# Date 2008-01-16 Time 05:01:34 PST -0800 (1200488494.26 s)
#phil __OFF__

Command line arguments: "../562.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 23966
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 562

-------------------------------------------------------------------------------
  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.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 47.3993, 84.6622, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.3993, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.857 1.96136
Completeness in resolution range: 0.94505
Completeness with d_max=infinity: 0.942141

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8570
                             d_min =   1.9614

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 47.3993, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.857 1.96136
Completeness in resolution range: 0.94505
Completeness with d_max=infinity: 0.942141

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8574 -  4.1968 [2183/2211]  1965   218  10.0%
  bin  2:  4.1968 -  3.3436 [2080/2103]  1872   208  10.0%
  bin  3:  3.3436 -  2.9247 [2058/2083]  1848   210  10.2%
  bin  4:  2.9247 -  2.6589 [2049/2065]  1851   198   9.7%
  bin  5:  2.6589 -  2.4693 [2035/2073]  1826   209  10.3%
  bin  6:  2.4693 -  2.3243 [2022/2055]  1828   194   9.6%
  bin  7:  2.3243 -  2.2082 [1992/2029]  1788   204  10.2%
  bin  8:  2.2082 -  2.1124 [2000/2042]  1800   200  10.0%
  bin  9:  2.1124 -  2.0313 [2007/2045]  1807   200  10.0%
  bin 10:  2.0313 -  1.9614 [1163/2022]  1045   118  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_562/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:
        1.70 -     2.34: 30
        2.34 -     2.98: 1838
        2.98 -     3.62: 4619
        3.62 -     4.26: 9221
        4.26 -     4.90: 12828
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.704 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.770 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.780 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.832 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28531 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 =====================


==================== 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/noshake/run_562/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_562/model_refine_001.geo

CPU time processing inputs: 9.08


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 47.3993 84.6622 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
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3819   r_free= 0.3777   ksol= 0.00   Bsol= 0.00   scale= 0.950    |
|                                                                             |
| 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:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.164590                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8574 -  4.6809 0.99   1412  157 0.3109 0.3218       6.421      6.4086|
|  2:  4.6809 -  3.7348 0.99   1365  147 0.3095 0.2933      6.5929      6.5676|
|  3:  3.7348 -  3.2685 0.99   1325  155 0.3319 0.3217      6.4742      6.5704|
|  4:  3.2685 -  2.9722 0.99   1330  146 0.3556 0.3451      6.3458      6.3218|
|  5:  2.9722 -  2.7606 0.98   1317  147 0.3817 0.3397      6.2195      6.1618|
|  6:  2.7606 -  2.5988 0.99   1303  143 0.4038 0.4039      6.1573       6.055|
|  7:  2.5988 -  2.4693 0.99   1310  148 0.4093 0.3679      6.1389      6.0758|
|  8:  2.4693 -  2.3622 0.99   1289  141 0.4215 0.4562       6.081      6.1306|
|  9:  2.3622 -  2.2716 0.99   1298  145 0.4357 0.4346      6.0542       6.067|
| 10:  2.2716 -  2.1935 0.98   1292  140 0.4424 0.4698      6.0289      6.0694|
| 11:  2.1935 -  2.1251 0.98   1274  142 0.4500 0.4705      5.9724      6.0376|
| 12:  2.1251 -  2.0645 1.00   1293  144 0.4340 0.4783       5.903      5.9446|
| 13:  2.0645 -  2.0103 0.96   1265  138 0.4684 0.4402      5.8223      5.8196|
| 14:  2.0103 -  1.9614 0.43    557   66 0.4955 0.4404      5.8328      5.6838|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8574 -  4.6809  1412   157  0.75  29.54   0.86     0.77      53045.70|
|  2:  4.6809 -  3.7348  1365   147  0.79  26.79   0.96     0.88      63452.91|
|  3:  3.7348 -  3.2685  1325   155  0.75  31.41   0.97     0.91      63658.55|
|  4:  3.2685 -  2.9722  1330   146  0.70  35.78   0.98     0.90      55556.45|
|  5:  2.9722 -  2.7606  1317   147  0.66  39.19   0.95     0.87      45074.81|
|  6:  2.7606 -  2.5988  1303   143  0.64  40.77   0.97     0.85      39338.59|
|  7:  2.5988 -  2.4693  1310   148  0.64  41.09   0.97     0.83      37289.37|
|  8:  2.4693 -  2.3622  1289   141  0.57  46.49   0.97     0.78      39025.72|
|  9:  2.3622 -  2.2716  1298   145  0.53  50.06   0.99     0.73      38534.61|
| 10:  2.2716 -  2.1935  1292   140  0.48  53.56   1.02     0.68      39753.12|
| 11:  2.1935 -  2.1251  1274   142  0.46  55.37   0.99     0.67      37611.99|
| 12:  2.1251 -  2.0645  1293   144  0.46  55.26   1.02     0.70      35600.43|
| 13:  2.0645 -  2.0103  1265   138  0.47  54.51   0.98     0.72      28309.40|
| 14:  2.0103 -  1.9614   557    66  0.54  48.66   0.97     0.76      20810.58|
|alpha:            min =        0.67 max =            0.91 mean =         0.79|
|beta:             min =    20810.58 max =        63658.55 mean =     43803.59|
|figures of merit: min =        0.00 max =            1.00 mean =         0.61|
|phase err.(work): min =        0.00 max =           89.98 mean =        43.01|
|phase err.(test): min =        0.00 max =           89.94 mean =        42.80|
|-----------------------------------------------------------------------------|

============================== 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 = 7.239363              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.495   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.220421              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.848   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.704 -  2.024:        9 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.024 -  2.343:       21 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.343 -  2.663:       72 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.663 -  2.983:     1766 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.983 -  3.302:     1937 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.302 -  3.622:     2682 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.622 -  3.941:     4722 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.941 -  4.261:     4499 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.261 -  4.580:     5825 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.580 -  4.900:     7003 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.174 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.704 |       0.363 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.718)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    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:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3819   r_free= 0.3777   ksol= 0.00   Bsol= 0.00   scale= 0.950    |
|                                                                             |
| 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:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.164590                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3694   r_free= 0.3634   ksol= 0.34   Bsol= 50.00   scale= 0.968   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.24,0.20,2.17,0.00,0.00,0.00); trace/3= -0.29                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.150508                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.189057              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.240   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.608907              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.818   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3694      final r-factor (work) = 0.2129          |
| start r-factor (free) = 0.3634      final r-factor (free) = 0.2361          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.2099 = 6.19 * 0.50 * 6.1515 + 1.00 * 0.1739                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.3465 = 6.19 * 0.50 * 5.8998 + 1.00 * 0.0895                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2129      final r-factor (work) = 0.1933          |
| start r-factor (free) = 0.2361      final r-factor (free) = 0.2476          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5988 = 0.61 * 1.00 * 5.8998 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4212 = 0.61 * 1.00 * 5.5954 + 1.00 * 0.0141                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.718)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.92   17.74    None  None   None       |
|    all(noH): 2823   0      0.00    80.92   17.74    None  None   None       |
|    Sol.    : 438    0      6.45    78.72   40.65    None  None   None       |
|    Mac.    : 2385   0      0.00    80.92   13.53    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 -   8.092:  624   |   5:    40.458 -  48.549:  116        |
|      1:     8.092 -  16.183: 1216   |   6:    48.549 -  56.641:   89        |
|      2:    16.183 -  24.275:  411   |   7:    56.641 -  64.732:   51        |
|      3:    24.275 -  32.366:  157   |   8:    64.732 -  72.824:   25        |
|      4:    32.366 -  40.458:  124   |   9:    72.824 -  80.915:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1933 r_free = 0.2476             target_work(ml) = 5.612         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1928 r_free = 0.2481             target_work(ml) = 5.611         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1928   r_free= 0.2481   ksol= 0.34   Bsol= 50.00   scale= 1.039   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.24,0.20,2.17,0.00,0.00,0.00); trace/3= -0.29                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.611192                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1892   r_free= 0.2450   ksol= 0.32   Bsol= 47.62   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.11,-1.38,-0.76,-0.00,-0.00,-0.00); trace/3= -1.75                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.601656                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.569718              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.503   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.244366              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.156   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1892      final r-factor (work) = 0.1385          |
| start r-factor (free) = 0.2450      final r-factor (free) = 0.1853          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0915 = 3.57 * 0.50 * 5.6038 + 1.00 * 0.0895                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8355 = 3.57 * 0.50 * 5.4769 + 1.00 * 0.0600                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1385      final r-factor (work) = 0.1285          |
| start r-factor (free) = 0.1853      final r-factor (free) = 0.1719          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3538 = 0.24 * 1.00 * 5.4769 + 1.00 * 0.0154                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3003 = 0.24 * 1.00 * 5.2876 + 1.00 * 0.0082                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.718)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.71    82.18   17.26    None  None   None       |
|    all(noH): 2823   0      1.71    82.18   17.26    None  None   None       |
|    Sol.    : 438    0      6.43    77.11   39.92    None  None   None       |
|    Mac.    : 2385   0      1.71    82.18   13.10    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.709 -   9.756:  947   |   5:    41.945 -  49.992:  124        |
|      1:     9.756 -  17.803: 1102   |   6:    49.992 -  58.039:   77        |
|      2:    17.803 -  25.850:  271   |   7:    58.039 -  66.086:   31        |
|      3:    25.850 -  33.898:  134   |   8:    66.086 -  74.134:   22        |
|      4:    33.898 -  41.945:  108   |   9:    74.134 -  82.181:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1285 r_free = 0.1719             target_work(ml) = 5.250         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1284 r_free = 0.1716             target_work(ml) = 5.249         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1284   r_free= 0.1716   ksol= 0.32   Bsol= 47.62   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.11,-1.38,-0.76,-0.00,-0.00,-0.00); trace/3= -1.75                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.249410                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1285   r_free= 0.1703   ksol= 0.32   Bsol= 46.14   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.85,-1.77,-1.54,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.247296                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.478778              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 119.841  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.236430              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.213  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1285      final r-factor (work) = 0.1146          |
| start r-factor (free) = 0.1703      final r-factor (free) = 0.1579          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6139 = 2.48 * 0.50 * 5.2882 + 1.00 * 0.0598                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5056 = 2.48 * 0.50 * 5.2001 + 1.00 * 0.0606                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1146      final r-factor (work) = 0.1121          |
| start r-factor (free) = 0.1579      final r-factor (free) = 0.1566          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2376 = 0.24 * 1.00 * 5.2001 + 1.00 * 0.0082                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2247 = 0.24 * 1.00 * 5.1473 + 1.00 * 0.0077                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.718)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.05    83.95   16.92    None  None   None       |
|    all(noH): 2823   0      2.05    83.95   16.92    None  None   None       |
|    Sol.    : 438    0      5.79    76.01   38.81    None  None   None       |
|    Mac.    : 2385   0      2.05    83.95   12.90    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.055 -  10.244: 1043   |   5:    43.002 -  51.191:  104        |
|      1:    10.244 -  18.434: 1081   |   6:    51.191 -  59.381:   77        |
|      2:    18.434 -  26.623:  229   |   7:    59.381 -  67.570:   23        |
|      3:    26.623 -  34.813:  130   |   8:    67.570 -  75.760:   14        |
|      4:    34.813 -  43.002:  118   |   9:    75.760 -  83.949:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1121 r_free = 0.1566             target_work(ml) = 5.142         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1120 r_free = 0.1565             target_work(ml) = 5.142         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1120   r_free= 0.1565   ksol= 0.32   Bsol= 46.14   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.85,-1.77,-1.54,-0.00,-0.00,-0.00); trace/3= -2.05                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.141810                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1120   r_free= 0.1564   ksol= 0.32   Bsol= 46.14   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.75,-1.89,-1.72,-0.00,-0.00,-0.00); trace/3= -2.12                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.141419                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.952354              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 143.384  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.399496              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 154.039  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1120      final r-factor (work) = 0.1074          |
| start r-factor (free) = 0.1564      final r-factor (free) = 0.1542          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6583 = 2.95 * 0.50 * 5.1469 + 1.00 * 0.0606                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6315 = 2.95 * 0.50 * 5.1238 + 1.00 * 0.0678                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1074      final r-factor (work) = 0.1066          |
| start r-factor (free) = 0.1542      final r-factor (free) = 0.1547          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0546 = 0.40 * 1.00 * 5.1238 + 1.00 * 0.0076                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0502 = 0.40 * 1.00 * 5.1117 + 1.00 * 0.0081                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.718)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.49    88.46   16.81    None  None   None       |
|    all(noH): 2823   0      1.49    88.46   16.81    None  None   None       |
|    Sol.    : 438    0      5.66    76.72   38.81    None  None   None       |
|    Mac.    : 2385   0      1.49    88.46   12.77    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.492 -  10.188: 1071   |   5:    44.975 -  53.671:  107        |
|      1:    10.188 -  18.885: 1080   |   6:    53.671 -  62.368:   54        |
|      2:    18.885 -  27.582:  224   |   7:    62.368 -  71.064:   20        |
|      3:    27.582 -  36.278:  130   |   8:    71.064 -  79.761:    9        |
|      4:    36.278 -  44.975:  125   |   9:    79.761 -  88.457:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1066 r_free = 0.1547             target_work(ml) = 5.115         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1066 r_free = 0.1547             target_work(ml) = 5.115         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1066   r_free= 0.1547   ksol= 0.32   Bsol= 46.14   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.75,-1.89,-1.72,-0.00,-0.00,-0.00); trace/3= -2.12                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.115127                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1065   r_free= 0.1547   ksol= 0.32   Bsol= 46.14   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.57,-1.78,-1.61,-0.00,-0.00,-0.00); trace/3= -1.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.115162                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.185779              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 162.551  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.797396              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.848  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1065      final r-factor (work) = 0.1074          |
| start r-factor (free) = 0.1547      final r-factor (free) = 0.1554          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6547 = 2.19 * 0.50 * 5.1121 + 1.00 * 0.0678                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6538 = 2.19 * 0.50 * 5.1196 + 1.00 * 0.0587                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1074      final r-factor (work) = 0.1068          |
| start r-factor (free) = 0.1554      final r-factor (free) = 0.1568          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.2100 = 1.80 * 1.00 * 5.1196 + 1.00 * 0.0081                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.2121 = 1.80 * 1.00 * 5.1199 + 1.00 * 0.0095                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.718)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.52    103.62  16.99    None  None   None       |
|    all(noH): 2823   0      0.52    103.62  16.99    None  None   None       |
|    Sol.    : 438    0      5.44    83.18   40.01    None  None   None       |
|    Mac.    : 2385   0      0.52    103.62  12.76    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:     0.517 -  10.827: 1269   |   5:    52.068 -  62.378:   83        |
|      1:    10.827 -  21.137:  966   |   6:    62.378 -  72.689:   34        |
|      2:    21.137 -  31.448:  195   |   7:    72.689 -  82.999:    9        |
|      3:    31.448 -  41.758:  130   |   8:    82.999 -  93.309:    6        |
|      4:    41.758 -  52.068:  130   |   9:    93.309 - 103.619:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1068 r_free = 0.1568             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1068 r_free = 0.1569             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1068   r_free= 0.1569   ksol= 0.32   Bsol= 46.14   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.57,-1.78,-1.61,-0.00,-0.00,-0.00); trace/3= -1.99                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.127014                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8574 -  4.6809 0.99   1412  157 0.0962 0.1257      5.3578      5.5118|
|  2:  4.6809 -  3.7348 0.99   1365  147 0.0808 0.1076      5.3924      5.6083|
|  3:  3.7348 -  3.2685 0.99   1325  155 0.1009 0.1507       5.435      5.8249|
|  4:  3.2685 -  2.9722 0.99   1330  146 0.1181 0.1504      5.4373      5.6005|
|  5:  2.9722 -  2.7606 0.98   1317  147 0.1238 0.1778      5.2938      5.5046|
|  6:  2.7606 -  2.5988 0.99   1303  143 0.1174 0.1868      5.1871      5.4236|
|  7:  2.5988 -  2.4693 0.99   1310  148 0.1183 0.1655      5.1202      5.3843|
|  8:  2.4693 -  2.3622 0.99   1289  141 0.1100 0.1684      5.0434      5.2541|
|  9:  2.3622 -  2.2716 0.99   1298  145 0.1114 0.1868      5.0073      5.3388|
| 10:  2.2716 -  2.1935 0.98   1292  140 0.1074 0.1781       4.952      5.2051|
| 11:  2.1935 -  2.1251 0.98   1274  142 0.1090 0.1760      4.9173      5.2598|
| 12:  2.1251 -  2.0645 1.00   1293  144 0.1041 0.1623      4.8435      5.1071|
| 13:  2.0645 -  2.0103 0.96   1265  138 0.1101 0.1820      4.7805      5.0893|
| 14:  2.0103 -  1.9614 0.43    557   66 0.1060 0.1665      4.7024      4.9081|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8574 -  4.6809  1412   157  0.94   8.72   0.98     0.96       6753.11|
|  2:  4.6809 -  3.7348  1365   147  0.95   7.63   1.02     1.00       8332.37|
|  3:  3.7348 -  3.2685  1325   155  0.94  10.85   1.03     1.03       9803.18|
|  4:  3.2685 -  2.9722  1330   146  0.92  13.97   1.01     0.99      10397.83|
|  5:  2.9722 -  2.7606  1317   147  0.90  15.69   0.99     0.97       8088.61|
|  6:  2.7606 -  2.5988  1303   143  0.90  15.76   0.98     0.96       6898.56|
|  7:  2.5988 -  2.4693  1310   148  0.91  14.74   0.99     0.96       5715.90|
|  8:  2.4693 -  2.3622  1289   141  0.91  15.25   0.99     0.97       5338.90|
|  9:  2.3622 -  2.2716  1298   145  0.91  15.30   1.00     0.96       4887.47|
| 10:  2.2716 -  2.1935  1292   140  0.90  15.72   0.99     0.95       4480.76|
| 11:  2.1935 -  2.1251  1274   142  0.90  16.36   1.00     0.96       4338.72|
| 12:  2.1251 -  2.0645  1293   144  0.92  14.63   0.99     0.98       3774.67|
| 13:  2.0645 -  2.0103  1265   138  0.90  16.69   1.00     0.99       3446.56|
| 14:  2.0103 -  1.9614   557    66  0.90  15.88   0.98     0.94       2847.55|
|alpha:            min =        0.94 max =            1.03 mean =         0.97|
|beta:             min =     2847.55 max =        10397.83 mean =      6252.17|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        13.94|
|phase err.(test): min =        0.00 max =           89.68 mean =        13.55|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1069   r_free= 0.1568   ksol= 0.32   Bsol= 46.26   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.34,-1.58,-1.44,-0.00,-0.00,-0.00); trace/3= -1.79                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.127526                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1069   r_free= 0.1568   ksol= 0.32   Bsol= 46.26   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.34,-1.58,-1.44,-0.00,-0.00,-0.00); trace/3= -1.79                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.127526                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8574 -  4.6809 0.99   1412  157 0.0959 0.1279      5.3617      5.5164|
|  2:  4.6809 -  3.7348 0.99   1365  147 0.0818 0.1067      5.4014      5.6153|
|  3:  3.7348 -  3.2685 0.99   1325  155 0.1008 0.1509      5.4361      5.8228|
|  4:  3.2685 -  2.9722 0.99   1330  146 0.1180 0.1491      5.4357      5.5931|
|  5:  2.9722 -  2.7606 0.98   1317  147 0.1239 0.1780       5.292      5.5034|
|  6:  2.7606 -  2.5988 0.99   1303  143 0.1173 0.1869      5.1857      5.4212|
|  7:  2.5988 -  2.4693 0.99   1310  148 0.1180 0.1657      5.1173      5.3844|
|  8:  2.4693 -  2.3622 0.99   1289  141 0.1100 0.1683      5.0431      5.2538|
|  9:  2.3622 -  2.2716 0.99   1298  145 0.1113 0.1869      5.0069      5.3397|
| 10:  2.2716 -  2.1935 0.98   1292  140 0.1071 0.1781      4.9517      5.2044|
| 11:  2.1935 -  2.1251 0.98   1274  142 0.1088 0.1761      4.9172      5.2601|
| 12:  2.1251 -  2.0645 1.00   1293  144 0.1040 0.1624      4.8437      5.1088|
| 13:  2.0645 -  2.0103 0.96   1265  138 0.1099 0.1823      4.7809      5.0909|
| 14:  2.0103 -  1.9614 0.43    557   66 0.1063 0.1664      4.7035      4.9094|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8574 -  4.6809  1412   157  0.94   8.82   0.98     0.96       6881.05|
|  2:  4.6809 -  3.7348  1365   147  0.95   7.78   1.02     1.01       8502.54|
|  3:  3.7348 -  3.2685  1325   155  0.94  10.93   1.03     1.03       9886.42|
|  4:  3.2685 -  2.9722  1330   146  0.92  13.95   1.01     0.99      10329.59|
|  5:  2.9722 -  2.7606  1317   147  0.90  15.62   1.00     0.98       8015.63|
|  6:  2.7606 -  2.5988  1303   143  0.90  15.75   0.99     0.97       6872.98|
|  7:  2.5988 -  2.4693  1310   148  0.91  14.69   1.00     0.97       5683.15|
|  8:  2.4693 -  2.3622  1289   141  0.91  15.25   1.00     0.97       5339.21|
|  9:  2.3622 -  2.2716  1298   145  0.91  15.32   1.01     0.97       4890.79|
| 10:  2.2716 -  2.1935  1292   140  0.90  15.73   1.00     0.96       4486.27|
| 11:  2.1935 -  2.1251  1274   142  0.90  16.36   1.01     0.97       4341.67|
| 12:  2.1251 -  2.0645  1293   144  0.92  14.64   1.00     0.99       3780.09|
| 13:  2.0645 -  2.0103  1265   138  0.90  16.71   1.01     1.00       3456.20|
| 14:  2.0103 -  1.9614   557    66  0.90  15.90   0.99     0.95       2853.80|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2853.80 max =        10329.59 mean =      6269.10|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.95 mean =        13.96|
|phase err.(test): min =        0.00 max =           89.81 mean =        13.58|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.718)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.50    103.60  16.97    None  None   None       |
|    all(noH): 2823   0      0.50    103.60  16.97    None  None   None       |
|    Sol.    : 438    0      5.42    83.16   40.00    None  None   None       |
|    Mac.    : 2385   0      0.50    103.60  12.74    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.501 -  10.811: 1269   |   5:    52.052 -  62.362:   83        |
|      1:    10.811 -  21.121:  966   |   6:    62.362 -  72.672:   34        |
|      2:    21.121 -  31.431:  195   |   7:    72.672 -  82.982:    9        |
|      3:    31.431 -  41.741:  130   |   8:    82.982 -  93.293:    6        |
|      4:    41.741 -  52.052:  130   |   9:    93.293 - 103.603:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 307         
Filter by distance & map next to the model:
   mapped sites are within: 0.647 - 4.406
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 302 from: 307
   mapped sites are within: 0.717 - 4.406

peak=    5.797 closest distance to " NH2 ARG A  56 " =    2.247
peak=    5.551 closest distance to " CG  PRO A  54 " =    1.231
peak=    5.407 closest distance to " CB  ARG A 275 " =    0.914
peak=    5.389 closest distance to " CB  GLN A 223 " =    1.426
peak=    5.350 closest distance to " CB  SER A  63 " =    1.162
peak=    5.096 closest distance to " CG  PRO A 213 " =    1.211
peak=    5.046 closest distance to " O   HOH Z 298 " =    1.805
peak=    4.939 closest distance to " O   HOH Z 126 " =    1.783
peak=    4.748 closest distance to " CG  PRO A  90 " =    1.150
peak=    4.745 closest distance to " O   HOH Z 272 " =    1.816
peak=    4.720 closest distance to " CB  GLN A 183 " =    1.353
peak=    4.656 closest distance to " O   HOH Z 232 " =    2.342
peak=    4.644 closest distance to " O   HOH Z  78 " =    1.783
peak=    4.608 closest distance to " O   HOH Z 142 " =    1.623
peak=    4.600 closest distance to " CA  TYR A  30 " =    0.937
peak=    4.571 closest distance to " C   PRO A 198 " =    1.494
peak=    4.521 closest distance to " NZ  LYS A 117 " =    3.220
peak=    4.499 closest distance to " O   HOH Z 124 " =    1.397
peak=    4.488 closest distance to " O   HOH Z 234 " =    3.685
peak=    4.475 closest distance to " O   HOH Z 193 " =    1.820
peak=    4.460 closest distance to " O   HOH Z  15 " =    2.094
peak=    4.445 closest distance to " NE2 GLN A  11 " =    1.031
peak=    4.432 closest distance to " O   HOH Z  40 " =    1.787
peak=    4.416 closest distance to " O   HOH Z 209 " =    2.263
peak=    4.403 closest distance to " O   HOH Z 403 " =    1.774
peak=    4.388 closest distance to " CB  TYR A 169 " =    0.780
peak=    4.369 closest distance to " O   HOH Z  97 " =    1.882
peak=    4.318 closest distance to " OD1 ASN A  69 " =    2.561
peak=    4.306 closest distance to " O   HOH Z  43 " =    2.021
peak=    4.303 closest distance to " OD2 ASP A 286 " =    2.786
peak=    4.295 closest distance to " CG  ARG A  66 " =    2.520
peak=    4.286 closest distance to " CB  ARG A  79 " =    1.394
peak=    4.282 closest distance to " O   HOH Z  54 " =    1.818
peak=    4.266 closest distance to " CB  GLU A 152 " =    1.195
peak=    4.259 closest distance to " CG  PRO A 198 " =    1.219
peak=    4.252 closest distance to " O   HOH Z 368 " =    2.026
peak=    4.220 closest distance to " CB  PRO A  54 " =    0.915
peak=    4.198 closest distance to " CB  SER A   3 " =    1.301
peak=    4.196 closest distance to " CB  GLU A 128 " =    1.159
peak=    4.194 closest distance to " O   HOH Z 427 " =    2.783
peak=    4.180 closest distance to " CG  PRO A 243 " =    1.150
peak=    4.159 closest distance to " O   HOH Z 144 " =    2.218
peak=    4.148 closest distance to " CB  GLU A 277 " =    3.528
peak=    4.141 closest distance to " CG1 ILE A  33 " =    1.263
peak=    4.129 closest distance to " O   HOH Z 189 " =    1.782
peak=    4.096 closest distance to " O   HOH Z 203 " =    1.835
peak=    4.084 closest distance to " CA  ALA A  21 " =    1.243
peak=    4.084 closest distance to " O   HOH Z 344 " =    2.991
peak=    4.083 closest distance to " O   SER A  87 " =    2.227
peak=    4.081 closest distance to " O   HOH Z  59 " =    2.121
peak=    4.072 closest distance to " CB  ASN A 148 " =    1.409
peak=    4.066 closest distance to " CB  ARG A 190 " =    1.695
peak=    4.064 closest distance to " O   HOH Z 316 " =    2.957
peak=    4.025 closest distance to " O   HOH Z 236 " =    1.964
peak=    3.985 closest distance to " O   HOH Z 371 " =    3.304
peak=    3.976 closest distance to " CB  TRP A 179 " =    1.303
peak=    3.963 closest distance to " ND2 ASN A 187 " =    1.459
peak=    3.928 closest distance to " OG BSER A 164 " =    2.292
peak=    3.925 closest distance to " O   HOH Z 345 " =    3.099
peak=    3.915 closest distance to " O   HOH Z   6 " =    2.208
peak=    3.913 closest distance to " O   HOH Z 108 " =    2.273
peak=    3.897 closest distance to " O   HOH Z 134 " =    1.386
peak=    3.886 closest distance to " O   HOH Z 416 " =    2.763
peak=    3.885 closest distance to " O   HOH Z 180 " =    2.283
peak=    3.872 closest distance to " O   HOH Z 303 " =    1.936
peak=    3.871 closest distance to " CD  ARG A 269 " =    1.017
peak=    3.869 closest distance to " O   HOH Z  44 " =    1.965
peak=    3.857 closest distance to " NH2BARG A 145 " =    2.036
peak=    3.850 closest distance to " CD2 LEU A 297 " =    0.914
peak=    3.849 closest distance to " O   HOH Z 369 " =    2.244
peak=    3.843 closest distance to " CB  ARG A 139 " =    0.911
peak=    3.840 closest distance to " O   MET A 105 " =    1.851
peak=    3.838 closest distance to " O   HOH Z 426 " =    1.520
peak=    3.831 closest distance to " CA  ASP A 140 " =    1.125
peak=    3.831 closest distance to " O   HOH Z 214 " =    2.156
peak=    3.824 closest distance to " O   HOH Z  68 " =    1.816
peak=    3.820 closest distance to " OD2 ASP A 298 " =    3.961
peak=    3.793 closest distance to " CA  ASN A 176 " =    1.176
peak=    3.783 closest distance to " CB  LEU A 228 " =    1.132
peak=    3.765 closest distance to " O   HOH Z 346 " =    1.748
peak=    3.761 closest distance to " O   HOH Z  61 " =    1.572
peak=    3.757 closest distance to " O   HOH Z 411 " =    3.660
peak=    3.738 closest distance to " CB  SER A 141 " =    1.031
peak=    3.735 closest distance to " O   HOH Z  19 " =    2.098
peak=    3.735 closest distance to " O   HOH Z  63 " =    1.912
peak=    3.733 closest distance to " O   HOH Z 402 " =    1.421
peak=    3.728 closest distance to " CA  THR A 221 " =    0.948
peak=    3.719 closest distance to " O   HOH Z 147 " =    1.758
peak=    3.717 closest distance to " O   HOH Z 284 " =    2.903
peak=    3.715 closest distance to " CG2 ILE A 120 " =    1.210
peak=    3.713 closest distance to " O   HOH Z  88 " =    3.266
peak=    3.711 closest distance to " CB  TYR A 169 " =    0.834
peak=    3.704 closest distance to " CG2 THR A 221 " =    1.122
peak=    3.703 closest distance to " O   HOH Z 368 " =    3.693
peak=    3.699 closest distance to " O   HOH Z 132 " =    2.590
peak=    3.698 closest distance to " O   HOH Z 183 " =    1.457
peak=    3.697 closest distance to " O   HOH Z 128 " =    2.045
peak=    3.690 closest distance to " O   HOH Z 247 " =    1.252
peak=    3.685 closest distance to " O   HOH Z 423 " =    1.986
peak=    3.684 closest distance to " O   HOH Z 389 " =    1.847
peak=    3.681 closest distance to " NH2 ARG A 156 " =    1.155
peak=    3.678 closest distance to " O   HOH Z  97 " =    2.687
peak=    3.673 closest distance to " ND2 ASN A 110 " =    1.724
peak=    3.672 closest distance to " CG1BVAL A  72 " =    1.592
peak=    3.665 closest distance to " CG  GLN A  58 " =    2.590
peak=    3.660 closest distance to " O   HOH Z 133 " =    2.473
peak=    3.652 closest distance to " CB  VAL A 265 " =    1.236
peak=    3.636 closest distance to " O   HOH Z  49 " =    2.068
peak=    3.626 closest distance to " CA  ASN A 215 " =    1.151
peak=    3.620 closest distance to " O   HOH Z 173 " =    1.994
peak=    3.616 closest distance to " CG2BVAL A  41 " =    0.820
peak=    3.616 closest distance to " CD1 LEU A 300 " =    1.260
peak=    3.613 closest distance to " O   HOH Z 193 " =    2.200
peak=    3.611 closest distance to " O   HOH Z 245 " =    1.332
peak=    3.608 closest distance to " O   HOH Z  61 " =    1.536
peak=    3.607 closest distance to " CD2 TRP A 179 " =    1.400
peak=    3.600 closest distance to " CD  ARG A 159 " =    0.759
peak=    3.598 closest distance to " O   HOH Z 227 " =    1.632
peak=    3.581 closest distance to " O   HOH Z 374 " =    2.595
peak=    3.575 closest distance to " CA  ARG A  36 " =    1.101
peak=    3.569 closest distance to " O   HOH Z 421 " =    1.594
peak=    3.567 closest distance to " O   HOH Z 326 " =    1.508
peak=    3.563 closest distance to " O   HOH Z 365 " =    2.868
peak=    3.560 closest distance to " CA  ARG A 195 " =    1.291
peak=    3.559 closest distance to " NZ  LYS A 119 " =    1.491
peak=    3.559 closest distance to " CA  MET A  40 " =    1.051
peak=    3.550 closest distance to " CD  ARG A  66 " =    2.680
peak=    3.539 closest distance to " O   HOH Z 158 " =    2.971
peak=    3.534 closest distance to " O   HOH Z 337 " =    3.672
peak=    3.531 closest distance to " O   HOH Z  21 " =    1.693
peak=    3.526 closest distance to " O   HOH Z 197 " =    2.889
peak=    3.526 closest distance to " O   HOH Z 250 " =    1.435
peak=    3.526 closest distance to " CG2AVAL A 121 " =    2.204
peak=    3.524 closest distance to " O   HOH Z 327 " =    1.720
peak=    3.521 closest distance to " N   ASN A  39 " =    1.262
peak=    3.521 closest distance to " O   HOH Z 185 " =    1.692
peak=    3.520 closest distance to " CA  LYS A 117 " =    1.215
peak=    3.504 closest distance to " CE1 TYR A 186 " =    1.243
peak=    3.500 closest distance to " O   HOH Z 427 " =    3.035
peak=    3.500 closest distance to " CD  LYS A 119 " =    1.302
peak=    3.498 closest distance to " CG2 VAL A 257 " =    0.856
peak=    3.494 closest distance to " O   HOH Z 261 " =    2.045
peak=    3.492 closest distance to " O   HOH Z  66 " =    2.207
peak=    3.479 closest distance to " NH1AARG A 145 " =    1.173
peak=    3.474 closest distance to " O   HOH Z 425 " =    2.087
peak=    3.473 closest distance to " CB  VAL A 202 " =    1.590
peak=    3.473 closest distance to " O   HOH Z 273 " =    2.745
peak=    3.469 closest distance to " O   HOH Z 261 " =    1.477
peak=    3.464 closest distance to " CB  ASN A  39 " =    0.868
peak=    3.464 closest distance to " O   HOH Z  54 " =    2.345
peak=    3.451 closest distance to " CG2 ILE A  20 " =    1.370
peak=    3.450 closest distance to " CB  SER A 216 " =    0.805
peak=    3.445 closest distance to " O   HOH Z 126 " =    2.015
peak=    3.442 closest distance to " O   HOH Z 406 " =    1.709
peak=    3.436 closest distance to " CD2 LEU A 255 " =    1.372
peak=    3.434 closest distance to " O   HOH Z 267 " =    2.069
peak=    3.428 closest distance to " O   HOH Z 250 " =    1.699
peak=    3.423 closest distance to " CB  ASP A 140 " =    0.915
peak=    3.418 closest distance to " O   HOH Z  89 " =    2.211
peak=    3.418 closest distance to " O   HOH Z 408 " =    1.329
peak=    3.417 closest distance to " O   HOH Z 145 " =    2.365
peak=    3.408 closest distance to " CD BLYS A 290 " =    1.174
peak=    3.401 closest distance to " O   HOH Z  80 " =    1.617
peak=    3.400 closest distance to " CA  ASP A 162 " =    1.197
peak=    3.396 closest distance to " CG2 VAL A  78 " =    0.914
peak=    3.393 closest distance to " CG  MET A 185 " =    1.117
peak=    3.389 closest distance to " CB  ALA A 291 " =    1.330
peak=    3.388 closest distance to " O   HOH Z  85 " =    1.382
peak=    3.387 closest distance to " O   HOH Z 163 " =    1.609
peak=    3.385 closest distance to " CA  ALA A  84 " =    1.321
peak=    3.382 closest distance to " O   HOH Z 133 " =    1.399
peak=    3.380 closest distance to " O   HOH Z 263 " =    2.295
peak=    3.371 closest distance to " CZ  PHE A 218 " =    1.020
peak=    3.367 closest distance to " CB  MET A  47 " =    0.996
peak=    3.366 closest distance to " CA  ALA A 160 " =    0.812
peak=    3.365 closest distance to " CA  ALA A  51 " =    0.942
peak=    3.365 closest distance to " O   HOH Z 299 " =    2.428
peak=    3.362 closest distance to " O   HOH Z  85 " =    2.058
peak=    3.353 closest distance to " CZ2 TRP A 179 " =    1.639
peak=    3.345 closest distance to " OG  SER A  62 " =    2.895
peak=    3.345 closest distance to " O   HOH Z 128 " =    2.237
peak=    3.345 closest distance to " CB  TRP A 266 " =    0.975
peak=    3.344 closest distance to " O   GLY A  91 " =    1.460
peak=    3.342 closest distance to " CB  SER A  62 " =    0.777
peak=    3.341 closest distance to " O   HOH Z 281 " =    4.406
peak=    3.339 closest distance to " CG2 VAL A 197 " =    1.130
peak=    3.339 closest distance to " CB  PRO A 198 " =    1.099
peak=    3.338 closest distance to " O   SER A  26 " =    1.688
peak=    3.334 closest distance to " CD2 HIS A  81 " =    1.174
peak=    3.330 closest distance to " O   HOH Z  10 " =    1.858
peak=    3.329 closest distance to " CB  GLN A  88 " =    1.139
peak=    3.327 closest distance to " CA  MET A 105 " =    1.056
peak=    3.326 closest distance to " O   GLY A  57 " =    2.595
peak=    3.307 closest distance to " O   HOH Z 102 " =    1.267
peak=    3.307 closest distance to " NH2AARG A 190 " =    1.215
peak=    3.304 closest distance to " O   HOH Z  50 " =    1.334
peak=    3.300 closest distance to " C   TYR A 214 " =    1.404
peak=    3.298 closest distance to " NH1BARG A 145 " =    1.057
peak=    3.298 closest distance to " CE  LYS A 119 " =    1.076
peak=    3.294 closest distance to " NH2 ARG A 219 " =    1.957
peak=    3.290 closest distance to " O   ALA A 165 " =    1.391
peak=    3.287 closest distance to " O   HOH Z 345 " =    1.578
peak=    3.287 closest distance to " O   HOH Z 357 " =    1.970
peak=    3.285 closest distance to " CB  ALA A  71 " =    1.226
peak=    3.279 closest distance to " O   HOH Z 435 " =    1.839
peak=    3.279 closest distance to " O   ALA A 158 " =    1.281
peak=    3.277 closest distance to " O   HOH Z 410 " =    1.824
peak=    3.276 closest distance to " O   HOH Z 313 " =    1.694
peak=    3.274 closest distance to " O   HOH Z 281 " =    1.803
peak=    3.271 closest distance to " O   HOH Z 299 " =    4.404
peak=    3.271 closest distance to " CB  SER A  26 " =    1.636
peak=    3.269 closest distance to " O   HOH Z 359 " =    1.739
peak=    3.269 closest distance to " O   HOH Z 417 " =    3.066
peak=    3.269 closest distance to " CD  LYS A 166 " =    1.302
peak=    3.268 closest distance to " O   HOH Z 135 " =    1.609
peak=    3.267 closest distance to " OE1 GLN A  11 " =    1.863
peak=    3.266 closest distance to " CG  GLN A  11 " =    1.376
peak=    3.256 closest distance to " O   HOH Z 163 " =    1.839
peak=    3.255 closest distance to " CG  LYS A  76 " =    1.081
peak=    3.253 closest distance to " O   HOH Z  50 " =    2.027
peak=    3.251 closest distance to " ND1 HIS A  81 " =    1.580
peak=    3.242 closest distance to " O   HOH Z 403 " =    1.270
peak=    3.241 closest distance to " CA  GLY A  80 " =    0.938
peak=    3.237 closest distance to " O   HOH Z 422 " =    2.670
peak=    3.237 closest distance to " CB  TYR A 116 " =    0.854
peak=    3.234 closest distance to " O   HOH Z   1 " =    2.119
peak=    3.231 closest distance to " CB  PRO A 163 " =    3.993
peak=    3.221 closest distance to " CG AARG A 275 " =    1.049
peak=    3.220 closest distance to " CA  ALA A 248 " =    1.177
peak=    3.220 closest distance to " CG  GLU A 277 " =    2.153
peak=    3.219 closest distance to " O   HOH Z 211 " =    2.751
peak=    3.213 closest distance to " OG  SER A  22 " =    2.715
peak=    3.212 closest distance to " O   HOH Z 417 " =    2.130
peak=    3.212 closest distance to " O   HOH Z 329 " =    3.563
peak=    3.211 closest distance to " CB  ASN A 285 " =    0.943
peak=    3.210 closest distance to " CA  ALA A 291 " =    0.861
peak=    3.208 closest distance to " CD1 ILE A 106 " =    0.840
peak=    3.208 closest distance to " O   TRP A 274 " =    1.947
peak=    3.206 closest distance to " CB  GLN A 278 " =    0.870
peak=    3.205 closest distance to " O   HOH Z 214 " =    2.298
peak=    3.203 closest distance to " O   HOH Z 189 " =    2.845
peak=    3.202 closest distance to " O   HOH Z 163 " =    1.323
peak=    3.202 closest distance to " CA  LEU A 282 " =    1.137
peak=    3.197 closest distance to " CB  ILE A 120 " =    1.341
peak=    3.196 closest distance to " CB  PHE A  16 " =    1.022
peak=    3.192 closest distance to " O   HOH Z  64 " =    2.114
peak=    3.189 closest distance to " CD1 LEU A  96 " =    0.737
peak=    3.186 closest distance to " O   HOH Z 279 " =    2.102
peak=    3.180 closest distance to " O   ALA A   1 " =    1.415
peak=    3.177 closest distance to " O   HOH Z 437 " =    1.369
peak=    3.175 closest distance to " CB  TYR A  30 " =    1.439
peak=    3.175 closest distance to " CA  ASP A 191 " =    0.816
peak=    3.174 closest distance to " N   TYR A 116 " =    1.484
peak=    3.174 closest distance to " CD1 LEU A 228 " =    1.586
peak=    3.171 closest distance to " CA  ASN A 217 " =    1.238
peak=    3.169 closest distance to " CB  SER A 212 " =    0.998
peak=    3.167 closest distance to " NZ  LYS A 166 " =    2.985
peak=    3.167 closest distance to " O   HOH Z 409 " =    3.304
peak=    3.165 closest distance to " O   HOH Z   4 " =    1.759
peak=    3.164 closest distance to " O   HOH Z 189 " =    1.115
peak=    3.163 closest distance to " O   HOH Z 305 " =    3.668
peak=    3.162 closest distance to " O   HOH Z 148 " =    3.097
peak=    3.157 closest distance to " CE  LYS A  48 " =    1.103
peak=    3.157 closest distance to " CA  ALA A  43 " =    1.260
peak=    3.156 closest distance to " OD1 ASP A 286 " =    1.644
peak=    3.152 closest distance to " CD  GLN A 240 " =    1.464
peak=    3.151 closest distance to " CB  ALA A   9 " =    1.586
peak=    3.150 closest distance to " O   THR A 251 " =    1.224
peak=    3.144 closest distance to " O   HOH Z 336 " =    1.695
peak=    3.142 closest distance to " O   HOH Z 334 " =    1.503
peak=    3.137 closest distance to " CA  PHE A 283 " =    1.446
peak=    3.136 closest distance to " CA  TYR A 116 " =    1.370
peak=    3.134 closest distance to " CB  LEU A 255 " =    0.717
peak=    3.132 closest distance to " N   ALA A 154 " =    1.183
peak=    3.129 closest distance to " CA  ALA A 233 " =    1.167
peak=    3.129 closest distance to " O   HOH Z  44 " =    3.535
peak=    3.124 closest distance to " NZ  LYS A  76 " =    1.298
peak=    3.123 closest distance to " CA  ILE A 234 " =    0.934
peak=    3.120 closest distance to " O   HOH Z 367 " =    3.593
peak=    3.115 closest distance to " O   HOH Z 393 " =    3.513
peak=    3.114 closest distance to " O   HOH Z 359 " =    1.407
peak=    3.110 closest distance to " CA  VAL A 126 " =    1.131
peak=    3.105 closest distance to " O   HOH Z 189 " =    2.185
peak=    3.105 closest distance to " O   HOH Z 438 " =    1.940
peak=    3.102 closest distance to " CB  ASN A 215 " =    1.143
peak=    3.101 closest distance to " O   HOH Z 194 " =    1.812
peak=    3.098 closest distance to " CB  ALA A 100 " =    1.184
peak=    3.095 closest distance to " CG2 VAL A 202 " =    1.130
peak=    3.095 closest distance to " O   HOH Z 112 " =    1.550
peak=    3.092 closest distance to " O   HOH Z  49 " =    2.424
peak=    3.092 closest distance to " CB  LYS A 289 " =    1.003
peak=    3.092 closest distance to " O   HOH Z  66 " =    1.839
peak=    3.088 closest distance to " N   ARG A 156 " =    1.332
peak=    3.081 closest distance to " CD  GLU A 152 " =    0.786
peak=    3.079 closest distance to " CB  SER A 273 " =    0.778
peak=    3.078 closest distance to " CG  GLN A  89 " =    1.507
peak=    3.073 closest distance to " CG  MET A 185 " =    1.004
peak=    3.069 closest distance to " C   ALA A 299 " =    0.955
peak=    3.057 closest distance to " N   ASN A 127 " =    1.269
peak=    3.046 closest distance to " O   HOH Z 336 " =    1.673
peak=    3.045 closest distance to " CD1AILE A 234 " =    0.966
peak=    3.024 closest distance to " O   HOH Z 271 " =    2.177

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 208         
Filter by distance & map next to the model:
   mapped sites are within: 0.848 - 5.705
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 207 from: 208
   mapped sites are within: 0.848 - 5.705

peak=   -4.798 closest distance to " O   HOH Z 266 " =    4.295
peak=   -4.359 closest distance to " CD  ARG A 156 " =    2.033
peak=   -4.301 closest distance to " O   HOH Z 372 " =    2.305
peak=   -4.287 closest distance to " C   HIS A 108 " =    1.080
peak=   -4.245 closest distance to " O   HOH Z  11 " =    1.948
peak=   -4.209 closest distance to " O   PRO A 163 " =    2.046
peak=   -4.185 closest distance to " SG  CYS A 254 " =    3.251
peak=   -4.181 closest distance to " N   ALA A 248 " =    1.727
peak=   -4.151 closest distance to " O   HOH Z 231 " =    2.274
peak=   -4.151 closest distance to " O   HOH Z 377 " =    2.043
peak=   -4.125 closest distance to " OXT GLY A 302 " =    2.767
peak=   -4.097 closest distance to " O   HOH Z  13 " =    1.654
peak=   -4.074 closest distance to " OG  SER A  97 " =    2.142
peak=   -4.011 closest distance to " ND2 ASN A  45 " =    0.966
peak=   -4.007 closest distance to " CB  PRO A 243 " =    2.597
peak=   -3.999 closest distance to " O   VAL A  67 " =    2.723
peak=   -3.967 closest distance to " O   HOH Z 198 " =    2.157
peak=   -3.964 closest distance to " CD1 LEU A 228 " =    2.197
peak=   -3.959 closest distance to " CB  ALA A 161 " =    2.581
peak=   -3.926 closest distance to " O   HOH Z 353 " =    2.268
peak=   -3.892 closest distance to " O   HOH Z 118 " =    3.057
peak=   -3.886 closest distance to " OG BSER A 134 " =    1.261
peak=   -3.883 closest distance to " CD1 LEU A 101 " =    2.478
peak=   -3.865 closest distance to " CB  TYR A  15 " =    2.234
peak=   -3.855 closest distance to " O   HOH Z  52 " =    1.490
peak=   -3.838 closest distance to " O   HOH Z  10 " =    1.495
peak=   -3.836 closest distance to " O   VAL A  67 " =    2.750
peak=   -3.833 closest distance to " CZ3 TRP A 179 " =    1.269
peak=   -3.831 closest distance to " N   ALA A  43 " =    2.610
peak=   -3.829 closest distance to " OE1 GLN A 223 " =    2.127
peak=   -3.823 closest distance to " CE2 TYR A  30 " =    2.771
peak=   -3.819 closest distance to " O   HOH Z 407 " =    3.065
peak=   -3.798 closest distance to " CG  ASP A 231 " =    0.848
peak=   -3.789 closest distance to " O   HOH Z 126 " =    1.828
peak=   -3.777 closest distance to " CD  ARG A 139 " =    1.604
peak=   -3.776 closest distance to " O   HOH Z 102 " =    1.653
peak=   -3.771 closest distance to " O   PRO A 198 " =    1.303
peak=   -3.752 closest distance to " O   HOH Z 185 " =    2.168
peak=   -3.736 closest distance to " CE  MET A 105 " =    2.077
peak=   -3.735 closest distance to " CD2 LEU A 300 " =    2.926
peak=   -3.728 closest distance to " O   HOH Z 234 " =    4.060
peak=   -3.719 closest distance to " O   HOH Z  43 " =    1.595
peak=   -3.710 closest distance to " CD1 PHE A  59 " =    1.854
peak=   -3.697 closest distance to " O   SER A 210 " =    1.932
peak=   -3.697 closest distance to " C   ALA A 158 " =    1.219
peak=   -3.693 closest distance to " O   HOH Z 165 " =    2.025
peak=   -3.693 closest distance to " OG  SER A   3 " =    1.725
peak=   -3.692 closest distance to " CG  ASP A 132 " =    2.364
peak=   -3.686 closest distance to " ND2 ASN A 187 " =    1.507
peak=   -3.686 closest distance to " N   GLN A  58 " =    1.642
peak=   -3.680 closest distance to " O   HOH Z 292 " =    4.516
peak=   -3.670 closest distance to " O   GLY A  80 " =    2.421
peak=   -3.665 closest distance to " CZ  PHE A  59 " =    1.689
peak=   -3.660 closest distance to " CA  GLY A 203 " =    2.161
peak=   -3.649 closest distance to " N   ALA A 248 " =    2.222
peak=   -3.646 closest distance to " CB  ALA A 291 " =    2.349
peak=   -3.635 closest distance to " O   HOH Z 166 " =    1.526
peak=   -3.632 closest distance to " O   HOH Z 283 " =    1.847
peak=   -3.613 closest distance to " O   PHE A 218 " =    1.591
peak=   -3.610 closest distance to " CB  PHE A 192 " =    1.965
peak=   -3.605 closest distance to " CZ  TYR A 169 " =    1.802
peak=   -3.605 closest distance to " OG BSER A 134 " =    1.722
peak=   -3.591 closest distance to " O   TRP A  92 " =    1.803
peak=   -3.586 closest distance to " O   SER A 135 " =    1.576
peak=   -3.577 closest distance to " OD1 ASN A 148 " =    1.565
peak=   -3.575 closest distance to " CB  ASN A  39 " =    2.279
peak=   -3.574 closest distance to " CA  ASP A 298 " =    1.047
peak=   -3.568 closest distance to " CG1 VAL A 250 " =    2.660
peak=   -3.567 closest distance to " C   LEU A 143 " =    1.144
peak=   -3.561 closest distance to " O   HOH Z  71 " =    1.523
peak=   -3.553 closest distance to " OG  SER A  62 " =    1.536
peak=   -3.553 closest distance to " NH2 ARG A  79 " =    1.918
peak=   -3.550 closest distance to " O   HOH Z 196 " =    1.948
peak=   -3.548 closest distance to " NH2AARG A 275 " =    5.170
peak=   -3.546 closest distance to " O   HOH Z 435 " =    2.673
peak=   -3.541 closest distance to " NH2 ARG A  66 " =    5.104
peak=   -3.530 closest distance to " O   HOH Z 395 " =    5.200
peak=   -3.520 closest distance to " O   HOH Z  38 " =    1.603
peak=   -3.510 closest distance to " O   HOH Z 311 " =    3.564
peak=   -3.488 closest distance to " CG1 VAL A 112 " =    2.780
peak=   -3.487 closest distance to " O   HOH Z 351 " =    1.415
peak=   -3.482 closest distance to " N   SER A 276 " =    1.332
peak=   -3.477 closest distance to " CG  PHE A 283 " =    2.615
peak=   -3.476 closest distance to " O   HOH Z 166 " =    1.728
peak=   -3.471 closest distance to " CG2 ILE A 263 " =    2.268
peak=   -3.467 closest distance to " O   HOH Z 436 " =    1.472
peak=   -3.464 closest distance to " O   HOH Z 417 " =    2.556
peak=   -3.457 closest distance to " CG  ASP A  50 " =    2.362
peak=   -3.457 closest distance to " O   HOH Z  19 " =    2.073
peak=   -3.451 closest distance to " O   VAL A 174 " =    2.035
peak=   -3.451 closest distance to " OD1 ASP A 191 " =    1.720
peak=   -3.448 closest distance to " OG BSER A 210 " =    2.039
peak=   -3.430 closest distance to " CD2 TYR A 247 " =    2.420
peak=   -3.429 closest distance to " CD  GLN A 223 " =    1.447
peak=   -3.427 closest distance to " NE2 GLN A 103 " =    1.614
peak=   -3.424 closest distance to " O   ALA A 160 " =    1.603
peak=   -3.422 closest distance to " O   HOH Z 361 " =    3.434
peak=   -3.421 closest distance to " O   HOH Z 111 " =    1.691
peak=   -3.415 closest distance to " O   HOH Z 326 " =    1.637
peak=   -3.401 closest distance to " CD1 TYR A 247 " =    2.458
peak=   -3.400 closest distance to " O   HOH Z  11 " =    1.809
peak=   -3.399 closest distance to " O   ALA A  34 " =    2.265
peak=   -3.392 closest distance to " CB  SER A 245 " =    2.431
peak=   -3.389 closest distance to " SG ACYS A 201 " =    2.038
peak=   -3.385 closest distance to " O   HOH Z 150 " =    1.757
peak=   -3.368 closest distance to " CD  GLN A  58 " =    1.246
peak=   -3.362 closest distance to " CB  ALA A 248 " =    2.286
peak=   -3.352 closest distance to " CG  GLU A  53 " =    1.356
peak=   -3.349 closest distance to " OG1 THR A 178 " =    1.348
peak=   -3.347 closest distance to " CB  ALA A  10 " =    2.185
peak=   -3.332 closest distance to " C   THR A 279 " =    1.130
peak=   -3.331 closest distance to " O   HOH Z  44 " =    2.145
peak=   -3.329 closest distance to " N   ASP A 171 " =    2.471
peak=   -3.327 closest distance to " N   GLN A 122 " =    1.483
peak=   -3.326 closest distance to " O   ASN A  45 " =    1.851
peak=   -3.311 closest distance to " O   HOH Z 298 " =    1.258
peak=   -3.309 closest distance to " OD2 ASP A 191 " =    1.538
peak=   -3.308 closest distance to " OE1 GLN A 223 " =    1.914
peak=   -3.305 closest distance to " NE2 GLN A  88 " =    1.840
peak=   -3.304 closest distance to " OG ASER A 134 " =    1.212
peak=   -3.294 closest distance to " O   LEU A 167 " =    1.542
peak=   -3.291 closest distance to " O   HOH Z 265 " =    2.092
peak=   -3.289 closest distance to " CE  MET A  93 " =    1.214
peak=   -3.288 closest distance to " OXT GLY A 302 " =    3.110
peak=   -3.288 closest distance to " O   HOH Z 148 " =    3.609
peak=   -3.284 closest distance to " OD2 ASP A 171 " =    2.328
peak=   -3.281 closest distance to " O   HOH Z 388 " =    2.042
peak=   -3.278 closest distance to " NE2 GLN A  58 " =    1.159
peak=   -3.277 closest distance to " CD1 LEU A  25 " =    2.440
peak=   -3.268 closest distance to " O   GLY A 196 " =    0.983
peak=   -3.266 closest distance to " O   HOH Z  15 " =    1.599
peak=   -3.262 closest distance to " OD1 ASP A 171 " =    1.561
peak=   -3.261 closest distance to " O   MET A  40 " =    2.689
peak=   -3.258 closest distance to " O   HOH Z 252 " =    3.537
peak=   -3.254 closest distance to " O   HOH Z 385 " =    1.946
peak=   -3.252 closest distance to " CA  GLY A 133 " =    1.921
peak=   -3.251 closest distance to " NH1 ARG A 195 " =    2.578
peak=   -3.248 closest distance to " O   HOH Z  93 " =    1.638
peak=   -3.246 closest distance to " O   HOH Z 116 " =    1.356
peak=   -3.243 closest distance to " C   ASN A 285 " =    2.321
peak=   -3.239 closest distance to " O   HOH Z 422 " =    1.530
peak=   -3.238 closest distance to " CB  ALA A 248 " =    1.983
peak=   -3.238 closest distance to " O   SER A  95 " =    1.512
peak=   -3.237 closest distance to " OE2 GLU A   2 " =    1.778
peak=   -3.236 closest distance to " O   HOH Z 193 " =    1.966
peak=   -3.235 closest distance to " O   LYS A 117 " =    1.644
peak=   -3.231 closest distance to " CB  PHE A 208 " =    2.179
peak=   -3.229 closest distance to " CD  LYS A 289 " =    2.491
peak=   -3.227 closest distance to " CE2 PHE A 192 " =    2.152
peak=   -3.226 closest distance to " O   HOH Z  97 " =    1.646
peak=   -3.225 closest distance to " C   GLN A 205 " =    1.889
peak=   -3.217 closest distance to " CA  VAL A 232 " =    2.488
peak=   -3.216 closest distance to " O   HOH Z 290 " =    1.147
peak=   -3.206 closest distance to " N   VAL A 189 " =    1.669
peak=   -3.205 closest distance to " O   HOH Z 414 " =    1.439
peak=   -3.199 closest distance to " N   ALA A 226 " =    1.998
peak=   -3.199 closest distance to " O   ASN A 187 " =    1.479
peak=   -3.197 closest distance to " O   HOH Z 250 " =    1.386
peak=   -3.195 closest distance to " O   HOH Z 389 " =    1.740
peak=   -3.195 closest distance to " NH2 ARG A  66 " =    1.989
peak=   -3.194 closest distance to " CG1AVAL A  41 " =    2.775
peak=   -3.194 closest distance to " CB  GLN A  11 " =    1.686
peak=   -3.190 closest distance to " CD2 LEU A 237 " =    2.610
peak=   -3.182 closest distance to " O   ALA A 256 " =    1.486
peak=   -3.182 closest distance to " CB  CYS A 254 " =    2.571
peak=   -3.181 closest distance to " CG  PRO A 163 " =    2.576
peak=   -3.181 closest distance to " CB  ASP A 286 " =    2.188
peak=   -3.174 closest distance to " O   HOH Z 263 " =    2.838
peak=   -3.171 closest distance to " CG  PRO A 243 " =    1.696
peak=   -3.170 closest distance to " O   HOH Z  90 " =    2.088
peak=   -3.165 closest distance to " OD2 ASP A  50 " =    1.432
peak=   -3.158 closest distance to " O   HOH Z 210 " =    0.994
peak=   -3.157 closest distance to " O   HOH Z 191 " =    5.705
peak=   -3.157 closest distance to " CA  GLY A  98 " =    2.044
peak=   -3.156 closest distance to " NH2 ARG A  66 " =    4.745
peak=   -3.150 closest distance to " CG  GLU A 152 " =    2.148
peak=   -3.150 closest distance to " O   HOH Z 297 " =    2.830
peak=   -3.149 closest distance to " O   HOH Z 423 " =    2.292
peak=   -3.140 closest distance to " O   HOH Z 198 " =    1.511
peak=   -3.134 closest distance to " OE1 GLN A  88 " =    1.071
peak=   -3.134 closest distance to " CB  ALA A 291 " =    2.226
peak=   -3.129 closest distance to " O   GLY A 111 " =    1.173
peak=   -3.127 closest distance to " O   HOH Z 324 " =    2.185
peak=   -3.125 closest distance to " OD2 ASP A 171 " =    1.778
peak=   -3.122 closest distance to " O   HOH Z   6 " =    1.717
peak=   -3.121 closest distance to " CD  ARG A  36 " =    1.901
peak=   -3.118 closest distance to " CB  PRO A 163 " =    2.603
peak=   -3.112 closest distance to " O   ASN A 249 " =    1.480
peak=   -3.109 closest distance to " O   HOH Z 211 " =    1.748
peak=   -3.106 closest distance to " CE3 TRP A 274 " =    2.421
peak=   -3.103 closest distance to " O   HOH Z  41 " =    2.285
peak=   -3.102 closest distance to " CZ  PHE A 130 " =    0.961
peak=   -3.098 closest distance to " CB  CYS A 201 " =    2.534
peak=   -3.095 closest distance to " O   HOH Z  47 " =    1.474
peak=   -3.091 closest distance to " O   HOH Z 134 " =    2.513
peak=   -3.090 closest distance to " O   VAL A 197 " =    1.149
peak=   -3.089 closest distance to " CG  ARG A 269 " =    2.217
peak=   -3.079 closest distance to " OG  SER A  87 " =    1.383
peak=   -3.078 closest distance to " N   SER A  12 " =    1.405
peak=   -3.073 closest distance to " O   HOH Z 111 " =    3.561
peak=   -3.072 closest distance to " O   HOH Z 262 " =    2.554
peak=   -3.062 closest distance to " O   HOH Z 193 " =    1.697
peak=   -3.051 closest distance to " CG2 VAL A 189 " =    2.182
peak=   -3.050 closest distance to " CG  GLU A 152 " =    1.358
peak=   -3.049 closest distance to " O   PRO A 198 " =    1.286
peak=   -3.039 closest distance to " O   HOH Z 411 " =    3.490
peak=   -3.021 closest distance to " O   HOH Z 244 " =    1.976

================= 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    :  0.3819 0.3777   6.164590e+00   6.160942e+00
   1_bss:  0.3694 0.3634   6.150508e+00   6.133465e+00
   1_xyz:  0.2129 0.2361   5.662015e+00   5.756779e+00
   1_adp:  0.1933 0.2476   5.612078e+00   5.794967e+00
   1_occ:  0.1928 0.2481   5.611192e+00   5.794374e+00
   2_bss:  0.1892 0.2450   5.601656e+00   5.784634e+00
   2_xyz:  0.1385 0.1853   5.320046e+00   5.539746e+00
   2_adp:  0.1285 0.1719   5.250430e+00   5.465421e+00
   2_occ:  0.1284 0.1716   5.249410e+00   5.464184e+00
   3_bss:  0.1285 0.1703   5.247296e+00   5.460066e+00
   3_xyz:  0.1146 0.1579   5.157558e+00   5.385006e+00
   3_adp:  0.1121 0.1566   5.142122e+00   5.374574e+00
   3_occ:  0.1120 0.1565   5.141810e+00   5.374595e+00
   4_bss:  0.1120 0.1564   5.141419e+00   5.374267e+00
   4_xyz:  0.1074 0.1542   5.115622e+00   5.361014e+00
   4_adp:  0.1066 0.1547   5.115079e+00   5.365185e+00
   4_occ:  0.1066 0.1547   5.115127e+00   5.365517e+00
   5_bss:  0.1065 0.1547   5.115162e+00   5.365525e+00
   5_xyz:  0.1074 0.1554   5.123201e+00   5.372407e+00
   5_adp:  0.1068 0.1568   5.126871e+00   5.382069e+00
   5_occ:  0.1068 0.1569   5.127014e+00   5.382428e+00
   5_bss:  0.1069 0.1568   5.127526e+00   5.382644e+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:  0.340  50.000  -3.238   0.204   2.173   0.000   0.000   0.000
   1_xyz:  0.340  50.000  -3.238   0.204   2.173   0.000   0.000   0.000
   1_adp:  0.340  50.000  -3.238   0.204   2.173   0.000   0.000   0.000
   1_occ:  0.340  50.000  -3.238   0.204   2.173   0.000   0.000   0.000
   2_bss:  0.324  47.621  -3.114  -1.382  -0.764  -0.000  -0.000  -0.000
   2_xyz:  0.324  47.621  -3.114  -1.382  -0.764  -0.000  -0.000  -0.000
   2_adp:  0.324  47.621  -3.114  -1.382  -0.764  -0.000  -0.000  -0.000
   2_occ:  0.324  47.621  -3.114  -1.382  -0.764  -0.000  -0.000  -0.000
   3_bss:  0.322  46.142  -2.851  -1.772  -1.541  -0.000  -0.000  -0.000
   3_xyz:  0.322  46.142  -2.851  -1.772  -1.541  -0.000  -0.000  -0.000
   3_adp:  0.322  46.142  -2.851  -1.772  -1.541  -0.000  -0.000  -0.000
   3_occ:  0.322  46.142  -2.851  -1.772  -1.541  -0.000  -0.000  -0.000
   4_bss:  0.322  46.142  -2.753  -1.890  -1.720  -0.000  -0.000  -0.000
   4_xyz:  0.322  46.142  -2.753  -1.890  -1.720  -0.000  -0.000  -0.000
   4_adp:  0.322  46.142  -2.753  -1.890  -1.720  -0.000  -0.000  -0.000
   4_occ:  0.322  46.142  -2.753  -1.890  -1.720  -0.000  -0.000  -0.000
   5_bss:  0.323  46.142  -2.570  -1.776  -1.615  -0.000  -0.000  -0.000
   5_xyz:  0.323  46.142  -2.570  -1.776  -1.615  -0.000  -0.000  -0.000
   5_adp:  0.323  46.142  -2.570  -1.776  -1.615  -0.000  -0.000  -0.000
   5_occ:  0.323  46.142  -2.570  -1.776  -1.615  -0.000  -0.000  -0.000
   5_bss:  0.320  46.256  -2.340  -1.583  -1.443  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  42.986 0.6080  0.7923    43803.394
   1_bss:  41.379 0.6254  0.8070    39534.498
   1_xyz:  22.933 0.8337  1.0057    14144.675
   1_adp:  24.367 0.8177  0.9919    15369.468
   1_occ:  24.347 0.8179  0.9916    15338.527
   2_bss:  23.902 0.8223  0.9461    14917.888
   2_xyz:  17.507 0.8841  0.9867     8608.671
   2_adp:  15.805 0.8998  0.9904     7519.429
   2_occ:  15.782 0.9000  0.9903     7496.149
   3_bss:  15.675 0.9009  0.9803     7413.197
   3_xyz:  14.136 0.9135  0.9863     6333.411
   3_adp:  13.856 0.9161  0.9843     6221.231
   3_occ:  13.852 0.9161  0.9842     6220.751
   4_bss:  13.842 0.9162  0.9820     6220.348
   4_xyz:  13.564 0.9184  0.9816     6036.202
   4_adp:  13.618 0.9181  0.9763     6063.003
   4_occ:  13.621 0.9181  0.9762     6066.453
   5_bss:  13.621 0.9181  0.9810     6067.757
   5_xyz:  13.696 0.9176  0.9807     6144.191
   5_adp:  13.894 0.9161  0.9742     6247.875
   5_occ:  13.899 0.9160  0.9742     6252.589
   5_bss:  13.920 0.9159  0.9804     6269.508
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.7394e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.7394e-01
   1_xyz:   1.267  0.010  0.079 15.525  0.005  4.112   8.9483e-02
   1_adp:   1.267  0.010  0.079 15.525  0.005  4.112   8.9483e-02
   1_occ:   1.267  0.010  0.079 15.525  0.005  4.112   8.9483e-02
   2_bss:   1.267  0.010  0.079 15.525  0.005  4.112   8.9483e-02
   2_xyz:   1.034  0.007  0.070 14.547  0.004  4.119   6.0022e-02
   2_adp:   1.034  0.007  0.070 14.547  0.004  4.119   6.0022e-02
   2_occ:   1.034  0.007  0.070 14.547  0.004  4.119   6.0022e-02
   3_bss:   1.034  0.007  0.070 14.547  0.004  4.119   6.0022e-02
   3_xyz:   1.019  0.007  0.076 14.814  0.004  4.114   6.0647e-02
   3_adp:   1.019  0.007  0.076 14.814  0.004  4.114   6.0647e-02
   3_occ:   1.019  0.007  0.076 14.814  0.004  4.114   6.0647e-02
   4_bss:   1.019  0.007  0.076 14.814  0.004  4.114   6.0647e-02
   4_xyz:   1.087  0.008  0.078 14.870  0.005  4.115   6.7782e-02
   4_adp:   1.087  0.008  0.078 14.870  0.005  4.115   6.7782e-02
   4_occ:   1.087  0.008  0.078 14.870  0.005  4.115   6.7782e-02
   5_bss:   1.087  0.008  0.078 14.870  0.005  4.115   6.7782e-02
   5_xyz:   1.001  0.007  0.074 14.608  0.004  4.115   5.8695e-02
   5_adp:   1.001  0.007  0.074 14.608  0.004  4.115   5.8695e-02
   5_occ:   1.001  0.007  0.074 14.608  0.004  4.115   5.8695e-02
   5_bss:   1.001  0.007  0.074 14.608  0.004  4.115   5.8695e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.704   2.3988e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.704   2.3988e-01
   1_xyz:   6.864  0.097  0.304 88.915  0.020  2.311   1.1596e-01
   1_adp:   6.864  0.097  0.304 88.915  0.020  2.311   1.1596e-01
   1_occ:   6.864  0.097  0.304 88.915  0.020  2.311   1.1596e-01
   2_bss:   6.864  0.097  0.304 88.915  0.020  2.311   1.1596e-01
   2_xyz:   7.024  0.042  0.232 82.775  0.035  2.338   4.7794e-02
   2_adp:   7.024  0.042  0.232 82.775  0.035  2.338   4.7794e-02
   2_occ:   7.024  0.042  0.232 82.775  0.035  2.338   4.7794e-02
   3_bss:   7.024  0.042  0.232 82.775  0.035  2.338   4.7794e-02
   3_xyz:   7.253  0.039  0.264 82.964  0.038  2.340   4.6578e-02
   3_adp:   7.253  0.039  0.264 82.964  0.038  2.340   4.6578e-02
   3_occ:   7.253  0.039  0.264 82.964  0.038  2.340   4.6578e-02
   4_bss:   7.253  0.039  0.264 82.964  0.038  2.340   4.6578e-02
   4_xyz:   7.487  0.047  0.253 82.002  0.039  2.275   5.3461e-02
   4_adp:   7.487  0.047  0.253 82.002  0.039  2.275   5.3461e-02
   4_occ:   7.487  0.047  0.253 82.002  0.039  2.275   5.3461e-02
   5_bss:   7.487  0.047  0.253 82.002  0.039  2.275   5.3461e-02
   5_xyz:   7.066  0.043  0.247 82.430  0.038  2.341   4.1723e-02
   5_adp:   7.066  0.043  0.247 82.430  0.038  2.341   4.1723e-02
   5_occ:   7.066  0.043  0.247 82.430  0.038  2.341   4.1723e-02
   5_bss:   7.066  0.043  0.247 82.430  0.038  2.341   4.1723e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  80.92   0.00  17.74  80.92   0.00  13.53  78.72   6.45  40.65
   1_occ:  80.92   0.00  17.74  80.92   0.00  13.53  78.72   6.45  40.65
   2_bss:  80.92   0.00  17.74  80.92   0.00  13.53  78.72   6.45  40.65
   2_xyz:  80.92   0.00  17.74  80.92   0.00  13.53  78.72   6.45  40.65
   2_adp:  82.18   1.71  17.26  82.18   1.71  13.10  77.11   6.43  39.92
   2_occ:  82.18   1.71  17.26  82.18   1.71  13.10  77.11   6.43  39.92
   3_bss:  82.18   1.71  17.26  82.18   1.71  13.10  77.11   6.43  39.92
   3_xyz:  82.18   1.71  17.26  82.18   1.71  13.10  77.11   6.43  39.92
   3_adp:  83.95   2.05  16.92  83.95   2.05  12.90  76.01   5.79  38.81
   3_occ:  83.95   2.05  16.92  83.95   2.05  12.90  76.01   5.79  38.81
   4_bss:  83.95   2.05  16.92  83.95   2.05  12.90  76.01   5.79  38.81
   4_xyz:  83.95   2.05  16.92  83.95   2.05  12.90  76.01   5.79  38.81
   4_adp:  88.46   1.49  16.81  88.46   1.49  12.77  76.72   5.66  38.81
   4_occ:  88.46   1.49  16.81  88.46   1.49  12.77  76.72   5.66  38.81
   5_bss:  88.46   1.49  16.81  88.46   1.49  12.77  76.72   5.66  38.81
   5_xyz:  88.46   1.49  16.81  88.46   1.49  12.77  76.72   5.66  38.81
   5_adp: 103.62   0.52  16.99 103.62   0.52  12.76  83.18   5.44  40.01
   5_occ: 103.62   0.52  16.99 103.62   0.52  12.76  83.18   5.44  40.01
   5_bss: 103.60   0.50  16.97 103.60   0.50  12.74  83.16   5.42  40.00
------------------------------------------------------------------------
 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:    1.656    0.028    0.388
   1_adp:    1.656    0.028    0.388
   1_occ:    1.656    0.028    0.388
   2_bss:    1.656    0.028    0.388
   2_xyz:    1.112    0.045    0.474
   2_adp:    1.112    0.045    0.474
   2_occ:    1.112    0.045    0.474
   3_bss:    1.112    0.045    0.474
   3_xyz:    1.259    0.025    0.517
   3_adp:    1.259    0.025    0.517
   3_occ:    1.259    0.025    0.517
   4_bss:    1.259    0.025    0.517
   4_xyz:    1.363    0.060    0.529
   4_adp:    1.363    0.060    0.529
   4_occ:    1.363    0.060    0.529
   5_bss:    1.363    0.060    0.529
   5_xyz:    1.418    0.052    0.536
   5_adp:    1.418    0.052    0.536
   5_occ:    1.418    0.052    0.536
   5_bss:    1.418    0.052    0.536
------------------------------------------------------------------------

CPU time actual refinement: 334.30


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_562/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/noshake/run_562/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_562/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_562/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_562/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 334.14 
  Macro-tasks:
    bulk solvent and scale       = 38.75  
    individual site refinement   = 137.68 
    weights calculation          = 29.67  
    collect and process          = 6.51   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 212.71 
  Micro-tasks:
    mask                            = 1.82   
    f_calc                          = 107.40 
    alpha_beta                      = 8.00   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 116.55 
    fmodel                         = 6.45   
    r_factors                      = 0.11   
    phase_errors                   = 11.02  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 252.83 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.725 micro seconds
Total CPU time: 5.79 minutes
from_scatterers_fft:    652 calls, 107.19 s
gradients_fft:          597 calls, 103.09 s

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

# Date 2008-01-16 Time 05:07:21 PST -0800 (1200488841.11 s)
Start R-work = 0.3819, R-free = 0.3777 (no bulk solvent and anisotropic scale)
Final R-work = 0.1304, R-free = 0.1762 (no bulk solvent and anisotropic scale)

Start R-work = 0.3694, R-free = 0.3634
Final R-work = 0.1069, R-free = 0.1568