# Date 2008-01-16 Time 03:13:26 PST -0800 (1200482006.43 s)
#phil __OFF__

Command line arguments: "../1148.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 17287
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1148

-------------------------------------------------------------------------------
  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: (71.655, 46.93, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 46.93, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1894 1.99104
Completeness in resolution range: 0.958835
Completeness with d_max=infinity: 0.955934

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1894
                             d_min =   1.9910

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: (71.655, 46.93, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1894 1.99104
Completeness in resolution range: 0.958835
Completeness with d_max=infinity: 0.955934

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1899 -  4.2610 [2142/2168]  1931   211   9.9%
  bin  2:  4.2610 -  3.3945 [2063/2082]  1855   208  10.1%
  bin  3:  3.3945 -  2.9690 [2032/2051]  1827   205  10.1%
  bin  4:  2.9690 -  2.6992 [2014/2044]  1813   201  10.0%
  bin  5:  2.6992 -  2.5067 [2014/2033]  1817   197   9.8%
  bin  6:  2.5067 -  2.3595 [1984/2009]  1778   206  10.4%
  bin  7:  2.3595 -  2.2417 [1991/2019]  1793   198   9.9%
  bin  8:  2.2417 -  2.1444 [1972/2008]  1780   192   9.7%
  bin  9:  2.1444 -  2.0620 [1972/2014]  1771   201  10.2%
  bin 10:  2.0620 -  1.9910 [1405/2002]  1265   140  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1148/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 11
        2.42 -     3.04: 2188
        3.04 -     3.66: 4634
        3.66 -     4.28: 9002
        4.28 -     4.90: 12260
  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 207 " - " O   HOH Z 341 "  1.851 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.057 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 208 " - " O   HOH Z 342 "  2.110 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  ... (remaining 28090 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_1148/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1148/model_refine_001.geo

CPU time processing inputs: 9.12


============================ 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 = 71.655 46.93 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4401   r_free= 0.4302   ksol= 0.00   Bsol= 0.00   scale= 0.812    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.238664                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1899 -  4.7528 0.99   1391  155 0.3727 0.3565      6.5409      6.4717|
|  2:  4.7528 -  3.7917 0.99   1343  146 0.3401 0.3521      6.6783      6.6865|
|  3:  3.7917 -  3.3181 0.99   1313  147 0.3860 0.3428      6.5736      6.5925|
|  4:  3.3181 -  3.0173 0.99   1316  153 0.4117 0.3958      6.4616      6.3957|
|  5:  3.0173 -  2.8025 0.99   1297  139 0.4552 0.4886      6.3241      6.3627|
|  6:  2.8025 -  2.6382 0.99   1284  143 0.4680 0.4581      6.2372      6.2178|
|  7:  2.6382 -  2.5067 0.99   1299  139 0.4968 0.5041      6.2384      6.2202|
|  8:  2.5067 -  2.3980 0.98   1263  151 0.4877 0.4622      6.1406      6.1339|
|  9:  2.3980 -  2.3060 0.98   1280  144 0.4758 0.4900      6.0963      6.1214|
| 10:  2.3060 -  2.2267 0.99   1277  139 0.4970 0.4693      6.0877      6.0686|
| 11:  2.2267 -  2.1573 0.98   1284  138 0.4989 0.4430      6.0314       5.982|
| 12:  2.1573 -  2.0958 0.97   1246  139 0.4881 0.5450       5.963      6.0268|
| 13:  2.0958 -  2.0407 1.00   1259  140 0.5232 0.5046      5.8845      5.8282|
| 14:  2.0407 -  1.9910 0.59    778   86 0.4976 0.4157      5.8552      5.7069|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1899 -  4.7528  1391   155  0.73  31.65   0.80     0.76      61064.89|
|  2:  4.7528 -  3.7917  1343   146  0.77  29.39   0.90     0.81      77990.74|
|  3:  3.7917 -  3.3181  1313   147  0.69  36.32   0.86     0.78      82408.54|
|  4:  3.3181 -  3.0173  1316   153  0.62  42.31   0.83     0.70      76719.26|
|  5:  3.0173 -  2.8025  1297   139  0.51  50.87   0.75     0.60      68407.92|
|  6:  2.8025 -  2.6382  1284   143  0.48  53.98   0.76     0.55      62857.19|
|  7:  2.6382 -  2.5067  1299   139  0.46  54.87   0.75     0.52      57218.21|
|  8:  2.5067 -  2.3980  1263   151  0.45  55.95   0.73     0.53      51293.33|
|  9:  2.3980 -  2.3060  1280   144  0.48  53.97   0.75     0.53      44421.36|
| 10:  2.3060 -  2.2267  1277   139  0.47  54.25   0.77     0.53      40089.46|
| 11:  2.2267 -  2.1573  1284   138  0.44  56.56   0.77     0.51      38823.37|
| 12:  2.1573 -  2.0958  1246   139  0.43  57.89   0.77     0.50      37544.26|
| 13:  2.0958 -  2.0407  1259   140  0.43  57.79   0.73     0.53      31637.33|
| 14:  2.0407 -  1.9910   778    86  0.56  47.71   0.73     0.60      20922.36|
|alpha:            min =        0.50 max =            0.81 mean =         0.61|
|beta:             min =    20922.36 max =        82408.54 mean =     54916.81|
|figures of merit: min =        0.00 max =            1.00 mean =         0.54|
|phase err.(work): min =        0.00 max =           89.99 mean =        48.61|
|phase err.(test): min =        0.00 max =           89.86 mean =        48.70|
|-----------------------------------------------------------------------------|

============================== 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 = 9.315687              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 75.268   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.686341              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 75.483   (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:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      165 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      674 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1502 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2617 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3890 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5029 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6525 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7679 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.044 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.628 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.098)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.098)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4474   r_free= 0.4383   ksol= 0.00   Bsol= 0.00   scale= 0.782    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.242113                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4323   r_free= 0.4187   ksol= 0.33   Bsol= 20.00   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (9.81,7.68,7.65,0.00,0.00,0.00); trace/3= 8.38                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.233208                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.407289              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.190   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.689926              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.650   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4323      final r-factor (work) = 0.3290          |
| start r-factor (free) = 0.4187      final r-factor (free) = 0.3570          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 80.2996 = 8.41 * 0.50 * 6.2460 + 1.00 * 54.0437                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.7307 = 8.41 * 0.50 * 6.0916 + 1.00 * 0.1239                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3290      final r-factor (work) = 0.2705          |
| start r-factor (free) = 0.3570      final r-factor (free) = 0.3105          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2175 = 0.69 * 1.00 * 6.0916 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1135 = 0.69 * 1.00 * 5.9449 + 1.00 * 0.0119                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.098)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    54.09   10.45    None  None   None       |
|    all(noH): 2823   0      0.00    54.09   10.45    None  None   None       |
|    Sol.    : 438    0      0.00    54.09   26.09    None  None   None       |
|    Mac.    : 2385   0      0.00    52.37   7.58     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 -   5.409: 1148   |   5:    27.047 -  32.457:  100        |
|      1:     5.409 -  10.819:  769   |   6:    32.457 -  37.866:   73        |
|      2:    10.819 -  16.228:  336   |   7:    37.866 -  43.275:   60        |
|      3:    16.228 -  21.638:  167   |   8:    43.275 -  48.685:   25        |
|      4:    21.638 -  27.047:  134   |   9:    48.685 -  54.094:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2705 r_free = 0.3105             target_work(ml) = 5.891         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2699 r_free = 0.3106             target_work(ml) = 5.890         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2699   r_free= 0.3106   ksol= 0.33   Bsol= 20.00   scale= 1.080   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (9.81,7.68,7.65,0.00,0.00,0.00); trace/3= 8.38                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.889703                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2658   r_free= 0.3054   ksol= 0.34   Bsol= 45.97   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.21,4.20,5.01,0.00,0.00,0.00); trace/3= 5.14                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.889181                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.454861              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.858   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.419792              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 117.932  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2658      final r-factor (work) = 0.1835          |
| start r-factor (free) = 0.3054      final r-factor (free) = 0.2315          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.3716 = 4.45 * 0.50 * 5.9477 + 1.00 * 0.1235                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.8330 = 4.45 * 0.50 * 5.7291 + 1.00 * 0.0719                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1835      final r-factor (work) = 0.1659          |
| start r-factor (free) = 0.2315      final r-factor (free) = 0.2141          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4364 = 0.42 * 1.00 * 5.7291 + 1.00 * 0.0314                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4040 = 0.42 * 1.00 * 5.5099 + 1.00 * 0.0910                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.098)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.63   10.99    None  None   None       |
|    all(noH): 2823   0      0.00    81.63   10.99    None  None   None       |
|    Sol.    : 438    0      0.58    58.25   30.25    None  None   None       |
|    Mac.    : 2385   0      0.00    81.63   7.46     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 -   8.163: 1656   |   5:    40.815 -  48.978:   71        |
|      1:     8.163 -  16.326:  597   |   6:    48.978 -  57.141:   22        |
|      2:    16.326 -  24.489:  174   |   7:    57.141 -  65.304:    1        |
|      3:    24.489 -  32.652:  143   |   8:    65.304 -  73.467:    0        |
|      4:    32.652 -  40.815:  158   |   9:    73.467 -  81.630:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1659 r_free = 0.2141             target_work(ml) = 5.472         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1657 r_free = 0.2140             target_work(ml) = 5.472         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1657   r_free= 0.2140   ksol= 0.34   Bsol= 45.97   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.21,4.20,5.01,0.00,0.00,0.00); trace/3= 5.14                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.471680                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1643   r_free= 0.2111   ksol= 0.34   Bsol= 52.55   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.89,3.15,4.04,0.00,0.00,0.00); trace/3= 3.69                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.469205                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.539935              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.024  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.020339              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.121   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1643      final r-factor (work) = 0.1305          |
| start r-factor (free) = 0.2111      final r-factor (free) = 0.1778          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8396 = 3.54 * 0.50 * 5.5186 + 1.00 * 0.0719                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5842 = 3.54 * 0.50 * 5.3729 + 1.00 * 0.0743                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1305      final r-factor (work) = 0.1219          |
| start r-factor (free) = 0.1778      final r-factor (free) = 0.1706          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.8694 = 2.02 * 1.00 * 5.3729 + 1.00 * 0.0143                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.6116 = 2.02 * 1.00 * 5.2452 + 1.00 * 0.0145                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.098)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.41   12.15    None  None   None       |
|    all(noH): 2823   0      0.00    81.41   12.15    None  None   None       |
|    Sol.    : 438    0      0.86    81.41   35.99    None  None   None       |
|    Mac.    : 2385   0      0.00    74.44   7.78     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 -   8.141: 1671   |   5:    40.704 -  48.845:   88        |
|      1:     8.141 -  16.282:  563   |   6:    48.845 -  56.986:   81        |
|      2:    16.282 -  24.423:  163   |   7:    56.986 -  65.127:   39        |
|      3:    24.423 -  32.564:  106   |   8:    65.127 -  73.268:   14        |
|      4:    32.564 -  40.704:   94   |   9:    73.268 -  81.409:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1219 r_free = 0.1706             target_work(ml) = 5.222         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1219 r_free = 0.1706             target_work(ml) = 5.222         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1219   r_free= 0.1706   ksol= 0.34   Bsol= 52.55   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.89,3.15,4.04,0.00,0.00,0.00); trace/3= 3.69                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.222028                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1221   r_free= 0.1700   ksol= 0.33   Bsol= 52.55   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.37,2.93,3.82,0.00,0.00,0.00); trace/3= 3.37                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.221102                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.646013              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 120.714  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.318204              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 110.570  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1221      final r-factor (work) = 0.1160          |
| start r-factor (free) = 0.1700      final r-factor (free) = 0.1653          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0148 = 2.65 * 0.50 * 5.2460 + 1.00 * 0.0743                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9522 = 2.65 * 0.50 * 5.2009 + 1.00 * 0.0713                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1160      final r-factor (work) = 0.1157          |
| start r-factor (free) = 0.1653      final r-factor (free) = 0.1629          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6699 = 0.32 * 1.00 * 5.2009 + 1.00 * 0.0150                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6618 = 0.32 * 1.00 * 5.1852 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.098)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.17   11.85    None  None   None       |
|    all(noH): 2823   0      0.00    80.17   11.85    None  None   None       |
|    Sol.    : 438    0      1.23    80.17   34.76    None  None   None       |
|    Mac.    : 2385   0      0.00    75.83   7.64     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 -   8.017: 1684   |   5:    40.083 -  48.100:   82        |
|      1:     8.017 -  16.033:  561   |   6:    48.100 -  56.116:   70        |
|      2:    16.033 -  24.050:  162   |   7:    56.116 -  64.133:   35        |
|      3:    24.050 -  32.066:  107   |   8:    64.133 -  72.149:   12        |
|      4:    32.066 -  40.083:  103   |   9:    72.149 -  80.166:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1157 r_free = 0.1629             target_work(ml) = 5.177         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1157 r_free = 0.1628             target_work(ml) = 5.176         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1157   r_free= 0.1628   ksol= 0.33   Bsol= 52.55   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.37,2.93,3.82,0.00,0.00,0.00); trace/3= 3.37                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.176348                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1157   r_free= 0.1628   ksol= 0.33   Bsol= 52.55   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.24,2.94,3.82,0.00,0.00,0.00); trace/3= 3.33                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.176340                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.933875              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 151.384  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.653054              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.700  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1157      final r-factor (work) = 0.1122          |
| start r-factor (free) = 0.1628      final r-factor (free) = 0.1606          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6770 = 2.93 * 0.50 * 5.1848 + 1.00 * 0.0711                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6503 = 2.93 * 0.50 * 5.1639 + 1.00 * 0.0752                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1122      final r-factor (work) = 0.1114          |
| start r-factor (free) = 0.1606      final r-factor (free) = 0.1616          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.5480 = 1.65 * 1.00 * 5.1639 + 1.00 * 0.0118                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.5309 = 1.65 * 1.00 * 5.1524 + 1.00 * 0.0136                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.098)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.09   11.90    None  None   None       |
|    all(noH): 2823   0      0.00    82.09   11.90    None  None   None       |
|    Sol.    : 438    0      1.33    82.09   35.10    None  None   None       |
|    Mac.    : 2385   0      0.00    77.92   7.64     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 -   8.209: 1689   |   5:    41.047 -  49.256:   88        |
|      1:     8.209 -  16.419:  553   |   6:    49.256 -  57.465:   63        |
|      2:    16.419 -  24.628:  162   |   7:    57.465 -  65.675:   32        |
|      3:    24.628 -  32.837:  118   |   8:    65.675 -  73.884:   11        |
|      4:    32.837 -  41.047:  102   |   9:    73.884 -  82.093:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1114 r_free = 0.1616             target_work(ml) = 5.157         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1113 r_free = 0.1615             target_work(ml) = 5.157         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1615   ksol= 0.33   Bsol= 52.55   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.24,2.94,3.82,0.00,0.00,0.00); trace/3= 3.33                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.157083                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1899 -  4.7528 0.99   1391  155 0.0972 0.1332      5.3741      5.5307|
|  2:  4.7528 -  3.7917 0.99   1343  146 0.0859 0.1115      5.4392       5.638|
|  3:  3.7917 -  3.3181 0.99   1313  147 0.1041 0.1583      5.4696      5.8827|
|  4:  3.3181 -  3.0173 0.99   1316  153 0.1180 0.1557      5.4543      5.5887|
|  5:  3.0173 -  2.8025 0.99   1297  139 0.1331 0.1836      5.3379      5.5841|
|  6:  2.8025 -  2.6382 0.99   1284  143 0.1223 0.1840       5.226      5.4918|
|  7:  2.6382 -  2.5067 0.99   1299  139 0.1267 0.1672        5.19      5.3784|
|  8:  2.5067 -  2.3980 0.98   1263  151 0.1178 0.1798       5.081      5.3779|
|  9:  2.3980 -  2.3060 0.98   1280  144 0.1183 0.1817      5.0644      5.3555|
| 10:  2.3060 -  2.2267 0.99   1277  139 0.1103 0.1758      4.9681       5.227|
| 11:  2.2267 -  2.1573 0.98   1284  138 0.1148 0.1810       4.963      5.3169|
| 12:  2.1573 -  2.0958 0.97   1246  139 0.1086 0.1664      4.8933      5.1332|
| 13:  2.0958 -  2.0407 1.00   1259  140 0.1199 0.1819      4.8164      5.1073|
| 14:  2.0407 -  1.9910 0.59    778   86 0.1023 0.1796      4.6623      4.9544|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1899 -  4.7528  1391   155  0.94   9.00   0.98     0.95       7190.11|
|  2:  4.7528 -  3.7917  1343   146  0.95   8.16   1.01     0.99       9224.11|
|  3:  3.7917 -  3.3181  1313   147  0.93  11.46   1.02     1.02      10533.43|
|  4:  3.3181 -  3.0173  1316   153  0.92  13.84   1.00     0.98      10620.27|
|  5:  3.0173 -  2.8025  1297   139  0.89  16.43   0.99     0.97       8608.62|
|  6:  2.8025 -  2.6382  1284   143  0.90  16.44   0.98     0.95       7563.55|
|  7:  2.6382 -  2.5067  1299   139  0.90  15.99   0.99     0.97       6629.91|
|  8:  2.5067 -  2.3980  1263   151  0.90  16.16   0.98     0.95       5617.62|
|  9:  2.3980 -  2.3060  1280   144  0.90  15.98   1.00     0.97       5413.41|
| 10:  2.3060 -  2.2267  1277   139  0.90  15.88   0.99     0.95       4545.04|
| 11:  2.2267 -  2.1573  1284   138  0.90  16.69   0.99     0.95       4615.63|
| 12:  2.1573 -  2.0958  1246   139  0.91  15.33   1.00     0.99       4198.68|
| 13:  2.0958 -  2.0407  1259   140  0.89  17.35   1.00     0.98       3625.61|
| 14:  2.0407 -  1.9910   778    86  0.91  14.92   0.97     0.94       2605.19|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2605.19 max =        10620.27 mean =      6651.33|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.47|
|phase err.(test): min =        0.00 max =           87.66 mean =        13.86|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1615   ksol= 0.33   Bsol= 55.97   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.10,-0.39,0.49,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.157134                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.19 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1615   ksol= 0.33   Bsol= 55.97   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.10,-0.39,0.49,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.157134                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1899 -  4.7528 0.99   1391  155 0.0972 0.1333      5.3744      5.5311|
|  2:  4.7528 -  3.7917 0.99   1343  146 0.0859 0.1115      5.4393      5.6378|
|  3:  3.7917 -  3.3181 0.99   1313  147 0.1041 0.1583      5.4695      5.8826|
|  4:  3.3181 -  3.0173 0.99   1316  153 0.1180 0.1557      5.4543      5.5888|
|  5:  3.0173 -  2.8025 0.99   1297  139 0.1331 0.1836       5.338      5.5841|
|  6:  2.8025 -  2.6382 0.99   1284  143 0.1223 0.1840       5.226      5.4917|
|  7:  2.6382 -  2.5067 0.99   1299  139 0.1266 0.1672      5.1899      5.3784|
|  8:  2.5067 -  2.3980 0.98   1263  151 0.1178 0.1798       5.081      5.3779|
|  9:  2.3980 -  2.3060 0.98   1280  144 0.1183 0.1817      5.0644      5.3554|
| 10:  2.3060 -  2.2267 0.99   1277  139 0.1103 0.1758      4.9681       5.227|
| 11:  2.2267 -  2.1573 0.98   1284  138 0.1148 0.1811       4.963      5.3171|
| 12:  2.1573 -  2.0958 0.97   1246  139 0.1086 0.1664      4.8934      5.1334|
| 13:  2.0958 -  2.0407 1.00   1259  140 0.1198 0.1820      4.8164      5.1073|
| 14:  2.0407 -  1.9910 0.59    778   86 0.1023 0.1796      4.6624      4.9544|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1899 -  4.7528  1391   155  0.94   9.01   0.98     0.95       7195.23|
|  2:  4.7528 -  3.7917  1343   146  0.95   8.16   1.01     0.99       9226.57|
|  3:  3.7917 -  3.3181  1313   147  0.93  11.46   1.02     1.02      10530.90|
|  4:  3.3181 -  3.0173  1316   153  0.92  13.84   1.01     0.98      10620.30|
|  5:  3.0173 -  2.8025  1297   139  0.89  16.43   1.00     0.97       8607.77|
|  6:  2.8025 -  2.6382  1284   143  0.90  16.44   0.98     0.96       7563.12|
|  7:  2.6382 -  2.5067  1299   139  0.90  15.99   0.99     0.97       6628.93|
|  8:  2.5067 -  2.3980  1263   151  0.90  16.16   0.98     0.95       5617.50|
|  9:  2.3980 -  2.3060  1280   144  0.90  15.98   1.00     0.97       5412.81|
| 10:  2.3060 -  2.2267  1277   139  0.90  15.88   1.00     0.95       4545.37|
| 11:  2.2267 -  2.1573  1284   138  0.90  16.69   0.99     0.95       4616.06|
| 12:  2.1573 -  2.0958  1246   139  0.91  15.33   1.01     0.99       4200.18|
| 13:  2.0958 -  2.0407  1259   140  0.89  17.35   1.00     0.99       3626.06|
| 14:  2.0407 -  1.9910   778    86  0.91  14.92   0.98     0.95       2605.64|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2605.64 max =        10620.30 mean =      6651.74|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.97 mean =        14.47|
|phase err.(test): min =        0.00 max =           87.66 mean =        13.87|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.098)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.42    85.51   15.32    None  None   None       |
|    all(noH): 2823   0      3.42    85.51   15.32    None  None   None       |
|    Sol.    : 438    0      4.75    85.51   38.52    None  None   None       |
|    Mac.    : 2385   0      3.42    81.34   11.06    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.420 -  11.629: 1689   |   5:    44.466 -  52.676:   88        |
|      1:    11.629 -  19.838:  553   |   6:    52.676 -  60.885:   63        |
|      2:    19.838 -  28.048:  162   |   7:    60.885 -  69.094:   32        |
|      3:    28.048 -  36.257:  118   |   8:    69.094 -  77.304:   11        |
|      4:    36.257 -  44.466:  102   |   9:    77.304 -  85.513:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 325         
Filter by distance & map next to the model:
   mapped sites are within: 0.353 - 4.696
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 319 from: 325
   mapped sites are within: 0.701 - 4.696

peak=   10.473 closest distance to " CG2 VAL A 230 " =    1.393
peak=    6.515 closest distance to " CG2 VAL A 296 " =    1.070
peak=    6.075 closest distance to " CG  LEU A   5 " =    1.158
peak=    6.061 closest distance to " O   HOH Z 111 " =    2.153
peak=    5.743 closest distance to " CG  LEU A 228 " =    1.152
peak=    5.679 closest distance to " CB  GLN A 223 " =    1.451
peak=    5.418 closest distance to " CD2 LEU A   5 " =    1.116
peak=    4.956 closest distance to " CB  VAL A 296 " =    1.117
peak=    4.950 closest distance to " CB  SER A  63 " =    1.307
peak=    4.941 closest distance to " CB  VAL A 230 " =    1.205
peak=    4.915 closest distance to " O   HOH Z 232 " =    2.293
peak=    4.880 closest distance to " CB  GLN A 183 " =    1.266
peak=    4.876 closest distance to " NE2 GLN A  11 " =    1.155
peak=    4.662 closest distance to " O   HOH Z 298 " =    1.844
peak=    4.601 closest distance to " O   HOH Z 126 " =    1.919
peak=    4.543 closest distance to " CG  PRO A 213 " =    1.208
peak=    4.515 closest distance to " O   HOH Z 369 " =    2.104
peak=    4.496 closest distance to " C   PRO A 198 " =    1.564
peak=    4.494 closest distance to " O   HOH Z 427 " =    3.153
peak=    4.370 closest distance to " O   HOH Z 316 " =    3.061
peak=    4.329 closest distance to " CB  GLU A 152 " =    1.195
peak=    4.323 closest distance to " OD1 ASN A  69 " =    2.696
peak=    4.313 closest distance to " O   HOH Z 425 " =    1.415
peak=    4.311 closest distance to " O   HOH Z 368 " =    2.218
peak=    4.293 closest distance to " O   HOH Z 403 " =    1.713
peak=    4.237 closest distance to " O   HOH Z 144 " =    1.638
peak=    4.228 closest distance to " O   HOH Z  78 " =    1.947
peak=    4.225 closest distance to " CB  ASN A 148 " =    1.383
peak=    4.216 closest distance to " CG  PRO A 243 " =    1.148
peak=    4.213 closest distance to " O   HOH Z 236 " =    1.900
peak=    4.213 closest distance to " CD2 LEU A 228 " =    1.165
peak=    4.190 closest distance to " CB  GLU A 128 " =    1.091
peak=    4.164 closest distance to " NH1AARG A 145 " =    1.137
peak=    4.159 closest distance to " CB  TRP A 266 " =    0.976
peak=    4.157 closest distance to " O   HOH Z 303 " =    2.094
peak=    4.147 closest distance to " O   HOH Z  54 " =    2.438
peak=    4.142 closest distance to " CB  ASP A 140 " =    0.962
peak=    4.104 closest distance to " CB  ARG A  79 " =    1.485
peak=    4.098 closest distance to " O   HOH Z 411 " =    3.681
peak=    4.093 closest distance to " CB  SER A   3 " =    1.391
peak=    4.082 closest distance to " ND2 ASN A 187 " =    1.502
peak=    4.076 closest distance to " CB  GLU A 277 " =    3.648
peak=    4.073 closest distance to " O   HOH Z 112 " =    1.580
peak=    4.049 closest distance to " CB  VAL A 265 " =    1.283
peak=    4.038 closest distance to " O   HOH Z 158 " =    3.030
peak=    4.021 closest distance to " CA  TYR A  30 " =    0.971
peak=    4.021 closest distance to " O   HOH Z 272 " =    1.865
peak=    4.001 closest distance to " CB  ARG A 275 " =    0.861
peak=    3.997 closest distance to " CB  LEU A 228 " =    1.263
peak=    3.997 closest distance to " CG  PRO A 198 " =    1.178
peak=    3.990 closest distance to " CB  SER A 212 " =    1.145
peak=    3.973 closest distance to " CD  ARG A  66 " =    2.405
peak=    3.965 closest distance to " CB  ASP A 124 " =    0.713
peak=    3.952 closest distance to " CB  TYR A 169 " =    0.701
peak=    3.942 closest distance to " CD  ARG A 159 " =    0.785
peak=    3.922 closest distance to " CG2 THR A 221 " =    1.150
peak=    3.917 closest distance to " CA  ALA A  51 " =    1.019
peak=    3.896 closest distance to " NH2 ARG A 156 " =    1.101
peak=    3.879 closest distance to " CG1 ILE A  33 " =    1.238
peak=    3.878 closest distance to " O   HOH Z 203 " =    1.834
peak=    3.850 closest distance to " CZ  PHE A 218 " =    1.055
peak=    3.849 closest distance to " O   HOH Z 247 " =    1.285
peak=    3.848 closest distance to " O   HOH Z 126 " =    1.693
peak=    3.846 closest distance to " O   HOH Z 346 " =    1.619
peak=    3.843 closest distance to " O   HOH Z 234 " =    3.741
peak=    3.843 closest distance to " O   HOH Z  15 " =    2.183
peak=    3.835 closest distance to " CD1 LEU A 300 " =    1.195
peak=    3.829 closest distance to " OD2 ASP A 286 " =    2.880
peak=    3.829 closest distance to " O   HOH Z 261 " =    2.103
peak=    3.825 closest distance to " O   HOH Z 193 " =    1.824
peak=    3.819 closest distance to " CB  SER A 216 " =    0.854
peak=    3.818 closest distance to " O   HOH Z  61 " =    1.641
peak=    3.811 closest distance to " CA  ASN A 215 " =    1.246
peak=    3.811 closest distance to " CG1BVAL A  72 " =    1.617
peak=    3.803 closest distance to " CB  TRP A 179 " =    1.452
peak=    3.799 closest distance to " O   HOH Z 193 " =    1.719
peak=    3.794 closest distance to " CB  ASN A 187 " =    1.115
peak=    3.786 closest distance to " O   SER A  87 " =    2.285
peak=    3.784 closest distance to " O   HOH Z 280 " =    2.934
peak=    3.783 closest distance to " O   HOH Z 371 " =    3.276
peak=    3.773 closest distance to " CD ALYS A 290 " =    1.021
peak=    3.770 closest distance to " O   HOH Z  88 " =    3.407
peak=    3.769 closest distance to " CB  LEU A 143 " =    1.160
peak=    3.766 closest distance to " CG  MET A 185 " =    1.270
peak=    3.754 closest distance to " O   HOH Z 193 " =    2.089
peak=    3.747 closest distance to " O   HOH Z 135 " =    1.920
peak=    3.745 closest distance to " O   HOH Z  20 " =    1.859
peak=    3.739 closest distance to " O   MET A 105 " =    1.814
peak=    3.736 closest distance to " NZ  LYS A 117 " =    3.288
peak=    3.736 closest distance to " CA  MET A  40 " =    1.117
peak=    3.732 closest distance to " CB  ALA A   9 " =    1.604
peak=    3.723 closest distance to " O   HOH Z  97 " =    2.062
peak=    3.709 closest distance to " O   HOH Z 197 " =    3.012
peak=    3.697 closest distance to " CB  PRO A  54 " =    0.743
peak=    3.694 closest distance to " O   HOH Z 189 " =    2.747
peak=    3.693 closest distance to " O   HOH Z 132 " =    2.678
peak=    3.686 closest distance to " O   HOH Z 423 " =    1.660
peak=    3.665 closest distance to " O   HOH Z  44 " =    2.230
peak=    3.663 closest distance to " ND2 ASN A 249 " =    1.858
peak=    3.661 closest distance to " NH1 ARG A  56 " =    0.948
peak=    3.661 closest distance to " CB  VAL A 202 " =    1.627
peak=    3.660 closest distance to " CA  GLY A 267 " =    0.761
peak=    3.651 closest distance to " O   TRP A 274 " =    1.877
peak=    3.650 closest distance to " CA  LYS A 117 " =    1.218
peak=    3.649 closest distance to " CA  THR A 264 " =    0.723
peak=    3.648 closest distance to " CZ  PHE A 192 " =    0.939
peak=    3.640 closest distance to " O   HOH Z 437 " =    1.817
peak=    3.638 closest distance to " CB  ARG A 190 " =    1.625
peak=    3.635 closest distance to " CB  THR A  82 " =    1.350
peak=    3.629 closest distance to " CA  ALA A  21 " =    1.213
peak=    3.627 closest distance to " O   ALA A 158 " =    1.410
peak=    3.627 closest distance to " O   HOH Z 133 " =    1.717
peak=    3.622 closest distance to " CG  GLN A  88 " =    1.062
peak=    3.619 closest distance to " CG BARG A 275 " =    1.502
peak=    3.607 closest distance to " CE  LYS A  76 " =    0.825
peak=    3.605 closest distance to " O   HOH Z 180 " =    2.061
peak=    3.603 closest distance to " O   HOH Z  43 " =    1.761
peak=    3.602 closest distance to " ND1 HIS A  81 " =    1.686
peak=    3.602 closest distance to " CB  GLN A  88 " =    1.285
peak=    3.596 closest distance to " CD  ARG A 269 " =    0.963
peak=    3.590 closest distance to " CA  ALA A 158 " =    1.187
peak=    3.590 closest distance to " O   HOH Z 126 " =    1.543
peak=    3.590 closest distance to " CB  TRP A 150 " =    1.400
peak=    3.588 closest distance to " O   HOH Z  80 " =    1.635
peak=    3.580 closest distance to " CA  ALA A 295 " =    1.066
peak=    3.573 closest distance to " OG BSER A 164 " =    2.175
peak=    3.569 closest distance to " O   HOH Z 171 " =    3.871
peak=    3.566 closest distance to " CB  ASN A  39 " =    0.908
peak=    3.553 closest distance to " N   SER A 135 " =    1.458
peak=    3.553 closest distance to " O   HOH Z  68 " =    2.151
peak=    3.552 closest distance to " ND1 HIS A  86 " =    1.774
peak=    3.552 closest distance to " O   GLN A 278 " =    1.304
peak=    3.543 closest distance to " O   HOH Z 213 " =    1.825
peak=    3.542 closest distance to " CD1 LEU A   5 " =    1.292
peak=    3.540 closest distance to " CG  LEU A 167 " =    1.192
peak=    3.540 closest distance to " CA  THR A 221 " =    0.919
peak=    3.539 closest distance to " CD2 LEU A   5 " =    0.721
peak=    3.538 closest distance to " CB AVAL A  41 " =    1.210
peak=    3.538 closest distance to " O   HOH Z 184 " =    1.417
peak=    3.535 closest distance to " CB  VAL A 268 " =    0.883
peak=    3.533 closest distance to " CD2 LEU A 255 " =    1.576
peak=    3.533 closest distance to " O   HOH Z 128 " =    2.103
peak=    3.530 closest distance to " CB  ALA A   1 " =    4.696
peak=    3.525 closest distance to " O   HOH Z 263 " =    1.635
peak=    3.523 closest distance to " O   HOH Z 214 " =    2.057
peak=    3.521 closest distance to " O   HOH Z  10 " =    1.832
peak=    3.508 closest distance to " O   HOH Z 271 " =    2.614
peak=    3.493 closest distance to " CA  ALA A 291 " =    0.940
peak=    3.492 closest distance to " O   HOH Z 147 " =    1.707
peak=    3.491 closest distance to " CB  ARG A 139 " =    0.915
peak=    3.487 closest distance to " O   HOH Z 313 " =    1.812
peak=    3.485 closest distance to " CB  ASN A 110 " =    1.285
peak=    3.472 closest distance to " O   HOH Z 132 " =    3.253
peak=    3.468 closest distance to " CG1 VAL A 153 " =    0.964
peak=    3.467 closest distance to " CB  LYS A 117 " =    1.154
peak=    3.463 closest distance to " OG  SER A  22 " =    2.917
peak=    3.463 closest distance to " O   HOH Z 345 " =    3.554
peak=    3.457 closest distance to " O   HOH Z  21 " =    1.669
peak=    3.454 closest distance to " NE2 HIS A 207 " =    1.572
peak=    3.446 closest distance to " O   HOH Z 425 " =    2.019
peak=    3.442 closest distance to " O   HOH Z 245 " =    1.342
peak=    3.438 closest distance to " O   HOH Z 302 " =    1.919
peak=    3.434 closest distance to " CG1 ILE A 151 " =    1.011
peak=    3.427 closest distance to " OD1 ASN A 217 " =    1.615
peak=    3.427 closest distance to " O   HOH Z  58 " =    1.508
peak=    3.425 closest distance to " O   HOH Z 250 " =    1.294
peak=    3.424 closest distance to " O   HOH Z 183 " =    1.349
peak=    3.423 closest distance to " CD  LYS A 166 " =    1.299
peak=    3.416 closest distance to " CG2 THR A 220 " =    0.969
peak=    3.416 closest distance to " NH2 ARG A 219 " =    1.843
peak=    3.416 closest distance to " CB  ASN A 142 " =    1.055
peak=    3.413 closest distance to " CE1 TYR A 186 " =    1.336
peak=    3.409 closest distance to " O   HOH Z 271 " =    2.150
peak=    3.408 closest distance to " CB  MET A  40 " =    0.828
peak=    3.403 closest distance to " O   HOH Z  97 " =    2.766
peak=    3.396 closest distance to " CG1 ILE A  49 " =    1.422
peak=    3.396 closest distance to " N   VAL A 126 " =    1.352
peak=    3.395 closest distance to " CA  ASP A 140 " =    1.231
peak=    3.392 closest distance to " O   HOH Z 248 " =    1.816
peak=    3.389 closest distance to " OG BSER A 210 " =    1.190
peak=    3.389 closest distance to " O   HOH Z 329 " =    3.874
peak=    3.388 closest distance to " CB  HIS A 108 " =    0.814
peak=    3.387 closest distance to " O   HOH Z 133 " =    2.498
peak=    3.379 closest distance to " O   HOH Z 368 " =    3.606
peak=    3.378 closest distance to " CB  THR A 157 " =    1.138
peak=    3.376 closest distance to " CB  THR A  31 " =    1.670
peak=    3.373 closest distance to " O   HOH Z 423 " =    2.824
peak=    3.372 closest distance to " O   HOH Z 305 " =    3.570
peak=    3.372 closest distance to " O   HOH Z 410 " =    1.413
peak=    3.361 closest distance to " O   HOH Z  68 " =    1.576
peak=    3.361 closest distance to " CA  ASN A  74 " =    1.279
peak=    3.361 closest distance to " CA  LEU A 282 " =    1.027
peak=    3.358 closest distance to " O   HOH Z 344 " =    3.052
peak=    3.357 closest distance to " CD1 LEU A 228 " =    1.831
peak=    3.357 closest distance to " CB  ALA A 248 " =    1.443
peak=    3.355 closest distance to " CB  ALA A  34 " =    0.942
peak=    3.354 closest distance to " CD1 ILE A  33 " =    1.573
peak=    3.351 closest distance to " CB  LEU A 255 " =    0.770
peak=    3.351 closest distance to " O   HOH Z 227 " =    1.643
peak=    3.349 closest distance to " O   HOH Z 290 " =    1.008
peak=    3.347 closest distance to " CB  ALA A 248 " =    1.001
peak=    3.345 closest distance to " CG BARG A 102 " =    1.859
peak=    3.343 closest distance to " ND2 ASN A 110 " =    1.694
peak=    3.342 closest distance to " CA  TYR A  30 " =    1.053
peak=    3.341 closest distance to " CB  LEU A 237 " =    0.798
peak=    3.340 closest distance to " O   HOH Z  53 " =    2.599
peak=    3.340 closest distance to " O   HOH Z   1 " =    1.840
peak=    3.337 closest distance to " N   PHE A 130 " =    1.305
peak=    3.336 closest distance to " O   ASP A 124 " =    1.037
peak=    3.336 closest distance to " O   HOH Z 116 " =    1.794
peak=    3.333 closest distance to " O   HOH Z 145 " =    3.554
peak=    3.325 closest distance to " O   HOH Z 134 " =    1.452
peak=    3.324 closest distance to " CB  ALA A 291 " =    1.425
peak=    3.321 closest distance to " O   HOH Z 426 " =    1.528
peak=    3.320 closest distance to " N   ASN A 127 " =    1.259
peak=    3.320 closest distance to " OG BSER A 134 " =    3.013
peak=    3.319 closest distance to " O   HOH Z 402 " =    1.459
peak=    3.316 closest distance to " O   HOH Z 273 " =    2.697
peak=    3.307 closest distance to " O   ARG A  56 " =    2.787
peak=    3.306 closest distance to " O   HOH Z 295 " =    1.495
peak=    3.303 closest distance to " CB  ILE A 120 " =    1.338
peak=    3.303 closest distance to " CG1 VAL A 296 " =    1.243
peak=    3.303 closest distance to " O   HOH Z 145 " =    1.711
peak=    3.296 closest distance to " CG  MET A 185 " =    1.088
peak=    3.296 closest distance to " CA  ARG A 195 " =    1.212
peak=    3.293 closest distance to " CB  ALA A 161 " =    0.904
peak=    3.293 closest distance to " CA  TYR A 116 " =    1.475
peak=    3.289 closest distance to " N   SER A 134 " =    1.776
peak=    3.288 closest distance to " CG2 VAL A 257 " =    0.898
peak=    3.281 closest distance to " O   HOH Z 383 " =    2.235
peak=    3.280 closest distance to " O   HOH Z 227 " =    2.136
peak=    3.280 closest distance to " O   HOH Z 282 " =    1.920
peak=    3.279 closest distance to " OG1 THR A 294 " =    2.387
peak=    3.279 closest distance to " OE1 GLU A 152 " =    0.885
peak=    3.275 closest distance to " O   HOH Z 355 " =    1.747
peak=    3.274 closest distance to " O   ALA A 291 " =    1.557
peak=    3.272 closest distance to " O   HOH Z 189 " =    3.211
peak=    3.269 closest distance to " O   HOH Z 291 " =    1.585
peak=    3.265 closest distance to " O   HOH Z 128 " =    2.269
peak=    3.265 closest distance to " CD  ARG A  14 " =    1.198
peak=    3.262 closest distance to " CG  ARG A 138 " =    1.119
peak=    3.259 closest distance to " O   HOH Z 286 " =    2.339
peak=    3.258 closest distance to " CA  SER A  87 " =    0.984
peak=    3.256 closest distance to " N   SER A 146 " =    1.716
peak=    3.254 closest distance to " O   HOH Z 172 " =    3.774
peak=    3.253 closest distance to " CA  ARG A  36 " =    1.141
peak=    3.248 closest distance to " CB  GLN A  89 " =    1.165
peak=    3.248 closest distance to " O   HOH Z 409 " =    3.076
peak=    3.247 closest distance to " OG  SER A  97 " =    2.699
peak=    3.247 closest distance to " C   LYS A 290 " =    1.341
peak=    3.244 closest distance to " CD1 TRP A 266 " =    1.132
peak=    3.241 closest distance to " CB  MET A  47 " =    1.132
peak=    3.238 closest distance to " CD2 TRP A 179 " =    1.366
peak=    3.238 closest distance to " O   HOH Z 201 " =    3.276
peak=    3.237 closest distance to " CA  ILE A  33 " =    1.654
peak=    3.236 closest distance to " O   HOH Z 353 " =    2.798
peak=    3.236 closest distance to " N   ASN A  39 " =    1.302
peak=    3.231 closest distance to " O   HOH Z 422 " =    2.669
peak=    3.230 closest distance to " O   HOH Z 285 " =    3.093
peak=    3.229 closest distance to " CB  GLU A  46 " =    1.063
peak=    3.226 closest distance to " C   SER A  32 " =    1.050
peak=    3.225 closest distance to " O   HOH Z 185 " =    1.923
peak=    3.221 closest distance to " CD  ARG A 219 " =    1.108
peak=    3.221 closest distance to " CA  ALA A 299 " =    0.959
peak=    3.214 closest distance to " O   HOH Z 313 " =    1.729
peak=    3.211 closest distance to " O   HOH Z 109 " =    2.627
peak=    3.210 closest distance to " CB  ALA A 104 " =    0.801
peak=    3.208 closest distance to " O   HOH Z 163 " =    1.539
peak=    3.207 closest distance to " O   HOH Z 407 " =    2.318
peak=    3.202 closest distance to " CB  ALA A 100 " =    1.245
peak=    3.202 closest distance to " O   HOH Z 175 " =    2.150
peak=    3.201 closest distance to " CD1 ILE A 106 " =    0.956
peak=    3.200 closest distance to " CB  ASN A 224 " =    0.993
peak=    3.199 closest distance to " O   HOH Z 102 " =    1.250
peak=    3.194 closest distance to " O   HOH Z  61 " =    1.548
peak=    3.187 closest distance to " O   HOH Z 350 " =    1.674
peak=    3.186 closest distance to " OG  SER A  62 " =    3.047
peak=    3.185 closest distance to " O   HOH Z 124 " =    1.855
peak=    3.184 closest distance to " CA  ALA A 154 " =    1.065
peak=    3.183 closest distance to " O   HOH Z 286 " =    2.504
peak=    3.182 closest distance to " NZ  LYS A  48 " =    1.479
peak=    3.179 closest distance to " O   HOH Z 163 " =    1.763
peak=    3.178 closest distance to " CG1 VAL A 174 " =    1.172
peak=    3.178 closest distance to " CB  TYR A 116 " =    0.879
peak=    3.176 closest distance to " CD2 HIS A  81 " =    1.026
peak=    3.165 closest distance to " NE2 GLN A  77 " =    3.359
peak=    3.162 closest distance to " CB  TYR A  30 " =    1.488
peak=    3.158 closest distance to " CA  ARG A  56 " =    2.102
peak=    3.155 closest distance to " CE2 TYR A 186 " =    0.870
peak=    3.155 closest distance to " OH  TYR A 214 " =    1.211
peak=    3.149 closest distance to " O   HOH Z  49 " =    2.702
peak=    3.141 closest distance to " O   HOH Z 148 " =    3.283
peak=    3.140 closest distance to " O   HOH Z 173 " =    2.156
peak=    3.136 closest distance to " CA  GLY A 211 " =    1.284
peak=    3.131 closest distance to " CA  VAL A  41 " =    0.953
peak=    3.128 closest distance to " O   HOH Z 187 " =    2.265
peak=    3.125 closest distance to " O   HOH Z 374 " =    2.735
peak=    3.124 closest distance to " O   HOH Z 334 " =    1.381
peak=    3.120 closest distance to " N   GLN A 278 " =    1.016
peak=    3.119 closest distance to " N   ARG A 156 " =    1.364
peak=    3.113 closest distance to " NH2BARG A 145 " =    2.091
peak=    3.112 closest distance to " CB  ALA A 227 " =    0.955
peak=    3.112 closest distance to " O   HOH Z 156 " =    2.902
peak=    3.111 closest distance to " OG  SER A 206 " =    1.186
peak=    3.099 closest distance to " O   HOH Z  59 " =    2.164
peak=    3.098 closest distance to " CB  ALA A 114 " =    1.242
peak=    3.096 closest distance to " NE  ARG A  79 " =    1.219
peak=    3.088 closest distance to " CA  ASN A 176 " =    1.198
peak=    3.087 closest distance to " CG  MET A 188 " =    1.102
peak=    3.080 closest distance to " O   HOH Z 213 " =    2.655
peak=    3.077 closest distance to " CA  ASP A 191 " =    0.771
peak=    3.075 closest distance to " CD  LYS A 119 " =    1.533
peak=    3.070 closest distance to " O   HOH Z 327 " =    2.082
peak=    3.058 closest distance to " O   HOH Z 391 " =    2.982
peak=    3.054 closest distance to " O   HOH Z 392 " =    1.936
peak=    3.049 closest distance to " CG  GLN A 278 " =    1.301
peak=    3.041 closest distance to " CB  ALA A  43 " =    0.863
peak=    3.039 closest distance to " O   HOH Z 173 " =    1.612
peak=    3.023 closest distance to " O   HOH Z 403 " =    1.382

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 209         
Filter by distance & map next to the model:
   mapped sites are within: 0.632 - 5.551
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 207 from: 209
   mapped sites are within: 0.780 - 5.551

peak=   -5.164 closest distance to " CG2 VAL A 230 " =    0.849
peak=   -4.577 closest distance to " CD  ARG A 156 " =    2.001
peak=   -4.159 closest distance to " CG  GLN A 223 " =    2.178
peak=   -4.123 closest distance to " O   HOH Z 266 " =    5.036
peak=   -4.101 closest distance to " O   HOH Z 231 " =    1.872
peak=   -4.056 closest distance to " CB  PRO A 243 " =    2.656
peak=   -4.035 closest distance to " O   HOH Z 389 " =    1.924
peak=   -4.030 closest distance to " SG  CYS A 254 " =    3.224
peak=   -4.013 closest distance to " CB  ALA A 161 " =    2.636
peak=   -4.002 closest distance to " CG2BVAL A  41 " =    2.591
peak=   -3.959 closest distance to " OG BSER A 134 " =    1.265
peak=   -3.957 closest distance to " O   HOH Z  52 " =    1.481
peak=   -3.922 closest distance to " CD2 LEU A 300 " =    2.846
peak=   -3.861 closest distance to " CZ3 TRP A 179 " =    1.158
peak=   -3.859 closest distance to " CG1 VAL A 250 " =    2.689
peak=   -3.847 closest distance to " OG  SER A  87 " =    1.497
peak=   -3.844 closest distance to " CE2 TYR A  30 " =    2.781
peak=   -3.831 closest distance to " CG1 VAL A 296 " =    1.427
peak=   -3.830 closest distance to " O   PRO A 163 " =    2.091
peak=   -3.826 closest distance to " O   HOH Z 290 " =    1.255
peak=   -3.801 closest distance to " NH2AARG A 275 " =    5.468
peak=   -3.791 closest distance to " CG1 VAL A 112 " =    2.922
peak=   -3.788 closest distance to " N   ALA A  43 " =    2.541
peak=   -3.783 closest distance to " NE2 GLN A  88 " =    2.161
peak=   -3.762 closest distance to " O   HOH Z 377 " =    1.953
peak=   -3.752 closest distance to " CD1 LEU A 228 " =    2.365
peak=   -3.744 closest distance to " O   SER A 271 " =    2.250
peak=   -3.743 closest distance to " CG1 VAL A 112 " =    2.609
peak=   -3.729 closest distance to " O   HOH Z  38 " =    1.559
peak=   -3.722 closest distance to " C   HIS A 108 " =    1.182
peak=   -3.714 closest distance to " CD  GLN A  58 " =    1.075
peak=   -3.714 closest distance to " CA  ASP A 298 " =    1.025
peak=   -3.708 closest distance to " O   HOH Z 353 " =    2.169
peak=   -3.707 closest distance to " OD1 ASN A 148 " =    1.489
peak=   -3.702 closest distance to " C   ALA A 158 " =    1.247
peak=   -3.700 closest distance to " CB  ALA A  43 " =    2.551
peak=   -3.694 closest distance to " O   HOH Z 426 " =    1.666
peak=   -3.680 closest distance to " CG2 VAL A 296 " =    1.390
peak=   -3.665 closest distance to " CA  GLY A 241 " =    3.071
peak=   -3.664 closest distance to " C   ASN A 187 " =    1.752
peak=   -3.653 closest distance to " OG  SER A  26 " =    1.304
peak=   -3.649 closest distance to " CB  PRO A 163 " =    2.550
peak=   -3.639 closest distance to " CG  LEU A 101 " =    2.522
peak=   -3.638 closest distance to " CG  ARG A 269 " =    2.339
peak=   -3.633 closest distance to " O   HOH Z  43 " =    1.650
peak=   -3.624 closest distance to " CD  LYS A 289 " =    2.458
peak=   -3.623 closest distance to " CG  MET A 105 " =    0.997
peak=   -3.622 closest distance to " O   HOH Z 196 " =    2.197
peak=   -3.612 closest distance to " O   HOH Z 118 " =    3.088
peak=   -3.609 closest distance to " N   THR A 157 " =    1.522
peak=   -3.598 closest distance to " O   VAL A 189 " =    2.635
peak=   -3.595 closest distance to " OG  SER A  97 " =    2.218
peak=   -3.595 closest distance to " O   HOH Z 103 " =    1.788
peak=   -3.587 closest distance to " O   HOH Z 166 " =    1.948
peak=   -3.584 closest distance to " CA  GLY A 241 " =    2.304
peak=   -3.583 closest distance to " O   HOH Z 351 " =    1.523
peak=   -3.581 closest distance to " CG1 VAL A 197 " =    2.323
peak=   -3.579 closest distance to " CG  TRP A 266 " =    1.755
peak=   -3.578 closest distance to " O   HOH Z 394 " =    1.570
peak=   -3.576 closest distance to " O   HOH Z  10 " =    1.513
peak=   -3.575 closest distance to " CG  ASP A 231 " =    0.780
peak=   -3.570 closest distance to " O   HOH Z  19 " =    2.492
peak=   -3.567 closest distance to " O   HOH Z  73 " =    2.165
peak=   -3.567 closest distance to " OG ASER A 134 " =    1.262
peak=   -3.552 closest distance to " CB  ALA A 291 " =    2.157
peak=   -3.537 closest distance to " O   HOH Z 275 " =    1.508
peak=   -3.531 closest distance to " CG  PRO A 163 " =    2.523
peak=   -3.530 closest distance to " O   HOH Z 435 " =    2.786
peak=   -3.529 closest distance to " OXT GLY A 302 " =    3.030
peak=   -3.527 closest distance to " O   HOH Z 407 " =    3.247
peak=   -3.521 closest distance to " O   HOH Z 211 " =    1.534
peak=   -3.507 closest distance to " CD2 TYR A 293 " =    2.081
peak=   -3.506 closest distance to " ND2 ASN A  45 " =    1.485
peak=   -3.502 closest distance to " CD1 LEU A 101 " =    2.582
peak=   -3.499 closest distance to " CG2 THR A   4 " =    1.954
peak=   -3.496 closest distance to " O   GLY A 211 " =    1.460
peak=   -3.495 closest distance to " CD1 TYR A 247 " =    2.822
peak=   -3.488 closest distance to " ND2 ASN A  45 " =    1.156
peak=   -3.485 closest distance to " OG BSER A 134 " =    1.738
peak=   -3.484 closest distance to " C   LEU A 222 " =    0.803
peak=   -3.477 closest distance to " O   PRO A 198 " =    1.257
peak=   -3.464 closest distance to " O   HOH Z 350 " =    1.703
peak=   -3.463 closest distance to " O   HOH Z  60 " =    2.232
peak=   -3.451 closest distance to " O   HOH Z 231 " =    1.221
peak=   -3.446 closest distance to " CD  ARG A 139 " =    1.622
peak=   -3.441 closest distance to " O   HOH Z  13 " =    1.418
peak=   -3.438 closest distance to " N   SER A 276 " =    1.373
peak=   -3.437 closest distance to " OD1 ASN A 187 " =    1.594
peak=   -3.437 closest distance to " CD1 PHE A  59 " =    1.867
peak=   -3.436 closest distance to " CB  ASP A 132 " =    2.295
peak=   -3.436 closest distance to " O   HOH Z 436 " =    1.522
peak=   -3.433 closest distance to " ND2 ASN A  60 " =    1.499
peak=   -3.418 closest distance to " N   ALA A 226 " =    2.176
peak=   -3.411 closest distance to " CE2 PHE A 218 " =    2.554
peak=   -3.410 closest distance to " O   GLY A 196 " =    1.201
peak=   -3.409 closest distance to " O   GLY A  80 " =    2.522
peak=   -3.407 closest distance to " CB  ALA A 291 " =    2.285
peak=   -3.407 closest distance to " O   HOH Z 198 " =    1.496
peak=   -3.405 closest distance to " O   VAL A  67 " =    2.659
peak=   -3.401 closest distance to " O   HOH Z 184 " =    1.737
peak=   -3.400 closest distance to " CD2 LEU A 167 " =    1.758
peak=   -3.400 closest distance to " CB  PHE A 192 " =    1.814
peak=   -3.399 closest distance to " CE1 TYR A 169 " =    2.486
peak=   -3.395 closest distance to " O   GLY A 203 " =    2.322
peak=   -3.390 closest distance to " O   HOH Z 311 " =    3.849
peak=   -3.386 closest distance to " CB  ASN A  39 " =    2.088
peak=   -3.385 closest distance to " CD2 PHE A  61 " =    1.933
peak=   -3.382 closest distance to " OH  TYR A 214 " =    1.249
peak=   -3.375 closest distance to " O   HOH Z 166 " =    1.523
peak=   -3.373 closest distance to " C   GLY A  17 " =    1.314
peak=   -3.369 closest distance to " CG2 ILE A 263 " =    2.422
peak=   -3.367 closest distance to " CA  GLY A 203 " =    2.362
peak=   -3.366 closest distance to " O   HOH Z 111 " =    2.347
peak=   -3.366 closest distance to " C   ALA A   8 " =    1.570
peak=   -3.358 closest distance to " CE  MET A 105 " =    2.103
peak=   -3.355 closest distance to " CG2 ILE A  49 " =    2.817
peak=   -3.350 closest distance to " CG  HIS A  86 " =    0.891
peak=   -3.343 closest distance to " O   HOH Z 388 " =    2.062
peak=   -3.343 closest distance to " O   PRO A 198 " =    1.431
peak=   -3.336 closest distance to " O   HOH Z 207 " =    2.189
peak=   -3.335 closest distance to " CG  GLN A  88 " =    0.875
peak=   -3.334 closest distance to " CB  VAL A 230 " =    1.059
peak=   -3.329 closest distance to " C   ASN A 285 " =    2.528
peak=   -3.320 closest distance to " O   HOH Z 292 " =    4.641
peak=   -3.320 closest distance to " CA  ASN A 127 " =    1.050
peak=   -3.317 closest distance to " CH2 TRP A 177 " =    2.174
peak=   -3.315 closest distance to " N   SER A 212 " =    2.016
peak=   -3.308 closest distance to " O   HOH Z 372 " =    2.440
peak=   -3.307 closest distance to " CG  PHE A 283 " =    2.835
peak=   -3.307 closest distance to " O   HOH Z 174 " =    2.607
peak=   -3.303 closest distance to " O   HOH Z 102 " =    1.716
peak=   -3.303 closest distance to " CD1 ILE A 151 " =    2.356
peak=   -3.299 closest distance to " OE1 GLN A  88 " =    1.128
peak=   -3.295 closest distance to " ND2BASN A 224 " =    1.679
peak=   -3.293 closest distance to " O   HOH Z 185 " =    2.325
peak=   -3.290 closest distance to " N   GLN A  58 " =    1.526
peak=   -3.289 closest distance to " O   HOH Z 417 " =    2.870
peak=   -3.288 closest distance to " CZ  PHE A  59 " =    1.592
peak=   -3.286 closest distance to " O   MET A  40 " =    2.759
peak=   -3.278 closest distance to " O   HOH Z  90 " =    3.174
peak=   -3.274 closest distance to " CB  ASP A 132 " =    2.267
peak=   -3.272 closest distance to " SD BMET A  47 " =    0.972
peak=   -3.268 closest distance to " OG  SER A 206 " =    1.798
peak=   -3.268 closest distance to " O   HOH Z 241 " =    1.252
peak=   -3.267 closest distance to " O   HOH Z 191 " =    5.551
peak=   -3.266 closest distance to " O   HOH Z 128 " =    4.176
peak=   -3.262 closest distance to " CG2 VAL A 112 " =    2.588
peak=   -3.261 closest distance to " NH1 ARG A 195 " =    2.630
peak=   -3.257 closest distance to " O   HOH Z  90 " =    1.500
peak=   -3.254 closest distance to " CB  ALA A 248 " =    2.008
peak=   -3.253 closest distance to " CD  GLN A 223 " =    1.370
peak=   -3.247 closest distance to " O   HOH Z 117 " =    4.601
peak=   -3.247 closest distance to " O   HOH Z 243 " =    1.932
peak=   -3.245 closest distance to " OG  SER A  62 " =    1.743
peak=   -3.244 closest distance to " O   HOH Z  60 " =    1.842
peak=   -3.240 closest distance to " O   HOH Z 396 " =    1.771
peak=   -3.231 closest distance to " CA  SER A 135 " =    1.355
peak=   -3.230 closest distance to " CD1 TYR A 247 " =    2.347
peak=   -3.222 closest distance to " CD  ARG A 195 " =    5.088
peak=   -3.222 closest distance to " C   LEU A 143 " =    1.245
peak=   -3.220 closest distance to " CE3 TRP A 150 " =    2.109
peak=   -3.216 closest distance to " ND2 ASN A 249 " =    2.390
peak=   -3.216 closest distance to " O   HOH Z 234 " =    4.356
peak=   -3.214 closest distance to " CA  GLY A 133 " =    2.247
peak=   -3.214 closest distance to " O   HOH Z 310 " =    2.036
peak=   -3.210 closest distance to " O   VAL A 125 " =    2.281
peak=   -3.205 closest distance to " CB  TRP A  85 " =    2.462
peak=   -3.204 closest distance to " CD1 ILE A 199 " =    2.606
peak=   -3.199 closest distance to " CE BMET A  47 " =    1.778
peak=   -3.199 closest distance to " O   HOH Z 359 " =    3.186
peak=   -3.191 closest distance to " O   HOH Z 128 " =    2.495
peak=   -3.184 closest distance to " O   HOH Z 140 " =    1.649
peak=   -3.179 closest distance to " OD2 ASP A  50 " =    2.339
peak=   -3.178 closest distance to " OD2 ASP A 171 " =    1.790
peak=   -3.176 closest distance to " O   HOH Z   6 " =    1.843
peak=   -3.170 closest distance to " N   ASN A  60 " =    1.312
peak=   -3.168 closest distance to " NH2 ARG A  66 " =    2.104
peak=   -3.168 closest distance to " OD1 ASP A 191 " =    1.582
peak=   -3.168 closest distance to " C   GLN A 240 " =    2.398
peak=   -3.164 closest distance to " O   HOH Z  51 " =    1.343
peak=   -3.162 closest distance to " CB  TYR A  15 " =    2.248
peak=   -3.159 closest distance to " O   HOH Z 123 " =    2.406
peak=   -3.156 closest distance to " CG  GLU A   2 " =    1.923
peak=   -3.155 closest distance to " CB  ALA A 227 " =    2.418
peak=   -3.154 closest distance to " NH2 ARG A  79 " =    1.979
peak=   -3.152 closest distance to " O   HOH Z 139 " =    3.022
peak=   -3.149 closest distance to " O   HOH Z 222 " =    1.523
peak=   -3.148 closest distance to " O   HOH Z  44 " =    2.141
peak=   -3.138 closest distance to " O   HOH Z 281 " =    2.579
peak=   -3.135 closest distance to " O   ASN A 301 " =    1.419
peak=   -3.125 closest distance to " N   PHE A  59 " =    2.103
peak=   -3.125 closest distance to " CZ  PHE A  38 " =    2.352
peak=   -3.118 closest distance to " SG ACYS A 201 " =    2.017
peak=   -3.117 closest distance to " O   HOH Z 189 " =    2.010
peak=   -3.114 closest distance to " CG  GLU A 277 " =    1.191
peak=   -3.109 closest distance to " O   HOH Z 369 " =    2.254
peak=   -3.107 closest distance to " NH2BARG A 275 " =    1.824
peak=   -3.104 closest distance to " O   TRP A  70 " =    1.518
peak=   -3.095 closest distance to " C   MET A 188 " =    1.397
peak=   -3.079 closest distance to " CG1 VAL A 112 " =    2.899
peak=   -3.074 closest distance to " N   MET A 105 " =    2.686
peak=   -3.071 closest distance to " OE1 GLN A  77 " =    1.925
peak=   -3.069 closest distance to " CD2 TYR A 247 " =    2.244
peak=   -3.060 closest distance to " N   ALA A 248 " =    2.510
peak=   -3.054 closest distance to " CE  MET A  93 " =    1.255
peak=   -3.048 closest distance to " CZ  TYR A 169 " =    1.677
peak=   -3.011 closest distance to " O   HOH Z 170 " =    1.947

================= 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    :  0.4401 0.4302   6.238664e+00   6.220717e+00
   1_bss:  0.4323 0.4187   6.233208e+00   6.209903e+00
   1_xyz:  0.3290 0.3570   6.044218e+00   6.103207e+00
   1_adp:  0.2705 0.3105   5.890531e+00   6.009817e+00
   1_occ:  0.2699 0.3106   5.889703e+00   6.011123e+00
   2_bss:  0.2658 0.3054   5.889181e+00   6.008849e+00
   2_xyz:  0.1835 0.2315   5.561014e+00   5.745484e+00
   2_adp:  0.1659 0.2141   5.471997e+00   5.670290e+00
   2_occ:  0.1657 0.2140   5.471680e+00   5.670051e+00
   3_bss:  0.1643 0.2111   5.469205e+00   5.667197e+00
   3_xyz:  0.1305 0.1778   5.275296e+00   5.505547e+00
   3_adp:  0.1219 0.1706   5.221895e+00   5.464316e+00
   3_occ:  0.1219 0.1706   5.222028e+00   5.464656e+00
   4_bss:  0.1221 0.1700   5.221102e+00   5.462130e+00
   4_xyz:  0.1160 0.1653   5.184656e+00   5.433360e+00
   4_adp:  0.1157 0.1629   5.176632e+00   5.419962e+00
   4_occ:  0.1157 0.1628   5.176348e+00   5.419570e+00
   5_bss:  0.1157 0.1628   5.176340e+00   5.419511e+00
   5_xyz:  0.1122 0.1606   5.156428e+00   5.408027e+00
   5_adp:  0.1114 0.1616   5.157122e+00   5.414754e+00
   5_occ:  0.1113 0.1615   5.157083e+00   5.414755e+00
   5_bss:  0.1113 0.1615   5.157134e+00   5.414770e+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:  0.335  20.001   9.807   7.677   7.647   0.000   0.000   0.000
   1_xyz:  0.335  20.001   9.807   7.677   7.647   0.000   0.000   0.000
   1_adp:  0.335  20.001   9.807   7.677   7.647   0.000   0.000   0.000
   1_occ:  0.335  20.001   9.807   7.677   7.647   0.000   0.000   0.000
   2_bss:  0.337  45.968   6.210   4.196   5.008   0.000   0.000   0.000
   2_xyz:  0.337  45.968   6.210   4.196   5.008   0.000   0.000   0.000
   2_adp:  0.337  45.968   6.210   4.196   5.008   0.000   0.000   0.000
   2_occ:  0.337  45.968   6.210   4.196   5.008   0.000   0.000   0.000
   3_bss:  0.338  52.552   3.889   3.151   4.039   0.000   0.000   0.000
   3_xyz:  0.338  52.552   3.889   3.151   4.039   0.000   0.000   0.000
   3_adp:  0.338  52.552   3.889   3.151   4.039   0.000   0.000   0.000
   3_occ:  0.338  52.552   3.889   3.151   4.039   0.000   0.000   0.000
   4_bss:  0.327  52.552   3.368   2.932   3.820   0.000   0.000   0.000
   4_xyz:  0.327  52.552   3.368   2.932   3.820   0.000   0.000   0.000
   4_adp:  0.327  52.552   3.368   2.932   3.820   0.000   0.000   0.000
   4_occ:  0.327  52.552   3.368   2.932   3.820   0.000   0.000   0.000
   5_bss:  0.327  52.552   3.242   2.944   3.817   0.000   0.000   0.000
   5_xyz:  0.327  52.552   3.242   2.944   3.817   0.000   0.000   0.000
   5_adp:  0.327  52.552   3.242   2.944   3.817   0.000   0.000   0.000
   5_occ:  0.327  52.552   3.242   2.944   3.817   0.000   0.000   0.000
   5_bss:  0.327  55.972  -0.105  -0.387   0.492   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  48.623 0.5392  0.6067    54921.486
   1_bss:  48.573 0.5378  0.7762    52436.885
   1_xyz:  39.539 0.6468  0.9082    36079.379
   1_adp:  32.635 0.7287  1.0075    26729.493
   1_occ:  32.655 0.7283  1.0066    26781.617
   2_bss:  32.478 0.7304  0.8998    26584.948
   2_xyz:  22.577 0.8361  0.9938    13680.418
   2_adp:  20.323 0.8590  1.0144    11678.448
   2_occ:  20.325 0.8589  1.0142    11678.932
   3_bss:  20.227 0.8599  0.9629    11577.146
   3_xyz:  16.438 0.8945  0.9812     8161.742
   3_adp:  15.531 0.9025  0.9835     7479.394
   3_occ:  15.537 0.9024  0.9833     7481.567
   4_bss:  15.494 0.9027  0.9714     7415.365
   4_xyz:  14.843 0.9083  0.9729     6922.657
   4_adp:  14.505 0.9112  0.9733     6748.855
   4_occ:  14.500 0.9113  0.9731     6739.430
   5_bss:  14.500 0.9113  0.9717     6737.891
   5_xyz:  14.280 0.9130  0.9725     6580.190
   5_adp:  14.407 0.9120  0.9692     6654.158
   5_occ:  14.407 0.9120  0.9692     6652.154
   5_bss:  14.408 0.9120  0.9721     6652.555
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4044e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4044e+01
   1_xyz:   1.559  0.012  0.103 18.032  0.006  4.124   1.2387e-01
   1_adp:   1.559  0.012  0.103 18.032  0.006  4.124   1.2387e-01
   1_occ:   1.559  0.012  0.103 18.032  0.006  4.124   1.2387e-01
   2_bss:   1.559  0.012  0.103 18.032  0.006  4.124   1.2387e-01
   2_xyz:   1.052  0.008  0.075 16.497  0.005  4.130   7.1941e-02
   2_adp:   1.052  0.008  0.075 16.497  0.005  4.130   7.1941e-02
   2_occ:   1.052  0.008  0.075 16.497  0.005  4.130   7.1941e-02
   3_bss:   1.052  0.008  0.075 16.497  0.005  4.130   7.1941e-02
   3_xyz:   1.112  0.008  0.086 16.243  0.004  4.114   7.4284e-02
   3_adp:   1.112  0.008  0.086 16.243  0.004  4.114   7.4284e-02
   3_occ:   1.112  0.008  0.086 16.243  0.004  4.114   7.4284e-02
   4_bss:   1.112  0.008  0.086 16.243  0.004  4.114   7.4284e-02
   4_xyz:   1.080  0.009  0.085 16.076  0.004  4.118   7.1344e-02
   4_adp:   1.080  0.009  0.085 16.076  0.004  4.118   7.1344e-02
   4_occ:   1.080  0.009  0.085 16.076  0.004  4.118   7.1344e-02
   5_bss:   1.080  0.009  0.085 16.076  0.004  4.118   7.1344e-02
   5_xyz:   1.105  0.010  0.089 15.872  0.004  4.122   7.5230e-02
   5_adp:   1.105  0.010  0.089 15.872  0.004  4.122   7.5230e-02
   5_occ:   1.105  0.010  0.089 15.872  0.004  4.122   7.5230e-02
   5_bss:   1.105  0.010  0.089 15.872  0.004  4.122   7.5230e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0077e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0077e+00
   1_xyz:  12.844  0.148  0.417 86.316  0.039  2.243   9.3311e-02
   1_adp:  12.844  0.148  0.417 86.316  0.039  2.243   9.3311e-02
   1_occ:  12.844  0.148  0.417 86.316  0.039  2.243   9.3311e-02
   2_bss:  12.844  0.148  0.417 86.316  0.039  2.243   9.3311e-02
   2_xyz:   7.005  0.096  0.245 86.837  0.042  2.301   6.5488e-02
   2_adp:   7.005  0.096  0.245 86.837  0.042  2.301   6.5488e-02
   2_occ:   7.005  0.096  0.245 86.837  0.042  2.301   6.5488e-02
   3_bss:   7.005  0.096  0.245 86.837  0.042  2.301   6.5488e-02
   3_xyz:   8.941  0.064  0.510 82.182  0.038  2.343   6.0285e-02
   3_adp:   8.941  0.064  0.510 82.182  0.038  2.343   6.0285e-02
   3_occ:   8.941  0.064  0.510 82.182  0.038  2.343   6.0285e-02
   4_bss:   8.941  0.064  0.510 82.182  0.038  2.343   6.0285e-02
   4_xyz:   8.677  0.064  0.548 83.864  0.040  2.331   4.6582e-02
   4_adp:   8.677  0.064  0.548 83.864  0.040  2.331   4.6582e-02
   4_occ:   8.677  0.064  0.548 83.864  0.040  2.331   4.6582e-02
   5_bss:   8.677  0.064  0.548 83.864  0.040  2.331   4.6582e-02
   5_xyz:   8.030  0.048  0.624 83.838  0.041  2.324   5.3818e-02
   5_adp:   8.030  0.048  0.624 83.838  0.041  2.324   5.3818e-02
   5_occ:   8.030  0.048  0.624 83.838  0.041  2.324   5.3818e-02
   5_bss:   8.030  0.048  0.624 83.838  0.041  2.324   5.3818e-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:  54.09   0.00  10.45  52.37   0.00   7.58  54.09   0.00  26.09
   1_occ:  54.09   0.00  10.45  52.37   0.00   7.58  54.09   0.00  26.09
   2_bss:  54.09   0.00  10.45  52.37   0.00   7.58  54.09   0.00  26.09
   2_xyz:  54.09   0.00  10.45  52.37   0.00   7.58  54.09   0.00  26.09
   2_adp:  81.63   0.00  10.99  81.63   0.00   7.46  58.25   0.58  30.25
   2_occ:  81.63   0.00  10.99  81.63   0.00   7.46  58.25   0.58  30.25
   3_bss:  81.63   0.00  10.99  81.63   0.00   7.46  58.25   0.58  30.25
   3_xyz:  81.63   0.00  10.99  81.63   0.00   7.46  58.25   0.58  30.25
   3_adp:  81.41   0.00  12.15  74.44   0.00   7.78  81.41   0.86  35.99
   3_occ:  81.41   0.00  12.15  74.44   0.00   7.78  81.41   0.86  35.99
   4_bss:  81.41   0.00  12.15  74.44   0.00   7.78  81.41   0.86  35.99
   4_xyz:  81.41   0.00  12.15  74.44   0.00   7.78  81.41   0.86  35.99
   4_adp:  80.17   0.00  11.85  75.83   0.00   7.64  80.17   1.23  34.76
   4_occ:  80.17   0.00  11.85  75.83   0.00   7.64  80.17   1.23  34.76
   5_bss:  80.17   0.00  11.85  75.83   0.00   7.64  80.17   1.23  34.76
   5_xyz:  80.17   0.00  11.85  75.83   0.00   7.64  80.17   1.23  34.76
   5_adp:  82.09   0.00  11.90  77.92   0.00   7.64  82.09   1.33  35.10
   5_occ:  82.09   0.00  11.90  77.92   0.00   7.64  82.09   1.33  35.10
   5_bss:  85.51   3.42  15.32  81.34   3.42  11.06  85.51   4.75  38.52
------------------------------------------------------------------------
 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:    1.175    0.018    0.406
   1_adp:    1.175    0.018    0.406
   1_occ:    1.175    0.018    0.406
   2_bss:    1.175    0.018    0.406
   2_xyz:    1.420    0.032    0.535
   2_adp:    1.420    0.032    0.535
   2_occ:    1.420    0.032    0.535
   3_bss:    1.420    0.032    0.535
   3_xyz:    1.422    0.019    0.576
   3_adp:    1.422    0.019    0.576
   3_occ:    1.422    0.019    0.576
   4_bss:    1.422    0.019    0.576
   4_xyz:    1.666    0.028    0.592
   4_adp:    1.666    0.028    0.592
   4_occ:    1.666    0.028    0.592
   5_bss:    1.666    0.028    0.592
   5_xyz:    1.720    0.024    0.599
   5_adp:    1.720    0.024    0.599
   5_occ:    1.720    0.024    0.599
   5_bss:    1.720    0.024    0.599
------------------------------------------------------------------------

CPU time actual refinement: 338.64


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1148/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_1148/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1148/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1148/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1148/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 338.48 
  Macro-tasks:
    bulk solvent and scale       = 41.56  
    individual site refinement   = 138.00 
    weights calculation          = 33.39  
    collect and process          = 6.76   
    model show statistics        = 0.15   
    TOTAL for macro-tasks        = 219.86 
  Micro-tasks:
    mask                            = 1.76   
    f_calc                          = 104.00 
    alpha_beta                      = 8.47   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 113.85 
    fmodel                         = 7.84   
    r_factors                      = 0.21   
    phase_errors                   = 10.92  
    foms                           = 0.19   
    TOTAL for micro-tasks          = 248.41 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.728 micro seconds
Total CPU time: 5.87 minutes
from_scatterers_fft:    654 calls, 103.72 s
gradients_fft:          598 calls, 100.17 s

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

# Date 2008-01-16 Time 03:19:17 PST -0800 (1200482357.57 s)
Start R-work = 0.4401, R-free = 0.4302 (no bulk solvent and anisotropic scale)
Final R-work = 0.1282, R-free = 0.1773 (no bulk solvent and anisotropic scale)

Start R-work = 0.4323, R-free = 0.4187
Final R-work = 0.1113, R-free = 0.1615