# Date 2008-01-16 Time 04:27:05 PST -0800 (1200486425.24 s)
#phil __OFF__

Command line arguments: "../324.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 1729
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 324

-------------------------------------------------------------------------------
  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: (69.1963, 47.3993, 86.39, 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: (69.1963, 47.3993, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8383 1.97069
Completeness in resolution range: 0.949908
Completeness with d_max=infinity: 0.946969

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8383
                             d_min =   1.9707

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.3993, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8383 1.97069
Completeness in resolution range: 0.949908
Completeness with d_max=infinity: 0.946969

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8387 -  4.2163 [2178/2206]  1957   221  10.1%
  bin  2:  4.2163 -  3.3594 [2064/2087]  1860   204   9.9%
  bin  3:  3.3594 -  2.9385 [2061/2083]  1855   206  10.0%
  bin  4:  2.9385 -  2.6715 [2034/2053]  1832   202   9.9%
  bin  5:  2.6715 -  2.4810 [2023/2052]  1812   211  10.4%
  bin  6:  2.4810 -  2.3353 [2006/2048]  1812   194   9.7%
  bin  7:  2.3353 -  2.2187 [2002/2038]  1805   197   9.8%
  bin  8:  2.2187 -  2.1224 [1998/2035]  1796   202  10.1%
  bin  9:  2.1224 -  2.0409 [1985/2017]  1788   197   9.9%
  bin 10:  2.0409 -  1.9707 [1238/2003]  1113   125  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_324/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:
        1.63 -     2.29: 15
        2.29 -     2.94: 1617
        2.94 -     3.59: 4505
        3.59 -     4.25: 9214
        4.25 -     4.90: 13022
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.635 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.713 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.844 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.991 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28368 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_324/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_324/model_refine_001.geo

CPU time processing inputs: 9.04


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 47.3993 86.39 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: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3287   r_free= 0.3210   ksol= 0.00   Bsol= 0.00   scale= 0.972    |
|                                                                             |
| 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:   0.37 A                  |
| x-ray target function (ml) for work reflections: 6.055395                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8387 -  4.7024 0.99   1403  157 0.2839 0.2968      6.3473       6.393|
|  2:  4.7024 -  3.7523 0.99   1363  151 0.2565 0.2369      6.4383      6.3881|
|  3:  3.7523 -  3.2838 0.99   1328  149 0.2796 0.2601      6.3352      6.3445|
|  4:  3.2838 -  2.9863 0.99   1312  137 0.3056 0.2982      6.2249      6.1665|
|  5:  2.9863 -  2.7737 0.99   1308  149 0.3412 0.2971      6.1172      6.0498|
|  6:  2.7737 -  2.6111 0.98   1304  149 0.3463 0.3753      6.0448       5.978|
|  7:  2.6111 -  2.4810 0.99   1298  152 0.3456 0.3168      6.0084      5.9219|
|  8:  2.4810 -  2.3734 0.99   1307  131 0.3590 0.3674      5.9719      6.0014|
|  9:  2.3734 -  2.2824 0.98   1295  148 0.3746 0.3633      5.9379      5.9231|
| 10:  2.2824 -  2.2039 0.98   1273  142 0.3664 0.3641        5.92      5.8804|
| 11:  2.2039 -  2.1352 0.98   1285  147 0.3816 0.3956      5.8699      5.8981|
| 12:  2.1352 -  2.0743 0.99   1289  137 0.3916 0.3877       5.824      5.8769|
| 13:  2.0743 -  2.0199 0.97   1268  137 0.4019 0.3922      5.7709      5.7322|
| 14:  2.0199 -  1.9707 0.47    597   73 0.4016 0.3850      5.7198      5.6071|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8387 -  4.7024  1403   157  0.77  27.66   0.87     0.78      46574.24|
|  2:  4.7024 -  3.7523  1363   151  0.84  22.22   0.98     0.91      46411.47|
|  3:  3.7523 -  3.2838  1328   149  0.82  24.92   0.99     0.96      42529.36|
|  4:  3.2838 -  2.9863  1312   137  0.79  27.60   0.99     0.95      36557.55|
|  5:  2.9863 -  2.7737  1308   149  0.73  32.77   0.98     0.91      31396.71|
|  6:  2.7737 -  2.6111  1304   149  0.72  34.13   0.99     0.90      28311.85|
|  7:  2.6111 -  2.4810  1298   152  0.73  33.26   1.01     0.91      25713.49|
|  8:  2.4810 -  2.3734  1307   131  0.72  34.33   1.01     0.93      24340.22|
|  9:  2.3734 -  2.2824  1295   148  0.70  35.74   1.01     0.94      22868.54|
| 10:  2.2824 -  2.2039  1273   142  0.69  36.44   1.04     0.92      21876.22|
| 11:  2.2039 -  2.1352  1285   147  0.67  38.26   1.02     0.93      22123.79|
| 12:  2.1352 -  2.0743  1289   137  0.64  40.75   1.04     0.92      21766.15|
| 13:  2.0743 -  2.0199  1268   137  0.63  42.05   1.03     0.89      19987.72|
| 14:  2.0199 -  1.9707   597    73  0.63  41.60   1.02     0.83      16220.46|
|alpha:            min =        0.78 max =            0.96 mean =         0.91|
|beta:             min =    16220.46 max =        46574.24 mean =     29789.91|
|figures of merit: min =        0.00 max =            1.00 mean =         0.72|
|phase err.(work): min =        0.00 max =           89.97 mean =        33.26|
|phase err.(test): min =        0.00 max =           89.79 mean =        33.54|
|-----------------------------------------------------------------------------|

============================== 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 = 3.379395              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.417   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.619110              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.718   (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 |  1.635 -  1.961:        4 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.961 -  2.288:       11 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.288 -  2.614:       44 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.614 -  2.941:     1573 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.941 -  3.267:     1907 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.267 -  3.594:     2598 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.594 -  3.920:     4746 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.920 -  4.247:     4468 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.247 -  4.573:     5939 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.573 -  4.900:     7083 |
|-----------------------------------------------------------------------------|
|-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 |        0.169 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.112    4.900  1.635 |       0.286 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.796)------------------------------------------|
|    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: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3287   r_free= 0.3210   ksol= 0.00   Bsol= 0.00   scale= 0.972    |
|                                                                             |
| 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:   0.37 A                  |
| x-ray target function (ml) for work reflections: 6.055395                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3169   r_free= 0.3089   ksol= 0.30   Bsol= 34.16   scale= 0.978   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.09,0.41,-1.62,0.00,-0.00,-0.00); trace/3= -0.77                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 6.034335                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.114229              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.295   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.338443              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.482   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3169      final r-factor (work) = 0.1907          |
| start r-factor (free) = 0.3089      final r-factor (free) = 0.2091          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.5868 = 3.11 * 0.50 * 6.0480 + 1.00 * 0.1695                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0243 = 3.11 * 0.50 * 5.7524 + 1.00 * 0.0671                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1907      final r-factor (work) = 0.1745          |
| start r-factor (free) = 0.2091      final r-factor (free) = 0.2138          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9530 = 0.34 * 1.00 * 5.7524 + 1.00 * 0.0061                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8744 = 0.34 * 1.00 * 5.5046 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.796)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    63.67   16.84    None  None   None       |
|    all(noH): 2823   0      0.00    63.67   16.84    None  None   None       |
|    Sol.    : 438    0      6.93    63.67   37.70    None  None   None       |
|    Mac.    : 2385   0      0.00    59.84   13.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.367:  283   |   5:    31.837 -  38.204:  114        |
|      1:     6.367 -  12.735: 1185   |   6:    38.204 -  44.571:  101        |
|      2:    12.735 -  19.102:  631   |   7:    44.571 -  50.939:   96        |
|      3:    19.102 -  25.469:  219   |   8:    50.939 -  57.306:   56        |
|      4:    25.469 -  31.837:  119   |   9:    57.306 -  63.673:   19        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1745 r_free = 0.2138             target_work(ml) = 5.514         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1741 r_free = 0.2138             target_work(ml) = 5.514         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1741   r_free= 0.2138   ksol= 0.30   Bsol= 34.16   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.09,0.41,-1.62,0.00,-0.00,-0.00); trace/3= -0.77                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.513627                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1721   r_free= 0.2114   ksol= 0.32   Bsol= 46.06   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.79,-1.38,-1.69,-0.00,-0.00,-0.00); trace/3= -1.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.508195                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.735123              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.638   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.178258              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 97.763   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1721      final r-factor (work) = 0.1329          |
| start r-factor (free) = 0.2114      final r-factor (free) = 0.1695          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8503 = 1.74 * 0.50 * 5.5133 + 1.00 * 0.0671                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7297 = 1.74 * 0.50 * 5.3941 + 1.00 * 0.0500                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1329      final r-factor (work) = 0.1273          |
| start r-factor (free) = 0.1695      final r-factor (free) = 0.1632          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9741 = 0.18 * 1.00 * 5.3941 + 1.00 * 0.0125                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9428 = 0.18 * 1.00 * 5.2489 + 1.00 * 0.0071                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.796)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.54    74.01   16.71    None  None   None       |
|    all(noH): 2823   0      1.54    74.01   16.71    None  None   None       |
|    Sol.    : 438    0      5.82    64.66   37.33    None  None   None       |
|    Mac.    : 2385   0      1.54    74.01   12.92    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:     1.544 -   8.790:  680   |   5:    37.777 -  45.024:  123        |
|      1:     8.790 -  16.037: 1251   |   6:    45.024 -  52.270:   92        |
|      2:    16.037 -  23.284:  364   |   7:    52.270 -  59.517:   52        |
|      3:    23.284 -  30.530:  121   |   8:    59.517 -  66.764:   19        |
|      4:    30.530 -  37.777:  120   |   9:    66.764 -  74.010:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1273 r_free = 0.1632             target_work(ml) = 5.229         |
| occupancies: max = 1.00  min = 0.19   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1272 r_free = 0.1632             target_work(ml) = 5.228         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1272   r_free= 0.1632   ksol= 0.32   Bsol= 46.06   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.79,-1.38,-1.69,-0.00,-0.00,-0.00); trace/3= -1.95                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.228242                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1274   r_free= 0.1625   ksol= 0.32   Bsol= 46.74   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.01,-1.80,-1.43,-0.00,-0.00,-0.00); trace/3= -2.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.228241                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.591733              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 116.588  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.169143              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 158.182  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1274      final r-factor (work) = 0.1122          |
| start r-factor (free) = 0.1625      final r-factor (free) = 0.1537          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8522 = 2.59 * 0.50 * 5.2492 + 1.00 * 0.0500                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7627 = 2.59 * 0.50 * 5.1687 + 1.00 * 0.0647                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1122      final r-factor (work) = 0.1109          |
| start r-factor (free) = 0.1537      final r-factor (free) = 0.1523          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8814 = 0.17 * 1.00 * 5.1687 + 1.00 * 0.0071                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8750 = 0.17 * 1.00 * 5.1319 + 1.00 * 0.0070                               |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.796)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.23    74.92   16.54    None  None   None       |
|    all(noH): 2823   0      2.23    74.92   16.54    None  None   None       |
|    Sol.    : 438    0      4.23    64.19   37.13    None  None   None       |
|    Mac.    : 2385   0      2.23    74.92   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:     2.226 -   9.495:  881   |   5:    38.571 -  45.840:  118        |
|      1:     9.495 -  16.764: 1135   |   6:    45.840 -  53.109:   96        |
|      2:    16.764 -  24.033:  297   |   7:    53.109 -  60.378:   41        |
|      3:    24.033 -  31.302:  125   |   8:    60.378 -  67.647:   15        |
|      4:    31.302 -  38.571:  114   |   9:    67.647 -  74.916:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1109 r_free = 0.1523             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1108 r_free = 0.1523             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1108   r_free= 0.1523   ksol= 0.32   Bsol= 46.74   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.01,-1.80,-1.43,-0.00,-0.00,-0.00); trace/3= -2.08                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.126968                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1108   r_free= 0.1523   ksol= 0.32   Bsol= 46.73   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.96,-1.89,-1.26,-0.00,-0.00,-0.00); trace/3= -2.04                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.127039                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.588530              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 139.245  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.241218              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 120.504  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1108      final r-factor (work) = 0.1118          |
| start r-factor (free) = 0.1523      final r-factor (free) = 0.1531          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1407 = 1.59 * 0.50 * 5.1318 + 1.00 * 0.0647                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1295 = 1.59 * 0.50 * 5.1328 + 1.00 * 0.0527                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1118      final r-factor (work) = 0.1103          |
| start r-factor (free) = 0.1531      final r-factor (free) = 0.1552          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 21.7762 = 4.24 * 1.00 * 5.1328 + 1.00 * 0.0070                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 21.7558 = 4.24 * 1.00 * 5.1273 + 1.00 * 0.0097                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.796)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.10   17.10    None  None   None       |
|    all(noH): 2823   0      0.00    91.10   17.10    None  None   None       |
|    Sol.    : 438    0      5.09    82.47   40.09    None  None   None       |
|    Mac.    : 2385   0      0.00    91.10   12.87    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.110:  837   |   5:    45.549 -  54.659:  106        |
|      1:     9.110 -  18.220: 1267   |   6:    54.659 -  63.769:   71        |
|      2:    18.220 -  27.329:  258   |   7:    63.769 -  72.878:   27        |
|      3:    27.329 -  36.439:  132   |   8:    72.878 -  81.988:    7        |
|      4:    36.439 -  45.549:  113   |   9:    81.988 -  91.098:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1103 r_free = 0.1552             target_work(ml) = 5.136         |
| occupancies: max = 1.00  min = 0.13   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1102 r_free = 0.1552             target_work(ml) = 5.136         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1102   r_free= 0.1552   ksol= 0.32   Bsol= 46.73   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.96,-1.89,-1.26,-0.00,-0.00,-0.00); trace/3= -2.04                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.135778                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1101   r_free= 0.1551   ksol= 0.32   Bsol= 49.38   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.76,-1.73,-1.05,-0.00,-0.00,-0.00); trace/3= -1.85                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.135516                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.345352              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 158.550  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.387546              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 116.394  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1101      final r-factor (work) = 0.1071          |
| start r-factor (free) = 0.1551      final r-factor (free) = 0.1554          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0661 = 2.35 * 0.50 * 5.1279 + 1.00 * 0.0527                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0692 = 2.35 * 0.50 * 5.1231 + 1.00 * 0.0615                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1071      final r-factor (work) = 0.1072          |
| start r-factor (free) = 0.1554      final r-factor (free) = 0.1543          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9951 = 0.39 * 1.00 * 5.1231 + 1.00 * 0.0096                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9938 = 0.39 * 1.00 * 5.1214 + 1.00 * 0.0091                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.796)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.91    91.28   16.81    None  None   None       |
|    all(noH): 2823   0      0.91    91.28   16.81    None  None   None       |
|    Sol.    : 438    0      5.50    82.87   39.47    None  None   None       |
|    Mac.    : 2385   0      0.91    91.28   12.65    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:     0.911 -   9.949: 1103   |   5:    46.097 -  55.134:  100        |
|      1:     9.949 -  18.986: 1063   |   6:    55.134 -  64.171:   70        |
|      2:    18.986 -  28.023:  211   |   7:    64.171 -  73.209:   20        |
|      3:    28.023 -  37.060:  133   |   8:    73.209 -  82.246:    6        |
|      4:    37.060 -  46.097:  112   |   9:    82.246 -  91.283:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1072 r_free = 0.1543             target_work(ml) = 5.118         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1072 r_free = 0.1543             target_work(ml) = 5.118         |
| occupancies: max = 1.00  min = 0.11   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1072   r_free= 0.1543   ksol= 0.32   Bsol= 49.38   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.76,-1.73,-1.05,-0.00,-0.00,-0.00); trace/3= -1.85                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.117804                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8387 -  4.7024 0.99   1403  157 0.0963 0.1265      5.3663      5.5359|
|  2:  4.7024 -  3.7523 0.99   1363  151 0.0817 0.1067      5.4023      5.5961|
|  3:  3.7523 -  3.2838 0.99   1328  149 0.1017 0.1492      5.4364       5.824|
|  4:  3.2838 -  2.9863 0.99   1312  137 0.1149 0.1474      5.4099      5.5702|
|  5:  2.9863 -  2.7737 0.99   1308  149 0.1261 0.1643      5.2909      5.4857|
|  6:  2.7737 -  2.6111 0.98   1304  149 0.1205 0.2005      5.1903      5.4711|
|  7:  2.6111 -  2.4810 0.99   1298  152 0.1154 0.1541      5.1202       5.313|
|  8:  2.4810 -  2.3734 0.99   1307  131 0.1095 0.1625      5.0419      5.2725|
|  9:  2.3734 -  2.2824 0.98   1295  148 0.1135 0.1869      4.9893      5.3181|
| 10:  2.2824 -  2.2039 0.98   1273  142 0.1074 0.1618      4.9353      5.1413|
| 11:  2.2039 -  2.1352 0.98   1285  147 0.1083 0.1766      4.8903      5.2118|
| 12:  2.1352 -  2.0743 0.99   1289  137 0.1065 0.1619      4.8309      5.1421|
| 13:  2.0743 -  2.0199 0.97   1268  137 0.1077 0.1663      4.7642      5.0012|
| 14:  2.0199 -  1.9707 0.47    597   73 0.1061 0.1837      4.6851      4.9579|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8387 -  4.7024  1403   157  0.94   9.11   0.97     0.95       6987.12|
|  2:  4.7024 -  3.7523  1363   151  0.95   7.83   1.01     1.00       8568.26|
|  3:  3.7523 -  3.2838  1328   149  0.94  10.88   1.02     1.02       9738.11|
|  4:  3.2838 -  2.9863  1312   137  0.93  12.99   1.01     1.00       9692.64|
|  5:  2.9863 -  2.7737  1308   149  0.90  15.51   1.00     0.97       7922.61|
|  6:  2.7737 -  2.6111  1304   149  0.90  16.05   0.98     0.95       6712.20|
|  7:  2.6111 -  2.4810  1298   152  0.91  14.71   0.98     0.95       5747.69|
|  8:  2.4810 -  2.3734  1307   131  0.91  14.59   0.99     0.97       5157.59|
|  9:  2.3734 -  2.2824  1295   148  0.91  15.41   0.99     0.96       4664.08|
| 10:  2.2824 -  2.2039  1273   142  0.90  15.26   0.99     0.95       4242.01|
| 11:  2.2039 -  2.1352  1285   147  0.91  15.35   0.99     0.96       4038.42|
| 12:  2.1352 -  2.0743  1289   137  0.91  14.82   1.00     0.99       3621.07|
| 13:  2.0743 -  2.0199  1268   137  0.91  15.35   0.99     0.98       3212.16|
| 14:  2.0199 -  1.9707   597    73  0.91  15.32   0.96     0.92       2660.76|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     2660.76 max =         9738.11 mean =      6092.22|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.89 mean =        13.68|
|phase err.(test): min =        0.00 max =           88.16 mean =        13.24|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1071   r_free= 0.1543   ksol= 0.32   Bsol= 49.35   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.53,-1.53,-0.80,-0.00,-0.00,-0.00); trace/3= -1.62                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.117933                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.84 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1071   r_free= 0.1543   ksol= 0.32   Bsol= 49.35   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.53,-1.53,-0.80,-0.00,-0.00,-0.00); trace/3= -1.62                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.117933                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8387 -  4.7024 0.99   1403  157 0.0964 0.1267      5.3674      5.5375|
|  2:  4.7024 -  3.7523 0.99   1363  151 0.0817 0.1067      5.4028      5.5959|
|  3:  3.7523 -  3.2838 0.99   1328  149 0.1017 0.1492      5.4364      5.8243|
|  4:  3.2838 -  2.9863 0.99   1312  137 0.1149 0.1474      5.4098      5.5702|
|  5:  2.9863 -  2.7737 0.99   1308  149 0.1261 0.1643      5.2908      5.4855|
|  6:  2.7737 -  2.6111 0.98   1304  149 0.1204 0.2004      5.1902      5.4706|
|  7:  2.6111 -  2.4810 0.99   1298  152 0.1154 0.1542      5.1202      5.3132|
|  8:  2.4810 -  2.3734 0.99   1307  131 0.1094 0.1626      5.0419      5.2724|
|  9:  2.3734 -  2.2824 0.98   1295  148 0.1135 0.1868      4.9895      5.3181|
| 10:  2.2824 -  2.2039 0.98   1273  142 0.1074 0.1620      4.9355      5.1422|
| 11:  2.2039 -  2.1352 0.98   1285  147 0.1082 0.1766      4.8904      5.2118|
| 12:  2.1352 -  2.0743 0.99   1289  137 0.1065 0.1620      4.8308      5.1425|
| 13:  2.0743 -  2.0199 0.97   1268  137 0.1077 0.1662      4.7641      5.0005|
| 14:  2.0199 -  1.9707 0.47    597   73 0.1060 0.1838      4.6851       4.958|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8387 -  4.7024  1403   157  0.94   9.12   0.98     0.95       7003.91|
|  2:  4.7024 -  3.7523  1363   151  0.95   7.84   1.02     1.00       8577.47|
|  3:  3.7523 -  3.2838  1328   149  0.94  10.88   1.03     1.02       9738.27|
|  4:  3.2838 -  2.9863  1312   137  0.93  12.99   1.01     1.00       9691.94|
|  5:  2.9863 -  2.7737  1308   149  0.90  15.51   1.00     0.98       7919.04|
|  6:  2.7737 -  2.6111  1304   149  0.90  16.05   0.98     0.95       6709.48|
|  7:  2.6111 -  2.4810  1298   152  0.91  14.71   0.99     0.96       5745.41|
|  8:  2.4810 -  2.3734  1307   131  0.91  14.59   1.00     0.98       5156.63|
|  9:  2.3734 -  2.2824  1295   148  0.91  15.41   1.00     0.96       4664.98|
| 10:  2.2824 -  2.2039  1273   142  0.90  15.27   1.00     0.96       4243.39|
| 11:  2.2039 -  2.1352  1285   147  0.91  15.36   1.00     0.97       4040.13|
| 12:  2.1352 -  2.0743  1289   137  0.91  14.83   1.01     1.00       3621.43|
| 13:  2.0743 -  2.0199  1268   137  0.91  15.35   1.00     0.99       3211.38|
| 14:  2.0199 -  1.9707   597    73  0.91  15.32   0.97     0.94       2659.57|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2659.57 max =         9738.27 mean =      6093.74|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.89 mean =        13.68|
|phase err.(test): min =        0.00 max =           88.17 mean =        13.25|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.796)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.88    91.25   16.78    None  None   None       |
|    all(noH): 2823   0      0.88    91.25   16.78    None  None   None       |
|    Sol.    : 438    0      5.47    82.84   39.44    None  None   None       |
|    Mac.    : 2385   0      0.88    91.25   12.62    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.880 -   9.917: 1103   |   5:    46.066 -  55.103:  100        |
|      1:     9.917 -  18.954: 1063   |   6:    55.103 -  64.140:   70        |
|      2:    18.954 -  27.992:  211   |   7:    64.140 -  73.177:   20        |
|      3:    27.992 -  37.029:  133   |   8:    73.177 -  82.214:    6        |
|      4:    37.029 -  46.066:  112   |   9:    82.214 -  91.252:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 280         
Filter by distance & map next to the model:
   mapped sites are within: 0.464 - 5.447
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 276 from: 280
   mapped sites are within: 0.727 - 5.447

peak=    5.692 closest distance to " NH2 ARG A  56 " =    2.289
peak=    5.535 closest distance to " CB  ARG A 275 " =    0.947
peak=    5.395 closest distance to " CG  PRO A  54 " =    1.274
peak=    5.151 closest distance to " CB  GLN A 223 " =    1.400
peak=    4.929 closest distance to " CB  SER A  63 " =    1.145
peak=    4.871 closest distance to " CB  GLN A 183 " =    1.307
peak=    4.782 closest distance to " O   HOH Z 142 " =    1.636
peak=    4.695 closest distance to " O   HOH Z 232 " =    2.378
peak=    4.662 closest distance to " C   PRO A 198 " =    1.466
peak=    4.645 closest distance to " O   HOH Z 126 " =    1.898
peak=    4.628 closest distance to " CG  PRO A 213 " =    1.224
peak=    4.607 closest distance to " O   HOH Z 403 " =    1.742
peak=    4.601 closest distance to " CB  GLU A 152 " =    1.141
peak=    4.587 closest distance to " O   HOH Z 298 " =    1.825
peak=    4.577 closest distance to " CA  TYR A  30 " =    0.923
peak=    4.503 closest distance to " O   HOH Z 402 " =    1.471
peak=    4.481 closest distance to " CB  ARG A 190 " =    1.724
peak=    4.392 closest distance to " CB  ARG A  79 " =    1.264
peak=    4.372 closest distance to " CB  TYR A 169 " =    0.801
peak=    4.368 closest distance to " O   HOH Z 234 " =    3.670
peak=    4.343 closest distance to " CG  PRO A  90 " =    1.191
peak=    4.323 closest distance to " O   HOH Z 369 " =    2.243
peak=    4.323 closest distance to " CD2 TRP A 179 " =    1.368
peak=    4.314 closest distance to " O   SER A  87 " =    2.157
peak=    4.313 closest distance to " NE2 GLN A  11 " =    1.016
peak=    4.287 closest distance to " O   HOH Z  15 " =    2.087
peak=    4.274 closest distance to " O   HOH Z 209 " =    2.252
peak=    4.272 closest distance to " O   HOH Z 287 " =    2.062
peak=    4.255 closest distance to " O   HOH Z  44 " =    1.935
peak=    4.209 closest distance to " CB  PRO A  54 " =    0.928
peak=    4.185 closest distance to " O   HOH Z 203 " =    1.751
peak=    4.181 closest distance to " O   HOH Z  97 " =    1.935
peak=    4.181 closest distance to " ND2 ASN A 187 " =    1.472
peak=    4.180 closest distance to " O   HOH Z 346 " =    1.608
peak=    4.178 closest distance to " O   HOH Z 193 " =    1.786
peak=    4.178 closest distance to " NH2BARG A 145 " =    2.114
peak=    4.177 closest distance to " NZ  LYS A 117 " =    3.036
peak=    4.143 closest distance to " CB  ASN A 148 " =    1.439
peak=    4.143 closest distance to " CG  PRO A 198 " =    1.227
peak=    4.136 closest distance to " O   HOH Z  78 " =    1.660
peak=    4.126 closest distance to " O   HOH Z 128 " =    1.923
peak=    4.125 closest distance to " O   HOH Z 250 " =    1.485
peak=    4.095 closest distance to " O   HOH Z 368 " =    2.069
peak=    4.045 closest distance to " O   HOH Z  97 " =    2.416
peak=    4.039 closest distance to " CB  VAL A 265 " =    1.236
peak=    4.036 closest distance to " O   HOH Z 272 " =    1.833
peak=    4.011 closest distance to " CB  GLU A 277 " =    3.590
peak=    3.995 closest distance to " CG  PRO A 243 " =    1.092
peak=    3.985 closest distance to " O   HOH Z 280 " =    2.978
peak=    3.982 closest distance to " O   HOH Z  40 " =    1.887
peak=    3.976 closest distance to " O   HOH Z  43 " =    1.979
peak=    3.974 closest distance to " O   HOH Z 316 " =    3.022
peak=    3.942 closest distance to " CG1BVAL A  72 " =    1.672
peak=    3.934 closest distance to " O   HOH Z  61 " =    1.563
peak=    3.926 closest distance to " CB  ARG A  79 " =    0.885
peak=    3.920 closest distance to " CG1 ILE A  33 " =    1.234
peak=    3.916 closest distance to " CD2 LEU A 297 " =    0.927
peak=    3.916 closest distance to " O   HOH Z 423 " =    1.990
peak=    3.914 closest distance to " CA  ALA A  21 " =    1.196
peak=    3.907 closest distance to " O   HOH Z 427 " =    2.883
peak=    3.906 closest distance to " O   HOH Z 158 " =    2.979
peak=    3.903 closest distance to " O   HOH Z 141 " =    1.702
peak=    3.902 closest distance to " CG  ARG A  66 " =    2.575
peak=    3.885 closest distance to " CA  ARG A  36 " =    1.035
peak=    3.875 closest distance to " O   HOH Z 189 " =    2.301
peak=    3.857 closest distance to " CZ  PHE A 218 " =    1.100
peak=    3.849 closest distance to " CG2 ILE A 120 " =    1.123
peak=    3.849 closest distance to " O   HOH Z  59 " =    2.282
peak=    3.835 closest distance to " CD  ARG A 269 " =    0.978
peak=    3.826 closest distance to " OD2 ASP A 298 " =    3.889
peak=    3.784 closest distance to " O   HOH Z 132 " =    2.710
peak=    3.783 closest distance to " CB  SER A   3 " =    1.237
peak=    3.773 closest distance to " OD1 ASN A  69 " =    2.483
peak=    3.764 closest distance to " O   HOH Z 371 " =    3.306
peak=    3.763 closest distance to " O   HOH Z 389 " =    1.867
peak=    3.758 closest distance to " CB  TRP A 266 " =    0.966
peak=    3.756 closest distance to " O   HOH Z 147 " =    1.758
peak=    3.754 closest distance to " CB  ASP A 140 " =    1.013
peak=    3.742 closest distance to " CB  GLU A 128 " =    1.188
peak=    3.742 closest distance to " O   HOH Z 126 " =    1.940
peak=    3.739 closest distance to " O   HOH Z 345 " =    2.962
peak=    3.733 closest distance to " O   HOH Z 291 " =    1.435
peak=    3.732 closest distance to " O   HOH Z 261 " =    1.727
peak=    3.732 closest distance to " CA  ASN A 176 " =    1.148
peak=    3.729 closest distance to " CB  ASN A  39 " =    0.853
peak=    3.729 closest distance to " O   HOH Z 303 " =    2.205
peak=    3.726 closest distance to " O   HOH Z 185 " =    1.748
peak=    3.723 closest distance to " O   HOH Z 411 " =    3.804
peak=    3.717 closest distance to " CB  LEU A 228 " =    1.127
peak=    3.715 closest distance to " O   HOH Z 406 " =    1.473
peak=    3.712 closest distance to " CG2 ILE A  20 " =    1.363
peak=    3.703 closest distance to " O   HOH Z 128 " =    2.227
peak=    3.703 closest distance to " CB  VAL A 202 " =    1.497
peak=    3.697 closest distance to " CA  ASN A 215 " =    1.131
peak=    3.689 closest distance to " CD  LYS A 166 " =    1.306
peak=    3.669 closest distance to " O   HOH Z 214 " =    2.284
peak=    3.663 closest distance to " CB  SER A 141 " =    1.030
peak=    3.654 closest distance to " O   HOH Z 108 " =    2.741
peak=    3.652 closest distance to " OD2 ASP A 286 " =    2.813
peak=    3.649 closest distance to " N   ASN A  39 " =    1.290
peak=    3.646 closest distance to " O   HOH Z 426 " =    1.485
peak=    3.644 closest distance to " O   HOH Z 180 " =    2.265
peak=    3.638 closest distance to " CB  TRP A 179 " =    1.267
peak=    3.637 closest distance to " CA  ARG A 195 " =    1.286
peak=    3.637 closest distance to " O   HOH Z 245 " =    1.364
peak=    3.631 closest distance to " O   HOH Z 392 " =    2.767
peak=    3.628 closest distance to " O   HOH Z 327 " =    1.587
peak=    3.620 closest distance to " O   HOH Z 227 " =    1.585
peak=    3.619 closest distance to " O   HOH Z 359 " =    1.447
peak=    3.610 closest distance to " O   HOH Z 421 " =    1.682
peak=    3.610 closest distance to " CB  ALA A 291 " =    1.288
peak=    3.610 closest distance to " O   HOH Z 416 " =    2.851
peak=    3.606 closest distance to " CA  LYS A 117 " =    1.253
peak=    3.599 closest distance to " O   HOH Z 265 " =    2.244
peak=    3.598 closest distance to " O   HOH Z 368 " =    3.682
peak=    3.587 closest distance to " O   HOH Z  19 " =    1.897
peak=    3.582 closest distance to " OE1 GLU A   2 " =    2.275
peak=    3.572 closest distance to " CB  SER A  26 " =    1.718
peak=    3.572 closest distance to " CG AARG A 275 " =    1.097
peak=    3.560 closest distance to " O   HOH Z  80 " =    1.665
peak=    3.558 closest distance to " OG BSER A 164 " =    2.304
peak=    3.556 closest distance to " CB  ARG A 139 " =    0.957
peak=    3.555 closest distance to " N   HIS A 108 " =    1.923
peak=    3.551 closest distance to " CB  TYR A 169 " =    0.880
peak=    3.551 closest distance to " O   HOH Z 298 " =    2.362
peak=    3.547 closest distance to " O   HOH Z 344 " =    3.105
peak=    3.546 closest distance to " CA  ALA A  84 " =    1.172
peak=    3.545 closest distance to " CA  ALA A 291 " =    0.806
peak=    3.533 closest distance to " O   HOH Z 261 " =    1.969
peak=    3.528 closest distance to " NH1AARG A 145 " =    1.262
peak=    3.519 closest distance to " O   HOH Z 357 " =    1.921
peak=    3.512 closest distance to " O   HOH Z 325 " =    2.267
peak=    3.509 closest distance to " CG  GLN A  58 " =    2.716
peak=    3.504 closest distance to " CB  ALA A 248 " =    1.299
peak=    3.492 closest distance to " O   HOH Z 305 " =    3.646
peak=    3.489 closest distance to " CD  ARG A 159 " =    0.743
peak=    3.484 closest distance to " O   HOH Z 193 " =    2.128
peak=    3.481 closest distance to " O   HOH Z 173 " =    2.031
peak=    3.479 closest distance to " CA  THR A 221 " =    0.963
peak=    3.479 closest distance to " NH2AARG A 275 " =    3.637
peak=    3.478 closest distance to " O   HOH Z 279 " =    2.165
peak=    3.474 closest distance to " O   HOH Z 365 " =    2.803
peak=    3.473 closest distance to " O   HOH Z 171 " =    1.778
peak=    3.462 closest distance to " CB  ILE A 120 " =    1.294
peak=    3.434 closest distance to " CB  SER A  62 " =    0.891
peak=    3.433 closest distance to " CE  LYS A  76 " =    0.849
peak=    3.426 closest distance to " O   HOH Z 258 " =    2.257
peak=    3.423 closest distance to " O   HOH Z 299 " =    4.388
peak=    3.421 closest distance to " CB  GLN A  89 " =    1.341
peak=    3.419 closest distance to " O   HOH Z  35 " =    2.394
peak=    3.417 closest distance to " O   HOH Z   1 " =    2.147
peak=    3.415 closest distance to " O   HOH Z 273 " =    2.843
peak=    3.411 closest distance to " O   HOH Z 353 " =    2.819
peak=    3.410 closest distance to " O   HOH Z 132 " =    2.560
peak=    3.409 closest distance to " O   HOH Z  88 " =    3.108
peak=    3.404 closest distance to " CA  ASP A 140 " =    1.143
peak=    3.401 closest distance to " O   HOH Z 285 " =    2.969
peak=    3.399 closest distance to " CB  GLU A  46 " =    0.956
peak=    3.398 closest distance to " O   HOH Z 313 " =    1.857
peak=    3.391 closest distance to " NE2 GLN A  77 " =    3.197
peak=    3.390 closest distance to " CA  ASP A 162 " =    1.098
peak=    3.388 closest distance to " CA  ALA A  51 " =    0.930
peak=    3.388 closest distance to " O   HOH Z 380 " =    1.959
peak=    3.380 closest distance to " CB  ASN A 110 " =    1.086
peak=    3.377 closest distance to " CG  MET A 185 " =    1.074
peak=    3.375 closest distance to " ND1 HIS A  81 " =    1.586
peak=    3.375 closest distance to " O   HOH Z 427 " =    3.091
peak=    3.373 closest distance to " CG2 THR A 221 " =    1.138
peak=    3.372 closest distance to " O   HOH Z 417 " =    3.149
peak=    3.369 closest distance to " O   HOH Z 187 " =    2.281
peak=    3.366 closest distance to " O   HOH Z  61 " =    1.517
peak=    3.365 closest distance to " O   HOH Z 183 " =    1.442
peak=    3.361 closest distance to " O   HOH Z 148 " =    3.249
peak=    3.357 closest distance to " O   ALA A 165 " =    1.408
peak=    3.353 closest distance to " N   TYR A 116 " =    1.547
peak=    3.352 closest distance to " O   HOH Z 126 " =    1.561
peak=    3.352 closest distance to " O   HOH Z 102 " =    1.249
peak=    3.352 closest distance to " O   HOH Z 109 " =    2.329
peak=    3.349 closest distance to " CB  THR A  31 " =    1.681
peak=    3.343 closest distance to " O   HOH Z 163 " =    1.482
peak=    3.338 closest distance to " O   HOH Z 345 " =    1.560
peak=    3.331 closest distance to " O   HOH Z 336 " =    1.660
peak=    3.330 closest distance to " O   HOH Z 281 " =    4.687
peak=    3.328 closest distance to " CG  LEU A 167 " =    1.218
peak=    3.327 closest distance to " ND2 ASN A 110 " =    1.541
peak=    3.319 closest distance to " CD1 ILE A 106 " =    0.972
peak=    3.316 closest distance to " CZ2 TRP A 179 " =    1.704
peak=    3.315 closest distance to " CA  ALA A 160 " =    0.884
peak=    3.312 closest distance to " CD  LYS A  76 " =    1.942
peak=    3.308 closest distance to " CA  MET A 105 " =    1.084
peak=    3.307 closest distance to " CG  LYS A  76 " =    1.005
peak=    3.301 closest distance to " CE1 TYR A 186 " =    1.244
peak=    3.299 closest distance to " CE  LYS A 119 " =    1.118
peak=    3.298 closest distance to " O   HOH Z 250 " =    1.587
peak=    3.294 closest distance to " CB  GLN A  88 " =    1.124
peak=    3.292 closest distance to " CG2 VAL A 257 " =    0.808
peak=    3.290 closest distance to " N   ARG A 156 " =    1.363
peak=    3.289 closest distance to " CA  ALA A 248 " =    1.218
peak=    3.284 closest distance to " CB  MET A  47 " =    1.012
peak=    3.281 closest distance to " CA  TYR A 116 " =    1.411
peak=    3.278 closest distance to " CB  ASN A 215 " =    1.143
peak=    3.277 closest distance to " CB  TYR A 116 " =    0.785
peak=    3.276 closest distance to " O   HOH Z 123 " =    2.215
peak=    3.275 closest distance to " CD1 LEU A 300 " =    1.253
peak=    3.270 closest distance to " O   HOH Z 425 " =    1.959
peak=    3.267 closest distance to " O   HOH Z 435 " =    1.871
peak=    3.266 closest distance to " O   HOH Z  66 " =    2.216
peak=    3.264 closest distance to " O   HOH Z 374 " =    2.570
peak=    3.259 closest distance to " NH2 ARG A 156 " =    1.123
peak=    3.254 closest distance to " CG2BVAL A  41 " =    0.864
peak=    3.251 closest distance to " O   HOH Z  49 " =    2.168
peak=    3.242 closest distance to " CA  ASP A 191 " =    0.887
peak=    3.239 closest distance to " CA  SER A  32 " =    1.610
peak=    3.237 closest distance to " N   CYS A 260 " =    0.816
peak=    3.236 closest distance to " CA  MET A  40 " =    1.099
peak=    3.234 closest distance to " CG  GLN A  77 " =    2.300
peak=    3.228 closest distance to " CD1 LEU A  96 " =    0.727
peak=    3.223 closest distance to " N   PHE A 130 " =    1.299
peak=    3.222 closest distance to " C   TYR A 214 " =    1.426
peak=    3.212 closest distance to " CB  ALA A 242 " =    0.990
peak=    3.212 closest distance to " OG  SER A  62 " =    2.772
peak=    3.210 closest distance to " O   HOH Z  85 " =    1.313
peak=    3.209 closest distance to " OH  TYR A 116 " =    1.047
peak=    3.209 closest distance to " O   HOH Z  89 " =    2.133
peak=    3.207 closest distance to " CB  SER A 212 " =    1.122
peak=    3.204 closest distance to " O   HOH Z 411 " =    1.664
peak=    3.203 closest distance to " CA  ASN A 217 " =    1.267
peak=    3.203 closest distance to " CB  ALA A   9 " =    1.559
peak=    3.199 closest distance to " CG2AVAL A 121 " =    2.203
peak=    3.192 closest distance to " CB  LYS A 290 " =    1.018
peak=    3.192 closest distance to " NH2 ARG A 219 " =    1.837
peak=    3.192 closest distance to " O   SER A  26 " =    1.679
peak=    3.192 closest distance to " CA  ALA A  43 " =    1.248
peak=    3.188 closest distance to " O   HOH Z 422 " =    2.658
peak=    3.182 closest distance to " CG2 VAL A 197 " =    1.096
peak=    3.180 closest distance to " CG1 VAL A 153 " =    0.956
peak=    3.178 closest distance to " CD2 HIS A  81 " =    1.114
peak=    3.174 closest distance to " OG  SER A 245 " =    1.573
peak=    3.174 closest distance to " OE1 GLU A 236 " =    1.146
peak=    3.166 closest distance to " CD  GLN A 194 " =    1.528
peak=    3.163 closest distance to " O   HOH Z 383 " =    2.014
peak=    3.161 closest distance to " CA  VAL A 125 " =    1.034
peak=    3.159 closest distance to " N   ASP A 162 " =    1.162
peak=    3.152 closest distance to " CG  ARG A  66 " =    0.939
peak=    3.147 closest distance to " OE2 GLU A  53 " =    2.063
peak=    3.145 closest distance to " O   HOH Z 403 " =    1.356
peak=    3.141 closest distance to " O   ASN A  74 " =    1.641
peak=    3.140 closest distance to " CA  SER A  87 " =    0.984
peak=    3.134 closest distance to " O   HOH Z 380 " =    1.921
peak=    3.114 closest distance to " CA  SER A 146 " =    1.775
peak=    3.114 closest distance to " O   HOH Z 313 " =    2.178
peak=    3.114 closest distance to " O   HOH Z 329 " =    3.918
peak=    3.111 closest distance to " O   HOH Z  88 " =    2.653
peak=    3.102 closest distance to " O   HOH Z 189 " =    2.481
peak=    3.097 closest distance to " CB  GLN A 205 " =    1.158
peak=    3.092 closest distance to " CD1AILE A 234 " =    0.936
peak=    3.086 closest distance to " CZ  PHE A  38 " =    1.297
peak=    3.084 closest distance to " O   HOH Z 425 " =    1.267
peak=    3.084 closest distance to " O   HOH Z  68 " =    1.699
peak=    3.078 closest distance to " O   HOH Z 417 " =    1.991
peak=    3.076 closest distance to " O   HOH Z 152 " =    1.863
peak=    3.073 closest distance to " CB  ASN A 142 " =    1.099
peak=    3.071 closest distance to " O   HOH Z 154 " =    1.943
peak=    3.071 closest distance to " NH1 ARG A 138 " =    1.273
peak=    3.069 closest distance to " O   HOH Z 251 " =    1.563
peak=    3.069 closest distance to " O   TRP A 274 " =    1.913
peak=    3.068 closest distance to " CB  GLN A 103 " =    0.883
peak=    3.060 closest distance to " CA  ASP A 191 " =    1.103
peak=    3.056 closest distance to " O   HOH Z 134 " =    1.168
peak=    3.054 closest distance to " CG  GLN A  11 " =    1.435
peak=    3.054 closest distance to " N   HIS A  86 " =    1.771
peak=    3.038 closest distance to " O   HOH Z 128 " =    1.699
peak=    3.032 closest distance to " O   HOH Z 271 " =    2.178
peak=    3.032 closest distance to " O   HOH Z 430 " =    5.447
peak=    3.029 closest distance to " O   HOH Z 129 " =    3.639
peak=    3.018 closest distance to " CB  VAL A 126 " =    1.177

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 197         
Filter by distance & map next to the model:
   mapped sites are within: 0.833 - 5.946
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 197 from: 197
   mapped sites are within: 0.833 - 5.946

peak=   -4.931 closest distance to " O   HOH Z 266 " =    4.932
peak=   -4.638 closest distance to " CD  GLN A  58 " =    1.094
peak=   -4.554 closest distance to " C   HIS A 108 " =    1.148
peak=   -4.471 closest distance to " SG  CYS A 254 " =    3.395
peak=   -4.460 closest distance to " CB  PRO A 243 " =    2.655
peak=   -4.379 closest distance to " O   HOH Z 377 " =    2.145
peak=   -4.281 closest distance to " OG BSER A 134 " =    1.243
peak=   -4.236 closest distance to " CD  ARG A 156 " =    2.083
peak=   -4.233 closest distance to " CG  GLN A 223 " =    2.030
peak=   -4.134 closest distance to " O   VAL A  67 " =    2.644
peak=   -4.096 closest distance to " OXT GLY A 302 " =    2.812
peak=   -4.078 closest distance to " O   HOH Z 198 " =    1.883
peak=   -4.070 closest distance to " O   HOH Z 231 " =    2.359
peak=   -4.055 closest distance to " O   HOH Z  13 " =    1.678
peak=   -4.048 closest distance to " O   PRO A 163 " =    2.110
peak=   -4.037 closest distance to " N   ALA A 248 " =    1.784
peak=   -4.000 closest distance to " CD1 LEU A 101 " =    2.397
peak=   -3.981 closest distance to " N   ALA A  43 " =    2.601
peak=   -3.962 closest distance to " O   HOH Z 290 " =    1.170
peak=   -3.961 closest distance to " CB  PHE A 192 " =    2.056
peak=   -3.953 closest distance to " CG1 VAL A 112 " =    2.778
peak=   -3.924 closest distance to " O   SER A 210 " =    1.925
peak=   -3.922 closest distance to " ND2 ASN A 187 " =    1.502
peak=   -3.901 closest distance to " OG  SER A  97 " =    2.193
peak=   -3.893 closest distance to " O   HOH Z 353 " =    2.229
peak=   -3.872 closest distance to " O   HOH Z 407 " =    2.823
peak=   -3.861 closest distance to " O   HOH Z 196 " =    1.970
peak=   -3.858 closest distance to " O   PRO A 198 " =    1.243
peak=   -3.853 closest distance to " CD1 LEU A  25 " =    2.508
peak=   -3.842 closest distance to " CG  ASP A 132 " =    2.327
peak=   -3.831 closest distance to " O   HOH Z 292 " =    4.502
peak=   -3.830 closest distance to " CA  ASP A 298 " =    1.074
peak=   -3.829 closest distance to " CB  ALA A 161 " =    2.569
peak=   -3.802 closest distance to " O   VAL A  67 " =    2.884
peak=   -3.796 closest distance to " O   HOH Z 351 " =    1.480
peak=   -3.785 closest distance to " CZ  TYR A 169 " =    1.821
peak=   -3.772 closest distance to " O   HOH Z 165 " =    1.936
peak=   -3.759 closest distance to " CB  ALA A 291 " =    2.324
peak=   -3.748 closest distance to " CG2 ILE A 263 " =    2.227
peak=   -3.724 closest distance to " CZ3 TRP A 179 " =    1.253
peak=   -3.724 closest distance to " O   HOH Z  10 " =    1.494
peak=   -3.708 closest distance to " CB  PHE A 208 " =    2.264
peak=   -3.696 closest distance to " O   HOH Z 114 " =    3.249
peak=   -3.682 closest distance to " N   GLN A  58 " =    1.684
peak=   -3.674 closest distance to " CE2 TYR A  30 " =    2.732
peak=   -3.673 closest distance to " N   ALA A 248 " =    2.242
peak=   -3.645 closest distance to " O   HOH Z 394 " =    1.515
peak=   -3.637 closest distance to " CB  ASN A  39 " =    2.325
peak=   -3.626 closest distance to " OD2 ASP A 171 " =    2.377
peak=   -3.626 closest distance to " O   HOH Z 389 " =    1.825
peak=   -3.620 closest distance to " O   HOH Z 166 " =    1.842
peak=   -3.613 closest distance to " OD1 ASN A 148 " =    1.523
peak=   -3.612 closest distance to " O   HOH Z  11 " =    2.130
peak=   -3.606 closest distance to " CD1 PHE A  59 " =    1.984
peak=   -3.604 closest distance to " O   PHE A 218 " =    1.576
peak=   -3.603 closest distance to " CB  ALA A 248 " =    2.263
peak=   -3.600 closest distance to " ND2 ASN A  45 " =    1.102
peak=   -3.589 closest distance to " O   HOH Z 126 " =    1.882
peak=   -3.589 closest distance to " O   LEU A 167 " =    1.500
peak=   -3.561 closest distance to " OD1 ASN A  39 " =    2.204
peak=   -3.559 closest distance to " CE  MET A 105 " =    2.289
peak=   -3.552 closest distance to " N   THR A  52 " =    1.708
peak=   -3.551 closest distance to " CD  ARG A 139 " =    1.605
peak=   -3.547 closest distance to " O   HOH Z 166 " =    1.616
peak=   -3.539 closest distance to " O   HOH Z  71 " =    1.856
peak=   -3.538 closest distance to " O   HOH Z 243 " =    1.995
peak=   -3.537 closest distance to " O   HOH Z  44 " =    2.255
peak=   -3.536 closest distance to " CD  ARG A 195 " =    5.159
peak=   -3.525 closest distance to " OG  SER A   3 " =    1.654
peak=   -3.522 closest distance to " CB  ASP A 286 " =    1.875
peak=   -3.521 closest distance to " OD1 ASP A 171 " =    1.551
peak=   -3.519 closest distance to " NE2 GLN A  88 " =    1.774
peak=   -3.517 closest distance to " CG1AVAL A  41 " =    2.706
peak=   -3.513 closest distance to " CB  ALA A 248 " =    2.094
peak=   -3.513 closest distance to " O   HOH Z 372 " =    2.292
peak=   -3.511 closest distance to " O   HOH Z 234 " =    4.045
peak=   -3.510 closest distance to " OD2 ASP A 191 " =    1.495
peak=   -3.498 closest distance to " O   VAL A 174 " =    2.114
peak=   -3.497 closest distance to " ND2 ASN A  45 " =    1.776
peak=   -3.475 closest distance to " O   HOH Z 301 " =    2.315
peak=   -3.474 closest distance to " OG BSER A 134 " =    1.798
peak=   -3.468 closest distance to " O   PRO A 198 " =    1.275
peak=   -3.465 closest distance to " O   GLY A  75 " =    1.744
peak=   -3.458 closest distance to " CB  ALA A 291 " =    2.290
peak=   -3.455 closest distance to " O   HOH Z 185 " =    2.455
peak=   -3.449 closest distance to " C   ILE A 234 " =    1.322
peak=   -3.446 closest distance to " CE1 TYR A 247 " =    2.717
peak=   -3.444 closest distance to " O   HOH Z 252 " =    3.635
peak=   -3.430 closest distance to " CG  ASP A 231 " =    0.833
peak=   -3.408 closest distance to " CD1 LEU A 255 " =    2.734
peak=   -3.408 closest distance to " CZ  ARG A  66 " =    1.212
peak=   -3.408 closest distance to " CD2 TYR A 247 " =    2.417
peak=   -3.407 closest distance to " CZ  PHE A  59 " =    1.653
peak=   -3.405 closest distance to " NE2 GLN A 194 " =    1.814
peak=   -3.397 closest distance to " O   ALA A 161 " =    1.753
peak=   -3.395 closest distance to " O   HOH Z  15 " =    1.496
peak=   -3.392 closest distance to " O   GLY A  80 " =    2.437
peak=   -3.392 closest distance to " O   ALA A  10 " =    1.809
peak=   -3.386 closest distance to " O   HOH Z 414 " =    1.469
peak=   -3.381 closest distance to " O   HOH Z 311 " =    3.638
peak=   -3.377 closest distance to " CG1 VAL A  78 " =    3.132
peak=   -3.376 closest distance to " O   HOH Z 422 " =    1.502
peak=   -3.375 closest distance to " O   HOH Z 283 " =    2.169
peak=   -3.369 closest distance to " CG1 VAL A 125 " =    2.279
peak=   -3.369 closest distance to " CG  GLU A  53 " =    1.508
peak=   -3.362 closest distance to " OE1 GLN A 183 " =    1.498
peak=   -3.345 closest distance to " CA  GLY A 133 " =    2.324
peak=   -3.344 closest distance to " CG  PHE A 283 " =    2.487
peak=   -3.342 closest distance to " CB  ALA A  43 " =    2.469
peak=   -3.335 closest distance to " O   HOH Z 171 " =    2.053
peak=   -3.333 closest distance to " CD1 LEU A 228 " =    2.095
peak=   -3.330 closest distance to " O   HOH Z  52 " =    1.449
peak=   -3.327 closest distance to " CG  GLU A   2 " =    1.839
peak=   -3.321 closest distance to " O   HOH Z 211 " =    1.554
peak=   -3.308 closest distance to " CD  LYS A 289 " =    2.400
peak=   -3.307 closest distance to " O   SER A 135 " =    1.542
peak=   -3.307 closest distance to " CD2 LEU A 237 " =    2.335
peak=   -3.305 closest distance to " O   HOH Z 102 " =    1.610
peak=   -3.304 closest distance to " O   VAL A 189 " =    1.755
peak=   -3.297 closest distance to " CA  GLY A 203 " =    2.346
peak=   -3.296 closest distance to " NH2 ARG A  79 " =    2.071
peak=   -3.295 closest distance to " O   HOH Z  38 " =    1.654
peak=   -3.295 closest distance to " O   ALA A  34 " =    2.195
peak=   -3.292 closest distance to " O   HOH Z 177 " =    1.629
peak=   -3.288 closest distance to " O   HOH Z 377 " =    1.702
peak=   -3.285 closest distance to " O   HOH Z 361 " =    3.432
peak=   -3.280 closest distance to " CD2 LEU A 237 " =    2.624
peak=   -3.278 closest distance to " CD2 LEU A 237 " =    2.185
peak=   -3.277 closest distance to " CG2 VAL A 189 " =    2.162
peak=   -3.273 closest distance to " O   VAL A 189 " =    2.593
peak=   -3.272 closest distance to " OG  SER A  62 " =    1.660
peak=   -3.266 closest distance to " NH1 ARG A 195 " =    2.577
peak=   -3.264 closest distance to " CG1 VAL A 112 " =    2.578
peak=   -3.260 closest distance to " O   HOH Z 367 " =    2.574
peak=   -3.259 closest distance to " CB  SER A 258 " =    2.051
peak=   -3.251 closest distance to " O   HOH Z 111 " =    2.033
peak=   -3.248 closest distance to " C   LEU A 143 " =    0.998
peak=   -3.243 closest distance to " CB  ALA A  10 " =    2.301
peak=   -3.242 closest distance to " O   TRP A  92 " =    1.731
peak=   -3.242 closest distance to " NH2AARG A 275 " =    5.036
peak=   -3.238 closest distance to " CD2 TYR A 293 " =    2.008
peak=   -3.237 closest distance to " CB  PRO A 163 " =    2.532
peak=   -3.227 closest distance to " O   HOH Z 427 " =    1.400
peak=   -3.226 closest distance to " NE2 GLN A 103 " =    1.657
peak=   -3.226 closest distance to " O   HOH Z 193 " =    1.743
peak=   -3.223 closest distance to " CD2 LEU A 300 " =    2.727
peak=   -3.220 closest distance to " O   HOH Z   9 " =    2.074
peak=   -3.218 closest distance to " SG ACYS A 201 " =    2.018
peak=   -3.213 closest distance to " O   ALA A  51 " =    1.268
peak=   -3.211 closest distance to " C   GLN A 205 " =    1.842
peak=   -3.208 closest distance to " NH2 ARG A 159 " =    2.360
peak=   -3.207 closest distance to " CD1 TYR A 247 " =    2.603
peak=   -3.207 closest distance to " CB  TRP A  85 " =    2.577
peak=   -3.206 closest distance to " O   HOH Z  43 " =    1.643
peak=   -3.203 closest distance to " OE1 GLN A 223 " =    1.968
peak=   -3.201 closest distance to " O   HOH Z 134 " =    2.898
peak=   -3.201 closest distance to " ND2 ASN A  39 " =    1.170
peak=   -3.199 closest distance to " OG  SER A  26 " =    1.273
peak=   -3.199 closest distance to " O   HOH Z 362 " =    5.897
peak=   -3.195 closest distance to " CA  PRO A 243 " =    2.344
peak=   -3.193 closest distance to " N   SER A 276 " =    1.365
peak=   -3.192 closest distance to " ND2 ASN A 249 " =    2.299
peak=   -3.186 closest distance to " N   ALA A 226 " =    1.968
peak=   -3.183 closest distance to " O   HOH Z   6 " =    1.673
peak=   -3.183 closest distance to " CE3 TRP A 150 " =    2.209
peak=   -3.181 closest distance to " C   PRO A  90 " =    1.509
peak=   -3.172 closest distance to " O   HOH Z 281 " =    2.593
peak=   -3.169 closest distance to " C   ALA A 158 " =    1.339
peak=   -3.161 closest distance to " O   ILE A 106 " =    1.856
peak=   -3.159 closest distance to " CA  GLY A 241 " =    3.234
peak=   -3.159 closest distance to " CG  PRO A 243 " =    1.722
peak=   -3.158 closest distance to " O   HOH Z 174 " =    4.059
peak=   -3.155 closest distance to " O   HOH Z 148 " =    3.798
peak=   -3.152 closest distance to " O   ASN A  45 " =    1.870
peak=   -3.151 closest distance to " OD1 ASN A 301 " =    1.999
peak=   -3.150 closest distance to " CB  PHE A  16 " =    2.613
peak=   -3.148 closest distance to " OH  TYR A 169 " =    0.959
peak=   -3.145 closest distance to " CG  GLN A  11 " =    1.848
peak=   -3.139 closest distance to " O   HOH Z  37 " =    1.768
peak=   -3.128 closest distance to " O   SER A   3 " =    1.095
peak=   -3.128 closest distance to " O   HOH Z 251 " =    1.536
peak=   -3.114 closest distance to " CD2 PHE A  61 " =    2.564
peak=   -3.108 closest distance to " N   VAL A 189 " =    1.636
peak=   -3.108 closest distance to " O   HOH Z 191 " =    5.946
peak=   -3.107 closest distance to " O   HOH Z 377 " =    1.886
peak=   -3.100 closest distance to " O   HOH Z  11 " =    1.742
peak=   -3.098 closest distance to " NE2 GLN A  88 " =    1.060
peak=   -3.091 closest distance to " O   ILE A 234 " =    1.254
peak=   -3.091 closest distance to " O   HOH Z 116 " =    1.435
peak=   -3.084 closest distance to " CB  ALA A   9 " =    2.554
peak=   -3.082 closest distance to " O   HOH Z 280 " =    2.454
peak=   -3.071 closest distance to " CZ3 TRP A 274 " =    2.422
peak=   -3.060 closest distance to " O   HOH Z 139 " =    3.165
peak=   -3.055 closest distance to " CE  MET A  93 " =    1.193
peak=   -3.053 closest distance to " ND2 ASN A  60 " =    1.400
peak=   -3.026 closest distance to " O   HOH Z 394 " =    1.219
peak=   -3.002 closest distance to " O   HOH Z 351 " =    1.364

================= 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    :  0.3287 0.3210   6.055395e+00   6.031294e+00
   1_bss:  0.3169 0.3089   6.034335e+00   6.008034e+00
   1_xyz:  0.1907 0.2091   5.566248e+00   5.655284e+00
   1_adp:  0.1745 0.2138   5.514268e+00   5.680999e+00
   1_occ:  0.1741 0.2138   5.513627e+00   5.681142e+00
   2_bss:  0.1721 0.2114   5.508195e+00   5.672388e+00
   2_xyz:  0.1329 0.1695   5.271771e+00   5.458939e+00
   2_adp:  0.1273 0.1632   5.228623e+00   5.418773e+00
   2_occ:  0.1272 0.1632   5.228242e+00   5.418458e+00
   3_bss:  0.1274 0.1625   5.228241e+00   5.415560e+00
   3_xyz:  0.1122 0.1537   5.138672e+00   5.363756e+00
   3_adp:  0.1109 0.1523   5.127012e+00   5.354819e+00
   3_occ:  0.1108 0.1523   5.126968e+00   5.355048e+00
   4_bss:  0.1108 0.1523   5.127039e+00   5.355146e+00
   4_xyz:  0.1118 0.1531   5.135730e+00   5.361681e+00
   4_adp:  0.1103 0.1552   5.135681e+00   5.373346e+00
   4_occ:  0.1102 0.1552   5.135778e+00   5.373644e+00
   5_bss:  0.1101 0.1551   5.135516e+00   5.373348e+00
   5_xyz:  0.1071 0.1554   5.121856e+00   5.371917e+00
   5_adp:  0.1072 0.1543   5.117806e+00   5.365296e+00
   5_occ:  0.1072 0.1543   5.117804e+00   5.365366e+00
   5_bss:  0.1071 0.1543   5.117933e+00   5.365492e+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:  0.305  34.160  -1.086   0.408  -1.617   0.000  -0.000  -0.000
   1_xyz:  0.305  34.160  -1.086   0.408  -1.617   0.000  -0.000  -0.000
   1_adp:  0.305  34.160  -1.086   0.408  -1.617   0.000  -0.000  -0.000
   1_occ:  0.305  34.160  -1.086   0.408  -1.617   0.000  -0.000  -0.000
   2_bss:  0.320  46.063  -2.788  -1.382  -1.689  -0.000  -0.000  -0.000
   2_xyz:  0.320  46.063  -2.788  -1.382  -1.689  -0.000  -0.000  -0.000
   2_adp:  0.320  46.063  -2.788  -1.382  -1.689  -0.000  -0.000  -0.000
   2_occ:  0.320  46.063  -2.788  -1.382  -1.689  -0.000  -0.000  -0.000
   3_bss:  0.322  46.736  -3.012  -1.795  -1.428  -0.000  -0.000  -0.000
   3_xyz:  0.322  46.736  -3.012  -1.795  -1.428  -0.000  -0.000  -0.000
   3_adp:  0.322  46.736  -3.012  -1.795  -1.428  -0.000  -0.000  -0.000
   3_occ:  0.322  46.736  -3.012  -1.795  -1.428  -0.000  -0.000  -0.000
   4_bss:  0.323  46.734  -2.958  -1.889  -1.261  -0.000  -0.000  -0.000
   4_xyz:  0.323  46.734  -2.958  -1.889  -1.261  -0.000  -0.000  -0.000
   4_adp:  0.323  46.734  -2.958  -1.889  -1.261  -0.000  -0.000  -0.000
   4_occ:  0.323  46.734  -2.958  -1.889  -1.261  -0.000  -0.000  -0.000
   5_bss:  0.321  49.380  -2.764  -1.728  -1.054  -0.000  -0.000  -0.000
   5_xyz:  0.321  49.380  -2.764  -1.728  -1.054  -0.000  -0.000  -0.000
   5_adp:  0.321  49.380  -2.764  -1.728  -1.054  -0.000  -0.000  -0.000
   5_occ:  0.321  49.380  -2.764  -1.728  -1.054  -0.000  -0.000  -0.000
   5_bss:  0.321  49.349  -2.529  -1.525  -0.802  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  33.287 0.7243  0.9086    29787.272
   1_bss:  32.142 0.7356  0.9005    26709.269
   1_xyz:  20.155 0.8612  0.9985    11308.467
   1_adp:  20.898 0.8534  0.9916    11868.910
   1_occ:  20.912 0.8532  0.9911    11874.132
   2_bss:  20.672 0.8554  0.9524    11604.888
   2_xyz:  15.771 0.8999  0.9787     7288.694
   2_adp:  14.840 0.9080  0.9786     6753.520
   2_occ:  14.840 0.9080  0.9785     6750.305
   3_bss:  14.789 0.9083  0.9740     6683.050
   3_xyz:  13.749 0.9168  0.9782     6089.359
   3_adp:  13.531 0.9186  0.9750     6009.475
   3_occ:  13.537 0.9185  0.9749     6009.645
   4_bss:  13.541 0.9185  0.9765     6012.341
   4_xyz:  13.575 0.9185  0.9756     6059.530
   4_adp:  13.794 0.9169  0.9686     6169.464
   4_occ:  13.797 0.9168  0.9686     6172.937
   5_bss:  13.791 0.9169  0.9752     6167.566
   5_xyz:  13.765 0.9171  0.9755     6169.519
   5_adp:  13.632 0.9180  0.9700     6091.351
   5_occ:  13.634 0.9180  0.9700     6091.279
   5_bss:  13.637 0.9180  0.9769     6092.802
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.112   1.6949e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.112   1.6949e-01
   1_xyz:   1.106  0.007  0.068 14.956  0.004  4.110   6.7129e-02
   1_adp:   1.106  0.007  0.068 14.956  0.004  4.110   6.7129e-02
   1_occ:   1.106  0.007  0.068 14.956  0.004  4.110   6.7129e-02
   2_bss:   1.106  0.007  0.068 14.956  0.004  4.110   6.7129e-02
   2_xyz:   0.921  0.005  0.067 14.360  0.004  4.117   4.9957e-02
   2_adp:   0.921  0.005  0.067 14.360  0.004  4.117   4.9957e-02
   2_occ:   0.921  0.005  0.067 14.360  0.004  4.117   4.9957e-02
   3_bss:   0.921  0.005  0.067 14.360  0.004  4.117   4.9957e-02
   3_xyz:   1.049  0.008  0.078 14.820  0.004  4.110   6.4749e-02
   3_adp:   1.049  0.008  0.078 14.820  0.004  4.110   6.4749e-02
   3_occ:   1.049  0.008  0.078 14.820  0.004  4.110   6.4749e-02
   4_bss:   1.049  0.008  0.078 14.820  0.004  4.110   6.4749e-02
   4_xyz:   0.930  0.006  0.071 14.447  0.004  4.110   5.2731e-02
   4_adp:   0.930  0.006  0.071 14.447  0.004  4.110   5.2731e-02
   4_occ:   0.930  0.006  0.071 14.447  0.004  4.110   5.2731e-02
   5_bss:   0.930  0.006  0.071 14.447  0.004  4.110   5.2731e-02
   5_xyz:   1.019  0.008  0.077 14.672  0.004  4.111   6.1501e-02
   5_adp:   1.019  0.008  0.077 14.672  0.004  4.111   6.1501e-02
   5_occ:   1.019  0.008  0.077 14.672  0.004  4.111   6.1501e-02
   5_bss:   1.019  0.008  0.077 14.672  0.004  4.111   6.1501e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.635   2.4072e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.635   2.4072e-01
   1_xyz:   7.324  0.037  0.254 86.104  0.038  2.288   9.2827e-02
   1_adp:   7.324  0.037  0.254 86.104  0.038  2.288   9.2827e-02
   1_occ:   7.324  0.037  0.254 86.104  0.038  2.288   9.2827e-02
   2_bss:   7.324  0.037  0.254 86.104  0.038  2.288   9.2827e-02
   2_xyz:   6.598  0.034  0.188 80.161  0.038  2.356   3.9592e-02
   2_adp:   6.598  0.034  0.188 80.161  0.038  2.356   3.9592e-02
   2_occ:   6.598  0.034  0.188 80.161  0.038  2.356   3.9592e-02
   3_bss:   6.598  0.034  0.188 80.161  0.038  2.356   3.9592e-02
   3_xyz:   7.742  0.047  0.244 83.662  0.037  2.338   5.7302e-02
   3_adp:   7.742  0.047  0.244 83.662  0.037  2.338   5.7302e-02
   3_occ:   7.742  0.047  0.244 83.662  0.037  2.338   5.7302e-02
   4_bss:   7.742  0.047  0.244 83.662  0.037  2.338   5.7302e-02
   4_xyz:   6.822  0.047  0.225 82.141  0.038  2.388   3.3857e-02
   4_adp:   6.822  0.047  0.225 82.141  0.038  2.388   3.3857e-02
   4_occ:   6.822  0.047  0.225 82.141  0.038  2.388   3.3857e-02
   5_bss:   6.822  0.047  0.225 82.141  0.038  2.388   3.3857e-02
   5_xyz:   7.464  0.049  0.254 82.780  0.037  2.315   4.4681e-02
   5_adp:   7.464  0.049  0.254 82.780  0.037  2.315   4.4681e-02
   5_occ:   7.464  0.049  0.254 82.780  0.037  2.315   4.4681e-02
   5_bss:   7.464  0.049  0.254 82.780  0.037  2.315   4.4681e-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:  63.67   0.00  16.84  59.84   0.00  13.00  63.67   6.93  37.70
   1_occ:  63.67   0.00  16.84  59.84   0.00  13.00  63.67   6.93  37.70
   2_bss:  63.67   0.00  16.84  59.84   0.00  13.00  63.67   6.93  37.70
   2_xyz:  63.67   0.00  16.84  59.84   0.00  13.00  63.67   6.93  37.70
   2_adp:  74.01   1.54  16.71  74.01   1.54  12.92  64.66   5.82  37.33
   2_occ:  74.01   1.54  16.71  74.01   1.54  12.92  64.66   5.82  37.33
   3_bss:  74.01   1.54  16.71  74.01   1.54  12.92  64.66   5.82  37.33
   3_xyz:  74.01   1.54  16.71  74.01   1.54  12.92  64.66   5.82  37.33
   3_adp:  74.92   2.23  16.54  74.92   2.23  12.76  64.19   4.23  37.13
   3_occ:  74.92   2.23  16.54  74.92   2.23  12.76  64.19   4.23  37.13
   4_bss:  74.92   2.23  16.54  74.92   2.23  12.76  64.19   4.23  37.13
   4_xyz:  74.92   2.23  16.54  74.92   2.23  12.76  64.19   4.23  37.13
   4_adp:  91.10   0.00  17.10  91.10   0.00  12.87  82.47   5.09  40.09
   4_occ:  91.10   0.00  17.10  91.10   0.00  12.87  82.47   5.09  40.09
   5_bss:  91.10   0.00  17.10  91.10   0.00  12.87  82.47   5.09  40.09
   5_xyz:  91.10   0.00  17.10  91.10   0.00  12.87  82.47   5.09  40.09
   5_adp:  91.28   0.91  16.81  91.28   0.91  12.65  82.87   5.50  39.47
   5_occ:  91.28   0.91  16.81  91.28   0.91  12.65  82.87   5.50  39.47
   5_bss:  91.25   0.88  16.78  91.25   0.88  12.62  82.84   5.47  39.44
------------------------------------------------------------------------
 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:    1.488    0.003    0.303
   1_adp:    1.488    0.003    0.303
   1_occ:    1.488    0.003    0.303
   2_bss:    1.488    0.003    0.303
   2_xyz:    1.012    0.027    0.360
   2_adp:    1.012    0.027    0.360
   2_occ:    1.012    0.027    0.360
   3_bss:    1.012    0.027    0.360
   3_xyz:    0.937    0.030    0.407
   3_adp:    0.937    0.030    0.407
   3_occ:    0.937    0.030    0.407
   4_bss:    0.937    0.030    0.407
   4_xyz:    1.041    0.051    0.414
   4_adp:    1.041    0.051    0.414
   4_occ:    1.041    0.051    0.414
   5_bss:    1.041    0.051    0.414
   5_xyz:    0.999    0.063    0.422
   5_adp:    0.999    0.063    0.422
   5_occ:    0.999    0.063    0.422
   5_bss:    0.999    0.063    0.422
------------------------------------------------------------------------

CPU time actual refinement: 340.15


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_324/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_324/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_324/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_324/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_324/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 340.00 
  Macro-tasks:
    bulk solvent and scale       = 37.77  
    individual site refinement   = 147.69 
    weights calculation          = 29.13  
    collect and process          = 6.58   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 221.26 
  Micro-tasks:
    mask                            = 1.21   
    f_calc                          = 109.20 
    alpha_beta                      = 8.30   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 120.37 
    fmodel                         = 6.99   
    r_factors                      = 0.19   
    phase_errors                   = 11.14  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 258.81 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.700 micro seconds
Total CPU time: 5.89 minutes
from_scatterers_fft:    670 calls, 108.75 s
gradients_fft:          615 calls, 105.86 s

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

# Date 2008-01-16 Time 04:32:58 PST -0800 (1200486778.28 s)
Start R-work = 0.3287, R-free = 0.3210 (no bulk solvent and anisotropic scale)
Final R-work = 0.1305, R-free = 0.1729 (no bulk solvent and anisotropic scale)

Start R-work = 0.3169, R-free = 0.3089
Final R-work = 0.1071, R-free = 0.1543