# Date 2008-01-16 Time 06:21:52 PST -0800 (1200493312.40 s)
#phil __OFF__

Command line arguments: "../1113.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 16612
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1113

-------------------------------------------------------------------------------
  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: (71.655, 46.2261, 85.0941, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 46.2261, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1461 1.97037
Completeness in resolution range: 0.952263
Completeness with d_max=infinity: 0.949447

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1461
                             d_min =   1.9704

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 46.2261, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1461 1.97037
Completeness in resolution range: 0.952263
Completeness with d_max=infinity: 0.949447

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1465 -  4.2174 [2153/2179]  1941   212   9.8%
  bin  2:  4.2174 -  3.3595 [2083/2103]  1873   210  10.1%
  bin  3:  3.3595 -  2.9383 [2035/2054]  1829   206  10.1%
  bin  4:  2.9383 -  2.6713 [2021/2051]  1824   197   9.7%
  bin  5:  2.6713 -  2.4807 [2043/2062]  1842   201   9.8%
  bin  6:  2.4807 -  2.3350 [2007/2032]  1795   212  10.6%
  bin  7:  2.3350 -  2.2184 [1996/2024]  1796   200  10.0%
  bin  8:  2.2184 -  2.1221 [1972/2008]  1781   191   9.7%
  bin  9:  2.1221 -  2.0406 [1992/2034]  1795   197   9.9%
  bin 10:  2.0406 -  1.9704 [1287/2024]  1154   133  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1113/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.73 -     2.37: 29
        2.37 -     3.00: 1945
        3.00 -     3.63: 4653
        3.63 -     4.27: 9197
        4.27 -     4.90: 12664
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.734 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 206 " - " O   HOH Z 341 "  1.862 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 107 " - " O   HOH Z 340 "  1.897 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 201 " - " O   HOH Z 349 "  2.041 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28483 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_1113/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1113/model_refine_001.geo

CPU time processing inputs: 9.18


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.655 46.22605 85.09415 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 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4486   r_free= 0.4460   ksol= 0.00   Bsol= 0.00   scale= 0.911    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.249336                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1465 -  4.7044 0.99   1405  158 0.3525 0.3585      6.4999      6.4986|
|  2:  4.7044 -  3.7527 0.99   1348  146 0.3788 0.3566      6.7543       6.728|
|  3:  3.7527 -  3.2839 0.99   1307  144 0.4096 0.3736      6.6064      6.6612|
|  4:  3.2839 -  2.9861 0.99   1329  156 0.4311 0.4761      6.4931      6.4711|
|  5:  2.9861 -  2.7735 0.99   1313  139 0.4714 0.4852      6.3383      6.3444|
|  6:  2.7735 -  2.6109 0.99   1286  149 0.4783 0.4677      6.2582      6.2489|
|  7:  2.6109 -  2.4807 0.99   1321  134 0.4891 0.4516      6.2254      6.1932|
|  8:  2.4807 -  2.3731 0.98   1255  151 0.5006 0.4751      6.1497      6.1274|
|  9:  2.3731 -  2.2821 0.98   1294  146 0.4868 0.4913      6.1136      6.1218|
| 10:  2.2821 -  2.2036 1.00   1285  143 0.5010 0.5211      6.0733      6.0967|
| 11:  2.2036 -  2.1349 0.98   1290  135 0.5138 0.5138      6.0348      6.0589|
| 12:  2.1349 -  2.0740 0.98   1254  148 0.5165 0.5678       5.962      6.0146|
| 13:  2.0740 -  2.0195 0.96   1242  137 0.5098 0.4929      5.8774       5.792|
| 14:  2.0195 -  1.9704 0.53    701   73 0.5311 0.4867      5.8298      5.8234|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1465 -  4.7044  1405   158  0.73  31.41   0.83     0.78      61532.58|
|  2:  4.7044 -  3.7527  1348   146  0.74  32.06   0.93     0.85      89439.59|
|  3:  3.7527 -  3.2839  1307   144  0.64  40.45   0.94     0.82      98562.91|
|  4:  3.2839 -  2.9861  1329   156  0.55  48.24   0.93     0.74      94757.18|
|  5:  2.9861 -  2.7735  1313   139  0.45  56.04   0.89     0.62      77439.22|
|  6:  2.7735 -  2.6109  1286   149  0.43  57.08   0.92     0.61      67754.97|
|  7:  2.6109 -  2.4807  1321   134  0.45  56.08   0.92     0.62      57164.36|
|  8:  2.4807 -  2.3731  1255   151  0.45  55.67   0.90     0.66      51682.43|
|  9:  2.3731 -  2.2821  1294   146  0.45  56.42   0.95     0.63      47435.55|
| 10:  2.2821 -  2.2036  1285   143  0.39  60.47   0.94     0.59      47206.66|
| 11:  2.2036 -  2.1349  1290   135  0.36  63.31   0.95     0.54      46543.15|
| 12:  2.1349 -  2.0740  1254   148  0.33  65.45   0.95     0.51      42932.99|
| 13:  2.0740 -  2.0195  1242   137  0.31  66.99   0.95     0.49      37410.52|
| 14:  2.0195 -  1.9704   701    73  0.30  67.90   0.92     0.44      32458.90|
|alpha:            min =        0.44 max =            0.85 mean =         0.64|
|beta:             min =    32458.90 max =        98562.91 mean =     62172.23|
|figures of merit: min =        0.00 max =            1.00 mean =         0.48|
|phase err.(work): min =        0.00 max =           89.99 mean =        53.35|
|phase err.(test): min =        0.00 max =           89.63 mean =        53.52|
|-----------------------------------------------------------------------------|

============================== 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 = 6.793279              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.159   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.300403              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.170   (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 |  1.734 -  2.051:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.051 -  2.367:       24 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.367 -  2.684:      113 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.684 -  3.001:     1832 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.001 -  3.317:     1918 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.317 -  3.634:     2735 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.634 -  3.950:     4754 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.950 -  4.267:     4443 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.267 -  4.583:     5771 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.583 -  4.900:     6893 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.169 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.109    4.900  1.734 |       0.292 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.787)------------------------------------------|
|    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 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4486   r_free= 0.4460   ksol= 0.00   Bsol= 0.00   scale= 0.911    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.249336                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4404   r_free= 0.4391   ksol= 0.30   Bsol= 20.00   scale= 0.950   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.75,0.73,0.14,0.00,0.00,0.00); trace/3= 0.54                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.244768                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.546381              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.308   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.062153              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.847   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4404      final r-factor (work) = 0.3138          |
| start r-factor (free) = 0.4391      final r-factor (free) = 0.3483          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.4751 = 5.55 * 0.50 * 6.2404 + 1.00 * 0.1693                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.0402 = 5.55 * 0.50 * 6.1033 + 1.00 * 0.1146                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3138      final r-factor (work) = 0.2864          |
| start r-factor (free) = 0.3483      final r-factor (free) = 0.3638          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.4888 = 1.06 * 1.00 * 6.1033 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.3379 = 1.06 * 1.00 * 5.9510 + 1.00 * 0.0170                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.787)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.98   18.45    None  None   None       |
|    all(noH): 2823   0      0.00    87.98   18.45    None  None   None       |
|    Sol.    : 438    0      0.00    87.98   39.60    None  None   None       |
|    Mac.    : 2385   0      0.00    80.83   14.56    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 -   8.798:  782   |   5:    43.988 -  52.785:   96        |
|      1:     8.798 -  17.595:  947   |   6:    52.785 -  61.583:   63        |
|      2:    17.595 -  26.393:  483   |   7:    61.583 -  70.380:   41        |
|      3:    26.393 -  35.190:  232   |   8:    70.380 -  79.178:    6        |
|      4:    35.190 -  43.988:  167   |   9:    79.178 -  87.975:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2864 r_free = 0.3638             target_work(ml) = 5.963         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2861 r_free = 0.3635             target_work(ml) = 5.962         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2861   r_free= 0.3635   ksol= 0.30   Bsol= 20.00   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.75,0.73,0.14,0.00,0.00,0.00); trace/3= 0.54                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 5.961732                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2852   r_free= 0.3623   ksol= 0.34   Bsol= 57.20   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.56,-0.98,-0.63,-0.00,-0.00,-0.00); trace/3= -0.72                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.45 A                  |
| x-ray target function (ml) for work reflections: 5.961214                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.871061              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 92.805   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.428645              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.070  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2852      final r-factor (work) = 0.2074          |
| start r-factor (free) = 0.3623      final r-factor (free) = 0.2671          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.6111 = 4.87 * 0.50 * 5.9521 + 1.00 * 0.1146                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.3205 = 4.87 * 0.50 * 5.8469 + 1.00 * 0.0802                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2074      final r-factor (work) = 0.1852          |
| start r-factor (free) = 0.2671      final r-factor (free) = 0.2430          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5232 = 0.43 * 1.00 * 5.8469 + 1.00 * 0.0170                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4261 = 0.43 * 1.00 * 5.6367 + 1.00 * 0.0100                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.787)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.32   17.61    None  None   None       |
|    all(noH): 2823   0      0.00    87.32   17.61    None  None   None       |
|    Sol.    : 438    0      4.07    87.32   40.89    None  None   None       |
|    Mac.    : 2385   0      0.00    81.72   13.34    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 -   8.732:  778   |   5:    43.659 -  52.391:  113        |
|      1:     8.732 -  17.464: 1174   |   6:    52.391 -  61.123:   73        |
|      2:    17.464 -  26.195:  342   |   7:    61.123 -  69.854:   34        |
|      3:    26.195 -  34.927:  158   |   8:    69.854 -  78.586:   12        |
|      4:    34.927 -  43.659:  135   |   9:    78.586 -  87.318:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1852 r_free = 0.2430             target_work(ml) = 5.590         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1850 r_free = 0.2428             target_work(ml) = 5.589         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1850   r_free= 0.2428   ksol= 0.34   Bsol= 57.20   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.56,-0.98,-0.63,-0.00,-0.00,-0.00); trace/3= -0.72                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.588505                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1853   r_free= 0.2423   ksol= 0.34   Bsol= 57.20   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.06,-1.82,-0.85,-0.00,-0.00,-0.00); trace/3= -1.24                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.586778                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.175764              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.880   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.372475              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 135.590  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1853      final r-factor (work) = 0.1440          |
| start r-factor (free) = 0.2423      final r-factor (free) = 0.1957          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0319 = 3.18 * 0.50 * 5.6376 + 1.00 * 0.0801                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.7629 = 3.18 * 0.50 * 5.4849 + 1.00 * 0.0534                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1440      final r-factor (work) = 0.1351          |
| start r-factor (free) = 0.1957      final r-factor (free) = 0.1843          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0529 = 0.37 * 1.00 * 5.4849 + 1.00 * 0.0099                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9963 = 0.37 * 1.00 * 5.3349 + 1.00 * 0.0092                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.787)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.06    88.06   17.39    None  None   None       |
|    all(noH): 2823   0      1.06    88.06   17.39    None  None   None       |
|    Sol.    : 438    0      6.33    84.48   41.84    None  None   None       |
|    Mac.    : 2385   0      1.06    88.06   12.90    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.065 -   9.764: 1009   |   5:    44.563 -  53.262:  102        |
|      1:     9.764 -  18.464: 1078   |   6:    53.262 -  61.962:   75        |
|      2:    18.464 -  27.163:  260   |   7:    61.962 -  70.661:   36        |
|      3:    27.163 -  35.863:  127   |   8:    70.661 -  79.361:   17        |
|      4:    35.863 -  44.563:  114   |   9:    79.361 -  88.060:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1351 r_free = 0.1843             target_work(ml) = 5.301         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1351 r_free = 0.1840             target_work(ml) = 5.301         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1351   r_free= 0.1840   ksol= 0.34   Bsol= 57.20   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.06,-1.82,-0.85,-0.00,-0.00,-0.00); trace/3= -1.24                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.300596                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1352   r_free= 0.1840   ksol= 0.33   Bsol= 53.02   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.71,-2.44,-1.42,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.301091                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.469300              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 119.669  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.297189              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.217  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1352      final r-factor (work) = 0.1244          |
| start r-factor (free) = 0.1840      final r-factor (free) = 0.1705          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9758 = 1.47 * 0.50 * 5.3390 + 1.00 * 0.0534                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9160 = 1.47 * 0.50 * 5.2674 + 1.00 * 0.0463                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1244      final r-factor (work) = 0.1222          |
| start r-factor (free) = 0.1705      final r-factor (free) = 0.1663          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5746 = 0.30 * 1.00 * 5.2674 + 1.00 * 0.0092                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5599 = 0.30 * 1.00 * 5.2194 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.787)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.83   17.14    None  None   None       |
|    all(noH): 2823   0      0.00    90.83   17.14    None  None   None       |
|    Sol.    : 438    0      5.89    86.72   40.94    None  None   None       |
|    Mac.    : 2385   0      0.00    90.83   12.77    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.083:  860   |   5:    45.416 -  54.499:   99        |
|      1:     9.083 -  18.167: 1238   |   6:    54.499 -  63.583:   73        |
|      2:    18.167 -  27.250:  269   |   7:    63.583 -  72.666:   25        |
|      3:    27.250 -  36.333:  128   |   8:    72.666 -  81.749:   13        |
|      4:    36.333 -  45.416:  113   |   9:    81.749 -  90.832:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1222 r_free = 0.1663             target_work(ml) = 5.207         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1221 r_free = 0.1660             target_work(ml) = 5.206         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1221   r_free= 0.1660   ksol= 0.33   Bsol= 53.02   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.71,-2.44,-1.42,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.206068                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1221   r_free= 0.1660   ksol= 0.32   Bsol= 47.93   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.71,-2.44,-1.42,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.206170                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.160502              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 140.724  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.934356              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.298  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1221      final r-factor (work) = 0.1138          |
| start r-factor (free) = 0.1660      final r-factor (free) = 0.1599          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6841 = 2.16 * 0.50 * 5.2189 + 1.00 * 0.0463                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6484 = 2.16 * 0.50 * 5.1740 + 1.00 * 0.0591                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1138      final r-factor (work) = 0.1125          |
| start r-factor (free) = 0.1599      final r-factor (free) = 0.1596          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8431 = 0.93 * 1.00 * 5.1740 + 1.00 * 0.0087                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8187 = 0.93 * 1.00 * 5.1468 + 1.00 * 0.0097                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.787)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.87   17.21    None  None   None       |
|    all(noH): 2823   0      0.00    97.87   17.21    None  None   None       |
|    Sol.    : 438    0      5.95    91.14   41.35    None  None   None       |
|    Mac.    : 2385   0      0.00    97.87   12.77    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.787: 1040   |   5:    48.933 -  58.719:  104        |
|      1:     9.787 -  19.573: 1127   |   6:    58.719 -  68.506:   43        |
|      2:    19.573 -  29.360:  233   |   7:    68.506 -  78.293:   20        |
|      3:    29.360 -  39.146:  125   |   8:    78.293 -  88.079:   10        |
|      4:    39.146 -  48.933:  116   |   9:    88.079 -  97.866:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1125 r_free = 0.1596             target_work(ml) = 5.148         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1124 r_free = 0.1595             target_work(ml) = 5.147         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1124   r_free= 0.1595   ksol= 0.32   Bsol= 47.93   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.71,-2.44,-1.42,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.147401                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1465 -  4.7044 0.99   1405  158 0.0959 0.1373       5.371      5.5843|
|  2:  4.7044 -  3.7527 0.99   1348  146 0.0852 0.1096      5.4405      5.6262|
|  3:  3.7527 -  3.2839 0.99   1307  144 0.1094 0.1568      5.4923      5.8523|
|  4:  3.2839 -  2.9861 0.99   1329  156 0.1268 0.1641      5.4858      5.6155|
|  5:  2.9861 -  2.7735 0.99   1313  139 0.1322 0.1833      5.3059      5.5739|
|  6:  2.7735 -  2.6109 0.99   1286  149 0.1189 0.1651      5.1846      5.4153|
|  7:  2.6109 -  2.4807 0.99   1321  134 0.1277 0.1612      5.1585      5.3208|
|  8:  2.4807 -  2.3731 0.98   1255  151 0.1181 0.1883       5.054      5.4167|
|  9:  2.3731 -  2.2821 0.98   1294  146 0.1173 0.1706      5.0429      5.2943|
| 10:  2.2821 -  2.2036 1.00   1285  143 0.1116 0.1766      4.9436      5.2325|
| 11:  2.2036 -  2.1349 0.98   1290  135 0.1162 0.1846      4.9642      5.3293|
| 12:  2.1349 -  2.0740 0.98   1254  148 0.1099 0.1534       4.862      5.0499|
| 13:  2.0740 -  2.0195 0.96   1242  137 0.1152 0.1804      4.8009       5.066|
| 14:  2.0195 -  1.9704 0.53    701   73 0.1052 0.1594      4.6604      4.9269|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1465 -  4.7044  1405   158  0.94   8.91   0.98     0.95       7087.72|
|  2:  4.7044 -  3.7527  1348   146  0.95   8.13   1.02     1.01       9146.37|
|  3:  3.7527 -  3.2839  1307   144  0.93  11.47   1.03     1.03      10618.25|
|  4:  3.2839 -  2.9861  1329   156  0.91  14.49   1.01     0.98      10892.36|
|  5:  2.9861 -  2.7735  1313   139  0.90  15.45   1.00     0.99       7748.41|
|  6:  2.7735 -  2.6109  1286   149  0.91  15.24   0.99     0.97       6613.34|
|  7:  2.6109 -  2.4807  1321   134  0.91  15.17   1.00     0.98       5997.17|
|  8:  2.4807 -  2.3731  1255   151  0.90  15.65   0.98     0.96       5172.42|
|  9:  2.3731 -  2.2821  1294   146  0.91  15.22   1.00     0.97       5061.26|
| 10:  2.2821 -  2.2036  1285   143  0.91  15.38   1.00     0.97       4270.78|
| 11:  2.2036 -  2.1349  1290   135  0.90  16.61   0.99     0.95       4553.02|
| 12:  2.1349 -  2.0740  1254   148  0.91  15.41   1.01     1.01       3922.32|
| 13:  2.0740 -  2.0195  1242   137  0.91  15.89   1.00     0.99       3378.93|
| 14:  2.0195 -  1.9704   701    73  0.91  15.05   0.99     0.96       2592.79|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2592.79 max =        10892.36 mean =      6385.54|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.76 mean =        14.05|
|phase err.(test): min =        0.00 max =           89.74 mean =        13.60|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1128   r_free= 0.1588   ksol= 0.32   Bsol= 50.51   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.71,-2.45,-1.42,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.147021                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.15 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1128   r_free= 0.1588   ksol= 0.32   Bsol= 50.51   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.71,-2.45,-1.42,-0.00,-0.00,-0.00); trace/3= -1.86                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.147021                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1465 -  4.7044 0.99   1405  158 0.0969 0.1326      5.3654      5.5629|
|  2:  4.7044 -  3.7527 0.99   1348  146 0.0864 0.1077      5.4429       5.619|
|  3:  3.7527 -  3.2839 0.99   1307  144 0.1101 0.1581      5.4932      5.8588|
|  4:  3.2839 -  2.9861 0.99   1329  156 0.1270 0.1632      5.4862       5.614|
|  5:  2.9861 -  2.7735 0.99   1313  139 0.1327 0.1828      5.3057      5.5699|
|  6:  2.7735 -  2.6109 0.99   1286  149 0.1190 0.1651      5.1841      5.4162|
|  7:  2.6109 -  2.4807 0.99   1321  134 0.1276 0.1608      5.1576      5.3188|
|  8:  2.4807 -  2.3731 0.98   1255  151 0.1177 0.1886      5.0537      5.4179|
|  9:  2.3731 -  2.2821 0.98   1294  146 0.1173 0.1706      5.0427      5.2963|
| 10:  2.2821 -  2.2036 1.00   1285  143 0.1113 0.1764      4.9427      5.2305|
| 11:  2.2036 -  2.1349 0.98   1290  135 0.1161 0.1848      4.9641      5.3315|
| 12:  2.1349 -  2.0740 0.98   1254  148 0.1098 0.1533      4.8622      5.0502|
| 13:  2.0740 -  2.0195 0.96   1242  137 0.1151 0.1805      4.8007      5.0665|
| 14:  2.0195 -  1.9704 0.53    701   73 0.1050 0.1595      4.6604      4.9283|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1465 -  4.7044  1405   158  0.94   8.93   0.97     0.95       6941.94|
|  2:  4.7044 -  3.7527  1348   146  0.95   7.98   1.02     1.01       8956.46|
|  3:  3.7527 -  3.2839  1307   144  0.93  11.34   1.03     1.03      10462.49|
|  4:  3.2839 -  2.9861  1329   156  0.91  14.52   1.01     0.98      10907.31|
|  5:  2.9861 -  2.7735  1313   139  0.90  15.38   1.00     0.99       7708.01|
|  6:  2.7735 -  2.6109  1286   149  0.91  15.21   0.99     0.97       6591.52|
|  7:  2.6109 -  2.4807  1321   134  0.91  15.16   1.00     0.98       5992.27|
|  8:  2.4807 -  2.3731  1255   151  0.90  15.69   0.98     0.96       5186.56|
|  9:  2.3731 -  2.2821  1294   146  0.91  15.22   1.00     0.97       5064.02|
| 10:  2.2821 -  2.2036  1285   143  0.91  15.39   1.00     0.97       4272.63|
| 11:  2.2036 -  2.1349  1290   135  0.90  16.63   0.99     0.95       4557.91|
| 12:  2.1349 -  2.0740  1254   148  0.91  15.43   1.01     1.01       3929.94|
| 13:  2.0740 -  2.0195  1242   137  0.91  15.91   1.00     0.99       3385.92|
| 14:  2.0195 -  1.9704   701    73  0.91  15.07   0.99     0.96       2594.86|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2594.86 max =        10907.31 mean =      6346.83|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.04|
|phase err.(test): min =        0.00 max =           89.62 mean =        13.61|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.787)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.87   17.21    None  None   None       |
|    all(noH): 2823   0      0.00    97.87   17.21    None  None   None       |
|    Sol.    : 438    0      5.95    91.14   41.35    None  None   None       |
|    Mac.    : 2385   0      0.00    97.87   12.78    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.790: 1040   |   5:    48.936 -  58.722:  104        |
|      1:     9.790 -  19.576: 1127   |   6:    58.722 -  68.509:   43        |
|      2:    19.576 -  29.363:  233   |   7:    68.509 -  78.296:   20        |
|      3:    29.363 -  39.149:  125   |   8:    78.296 -  88.082:   10        |
|      4:    39.149 -  48.936:  116   |   9:    88.082 -  97.869:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 314         
Filter by distance & map next to the model:
   mapped sites are within: 0.565 - 4.428
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 311 from: 314
   mapped sites are within: 0.753 - 4.428

peak=    6.216 closest distance to " NE2 GLN A  11 " =    1.260
peak=    5.648 closest distance to " NH2 ARG A  56 " =    2.132
peak=    5.465 closest distance to " CG  PRO A  54 " =    1.219
peak=    5.393 closest distance to " CB  GLN A 223 " =    1.470
peak=    5.199 closest distance to " O   HOH Z 144 " =    1.704
peak=    5.157 closest distance to " CB  SER A  63 " =    1.318
peak=    5.152 closest distance to " CG  PRO A 213 " =    1.258
peak=    5.061 closest distance to " O   HOH Z 232 " =    2.260
peak=    5.019 closest distance to " O   HOH Z 126 " =    2.007
peak=    4.907 closest distance to " CG  PRO A 198 " =    1.274
peak=    4.811 closest distance to " CB  GLN A 183 " =    1.217
peak=    4.773 closest distance to " O   HOH Z 369 " =    2.106
peak=    4.686 closest distance to " O   HOH Z 425 " =    1.402
peak=    4.666 closest distance to " O   HOH Z 423 " =    1.845
peak=    4.656 closest distance to " O   HOH Z   7 " =    1.282
peak=    4.646 closest distance to " CB  PRO A  54 " =    0.942
peak=    4.616 closest distance to " O   HOH Z 298 " =    1.951
peak=    4.555 closest distance to " O   HOH Z 135 " =    1.841
peak=    4.527 closest distance to " O   HOH Z 427 " =    2.657
peak=    4.515 closest distance to " O   HOH Z 183 " =    1.478
peak=    4.484 closest distance to " O   HOH Z 214 " =    1.250
peak=    4.434 closest distance to " CB  GLU A 152 " =    1.372
peak=    4.417 closest distance to " CA  TYR A  30 " =    1.018
peak=    4.413 closest distance to " CB  GLU A 128 " =    1.032
peak=    4.411 closest distance to " O   HOH Z  78 " =    1.967
peak=    4.404 closest distance to " C   PRO A 198 " =    1.546
peak=    4.375 closest distance to " O   HOH Z 403 " =    1.385
peak=    4.356 closest distance to " O   HOH Z   2 " =    1.713
peak=    4.351 closest distance to " CB  SER A   3 " =    1.467
peak=    4.339 closest distance to " CB  ARG A 275 " =    0.927
peak=    4.319 closest distance to " CB  ASN A 148 " =    1.346
peak=    4.294 closest distance to " O   HOH Z 193 " =    1.738
peak=    4.258 closest distance to " O   HOH Z 134 " =    1.333
peak=    4.252 closest distance to " O   HOH Z  63 " =    1.480
peak=    4.221 closest distance to " ND2 ASN A 187 " =    1.510
peak=    4.210 closest distance to " O   HOH Z 217 " =    2.884
peak=    4.205 closest distance to " O   HOH Z 272 " =    1.855
peak=    4.198 closest distance to " O   HOH Z 236 " =    1.458
peak=    4.160 closest distance to " O   HOH Z 287 " =    1.996
peak=    4.120 closest distance to " O   HOH Z 316 " =    3.113
peak=    4.084 closest distance to " O   HOH Z 193 " =    1.881
peak=    4.074 closest distance to " O   HOH Z  10 " =    1.793
peak=    4.045 closest distance to " CG  PRO A  90 " =    1.024
peak=    4.038 closest distance to " CB  LEU A 228 " =    1.093
peak=    4.028 closest distance to " CB  TRP A 266 " =    1.026
peak=    4.027 closest distance to " CG2 VAL A 257 " =    0.993
peak=    4.020 closest distance to " O   HOH Z 261 " =    1.689
peak=    4.006 closest distance to " CB  SER A 216 " =    0.853
peak=    4.005 closest distance to " OD1 ASN A  69 " =    2.639
peak=    3.994 closest distance to " CB  ARG A 139 " =    1.069
peak=    3.985 closest distance to " CG1 ILE A  33 " =    1.244
peak=    3.983 closest distance to " O   HOH Z 368 " =    1.935
peak=    3.974 closest distance to " O   HOH Z   1 " =    1.837
peak=    3.969 closest distance to " O   HOH Z 132 " =    2.234
peak=    3.959 closest distance to " O   HOH Z 180 " =    2.077
peak=    3.959 closest distance to " CD  ARG A 159 " =    0.870
peak=    3.940 closest distance to " O   HOH Z   9 " =    2.289
peak=    3.937 closest distance to " O   HOH Z 437 " =    1.906
peak=    3.934 closest distance to " CG  TRP A 179 " =    2.248
peak=    3.924 closest distance to " OD2 ASP A 286 " =    2.816
peak=    3.917 closest distance to " CD BLYS A 290 " =    1.013
peak=    3.916 closest distance to " O   HOH Z 260 " =    1.234
peak=    3.909 closest distance to " NH2BARG A 102 " =    1.060
peak=    3.907 closest distance to " CB  ARG A  79 " =    1.387
peak=    3.905 closest distance to " O   HOH Z  44 " =    1.727
peak=    3.905 closest distance to " O   HOH Z 234 " =    3.819
peak=    3.900 closest distance to " CB  TYR A 169 " =    0.874
peak=    3.897 closest distance to " O   HOH Z  21 " =    1.705
peak=    3.893 closest distance to " O   HOH Z 419 " =    2.078
peak=    3.877 closest distance to " ND1 HIS A  86 " =    1.810
peak=    3.853 closest distance to " NH1AARG A 145 " =    1.115
peak=    3.846 closest distance to " CB  ASN A 187 " =    1.091
peak=    3.845 closest distance to " O   HOH Z 411 " =    3.624
peak=    3.837 closest distance to " O   HOH Z 344 " =    3.255
peak=    3.832 closest distance to " O   HOH Z  61 " =    1.575
peak=    3.829 closest distance to " CA  MET A  40 " =    1.090
peak=    3.821 closest distance to " CB  VAL A 265 " =    1.307
peak=    3.818 closest distance to " O   HOH Z 352 " =    1.820
peak=    3.814 closest distance to " O   MET A 105 " =    1.860
peak=    3.814 closest distance to " O   HOH Z  88 " =    3.302
peak=    3.797 closest distance to " CA  THR A 264 " =    0.842
peak=    3.793 closest distance to " O   HOH Z 108 " =    1.640
peak=    3.783 closest distance to " N   ALA A   1 " =    2.051
peak=    3.780 closest distance to " O   HOH Z 282 " =    1.607
peak=    3.773 closest distance to " O   HOH Z 394 " =    1.589
peak=    3.769 closest distance to " OD1BASN A 224 " =    2.267
peak=    3.764 closest distance to " CE  LYS A  76 " =    0.890
peak=    3.761 closest distance to " CB  VAL A 202 " =    1.660
peak=    3.754 closest distance to " CA  GLY A 267 " =    1.307
peak=    3.747 closest distance to " O   HOH Z   1 " =    1.719
peak=    3.747 closest distance to " N   PHE A 130 " =    1.280
peak=    3.745 closest distance to " CB  TRP A 179 " =    1.511
peak=    3.744 closest distance to " O   HOH Z 126 " =    1.456
peak=    3.737 closest distance to " O   HOH Z  64 " =    2.269
peak=    3.733 closest distance to " O   HOH Z  44 " =    3.042
peak=    3.731 closest distance to " O   HOH Z 391 " =    2.939
peak=    3.726 closest distance to " O   SER A  87 " =    2.281
peak=    3.726 closest distance to " CG2 THR A 221 " =    1.045
peak=    3.722 closest distance to " O   HOH Z 189 " =    2.175
peak=    3.710 closest distance to " CB  MET A  47 " =    1.158
peak=    3.703 closest distance to " CG  PRO A 243 " =    1.108
peak=    3.701 closest distance to " NE AARG A 275 " =    1.496
peak=    3.700 closest distance to " O   HOH Z  48 " =    1.453
peak=    3.694 closest distance to " O   HOH Z  40 " =    2.271
peak=    3.692 closest distance to " CG  LEU A 167 " =    1.237
peak=    3.689 closest distance to " O   HOH Z 380 " =    1.557
peak=    3.661 closest distance to " O   HOH Z 115 " =    1.913
peak=    3.644 closest distance to " O   HOH Z 371 " =    1.909
peak=    3.642 closest distance to " O   HOH Z 371 " =    2.736
peak=    3.639 closest distance to " O   HOH Z 133 " =    2.377
peak=    3.632 closest distance to " CB  GLU A 236 " =    1.260
peak=    3.623 closest distance to " O   HOH Z 409 " =    2.436
peak=    3.622 closest distance to " O   HOH Z 334 " =    3.059
peak=    3.619 closest distance to " CD  PRO A 243 " =    1.821
peak=    3.617 closest distance to " O   HOH Z  61 " =    1.627
peak=    3.615 closest distance to " CA  ILE A 234 " =    1.086
peak=    3.614 closest distance to " O   HOH Z 288 " =    2.056
peak=    3.607 closest distance to " O   HOH Z 302 " =    1.647
peak=    3.604 closest distance to " ND2 ASN A  60 " =    3.068
peak=    3.603 closest distance to " CA  ALA A 299 " =    0.935
peak=    3.599 closest distance to " CB  ASP A 132 " =    3.888
peak=    3.596 closest distance to " O   HOH Z 407 " =    2.022
peak=    3.594 closest distance to " N   ASN A 127 " =    1.265
peak=    3.586 closest distance to " CB  TYR A 116 " =    0.922
peak=    3.585 closest distance to " O   HOH Z  58 " =    1.782
peak=    3.583 closest distance to " O   HOH Z 271 " =    2.403
peak=    3.578 closest distance to " CG  ARG A 159 " =    0.851
peak=    3.563 closest distance to " O   HOH Z 108 " =    1.998
peak=    3.562 closest distance to " O   HOH Z  64 " =    2.019
peak=    3.561 closest distance to " O   HOH Z 182 " =    1.178
peak=    3.555 closest distance to " O   HOH Z  66 " =    2.087
peak=    3.547 closest distance to " NH1 ARG A  56 " =    1.149
peak=    3.543 closest distance to " O   HOH Z 247 " =    1.234
peak=    3.541 closest distance to " CD1 ILE A  33 " =    1.587
peak=    3.534 closest distance to " CD1 LEU A 300 " =    1.303
peak=    3.528 closest distance to " O   HOH Z 281 " =    4.428
peak=    3.521 closest distance to " O   HOH Z 368 " =    3.697
peak=    3.520 closest distance to " CD2 LEU A 255 " =    1.510
peak=    3.518 closest distance to " CA  SER A  87 " =    0.979
peak=    3.518 closest distance to " O   HOH Z 365 " =    2.849
peak=    3.517 closest distance to " O   THR A 220 " =    1.477
peak=    3.516 closest distance to " O   HOH Z 207 " =    2.067
peak=    3.512 closest distance to " O   HOH Z  20 " =    1.798
peak=    3.511 closest distance to " CA  ASN A 215 " =    1.283
peak=    3.510 closest distance to " CB  ARG A 190 " =    1.716
peak=    3.509 closest distance to " O   HOH Z 158 " =    2.869
peak=    3.507 closest distance to " CB  SER A 276 " =    1.149
peak=    3.506 closest distance to " O   HOH Z 227 " =    1.692
peak=    3.501 closest distance to " O   HOH Z 188 " =    2.049
peak=    3.499 closest distance to " CB  GLU A 277 " =    3.575
peak=    3.497 closest distance to " N   ARG A 156 " =    1.264
peak=    3.495 closest distance to " CD  LYS A 166 " =    1.335
peak=    3.495 closest distance to " O   HOH Z 193 " =    2.134
peak=    3.481 closest distance to " O   HOH Z 234 " =    3.916
peak=    3.481 closest distance to " O   TYR A 116 " =    1.352
peak=    3.480 closest distance to " O   HOH Z  97 " =    1.930
peak=    3.478 closest distance to " O   HOH Z 217 " =    1.599
peak=    3.475 closest distance to " OG  SER A  62 " =    3.049
peak=    3.473 closest distance to " O   HOH Z  59 " =    1.667
peak=    3.473 closest distance to " O   HOH Z 258 " =    2.190
peak=    3.472 closest distance to " CB  ALA A 291 " =    1.478
peak=    3.468 closest distance to " N   TYR A  15 " =    0.927
peak=    3.468 closest distance to " CA  TYR A 186 " =    1.500
peak=    3.467 closest distance to " O   HOH Z 207 " =    1.706
peak=    3.466 closest distance to " N   ASN A  39 " =    1.396
peak=    3.466 closest distance to " CG  GLN A  88 " =    1.049
peak=    3.464 closest distance to " O   HOH Z 405 " =    1.302
peak=    3.463 closest distance to " CD  LYS A 119 " =    1.151
peak=    3.457 closest distance to " NE2 GLN A  73 " =    3.596
peak=    3.454 closest distance to " O   HOH Z 313 " =    1.692
peak=    3.453 closest distance to " CA  ALA A 154 " =    0.972
peak=    3.452 closest distance to " CB  SER A 212 " =    0.957
peak=    3.450 closest distance to " CB  THR A 157 " =    1.163
peak=    3.444 closest distance to " CB  LEU A 143 " =    1.081
peak=    3.444 closest distance to " CA  GLU A 152 " =    1.358
peak=    3.442 closest distance to " O   HOH Z 116 " =    3.002
peak=    3.437 closest distance to " O   HOH Z 153 " =    1.634
peak=    3.435 closest distance to " O   HOH Z 374 " =    2.740
peak=    3.427 closest distance to " CD BARG A 102 " =    1.209
peak=    3.426 closest distance to " O   HOH Z 119 " =    1.492
peak=    3.421 closest distance to " O   HOH Z  59 " =    1.859
peak=    3.420 closest distance to " CA  ALA A 233 " =    1.293
peak=    3.415 closest distance to " CA  ALA A  21 " =    1.157
peak=    3.409 closest distance to " O   HOH Z 184 " =    1.757
peak=    3.405 closest distance to " CA  ALA A 160 " =    0.811
peak=    3.404 closest distance to " O   HOH Z 389 " =    1.913
peak=    3.396 closest distance to " O   HOH Z 112 " =    1.111
peak=    3.396 closest distance to " CA  THR A 221 " =    0.953
peak=    3.390 closest distance to " O   HOH Z 345 " =    3.469
peak=    3.390 closest distance to " O   HOH Z 289 " =    1.635
peak=    3.382 closest distance to " O   HOH Z 209 " =    2.292
peak=    3.380 closest distance to " O   HOH Z  40 " =    2.113
peak=    3.374 closest distance to " O   HOH Z 211 " =    2.478
peak=    3.373 closest distance to " O   HOH Z 282 " =    2.088
peak=    3.371 closest distance to " OD1 ASN A 217 " =    1.575
peak=    3.368 closest distance to " O   HOH Z  17 " =    1.836
peak=    3.366 closest distance to " CE1 TYR A 186 " =    1.346
peak=    3.366 closest distance to " CB  THR A  82 " =    1.253
peak=    3.363 closest distance to " CB  ALA A  34 " =    1.200
peak=    3.360 closest distance to " O   HOH Z 380 " =    2.067
peak=    3.360 closest distance to " OG BSER A  99 " =    2.211
peak=    3.356 closest distance to " O   HOH Z 417 " =    1.332
peak=    3.356 closest distance to " O   HOH Z 175 " =    2.155
peak=    3.352 closest distance to " O   HOH Z 133 " =    1.683
peak=    3.346 closest distance to " O   HOH Z 327 " =    1.863
peak=    3.344 closest distance to " O   HOH Z  68 " =    1.624
peak=    3.337 closest distance to " O   HOH Z 145 " =    2.351
peak=    3.333 closest distance to " CA  LEU A 282 " =    1.116
peak=    3.332 closest distance to " O   ALA A 165 " =    1.344
peak=    3.331 closest distance to " CB  ASN A  39 " =    0.912
peak=    3.331 closest distance to " O   HOH Z 214 " =    1.700
peak=    3.331 closest distance to " O   HOH Z 175 " =    3.590
peak=    3.321 closest distance to " CG  PRO A 280 " =    0.758
peak=    3.317 closest distance to " O   HOH Z 379 " =    1.912
peak=    3.315 closest distance to " O   GLY A  57 " =    2.585
peak=    3.304 closest distance to " CA  TYR A 116 " =    1.381
peak=    3.304 closest distance to " O   HOH Z 152 " =    2.395
peak=    3.303 closest distance to " CD  GLN A 240 " =    1.677
peak=    3.303 closest distance to " O   HOH Z 209 " =    2.548
peak=    3.297 closest distance to " N   GLN A 278 " =    0.950
peak=    3.296 closest distance to " OG  SER A  97 " =    3.280
peak=    3.291 closest distance to " O   HOH Z 281 " =    1.910
peak=    3.291 closest distance to " CA  ALA A 158 " =    1.162
peak=    3.287 closest distance to " NH1BARG A 145 " =    1.222
peak=    3.286 closest distance to " NH2AARG A 190 " =    1.371
peak=    3.285 closest distance to " CA  ARG A 102 " =    1.221
peak=    3.281 closest distance to " O   HOH Z 392 " =    1.273
peak=    3.280 closest distance to " O   HOH Z 128 " =    2.148
peak=    3.271 closest distance to " CB  ALA A 233 " =    1.307
peak=    3.271 closest distance to " O   HOH Z  51 " =    1.729
peak=    3.270 closest distance to " O   HOH Z 369 " =    1.645
peak=    3.268 closest distance to " O   HOH Z 147 " =    1.709
peak=    3.268 closest distance to " O   HOH Z 423 " =    2.148
peak=    3.268 closest distance to " O   HOH Z 154 " =    2.017
peak=    3.263 closest distance to " OG BSER A 164 " =    2.590
peak=    3.262 closest distance to " CD  ARG A  14 " =    1.343
peak=    3.255 closest distance to " NE  ARG A  66 " =    3.670
peak=    3.255 closest distance to " O   HOH Z 373 " =    1.446
peak=    3.254 closest distance to " CB  LYS A 117 " =    1.179
peak=    3.253 closest distance to " CB  ASP A 171 " =    0.944
peak=    3.251 closest distance to " O   HOH Z  43 " =    1.895
peak=    3.249 closest distance to " CB  TYR A 169 " =    0.856
peak=    3.249 closest distance to " CB  ALA A  43 " =    0.919
peak=    3.246 closest distance to " CB  VAL A 265 " =    2.091
peak=    3.243 closest distance to " CB  LEU A 255 " =    0.813
peak=    3.241 closest distance to " O   HOH Z 362 " =    2.451
peak=    3.234 closest distance to " O   HOH Z 387 " =    3.251
peak=    3.234 closest distance to " CG  GLN A 144 " =    0.945
peak=    3.233 closest distance to " O   HOH Z 172 " =    3.201
peak=    3.227 closest distance to " N   SER A 134 " =    1.379
peak=    3.227 closest distance to " CG1 VAL A 153 " =    0.955
peak=    3.226 closest distance to " C   GLU A 277 " =    1.366
peak=    3.222 closest distance to " CB  LEU A 237 " =    0.753
peak=    3.218 closest distance to " NH2BARG A 145 " =    2.033
peak=    3.215 closest distance to " O   HOH Z 295 " =    1.505
peak=    3.207 closest distance to " NH1 ARG A  14 " =    1.051
peak=    3.205 closest distance to " CB  TRP A 150 " =    1.263
peak=    3.204 closest distance to " O   HOH Z  15 " =    1.418
peak=    3.202 closest distance to " O   HOH Z 148 " =    3.382
peak=    3.201 closest distance to " O   HOH Z 281 " =    1.932
peak=    3.201 closest distance to " O   HOH Z   3 " =    2.025
peak=    3.198 closest distance to " NH2 ARG A 219 " =    1.791
peak=    3.187 closest distance to " O   HOH Z 425 " =    2.027
peak=    3.187 closest distance to " O   HOH Z 155 " =    1.401
peak=    3.183 closest distance to " O   HOH Z 329 " =    3.707
peak=    3.180 closest distance to " O   HOH Z 422 " =    2.711
peak=    3.180 closest distance to " CB  ILE A 234 " =    1.100
peak=    3.175 closest distance to " O   HOH Z  88 " =    2.660
peak=    3.173 closest distance to " CD  PRO A 280 " =    0.896
peak=    3.172 closest distance to " CA  LYS A  48 " =    1.429
peak=    3.170 closest distance to " O   HOH Z 213 " =    1.817
peak=    3.168 closest distance to " CB  ARG A 138 " =    0.974
peak=    3.164 closest distance to " OH  TYR A 186 " =    1.129
peak=    3.164 closest distance to " O   HOH Z 110 " =    1.632
peak=    3.164 closest distance to " CA  ASP A 191 " =    0.758
peak=    3.161 closest distance to " O   ASN A 209 " =    1.356
peak=    3.157 closest distance to " O   HOH Z 410 " =    1.696
peak=    3.151 closest distance to " CA  ARG A  56 " =    2.167
peak=    3.150 closest distance to " O   HOH Z 303 " =    1.755
peak=    3.150 closest distance to " CG1 VAL A 202 " =    1.976
peak=    3.150 closest distance to " CB  ALA A  21 " =    1.722
peak=    3.147 closest distance to " CB  ILE A 120 " =    1.296
peak=    3.147 closest distance to " CD  ARG A 138 " =    0.760
peak=    3.145 closest distance to " O   HOH Z  53 " =    2.536
peak=    3.144 closest distance to " O   HOH Z 255 " =    1.714
peak=    3.143 closest distance to " CB  LEU A 300 " =    0.965
peak=    3.141 closest distance to " CB  THR A  31 " =    1.750
peak=    3.141 closest distance to " OG  SER A 206 " =    1.214
peak=    3.137 closest distance to " O   HOH Z 186 " =    1.127
peak=    3.135 closest distance to " OG  SER A  22 " =    2.890
peak=    3.133 closest distance to " CG  GLN A 278 " =    3.684
peak=    3.130 closest distance to " O   HOH Z 128 " =    2.185
peak=    3.123 closest distance to " O   HOH Z 368 " =    4.309
peak=    3.123 closest distance to " CA  LEU A 101 " =    1.416
peak=    3.116 closest distance to " CB  ALA A  71 " =    1.415
peak=    3.111 closest distance to " CG BARG A 275 " =    1.533
peak=    3.110 closest distance to " O   HOH Z 286 " =    2.322
peak=    3.108 closest distance to " O   HOH Z 109 " =    2.761
peak=    3.108 closest distance to " O   HOH Z 116 " =    1.743
peak=    3.105 closest distance to " O   HOH Z 188 " =    2.542
peak=    3.099 closest distance to " CG  GLU A 277 " =    2.067
peak=    3.098 closest distance to " CZ  PHE A 218 " =    1.034
peak=    3.096 closest distance to " CG1BVAL A  72 " =    1.523
peak=    3.094 closest distance to " NZ ALYS A 290 " =    0.961
peak=    3.077 closest distance to " CG  LYS A  76 " =    1.051
peak=    3.076 closest distance to " CB  ASN A 142 " =    0.907
peak=    3.074 closest distance to " O   HOH Z 359 " =    4.030
peak=    3.069 closest distance to " NE2 GLN A  58 " =    3.245
peak=    3.064 closest distance to " O   HOH Z 173 " =    1.768
peak=    3.058 closest distance to " CD1AILE A 234 " =    1.024
peak=    3.015 closest distance to " NZ  LYS A  76 " =    1.346

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 203         
Filter by distance & map next to the model:
   mapped sites are within: 0.534 - 5.932
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 200 from: 203
   mapped sites are within: 0.789 - 5.932

peak=   -4.928 closest distance to " O   HOH Z 377 " =    1.721
peak=   -4.391 closest distance to " CB  PRO A 243 " =    2.505
peak=   -4.304 closest distance to " CD  ARG A  14 " =    3.265
peak=   -4.293 closest distance to " CD  ARG A 156 " =    1.919
peak=   -4.184 closest distance to " CB  ASP A  27 " =    2.441
peak=   -4.177 closest distance to " O   PRO A 198 " =    1.284
peak=   -4.162 closest distance to " O   HOH Z 266 " =    4.575
peak=   -4.076 closest distance to " CA  GLY A  98 " =    1.975
peak=   -4.074 closest distance to " CG  MET A 105 " =    0.974
peak=   -3.990 closest distance to " CG  GLN A 223 " =    2.031
peak=   -3.990 closest distance to " O   HOH Z 290 " =    1.244
peak=   -3.978 closest distance to " CG  LYS A 193 " =    2.506
peak=   -3.969 closest distance to " O   HOH Z 407 " =    3.386
peak=   -3.951 closest distance to " O   HOH Z 166 " =    1.274
peak=   -3.929 closest distance to " OG  SER A  87 " =    1.310
peak=   -3.924 closest distance to " O   HOH Z 388 " =    1.995
peak=   -3.907 closest distance to " C   ALA A 158 " =    1.322
peak=   -3.902 closest distance to " CG  GLN A  88 " =    0.833
peak=   -3.873 closest distance to " ND2 ASN A  45 " =    1.040
peak=   -3.871 closest distance to " CD  ARG A 195 " =    5.124
peak=   -3.840 closest distance to " O   HOH Z 231 " =    1.849
peak=   -3.833 closest distance to " O   HOH Z 198 " =    2.061
peak=   -3.831 closest distance to " C   ASN A 285 " =    2.469
peak=   -3.824 closest distance to " CB  ALA A 291 " =    2.166
peak=   -3.784 closest distance to " CB  CYS A 254 " =    2.163
peak=   -3.780 closest distance to " OD1 ASN A 187 " =    1.518
peak=   -3.778 closest distance to " O   TYR A 247 " =    2.845
peak=   -3.704 closest distance to " OG BSER A 134 " =    1.198
peak=   -3.701 closest distance to " O   HOH Z 389 " =    1.946
peak=   -3.672 closest distance to " NE BARG A 102 " =    2.250
peak=   -3.671 closest distance to " CZ3 TRP A 179 " =    1.046
peak=   -3.650 closest distance to " CA  GLY A 203 " =    2.218
peak=   -3.649 closest distance to " O   PRO A 163 " =    1.948
peak=   -3.636 closest distance to " CZ BARG A 275 " =    1.700
peak=   -3.634 closest distance to " O   HOH Z 353 " =    2.107
peak=   -3.624 closest distance to " NH2AARG A 275 " =    5.588
peak=   -3.620 closest distance to " O   HOH Z 102 " =    1.707
peak=   -3.619 closest distance to " O   HOH Z 185 " =    2.169
peak=   -3.617 closest distance to " O   HOH Z  71 " =    1.080
peak=   -3.617 closest distance to " N   GLN A  58 " =    1.685
peak=   -3.604 closest distance to " O   HOH Z  43 " =    1.562
peak=   -3.587 closest distance to " O   SER A 135 " =    1.467
peak=   -3.582 closest distance to " CG  ASP A 231 " =    0.789
peak=   -3.579 closest distance to " OH  TYR A 214 " =    1.186
peak=   -3.576 closest distance to " C   ASN A 187 " =    1.819
peak=   -3.556 closest distance to " CG1 VAL A 112 " =    3.019
peak=   -3.549 closest distance to " CB  ALA A 248 " =    1.916
peak=   -3.542 closest distance to " O   HOH Z 435 " =    2.788
peak=   -3.529 closest distance to " CG1 VAL A 197 " =    2.267
peak=   -3.529 closest distance to " O   HOH Z 316 " =    1.887
peak=   -3.529 closest distance to " CE2 TYR A  30 " =    2.751
peak=   -3.525 closest distance to " CZ  PHE A  59 " =    1.572
peak=   -3.524 closest distance to " O   HOH Z 385 " =    1.918
peak=   -3.519 closest distance to " CB  PRO A  54 " =    2.365
peak=   -3.506 closest distance to " C   HIS A 108 " =    1.092
peak=   -3.501 closest distance to " O   HOH Z  38 " =    1.541
peak=   -3.497 closest distance to " O   HOH Z 409 " =    5.932
peak=   -3.489 closest distance to " CD1 PHE A  59 " =    1.929
peak=   -3.487 closest distance to " O   HOH Z  13 " =    1.363
peak=   -3.479 closest distance to " O   HOH Z 168 " =    1.923
peak=   -3.466 closest distance to " CB  PHE A 283 " =    2.702
peak=   -3.465 closest distance to " O   HOH Z 298 " =    1.173
peak=   -3.450 closest distance to " CB  ALA A  43 " =    2.447
peak=   -3.447 closest distance to " CG  PRO A 163 " =    2.311
peak=   -3.440 closest distance to " O   HOH Z 417 " =    2.894
peak=   -3.440 closest distance to " CD1 LEU A 101 " =    2.400
peak=   -3.440 closest distance to " O   HOH Z  52 " =    1.333
peak=   -3.438 closest distance to " CB  ASN A  39 " =    2.253
peak=   -3.434 closest distance to " CD  ARG A 139 " =    1.594
peak=   -3.430 closest distance to " O   VAL A 189 " =    2.437
peak=   -3.429 closest distance to " CB  ALA A   7 " =    2.018
peak=   -3.427 closest distance to " O   GLY A 211 " =    1.346
peak=   -3.423 closest distance to " CG1 VAL A 250 " =    2.612
peak=   -3.423 closest distance to " O   HOH Z 111 " =    0.993
peak=   -3.416 closest distance to " CD1 LEU A 228 " =    2.282
peak=   -3.412 closest distance to " O   HOH Z 234 " =    4.070
peak=   -3.412 closest distance to " C   LEU A 143 " =    1.327
peak=   -3.412 closest distance to " N   ALA A  43 " =    2.199
peak=   -3.407 closest distance to " O   HOH Z 351 " =    1.563
peak=   -3.405 closest distance to " OG ASER A 134 " =    1.124
peak=   -3.404 closest distance to " NH2 ARG A  79 " =    1.803
peak=   -3.402 closest distance to " O   HOH Z 198 " =    1.566
peak=   -3.401 closest distance to " CE  MET A 105 " =    2.223
peak=   -3.398 closest distance to " O   HOH Z  51 " =    1.087
peak=   -3.393 closest distance to " O   HOH Z 281 " =    2.962
peak=   -3.386 closest distance to " O   HOH Z 313 " =    1.954
peak=   -3.382 closest distance to " O   HOH Z 140 " =    4.975
peak=   -3.381 closest distance to " CE  MET A  93 " =    1.146
peak=   -3.379 closest distance to " CD  LYS A 289 " =    2.429
peak=   -3.378 closest distance to " O   ALA A 161 " =    1.611
peak=   -3.378 closest distance to " N   ARG A  14 " =    1.008
peak=   -3.366 closest distance to " CB  PHE A 192 " =    1.691
peak=   -3.354 closest distance to " O   HOH Z  60 " =    1.911
peak=   -3.353 closest distance to " OD1 ASP A 171 " =    1.523
peak=   -3.351 closest distance to " CA  GLY A 241 " =    2.205
peak=   -3.349 closest distance to " O   SER A  62 " =    2.248
peak=   -3.335 closest distance to " O   HOH Z  90 " =    2.982
peak=   -3.334 closest distance to " O   HOH Z 211 " =    1.529
peak=   -3.333 closest distance to " O   ASP A  50 " =    1.622
peak=   -3.332 closest distance to " CG  TRP A 266 " =    1.591
peak=   -3.330 closest distance to " CE2 PHE A 218 " =    2.489
peak=   -3.313 closest distance to " O   PHE A 218 " =    1.364
peak=   -3.313 closest distance to " O   VAL A  67 " =    2.599
peak=   -3.310 closest distance to " OE1 GLN A  88 " =    1.275
peak=   -3.307 closest distance to " O   HOH Z 317 " =    2.523
peak=   -3.307 closest distance to " ND2 ASN A  69 " =    1.636
peak=   -3.306 closest distance to " CB  TYR A  15 " =    2.149
peak=   -3.305 closest distance to " OXT GLY A 302 " =    3.029
peak=   -3.304 closest distance to " OG  SER A  97 " =    2.116
peak=   -3.300 closest distance to " O   HOH Z 350 " =    1.444
peak=   -3.296 closest distance to " O   GLY A  80 " =    2.356
peak=   -3.294 closest distance to " O   HOH Z  65 " =    1.295
peak=   -3.289 closest distance to " O   HOH Z 426 " =    2.281
peak=   -3.289 closest distance to " O   ARG A 145 " =    1.435
peak=   -3.288 closest distance to " O   HOH Z 275 " =    1.554
peak=   -3.279 closest distance to " CB  ALA A   9 " =    2.430
peak=   -3.279 closest distance to " O   HOH Z 247 " =    1.720
peak=   -3.278 closest distance to " OD2 ASP A 171 " =    1.762
peak=   -3.270 closest distance to " CD2 LEU A 143 " =    2.564
peak=   -3.269 closest distance to " CE  LYS A  76 " =    2.706
peak=   -3.265 closest distance to " O   ILE A 109 " =    2.595
peak=   -3.265 closest distance to " O   HOH Z 438 " =    1.034
peak=   -3.265 closest distance to " O   ASN A 301 " =    1.430
peak=   -3.263 closest distance to " N   ASP A 171 " =    2.436
peak=   -3.262 closest distance to " O   HOH Z  11 " =    1.941
peak=   -3.259 closest distance to " O   HOH Z  39 " =    1.261
peak=   -3.258 closest distance to " O   VAL A 153 " =    2.255
peak=   -3.256 closest distance to " O   ILE A  49 " =    1.764
peak=   -3.255 closest distance to " O   HOH Z  22 " =    2.557
peak=   -3.252 closest distance to " O   HOH Z 410 " =    2.184
peak=   -3.247 closest distance to " CE1 TYR A 169 " =    2.485
peak=   -3.246 closest distance to " O   HOH Z  98 " =    2.292
peak=   -3.239 closest distance to " O   HOH Z 417 " =    2.376
peak=   -3.236 closest distance to " O   ALA A  51 " =    1.465
peak=   -3.235 closest distance to " CB  SER A 271 " =    1.125
peak=   -3.235 closest distance to " O   ALA A   1 " =    1.057
peak=   -3.231 closest distance to " O   HOH Z 339 " =    1.858
peak=   -3.228 closest distance to " CB  SER A 245 " =    2.422
peak=   -3.222 closest distance to " O   HOH Z  44 " =    2.117
peak=   -3.222 closest distance to " O   HOH Z 231 " =    1.124
peak=   -3.219 closest distance to " ND2 ASN A  60 " =    1.961
peak=   -3.217 closest distance to " OE1 GLN A  58 " =    2.934
peak=   -3.215 closest distance to " OXT GLY A 302 " =    3.228
peak=   -3.214 closest distance to " CB  PRO A 163 " =    2.465
peak=   -3.212 closest distance to " CZ2 TRP A 179 " =    2.332
peak=   -3.201 closest distance to " O   HOH Z 377 " =    1.226
peak=   -3.199 closest distance to " CG  ARG A 269 " =    2.613
peak=   -3.198 closest distance to " OG BSER A 134 " =    1.613
peak=   -3.196 closest distance to " O   HOH Z   9 " =    1.917
peak=   -3.195 closest distance to " O   HOH Z 193 " =    1.458
peak=   -3.193 closest distance to " N   SER A 276 " =    1.132
peak=   -3.189 closest distance to " CD2 TYR A 293 " =    1.966
peak=   -3.187 closest distance to " O   HOH Z 222 " =    3.129
peak=   -3.185 closest distance to " NH1AARG A 275 " =    1.891
peak=   -3.183 closest distance to " CE  MET A 113 " =    2.243
peak=   -3.183 closest distance to " CB  ALA A 131 " =    1.906
peak=   -3.183 closest distance to " O   PRO A 198 " =    1.316
peak=   -3.177 closest distance to " CB  TRP A  85 " =    2.434
peak=   -3.174 closest distance to " CB  ASP A 132 " =    2.275
peak=   -3.170 closest distance to " O   SER A  22 " =    2.483
peak=   -3.168 closest distance to " CE3 TRP A 123 " =    1.399
peak=   -3.167 closest distance to " OG ASER A 216 " =    0.985
peak=   -3.164 closest distance to " O   HOH Z 337 " =    1.586
peak=   -3.158 closest distance to " O   PRO A 243 " =    2.159
peak=   -3.154 closest distance to " O   HOH Z 222 " =    0.916
peak=   -3.141 closest distance to " O   PRO A 243 " =    2.355
peak=   -3.138 closest distance to " O   VAL A  67 " =    2.628
peak=   -3.134 closest distance to " CG  GLU A 152 " =    1.370
peak=   -3.132 closest distance to " ND2 ASN A 249 " =    2.019
peak=   -3.131 closest distance to " O   TYR A  30 " =    2.823
peak=   -3.131 closest distance to " O   VAL A 197 " =    1.430
peak=   -3.130 closest distance to " OD2 ASP A 171 " =    2.061
peak=   -3.130 closest distance to " O   HOH Z 352 " =    1.931
peak=   -3.127 closest distance to " O   HOH Z 346 " =    1.669
peak=   -3.124 closest distance to " O   HOH Z 409 " =    4.444
peak=   -3.122 closest distance to " O   HOH Z  73 " =    2.302
peak=   -3.116 closest distance to " O   HOH Z 298 " =    2.601
peak=   -3.116 closest distance to " OD1 ASN A 148 " =    1.658
peak=   -3.116 closest distance to " OD1 ASP A 200 " =    1.361
peak=   -3.115 closest distance to " O   HOH Z 168 " =    1.801
peak=   -3.114 closest distance to " O   HOH Z 324 " =    2.156
peak=   -3.114 closest distance to " CA  GLY A 133 " =    1.935
peak=   -3.113 closest distance to " O   HOH Z 207 " =    2.130
peak=   -3.107 closest distance to " CG2 THR A  18 " =    2.851
peak=   -3.106 closest distance to " C   LEU A 101 " =    0.937
peak=   -3.106 closest distance to " O   HOH Z 418 " =    1.509
peak=   -3.104 closest distance to " CZ  TYR A 169 " =    1.721
peak=   -3.095 closest distance to " OD1 ASN A 301 " =    1.839
peak=   -3.093 closest distance to " O   HOH Z 150 " =    1.617
peak=   -3.088 closest distance to " CD2 PHE A 192 " =    2.255
peak=   -3.087 closest distance to " OG  SER A 245 " =    1.111
peak=   -3.075 closest distance to " N   VAL A  72 " =    1.350
peak=   -3.071 closest distance to " O   HOH Z 191 " =    5.455
peak=   -3.069 closest distance to " O   HOH Z 412 " =    5.394
peak=   -3.057 closest distance to " ND2 ASN A  39 " =    1.975
peak=   -3.057 closest distance to " CE3 TRP A 150 " =    1.867
peak=   -3.045 closest distance to " CG1 VAL A 197 " =    2.139
peak=   -3.037 closest distance to " NH2 ARG A 219 " =    1.740
peak=   -3.021 closest distance to " CB  CYS A 201 " =    2.358
peak=   -3.009 closest distance to " CD1 ILE A 263 " =    2.550

================= 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    :  0.4486 0.4460   6.249336e+00   6.247157e+00
   1_bss:  0.4404 0.4391   6.244768e+00   6.236929e+00
   1_xyz:  0.3138 0.3483   6.009391e+00   6.076574e+00
   1_adp:  0.2864 0.3638   5.962790e+00   6.102471e+00
   1_occ:  0.2861 0.3635   5.961732e+00   6.101658e+00
   2_bss:  0.2852 0.3623   5.961214e+00   6.099667e+00
   2_xyz:  0.2074 0.2671   5.683108e+00   5.874847e+00
   2_adp:  0.1852 0.2430   5.589636e+00   5.794028e+00
   2_occ:  0.1850 0.2428   5.588505e+00   5.792507e+00
   3_bss:  0.1853 0.2423   5.586778e+00   5.790289e+00
   3_xyz:  0.1440 0.1957   5.360405e+00   5.594574e+00
   3_adp:  0.1351 0.1843   5.301440e+00   5.534792e+00
   3_occ:  0.1351 0.1840   5.300596e+00   5.533678e+00
   4_bss:  0.1352 0.1840   5.301091e+00   5.533770e+00
   4_xyz:  0.1244 0.1705   5.226804e+00   5.459881e+00
   4_adp:  0.1222 0.1663   5.207040e+00   5.438975e+00
   4_occ:  0.1221 0.1660   5.206068e+00   5.438082e+00
   5_bss:  0.1221 0.1660   5.206170e+00   5.438190e+00
   5_xyz:  0.1138 0.1599   5.152717e+00   5.400272e+00
   5_adp:  0.1125 0.1596   5.147751e+00   5.399232e+00
   5_occ:  0.1124 0.1595   5.147401e+00   5.399093e+00
   5_bss:  0.1128 0.1588   5.147021e+00   5.397190e+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:  0.300  20.000   0.754   0.726   0.138   0.000   0.000   0.000
   1_xyz:  0.300  20.000   0.754   0.726   0.138   0.000   0.000   0.000
   1_adp:  0.300  20.000   0.754   0.726   0.138   0.000   0.000   0.000
   1_occ:  0.300  20.000   0.754   0.726   0.138   0.000   0.000   0.000
   2_bss:  0.341  57.200  -0.556  -0.979  -0.625  -0.000  -0.000  -0.000
   2_xyz:  0.341  57.200  -0.556  -0.979  -0.625  -0.000  -0.000  -0.000
   2_adp:  0.341  57.200  -0.556  -0.979  -0.625  -0.000  -0.000  -0.000
   2_occ:  0.341  57.200  -0.556  -0.979  -0.625  -0.000  -0.000  -0.000
   3_bss:  0.336  57.200  -1.055  -1.821  -0.854  -0.000  -0.000  -0.000
   3_xyz:  0.336  57.200  -1.055  -1.821  -0.854  -0.000  -0.000  -0.000
   3_adp:  0.336  57.200  -1.055  -1.821  -0.854  -0.000  -0.000  -0.000
   3_occ:  0.336  57.200  -1.055  -1.821  -0.854  -0.000  -0.000  -0.000
   4_bss:  0.328  53.023  -1.712  -2.444  -1.418  -0.000  -0.000  -0.000
   4_xyz:  0.328  53.023  -1.712  -2.444  -1.418  -0.000  -0.000  -0.000
   4_adp:  0.328  53.023  -1.712  -2.444  -1.418  -0.000  -0.000  -0.000
   4_occ:  0.328  53.023  -1.712  -2.444  -1.418  -0.000  -0.000  -0.000
   5_bss:  0.319  47.934  -1.712  -2.444  -1.418  -0.000  -0.000  -0.000
   5_xyz:  0.319  47.934  -1.712  -2.444  -1.418  -0.000  -0.000  -0.000
   5_adp:  0.319  47.934  -1.712  -2.444  -1.418  -0.000  -0.000  -0.000
   5_occ:  0.319  47.934  -1.712  -2.444  -1.418  -0.000  -0.000  -0.000
   5_bss:  0.320  50.513  -1.715  -2.447  -1.421  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.365 0.4784  0.6439    62176.924
   1_bss:  52.389 0.4891  0.6732    59239.953
   1_xyz:  36.498 0.6849  0.9017    33419.707
   1_adp:  38.584 0.6588  0.8736    35819.662
   1_occ:  38.608 0.6584  0.8720    35756.285
   2_bss:  38.415 0.6606  0.8392    35455.025
   2_xyz:  27.313 0.7862  0.9632    18712.846
   2_adp:  23.961 0.8228  0.9787    15495.608
   2_occ:  23.920 0.8232  0.9786    15432.040
   3_bss:  23.834 0.8238  0.9606    15278.950
   3_xyz:  18.558 0.8749  0.9949     9679.136
   3_adp:  16.964 0.8901  0.9985     8586.020
   3_occ:  16.938 0.8903  0.9984     8558.020
   4_bss:  16.935 0.8903  0.9762     8553.656
   4_xyz:  15.304 0.9042  0.9814     7211.034
   4_adp:  14.761 0.9091  0.9804     6929.499
   4_occ:  14.733 0.9094  0.9803     6905.046
   5_bss:  14.737 0.9093  0.9801     6902.473
   5_xyz:  14.055 0.9145  0.9840     6411.925
   5_adp:  14.018 0.9150  0.9803     6393.651
   5_occ:  14.009 0.9150  0.9803     6386.470
   5_bss:  13.995 0.9150  0.9805     6347.820
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   1.6931e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   1.6931e-01
   1_xyz:   1.447  0.011  0.098 15.473  0.006  4.108   1.1460e-01
   1_adp:   1.447  0.011  0.098 15.473  0.006  4.108   1.1460e-01
   1_occ:   1.447  0.011  0.098 15.473  0.006  4.108   1.1460e-01
   2_bss:   1.447  0.011  0.098 15.473  0.006  4.108   1.1460e-01
   2_xyz:   1.235  0.009  0.086 14.431  0.005  4.124   8.0206e-02
   2_adp:   1.235  0.009  0.086 14.431  0.005  4.124   8.0206e-02
   2_occ:   1.235  0.009  0.086 14.431  0.005  4.124   8.0206e-02
   3_bss:   1.235  0.009  0.086 14.431  0.005  4.124   8.0206e-02
   3_xyz:   0.956  0.006  0.069 14.090  0.003  4.115   5.3445e-02
   3_adp:   0.956  0.006  0.069 14.090  0.003  4.115   5.3445e-02
   3_occ:   0.956  0.006  0.069 14.090  0.003  4.115   5.3445e-02
   4_bss:   0.956  0.006  0.069 14.090  0.003  4.115   5.3445e-02
   4_xyz:   0.871  0.005  0.064 13.962  0.003  4.120   4.6336e-02
   4_adp:   0.871  0.005  0.064 13.962  0.003  4.120   4.6336e-02
   4_occ:   0.871  0.005  0.064 13.962  0.003  4.120   4.6336e-02
   5_bss:   0.871  0.005  0.064 13.962  0.003  4.120   4.6336e-02
   5_xyz:   1.006  0.007  0.073 14.450  0.004  4.110   5.9144e-02
   5_adp:   1.006  0.007  0.073 14.450  0.004  4.110   5.9144e-02
   5_occ:   1.006  0.007  0.073 14.450  0.004  4.110   5.9144e-02
   5_bss:   1.006  0.007  0.073 14.450  0.004  4.110   5.9144e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.734   2.3984e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.734   2.3984e-01
   1_xyz:   9.504  0.065  0.479 86.182  0.035  2.057   1.3149e-01
   1_adp:   9.504  0.065  0.479 86.182  0.035  2.057   1.3149e-01
   1_occ:   9.504  0.065  0.479 86.182  0.035  2.057   1.3149e-01
   2_bss:   9.504  0.065  0.479 86.182  0.035  2.057   1.3149e-01
   2_xyz:   8.605  0.058  0.267 83.692  0.047  2.288   1.1762e-01
   2_adp:   8.605  0.058  0.267 83.692  0.047  2.288   1.1762e-01
   2_occ:   8.605  0.058  0.267 83.692  0.047  2.288   1.1762e-01
   3_bss:   8.605  0.058  0.267 83.692  0.047  2.288   1.1762e-01
   3_xyz:   8.717  0.056  0.277 80.996  0.021  2.314   3.9974e-02
   3_adp:   8.717  0.056  0.277 80.996  0.021  2.314   3.9974e-02
   3_occ:   8.717  0.056  0.277 80.996  0.021  2.314   3.9974e-02
   4_bss:   8.717  0.056  0.277 80.996  0.021  2.314   3.9974e-02
   4_xyz:   8.019  0.044  0.207 84.563  0.031  2.387   2.9001e-02
   4_adp:   8.019  0.044  0.207 84.563  0.031  2.387   2.9001e-02
   4_occ:   8.019  0.044  0.207 84.563  0.031  2.387   2.9001e-02
   5_bss:   8.019  0.044  0.207 84.563  0.031  2.387   2.9001e-02
   5_xyz:   8.346  0.047  0.218 85.375  0.033  2.250   5.8215e-02
   5_adp:   8.346  0.047  0.218 85.375  0.033  2.250   5.8215e-02
   5_occ:   8.346  0.047  0.218 85.375  0.033  2.250   5.8215e-02
   5_bss:   8.346  0.047  0.218 85.375  0.033  2.250   5.8215e-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:  87.98   0.00  18.45  80.83   0.00  14.56  87.98   0.00  39.60
   1_occ:  87.98   0.00  18.45  80.83   0.00  14.56  87.98   0.00  39.60
   2_bss:  87.98   0.00  18.45  80.83   0.00  14.56  87.98   0.00  39.60
   2_xyz:  87.98   0.00  18.45  80.83   0.00  14.56  87.98   0.00  39.60
   2_adp:  87.32   0.00  17.61  81.72   0.00  13.34  87.32   4.07  40.89
   2_occ:  87.32   0.00  17.61  81.72   0.00  13.34  87.32   4.07  40.89
   3_bss:  87.32   0.00  17.61  81.72   0.00  13.34  87.32   4.07  40.89
   3_xyz:  87.32   0.00  17.61  81.72   0.00  13.34  87.32   4.07  40.89
   3_adp:  88.06   1.06  17.39  88.06   1.06  12.90  84.48   6.33  41.84
   3_occ:  88.06   1.06  17.39  88.06   1.06  12.90  84.48   6.33  41.84
   4_bss:  88.06   1.06  17.39  88.06   1.06  12.90  84.48   6.33  41.84
   4_xyz:  88.06   1.06  17.39  88.06   1.06  12.90  84.48   6.33  41.84
   4_adp:  90.83   0.00  17.14  90.83   0.00  12.77  86.72   5.89  40.94
   4_occ:  90.83   0.00  17.14  90.83   0.00  12.77  86.72   5.89  40.94
   5_bss:  90.83   0.00  17.14  90.83   0.00  12.77  86.72   5.89  40.94
   5_xyz:  90.83   0.00  17.14  90.83   0.00  12.77  86.72   5.89  40.94
   5_adp:  97.87   0.00  17.21  97.87   0.00  12.77  91.14   5.95  41.35
   5_occ:  97.87   0.00  17.21  97.87   0.00  12.77  91.14   5.95  41.35
   5_bss:  97.87   0.00  17.21  97.87   0.00  12.78  91.14   5.95  41.35
------------------------------------------------------------------------
 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:    1.948    0.022    0.337
   1_adp:    1.948    0.022    0.337
   1_occ:    1.948    0.022    0.337
   2_bss:    1.948    0.022    0.337
   2_xyz:    1.180    0.040    0.524
   2_adp:    1.180    0.040    0.524
   2_occ:    1.180    0.040    0.524
   3_bss:    1.180    0.040    0.524
   3_xyz:    1.188    0.049    0.613
   3_adp:    1.188    0.049    0.613
   3_occ:    1.188    0.049    0.613
   4_bss:    1.188    0.049    0.613
   4_xyz:    1.236    0.116    0.650
   4_adp:    1.236    0.116    0.650
   4_occ:    1.236    0.116    0.650
   5_bss:    1.236    0.116    0.650
   5_xyz:    1.324    0.085    0.670
   5_adp:    1.324    0.085    0.670
   5_occ:    1.324    0.085    0.670
   5_bss:    1.324    0.085    0.670
------------------------------------------------------------------------

CPU time actual refinement: 356.38


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1113/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_1113/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1113/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1113/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1113/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 356.23 
  Macro-tasks:
    bulk solvent and scale       = 42.69  
    individual site refinement   = 141.88 
    weights calculation          = 30.17  
    collect and process          = 6.58   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 221.42 
  Micro-tasks:
    mask                            = 2.46   
    f_calc                          = 116.51 
    alpha_beta                      = 8.66   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 123.89 
    fmodel                         = 7.43   
    r_factors                      = 0.26   
    phase_errors                   = 10.81  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 271.47 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.044 micro seconds
Total CPU time: 6.16 minutes
from_scatterers_fft:    661 calls, 116.07 s
gradients_fft:          606 calls, 110.72 s

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

# Date 2008-01-16 Time 06:28:01 PST -0800 (1200493681.48 s)
Start R-work = 0.4486, R-free = 0.4460 (no bulk solvent and anisotropic scale)
Final R-work = 0.1358, R-free = 0.1792 (no bulk solvent and anisotropic scale)

Start R-work = 0.4404, R-free = 0.4391
Final R-work = 0.1128, R-free = 0.1588