 1.00 * 5.9669 + 1.00 * 0.0135                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.765)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    69.42   11.30    None  None   None       |
|    all(noH): 2823   0      0.00    69.42   11.30    None  None   None       |
|    Sol.    : 438    0      0.00    69.42   27.26    None  None   None       |
|    Mac.    : 2385   0      0.00    68.53   8.37     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 -   6.942: 1365   |   5:    34.709 -  41.650:   81        |
|      1:     6.942 -  13.884:  696   |   6:    41.650 -  48.592:   55        |
|      2:    13.884 -  20.825:  309   |   7:    48.592 -  55.534:   30        |
|      3:    20.825 -  27.767:  153   |   8:    55.534 -  62.476:   10        |
|      4:    27.767 -  34.709:  121   |   9:    62.476 -  69.417:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2853 r_free = 0.3219             target_work(ml) = 5.920         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2846 r_free = 0.3214             target_work(ml) = 5.919         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2846   r_free= 0.3214   ksol= 0.35   Bsol= 17.11   scale= 1.092   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.31,9.58,8.13,0.00,0.00,0.00); trace/3= 8.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.919448                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2810   r_free= 0.3176   ksol= 0.32   Bsol= 37.11   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.86,5.73,5.14,0.00,0.00,0.00); trace/3= 4.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.919128                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.474854              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.221   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.349279              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 120.923  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2810      final r-factor (work) = 0.1870          |
| start r-factor (free) = 0.3176      final r-factor (free) = 0.2247          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.4878 = 4.47 * 0.50 * 5.9696 + 1.00 * 0.1313                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.9142 = 4.47 * 0.50 * 5.7422 + 1.00 * 0.0664                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1870      final r-factor (work) = 0.1671          |
| start r-factor (free) = 0.2247      final r-factor (free) = 0.2083          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0204 = 0.35 * 1.00 * 5.7422 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9330 = 0.35 * 1.00 * 5.5039 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.765)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.72   11.71    None  None   None       |
|    all(noH): 2823   0      0.00    74.72   11.71    None  None   None       |
|    Sol.    : 438    0      0.83    66.18   32.43    None  None   None       |
|    Mac.    : 2385   0      0.00    74.72   7.91     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 -   7.473: 1539   |   5:    37.362 -  44.835:  100        |
|      1:     7.473 -  14.945:  654   |   6:    44.835 -  52.307:   64        |
|      2:    14.945 -  22.417:  190   |   7:    52.307 -  59.780:   38        |
|      3:    22.417 -  29.890:  110   |   8:    59.780 -  67.252:   11        |
|      4:    29.890 -  37.362:  112   |   9:    67.252 -  74.724:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1671 r_free = 0.2083             target_work(ml) = 5.466         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1669 r_free = 0.2083             target_work(ml) = 5.465         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1669   r_free= 0.2083   ksol= 0.32   Bsol= 37.11   scale= 1.040   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.86,5.73,5.14,0.00,0.00,0.00); trace/3= 4.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.464829                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1656   r_free= 0.2080   ksol= 0.32   Bsol= 37.11   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.53,3.92,3.97,0.00,0.00,0.00); trace/3= 3.48                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.464202                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.376985              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.066  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.202745              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.090  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1656      final r-factor (work) = 0.1294          |
| start r-factor (free) = 0.2080      final r-factor (free) = 0.1681          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6191 = 2.38 * 0.50 * 5.5135 + 1.00 * 0.0664                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4287 = 2.38 * 0.50 * 5.3579 + 1.00 * 0.0609                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1294      final r-factor (work) = 0.1242          |
| start r-factor (free) = 0.1681      final r-factor (free) = 0.1605          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0969 = 0.20 * 1.00 * 5.3579 + 1.00 * 0.0106                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0693 = 0.20 * 1.00 * 5.2269 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.765)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    74.41   11.65    None  None   None       |
|    all(noH): 2823   0      0.00    74.41   11.65    None  None   None       |
|    Sol.    : 438    0      1.46    65.23   32.90    None  None   None       |
|    Mac.    : 2385   0      0.00    74.41   7.75     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 -   7.441: 1588   |   5:    37.204 -  44.645:  101        |
|      1:     7.441 -  14.882:  621   |   6:    44.645 -  52.086:   62        |
|      2:    14.882 -  22.323:  166   |   7:    52.086 -  59.527:   37        |
|      3:    22.323 -  29.764:  114   |   8:    59.527 -  66.968:   10        |
|      4:    29.764 -  37.204:  119   |   9:    66.968 -  74.409:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1242 r_free = 0.1605             target_work(ml) = 5.206         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1239 r_free = 0.1605             target_work(ml) = 5.206         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1239   r_free= 0.1605   ksol= 0.32   Bsol= 37.11   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.53,3.92,3.97,0.00,0.00,0.00); trace/3= 3.48                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.205810                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1243   r_free= 0.1607   ksol= 0.32   Bsol= 41.34   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.24,3.32,3.62,0.00,0.00,0.00); trace/3= 3.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.208387                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.918089              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.021  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.988499              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 115.149  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1243      final r-factor (work) = 0.1132          |
| start r-factor (free) = 0.1607      final r-factor (free) = 0.1556          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6903 = 2.92 * 0.50 * 5.2289 + 1.00 * 0.0611                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6093 = 2.92 * 0.50 * 5.1650 + 1.00 * 0.0734                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1132      final r-factor (work) = 0.1105          |
| start r-factor (free) = 0.1556      final r-factor (free) = 0.1566          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1154 = 0.99 * 1.00 * 5.1650 + 1.00 * 0.0098                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0884 = 0.99 * 1.00 * 5.1328 + 1.00 * 0.0147                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.765)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.34   11.97    None  None   None       |
|    all(noH): 2823   0      0.00    82.34   11.97    None  None   None       |
|    Sol.    : 438    0      1.12    70.40   34.88    None  None   None       |
|    Mac.    : 2385   0      0.00    82.34   7.77     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 -   8.234: 1702   |   5:    41.171 -  49.405:   93        |
|      1:     8.234 -  16.468:  555   |   6:    49.405 -  57.639:   62        |
|      2:    16.468 -  24.702:  151   |   7:    57.639 -  65.873:   32        |
|      3:    24.702 -  32.937:  104   |   8:    65.873 -  74.107:    8        |
|      4:    32.937 -  41.171:  110   |   9:    74.107 -  82.341:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1105 r_free = 0.1566             target_work(ml) = 5.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1104 r_free = 0.1568             target_work(ml) = 5.137         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1104   r_free= 0.1568   ksol= 0.32   Bsol= 41.34   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.24,3.32,3.62,0.00,0.00,0.00); trace/3= 3.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.136892                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1103   r_free= 0.1567   ksol= 0.32   Bsol= 41.34   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.38,3.32,3.71,0.00,0.00,0.00); trace/3= 3.14                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.136887                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.050318              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 154.439  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.219869              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 103.877  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1103      final r-factor (work) = 0.1111          |
| start r-factor (free) = 0.1567      final r-factor (free) = 0.1566          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3351 = 2.05 * 0.50 * 5.1326 + 1.00 * 0.0734                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3312 = 2.05 * 0.50 * 5.1412 + 1.00 * 0.0606                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1111      final r-factor (work) = 0.1121          |
| start r-factor (free) = 0.1566      final r-factor (free) = 0.1552          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1452 = 0.22 * 1.00 * 5.1412 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1418 = 0.22 * 1.00 * 5.1462 + 1.00 * 0.0103                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.765)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.55   11.64    None  None   None       |
|    all(noH): 2823   0      0.00    81.55   11.64    None  None   None       |
|    Sol.    : 438    0      1.04    69.36   33.53    None  None   None       |
|    Mac.    : 2385   0      0.00    81.55   7.62     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 -   8.155: 1724   |   5:    40.775 -  48.930:   88        |
|      1:     8.155 -  16.310:  544   |   6:    48.930 -  57.085:   60        |
|      2:    16.310 -  24.465:  150   |   7:    57.085 -  65.240:   23        |
|      3:    24.465 -  32.620:  108   |   8:    65.240 -  73.395:    7        |
|      4:    32.620 -  40.775:  113   |   9:    73.395 -  81.550:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1121 r_free = 0.1552             target_work(ml) = 5.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1121 r_free = 0.1553             target_work(ml) = 5.141         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1553   ksol= 0.32   Bsol= 41.34   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.38,3.32,3.71,0.00,0.00,0.00); trace/3= 3.14                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.141331                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8444 -  4.7251 0.99   1380  154 0.1017 0.1272      5.3926      5.5147|
|  2:  4.7251 -  3.7707 0.99   1329  146 0.0876 0.1119        5.45      5.6453|
|  3:  3.7707 -  3.3000 0.99   1305  147 0.1044 0.1475      5.4663        5.86|
|  4:  3.3000 -  3.0010 0.99   1293  138 0.1213 0.1537       5.447      5.6118|
|  5:  3.0010 -  2.7875 0.99   1283  146 0.1295 0.1607      5.3217      5.4708|
|  6:  2.7875 -  2.6241 0.98   1281  142 0.1250 0.1918      5.2222      5.4755|
|  7:  2.6241 -  2.4933 0.99   1274  143 0.1219 0.1635      5.1563      5.3472|
|  8:  2.4933 -  2.3852 0.98   1267  140 0.1165 0.1746      5.0785      5.3722|
|  9:  2.3852 -  2.2937 0.98   1276  146 0.1187 0.1772      5.0282      5.3007|
| 10:  2.2937 -  2.2148 0.97   1235  132 0.1139 0.1688      4.9704      5.1661|
| 11:  2.2148 -  2.1458 0.99   1273  144 0.1140 0.1658      4.9147      5.2546|
| 12:  2.1458 -  2.0846 0.98   1270  133 0.1084 0.1657      4.8495      5.1379|
| 13:  2.0846 -  2.0299 0.97   1227  139 0.1155 0.1664      4.7929      5.0219|
| 14:  2.0299 -  1.9805 0.73    937  109 0.1096 0.1731       4.705      4.9473|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8444 -  4.7251  1380   154  0.94   8.99   0.98     0.96       7108.79|
|  2:  4.7251 -  3.7707  1329   146  0.95   7.94   1.02     1.00       8966.86|
|  3:  3.7707 -  3.3000  1305   147  0.94  11.08   1.03     1.02      10331.84|
|  4:  3.3000 -  3.0010  1293   138  0.92  13.17   1.01     0.99       9968.38|
|  5:  3.0010 -  2.7875  1283   146  0.90  15.66   0.99     0.96       8114.87|
|  6:  2.7875 -  2.6241  1281   142  0.90  15.93   0.98     0.95       7068.04|
|  7:  2.6241 -  2.4933  1274   143  0.91  15.31   0.99     0.96       6058.14|
|  8:  2.4933 -  2.3852  1267   140  0.91  14.89   0.99     0.97       5388.03|
|  9:  2.3852 -  2.2937  1276   146  0.91  15.64   1.00     0.98       4927.53|
| 10:  2.2937 -  2.2148  1235   132  0.90  15.40   1.00     0.98       4408.94|
| 11:  2.2148 -  2.1458  1273   144  0.91  15.29   1.00     0.97       4056.44|
| 12:  2.1458 -  2.0846  1270   133  0.92  14.18   1.01     0.99       3629.64|
| 13:  2.0846 -  2.0299  1227   139  0.91  15.44   1.00     0.99       3284.93|
| 14:  2.0299 -  1.9805   937   109  0.91  15.52   0.98     0.95       2747.80|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2747.80 max =        10331.84 mean =      6251.89|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.94 mean =        13.80|
|phase err.(test): min =        0.00 max =           89.09 mean =        13.33|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1553   ksol= 0.32   Bsol= 45.43   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.76,0.17,0.60,0.00,0.00,0.00); trace/3= -0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.141336                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1121   r_free= 0.1553   ksol= 0.32   Bsol= 45.43   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.76,0.17,0.60,0.00,0.00,0.00); trace/3= -0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.141336                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8444 -  4.7251 0.99   1380  154 0.1017 0.1273      5.3935      5.5156|
|  2:  4.7251 -  3.7707 0.99   1329  146 0.0877 0.1119      5.4507       5.646|
|  3:  3.7707 -  3.3000 0.99   1305  147 0.1044 0.1475      5.4666      5.8601|
|  4:  3.3000 -  3.0010 0.99   1293  138 0.1212 0.1536      5.4468      5.6116|
|  5:  3.0010 -  2.7875 0.99   1283  146 0.1295 0.1607      5.3214      5.4706|
|  6:  2.7875 -  2.6241 0.98   1281  142 0.1249 0.1916      5.2218      5.4749|
|  7:  2.6241 -  2.4933 0.99   1274  143 0.1219 0.1636       5.156      5.3471|
|  8:  2.4933 -  2.3852 0.98   1267  140 0.1164 0.1745      5.0782      5.3718|
|  9:  2.3852 -  2.2937 0.98   1276  146 0.1186 0.1772       5.028      5.3007|
| 10:  2.2937 -  2.2148 0.97   1235  132 0.1139 0.1688      4.9704      5.1661|
| 11:  2.2148 -  2.1458 0.99   1273  144 0.1139 0.1658      4.9147      5.2548|
| 12:  2.1458 -  2.0846 0.98   1270  133 0.1084 0.1657      4.8495      5.1381|
| 13:  2.0846 -  2.0299 0.97   1227  139 0.1155 0.1664      4.7929      5.0219|
| 14:  2.0299 -  1.9805 0.73    937  109 0.1096 0.1730      4.7046      4.9468|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8444 -  4.7251  1380   154  0.94   9.00   0.98     0.96       7124.24|
|  2:  4.7251 -  3.7707  1329   146  0.95   7.95   1.02     1.00       8979.82|
|  3:  3.7707 -  3.3000  1305   147  0.94  11.09   1.03     1.02      10338.39|
|  4:  3.3000 -  3.0010  1293   138  0.92  13.17   1.01     0.99       9965.22|
|  5:  3.0010 -  2.7875  1283   146  0.90  15.65   0.99     0.96       8107.61|
|  6:  2.7875 -  2.6241  1281   142  0.90  15.93   0.98     0.95       7062.72|
|  7:  2.6241 -  2.4933  1274   143  0.91  15.30   0.99     0.96       6053.27|
|  8:  2.4933 -  2.3852  1267   140  0.91  14.89   1.00     0.98       5385.67|
|  9:  2.3852 -  2.2937  1276   146  0.91  15.64   1.01     0.98       4925.99|
| 10:  2.2937 -  2.2148  1235   132  0.90  15.40   1.01     0.98       4408.98|
| 11:  2.2148 -  2.1458  1273   144  0.91  15.29   1.00     0.97       4056.89|
| 12:  2.1458 -  2.0846  1270   133  0.92  14.18   1.01     0.99       3630.48|
| 13:  2.0846 -  2.0299  1227   139  0.91  15.44   1.00     1.00       3284.23|
| 14:  2.0299 -  1.9805   937   109  0.91  15.52   0.99     0.95       2745.25|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2745.25 max =        10338.39 mean =      6252.69|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.94 mean =        13.80|
|phase err.(test): min =        0.00 max =           89.51 mean =        13.34|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.765)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.18    84.73   14.83    None  None   None       |
|    all(noH): 2823   0      3.18    84.73   14.83    None  None   None       |
|    Sol.    : 438    0      4.22    72.55   36.71    None  None   None       |
|    Mac.    : 2385   0      3.18    84.73   10.81    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.184 -  11.339: 1724   |   5:    43.959 -  52.114:   88        |
|      1:    11.339 -  19.494:  544   |   6:    52.114 -  60.269:   60        |
|      2:    19.494 -  27.649:  150   |   7:    60.269 -  68.424:   23        |
|      3:    27.649 -  35.804:  108   |   8:    68.424 -  76.579:    7        |
|      4:    35.804 -  43.959:  113   |   9:    76.579 -  84.734:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 312         
Filter by distance & map next to the model:
   mapped sites are within: 0.263 - 4.832
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 304 from: 312
   mapped sites are within: 0.720 - 4.832

peak=   10.942 closest distance to " CB  VAL A 230 " =    1.464
peak=    6.981 closest distance to " CG2 VAL A 296 " =    1.109
peak=    6.394 closest distance to " CG  LEU A   5 " =    1.275
peak=    5.716 closest distance to " NH2 ARG A  56 " =    2.213
peak=    5.520 closest distance to " CB  VAL A 296 " =    1.128
peak=    5.423 closest distance to " CG  PRO A  54 " =    1.312
peak=    5.204 closest distance to " CG  LEU A 228 " =    1.228
peak=    5.182 closest distance to " CB  ARG A 275 " =    0.924
peak=    5.073 closest distance to " CB  SER A  63 " =    1.191
peak=    5.057 closest distance to " CB  GLN A 223 " =    1.397
peak=    4.970 closest distance to " CD2 LEU A   5 " =    1.162
peak=    4.865 closest distance to " CG  PRO A 213 " =    1.277
peak=    4.839 closest distance to " CB  ASN A 187 " =    1.941
peak=    4.782 closest distance to " O   HOH Z 193 " =    1.823
peak=    4.717 closest distance to " O   HOH Z 402 " =    1.514
peak=    4.688 closest distance to " O   HOH Z 142 " =    1.691
peak=    4.674 closest distance to " CB  GLN A 183 " =    1.304
peak=    4.665 closest distance to " O   SER A  87 " =    2.186
peak=    4.656 closest distance to " C   PRO A 198 " =    1.497
peak=    4.645 closest distance to " CB  PRO A  54 " =    0.939
peak=    4.620 closest distance to " CB  VAL A 230 " =    1.231
peak=    4.620 closest distance to " O   HOH Z 232 " =    2.273
peak=    4.587 closest distance to " O   HOH Z 272 " =    1.882
peak=    4.549 closest distance to " O   HOH Z 234 " =    3.592
peak=    4.530 closest distance to " O   HOH Z 124 " =    1.468
peak=    4.523 closest distance to " O   HOH Z 209 " =    2.324
peak=    4.523 closest distance to " CB  GLU A 152 " =    1.130
peak=    4.520 closest distance to " CG  PRO A 198 " =    1.219
peak=    4.515 closest distance to " NE2 GLN A  11 " =    1.070
peak=    4.501 closest distance to " O   HOH Z  85 " =    1.392
peak=    4.492 closest distance to " O   HOH Z 236 " =    1.835
peak=    4.465 closest distance to " CG  PRO A 243 " =    1.139
peak=    4.415 closest distance to " CB  SER A   3 " =    1.276
peak=    4.388 closest distance to " O   HOH Z 423 " =    1.855
peak=    4.349 closest distance to " O   HOH Z 403 " =    1.706
peak=    4.343 closest distance to " O   HOH Z  48 " =    1.660
peak=    4.327 closest distance to " O   HOH Z 298 " =    1.793
peak=    4.321 closest distance to " O   HOH Z  97 " =    1.938
peak=    4.293 closest distance to " O   HOH Z 316 " =    2.954
peak=    4.252 closest distance to " ND2 ASN A 187 " =    1.526
peak=    4.234 closest distance to " O   HOH Z  59 " =    2.222
peak=    4.227 closest distance to " CB  TYR A 169 " =    0.732
peak=    4.207 closest distance to " O   HOH Z 346 " =    1.533
peak=    4.164 closest distance to " O   HOH Z  80 " =    1.788
peak=    4.121 closest distance to " CG1BVAL A  72 " =    1.620
peak=    4.116 closest distance to " CB  TRP A 179 " =    1.299
peak=    4.115 closest distance to " CB  ASN A 148 " =    1.340
peak=    4.110 closest distance to " CA  TYR A  30 " =    0.971
peak=    4.084 closest distance to " O   HOH Z 368 " =    2.189
peak=    4.078 closest distance to " OD1 ASN A  69 " =    2.525
peak=    4.069 closest distance to " CD2 LEU A 228 " =    1.148
peak=    4.066 closest distance to " O   HOH Z 203 " =    1.730
peak=    4.057 closest distance to " CB  ARG A  79 " =    1.332
peak=    4.053 closest distance to " O   HOH Z 369 " =    2.170
peak=    4.037 closest distance to " CB  ARG A 139 " =    0.914
peak=    4.020 closest distance to " O   HOH Z  54 " =    1.568
peak=    4.017 closest distance to " O   HOH Z 128 " =    2.207
peak=    4.016 closest distance to " CA  ALA A  21 " =    1.133
peak=    4.011 closest distance to " O   HOH Z 345 " =    2.978
peak=    4.005 closest distance to " CB  ASN A  39 " =    0.808
peak=    4.000 closest distance to " N   ASN A  39 " =    1.172
peak=    3.992 closest distance to " O   HOH Z  97 " =    2.472
peak=    3.970 closest distance to " CB  GLU A 277 " =    3.548
peak=    3.964 closest distance to " O   HOH Z 389 " =    1.894
peak=    3.952 closest distance to " O   HOH Z 303 " =    2.109
peak=    3.950 closest distance to " CZ  PHE A 218 " =    1.084
peak=    3.945 closest distance to " CA  VAL A  41 " =    0.783
peak=    3.927 closest distance to " O   HOH Z 280 " =    2.962
peak=    3.911 closest distance to " CB  GLU A 128 " =    1.023
peak=    3.896 closest distance to " O   HOH Z  48 " =    1.636
peak=    3.887 closest distance to " O   HOH Z 227 " =    1.595
peak=    3.883 closest distance to " O   HOH Z  61 " =    1.567
peak=    3.858 closest distance to " O   HOH Z  43 " =    2.233
peak=    3.850 closest distance to " CG  ARG A  66 " =    2.840
peak=    3.849 closest distance to " O   HOH Z 189 " =    2.578
peak=    3.846 closest distance to " O   HOH Z 357 " =    1.938
peak=    3.839 closest distance to " CB  ALA A 248 " =    1.370
peak=    3.838 closest distance to " O   HOH Z 247 " =    1.344
peak=    3.831 closest distance to " O   TRP A 274 " =    1.940
peak=    3.826 closest distance to " CA  ALA A  51 " =    0.971
peak=    3.822 closest distance to " O   HOH Z 102 " =    1.272
peak=    3.814 closest distance to " CG1 ILE A  33 " =    1.343
peak=    3.811 closest distance to " O   HOH Z 371 " =    3.236
peak=    3.805 closest distance to " CB  VAL A 265 " =    1.280
peak=    3.803 closest distance to " O   HOH Z 128 " =    1.976
peak=    3.788 closest distance to " O   HOH Z 263 " =    1.604
peak=    3.770 closest distance to " O   HOH Z 416 " =    2.696
peak=    3.769 closest distance to " O   HOH Z  63 " =    2.342
peak=    3.768 closest distance to " O   HOH Z  54 " =    2.413
peak=    3.767 closest distance to " CD  LYS A 166 " =    1.300
peak=    3.761 closest distance to " O   HOH Z  78 " =    1.639
peak=    3.752 closest distance to " O   HOH Z 273 " =    2.750
peak=    3.745 closest distance to " O   HOH Z 411 " =    3.670
peak=    3.740 closest distance to " CB  ALA A   9 " =    1.606
peak=    3.737 closest distance to " CB  ARG A 190 " =    1.686
peak=    3.731 closest distance to " CG2 ILE A  20 " =    1.449
peak=    3.722 closest distance to " O   HOH Z  48 " =    2.321
peak=    3.722 closest distance to " CD  ARG A 269 " =    1.026
peak=    3.714 closest distance to " O   HOH Z 344 " =    2.846
peak=    3.712 closest distance to " NZ  LYS A 117 " =    2.952
peak=    3.712 closest distance to " O   HOH Z 197 " =    2.794
peak=    3.708 closest distance to " CA  LYS A 117 " =    1.297
peak=    3.704 closest distance to " O   HOH Z 427 " =    2.855
peak=    3.696 closest distance to " O   HOH Z 245 " =    1.447
peak=    3.692 closest distance to " CB  TRP A 266 " =    0.959
peak=    3.688 closest distance to " CB  VAL A 202 " =    1.492
peak=    3.686 closest distance to " O   HOH Z  40 " =    1.682
peak=    3.682 closest distance to " NH2 ARG A 156 " =    1.119
peak=    3.677 closest distance to " OD2 ASP A 286 " =    2.827
peak=    3.657 closest distance to " O   HOH Z 193 " =    1.992
peak=    3.654 closest distance to " O   HOH Z 366 " =    2.883
peak=    3.648 closest distance to " OD2 ASP A 298 " =    3.914
peak=    3.648 closest distance to " OG BSER A 164 " =    2.253
peak=    3.642 closest distance to " O   HOH Z 158 " =    3.052
peak=    3.639 closest distance to " CE1 HIS A 108 " =    1.118
peak=    3.638 closest distance to " O   HOH Z 250 " =    1.410
peak=    3.637 closest distance to " CB  SER A  26 " =    1.702
peak=    3.625 closest distance to " CB  ALA A 295 " =    1.169
peak=    3.618 closest distance to " O   HOH Z 414 " =    1.547
peak=    3.615 closest distance to " O   HOH Z 214 " =    2.496
peak=    3.613 closest distance to " O   HOH Z  68 " =    1.960
peak=    3.613 closest distance to " O   HOH Z 248 " =    1.633
peak=    3.596 closest distance to " O   HOH Z 421 " =    1.592
peak=    3.593 closest distance to " CG  ARG A  66 " =    0.965
peak=    3.575 closest distance to " O   HOH Z 261 " =    2.120
peak=    3.570 closest distance to " CD2 TRP A 179 " =    1.376
peak=    3.568 closest distance to " O   HOH Z 322 " =    2.159
peak=    3.568 closest distance to " O   HOH Z  15 " =    2.093
peak=    3.561 closest distance to " O   HOH Z 134 " =    1.420
peak=    3.558 closest distance to " O   HOH Z 419 " =    1.658
peak=    3.555 closest distance to " CA  ASP A 191 " =    0.999
peak=    3.553 closest distance to " O   HOH Z 383 " =    1.992
peak=    3.553 closest distance to " O   HOH Z 261 " =    2.191
peak=    3.544 closest distance to " OG1 THR A 294 " =    2.300
peak=    3.541 closest distance to " CA  ASP A 140 " =    1.209
peak=    3.539 closest distance to " CG2 THR A 221 " =    1.185
peak=    3.535 closest distance to " OE1 GLU A   2 " =    2.122
peak=    3.533 closest distance to " O   HOH Z 426 " =    1.500
peak=    3.531 closest distance to " CA  ASN A 176 " =    1.074
peak=    3.526 closest distance to " O   HOH Z  21 " =    1.777
peak=    3.526 closest distance to " CA  ASP A 162 " =    1.042
peak=    3.525 closest distance to " O   HOH Z 227 " =    2.159
peak=    3.525 closest distance to " CB BVAL A  41 " =    1.021
peak=    3.524 closest distance to " CG  GLN A  58 " =    2.728
peak=    3.518 closest distance to " CG1 VAL A 296 " =    1.154
peak=    3.511 closest distance to " CG  GLN A  77 " =    2.241
peak=    3.508 closest distance to " CE1 TYR A 186 " =    1.264
peak=    3.504 closest distance to " O   HOH Z 422 " =    2.658
peak=    3.503 closest distance to " O   HOH Z 327 " =    1.535
peak=    3.502 closest distance to " CA  ARG A  36 " =    1.043
peak=    3.501 closest distance to " O   HOH Z 154 " =    1.434
peak=    3.498 closest distance to " O   HOH Z 367 " =    3.455
peak=    3.489 closest distance to " CG1 VAL A 153 " =    0.934
peak=    3.487 closest distance to " NZ  LYS A 166 " =    2.966
peak=    3.481 closest distance to " CG AARG A 275 " =    1.135
peak=    3.480 closest distance to " O   HOH Z 417 " =    3.187
peak=    3.477 closest distance to " NH2BARG A 145 " =    2.154
peak=    3.477 closest distance to " O   HOH Z 250 " =    1.463
peak=    3.476 closest distance to " O   HOH Z  44 " =    1.796
peak=    3.473 closest distance to " CD  ARG A 159 " =    0.742
peak=    3.467 closest distance to " O   HOH Z 406 " =    1.571
peak=    3.465 closest distance to " O   HOH Z 132 " =    2.600
peak=    3.463 closest distance to " CB  GLN A 278 " =    0.862
peak=    3.461 closest distance to " O   HOH Z 214 " =    2.375
peak=    3.445 closest distance to " O   HOH Z 404 " =    2.208
peak=    3.442 closest distance to " O   HOH Z 435 " =    1.886
peak=    3.437 closest distance to " O   HOH Z 313 " =    1.773
peak=    3.435 closest distance to " CG BARG A 102 " =    1.796
peak=    3.433 closest distance to " CD2 TYR A  30 " =    0.823
peak=    3.432 closest distance to " O   HOH Z 257 " =    2.278
peak=    3.429 closest distance to " NZ  LYS A  76 " =    1.302
peak=    3.428 closest distance to " CB  ASP A 140 " =    0.861
peak=    3.427 closest distance to " O   ASP A 124 " =    1.270
peak=    3.427 closest distance to " CB  ALA A 291 " =    1.314
peak=    3.424 closest distance to " O   HOH Z  88 " =    2.720
peak=    3.418 closest distance to " O   HOH Z 251 " =    1.701
peak=    3.415 closest distance to " CD1 LEU A 300 " =    1.248
peak=    3.414 closest distance to " O   HOH Z 420 " =    1.923
peak=    3.412 closest distance to " CG2 ILE A 120 " =    1.286
peak=    3.411 closest distance to " CA  ALA A 158 " =    1.251
peak=    3.403 closest distance to " O   GLY A  91 " =    1.358
peak=    3.400 closest distance to " CA  ARG A 195 " =    1.154
peak=    3.398 closest distance to " CG  MET A 185 " =    1.140
peak=    3.391 closest distance to " CB  SER A 273 " =    0.820
peak=    3.388 closest distance to " OE1 GLN A  11 " =    1.784
peak=    3.386 closest distance to " CG1 ILE A  49 " =    1.497
peak=    3.379 closest distance to " CA  ASN A 215 " =    1.177
peak=    3.374 closest distance to " CD2 HIS A  81 " =    1.121
peak=    3.369 closest distance to " CD BLYS A 290 " =    1.128
peak=    3.367 closest distance to " CD2 LEU A 297 " =    0.906
peak=    3.366 closest distance to " O   HOH Z 291 " =    1.481
peak=    3.366 closest distance to " CB  PRO A 198 " =    1.004
peak=    3.365 closest distance to " CB  THR A  31 " =    1.735
peak=    3.364 closest distance to " NH2 ARG A  79 " =    1.260
peak=    3.352 closest distance to " CB  ASN A 148 " =    1.912
peak=    3.349 closest distance to " O   HOH Z 271 " =    2.558
peak=    3.348 closest distance to " O   HOH Z  66 " =    2.197
peak=    3.346 closest distance to " O   HOH Z 185 " =    1.704
peak=    3.346 closest distance to " ND2 ASN A 110 " =    1.634
peak=    3.345 closest distance to " CB  GLU A  46 " =    1.078
peak=    3.342 closest distance to " O   HOH Z  49 " =    2.427
peak=    3.339 closest distance to " O   HOH Z 380 " =    1.963
peak=    3.336 closest distance to " OG  SER A 276 " =    1.303
peak=    3.336 closest distance to " CA  ALA A 295 " =    0.996
peak=    3.333 closest distance to " O   HOH Z 147 " =    1.769
peak=    3.330 closest distance to " O   HOH Z 374 " =    2.577
peak=    3.325 closest distance to " O   HOH Z 234 " =    1.794
peak=    3.325 closest distance to " CB  GLN A 205 " =    1.131
peak=    3.323 closest distance to " O   HOH Z 357 " =    2.209
peak=    3.321 closest distance to " O   HOH Z  88 " =    2.927
peak=    3.317 closest distance to " O   HOH Z 438 " =    1.989
peak=    3.314 closest distance to " C   ALA A 299 " =    0.931
peak=    3.313 closest distance to " O   HOH Z 329 " =    3.825
peak=    3.311 closest distance to " O   HOH Z 180 " =    2.138
peak=    3.301 closest distance to " CA  THR A 264 " =    0.798
peak=    3.300 closest distance to " CD1 ILE A 106 " =    1.126
peak=    3.298 closest distance to " CG2AVAL A 121 " =    2.263
peak=    3.293 closest distance to " O   HOH Z 155 " =    3.172
peak=    3.292 closest distance to " CB  ASN A 142 " =    1.096
peak=    3.280 closest distance to " N   SER A 135 " =    1.398
peak=    3.278 closest distance to " CA  PHE A 283 " =    1.124
peak=    3.277 closest distance to " CA  THR A 221 " =    0.894
peak=    3.270 closest distance to " N   ARG A 190 " =    1.021
peak=    3.270 closest distance to " CB  ALA A   1 " =    1.219
peak=    3.270 closest distance to " CB  TRP A 150 " =    1.506
peak=    3.268 closest distance to " O   HOH Z 411 " =    1.738
peak=    3.268 closest distance to " CB  LEU A 143 " =    1.156
peak=    3.265 closest distance to " O   HOH Z 135 " =    1.765
peak=    3.265 closest distance to " CG2 THR A 294 " =    1.641
peak=    3.264 closest distance to " CD  LYS A 119 " =    1.982
peak=    3.257 closest distance to " CA  GLN A 194 " =    1.189
peak=    3.249 closest distance to " O   HOH Z 280 " =    2.442
peak=    3.247 closest distance to " O   HOH Z 389 " =    1.797
peak=    3.241 closest distance to " CG2 VAL A 202 " =    1.175
peak=    3.241 closest distance to " CA  VAL A 126 " =    0.877
peak=    3.236 closest distance to " CG2 ILE A 234 " =    2.021
peak=    3.235 closest distance to " O   HOH Z 123 " =    2.071
peak=    3.232 closest distance to " CB  HIS A 108 " =    0.796
peak=    3.230 closest distance to " NH1 ARG A 138 " =    1.280
peak=    3.225 closest distance to " O   GLN A 278 " =    1.270
peak=    3.224 closest distance to " OG  SER A  22 " =    2.687
peak=    3.222 closest distance to " O   HOH Z  35 " =    2.322
peak=    3.220 closest distance to " O   HOH Z 261 " =    1.735
peak=    3.219 closest distance to " CB  ASN A 215 " =    1.098
peak=    3.216 closest distance to " O   HOH Z 345 " =    1.574
peak=    3.214 closest distance to " CZ3 TRP A  85 " =    0.963
peak=    3.209 closest distance to " CG1 ILE A 120 " =    1.147
peak=    3.208 closest distance to " CA  ALA A  84 " =    1.314
peak=    3.208 closest distance to " CA  LEU A 282 " =    1.115
peak=    3.207 closest distance to " O   HOH Z 387 " =    2.980
peak=    3.204 closest distance to " O   HOH Z 425 " =    2.065
peak=    3.204 closest distance to " CB  ILE A 120 " =    1.336
peak=    3.201 closest distance to " O   MET A 105 " =    1.802
peak=    3.199 closest distance to " O   HOH Z 148 " =    3.167
peak=    3.196 closest distance to " O   HOH Z 112 " =    1.624
peak=    3.196 closest distance to " O   HOH Z 423 " =    3.321
peak=    3.195 closest distance to " O   HOH Z 313 " =    1.736
peak=    3.194 closest distance to " NH1AARG A 145 " =    1.092
peak=    3.190 closest distance to " O   HOH Z 362 " =    3.528
peak=    3.189 closest distance to " O   HOH Z 299 " =    4.293
peak=    3.186 closest distance to " CG  LEU A 167 " =    1.149
peak=    3.183 closest distance to " N   VAL A 126 " =    1.424
peak=    3.182 closest distance to " O   HOH Z 361 " =    3.075
peak=    3.178 closest distance to " OG BSER A 258 " =    3.289
peak=    3.177 closest distance to " O   HOH Z 329 " =    2.814
peak=    3.175 closest distance to " OH  TYR A 116 " =    1.112
peak=    3.174 closest distance to " O   HOH Z 279 " =    2.083
peak=    3.167 closest distance to " O   HOH Z 417 " =    2.392
peak=    3.151 closest distance to " CZ2 TRP A 274 " =    1.553
peak=    3.148 closest distance to " CB  ARG A 219 " =    1.354
peak=    3.147 closest distance to " CA  ASN A 217 " =    1.339
peak=    3.147 closest distance to " O   HOH Z 303 " =    1.652
peak=    3.144 closest distance to " CB  MET A  40 " =    0.784
peak=    3.143 closest distance to " CE  LYS A 119 " =    1.002
peak=    3.142 closest distance to " CD1 ILE A  33 " =    1.612
peak=    3.140 closest distance to " N   SER A 288 " =    1.768
peak=    3.139 closest distance to " CA  ALA A 233 " =    1.190
peak=    3.134 closest distance to " CG  MET A 185 " =    1.094
peak=    3.125 closest distance to " O   HOH Z 298 " =    4.832
peak=    3.120 closest distance to " OG BSER A 134 " =    2.934
peak=    3.117 closest distance to " CB  THR A 157 " =    1.136
peak=    3.116 closest distance to " CB  LEU A   5 " =    1.265
peak=    3.110 closest distance to " O   HOH Z 353 " =    2.787
peak=    3.109 closest distance to " N   ASP A 162 " =    1.317
peak=    3.109 closest distance to " CB  SER A 212 " =    1.245
peak=    3.102 closest distance to " O   HOH Z 392 " =    1.606
peak=    3.093 closest distance to " O   HOH Z  90 " =    3.412
peak=    3.091 closest distance to " CB  PRO A 243 " =    1.251
peak=    3.090 closest distance to " CA  THR A  52 " =    1.052
peak=    3.085 closest distance to " CA  ILE A 106 " =    0.720
peak=    3.084 closest distance to " O   ILE A  33 " =    1.251
peak=    3.082 closest distance to " O   HOH Z 281 " =    4.646
peak=    3.080 closest distance to " CB  LYS A 290 " =    1.033
peak=    3.079 closest distance to " O   HOH Z 292 " =    1.601
peak=    3.076 closest distance to " O   HOH Z 336 " =    1.690
peak=    3.070 closest distance to " O   ALA A 158 " =    1.302
peak=    3.066 closest distance to " CB  ALA A 100 " =    1.170
peak=    3.065 closest distance to " O   ASP A 124 " =    1.754
peak=    3.053 closest distance to " O   HOH Z  68 " =    1.553
peak=    3.051 closest distance to " O   HOH Z 302 " =    1.854
peak=    3.050 closest distance to " O   HOH Z 294 " =    1.527
peak=    3.047 closest distance to " O   HOH Z 327 " =    2.490
peak=    3.035 closest distance to " O   HOH Z  48 " =    3.024
peak=    3.032 closest distance to " ND1 HIS A  81 " =    1.590

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 197         
Filter by distance & map next to the model:
   mapped sites are within: 0.716 - 5.453
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 196 from: 197
   mapped sites are within: 0.716 - 5.453

peak=   -5.809 closest distance to " CG2 VAL A 230 " =    0.716
peak=   -4.750 closest distance to " SG  CYS A 254 " =    3.237
peak=   -4.617 closest distance to " CD  ARG A 156 " =    2.056
peak=   -4.469 closest distance to " CG2BVAL A  41 " =    2.622
peak=   -4.435 closest distance to " O   HOH Z 266 " =    4.733
peak=   -4.304 closest distance to " O   PRO A 163 " =    2.147
peak=   -4.274 closest distance to " C   HIS A 108 " =    1.215
peak=   -4.246 closest distance to " O   HOH Z 290 " =    1.039
peak=   -4.233 closest distance to " CG  ASP A 231 " =    0.841
peak=   -4.233 closest distance to " CE2 TYR A  30 " =    2.786
peak=   -4.188 closest distance to " CD1 LEU A 101 " =    2.462
peak=   -4.161 closest distance to " CG  GLN A 223 " =    2.057
peak=   -4.129 closest distance to " OXT GLY A 302 " =    2.735
peak=   -4.053 closest distance to " O   HOH Z 351 " =    1.483
peak=   -4.049 closest distance to " CB  ALA A 161 " =    2.545
peak=   -4.011 closest distance to " O   HOH Z 166 " =    1.757
peak=   -3.984 closest distance to " CD  GLN A  58 " =    1.197
peak=   -3.920 closest distance to " N   GLN A  58 " =    1.909
peak=   -3.888 closest distance to " ND2 ASN A  45 " =    0.978
peak=   -3.837 closest distance to " OG BSER A 134 " =    1.205
peak=   -3.834 closest distance to " CB  PRO A 243 " =    2.651
peak=   -3.830 closest distance to " O   HOH Z 196 " =    2.090
peak=   -3.820 closest distance to " O   HOH Z 118 " =    3.213
peak=   -3.810 closest distance to " O   HOH Z  13 " =    1.536
peak=   -3.789 closest distance to " O   HOH Z  37 " =    1.906
peak=   -3.750 closest distance to " CE2 PHE A 218 " =    2.750
peak=   -3.748 closest distance to " O   HOH Z 407 " =    2.933
peak=   -3.738 closest distance to " ND2 ASN A 187 " =    1.626
peak=   -3.715 closest distance to " CE  MET A 105 " =    2.146
peak=   -3.712 closest distance to " CG2 VAL A 296 " =    1.101
peak=   -3.712 closest distance to " OG  SER A  97 " =    2.329
peak=   -3.708 closest distance to " O   HOH Z  11 " =    1.883
peak=   -3.700 closest distance to " CD  LYS A 289 " =    2.454
peak=   -3.694 closest distance to " CD2 LEU A 300 " =    2.697
peak=   -3.685 closest distance to " O   HOH Z 166 " =    1.630
peak=   -3.684 closest distance to " O   HOH Z 423 " =    2.206
peak=   -3.664 closest distance to " CB  ALA A 248 " =    2.309
peak=   -3.655 closest distance to " C   THR A 279 " =    1.189
peak=   -3.644 closest distance to " NE2 GLN A  88 " =    1.042
peak=   -3.626 closest distance to " NH2AARG A 275 " =    4.901
peak=   -3.625 closest distance to " C   MET A 188 " =    1.557
peak=   -3.624 closest distance to " CZ3 TRP A 179 " =    1.284
peak=   -3.617 closest distance to " NE2 GLN A  88 " =    1.950
peak=   -3.605 closest distance to " CB  ALA A 248 " =    1.979
peak=   -3.604 closest distance to " O   VAL A  67 " =    2.679
peak=   -3.603 closest distance to " C   GLN A  58 " =    2.331
peak=   -3.601 closest distance to " O   HOH Z 231 " =    2.058
peak=   -3.595 closest distance to " CG2 THR A 178 " =    2.181
peak=   -3.586 closest distance to " N   ALA A 226 " =    1.986
peak=   -3.583 closest distance to " O   SER A 210 " =    1.990
peak=   -3.583 closest distance to " CB  PRO A 163 " =    2.721
peak=   -3.581 closest distance to " NH2 ARG A  79 " =    2.001
peak=   -3.574 closest distance to " O   GLY A 196 " =    1.093
peak=   -3.570 closest distance to " CD1 PHE A  59 " =    1.829
peak=   -3.569 closest distance to " CB  PHE A 192 " =    2.035
peak=   -3.566 closest distance to " ND2 ASN A  45 " =    1.122
peak=   -3.566 closest distance to " CD  ARG A 139 " =    1.682
peak=   -3.566 closest distance to " OG  SER A   3 " =    1.656
peak=   -3.563 closest distance to " O   HOH Z 394 " =    1.600
peak=   -3.554 closest distance to " N   THR A 235 " =    1.325
peak=   -3.531 closest distance to " O   HOH Z 426 " =    1.797
peak=   -3.518 closest distance to " O   HOH Z 353 " =    2.138
peak=   -3.517 closest distance to " O   HOH Z 165 " =    1.930
peak=   -3.517 closest distance to " OG BSER A 134 " =    1.706
peak=   -3.515 closest distance to " NH2 ARG A  66 " =    1.592
peak=   -3.512 closest distance to " O   PRO A 198 " =    1.199
peak=   -3.508 closest distance to " OG ASER A 134 " =    1.365
peak=   -3.504 closest distance to " C   ALA A 158 " =    1.301
peak=   -3.504 closest distance to " O   HOH Z  52 " =    1.622
peak=   -3.481 closest distance to " CB  TYR A  15 " =    2.214
peak=   -3.479 closest distance to " O   HOH Z 222 " =    1.309
peak=   -3.475 closest distance to " O   HOH Z 283 " =    1.863
peak=   -3.472 closest distance to " O   HOH Z 136 " =    2.201
peak=   -3.472 closest distance to " O   HOH Z  17 " =    1.358
peak=   -3.470 closest distance to " O   HOH Z  88 " =    4.367
peak=   -3.469 closest distance to " N   THR A 157 " =    1.564
peak=   -3.467 closest distance to " CG1 VAL A 296 " =    1.224
peak=   -3.443 closest distance to " O   GLY A  75 " =    1.790
peak=   -3.432 closest distance to " CA  ASP A 298 " =    1.068
peak=   -3.423 closest distance to " CB  GLN A  11 " =    1.785
peak=   -3.422 closest distance to " O   ALA A 161 " =    1.729
peak=   -3.421 closest distance to " O   HOH Z 234 " =    4.048
peak=   -3.420 closest distance to " CD1 LEU A 228 " =    2.193
peak=   -3.411 closest distance to " CG  ASP A 132 " =    2.306
peak=   -3.411 closest distance to " O   HOH Z 174 " =    4.291
peak=   -3.411 closest distance to " O   SER A  95 " =    1.593
peak=   -3.409 closest distance to " O   HOH Z 123 " =    2.352
peak=   -3.407 closest distance to " N   ALA A 248 " =    1.621
peak=   -3.404 closest distance to " CZ  TYR A 169 " =    1.776
peak=   -3.403 closest distance to " CG1 VAL A 112 " =    2.710
peak=   -3.402 closest distance to " CB  ASN A  39 " =    2.174
peak=   -3.395 closest distance to " C   ASP A 231 " =    2.521
peak=   -3.391 closest distance to " CD2 LEU A 237 " =    2.717
peak=   -3.390 closest distance to " CE3 TRP A 150 " =    2.029
peak=   -3.390 closest distance to " CD1 LEU A  25 " =    2.469
peak=   -3.383 closest distance to " NE1 TRP A 266 " =    2.362
peak=   -3.374 closest distance to " OG BSER A 210 " =    2.182
peak=   -3.373 closest distance to " O   ASN A  45 " =    1.878
peak=   -3.372 closest distance to " CG  GLU A  53 " =    1.490
peak=   -3.371 closest distance to " CE BMET A  47 " =    1.650
peak=   -3.366 closest distance to " CB  ALA A 291 " =    2.241
peak=   -3.364 closest distance to " CB  ALA A 291 " =    2.181
peak=   -3.361 closest distance to " NE2 GLN A 103 " =    1.703
peak=   -3.359 closest distance to " CB  PRO A 280 " =    2.184
peak=   -3.358 closest distance to " ND2 ASN A  69 " =    1.679
peak=   -3.356 closest distance to " CG2 ILE A 263 " =    2.305
peak=   -3.354 closest distance to " O   HOH Z 193 " =    1.729
peak=   -3.351 closest distance to " O   HOH Z 389 " =    1.774
peak=   -3.348 closest distance to " O   ASN A 187 " =    1.540
peak=   -3.346 closest distance to " CG  TRP A 266 " =    1.938
peak=   -3.343 closest distance to " OG  SER A  62 " =    1.475
peak=   -3.340 closest distance to " O   HOH Z 427 " =    1.370
peak=   -3.340 closest distance to " N   SER A 276 " =    1.340
peak=   -3.338 closest distance to " OD2 ASP A 171 " =    2.217
peak=   -3.337 closest distance to " O   ALA A  51 " =    1.484
peak=   -3.330 closest distance to " N   ALA A  43 " =    2.591
peak=   -3.326 closest distance to " CE  LYS A 166 " =    3.075
peak=   -3.319 closest distance to " O   HOH Z 185 " =    2.427
peak=   -3.318 closest distance to " CB  ALA A  10 " =    2.284
peak=   -3.317 closest distance to " O   VAL A 125 " =    2.178
peak=   -3.317 closest distance to " O   VAL A 189 " =    2.571
peak=   -3.308 closest distance to " O   PHE A 218 " =    1.679
peak=   -3.308 closest distance to " OD1 ASN A 301 " =    2.053
peak=   -3.306 closest distance to " O   HOH Z 411 " =    1.573
peak=   -3.304 closest distance to " CG  GLU A 277 " =    1.114
peak=   -3.303 closest distance to " ND2 ASN A  39 " =    1.181
peak=   -3.299 closest distance to " CB  VAL A 296 " =    1.129
peak=   -3.297 closest distance to " C   GLN A 205 " =    1.929
peak=   -3.286 closest distance to " O   HOH Z 435 " =    2.735
peak=   -3.285 closest distance to " NH2 ARG A  66 " =    4.863
peak=   -3.279 closest distance to " CB  ASN A  69 " =    1.116
peak=   -3.271 closest distance to " N   GLY A  23 " =    2.132
peak=   -3.271 closest distance to " O   VAL A 197 " =    1.270
peak=   -3.270 closest distance to " O   HOH Z 211 " =    1.674
peak=   -3.270 closest distance to " O   HOH Z 377 " =    1.481
peak=   -3.267 closest distance to " O   HOH Z  47 " =    1.509
peak=   -3.264 closest distance to " O   HOH Z  15 " =    1.558
peak=   -3.260 closest distance to " CG  ASP A  50 " =    2.350
peak=   -3.258 closest distance to " OG1 THR A  82 " =    1.317
peak=   -3.253 closest distance to " O   HOH Z 311 " =    3.528
peak=   -3.243 closest distance to " CG1 VAL A  78 " =    2.512
peak=   -3.239 closest distance to " O   HOH Z 126 " =    1.886
peak=   -3.237 closest distance to " CG  LEU A 228 " =    0.928
peak=   -3.236 closest distance to " CB  ASP A 132 " =    2.386
peak=   -3.223 closest distance to " OXT GLY A 302 " =    3.429
peak=   -3.223 closest distance to " O   LYS A 117 " =    1.654
peak=   -3.219 closest distance to " CA  GLY A 133 " =    1.993
peak=   -3.214 closest distance to " O   HOH Z 313 " =    1.146
peak=   -3.211 closest distance to " CA  GLY A 133 " =    2.263
peak=   -3.200 closest distance to " O   HOH Z 431 " =    1.849
peak=   -3.197 closest distance to " CG  ARG A 219 " =    2.821
peak=   -3.197 closest distance to " OD1 ASN A 148 " =    1.529
peak=   -3.192 closest distance to " CB  ASP A 162 " =    2.574
peak=   -3.189 closest distance to " N   HIS A 115 " =    2.114
peak=   -3.187 closest distance to " O   MET A  40 " =    2.695
peak=   -3.186 closest distance to " O   HOH Z 372 " =    2.381
peak=   -3.185 closest distance to " C   VAL A 265 " =    0.808
peak=   -3.185 closest distance to " O   HOH Z  97 " =    1.288
peak=   -3.178 closest distance to " CB  ALA A 100 " =    2.562
peak=   -3.176 closest distance to " NH1 ARG A 195 " =    2.573
peak=   -3.175 closest distance to " NE2 GLN A 194 " =    1.737
peak=   -3.174 closest distance to " C   SER A 206 " =    1.577
peak=   -3.173 closest distance to " O   HOH Z  43 " =    1.816
peak=   -3.172 closest distance to " CG  PHE A 283 " =    2.669
peak=   -3.172 closest distance to " O   SER A 258 " =    1.893
peak=   -3.171 closest distance to " O   HOH Z 252 " =    3.986
peak=   -3.165 closest distance to " O   GLY A  80 " =    2.395
peak=   -3.157 closest distance to " O   HOH Z 414 " =    1.984
peak=   -3.156 closest distance to " CG  GLU A   2 " =    1.708
peak=   -3.156 closest distance to " CD2 TYR A 293 " =    2.085
peak=   -3.152 closest distance to " CB  ALA A  64 " =    2.531
peak=   -3.148 closest distance to " CG1 VAL A 230 " =    1.810
peak=   -3.147 closest distance to " N   VAL A 230 " =    1.092
peak=   -3.146 closest distance to " O   PRO A 198 " =    1.266
peak=   -3.145 closest distance to " N   MET A 105 " =    2.628
peak=   -3.144 closest distance to " CD  GLN A 223 " =    0.731
peak=   -3.143 closest distance to " O   HOH Z 191 " =    5.453
peak=   -3.141 closest distance to " O   HOH Z  10 " =    1.525
peak=   -3.136 closest distance to " O   HOH Z  11 " =    1.993
peak=   -3.132 closest distance to " O   TRP A  92 " =    1.873
peak=   -3.132 closest distance to " O   HOH Z 377 " =    1.518
peak=   -3.127 closest distance to " O   VAL A 174 " =    2.043
peak=   -3.127 closest distance to " OG  SER A  26 " =    1.249
peak=   -3.124 closest distance to " O   LEU A 167 " =    1.539
peak=   -3.107 closest distance to " CG  ARG A 269 " =    2.245
peak=   -3.105 closest distance to " O   HOH Z  60 " =    2.222
peak=   -3.102 closest distance to " CD1 TYR A 247 " =    2.332
peak=   -3.101 closest distance to " O   HOH Z 151 " =    1.644
peak=   -3.099 closest distance to " O   HOH Z 407 " =    3.039
peak=   -3.095 closest distance to " CG1 VAL A 197 " =    2.194
peak=   -3.094 closest distance to " O   HOH Z 295 " =    1.463
peak=   -3.090 closest distance to " NH2 ARG A  79 " =    1.594
peak=   -3.089 closest distance to " CG  MET A 105 " =    0.847
peak=   -3.073 closest distance to " CG2 VAL A 189 " =    2.148
peak=   -3.069 closest distance to " O   ASP A 171 " =    1.994
peak=   -3.067 closest distance to " O   HOH Z 250 " =    1.374

================= 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    :  0.4518 0.4417   6.248795e+00   6.232406e+00
   1_bss:  0.4431 0.4355   6.241570e+00   6.221035e+00
   1_xyz:  0.3408 0.3638   6.063205e+00   6.106573e+00
   1_adp:  0.2853 0.3219   5.920462e+00   6.019516e+00
   1_occ:  0.2846 0.3214   5.919448e+00   6.019538e+00
   2_bss:  0.2810 0.3176   5.919128e+00   6.014724e+00
   2_xyz:  0.1870 0.2247   5.564371e+00   5.728592e+00
   2_adp:  0.1671 0.2083   5.465585e+00   5.647575e+00
   2_occ:  0.1669 0.2083   5.464829e+00   5.647192e+00
   3_bss:  0.1656 0.2080   5.464202e+00   5.644580e+00
   3_xyz:  0.1294 0.1681   5.246974e+00   5.451645e+00
   3_adp:  0.1242 0.1605   5.206247e+00   5.410899e+00
   3_occ:  0.1239 0.1605   5.205810e+00   5.411358e+00
   4_bss:  0.1243 0.1607   5.208387e+00   5.412701e+00
   4_xyz:  0.1132 0.1556   5.145044e+00   5.379157e+00
   4_adp:  0.1105 0.1566   5.137265e+00   5.383945e+00
   4_occ:  0.1104 0.1568   5.136892e+00   5.383901e+00
   5_bss:  0.1103 0.1567   5.136887e+00   5.383964e+00
   5_xyz:  0.1111 0.1566   5.142659e+00   5.385709e+00
   5_adp:  0.1121 0.1552   5.141301e+00   5.377708e+00
   5_occ:  0.1121 0.1553   5.141331e+00   5.377993e+00
   5_bss:  0.1121 0.1553   5.141336e+00   5.377999e+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:  0.349  17.106   7.312   9.578   8.128   0.000   0.000   0.000
   1_xyz:  0.349  17.106   7.312   9.578   8.128   0.000   0.000   0.000
   1_adp:  0.349  17.106   7.312   9.578   8.128   0.000   0.000   0.000
   1_occ:  0.349  17.106   7.312   9.578   8.128   0.000   0.000   0.000
   2_bss:  0.317  37.112   3.855   5.728   5.144   0.000   0.000   0.000
   2_xyz:  0.317  37.112   3.855   5.728   5.144   0.000   0.000   0.000
   2_adp:  0.317  37.112   3.855   5.728   5.144   0.000   0.000   0.000
   2_occ:  0.317  37.112   3.855   5.728   5.144   0.000   0.000   0.000
   3_bss:  0.318  37.112   2.528   3.924   3.975   0.000   0.000   0.000
   3_xyz:  0.318  37.112   2.528   3.924   3.975   0.000   0.000   0.000
   3_adp:  0.318  37.112   2.528   3.924   3.975   0.000   0.000   0.000
   3_occ:  0.318  37.112   2.528   3.924   3.975   0.000   0.000   0.000
   4_bss:  0.322  41.338   2.243   3.317   3.623   0.000   0.000   0.000
   4_xyz:  0.322  41.338   2.243   3.317   3.623   0.000   0.000   0.000
   4_adp:  0.322  41.338   2.243   3.317   3.623   0.000   0.000   0.000
   4_occ:  0.322  41.338   2.243   3.317   3.623   0.000   0.000   0.000
   5_bss:  0.322  41.338   2.376   3.316   3.712   0.000   0.000   0.000
   5_xyz:  0.322  41.338   2.376   3.316   3.712   0.000   0.000   0.000
   5_adp:  0.322  41.338   2.376   3.316   3.712   0.000   0.000   0.000
   5_occ:  0.322  41.338   2.376   3.316   3.712   0.000   0.000   0.000
   5_bss:  0.323  45.432  -0.765   0.168   0.597   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  50.129 0.5205  0.5873    56925.414
   1_bss:  50.411 0.5144  0.7433    54803.056
   1_xyz:  40.223 0.6385  0.9051    36640.439
   1_adp:  33.405 0.7200  1.0143    27686.881
   1_occ:  33.377 0.7203  1.0132    27643.869
   2_bss:  33.097 0.7234  0.8992    27225.486
   2_xyz:  22.389 0.8376  1.0026    13147.759
   2_adp:  20.003 0.8616  1.0199    11037.369
   2_occ:  19.995 0.8617  1.0198    11024.998
   3_bss:  19.931 0.8623  0.9679    10971.508
   3_xyz:  15.430 0.9029  0.9906     7177.242
   3_adp:  14.495 0.9111  0.9952     6685.059
   3_occ:  14.505 0.9111  0.9950     6689.726
   4_bss:  14.525 0.9109  0.9800     6739.573
   4_xyz:  13.812 0.9167  0.9804     6297.576
   4_adp:  13.914 0.9160  0.9751     6337.660
   4_occ:  13.911 0.9160  0.9750     6341.012
   5_bss:  13.911 0.9160  0.9778     6342.368
   5_xyz:  13.924 0.9160  0.9775     6342.799
   5_adp:  13.750 0.9173  0.9766     6246.584
   5_occ:  13.751 0.9173  0.9765     6251.092
   5_bss:  13.751 0.9173  0.9783     6251.892
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3544e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3544e+01
   1_xyz:   1.636  0.013  0.108 17.902  0.007  4.110   1.3135e-01
   1_adp:   1.636  0.013  0.108 17.902  0.007  4.110   1.3135e-01
   1_occ:   1.636  0.013  0.108 17.902  0.007  4.110   1.3135e-01
   2_bss:   1.636  0.013  0.108 17.902  0.007  4.110   1.3135e-01
   2_xyz:   1.048  0.007  0.076 16.199  0.004  4.123   6.6433e-02
   2_adp:   1.048  0.007  0.076 16.199  0.004  4.123   6.6433e-02
   2_occ:   1.048  0.007  0.076 16.199  0.004  4.123   6.6433e-02
   3_bss:   1.048  0.007  0.076 16.199  0.004  4.123   6.6433e-02
   3_xyz:   0.996  0.006  0.078 15.592  0.004  4.130   6.0922e-02
   3_adp:   0.996  0.006  0.078 15.592  0.004  4.130   6.0922e-02
   3_occ:   0.996  0.006  0.078 15.592  0.004  4.130   6.0922e-02
   4_bss:   0.996  0.006  0.078 15.592  0.004  4.130   6.0922e-02
   4_xyz:   1.127  0.008  0.091 15.757  0.004  4.113   7.3379e-02
   4_adp:   1.127  0.008  0.091 15.757  0.004  4.113   7.3379e-02
   4_occ:   1.127  0.008  0.091 15.757  0.004  4.113   7.3379e-02
   5_bss:   1.127  0.008  0.091 15.757  0.004  4.113   7.3379e-02
   5_xyz:   1.001  0.007  0.080 15.368  0.004  4.113   6.0599e-02
   5_adp:   1.001  0.007  0.080 15.368  0.004  4.113   6.0599e-02
   5_occ:   1.001  0.007  0.080 15.368  0.004  4.113   6.0599e-02
   5_bss:   1.001  0.007  0.080 15.368  0.004  4.113   6.0599e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9409e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9409e+00
   1_xyz:  14.820  0.157  0.519 86.156  0.046  2.262   9.8530e-02
   1_adp:  14.820  0.157  0.519 86.156  0.046  2.262   9.8530e-02
   1_occ:  14.820  0.157  0.519 86.156  0.046  2.262   9.8530e-02
   2_bss:  14.820  0.157  0.519 86.156  0.046  2.262   9.8530e-02
   2_xyz:   7.101  0.067  0.264 83.431  0.025  2.212   5.0548e-02
   2_adp:   7.101  0.067  0.264 83.431  0.025  2.212   5.0548e-02
   2_occ:   7.101  0.067  0.264 83.431  0.025  2.212   5.0548e-02
   3_bss:   7.101  0.067  0.264 83.431  0.025  2.212   5.0548e-02
   3_xyz:   6.529  0.047  0.530 81.237  0.036  2.325   6.8567e-02
   3_adp:   6.529  0.047  0.530 81.237  0.036  2.325   6.8567e-02
   3_occ:   6.529  0.047  0.530 81.237  0.036  2.325   6.8567e-02
   4_bss:   6.529  0.047  0.530 81.237  0.036  2.325   6.8567e-02
   4_xyz:   7.669  0.046  0.719 82.637  0.041  2.304   5.2717e-02
   4_adp:   7.669  0.046  0.719 82.637  0.041  2.304   5.2717e-02
   4_occ:   7.669  0.046  0.719 82.637  0.041  2.304   5.2717e-02
   5_bss:   7.669  0.046  0.719 82.637  0.041  2.304   5.2717e-02
   5_xyz:   6.931  0.046  0.564 81.943  0.036  2.346   3.7957e-02
   5_adp:   6.931  0.046  0.564 81.943  0.036  2.346   3.7957e-02
   5_occ:   6.931  0.046  0.564 81.943  0.036  2.346   3.7957e-02
   5_bss:   6.931  0.046  0.564 81.943  0.036  2.346   3.7957e-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:  69.42   0.00  11.30  68.53   0.00   8.37  69.42   0.00  27.26
   1_occ:  69.42   0.00  11.30  68.53   0.00   8.37  69.42   0.00  27.26
   2_bss:  69.42   0.00  11.30  68.53   0.00   8.37  69.42   0.00  27.26
   2_xyz:  69.42   0.00  11.30  68.53   0.00   8.37  69.42   0.00  27.26
   2_adp:  74.72   0.00  11.71  74.72   0.00   7.91  66.18   0.83  32.43
   2_occ:  74.72   0.00  11.71  74.72   0.00   7.91  66.18   0.83  32.43
   3_bss:  74.72   0.00  11.71  74.72   0.00   7.91  66.18   0.83  32.43
   3_xyz:  74.72   0.00  11.71  74.72   0.00   7.91  66.18   0.83  32.43
   3_adp:  74.41   0.00  11.65  74.41   0.00   7.75  65.23   1.46  32.90
   3_occ:  74.41   0.00  11.65  74.41   0.00   7.75  65.23   1.46  32.90
   4_bss:  74.41   0.00  11.65  74.41   0.00   7.75  65.23   1.46  32.90
   4_xyz:  74.41   0.00  11.65  74.41   0.00   7.75  65.23   1.46  32.90
   4_adp:  82.34   0.00  11.97  82.34   0.00   7.77  70.40   1.12  34.88
   4_occ:  82.34   0.00  11.97  82.34   0.00   7.77  70.40   1.12  34.88
   5_bss:  82.34   0.00  11.97  82.34   0.00   7.77  70.40   1.12  34.88
   5_xyz:  82.34   0.00  11.97  82.34   0.00   7.77  70.40   1.12  34.88
   5_adp:  81.55   0.00  11.64  81.55   0.00   7.62  69.36   1.04  33.53
   5_occ:  81.55   0.00  11.64  81.55   0.00   7.62  69.36   1.04  33.53
   5_bss:  84.73   3.18  14.83  84.73   3.18  10.81  72.55   4.22  36.71
------------------------------------------------------------------------
 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:    1.187    0.012    0.412
   1_adp:    1.187    0.012    0.412
   1_occ:    1.187    0.012    0.412
   2_bss:    1.187    0.012    0.412
   2_xyz:    1.553    0.033    0.545
   2_adp:    1.553    0.033    0.545
   2_occ:    1.553    0.033    0.545
   3_bss:    1.553    0.033    0.545
   3_xyz:    1.564    0.069    0.593
   3_adp:    1.564    0.069    0.593
   3_occ:    1.564    0.069    0.593
   4_bss:    1.564    0.069    0.593
   4_xyz:    1.565    0.055    0.616
   4_adp:    1.565    0.055    0.616
   4_occ:    1.565    0.055    0.616
   5_bss:    1.565    0.055    0.616
   5_xyz:    1.700    0.018    0.623
   5_adp:    1.700    0.018    0.623
   5_occ:    1.700    0.018    0.623
   5_bss:    1.700    0.018    0.623
------------------------------------------------------------------------

CPU time actual refinement: 338.79


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_443/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_443/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_443/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_443/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_443/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 338.64 
  Macro-tasks:
    bulk solvent and scale       = 43.72  
    individual site refinement   = 136.29 
    weights calculation          = 32.65  
    collect and process          = 6.67   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 219.43 
  Micro-tasks:
    mask                            = 1.66   
    f_calc                          = 105.20 
    alpha_beta                      = 8.52   
    target                          = 1.26   
    gradients_wrt_atomic_parameters = 110.46 
    fmodel                         = 8.03   
    r_factors                      = 0.20   
    phase_errors                   = 11.71  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 247.32 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.739 micro seconds
Total CPU time: 5.87 minutes
from_scatterers_fft:    665 calls, 104.77 s
gradients_fft:          609 calls,  98.80 s

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

# Date 2008-01-16 Time 01:34:29 PST -0800 (1200476069.81 s)
Start R-work = 0.4518, R-free = 0.4417 (no bulk solvent and anisotropic scale)
Final R-work = 0.1295, R-free = 0.1712 (no bulk solvent and anisotropic scale)

Start R-work = 0.4431, R-free = 0.4355
Final R-work = 0.1121, R-free = 0.1553