# Date 2008-01-16 Time 04:29:48 PST -0800 (1200486588.36 s)
#phil __OFF__

Command line arguments: "../338.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 7421
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 338

-------------------------------------------------------------------------------
  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, 47.6339, 87.6859, 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: 3.35, per 1000 atoms: 1.19


================================== 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, 47.6339, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9291 1.97084
Completeness in resolution range: 0.93024
Completeness with d_max=infinity: 0.927422

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9291
                             d_min =   1.9708

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, 47.6339, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9291 1.97084
Completeness in resolution range: 0.93024
Completeness with d_max=infinity: 0.927422

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9295 -  4.2171 [2211/2239]  1988   223  10.1%
  bin  2:  4.2171 -  3.3598 [2119/2142]  1903   216  10.2%
  bin  3:  3.3598 -  2.9388 [2085/2110]  1884   201   9.6%
  bin  4:  2.9388 -  2.6718 [2085/2101]  1872   213  10.2%
  bin  5:  2.6718 -  2.4812 [2040/2078]  1831   209  10.2%
  bin  6:  2.4812 -  2.3355 [2069/2102]  1866   203   9.8%
  bin  7:  2.3355 -  2.2189 [2039/2076]  1839   200   9.8%
  bin  8:  2.2189 -  2.1226 [2037/2079]  1830   207  10.2%
  bin  9:  2.1226 -  2.0411 [2015/2054]  1820   195   9.7%
  bin 10:  2.0411 -  1.9708 [ 889/2077]   797    92  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_338/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.55 -     2.22: 14
        2.22 -     2.89: 1329
        2.89 -     3.56: 4437
        3.56 -     4.23: 9115
        4.23 -     4.90: 13254
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.553 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.692 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.718 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.792 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28144 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_338/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_338/model_refine_001.geo

CPU time processing inputs: 8.99


============================ 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 47.63395 87.68585 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 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4270   r_free= 0.4191   ksol= 0.00   Bsol= 0.00   scale= 0.916    |
|                                                                             |
| 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:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.225274                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9295 -  4.7036 0.99   1436  159 0.3275 0.3438      6.4664      6.4795|
|  2:  4.7036 -  3.7529 0.99   1387  154 0.3512 0.3560      6.6861       6.712|
|  3:  3.7529 -  3.2843 0.99   1346  149 0.3959 0.3657      6.5872      6.5391|
|  4:  3.2843 -  2.9866 0.99   1353  147 0.4139 0.4077       6.421      6.4111|
|  5:  2.9866 -  2.7740 0.98   1325  152 0.4525 0.4104      6.2992      6.2915|
|  6:  2.7740 -  2.6114 0.99   1346  145 0.4553 0.4924      6.2196      6.1416|
|  7:  2.6114 -  2.4812 0.99   1285  156 0.4511 0.4222      6.1692      6.0888|
|  8:  2.4812 -  2.3736 0.99   1343  134 0.4869 0.4504       6.143       6.111|
|  9:  2.3736 -  2.2826 0.99   1327  151 0.4839 0.4464      6.0923      6.1022|
| 10:  2.2826 -  2.2041 0.98   1317  142 0.4855 0.4639       6.064       6.026|
| 11:  2.2041 -  2.1354 0.98   1278  154 0.4938 0.4845      6.0032      6.0149|
| 12:  2.1354 -  2.0745 1.00   1322  143 0.4916 0.4892      5.9221      5.9586|
| 13:  2.0745 -  2.0200 0.91   1238  132 0.5087 0.5640      5.8614      5.8402|
| 14:  2.0200 -  1.9708 0.25    327   41 0.4582 0.4430      5.8554      5.6837|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9295 -  4.7036  1436   159  0.74  30.92   0.85     0.75      58121.19|
|  2:  4.7036 -  3.7529  1387   154  0.76  29.69   0.94     0.85      78681.70|
|  3:  3.7529 -  3.2843  1346   149  0.69  36.17   0.92     0.85      80825.55|
|  4:  3.2843 -  2.9866  1353   147  0.62  42.04   0.93     0.80      70829.62|
|  5:  2.9866 -  2.7740  1325   152  0.56  47.35   0.91     0.74      58192.40|
|  6:  2.7740 -  2.6114  1346   145  0.53  49.43   0.93     0.70      52114.63|
|  7:  2.6114 -  2.4812  1285   156  0.53  49.74   0.95     0.70      47463.99|
|  8:  2.4812 -  2.3736  1343   134  0.53  49.79   0.93     0.72      42123.92|
|  9:  2.3736 -  2.2826  1327   151  0.54  49.13   0.92     0.75      38436.65|
| 10:  2.2826 -  2.2041  1317   142  0.53  50.15   0.94     0.74      35538.70|
| 11:  2.2041 -  2.1354  1278   154  0.46  55.54   0.95     0.69      38418.48|
| 12:  2.1354 -  2.0745  1322   143  0.38  61.48   0.94     0.60      39355.22|
| 13:  2.0745 -  2.0200  1238   132  0.34  64.52   0.92     0.54      36317.99|
| 14:  2.0200 -  1.9708   327    41  0.42  58.30   1.01     0.53      27142.20|
|alpha:            min =        0.53 max =            0.85 mean =         0.72|
|beta:             min =    27142.20 max =        80825.55 mean =     51889.14|
|figures of merit: min =        0.00 max =            1.00 mean =         0.56|
|phase err.(work): min =        0.00 max =           89.99 mean =        47.29|
|phase err.(test): min =        0.00 max =           89.97 mean =        47.49|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.318413              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.850   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.247847              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.745   (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 |  1.553 -  1.888:        6 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.888 -  2.223:        8 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.223 -  2.557:       33 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.557 -  2.892:     1296 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.892 -  3.227:     1887 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.227 -  3.561:     2550 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.561 -  3.896:     4641 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.896 -  4.231:     4474 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.231 -  4.565:     6039 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.565 -  4.900:     7215 |
|-----------------------------------------------------------------------------|
|-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 |        0.175 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.113    4.900  1.553 |       0.354 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.977)------------------------------------------|
|    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 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4270   r_free= 0.4191   ksol= 0.00   Bsol= 0.00   scale= 0.916    |
|                                                                             |
| 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:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.225274                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4187   r_free= 0.4087   ksol= 0.30   Bsol= 34.26   scale= 0.957   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.76,2.22,1.72,0.00,0.00,0.00); trace/3= 0.73                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.215697                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.218902              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.491   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.721277              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.505   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4187      final r-factor (work) = 0.2554          |
| start r-factor (free) = 0.4087      final r-factor (free) = 0.2814          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.7199 = 8.22 * 0.50 * 6.2161 + 1.00 * 0.1752                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 24.7550 = 8.22 * 0.50 * 5.9979 + 1.00 * 0.1070                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2554      final r-factor (work) = 0.2341          |
| start r-factor (free) = 0.2814      final r-factor (free) = 0.2909          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3325 = 0.72 * 1.00 * 5.9979 + 1.00 * 0.0063                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1968 = 0.72 * 1.00 * 5.7665 + 1.00 * 0.0375                               |
|-----------------------------------------------------------------------------|
| number of iterations = 7       |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.977)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.15   17.15    None  None   None       |
|    all(noH): 2823   0      0.00    92.15   17.15    None  None   None       |
|    Sol.    : 438    0      4.29    67.78   38.20    None  None   None       |
|    Mac.    : 2385   0      0.00    92.15   13.29    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 -   9.215:  826   |   5:    46.077 -  55.292:  111        |
|      1:     9.215 -  18.431: 1122   |   6:    55.292 -  64.508:   36        |
|      2:    18.431 -  27.646:  401   |   7:    64.508 -  73.723:    2        |
|      3:    27.646 -  36.862:  171   |   8:    73.723 -  82.938:    0        |
|      4:    36.862 -  46.077:  153   |   9:    82.938 -  92.154:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2341 r_free = 0.2909             target_work(ml) = 5.780         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2339 r_free = 0.2913             target_work(ml) = 5.780         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2339   r_free= 0.2913   ksol= 0.30   Bsol= 34.26   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.76,2.22,1.72,0.00,0.00,0.00); trace/3= 0.73                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.779810                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2309   r_free= 0.2886   ksol= 0.33   Bsol= 64.18   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.83,-0.32,-0.24,-0.00,-0.00,-0.00); trace/3= -1.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.775092                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.136315              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.591   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.409799              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.221   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2309      final r-factor (work) = 0.1650          |
| start r-factor (free) = 0.2886      final r-factor (free) = 0.2068          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.0535 = 4.14 * 0.50 * 5.7764 + 1.00 * 0.1070                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.7606 = 4.14 * 0.50 * 5.6538 + 1.00 * 0.0677                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1650      final r-factor (work) = 0.1487          |
| start r-factor (free) = 0.2068      final r-factor (free) = 0.1909          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3411 = 0.41 * 1.00 * 5.6538 + 1.00 * 0.0242                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2298 = 0.41 * 1.00 * 5.4163 + 1.00 * 0.0102                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.977)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.68    84.47   17.53    None  None   None       |
|    all(noH): 2823   0      0.68    84.47   17.53    None  None   None       |
|    Sol.    : 438    0      6.27    76.70   41.36    None  None   None       |
|    Mac.    : 2385   0      0.68    84.47   13.16    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:     0.678 -   9.057:  845   |   5:    42.576 -  50.956:  107        |
|      1:     9.057 -  17.437: 1170   |   6:    50.956 -  59.335:   82        |
|      2:    17.437 -  25.817:  304   |   7:    59.335 -  67.715:   55        |
|      3:    25.817 -  34.196:  125   |   8:    67.715 -  76.095:   22        |
|      4:    34.196 -  42.576:  107   |   9:    76.095 -  84.474:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1487 r_free = 0.1909             target_work(ml) = 5.380         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1485 r_free = 0.1908             target_work(ml) = 5.379         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1485   r_free= 0.1908   ksol= 0.33   Bsol= 64.18   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.83,-0.32,-0.24,-0.00,-0.00,-0.00); trace/3= -1.13                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.379342                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1484   r_free= 0.1906   ksol= 0.33   Bsol= 64.18   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.90,-1.15,-0.46,-0.00,-0.00,-0.00); trace/3= -1.50                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.378372                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.917027              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.885   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.216046              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.569  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1484      final r-factor (work) = 0.1249          |
| start r-factor (free) = 0.1906      final r-factor (free) = 0.1686          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9681 = 2.92 * 0.50 * 5.4168 + 1.00 * 0.0677                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7993 = 2.92 * 0.50 * 5.3037 + 1.00 * 0.0638                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1249      final r-factor (work) = 0.1219          |
| start r-factor (free) = 0.1686      final r-factor (free) = 0.1642          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1560 = 0.22 * 1.00 * 5.3037 + 1.00 * 0.0102                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3578 = 0.22 * 1.00 * 5.2262 + 1.00 * 0.2287                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 8      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.977)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.96   17.26    None  None   None       |
|    all(noH): 2823   0      0.00    84.96   17.26    None  None   None       |
|    Sol.    : 438    0      6.12    77.26   40.85    None  None   None       |
|    Mac.    : 2385   0      0.00    84.96   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:     0.000 -   8.496:  719   |   5:    42.482 -  50.978:  114        |
|      1:     8.496 -  16.993: 1297   |   6:    50.978 -  59.474:   74        |
|      2:    16.993 -  25.489:  309   |   7:    59.474 -  67.970:   54        |
|      3:    25.489 -  33.985:  126   |   8:    67.970 -  76.467:   21        |
|      4:    33.985 -  42.482:  105   |   9:    76.467 -  84.963:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1219 r_free = 0.1642             target_work(ml) = 5.212         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1217 r_free = 0.1642             target_work(ml) = 5.212         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1217   r_free= 0.1642   ksol= 0.33   Bsol= 64.18   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.90,-1.15,-0.46,-0.00,-0.00,-0.00); trace/3= -1.50                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.211812                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1220   r_free= 0.1648   ksol= 0.33   Bsol= 61.57   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.88,-1.54,-0.58,-0.00,-0.00,-0.00); trace/3= -1.67                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.213925                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.505912              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 131.317  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.977303              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.230   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1220      final r-factor (work) = 0.1155          |
| start r-factor (free) = 0.1648      final r-factor (free) = 0.1599          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6128 = 2.51 * 0.50 * 5.2266 + 1.00 * 0.0641                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5707 = 2.51 * 0.50 * 5.1913 + 1.00 * 0.0662                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1155      final r-factor (work) = 0.1137          |
| start r-factor (free) = 0.1599      final r-factor (free) = 0.1609          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.2856 = 1.98 * 1.00 * 5.1913 + 1.00 * 0.0208                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.2226 = 1.98 * 1.00 * 5.1646 + 1.00 * 0.0107                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.977)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.66   17.22    None  None   None       |
|    all(noH): 2823   0      0.00    93.66   17.22    None  None   None       |
|    Sol.    : 438    0      0.00    88.56   41.55    None  None   None       |
|    Mac.    : 2385   0      0.21    93.66   12.75    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.366:  960   |   5:    46.828 -  56.193:   95        |
|      1:     9.366 -  18.731: 1179   |   6:    56.193 -  65.559:   75        |
|      2:    18.731 -  28.097:  222   |   7:    65.559 -  74.924:   34        |
|      3:    28.097 -  37.462:  135   |   8:    74.924 -  84.290:   12        |
|      4:    37.462 -  46.828:  107   |   9:    84.290 -  93.655:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1137 r_free = 0.1609             target_work(ml) = 5.168         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1135 r_free = 0.1609             target_work(ml) = 5.168         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1135   r_free= 0.1609   ksol= 0.33   Bsol= 61.57   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.88,-1.54,-0.58,-0.00,-0.00,-0.00); trace/3= -1.67                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.167561                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1135   r_free= 0.1607   ksol= 0.32   Bsol= 61.57   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.64,-1.42,-0.40,-0.00,-0.00,-0.00); trace/3= -1.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.167687                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.466767              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 154.797  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.186684              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 118.601  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1135      final r-factor (work) = 0.1157          |
| start r-factor (free) = 0.1607      final r-factor (free) = 0.1624          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8538 = 1.47 * 0.50 * 5.1646 + 1.00 * 0.0662                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8493 = 1.47 * 0.50 * 5.1781 + 1.00 * 0.0518                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1157      final r-factor (work) = 0.1170          |
| start r-factor (free) = 0.1624      final r-factor (free) = 0.1602          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9773 = 0.19 * 1.00 * 5.1781 + 1.00 * 0.0106                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9771 = 0.19 * 1.00 * 5.1901 + 1.00 * 0.0082                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.977)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.23    90.00   16.38    None  None   None       |
|    all(noH): 2823   0      1.23    90.00   16.38    None  None   None       |
|    Sol.    : 438    0      1.38    85.82   38.21    None  None   None       |
|    Mac.    : 2385   0      1.23    90.00   12.37    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.229 -  10.107: 1146   |   5:    45.617 -  54.495:   84        |
|      1:    10.107 -  18.984: 1027   |   6:    54.495 -  63.372:   54        |
|      2:    18.984 -  27.862:  216   |   7:    63.372 -  72.250:   25        |
|      3:    27.862 -  36.739:  139   |   8:    72.250 -  81.127:    7        |
|      4:    36.739 -  45.617:  122   |   9:    81.127 -  90.005:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1170 r_free = 0.1602             target_work(ml) = 5.186         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1169 r_free = 0.1602             target_work(ml) = 5.185         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1169   r_free= 0.1602   ksol= 0.32   Bsol= 61.57   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.64,-1.42,-0.40,-0.00,-0.00,-0.00); trace/3= -1.49                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.185428                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9295 -  4.7036 0.99   1436  159 0.1001 0.1300      5.4021      5.5649|
|  2:  4.7036 -  3.7529 0.99   1387  154 0.0876 0.1079      5.4451      5.6298|
|  3:  3.7529 -  3.2843 0.99   1346  149 0.1099 0.1497      5.4834      5.8305|
|  4:  3.2843 -  2.9866 0.99   1353  147 0.1295 0.1627      5.4774      5.6294|
|  5:  2.9866 -  2.7740 0.98   1325  152 0.1383 0.1657      5.3589      5.5176|
|  6:  2.7740 -  2.6114 0.99   1346  145 0.1314 0.2170      5.2599       5.535|
|  7:  2.6114 -  2.4812 0.99   1285  156 0.1313 0.1706      5.2051      5.3963|
|  8:  2.4812 -  2.3736 0.99   1343  134 0.1212 0.1670      5.1246      5.2793|
|  9:  2.3736 -  2.2826 0.99   1327  151 0.1220 0.1950      5.0537      5.3619|
| 10:  2.2826 -  2.2041 0.98   1317  142 0.1213 0.1799      4.9934      5.1887|
| 11:  2.2041 -  2.1354 0.98   1278  154 0.1229 0.1816      4.9485       5.285|
| 12:  2.1354 -  2.0745 1.00   1322  143 0.1213 0.1582      4.8891      5.0823|
| 13:  2.0745 -  2.0200 0.91   1238  132 0.1185 0.1776      4.8019      5.0416|
| 14:  2.0200 -  1.9708 0.25    327   41 0.1084 0.1792      4.7446      4.9413|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9295 -  4.7036  1436   159  0.94   9.43   0.97     0.94       7497.40|
|  2:  4.7036 -  3.7529  1387   154  0.95   7.99   1.00     0.99       9010.90|
|  3:  3.7529 -  3.2843  1346   149  0.93  11.37   1.01     1.01      10342.99|
|  4:  3.2843 -  2.9866  1353   147  0.91  14.46   1.00     0.98      10684.58|
|  5:  2.9866 -  2.7740  1325   152  0.90  16.35   0.99     0.96       8704.18|
|  6:  2.7740 -  2.6114  1346   145  0.89  16.98   0.98     0.96       7652.17|
|  7:  2.6114 -  2.4812  1285   156  0.90  16.19   0.98     0.95       6583.84|
|  8:  2.4812 -  2.3736  1343   134  0.90  16.43   0.99     0.96       6060.66|
|  9:  2.3736 -  2.2826  1327   151  0.90  16.49   0.99     0.95       5222.24|
| 10:  2.2826 -  2.2041  1317   142  0.90  16.33   0.99     0.95       4715.28|
| 11:  2.2041 -  2.1354  1278   154  0.90  16.06   0.98     0.94       4262.02|
| 12:  2.1354 -  2.0745  1322   143  0.90  16.14   0.99     0.99       3912.82|
| 13:  2.0745 -  2.0200  1238   132  0.90  16.54   0.97     0.96       3368.06|
| 14:  2.0200 -  1.9708   327    41  0.92  14.35   0.96     0.92       2821.41|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2821.41 max =        10684.58 mean =      6745.70|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.84 mean =        14.59|
|phase err.(test): min =        0.00 max =           89.46 mean =        14.13|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1169   r_free= 0.1602   ksol= 0.33   Bsol= 61.53   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.53,-1.35,-0.27,-0.00,-0.00,-0.00); trace/3= -1.38                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.185582                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.93 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1169   r_free= 0.1602   ksol= 0.33   Bsol= 61.53   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.53,-1.35,-0.27,-0.00,-0.00,-0.00); trace/3= -1.38                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.185582                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9295 -  4.7036 0.99   1436  159 0.1002 0.1302      5.4039      5.5659|
|  2:  4.7036 -  3.7529 0.99   1387  154 0.0875 0.1079      5.4448      5.6293|
|  3:  3.7529 -  3.2843 0.99   1346  149 0.1099 0.1497      5.4831      5.8308|
|  4:  3.2843 -  2.9866 0.99   1353  147 0.1296 0.1628      5.4775      5.6294|
|  5:  2.9866 -  2.7740 0.98   1325  152 0.1383 0.1657       5.359      5.5175|
|  6:  2.7740 -  2.6114 0.99   1346  145 0.1314 0.2169      5.2598      5.5349|
|  7:  2.6114 -  2.4812 0.99   1285  156 0.1313 0.1708      5.2052      5.3965|
|  8:  2.4812 -  2.3736 0.99   1343  134 0.1212 0.1670      5.1246      5.2793|
|  9:  2.3736 -  2.2826 0.99   1327  151 0.1220 0.1951      5.0539      5.3621|
| 10:  2.2826 -  2.2041 0.98   1317  142 0.1213 0.1800      4.9936      5.1891|
| 11:  2.2041 -  2.1354 0.98   1278  154 0.1228 0.1816      4.9487      5.2854|
| 12:  2.1354 -  2.0745 1.00   1322  143 0.1213 0.1582      4.8891      5.0822|
| 13:  2.0745 -  2.0200 0.91   1238  132 0.1185 0.1776      4.8019      5.0412|
| 14:  2.0200 -  1.9708 0.25    327   41 0.1084 0.1791      4.7445      4.9413|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9295 -  4.7036  1436   159  0.94   9.46   0.97     0.94       7528.25|
|  2:  4.7036 -  3.7529  1387   154  0.95   7.99   1.00     0.99       9016.27|
|  3:  3.7529 -  3.2843  1346   149  0.93  11.37   1.01     1.01      10333.81|
|  4:  3.2843 -  2.9866  1353   147  0.91  14.46   1.00     0.98      10686.74|
|  5:  2.9866 -  2.7740  1325   152  0.90  16.35   0.99     0.96       8702.46|
|  6:  2.7740 -  2.6114  1346   145  0.89  16.98   0.98     0.96       7651.69|
|  7:  2.6114 -  2.4812  1285   156  0.90  16.19   0.98     0.95       6583.06|
|  8:  2.4812 -  2.3736  1343   134  0.90  16.43   1.00     0.96       6061.29|
|  9:  2.3736 -  2.2826  1327   151  0.90  16.50   0.99     0.95       5224.52|
| 10:  2.2826 -  2.2041  1317   142  0.90  16.34   0.99     0.95       4718.32|
| 11:  2.2041 -  2.1354  1278   154  0.90  16.07   0.98     0.94       4265.25|
| 12:  2.1354 -  2.0745  1322   143  0.90  16.15   1.00     0.99       3913.57|
| 13:  2.0745 -  2.0200  1238   132  0.90  16.54   0.98     0.97       3367.22|
| 14:  2.0200 -  1.9708   327    41  0.92  14.34   0.97     0.92       2819.69|
|alpha:            min =        0.92 max =            1.01 mean =         0.96|
|beta:             min =     2819.69 max =        10686.74 mean =      6748.52|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.83 mean =        14.60|
|phase err.(test): min =        0.00 max =           89.54 mean =        14.14|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.977)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.19    89.96   16.33    None  None   None       |
|    all(noH): 2823   0      1.19    89.96   16.33    None  None   None       |
|    Sol.    : 438    0      1.34    85.78   38.17    None  None   None       |
|    Mac.    : 2385   0      1.19    89.96   12.32    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:     1.186 -  10.064: 1146   |   5:    45.574 -  54.451:   84        |
|      1:    10.064 -  18.941: 1027   |   6:    54.451 -  63.329:   54        |
|      2:    18.941 -  27.819:  216   |   7:    63.329 -  72.207:   25        |
|      3:    27.819 -  36.696:  139   |   8:    72.207 -  81.084:    7        |
|      4:    36.696 -  45.574:  122   |   9:    81.084 -  89.962:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 300         
Filter by distance & map next to the model:
   mapped sites are within: 0.428 - 4.756
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 296 from: 300
   mapped sites are within: 0.738 - 4.756

peak=    5.448 closest distance to " O   HOH Z 113 " =    2.199
peak=    5.430 closest distance to " CG  PRO A 280 " =    0.863
peak=    5.175 closest distance to " CG  PRO A  54 " =    1.393
peak=    5.161 closest distance to " CG  PRO A  90 " =    1.297
peak=    5.033 closest distance to " CB  ARG A 275 " =    0.922
peak=    4.961 closest distance to " CB  GLN A 223 " =    1.400
peak=    4.867 closest distance to " CG  PRO A 198 " =    1.250
peak=    4.723 closest distance to " O   HOH Z 403 " =    1.823
peak=    4.594 closest distance to " CB  ARG A 190 " =    1.733
peak=    4.574 closest distance to " CG  PRO A 213 " =    1.314
peak=    4.569 closest distance to " O   HOH Z 232 " =    2.293
peak=    4.562 closest distance to " CB  GLU A 152 " =    1.174
peak=    4.510 closest distance to " C   PRO A 198 " =    1.536
peak=    4.505 closest distance to " CA  ARG A  36 " =    1.052
peak=    4.495 closest distance to " O   HOH Z 234 " =    3.810
peak=    4.483 closest distance to " CZ  PHE A 218 " =    1.058
peak=    4.461 closest distance to " CA  TYR A  30 " =    0.915
peak=    4.457 closest distance to " O  BHOH Z  74 " =    1.133
peak=    4.419 closest distance to " CB  PRO A  54 " =    1.014
peak=    4.413 closest distance to " CB  GLN A 183 " =    1.260
peak=    4.360 closest distance to " CD2 TRP A 179 " =    1.307
peak=    4.359 closest distance to " CB  SER A  63 " =    1.146
peak=    4.347 closest distance to " ND2 ASN A 187 " =    1.619
peak=    4.332 closest distance to " CG  PRO A 243 " =    1.139
peak=    4.296 closest distance to " O   HOH Z 189 " =    2.855
peak=    4.222 closest distance to " CB  ARG A  79 " =    1.370
peak=    4.213 closest distance to " O   HOH Z  43 " =    2.199
peak=    4.209 closest distance to " CD  ARG A 269 " =    1.007
peak=    4.167 closest distance to " O   HOH Z 126 " =    1.870
peak=    4.166 closest distance to " O   SER A  87 " =    2.230
peak=    4.161 closest distance to " O   HOH Z  40 " =    1.937
peak=    4.152 closest distance to " O   HOH Z 402 " =    1.474
peak=    4.121 closest distance to " O   HOH Z 142 " =    1.634
peak=    4.110 closest distance to " O   HOH Z 369 " =    2.152
peak=    4.084 closest distance to " O   HOH Z  63 " =    1.946
peak=    4.070 closest distance to " O   HOH Z 210 " =    1.146
peak=    4.070 closest distance to " CG2 ILE A 120 " =    1.195
peak=    4.063 closest distance to " O   HOH Z  49 " =    1.069
peak=    4.055 closest distance to " O   HOH Z 209 " =    2.231
peak=    4.022 closest distance to " O   HOH Z 298 " =    1.776
peak=    4.013 closest distance to " O   HOH Z 287 " =    1.943
peak=    4.010 closest distance to " CB  ASN A 148 " =    1.445
peak=    3.998 closest distance to " O   HOH Z 423 " =    1.935
peak=    3.961 closest distance to " CB  ARG A  79 " =    0.933
peak=    3.935 closest distance to " O   HOH Z  97 " =    2.027
peak=    3.933 closest distance to " CG  ARG A  66 " =    2.690
peak=    3.909 closest distance to " ND2 ASN A 249 " =    0.929
peak=    3.901 closest distance to " CB  ASN A 187 " =    1.367
peak=    3.900 closest distance to " O   HOH Z 346 " =    1.592
peak=    3.896 closest distance to " CD  LYS A 166 " =    1.317
peak=    3.887 closest distance to " O   HOH Z  15 " =    2.270
peak=    3.882 closest distance to " O   HOH Z 227 " =    1.667
peak=    3.872 closest distance to " O   HOH Z 389 " =    1.881
peak=    3.867 closest distance to " N   ASN A  39 " =    1.235
peak=    3.858 closest distance to " O   HOH Z 248 " =    1.516
peak=    3.858 closest distance to " O   HOH Z 265 " =    2.035
peak=    3.852 closest distance to " CZ  PHE A  38 " =    1.251
peak=    3.844 closest distance to " O   HOH Z 250 " =    1.504
peak=    3.827 closest distance to " O   HOH Z 128 " =    1.965
peak=    3.827 closest distance to " O   HOH Z 406 " =    1.586
peak=    3.823 closest distance to " CB  GLU A 277 " =    3.700
peak=    3.822 closest distance to " O   HOH Z 251 " =    1.642
peak=    3.821 closest distance to " CA  ALA A  51 " =    0.964
peak=    3.813 closest distance to " O   HOH Z  97 " =    2.200
peak=    3.804 closest distance to " CB  TRP A 266 " =    1.026
peak=    3.801 closest distance to " CB  GLU A  46 " =    1.011
peak=    3.797 closest distance to " NZ  LYS A 117 " =    3.063
peak=    3.791 closest distance to " O   HOH Z  44 " =    2.046
peak=    3.775 closest distance to " CG2 VAL A 257 " =    0.849
peak=    3.774 closest distance to " CB  ALA A 248 " =    1.247
peak=    3.772 closest distance to " CB  GLU A 128 " =    1.024
peak=    3.769 closest distance to " O   HOH Z 362 " =    3.582
peak=    3.766 closest distance to " O   HOH Z  21 " =    1.882
peak=    3.761 closest distance to " CB  VAL A 202 " =    1.478
peak=    3.760 closest distance to " CZ3 TRP A 266 " =    1.086
peak=    3.757 closest distance to " CB  ASN A  39 " =    0.826
peak=    3.749 closest distance to " CG2AVAL A  72 " =    1.777
peak=    3.741 closest distance to " NE2 GLN A  11 " =    1.203
peak=    3.740 closest distance to " O   HOH Z 280 " =    2.993
peak=    3.740 closest distance to " CB  SER A 141 " =    1.063
peak=    3.739 closest distance to " CB  THR A  31 " =    1.447
peak=    3.735 closest distance to " O   HOH Z 261 " =    2.052
peak=    3.732 closest distance to " NH2BARG A 145 " =    2.080
peak=    3.732 closest distance to " O   HOH Z 316 " =    3.066
peak=    3.731 closest distance to " CA  ARG A 195 " =    1.217
peak=    3.720 closest distance to " OG BSER A 212 " =    2.571
peak=    3.719 closest distance to " O   HOH Z 291 " =    1.500
peak=    3.719 closest distance to " CG  MET A 185 " =    1.141
peak=    3.715 closest distance to " O   HOH Z 258 " =    2.183
peak=    3.709 closest distance to " CA  SER A  87 " =    1.055
peak=    3.706 closest distance to " NE2 GLN A  77 " =    3.239
peak=    3.706 closest distance to " CB  TRP A 179 " =    1.344
peak=    3.696 closest distance to " O   HOH Z 368 " =    2.067
peak=    3.695 closest distance to " O   HOH Z 303 " =    2.262
peak=    3.691 closest distance to " NH1AARG A 145 " =    1.395
peak=    3.683 closest distance to " CB  ASP A 124 " =    0.748
peak=    3.682 closest distance to " CB  TYR A 169 " =    0.738
peak=    3.680 closest distance to " O   HOH Z 421 " =    2.013
peak=    3.670 closest distance to " O   ASN A  74 " =    1.532
peak=    3.668 closest distance to " O   HOH Z 203 " =    1.745
peak=    3.666 closest distance to " O   HOH Z 146 " =    2.353
peak=    3.662 closest distance to " O   HOH Z 185 " =    1.804
peak=    3.661 closest distance to " CE  LYS A  76 " =    0.886
peak=    3.658 closest distance to " CA  ILE A 106 " =    0.815
peak=    3.653 closest distance to " CB  SER A  26 " =    1.809
peak=    3.650 closest distance to " O   HOH Z  80 " =    1.899
peak=    3.647 closest distance to " CD2 LEU A 297 " =    0.944
peak=    3.645 closest distance to " CB  LEU A 228 " =    1.102
peak=    3.643 closest distance to " CB  ALA A 291 " =    1.116
peak=    3.638 closest distance to " CA  ASN A 176 " =    1.197
peak=    3.637 closest distance to " O   HOH Z 214 " =    2.526
peak=    3.637 closest distance to " O   HOH Z 128 " =    2.368
peak=    3.630 closest distance to " CB  VAL A 265 " =    1.205
peak=    3.621 closest distance to " O   HOH Z 412 " =    3.783
peak=    3.620 closest distance to " O   HOH Z 173 " =    2.128
peak=    3.617 closest distance to " O   HOH Z 132 " =    2.737
peak=    3.609 closest distance to " O   HOH Z  59 " =    2.310
peak=    3.600 closest distance to " CB  PHE A 204 " =    0.780
peak=    3.594 closest distance to " O   HOH Z 193 " =    1.826
peak=    3.591 closest distance to " CB  ASN A 142 " =    1.098
peak=    3.583 closest distance to " O   TYR A 116 " =    1.446
peak=    3.581 closest distance to " O   HOH Z 102 " =    1.302
peak=    3.578 closest distance to " O   HOH Z 359 " =    1.660
peak=    3.577 closest distance to " CB  PRO A  90 " =    1.068
peak=    3.576 closest distance to " O   HOH Z 246 " =    1.410
peak=    3.576 closest distance to " O   HOH Z 353 " =    2.731
peak=    3.573 closest distance to " CB  LEU A  83 " =    0.765
peak=    3.568 closest distance to " O   HOH Z 345 " =    1.696
peak=    3.563 closest distance to " CA  ALA A 295 " =    1.045
peak=    3.562 closest distance to " O   HOH Z  61 " =    1.563
peak=    3.556 closest distance to " CB  SER A   3 " =    1.269
peak=    3.548 closest distance to " O   HOH Z 383 " =    1.984
peak=    3.536 closest distance to " O   HOH Z 148 " =    3.376
peak=    3.535 closest distance to " O   HOH Z 285 " =    2.714
peak=    3.531 closest distance to " CG  LEU A 167 " =    1.106
peak=    3.531 closest distance to " N   ARG A 156 " =    1.474
peak=    3.528 closest distance to " O   HOH Z 158 " =    3.060
peak=    3.528 closest distance to " CB  PRO A 198 " =    1.047
peak=    3.525 closest distance to " CB  SER A  62 " =    0.910
peak=    3.524 closest distance to " CG2 ILE A  20 " =    1.369
peak=    3.524 closest distance to " OD2 ASP A 298 " =    3.827
peak=    3.508 closest distance to " CG  GLU A  37 " =    0.944
peak=    3.506 closest distance to " O   ALA A 165 " =    1.435
peak=    3.503 closest distance to " CG  GLN A  11 " =    1.334
peak=    3.502 closest distance to " CG1 ILE A  20 " =    1.290
peak=    3.497 closest distance to " CG AARG A 275 " =    1.095
peak=    3.495 closest distance to " CG2BVAL A  41 " =    0.898
peak=    3.495 closest distance to " O  BHOH Z 338 " =    2.236
peak=    3.494 closest distance to " CA  TYR A 116 " =    1.378
peak=    3.492 closest distance to " O   HOH Z  19 " =    1.584
peak=    3.491 closest distance to " OG BSER A 164 " =    2.319
peak=    3.487 closest distance to " O   HOH Z 380 " =    1.894
peak=    3.487 closest distance to " NZ  LYS A  48 " =    1.198
peak=    3.485 closest distance to " CA  ALA A 248 " =    1.200
peak=    3.484 closest distance to " O   HOH Z 126 " =    1.578
peak=    3.483 closest distance to " O   HOH Z 272 " =    1.897
peak=    3.478 closest distance to " O   ASN A  74 " =    1.829
peak=    3.473 closest distance to " NH2 ARG A 156 " =    1.164
peak=    3.472 closest distance to " CA  ALA A  21 " =    1.132
peak=    3.469 closest distance to " O   HOH Z 371 " =    3.018
peak=    3.466 closest distance to " CB  ASP A 191 " =    1.180
peak=    3.462 closest distance to " CD  PRO A  54 " =    0.921
peak=    3.453 closest distance to " O   HOH Z 365 " =    2.733
peak=    3.453 closest distance to " OG  SER A 276 " =    1.329
peak=    3.452 closest distance to " CD1 LEU A  96 " =    0.815
peak=    3.451 closest distance to " CA  ALA A  84 " =    1.156
peak=    3.450 closest distance to " CG1 VAL A 153 " =    0.991
peak=    3.448 closest distance to " O   THR A 182 " =    1.402
peak=    3.446 closest distance to " O   HOH Z 357 " =    2.089
peak=    3.445 closest distance to " O   HOH Z  48 " =    1.625
peak=    3.443 closest distance to " O   HOH Z 109 " =    2.136
peak=    3.442 closest distance to " CG1 ILE A  33 " =    1.248
peak=    3.441 closest distance to " CB  ALA A 114 " =    0.859
peak=    3.439 closest distance to " CA  ALA A 160 " =    0.927
peak=    3.434 closest distance to " O   HOH Z 361 " =    2.491
peak=    3.434 closest distance to " OG  SER A  28 " =    1.466
peak=    3.433 closest distance to " O   THR A 251 " =    1.069
peak=    3.432 closest distance to " O   HOH Z  78 " =    1.677
peak=    3.428 closest distance to " NH2AARG A 275 " =    3.616
peak=    3.427 closest distance to " O   HOH Z 417 " =    2.983
peak=    3.427 closest distance to " O   HOH Z 404 " =    2.316
peak=    3.425 closest distance to " O   HOH Z 313 " =    1.980
peak=    3.425 closest distance to " CD1 ILE A 199 " =    1.174
peak=    3.424 closest distance to " O   HOH Z  63 " =    2.190
peak=    3.423 closest distance to " O   HOH Z 325 " =    2.179
peak=    3.422 closest distance to " O   HOH Z 426 " =    1.498
peak=    3.417 closest distance to " CA  THR A 264 " =    0.912
peak=    3.417 closest distance to " CA  ASP A 162 " =    1.093
peak=    3.415 closest distance to " CB  PHE A  16 " =    1.086
peak=    3.413 closest distance to " O   HOH Z 139 " =    4.756
peak=    3.413 closest distance to " O   HOH Z 298 " =    2.365
peak=    3.411 closest distance to " O   HOH Z 180 " =    2.188
peak=    3.403 closest distance to " CB  GLN A  89 " =    1.339
peak=    3.402 closest distance to " O   HOH Z 427 " =    2.941
peak=    3.402 closest distance to " O   HOH Z 132 " =    2.697
peak=    3.398 closest distance to " CB  GLN A 103 " =    0.845
peak=    3.396 closest distance to " CD  ARG A 159 " =    0.773
peak=    3.389 closest distance to " CA  ASN A 215 " =    0.979
peak=    3.389 closest distance to " CB  ALA A 104 " =    0.751
peak=    3.388 closest distance to " CA  GLY A 241 " =    1.001
peak=    3.386 closest distance to " CB  GLN A  88 " =    1.122
peak=    3.385 closest distance to " O   THR A 220 " =    1.128
peak=    3.380 closest distance to " CG2 THR A 220 " =    0.771
peak=    3.374 closest distance to " CB  PRO A 243 " =    1.418
peak=    3.365 closest distance to " O   HOH Z  66 " =    2.206
peak=    3.360 closest distance to " O   HOH Z 327 " =    1.660
peak=    3.353 closest distance to " O   HOH Z 392 " =    2.343
peak=    3.352 closest distance to " N   HIS A 108 " =    1.793
peak=    3.344 closest distance to " N   PHE A 130 " =    1.289
peak=    3.337 closest distance to " CE1 TYR A 186 " =    1.314
peak=    3.333 closest distance to " CA  ASP A 191 " =    0.871
peak=    3.328 closest distance to " N   CYS A 260 " =    0.831
peak=    3.325 closest distance to " O   HOH Z 234 " =    1.889
peak=    3.322 closest distance to " OG BSER A 134 " =    2.757
peak=    3.320 closest distance to " O   HOH Z 163 " =    1.565
peak=    3.319 closest distance to " O   ASP A 124 " =    1.608
peak=    3.319 closest distance to " CA  SER A  32 " =    1.633
peak=    3.318 closest distance to " O   HOH Z 299 " =    4.371
peak=    3.315 closest distance to " OH  TYR A 116 " =    1.132
peak=    3.315 closest distance to " CB  MET A  47 " =    0.933
peak=    3.314 closest distance to " N   TYR A 116 " =    1.532
peak=    3.309 closest distance to " O   HOH Z 273 " =    2.882
peak=    3.305 closest distance to " NE  ARG A  24 " =    1.001
peak=    3.302 closest distance to " O   HOH Z 261 " =    2.496
peak=    3.294 closest distance to " O   HOH Z 427 " =    3.127
peak=    3.293 closest distance to " O   HOH Z  96 " =    2.149
peak=    3.290 closest distance to " OE1 GLU A 236 " =    1.109
peak=    3.289 closest distance to " O   HOH Z 422 " =    2.677
peak=    3.286 closest distance to " O   HOH Z 336 " =    1.769
peak=    3.284 closest distance to " O   PRO A 213 " =    1.450
peak=    3.276 closest distance to " O   HOH Z 271 " =    2.672
peak=    3.275 closest distance to " CG2 THR A 221 " =    1.079
peak=    3.272 closest distance to " CA  GLU A 152 " =    0.846
peak=    3.270 closest distance to " CA  MET A 105 " =    1.038
peak=    3.262 closest distance to " O   HOH Z 183 " =    1.552
peak=    3.260 closest distance to " O   HOH Z 250 " =    1.630
peak=    3.256 closest distance to " CA  ILE A 234 " =    0.861
peak=    3.256 closest distance to " CD  LYS A 119 " =    1.772
peak=    3.254 closest distance to " O   HOH Z 294 " =    1.559
peak=    3.249 closest distance to " CB  ASP A 298 " =    1.190
peak=    3.249 closest distance to " O   HOH Z 141 " =    1.716
peak=    3.241 closest distance to " O   HOH Z 375 " =    2.156
peak=    3.239 closest distance to " CB  ASN A 110 " =    1.077
peak=    3.238 closest distance to " CA  ALA A 154 " =    1.006
peak=    3.237 closest distance to " CG2AVAL A 121 " =    2.158
peak=    3.237 closest distance to " O   HOH Z 146 " =    2.307
peak=    3.236 closest distance to " CA  ARG A 275 " =    1.836
peak=    3.235 closest distance to " CB  ASN A 215 " =    1.204
peak=    3.234 closest distance to " O   HOH Z 134 " =    1.326
peak=    3.229 closest distance to " CE  LYS A 119 " =    1.109
peak=    3.228 closest distance to " CB  SER A 210 " =    0.842
peak=    3.224 closest distance to " O   HOH Z 402 " =    2.967
peak=    3.211 closest distance to " O   ALA A 158 " =    1.069
peak=    3.211 closest distance to " CB  ASN A 285 " =    0.976
peak=    3.201 closest distance to " OD1 ASN A  69 " =    2.425
peak=    3.200 closest distance to " CA  ALA A 233 " =    1.414
peak=    3.198 closest distance to " CG  ARG A 138 " =    1.191
peak=    3.194 closest distance to " O   HOH Z  54 " =    1.647
peak=    3.193 closest distance to " CG2 VAL A 197 " =    1.068
peak=    3.188 closest distance to " O   HOH Z 245 " =    1.393
peak=    3.184 closest distance to " N   ASP A 162 " =    1.181
peak=    3.172 closest distance to " O   HOH Z  35 " =    2.336
peak=    3.158 closest distance to " O   HOH Z  94 " =    2.660
peak=    3.153 closest distance to " ND2 ASN A 110 " =    1.494
peak=    3.152 closest distance to " CB  ALA A   9 " =    1.643
peak=    3.150 closest distance to " O   HOH Z   1 " =    2.513
peak=    3.144 closest distance to " ND2 ASN A 217 " =    1.037
peak=    3.142 closest distance to " O   GLY A  91 " =    1.381
peak=    3.141 closest distance to " CB  ASP A 140 " =    1.033
peak=    3.137 closest distance to " CD1 LEU A 300 " =    1.239
peak=    3.134 closest distance to " CA  VAL A 125 " =    1.187
peak=    3.128 closest distance to " N   ASP A 132 " =    1.022
peak=    3.126 closest distance to " O   HOH Z  47 " =    1.789
peak=    3.125 closest distance to " CD  ARG A 139 " =    1.197
peak=    3.123 closest distance to " CG2 VAL A 126 " =    0.774
peak=    3.121 closest distance to " O   HOH Z  28 " =    1.832
peak=    3.117 closest distance to " O   HOH Z 394 " =    1.674
peak=    3.116 closest distance to " O   HOH Z 279 " =    2.177
peak=    3.112 closest distance to " CG2 VAL A 296 " =    1.089
peak=    3.111 closest distance to " O   HOH Z 200 " =    2.655
peak=    3.103 closest distance to " N   VAL A 265 " =    1.338
peak=    3.100 closest distance to " CB  HIS A 108 " =    0.782
peak=    3.098 closest distance to " OG1 THR A 264 " =    0.751
peak=    3.097 closest distance to " CA  ALA A 100 " =    1.003
peak=    3.096 closest distance to " O   HOH Z 162 " =    1.690
peak=    3.086 closest distance to " CB  GLN A 278 " =    0.826
peak=    3.081 closest distance to " OG  SER A  22 " =    2.623
peak=    3.080 closest distance to " N   ARG A 190 " =    0.976
peak=    3.077 closest distance to " OG  SER A 245 " =    1.557
peak=    3.075 closest distance to " O   HOH Z 193 " =    1.886
peak=    3.073 closest distance to " CA  TRP A  85 " =    1.082
peak=    3.069 closest distance to " CB  ALA A 299 " =    0.773
peak=    3.046 closest distance to " CB  GLN A 240 " =    1.497
peak=    3.040 closest distance to " O   HOH Z 305 " =    3.773
peak=    3.040 closest distance to " CE1 TYR A  30 " =    1.012
peak=    3.033 closest distance to " OD1 ASP A 171 " =    1.221

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 199         
Filter by distance & map next to the model:
   mapped sites are within: 0.597 - 5.305
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 195 from: 199
   mapped sites are within: 0.790 - 5.305

peak=   -5.134 closest distance to " O   HOH Z 210 " =    0.790
peak=   -4.716 closest distance to " CD  GLN A  58 " =    1.008
peak=   -4.442 closest distance to " CD  ARG A  14 " =    3.453
peak=   -4.387 closest distance to " O   HOH Z 266 " =    5.305
peak=   -4.305 closest distance to " CB  PRO A 243 " =    2.708
peak=   -4.248 closest distance to " C   HIS A 108 " =    1.089
peak=   -4.218 closest distance to " O   PRO A 198 " =    1.260
peak=   -4.202 closest distance to " CD1 LEU A 101 " =    2.413
peak=   -4.157 closest distance to " O   HOH Z 290 " =    0.940
peak=   -4.151 closest distance to " CH2 TRP A 179 " =    1.268
peak=   -4.136 closest distance to " CD  ARG A 156 " =    2.141
peak=   -4.099 closest distance to " OXT GLY A 302 " =    2.941
peak=   -4.022 closest distance to " O   HOH Z 166 " =    1.719
peak=   -4.012 closest distance to " CD1 LEU A  25 " =    2.541
peak=   -3.968 closest distance to " O   VAL A  67 " =    2.662
peak=   -3.952 closest distance to " O   HOH Z  10 " =    1.618
peak=   -3.942 closest distance to " CD2 LEU A 237 " =    2.599
peak=   -3.940 closest distance to " CE2 TYR A  30 " =    2.801
peak=   -3.908 closest distance to " CD2 TYR A 293 " =    1.959
peak=   -3.905 closest distance to " O   HOH Z 394 " =    1.544
peak=   -3.898 closest distance to " CB  PHE A 192 " =    2.102
peak=   -3.897 closest distance to " CG1 VAL A 112 " =    2.633
peak=   -3.880 closest distance to " CG2 ILE A  49 " =    2.766
peak=   -3.844 closest distance to " CZ  TYR A 169 " =    1.813
peak=   -3.837 closest distance to " CD  ARG A  79 " =    1.178
peak=   -3.793 closest distance to " CB  ALA A 184 " =    2.353
peak=   -3.792 closest distance to " OG  SER A  97 " =    2.270
peak=   -3.784 closest distance to " OG BSER A 134 " =    1.236
peak=   -3.779 closest distance to " CA  GLY A 241 " =    2.388
peak=   -3.769 closest distance to " O   HOH Z 377 " =    2.002
peak=   -3.759 closest distance to " CG  GLU A  53 " =    1.433
peak=   -3.755 closest distance to " O   PRO A 163 " =    2.065
peak=   -3.752 closest distance to " CD  GLN A 223 " =    1.369
peak=   -3.739 closest distance to " O   HOH Z 198 " =    1.490
peak=   -3.732 closest distance to " CA  GLY A 241 " =    3.195
peak=   -3.718 closest distance to " NH2 ARG A  79 " =    1.600
peak=   -3.718 closest distance to " O   HOH Z 351 " =    1.538
peak=   -3.707 closest distance to " CA  VAL A  67 " =    2.969
peak=   -3.697 closest distance to " CG1 VAL A 112 " =    2.732
peak=   -3.694 closest distance to " CB  PHE A 208 " =    2.322
peak=   -3.683 closest distance to " N   THR A  52 " =    1.705
peak=   -3.682 closest distance to " O   HOH Z  71 " =    2.228
peak=   -3.666 closest distance to " CE3 TRP A 150 " =    2.278
peak=   -3.659 closest distance to " O   HOH Z 165 " =    1.847
peak=   -3.656 closest distance to " NE2 GLN A  88 " =    1.033
peak=   -3.649 closest distance to " O   SER A 210 " =    1.991
peak=   -3.641 closest distance to " ND2 ASN A 187 " =    1.594
peak=   -3.640 closest distance to " CB  ALA A 161 " =    2.491
peak=   -3.634 closest distance to " CE2 PHE A  61 " =    2.650
peak=   -3.627 closest distance to " O   HOH Z 374 " =    1.888
peak=   -3.615 closest distance to " OD1 ASN A 148 " =    1.402
peak=   -3.609 closest distance to " CD1 PHE A  59 " =    2.049
peak=   -3.601 closest distance to " O   HOH Z 372 " =    2.348
peak=   -3.601 closest distance to " CG  ASP A 132 " =    2.316
peak=   -3.590 closest distance to " O   HOH Z  13 " =    1.689
peak=   -3.566 closest distance to " CG1AVAL A  41 " =    2.651
peak=   -3.565 closest distance to " CE BMET A  47 " =    1.606
peak=   -3.561 closest distance to " O   HOH Z 102 " =    1.600
peak=   -3.555 closest distance to " ND2 ASN A  45 " =    1.931
peak=   -3.549 closest distance to " CZ  TYR A 172 " =    1.967
peak=   -3.544 closest distance to " CA  ASP A 298 " =    1.094
peak=   -3.541 closest distance to " CB  ALA A  10 " =    2.256
peak=   -3.535 closest distance to " O   ALA A  10 " =    1.850
peak=   -3.519 closest distance to " C   THR A 279 " =    1.172
peak=   -3.519 closest distance to " CH2 TRP A 150 " =    1.156
peak=   -3.517 closest distance to " O   HOH Z 196 " =    1.968
peak=   -3.514 closest distance to " ND2 ASN A 249 " =    2.303
peak=   -3.513 closest distance to " O   HOH Z 193 " =    1.518
peak=   -3.510 closest distance to " CG2 ILE A 263 " =    2.280
peak=   -3.494 closest distance to " O   HOH Z 264 " =    1.745
peak=   -3.488 closest distance to " N   ALA A 248 " =    1.788
peak=   -3.484 closest distance to " CB  ALA A 248 " =    2.305
peak=   -3.484 closest distance to " O   ALA A  34 " =    2.393
peak=   -3.482 closest distance to " O   HOH Z 171 " =    2.310
peak=   -3.481 closest distance to " O   HOH Z 113 " =    1.970
peak=   -3.479 closest distance to " OD1 ASP A 171 " =    1.535
peak=   -3.474 closest distance to " O   VAL A 174 " =    2.136
peak=   -3.468 closest distance to " N   ASP A 286 " =    2.195
peak=   -3.467 closest distance to " OE1 GLN A 223 " =    2.243
peak=   -3.463 closest distance to " CG  GLN A  11 " =    1.650
peak=   -3.457 closest distance to " O   HOH Z 185 " =    2.512
peak=   -3.447 closest distance to " C   SER A 206 " =    1.557
peak=   -3.435 closest distance to " CZ3 TRP A 274 " =    2.458
peak=   -3.433 closest distance to " O   HOH Z 154 " =    1.680
peak=   -3.429 closest distance to " CD2 TYR A 247 " =    2.404
peak=   -3.422 closest distance to " O   HOH Z 283 " =    2.281
peak=   -3.421 closest distance to " CD2 LEU A 300 " =    2.788
peak=   -3.407 closest distance to " CD  ARG A 195 " =    5.131
peak=   -3.389 closest distance to " CD  PRO A 243 " =    2.052
peak=   -3.388 closest distance to " O   HOH Z 174 " =    3.679
peak=   -3.386 closest distance to " OD1 ASP A 191 " =    1.348
peak=   -3.377 closest distance to " CG  LEU A  83 " =    2.029
peak=   -3.368 closest distance to " CG  PRO A 243 " =    1.697
peak=   -3.366 closest distance to " CG  GLN A  58 " =    1.250
peak=   -3.363 closest distance to " CZ  PHE A 155 " =    1.069
peak=   -3.363 closest distance to " O   PHE A 218 " =    1.511
peak=   -3.362 closest distance to " N   ALA A  43 " =    2.734
peak=   -3.362 closest distance to " CB  TRP A  85 " =    2.462
peak=   -3.361 closest distance to " O   HOH Z 421 " =    3.974
peak=   -3.361 closest distance to " OD2 ASP A 171 " =    2.469
peak=   -3.358 closest distance to " O   HOH Z 197 " =    2.057
peak=   -3.352 closest distance to " O   GLN A  94 " =    2.271
peak=   -3.352 closest distance to " CG1 VAL A 125 " =    1.977
peak=   -3.348 closest distance to " O   HOH Z  15 " =    1.539
peak=   -3.339 closest distance to " ND2 ASN A  45 " =    1.119
peak=   -3.335 closest distance to " CB  ALA A 291 " =    2.417
peak=   -3.335 closest distance to " O   HOH Z  63 " =    1.214
peak=   -3.333 closest distance to " O   HOH Z 252 " =    3.957
peak=   -3.331 closest distance to " O   GLY A 196 " =    1.088
peak=   -3.329 closest distance to " O   HOH Z 366 " =    1.579
peak=   -3.326 closest distance to " OD1 ASN A 301 " =    2.025
peak=   -3.322 closest distance to " CA  ILE A 263 " =    1.253
peak=   -3.321 closest distance to " OG BSER A 134 " =    2.031
peak=   -3.316 closest distance to " CA  TYR A  68 " =    3.082
peak=   -3.315 closest distance to " SD  MET A 105 " =    1.002
peak=   -3.312 closest distance to " O   SER A 276 " =    1.747
peak=   -3.310 closest distance to " CD  GLN A 223 " =    0.974
peak=   -3.302 closest distance to " N   ALA A 226 " =    1.951
peak=   -3.301 closest distance to " O   HOH Z 150 " =    2.228
peak=   -3.301 closest distance to " O   HOH Z 174 " =    2.327
peak=   -3.294 closest distance to " O   HOH Z 423 " =    2.378
peak=   -3.292 closest distance to " O   VAL A 189 " =    2.663
peak=   -3.291 closest distance to " O   VAL A 189 " =    1.828
peak=   -3.281 closest distance to " ND2BASN A 224 " =    1.815
peak=   -3.275 closest distance to " CG  ARG A 219 " =    2.483
peak=   -3.275 closest distance to " NE  ARG A  66 " =    4.277
peak=   -3.268 closest distance to " OD2 ASP A  50 " =    2.174
peak=   -3.266 closest distance to " O   HOH Z   6 " =    2.143
peak=   -3.259 closest distance to " O   HOH Z 211 " =    1.559
peak=   -3.255 closest distance to " NH2AARG A 275 " =    5.100
peak=   -3.255 closest distance to " O   HOH Z  38 " =    1.617
peak=   -3.253 closest distance to " NE2 GLN A 103 " =    1.812
peak=   -3.251 closest distance to " O   HOH Z 114 " =    3.371
peak=   -3.245 closest distance to " CG  TRP A 266 " =    1.976
peak=   -3.245 closest distance to " CD2 HIS A 207 " =    2.350
peak=   -3.236 closest distance to " O   HOH Z 301 " =    2.486
peak=   -3.235 closest distance to " CG  GLN A 103 " =    2.464
peak=   -3.227 closest distance to " O   HOH Z 252 " =    3.799
peak=   -3.222 closest distance to " C   GLY A 262 " =    1.928
peak=   -3.221 closest distance to " NH2 ARG A  66 " =    0.998
peak=   -3.220 closest distance to " O   SER A 271 " =    2.101
peak=   -3.213 closest distance to " O   HOH Z 198 " =    1.562
peak=   -3.211 closest distance to " O   HOH Z 407 " =    2.928
peak=   -3.210 closest distance to " O   HOH Z 106 " =    1.995
peak=   -3.207 closest distance to " O   SER A   3 " =    1.055
peak=   -3.205 closest distance to " O  BHOH Z 338 " =    1.130
peak=   -3.205 closest distance to " O   HOH Z 128 " =    2.628
peak=   -3.204 closest distance to " CZ  PHE A  38 " =    2.019
peak=   -3.201 closest distance to " O   HOH Z  78 " =    1.835
peak=   -3.201 closest distance to " CA  GLY A 241 " =    2.895
peak=   -3.197 closest distance to " O   HOH Z 156 " =    3.506
peak=   -3.197 closest distance to " O   HOH Z 357 " =    2.047
peak=   -3.191 closest distance to " CG  PHE A 283 " =    2.561
peak=   -3.186 closest distance to " OE1 GLN A 183 " =    1.578
peak=   -3.183 closest distance to " CB  PRO A 163 " =    2.584
peak=   -3.182 closest distance to " CG  ASP A 231 " =    0.801
peak=   -3.180 closest distance to " O   HOH Z 116 " =    1.308
peak=   -3.179 closest distance to " O   HOH Z 422 " =    1.415
peak=   -3.176 closest distance to " O   HOH Z 193 " =    2.095
peak=   -3.169 closest distance to " O   HOH Z  37 " =    1.888
peak=   -3.164 closest distance to " O   HOH Z  43 " =    1.406
peak=   -3.163 closest distance to " O   TRP A  92 " =    2.013
peak=   -3.159 closest distance to " NE2 GLN A  88 " =    1.795
peak=   -3.157 closest distance to " O   SER A  95 " =    1.647
peak=   -3.155 closest distance to " N   SER A 276 " =    1.438
peak=   -3.149 closest distance to " O   GLY A  80 " =    2.511
peak=   -3.145 closest distance to " O   HOH Z 396 " =    2.028
peak=   -3.143 closest distance to " O   HOH Z 353 " =    2.307
peak=   -3.140 closest distance to " CD1 ILE A 106 " =    2.225
peak=   -3.139 closest distance to " O   HOH Z 139 " =    5.016
peak=   -3.136 closest distance to " CG1 VAL A  78 " =    2.575
peak=   -3.130 closest distance to " CZ  TYR A  68 " =    1.138
peak=   -3.121 closest distance to " CD  LYS A 289 " =    2.386
peak=   -3.119 closest distance to " CD  ARG A 139 " =    1.575
peak=   -3.118 closest distance to " CB  ALA A   9 " =    2.593
peak=   -3.112 closest distance to " C   MET A 188 " =    1.597
peak=   -3.112 closest distance to " N   GLN A  58 " =    1.701
peak=   -3.109 closest distance to " CD2 PHE A  61 " =    2.151
peak=   -3.105 closest distance to " O   HOH Z 111 " =    3.819
peak=   -3.103 closest distance to " O   HOH Z 236 " =    1.671
peak=   -3.102 closest distance to " O   SER A  62 " =    2.103
peak=   -3.099 closest distance to " O   HOH Z 145 " =    2.847
peak=   -3.098 closest distance to " CG  ARG A 269 " =    2.276
peak=   -3.090 closest distance to " CB  PHE A  16 " =    2.498
peak=   -3.089 closest distance to " CD1 ILE A 151 " =    2.366
peak=   -3.080 closest distance to " O   HOH Z 166 " =    1.710
peak=   -3.080 closest distance to " CG2 VAL A 189 " =    2.211
peak=   -3.078 closest distance to " CA  GLY A 133 " =    2.378
peak=   -3.076 closest distance to " CG  HIS A  86 " =    1.166
peak=   -3.070 closest distance to " O   HOH Z 418 " =    1.303
peak=   -3.070 closest distance to " O   HOH Z 234 " =    4.143
peak=   -3.065 closest distance to " O   HOH Z 414 " =    1.449
peak=   -3.043 closest distance to " OH  TYR A 172 " =    1.981
peak=   -3.042 closest distance to " C   GLN A 144 " =    0.884
peak=   -3.029 closest distance to " O   HOH Z 377 " =    1.737

================= 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    :  0.4270 0.4191   6.225274e+00   6.205028e+00
   1_bss:  0.4187 0.4087   6.215697e+00   6.192202e+00
   1_xyz:  0.2554 0.2814   5.822032e+00   5.908374e+00
   1_adp:  0.2341 0.2909   5.779640e+00   5.939054e+00
   1_occ:  0.2339 0.2913   5.779810e+00   5.940331e+00
   2_bss:  0.2309 0.2886   5.775092e+00   5.934798e+00
   2_xyz:  0.1650 0.2068   5.465862e+00   5.649943e+00
   2_adp:  0.1487 0.1909   5.379931e+00   5.578810e+00
   2_occ:  0.1485 0.1908   5.379342e+00   5.578530e+00
   3_bss:  0.1484 0.1906   5.378372e+00   5.576050e+00
   3_xyz:  0.1249 0.1686   5.236351e+00   5.455412e+00
   3_adp:  0.1219 0.1642   5.212029e+00   5.429046e+00
   3_occ:  0.1217 0.1642   5.211812e+00   5.429093e+00
   4_bss:  0.1220 0.1648   5.213925e+00   5.430947e+00
   4_xyz:  0.1155 0.1599   5.173659e+00   5.401096e+00
   4_adp:  0.1137 0.1609   5.168097e+00   5.404085e+00
   4_occ:  0.1135 0.1609   5.167561e+00   5.403804e+00
   5_bss:  0.1135 0.1607   5.167687e+00   5.403909e+00
   5_xyz:  0.1157 0.1624   5.184654e+00   5.416102e+00
   5_adp:  0.1170 0.1602   5.185670e+00   5.407838e+00
   5_occ:  0.1169 0.1602   5.185428e+00   5.407756e+00
   5_bss:  0.1169 0.1602   5.185582e+00   5.407849e+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:  0.302  34.262  -1.758   2.222   1.721   0.000   0.000   0.000
   1_xyz:  0.302  34.262  -1.758   2.222   1.721   0.000   0.000   0.000
   1_adp:  0.302  34.262  -1.758   2.222   1.721   0.000   0.000   0.000
   1_occ:  0.302  34.262  -1.758   2.222   1.721   0.000   0.000   0.000
   2_bss:  0.330  64.176  -2.829  -0.319  -0.238  -0.000  -0.000  -0.000
   2_xyz:  0.330  64.176  -2.829  -0.319  -0.238  -0.000  -0.000  -0.000
   2_adp:  0.330  64.176  -2.829  -0.319  -0.238  -0.000  -0.000  -0.000
   2_occ:  0.330  64.176  -2.829  -0.319  -0.238  -0.000  -0.000  -0.000
   3_bss:  0.330  64.176  -2.897  -1.149  -0.458  -0.000  -0.000  -0.000
   3_xyz:  0.330  64.176  -2.897  -1.149  -0.458  -0.000  -0.000  -0.000
   3_adp:  0.330  64.176  -2.897  -1.149  -0.458  -0.000  -0.000  -0.000
   3_occ:  0.330  64.176  -2.897  -1.149  -0.458  -0.000  -0.000  -0.000
   4_bss:  0.326  61.572  -2.878  -1.544  -0.580  -0.000  -0.000  -0.000
   4_xyz:  0.326  61.572  -2.878  -1.544  -0.580  -0.000  -0.000  -0.000
   4_adp:  0.326  61.572  -2.878  -1.544  -0.580  -0.000  -0.000  -0.000
   4_occ:  0.326  61.572  -2.878  -1.544  -0.580  -0.000  -0.000  -0.000
   5_bss:  0.324  61.572  -2.639  -1.419  -0.400  -0.000  -0.000  -0.000
   5_xyz:  0.324  61.572  -2.639  -1.419  -0.400  -0.000  -0.000  -0.000
   5_adp:  0.324  61.572  -2.639  -1.419  -0.400  -0.000  -0.000  -0.000
   5_occ:  0.324  61.572  -2.639  -1.419  -0.400  -0.000  -0.000  -0.000
   5_bss:  0.328  61.529  -2.535  -1.350  -0.270  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  47.306 0.5551  0.7242    51884.788
   1_bss:  46.374 0.5648  0.7583    48925.096
   1_xyz:  28.889 0.7708  0.9749    21150.204
   1_adp:  30.234 0.7553  0.9591    22760.884
   1_occ:  30.314 0.7543  0.9578    22851.197
   2_bss:  29.950 0.7583  0.9037    22398.998
   2_xyz:  20.432 0.8565  0.9761    10978.931
   2_adp:  18.409 0.8765  0.9785     9518.689
   2_occ:  18.398 0.8766  0.9785     9509.819
   3_bss:  18.324 0.8772  0.9661     9436.634
   3_xyz:  15.766 0.8998  0.9777     7348.313
   3_adp:  15.139 0.9055  0.9746     7048.572
   3_occ:  15.141 0.9055  0.9745     7050.051
   4_bss:  15.177 0.9052  0.9687     7099.573
   4_xyz:  14.468 0.9113  0.9710     6608.775
   4_adp:  14.519 0.9110  0.9623     6646.770
   4_occ:  14.515 0.9110  0.9622     6639.905
   5_bss:  14.518 0.9110  0.9684     6641.090
   5_xyz:  14.708 0.9096  0.9681     6807.259
   5_adp:  14.551 0.9109  0.9629     6747.206
   5_occ:  14.549 0.9109  0.9628     6744.817
   5_bss:  14.553 0.9109  0.9648     6747.641
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.113   1.7517e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.113   1.7517e-01
   1_xyz:   1.397  0.012  0.085 15.309  0.006  4.112   1.0702e-01
   1_adp:   1.397  0.012  0.085 15.309  0.006  4.112   1.0702e-01
   1_occ:   1.397  0.012  0.085 15.309  0.006  4.112   1.0702e-01
   2_bss:   1.397  0.012  0.085 15.309  0.006  4.112   1.0702e-01
   2_xyz:   1.068  0.008  0.075 14.614  0.004  4.129   6.7671e-02
   2_adp:   1.068  0.008  0.075 14.614  0.004  4.129   6.7671e-02
   2_occ:   1.068  0.008  0.075 14.614  0.004  4.129   6.7671e-02
   3_bss:   1.068  0.008  0.075 14.614  0.004  4.129   6.7671e-02
   3_xyz:   1.062  0.008  0.076 14.526  0.004  4.137   6.3761e-02
   3_adp:   1.062  0.008  0.076 14.526  0.004  4.137   6.3761e-02
   3_occ:   1.062  0.008  0.076 14.526  0.004  4.137   6.3761e-02
   4_bss:   1.062  0.008  0.076 14.526  0.004  4.137   6.3761e-02
   4_xyz:   1.078  0.009  0.080 14.476  0.004  4.123   6.6155e-02
   4_adp:   1.078  0.009  0.080 14.476  0.004  4.123   6.6155e-02
   4_occ:   1.078  0.009  0.080 14.476  0.004  4.123   6.6155e-02
   5_bss:   1.078  0.009  0.080 14.476  0.004  4.123   6.6155e-02
   5_xyz:   0.934  0.006  0.071 14.156  0.003  4.122   5.1811e-02
   5_adp:   0.934  0.006  0.071 14.156  0.003  4.122   5.1811e-02
   5_occ:   0.934  0.006  0.071 14.156  0.003  4.122   5.1811e-02
   5_bss:   0.934  0.006  0.071 14.156  0.003  4.122   5.1811e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.553   2.4246e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.553   2.4246e-01
   1_xyz:   8.888  0.090  0.327 84.493  0.024  2.076   1.1243e-01
   1_adp:   8.888  0.090  0.327 84.493  0.024  2.076   1.1243e-01
   1_occ:   8.888  0.090  0.327 84.493  0.024  2.076   1.1243e-01
   2_bss:   8.888  0.090  0.327 84.493  0.024  2.076   1.1243e-01
   2_xyz:   7.434  0.049  0.234 80.435  0.051  2.327   1.2876e-01
   2_adp:   7.434  0.049  0.234 80.435  0.051  2.327   1.2876e-01
   2_occ:   7.434  0.049  0.234 80.435  0.051  2.327   1.2876e-01
   3_bss:   7.434  0.049  0.234 80.435  0.051  2.327   1.2876e-01
   3_xyz:   7.977  0.043  0.233 81.927  0.030  2.256   5.1567e-02
   3_adp:   7.977  0.043  0.233 81.927  0.030  2.256   5.1567e-02
   3_occ:   7.977  0.043  0.233 81.927  0.030  2.256   5.1567e-02
   4_bss:   7.977  0.043  0.233 81.927  0.030  2.256   5.1567e-02
   4_xyz:   8.021  0.045  0.275 82.191  0.035  2.365   4.6257e-02
   4_adp:   8.021  0.045  0.275 82.191  0.035  2.365   4.6257e-02
   4_occ:   8.021  0.045  0.275 82.191  0.035  2.365   4.6257e-02
   5_bss:   8.021  0.045  0.275 82.191  0.035  2.365   4.6257e-02
   5_xyz:   6.980  0.045  0.226 81.381  0.029  2.419   3.3991e-02
   5_adp:   6.980  0.045  0.226 81.381  0.029  2.419   3.3991e-02
   5_occ:   6.980  0.045  0.226 81.381  0.029  2.419   3.3991e-02
   5_bss:   6.980  0.045  0.226 81.381  0.029  2.419   3.3991e-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:  92.15   0.00  17.15  92.15   0.00  13.29  67.78   4.29  38.20
   1_occ:  92.15   0.00  17.15  92.15   0.00  13.29  67.78   4.29  38.20
   2_bss:  92.15   0.00  17.15  92.15   0.00  13.29  67.78   4.29  38.20
   2_xyz:  92.15   0.00  17.15  92.15   0.00  13.29  67.78   4.29  38.20
   2_adp:  84.47   0.68  17.53  84.47   0.68  13.16  76.70   6.27  41.36
   2_occ:  84.47   0.68  17.53  84.47   0.68  13.16  76.70   6.27  41.36
   3_bss:  84.47   0.68  17.53  84.47   0.68  13.16  76.70   6.27  41.36
   3_xyz:  84.47   0.68  17.53  84.47   0.68  13.16  76.70   6.27  41.36
   3_adp:  84.96   0.00  17.26  84.96   0.00  12.92  77.26   6.12  40.85
   3_occ:  84.96   0.00  17.26  84.96   0.00  12.92  77.26   6.12  40.85
   4_bss:  84.96   0.00  17.26  84.96   0.00  12.92  77.26   6.12  40.85
   4_xyz:  84.96   0.00  17.26  84.96   0.00  12.92  77.26   6.12  40.85
   4_adp:  93.66   0.00  17.22  93.66   0.21  12.75  88.56   0.00  41.55
   4_occ:  93.66   0.00  17.22  93.66   0.21  12.75  88.56   0.00  41.55
   5_bss:  93.66   0.00  17.22  93.66   0.21  12.75  88.56   0.00  41.55
   5_xyz:  93.66   0.00  17.22  93.66   0.21  12.75  88.56   0.00  41.55
   5_adp:  90.00   1.23  16.38  90.00   1.23  12.37  85.82   1.38  38.21
   5_occ:  90.00   1.23  16.38  90.00   1.23  12.37  85.82   1.38  38.21
   5_bss:  89.96   1.19  16.33  89.96   1.19  12.32  85.78   1.34  38.17
------------------------------------------------------------------------
 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:    1.584    0.020    0.429
   1_adp:    1.584    0.020    0.429
   1_occ:    1.584    0.020    0.429
   2_bss:    1.584    0.020    0.429
   2_xyz:    1.297    0.025    0.532
   2_adp:    1.297    0.025    0.532
   2_occ:    1.297    0.025    0.532
   3_bss:    1.297    0.025    0.532
   3_xyz:    1.183    0.030    0.600
   3_adp:    1.183    0.030    0.600
   3_occ:    1.183    0.030    0.600
   4_bss:    1.183    0.030    0.600
   4_xyz:    1.103    0.076    0.622
   4_adp:    1.103    0.076    0.622
   4_occ:    1.103    0.076    0.622
   5_bss:    1.103    0.076    0.622
   5_xyz:    1.244    0.084    0.629
   5_adp:    1.244    0.084    0.629
   5_occ:    1.244    0.084    0.629
   5_bss:    1.244    0.084    0.629
------------------------------------------------------------------------

CPU time actual refinement: 332.75


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_338/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_338/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_338/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_338/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_338/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 332.61 
  Macro-tasks:
    bulk solvent and scale       = 41.47  
    individual site refinement   = 137.55 
    weights calculation          = 30.04  
    collect and process          = 6.71   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 215.87 
  Micro-tasks:
    mask                            = 1.69   
    f_calc                          = 107.10 
    alpha_beta                      = 8.57   
    target                          = 1.24   
    gradients_wrt_atomic_parameters = 110.90 
    fmodel                         = 6.79   
    r_factors                      = 0.12   
    phase_errors                   = 11.77  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 248.41 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.736 micro seconds
Total CPU time: 5.76 minutes
from_scatterers_fft:    627 calls, 106.82 s
gradients_fft:          572 calls,  99.64 s

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

# Date 2008-01-16 Time 04:35:34 PST -0800 (1200486934.32 s)
Start R-work = 0.4270, R-free = 0.4191 (no bulk solvent and anisotropic scale)
Final R-work = 0.1388, R-free = 0.1769 (no bulk solvent and anisotropic scale)

Start R-work = 0.4187, R-free = 0.4087
Final R-work = 0.1169, R-free = 0.1602