# Date 2008-01-16 Time 04:45:28 PST -0800 (1200487528.83 s)
#phil __OFF__

Command line arguments: "../452.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 12386
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 452

-------------------------------------------------------------------------------
  PHENIX: Python-based Hierarchical ENvironment for Integrated Xtallography
  User: phzwart
-------------------------------------------------------------------------------

              phenix.refine: Macromolecular Structure Refinement

-------------------------------------------------------------------------------
Phenix developers include:
  Paul Adams, Pavel Afonine, Vicent Chen, Ian Davis, Kreshna Gopal,
  Ralf Grosse-Kunstleve, Li-Wei Hung, Robert Immormino, Tom Ioerger,
  Airlie McCoy, Erik McKee, Nigel Moriarty, Reetal Pai, Randy Read,
  Jane Richardson, David Richardson, Tod Romo, Jim Sacchettini,
  Nicholas Sauter, Jacob Smith, Laurent Storoni, Tom Terwilliger,
  Peter Zwart
Phenix home page:
  http://www.phenix-online.org/
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Phenix components are copyrighted by:
  - Lawrence Berkeley National Laboratory
  - Los Alamos National Laboratory
  - University of Cambridge
  - Duke University
  - Texas Agricultural Experiment Station &
    Texas Engineering Experiment Station
-------------------------------------------------------------------------------

-------------------------------------------------------------------------------
Major third-party components of Phenix include:
    Python, wxwidgets, wxPython, Boost, SCons, Clipper,
    CCP4 Monomer Library, CCP4 I/O libraries, PyCifRW, FFTPACK, L-BFGS
  Enter phenix.acknowledgments for details.
-------------------------------------------------------------------------------

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.5475, 47.6339, 84.6622, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 47.6339, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8666 1.96141
Completeness in resolution range: 0.945643
Completeness with d_max=infinity: 0.942776

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8666
                             d_min =   1.9614

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 47.6339, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8666 1.96141
Completeness in resolution range: 0.945643
Completeness with d_max=infinity: 0.942776

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8670 -  4.1970 [2178/2207]  1960   218  10.0%
  bin  2:  4.1970 -  3.3438 [2086/2109]  1876   210  10.1%
  bin  3:  3.3438 -  2.9247 [2065/2090]  1856   209  10.1%
  bin  4:  2.9247 -  2.6590 [2039/2055]  1841   198   9.7%
  bin  5:  2.6590 -  2.4693 [2030/2074]  1821   209  10.3%
  bin  6:  2.4693 -  2.3243 [2023/2051]  1833   190   9.4%
  bin  7:  2.3243 -  2.2083 [1999/2035]  1792   207  10.4%
  bin  8:  2.2083 -  2.1125 [1988/2030]  1794   194   9.8%
  bin  9:  2.1125 -  2.0313 [2002/2048]  1805   197   9.8%
  bin 10:  2.0313 -  1.9614 [1179/2016]  1052   127  10.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_452/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:
        1.62 -     2.27: 29
        2.27 -     2.93: 1582
        2.93 -     3.59: 4504
        3.59 -     4.24: 9280
        4.24 -     4.90: 13172
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.616 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 294 "  1.646 3.040 -x+1/2,-y+1,z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.725 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.753 3.040 -x+1/2,-y+1,z+1/2
  " OG  SER A  95 " - " O   SER A 271 "  1.770 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28562 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_452/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_452/model_refine_001.geo

CPU time processing inputs: 9.20


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.5475 47.63395 84.6622 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4305   r_free= 0.4264   ksol= 0.00   Bsol= 0.00   scale= 0.924    |
|                                                                             |
| 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:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.233781                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8670 -  4.6812 0.99   1409  157 0.3405 0.3567        6.49      6.5017|
|  2:  4.6812 -  3.7350 0.99   1366  150 0.3588 0.3471      6.7116      6.6874|
|  3:  3.7350 -  3.2686 0.99   1328  152 0.3849 0.3720      6.5798      6.6479|
|  4:  3.2686 -  2.9723 0.99   1324  143 0.4052 0.3933      6.4351      6.4039|
|  5:  2.9723 -  2.7607 0.98   1325  148 0.4386 0.3981      6.3108      6.2468|
|  6:  2.7607 -  2.5989 0.99   1307  146 0.4567 0.4455      6.2263      6.1258|
|  7:  2.5989 -  2.4693 0.98   1295  148 0.4669 0.4138      6.2086      6.1379|
|  8:  2.4693 -  2.3623 0.99   1295  141 0.4803 0.5174      6.1482      6.1785|
|  9:  2.3623 -  2.2717 0.99   1300  142 0.4964 0.4906      6.1018      6.1403|
| 10:  2.2717 -  2.1935 0.98   1293  143 0.4832 0.5334      6.0896      6.1301|
| 11:  2.1935 -  2.1252 0.97   1275  139 0.5120 0.5047       6.021      6.0053|
| 12:  2.1252 -  2.0646 0.99   1277  150 0.4804 0.5200      5.9465      5.9878|
| 13:  2.0646 -  2.0104 0.94   1257  134 0.5114 0.5133      5.8651      5.8638|
| 14:  2.0104 -  1.9614 0.45    579   66 0.5256 0.4516      5.8382      5.7116|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8670 -  4.6812  1409   157  0.72  32.89   0.85     0.74      65024.21|
|  2:  4.6812 -  3.7350  1366   150  0.75  30.82   0.94     0.84      82143.05|
|  3:  3.7350 -  3.2686  1328   152  0.68  36.88   0.95     0.87      83846.91|
|  4:  3.2686 -  2.9723  1324   143  0.63  41.65   0.95     0.84      72736.30|
|  5:  2.9723 -  2.7607  1325   148  0.58  45.67   0.92     0.80      59089.65|
|  6:  2.7607 -  2.5989  1307   146  0.55  48.06   0.94     0.76      51538.77|
|  7:  2.5989 -  2.4693  1295   148  0.53  49.62   0.94     0.72      49414.45|
|  8:  2.4693 -  2.3623  1295   141  0.46  55.55   0.92     0.64      50581.79|
|  9:  2.3623 -  2.2717  1300   142  0.40  60.12   0.94     0.58      49836.50|
| 10:  2.2717 -  2.1935  1293   143  0.35  63.63   0.98     0.51      49573.68|
| 11:  2.1935 -  2.1252  1275   139  0.31  66.84   0.94     0.48      47313.50|
| 12:  2.1252 -  2.0646  1277   150  0.31  66.82   0.98     0.49      44542.18|
| 13:  2.0646 -  2.0104  1257   134  0.33  65.37   0.96     0.53      36209.11|
| 14:  2.0104 -  1.9614   579    66  0.42  58.63   0.94     0.60      26743.91|
|alpha:            min =        0.48 max =            0.87 mean =         0.68|
|beta:             min =    26743.91 max =        83846.91 mean =     56365.23|
|figures of merit: min =        0.00 max =            1.00 mean =         0.51|
|phase err.(work): min =        0.00 max =           90.00 mean =        51.00|
|phase err.(test): min =        0.00 max =           89.95 mean =        51.03|
|-----------------------------------------------------------------------------|

============================== 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 = 8.662615              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.664   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.938946              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.886   (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 |  1.616 -  1.945:        9 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.945 -  2.273:       20 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.273 -  2.601:       48 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.601 -  2.930:     1534 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.930 -  3.258:     1921 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.258 -  3.587:     2583 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.587 -  3.915:     4770 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.915 -  4.243:     4510 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.243 -  4.572:     6005 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.572 -  4.900:     7167 |
|-----------------------------------------------------------------------------|
|-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 |        0.182 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.616 |       0.490 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.690)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4305   r_free= 0.4264   ksol= 0.00   Bsol= 0.00   scale= 0.924    |
|                                                                             |
| 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:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.233781                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4206   r_free= 0.4157   ksol= 0.31   Bsol= 24.63   scale= 0.955   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.77,2.23,1.60,0.00,0.00,0.00); trace/3= 0.35                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.223551                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.443554              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.339   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.925397              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.750   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4206      final r-factor (work) = 0.2788          |
| start r-factor (free) = 0.4157      final r-factor (free) = 0.3035          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.3463 = 7.44 * 0.50 * 6.2239 + 1.00 * 0.1824                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.5938 = 7.44 * 0.50 * 6.0424 + 1.00 * 0.1053                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2788      final r-factor (work) = 0.2542          |
| start r-factor (free) = 0.3035      final r-factor (free) = 0.3149          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5978 = 0.93 * 1.00 * 6.0424 + 1.00 * 0.0062                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4196 = 0.93 * 1.00 * 5.8356 + 1.00 * 0.0193                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.690)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    68.31   17.79    None  None   None       |
|    all(noH): 2823   0      0.00    68.31   17.79    None  None   None       |
|    Sol.    : 438    0      2.83    68.31   38.88    None  None   None       |
|    Mac.    : 2385   0      0.00    57.71   13.92    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.831:  504   |   5:    34.153 -  40.983:  139        |
|      1:     6.831 -  13.661:  921   |   6:    40.983 -  47.814:  105        |
|      2:    13.661 -  20.492:  563   |   7:    47.814 -  54.644:   86        |
|      3:    20.492 -  27.322:  273   |   8:    54.644 -  61.475:   46        |
|      4:    27.322 -  34.153:  173   |   9:    61.475 -  68.305:   13        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2542 r_free = 0.3149             target_work(ml) = 5.847         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2537 r_free = 0.3154             target_work(ml) = 5.846         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2537   r_free= 0.3154   ksol= 0.31   Bsol= 24.63   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.77,2.23,1.60,0.00,0.00,0.00); trace/3= 0.35                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.845944                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2506   r_free= 0.3129   ksol= 0.33   Bsol= 50.00   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.88,0.07,-0.57,0.00,-0.00,-0.00); trace/3= -1.13                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.841374                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.162608              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.061   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.355339              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.551   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2506      final r-factor (work) = 0.1805          |
| start r-factor (free) = 0.3129      final r-factor (free) = 0.2274          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.2529 = 4.16 * 0.50 * 5.8365 + 1.00 * 0.1053                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.9595 = 4.16 * 0.50 * 5.7144 + 1.00 * 0.0661                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1805      final r-factor (work) = 0.1621          |
| start r-factor (free) = 0.2274      final r-factor (free) = 0.2085          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0510 = 0.36 * 1.00 * 5.7144 + 1.00 * 0.0205                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9622 = 0.36 * 1.00 * 5.4964 + 1.00 * 0.0091                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.690)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.49    79.49   17.44    None  None   None       |
|    all(noH): 2823   0      0.49    79.49   17.44    None  None   None       |
|    Sol.    : 438    0      5.81    74.08   40.08    None  None   None       |
|    Mac.    : 2385   0      0.49    79.49   13.29    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.491 -   8.391:  683   |   5:    39.993 -  47.893:  122        |
|      1:     8.391 -  16.292: 1205   |   6:    47.893 -  55.793:   86        |
|      2:    16.292 -  24.192:  369   |   7:    55.793 -  63.693:   55        |
|      3:    24.192 -  32.092:  163   |   8:    63.693 -  71.594:   20        |
|      4:    32.092 -  39.993:  111   |   9:    71.594 -  79.494:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1621 r_free = 0.2085             target_work(ml) = 5.455         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1619 r_free = 0.2085             target_work(ml) = 5.454         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1619   r_free= 0.2085   ksol= 0.33   Bsol= 50.00   scale= 1.024   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.88,0.07,-0.57,0.00,-0.00,-0.00); trace/3= -1.13                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.454363                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1621   r_free= 0.2073   ksol= 0.32   Bsol= 47.67   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.80,-0.94,-1.38,-0.00,-0.00,-0.00); trace/3= -1.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.451876                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.320288              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.719  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.440830              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.132  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1621      final r-factor (work) = 0.1283          |
| start r-factor (free) = 0.2073      final r-factor (free) = 0.1721          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1937 = 3.32 * 0.50 * 5.4981 + 1.00 * 0.0661                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9419 = 3.32 * 0.50 * 5.3490 + 1.00 * 0.0618                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1283      final r-factor (work) = 0.1214          |
| start r-factor (free) = 0.1721      final r-factor (free) = 0.1654          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3670 = 0.44 * 1.00 * 5.3490 + 1.00 * 0.0090                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3128 = 0.44 * 1.00 * 5.2257 + 1.00 * 0.0091                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.690)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.52   17.37    None  None   None       |
|    all(noH): 2823   0      0.00    89.52   17.37    None  None   None       |
|    Sol.    : 438    0      0.00    81.10   41.06    None  None   None       |
|    Mac.    : 2385   0      1.22    89.52   13.02    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 -   8.952:  781   |   5:    44.759 -  53.711:  116        |
|      1:     8.952 -  17.904: 1291   |   6:    53.711 -  62.663:   80        |
|      2:    17.904 -  26.856:  278   |   7:    62.663 -  71.615:   28        |
|      3:    26.856 -  35.807:  118   |   8:    71.615 -  80.567:   13        |
|      4:    35.807 -  44.759:  113   |   9:    80.567 -  89.518:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1214 r_free = 0.1654             target_work(ml) = 5.205         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1213 r_free = 0.1653             target_work(ml) = 5.204         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1213   r_free= 0.1653   ksol= 0.32   Bsol= 47.67   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.80,-0.94,-1.38,-0.00,-0.00,-0.00); trace/3= -1.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.204313                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1217   r_free= 0.1656   ksol= 0.32   Bsol= 48.17   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.80,-1.45,-1.65,-0.00,-0.00,-0.00); trace/3= -1.97                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.207367                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.640973              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 132.697  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.300132              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.947  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1217      final r-factor (work) = 0.1162          |
| start r-factor (free) = 0.1656      final r-factor (free) = 0.1606          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3513 = 1.64 * 0.50 * 5.2280 + 1.00 * 0.0618                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3099 = 1.64 * 0.50 * 5.1902 + 1.00 * 0.0514                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1162      final r-factor (work) = 0.1150          |
| start r-factor (free) = 0.1606      final r-factor (free) = 0.1596          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5668 = 0.30 * 1.00 * 5.1902 + 1.00 * 0.0091                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5595 = 0.30 * 1.00 * 5.1676 + 1.00 * 0.0085                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.690)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.54    91.97   17.04    None  None   None       |
|    all(noH): 2823   0      1.54    91.97   17.04    None  None   None       |
|    Sol.    : 438    0      1.66    83.23   39.98    None  None   None       |
|    Mac.    : 2385   0      1.54    91.97   12.83    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.544 -  10.586: 1166   |   5:    46.755 -  55.798:   91        |
|      1:    10.586 -  19.628: 1017   |   6:    55.798 -  64.840:   65        |
|      2:    19.628 -  28.671:  209   |   7:    64.840 -  73.883:   19        |
|      3:    28.671 -  37.713:  125   |   8:    73.883 -  82.925:    8        |
|      4:    37.713 -  46.755:  118   |   9:    82.925 -  91.967:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1150 r_free = 0.1596             target_work(ml) = 5.164         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1150 r_free = 0.1596             target_work(ml) = 5.164         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1150   r_free= 0.1596   ksol= 0.32   Bsol= 48.17   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.80,-1.45,-1.65,-0.00,-0.00,-0.00); trace/3= -1.97                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.164037                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1150   r_free= 0.1596   ksol= 0.33   Bsol= 48.17   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.68,-1.50,-1.63,-0.00,-0.00,-0.00); trace/3= -1.94                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.164075                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.610206              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 139.109  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.279287              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.023  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1150      final r-factor (work) = 0.1089          |
| start r-factor (free) = 0.1596      final r-factor (free) = 0.1567          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7954 = 2.61 * 0.50 * 5.1674 + 1.00 * 0.0514                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7738 = 2.61 * 0.50 * 5.1401 + 1.00 * 0.0654                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1089      final r-factor (work) = 0.1089          |
| start r-factor (free) = 0.1567      final r-factor (free) = 0.1561          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4441 = 0.28 * 1.00 * 5.1401 + 1.00 * 0.0085                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4401 = 0.28 * 1.00 * 5.1274 + 1.00 * 0.0081                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.690)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.35    92.69   16.71    None  None   None       |
|    all(noH): 2823   0      1.35    92.69   16.71    None  None   None       |
|    Sol.    : 438    0      3.76    83.66   38.92    None  None   None       |
|    Mac.    : 2385   0      1.35    92.69   12.64    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.350 -  10.485: 1173   |   5:    47.022 -  56.156:   96        |
|      1:    10.485 -  19.619: 1027   |   6:    56.156 -  65.291:   52        |
|      2:    19.619 -  28.753:  203   |   7:    65.291 -  74.425:   15        |
|      3:    28.753 -  37.888:  124   |   8:    74.425 -  83.559:    5        |
|      4:    37.888 -  47.022:  123   |   9:    83.559 -  92.694:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1089 r_free = 0.1561             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1088 r_free = 0.1561             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.04   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1088   r_free= 0.1561   ksol= 0.33   Bsol= 48.17   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.68,-1.50,-1.63,-0.00,-0.00,-0.00); trace/3= -1.94                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.126983                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8670 -  4.6812 0.99   1409  157 0.0966 0.1271      5.3581      5.5144|
|  2:  4.6812 -  3.7350 0.99   1366  150 0.0820 0.1072      5.4012      5.6085|
|  3:  3.7350 -  3.2686 0.99   1328  152 0.1028 0.1530      5.4402      5.8317|
|  4:  3.2686 -  2.9723 0.99   1324  143 0.1214 0.1554      5.4393      5.6085|
|  5:  2.9723 -  2.7607 0.98   1325  148 0.1265 0.1713      5.2969      5.4845|
|  6:  2.7607 -  2.5989 0.99   1307  146 0.1209 0.1904      5.2016      5.4206|
|  7:  2.5989 -  2.4693 0.98   1295  148 0.1199 0.1640      5.1223      5.3816|
|  8:  2.4693 -  2.3623 0.99   1295  141 0.1140 0.1663      5.0567      5.2516|
|  9:  2.3623 -  2.2717 0.99   1300  142 0.1153 0.1773      5.0103      5.3043|
| 10:  2.2717 -  2.1935 0.98   1293  143 0.1113 0.1838      4.9726      5.2446|
| 11:  2.1935 -  2.1252 0.97   1275  139 0.1081 0.1745      4.8904      5.2095|
| 12:  2.1252 -  2.0646 0.99   1277  150 0.1066 0.1586      4.8303      5.0674|
| 13:  2.0646 -  2.0104 0.94   1257  134 0.1101 0.1803      4.7567      5.0654|
| 14:  2.0104 -  1.9614 0.45    579   66 0.1100 0.1606      4.6814       4.865|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8670 -  4.6812  1409   157  0.94   8.73   0.98     0.96       6753.44|
|  2:  4.6812 -  3.7350  1366   150  0.95   7.71   1.02     1.00       8487.04|
|  3:  3.7350 -  3.2686  1328   152  0.94  11.02   1.03     1.02       9830.74|
|  4:  3.2686 -  2.9723  1324   143  0.92  13.85   1.01     0.99      10118.91|
|  5:  2.9723 -  2.7607  1325   148  0.90  15.51   1.00     0.97       7868.76|
|  6:  2.7607 -  2.5989  1307   146  0.90  15.65   0.99     0.95       6886.29|
|  7:  2.5989 -  2.4693  1295   148  0.91  14.76   0.99     0.96       5638.81|
|  8:  2.4693 -  2.3623  1295   141  0.91  15.30   1.00     0.98       5395.07|
|  9:  2.3623 -  2.2717  1300   142  0.91  15.30   1.00     0.96       4800.82|
| 10:  2.2717 -  2.1935  1293   143  0.90  15.64   0.99     0.96       4593.65|
| 11:  2.1935 -  2.1252  1275   139  0.90  16.01   1.00     0.97       4086.85|
| 12:  2.1252 -  2.0646  1277   150  0.92  14.08   1.00     0.99       3536.91|
| 13:  2.0646 -  2.0104  1257   134  0.91  15.59   1.00     1.00       3122.11|
| 14:  2.0104 -  1.9614   579    66  0.90  15.32   0.98     0.94       2615.19|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2615.19 max =        10118.91 mean =      6161.29|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.77|
|phase err.(test): min =        0.00 max =           89.61 mean =        13.40|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1088   r_free= 0.1562   ksol= 0.33   Bsol= 48.13   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.50,-1.40,-1.45,-0.00,-0.00,-0.00); trace/3= -1.78                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.127126                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.87 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1088   r_free= 0.1562   ksol= 0.33   Bsol= 48.13   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.50,-1.40,-1.45,-0.00,-0.00,-0.00); trace/3= -1.78                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.127126                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8670 -  4.6812 0.99   1409  157 0.0967 0.1274      5.3595      5.5159|
|  2:  4.6812 -  3.7350 0.99   1366  150 0.0820 0.1072      5.4015      5.6084|
|  3:  3.7350 -  3.2686 0.99   1328  152 0.1028 0.1530      5.4403       5.832|
|  4:  3.2686 -  2.9723 0.99   1324  143 0.1214 0.1554      5.4394      5.6085|
|  5:  2.9723 -  2.7607 0.98   1325  148 0.1265 0.1712      5.2967      5.4841|
|  6:  2.7607 -  2.5989 0.99   1307  146 0.1208 0.1903      5.2013      5.4202|
|  7:  2.5989 -  2.4693 0.98   1295  148 0.1199 0.1640      5.1223      5.3818|
|  8:  2.4693 -  2.3623 0.99   1295  141 0.1140 0.1663      5.0568      5.2515|
|  9:  2.3623 -  2.2717 0.99   1300  142 0.1153 0.1774      5.0104      5.3049|
| 10:  2.2717 -  2.1935 0.98   1293  143 0.1113 0.1839      4.9728      5.2449|
| 11:  2.1935 -  2.1252 0.97   1275  139 0.1080 0.1744      4.8905      5.2092|
| 12:  2.1252 -  2.0646 0.99   1277  150 0.1066 0.1588      4.8303       5.068|
| 13:  2.0646 -  2.0104 0.94   1257  134 0.1101 0.1802      4.7567      5.0647|
| 14:  2.0104 -  1.9614 0.45    579   66 0.1100 0.1605      4.6813      4.8646|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8670 -  4.6812  1409   157  0.94   8.74   0.98     0.96       6774.15|
|  2:  4.6812 -  3.7350  1366   150  0.95   7.72   1.02     1.00       8497.61|
|  3:  3.7350 -  3.2686  1328   152  0.94  11.02   1.03     1.02       9832.53|
|  4:  3.2686 -  2.9723  1324   143  0.92  13.85   1.01     0.99      10119.62|
|  5:  2.9723 -  2.7607  1325   148  0.90  15.50   1.00     0.97       7861.49|
|  6:  2.7607 -  2.5989  1307   146  0.90  15.64   0.99     0.96       6879.92|
|  7:  2.5989 -  2.4693  1295   148  0.91  14.76   0.99     0.97       5637.14|
|  8:  2.4693 -  2.3623  1295   141  0.91  15.31   1.00     0.98       5396.69|
|  9:  2.3623 -  2.2717  1300   142  0.91  15.31   1.00     0.97       4805.46|
| 10:  2.2717 -  2.1935  1293   143  0.90  15.64   1.00     0.97       4595.02|
| 11:  2.1935 -  2.1252  1275   139  0.90  16.02   1.00     0.97       4088.38|
| 12:  2.1252 -  2.0646  1277   150  0.92  14.08   1.00     0.99       3537.11|
| 13:  2.0646 -  2.0104  1257   134  0.91  15.59   1.01     1.01       3120.87|
| 14:  2.0104 -  1.9614   579    66  0.90  15.32   0.99     0.95       2612.22|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2612.22 max =        10119.62 mean =      6163.32|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.77|
|phase err.(test): min =        0.00 max =           89.59 mean =        13.40|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.690)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.30    92.65   16.67    None  None   None       |
|    all(noH): 2823   0      1.30    92.65   16.67    None  None   None       |
|    Sol.    : 438    0      3.71    83.61   38.87    None  None   None       |
|    Mac.    : 2385   0      1.30    92.65   12.59    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:     1.303 -  10.437: 1173   |   5:    46.974 -  56.109:   96        |
|      1:    10.437 -  19.571: 1027   |   6:    56.109 -  65.243:   52        |
|      2:    19.571 -  28.706:  203   |   7:    65.243 -  74.377:   15        |
|      3:    28.706 -  37.840:  124   |   8:    74.377 -  83.512:    5        |
|      4:    37.840 -  46.974:  123   |   9:    83.512 -  92.646:    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)= 281         
Filter by distance & map next to the model:
   mapped sites are within: 0.618 - 4.436
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 280 from: 281
   mapped sites are within: 0.710 - 4.436

peak=    5.776 closest distance to " NH2 ARG A  56 " =    2.264
peak=    5.448 closest distance to " CB  SER A  63 " =    1.126
peak=    5.235 closest distance to " CG  PRO A  54 " =    1.207
peak=    5.195 closest distance to " CB  GLN A 223 " =    1.390
peak=    5.043 closest distance to " CB  ARG A 275 " =    0.911
peak=    4.955 closest distance to " O   HOH Z 124 " =    1.441
peak=    4.848 closest distance to " O   HOH Z 234 " =    3.753
peak=    4.776 closest distance to " O   HOH Z 298 " =    1.877
peak=    4.754 closest distance to " CG  PRO A 213 " =    1.211
peak=    4.700 closest distance to " O   HOH Z  15 " =    2.065
peak=    4.681 closest distance to " CB  GLN A 183 " =    1.317
peak=    4.659 closest distance to " O   HOH Z 142 " =    1.578
peak=    4.608 closest distance to " O   HOH Z 193 " =    1.830
peak=    4.583 closest distance to " O   HOH Z 126 " =    1.860
peak=    4.569 closest distance to " C   PRO A 198 " =    1.502
peak=    4.501 closest distance to " CA  TYR A  30 " =    0.967
peak=    4.490 closest distance to " CB  SER A   3 " =    1.286
peak=    4.488 closest distance to " CB  TYR A 169 " =    0.872
peak=    4.482 closest distance to " CB  GLU A 152 " =    1.148
peak=    4.469 closest distance to " O   HOH Z 368 " =    2.024
peak=    4.443 closest distance to " O   HOH Z 272 " =    1.862
peak=    4.437 closest distance to " O   HOH Z 403 " =    1.820
peak=    4.433 closest distance to " O   HOH Z 232 " =    2.352
peak=    4.394 closest distance to " NE2 GLN A  11 " =    1.058
peak=    4.393 closest distance to " O   SER A  87 " =    2.169
peak=    4.385 closest distance to " CA  ALA A  21 " =    1.227
peak=    4.378 closest distance to " CB  GLU A 128 " =    1.139
peak=    4.341 closest distance to " NH2BARG A 145 " =    2.034
peak=    4.328 closest distance to " CB  ARG A  79 " =    1.405
peak=    4.327 closest distance to " O   HOH Z  97 " =    1.878
peak=    4.322 closest distance to " CB  GLU A 277 " =    3.525
peak=    4.283 closest distance to " O   HOH Z 316 " =    2.887
peak=    4.272 closest distance to " OD1 ASN A  69 " =    2.578
peak=    4.222 closest distance to " O   HOH Z 402 " =    1.457
peak=    4.216 closest distance to " O   HOH Z 426 " =    1.503
peak=    4.205 closest distance to " O   HOH Z 203 " =    1.745
peak=    4.196 closest distance to " O   HOH Z 132 " =    1.097
peak=    4.174 closest distance to " O   HOH Z  97 " =    2.498
peak=    4.163 closest distance to " OD2 ASP A 286 " =    2.778
peak=    4.161 closest distance to " O   HOH Z  78 " =    1.669
peak=    4.157 closest distance to " O   HOH Z 279 " =    2.045
peak=    4.155 closest distance to " O   HOH Z 236 " =    1.954
peak=    4.130 closest distance to " O   HOH Z  80 " =    1.653
peak=    4.120 closest distance to " O   HOH Z  44 " =    2.090
peak=    4.113 closest distance to " O   HOH Z 389 " =    1.889
peak=    4.100 closest distance to " NZ  LYS A 117 " =    3.114
peak=    4.079 closest distance to " O   HOH Z  49 " =    2.222
peak=    4.075 closest distance to " O   HOH Z  59 " =    2.321
peak=    4.065 closest distance to " O   HOH Z 128 " =    1.964
peak=    4.051 closest distance to " O   HOH Z 374 " =    2.582
peak=    4.038 closest distance to " O   HOH Z 209 " =    2.299
peak=    4.020 closest distance to " CG  ARG A  66 " =    2.766
peak=    4.016 closest distance to " CB  ASN A 148 " =    1.588
peak=    4.013 closest distance to " CG1 ILE A  33 " =    1.276
peak=    4.011 closest distance to " O   HOH Z 313 " =    1.767
peak=    3.997 closest distance to " O   HOH Z 134 " =    1.500
peak=    3.994 closest distance to " O   HOH Z 357 " =    1.919
peak=    3.984 closest distance to " CG1BVAL A  72 " =    1.640
peak=    3.979 closest distance to " OG BSER A 164 " =    2.450
peak=    3.975 closest distance to " O   HOH Z  63 " =    1.890
peak=    3.957 closest distance to " O   HOH Z  40 " =    1.772
peak=    3.914 closest distance to " O   HOH Z 344 " =    2.874
peak=    3.907 closest distance to " CA  THR A 221 " =    0.923
peak=    3.897 closest distance to " O   HOH Z 369 " =    2.248
peak=    3.895 closest distance to " CB  ARG A 190 " =    1.682
peak=    3.886 closest distance to " O   HOH Z 227 " =    1.664
peak=    3.885 closest distance to " O   HOH Z 406 " =    1.632
peak=    3.878 closest distance to " NH2 ARG A 156 " =    1.153
peak=    3.873 closest distance to " CG  PRO A  90 " =    1.152
peak=    3.872 closest distance to " O   HOH Z 427 " =    2.737
peak=    3.871 closest distance to " O   HOH Z 423 " =    2.009
peak=    3.860 closest distance to " CA  ASN A 176 " =    1.119
peak=    3.860 closest distance to " NH2AARG A 145 " =    2.260
peak=    3.859 closest distance to " O   HOH Z 102 " =    1.288
peak=    3.858 closest distance to " CD2 TRP A 179 " =    1.382
peak=    3.844 closest distance to " CB  ARG A 139 " =    0.938
peak=    3.842 closest distance to " O   HOH Z   6 " =    2.239
peak=    3.837 closest distance to " O   HOH Z 365 " =    2.775
peak=    3.835 closest distance to " CA  ARG A  36 " =    1.101
peak=    3.832 closest distance to " O   HOH Z 345 " =    1.686
peak=    3.819 closest distance to " ND2 ASN A 187 " =    1.611
peak=    3.814 closest distance to " CB  ASN A  39 " =    0.843
peak=    3.814 closest distance to " O   HOH Z 326 " =    1.529
peak=    3.813 closest distance to " O   HOH Z  67 " =    1.964
peak=    3.805 closest distance to " O   HOH Z 284 " =    2.861
peak=    3.802 closest distance to " CB  SER A 141 " =    1.036
peak=    3.794 closest distance to " O   HOH Z 128 " =    2.180
peak=    3.793 closest distance to " CB  LEU A 228 " =    1.173
peak=    3.783 closest distance to " O   HOH Z 132 " =    2.779
peak=    3.780 closest distance to " O   HOH Z 189 " =    1.758
peak=    3.779 closest distance to " O   HOH Z 214 " =    2.158
peak=    3.767 closest distance to " N   ASN A  39 " =    1.226
peak=    3.754 closest distance to " O   HOH Z  54 " =    1.640
peak=    3.752 closest distance to " O   HOH Z 193 " =    2.221
peak=    3.750 closest distance to " CG  GLN A  58 " =    2.486
peak=    3.748 closest distance to " O   HOH Z 416 " =    2.786
peak=    3.747 closest distance to " CB  VAL A 202 " =    1.541
peak=    3.745 closest distance to " O   HOH Z 132 " =    2.147
peak=    3.740 closest distance to " O   HOH Z 303 " =    1.997
peak=    3.739 closest distance to " O   HOH Z 346 " =    1.512
peak=    3.734 closest distance to " O   HOH Z  43 " =    2.222
peak=    3.731 closest distance to " O   HOH Z 108 " =    2.407
peak=    3.728 closest distance to " O   HOH Z  21 " =    1.788
peak=    3.726 closest distance to " CB  PRO A  54 " =    0.828
peak=    3.725 closest distance to " CD  ARG A 269 " =    0.987
peak=    3.723 closest distance to " O   HOH Z 411 " =    3.502
peak=    3.723 closest distance to " CG  PRO A 198 " =    1.300
peak=    3.721 closest distance to " O   HOH Z 427 " =    3.022
peak=    3.720 closest distance to " CG  PRO A 243 " =    1.179
peak=    3.720 closest distance to " O   HOH Z 247 " =    1.335
peak=    3.719 closest distance to " O   HOH Z 154 " =    1.339
peak=    3.715 closest distance to " CG2 ILE A  20 " =    1.396
peak=    3.711 closest distance to " O   HOH Z 327 " =    1.741
peak=    3.710 closest distance to " O   HOH Z 250 " =    1.448
peak=    3.704 closest distance to " O   HOH Z 345 " =    2.770
peak=    3.702 closest distance to " CB  TRP A 179 " =    1.292
peak=    3.701 closest distance to " O   HOH Z 371 " =    3.285
peak=    3.686 closest distance to " O   HOH Z 173 " =    2.110
peak=    3.686 closest distance to " OD2 ASP A 298 " =    3.988
peak=    3.685 closest distance to " O   HOH Z 144 " =    2.137
peak=    3.679 closest distance to " CG2 THR A 221 " =    1.117
peak=    3.675 closest distance to " CG  ARG A  66 " =    0.965
peak=    3.671 closest distance to " O   HOH Z  61 " =    1.513
peak=    3.667 closest distance to " CD2 LEU A 297 " =    0.902
peak=    3.664 closest distance to " CA  ARG A 195 " =    1.245
peak=    3.653 closest distance to " O   HOH Z 147 " =    1.776
peak=    3.642 closest distance to " CB  TYR A 169 " =    0.875
peak=    3.640 closest distance to " O   HOH Z 334 " =    1.445
peak=    3.635 closest distance to " O   HOH Z 163 " =    1.485
peak=    3.635 closest distance to " O   HOH Z 419 " =    1.531
peak=    3.632 closest distance to " OE1 GLN A  11 " =    1.903
peak=    3.627 closest distance to " OG  SER A  62 " =    2.922
peak=    3.626 closest distance to " O   HOH Z 197 " =    2.622
peak=    3.594 closest distance to " O   HOH Z 362 " =    3.553
peak=    3.586 closest distance to " O   HOH Z 358 " =    2.129
peak=    3.571 closest distance to " C   ILE A 106 " =    1.886
peak=    3.571 closest distance to " CG AARG A 275 " =    1.019
peak=    3.565 closest distance to " O   HOH Z 260 " =    1.353
peak=    3.556 closest distance to " O   HOH Z  10 " =    1.796
peak=    3.552 closest distance to " O   HOH Z 163 " =    1.938
peak=    3.540 closest distance to " O   HOH Z 130 " =    2.343
peak=    3.540 closest distance to " O   ALA A 165 " =    1.357
peak=    3.537 closest distance to " O   HOH Z 126 " =    1.665
peak=    3.534 closest distance to " O   HOH Z 123 " =    2.117
peak=    3.529 closest distance to " O   HOH Z 183 " =    1.589
peak=    3.528 closest distance to " O   HOH Z 336 " =    1.684
peak=    3.528 closest distance to " O   HOH Z 281 " =    4.316
peak=    3.527 closest distance to " O   HOH Z  66 " =    2.190
peak=    3.525 closest distance to " CB  ALA A 248 " =    1.394
peak=    3.523 closest distance to " CA  LYS A 117 " =    1.276
peak=    3.520 closest distance to " CG2AVAL A 121 " =    2.179
peak=    3.517 closest distance to " O   HOH Z 421 " =    1.619
peak=    3.517 closest distance to " O   HOH Z 380 " =    1.908
peak=    3.513 closest distance to " O   HOH Z 299 " =    4.436
peak=    3.510 closest distance to " O   HOH Z 438 " =    2.184
peak=    3.506 closest distance to " CA  ASP A 140 " =    1.116
peak=    3.501 closest distance to " O   HOH Z  88 " =    3.189
peak=    3.496 closest distance to " O   HOH Z 245 " =    1.371
peak=    3.496 closest distance to " NZ  LYS A 119 " =    1.775
peak=    3.492 closest distance to " NH1AARG A 145 " =    1.183
peak=    3.490 closest distance to " O   HOH Z 425 " =    2.097
peak=    3.484 closest distance to " O   HOH Z  35 " =    2.411
peak=    3.470 closest distance to " CB  TRP A 266 " =    0.973
peak=    3.464 closest distance to " CD  PRO A  54 " =    1.113
peak=    3.461 closest distance to " NH2AARG A 190 " =    1.179
peak=    3.461 closest distance to " O   HOH Z  19 " =    1.636
peak=    3.456 closest distance to " CG2 VAL A 197 " =    1.077
peak=    3.452 closest distance to " CB  SER A  62 " =    0.793
peak=    3.444 closest distance to " CA  ASP A 162 " =    1.142
peak=    3.443 closest distance to " O   HOH Z 291 " =    1.484
peak=    3.442 closest distance to " CB  ALA A 291 " =    1.259
peak=    3.442 closest distance to " OG1 THR A 294 " =    2.308
peak=    3.441 closest distance to " CD  LYS A 166 " =    1.331
peak=    3.439 closest distance to " O   TRP A 274 " =    1.889
peak=    3.431 closest distance to " O   HOH Z 263 " =    2.351
peak=    3.422 closest distance to " O   HOH Z 255 " =    1.553
peak=    3.420 closest distance to " O   HOH Z 408 " =    1.491
peak=    3.412 closest distance to " O  BHOH Z  74 " =    1.372
peak=    3.406 closest distance to " O   HOH Z 250 " =    1.716
peak=    3.405 closest distance to " CE  LYS A 119 " =    1.137
peak=    3.393 closest distance to " O   HOH Z 261 " =    1.593
peak=    3.390 closest distance to " CB  ALA A 100 " =    1.209
peak=    3.388 closest distance to " CB  VAL A 265 " =    1.240
peak=    3.388 closest distance to " CB  SER A  26 " =    1.625
peak=    3.386 closest distance to " O   SER A  26 " =    1.711
peak=    3.380 closest distance to " CG2BVAL A  41 " =    0.863
peak=    3.380 closest distance to " CD2 LEU A 255 " =    1.246
peak=    3.380 closest distance to " CA  ALA A  84 " =    1.290
peak=    3.377 closest distance to " CA  ASP A 191 " =    0.832
peak=    3.375 closest distance to " CA  ASN A 215 " =    1.133
peak=    3.370 closest distance to " CD1 LEU A 300 " =    1.240
peak=    3.367 closest distance to " CA  ALA A  51 " =    0.874
peak=    3.361 closest distance to " O   HOH Z 185 " =    1.671
peak=    3.360 closest distance to " CB  PRO A 198 " =    1.161
peak=    3.360 closest distance to " O   HOH Z  20 " =    1.386
peak=    3.353 closest distance to " CG2 ILE A 120 " =    1.208
peak=    3.352 closest distance to " O   HOH Z 217 " =    2.104
peak=    3.351 closest distance to " CB  ARG A 259 " =    1.903
peak=    3.351 closest distance to " O   HOH Z 214 " =    2.274
peak=    3.350 closest distance to " O   HOH Z 280 " =    2.493
peak=    3.342 closest distance to " O   HOH Z 337 " =    3.644
peak=    3.338 closest distance to " O   HOH Z 158 " =    2.934
peak=    3.336 closest distance to " O   HOH Z 133 " =    1.323
peak=    3.334 closest distance to " CG  GLN A  77 " =    2.136
peak=    3.323 closest distance to " CB  ILE A 120 " =    1.334
peak=    3.319 closest distance to " CZ2 TRP A 179 " =    1.702
peak=    3.319 closest distance to " O   HOH Z 417 " =    3.119
peak=    3.317 closest distance to " O   HOH Z  61 " =    1.563
peak=    3.303 closest distance to " CA  VAL A  41 " =    0.890
peak=    3.301 closest distance to " CD  ARG A 159 " =    0.762
peak=    3.301 closest distance to " O   HOH Z 273 " =    2.619
peak=    3.296 closest distance to " CA  ALA A 291 " =    0.876
peak=    3.291 closest distance to " CB  MET A  47 " =    1.028
peak=    3.286 closest distance to " O   HOH Z 423 " =    3.338
peak=    3.282 closest distance to " CA  ARG A  66 " =    1.209
peak=    3.278 closest distance to " O   HOH Z 411 " =    1.649
peak=    3.263 closest distance to " ND2 ASN A 110 " =    1.624
peak=    3.259 closest distance to " O   GLY A  57 " =    2.576
peak=    3.256 closest distance to " O   HOH Z 166 " =    3.621
peak=    3.256 closest distance to " CE1 TYR A 186 " =    1.196
peak=    3.255 closest distance to " CG BARG A 102 " =    1.833
peak=    3.244 closest distance to " O   ALA A   1 " =    1.607
peak=    3.238 closest distance to " O   HOH Z 267 " =    2.011
peak=    3.232 closest distance to " CD1 LEU A  96 " =    0.756
peak=    3.230 closest distance to " O   HOH Z  59 " =    1.663
peak=    3.230 closest distance to " CA  GLY A  80 " =    0.870
peak=    3.229 closest distance to " CG  MET A 185 " =    1.143
peak=    3.228 closest distance to " OG  SER A  22 " =    2.726
peak=    3.225 closest distance to " O   HOH Z 383 " =    2.014
peak=    3.221 closest distance to " O  BHOH Z  74 " =    1.577
peak=    3.220 closest distance to " O   HOH Z 368 " =    2.502
peak=    3.218 closest distance to " CA  ASP A 124 " =    0.710
peak=    3.211 closest distance to " O   HOH Z   1 " =    2.355
peak=    3.208 closest distance to " CB  THR A  52 " =    1.108
peak=    3.206 closest distance to " CB  ASP A 140 " =    0.782
peak=    3.204 closest distance to " CA  ASN A 217 " =    1.293
peak=    3.202 closest distance to " O   HOH Z  89 " =    2.276
peak=    3.201 closest distance to " O   ALA A 158 " =    1.220
peak=    3.200 closest distance to " CA  ALA A 160 " =    0.826
peak=    3.188 closest distance to " CA  MET A  40 " =    1.043
peak=    3.186 closest distance to " O   HOH Z 353 " =    2.791
peak=    3.183 closest distance to " O   HOH Z 261 " =    1.963
peak=    3.183 closest distance to " OG BSER A 210 " =    1.221
peak=    3.183 closest distance to " OG BSER A 258 " =    3.156
peak=    3.179 closest distance to " CB  PRO A  90 " =    1.942
peak=    3.179 closest distance to " O   HOH Z  48 " =    1.586
peak=    3.177 closest distance to " O   HOH Z 148 " =    3.084
peak=    3.172 closest distance to " CB  ALA A   9 " =    1.513
peak=    3.171 closest distance to " NH2 ARG A 219 " =    1.943
peak=    3.170 closest distance to " O   GLY A 147 " =    1.605
peak=    3.167 closest distance to " O   HOH Z 189 " =    1.341
peak=    3.163 closest distance to " NH1BARG A 145 " =    1.101
peak=    3.154 closest distance to " NZ  LYS A  76 " =    1.308
peak=    3.148 closest distance to " CZ  PHE A 218 " =    1.033
peak=    3.144 closest distance to " CD1 LEU A 228 " =    1.614
peak=    3.140 closest distance to " CB  MET A  40 " =    0.980
peak=    3.139 closest distance to " CZ  PHE A  38 " =    1.456
peak=    3.137 closest distance to " O   HOH Z 227 " =    1.657
peak=    3.125 closest distance to " O   HOH Z 135 " =    1.716
peak=    3.124 closest distance to " CD  GLN A 194 " =    1.566
peak=    3.122 closest distance to " CA  GLU A  46 " =    0.714
peak=    3.120 closest distance to " O   HOH Z 194 " =    1.860
peak=    3.117 closest distance to " O   HOH Z 299 " =    2.304
peak=    3.117 closest distance to " O   HOH Z 234 " =    1.763
peak=    3.113 closest distance to " O   HOH Z 435 " =    1.827
peak=    3.106 closest distance to " O   HOH Z  30 " =    1.957
peak=    3.098 closest distance to " O   HOH Z 197 " =    1.951
peak=    3.097 closest distance to " OD1 ASP A 238 " =    0.983
peak=    3.094 closest distance to " O   HOH Z 394 " =    1.667
peak=    3.089 closest distance to " CA  ILE A  33 " =    1.406
peak=    3.083 closest distance to " CB  ALA A  71 " =    1.187
peak=    3.079 closest distance to " CB  SER A 273 " =    0.764
peak=    3.079 closest distance to " CG  MET A  93 " =    1.023
peak=    3.074 closest distance to " CB  ASN A 215 " =    1.106
peak=    3.068 closest distance to " C   ARG A  56 " =    1.426
peak=    3.057 closest distance to " N   ARG A 156 " =    1.389
peak=    3.056 closest distance to " CD  GLN A 240 " =    1.475
peak=    3.052 closest distance to " OH  TYR A 116 " =    1.072
peak=    3.022 closest distance to " O   PHE A 155 " =    1.875
peak=    3.008 closest distance to " O   HOH Z 156 " =    2.829

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 205         
Filter by distance & map next to the model:
   mapped sites are within: 0.573 - 5.751
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 205
   mapped sites are within: 0.747 - 5.751

peak=   -4.866 closest distance to " O   HOH Z 266 " =    4.175
peak=   -4.384 closest distance to " CD  ARG A 156 " =    2.027
peak=   -4.317 closest distance to " C   HIS A 108 " =    1.118
peak=   -4.312 closest distance to " O   VAL A  67 " =    2.737
peak=   -4.305 closest distance to " OXT GLY A 302 " =    2.799
peak=   -4.303 closest distance to " O   HOH Z  13 " =    1.587
peak=   -4.271 closest distance to " SG  CYS A 254 " =    3.332
peak=   -4.262 closest distance to " O   PRO A 163 " =    2.086
peak=   -4.145 closest distance to " CG  MET A  93 " =    2.478
peak=   -4.047 closest distance to " O   HOH Z 234 " =    4.201
peak=   -4.023 closest distance to " O   HOH Z 353 " =    2.270
peak=   -4.017 closest distance to " O   HOH Z 407 " =    3.087
peak=   -4.010 closest distance to " O   HOH Z 377 " =    2.016
peak=   -3.977 closest distance to " CA  VAL A  67 " =    2.794
peak=   -3.970 closest distance to " O   HOH Z 292 " =    4.535
peak=   -3.935 closest distance to " CH2 TRP A 179 " =    1.305
peak=   -3.933 closest distance to " N   GLN A  58 " =    1.598
peak=   -3.933 closest distance to " O   HOH Z 165 " =    1.994
peak=   -3.908 closest distance to " OG  SER A  97 " =    2.117
peak=   -3.903 closest distance to " O   HOH Z 290 " =    0.938
peak=   -3.894 closest distance to " CD  ARG A 139 " =    1.629
peak=   -3.887 closest distance to " O   HOH Z 118 " =    3.307
peak=   -3.886 closest distance to " CD1 PHE A  59 " =    1.930
peak=   -3.867 closest distance to " CB  TYR A  15 " =    2.240
peak=   -3.859 closest distance to " O   PRO A 198 " =    1.310
peak=   -3.858 closest distance to " O   SER A 210 " =    1.879
peak=   -3.855 closest distance to " CE2 TYR A  30 " =    2.779
peak=   -3.852 closest distance to " CD1 LEU A 228 " =    2.204
peak=   -3.823 closest distance to " CB  ALA A 291 " =    2.344
peak=   -3.815 closest distance to " O   HOH Z  10 " =    1.570
peak=   -3.803 closest distance to " O   ILE A 109 " =    2.585
peak=   -3.799 closest distance to " CD1 PHE A 130 " =    2.281
peak=   -3.787 closest distance to " CG  ASP A 132 " =    2.312
peak=   -3.755 closest distance to " O   TRP A  92 " =    1.820
peak=   -3.755 closest distance to " O   HOH Z  11 " =    1.802
peak=   -3.752 closest distance to " CG  GLU A  53 " =    1.424
peak=   -3.745 closest distance to " O   HOH Z  71 " =    1.444
peak=   -3.733 closest distance to " OG  SER A  62 " =    1.341
peak=   -3.728 closest distance to " N   ALA A  43 " =    2.623
peak=   -3.726 closest distance to " CZ  TYR A 169 " =    1.843
peak=   -3.716 closest distance to " CB  PRO A 243 " =    2.605
peak=   -3.700 closest distance to " CD  GLN A  58 " =    1.084
peak=   -3.699 closest distance to " ND2 ASN A 187 " =    1.484
peak=   -3.697 closest distance to " OG ASER A 134 " =    1.271
peak=   -3.695 closest distance to " CB  ASN A  39 " =    2.318
peak=   -3.692 closest distance to " C   ALA A 158 " =    1.196
peak=   -3.692 closest distance to " CG  ASP A 231 " =    0.870
peak=   -3.677 closest distance to " NH2 ARG A  79 " =    1.949
peak=   -3.673 closest distance to " CD2 LEU A 300 " =    2.835
peak=   -3.668 closest distance to " ND2 ASN A  45 " =    0.987
peak=   -3.661 closest distance to " OG BSER A 134 " =    1.281
peak=   -3.650 closest distance to " CB  PHE A 192 " =    1.906
peak=   -3.647 closest distance to " O   HOH Z  17 " =    1.341
peak=   -3.643 closest distance to " O   HOH Z 372 " =    2.336
peak=   -3.642 closest distance to " ND2 ASN A  45 " =    1.276
peak=   -3.641 closest distance to " O   HOH Z  52 " =    1.648
peak=   -3.635 closest distance to " O   ALA A 256 " =    1.489
peak=   -3.626 closest distance to " NH1 ARG A 195 " =    2.535
peak=   -3.618 closest distance to " N   SER A 276 " =    1.401
peak=   -3.617 closest distance to " NH2 ARG A  66 " =    4.987
peak=   -3.609 closest distance to " CD  GLN A  58 " =    1.244
peak=   -3.603 closest distance to " O   HOH Z 196 " =    1.908
peak=   -3.603 closest distance to " OE1 GLN A 223 " =    2.182
peak=   -3.586 closest distance to " O   HOH Z 166 " =    1.643
peak=   -3.581 closest distance to " CA  ASP A 298 " =    1.071
peak=   -3.578 closest distance to " N   ALA A 248 " =    1.711
peak=   -3.554 closest distance to " C   THR A 279 " =    1.198
peak=   -3.539 closest distance to " O   HOH Z  43 " =    1.579
peak=   -3.538 closest distance to " OG BSER A 210 " =    2.125
peak=   -3.527 closest distance to " O   HOH Z  11 " =    1.834
peak=   -3.517 closest distance to " O   VAL A 174 " =    2.072
peak=   -3.516 closest distance to " O   LEU A 167 " =    1.595
peak=   -3.514 closest distance to " O   PHE A 218 " =    1.521
peak=   -3.513 closest distance to " OG BSER A 134 " =    1.748
peak=   -3.511 closest distance to " O   HOH Z 283 " =    1.776
peak=   -3.510 closest distance to " C   ASN A 285 " =    2.314
peak=   -3.507 closest distance to " CD1 LEU A  25 " =    2.462
peak=   -3.492 closest distance to " CD  ARG A 195 " =    5.124
peak=   -3.487 closest distance to " O   HOH Z 185 " =    2.333
peak=   -3.483 closest distance to " O   HOH Z 198 " =    2.116
peak=   -3.470 closest distance to " O   HOH Z 126 " =    1.919
peak=   -3.466 closest distance to " N   GLN A 122 " =    1.538
peak=   -3.463 closest distance to " OD1 ASN A 148 " =    1.652
peak=   -3.446 closest distance to " NH2 ARG A  66 " =    1.720
peak=   -3.442 closest distance to " O   GLY A 196 " =    0.969
peak=   -3.442 closest distance to " CG  ASP A  50 " =    2.386
peak=   -3.439 closest distance to " O   ALA A 161 " =    1.601
peak=   -3.436 closest distance to " O   HOH Z 166 " =    1.913
peak=   -3.433 closest distance to " O   HOH Z 385 " =    1.959
peak=   -3.433 closest distance to " O   ASN A 187 " =    1.464
peak=   -3.430 closest distance to " OD2 ASP A 171 " =    2.331
peak=   -3.422 closest distance to " N   GLY A 133 " =    1.830
peak=   -3.420 closest distance to " O   HOH Z  15 " =    1.546
peak=   -3.417 closest distance to " O   HOH Z  93 " =    1.363
peak=   -3.412 closest distance to " O   ALA A 160 " =    1.470
peak=   -3.411 closest distance to " CB  ASP A 286 " =    2.063
peak=   -3.403 closest distance to " O   SER A 135 " =    1.621
peak=   -3.402 closest distance to " C   GLY A  80 " =    2.355
peak=   -3.401 closest distance to " O   HOH Z 311 " =    3.483
peak=   -3.397 closest distance to " CG2 THR A 178 " =    2.211
peak=   -3.394 closest distance to " OE2 GLU A   2 " =    1.616
peak=   -3.393 closest distance to " O   HOH Z 361 " =    3.437
peak=   -3.389 closest distance to " CD2 LEU A 237 " =    2.602
peak=   -3.384 closest distance to " OG  SER A   3 " =    1.547
peak=   -3.380 closest distance to " O   MET A  40 " =    2.726
peak=   -3.375 closest distance to " O   HOH Z 360 " =    2.558
peak=   -3.372 closest distance to " CD2 LEU A 237 " =    2.695
peak=   -3.372 closest distance to " CB  PHE A 208 " =    2.229
peak=   -3.371 closest distance to " CB  PRO A 163 " =    2.712
peak=   -3.371 closest distance to " SG ACYS A 201 " =    2.164
peak=   -3.363 closest distance to " N   VAL A 189 " =    1.702
peak=   -3.363 closest distance to " O   ALA A   1 " =    1.875
peak=   -3.357 closest distance to " OD1 ASP A 191 " =    1.771
peak=   -3.355 closest distance to " CB  ALA A 248 " =    1.930
peak=   -3.351 closest distance to " CE  MET A 105 " =    1.943
peak=   -3.350 closest distance to " CB  CYS A 254 " =    2.620
peak=   -3.349 closest distance to " O   SER A 146 " =    0.985
peak=   -3.349 closest distance to " O   SER A 273 " =    1.387
peak=   -3.348 closest distance to " O   HOH Z 417 " =    2.638
peak=   -3.341 closest distance to " O   HOH Z 377 " =    1.487
peak=   -3.338 closest distance to " CG  LYS A 119 " =    2.914
peak=   -3.330 closest distance to " O   HOH Z 388 " =    2.071
peak=   -3.326 closest distance to " O   HOH Z 102 " =    1.715
peak=   -3.324 closest distance to " NH1 ARG A  66 " =    0.815
peak=   -3.320 closest distance to " O   HOH Z  38 " =    1.510
peak=   -3.318 closest distance to " O   HOH Z 265 " =    2.037
peak=   -3.313 closest distance to " O   HOH Z 297 " =    2.799
peak=   -3.306 closest distance to " O   HOH Z 427 " =    1.367
peak=   -3.305 closest distance to " C   LEU A 143 " =    1.107
peak=   -3.295 closest distance to " ND2 ASN A  39 " =    1.184
peak=   -3.295 closest distance to " CE  MET A  93 " =    1.207
peak=   -3.294 closest distance to " CG  LEU A  83 " =    1.950
peak=   -3.294 closest distance to " NE2 GLN A 103 " =    1.636
peak=   -3.287 closest distance to " O   HOH Z 313 " =    1.021
peak=   -3.286 closest distance to " O   PRO A 198 " =    1.317
peak=   -3.285 closest distance to " O   HOH Z 418 " =    1.346
peak=   -3.277 closest distance to " CG1AVAL A  41 " =    2.761
peak=   -3.273 closest distance to " CG  GLU A 277 " =    1.129
peak=   -3.273 closest distance to " O   HOH Z  61 " =    1.601
peak=   -3.267 closest distance to " O   ASN A  45 " =    1.858
peak=   -3.267 closest distance to " O   HOH Z 351 " =    1.507
peak=   -3.261 closest distance to " O   GLN A  11 " =    1.387
peak=   -3.257 closest distance to " CG1 VAL A 112 " =    2.713
peak=   -3.251 closest distance to " CD  LYS A 289 " =    2.363
peak=   -3.251 closest distance to " O   VAL A 125 " =    2.258
peak=   -3.240 closest distance to " O   HOH Z 414 " =    1.343
peak=   -3.238 closest distance to " CD1 TYR A 247 " =    2.307
peak=   -3.236 closest distance to " CG1 VAL A  78 " =    2.896
peak=   -3.235 closest distance to " ND2 ASN A 209 " =    1.570
peak=   -3.234 closest distance to " CG2 ILE A 263 " =    2.202
peak=   -3.229 closest distance to " O   HOH Z 151 " =    1.468
peak=   -3.229 closest distance to " O   HOH Z 385 " =    3.550
peak=   -3.228 closest distance to " O   HOH Z  90 " =    2.863
peak=   -3.223 closest distance to " O   HOH Z 435 " =    2.613
peak=   -3.219 closest distance to " OG  SER A  63 " =    1.381
peak=   -3.218 closest distance to " C   SER A 206 " =    1.630
peak=   -3.218 closest distance to " O   HOH Z 326 " =    1.710
peak=   -3.217 closest distance to " O   ALA A  34 " =    2.387
peak=   -3.213 closest distance to " CB  SER A 258 " =    1.987
peak=   -3.211 closest distance to " CA  GLY A 203 " =    2.189
peak=   -3.208 closest distance to " NE2 GLN A  88 " =    1.851
peak=   -3.207 closest distance to " CE3 TRP A 150 " =    2.160
peak=   -3.204 closest distance to " CZ3 TRP A 274 " =    2.413
peak=   -3.199 closest distance to " CZ  PHE A  59 " =    1.691
peak=   -3.189 closest distance to " O   HOH Z  97 " =    1.484
peak=   -3.187 closest distance to " CG  GLN A 223 " =    1.513
peak=   -3.185 closest distance to " N   SER A 206 " =    1.839
peak=   -3.175 closest distance to " O   HOH Z 423 " =    2.289
peak=   -3.175 closest distance to " CB  ALA A 248 " =    2.323
peak=   -3.174 closest distance to " O   HOH Z 171 " =    2.003
peak=   -3.172 closest distance to " CG2 VAL A 189 " =    2.180
peak=   -3.170 closest distance to " OG  SER A  26 " =    1.294
peak=   -3.170 closest distance to " O   HOH Z   6 " =    1.774
peak=   -3.169 closest distance to " O   HOH Z 252 " =    3.341
peak=   -3.166 closest distance to " CG  PRO A 163 " =    2.627
peak=   -3.164 closest distance to " CD  GLN A  88 " =    0.747
peak=   -3.161 closest distance to " O   HOH Z 384 " =    2.352
peak=   -3.154 closest distance to " O   HOH Z 116 " =    1.247
peak=   -3.144 closest distance to " OD1 ASP A 171 " =    1.635
peak=   -3.143 closest distance to " CA  GLY A 241 " =    2.315
peak=   -3.133 closest distance to " CG  GLU A 152 " =    2.282
peak=   -3.120 closest distance to " ND2 ASN A  60 " =    1.439
peak=   -3.119 closest distance to " O   HOH Z  41 " =    2.326
peak=   -3.116 closest distance to " O   HOH Z 396 " =    1.657
peak=   -3.115 closest distance to " O   VAL A 153 " =    2.332
peak=   -3.113 closest distance to " O   HOH Z 298 " =    2.677
peak=   -3.109 closest distance to " O   HOH Z 411 " =    3.479
peak=   -3.103 closest distance to " O   HOH Z 263 " =    2.929
peak=   -3.100 closest distance to " O   HOH Z 191 " =    5.751
peak=   -3.098 closest distance to " O   HOH Z 219 " =    3.600
peak=   -3.090 closest distance to " O   ALA A  51 " =    1.468
peak=   -3.087 closest distance to " OH  TYR A 169 " =    0.973
peak=   -3.087 closest distance to " N   ALA A 248 " =    2.242
peak=   -3.086 closest distance to " N   ALA A 226 " =    1.991
peak=   -3.084 closest distance to " CG2 VAL A 189 " =    2.324
peak=   -3.074 closest distance to " OD2 ASP A 171 " =    2.307
peak=   -3.067 closest distance to " CB  LEU A 167 " =    2.166
peak=   -3.064 closest distance to " OG  SER A 206 " =    1.677
peak=   -3.054 closest distance to " CG2AVAL A  41 " =    2.696
peak=   -3.054 closest distance to " O   PRO A 198 " =    1.689
peak=   -3.049 closest distance to " O   ASN A 301 " =    1.333
peak=   -3.048 closest distance to " O   VAL A 197 " =    1.166
peak=   -2.973 closest distance to " SG  CYS A 254 " =    2.784

================= 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    :  0.4305 0.4264   6.233781e+00   6.223953e+00
   1_bss:  0.4206 0.4157   6.223551e+00   6.204609e+00
   1_xyz:  0.2788 0.3035   5.898254e+00   5.966303e+00
   1_adp:  0.2542 0.3149   5.846793e+00   5.993415e+00
   1_occ:  0.2537 0.3154   5.845944e+00   5.992932e+00
   2_bss:  0.2506 0.3129   5.841374e+00   5.989538e+00
   2_xyz:  0.1805 0.2274   5.545265e+00   5.732039e+00
   2_adp:  0.1621 0.2085   5.454838e+00   5.647534e+00
   2_occ:  0.1619 0.2085   5.454363e+00   5.647366e+00
   3_bss:  0.1621 0.2073   5.451876e+00   5.641959e+00
   3_xyz:  0.1283 0.1721   5.248785e+00   5.469378e+00
   3_adp:  0.1214 0.1654   5.204720e+00   5.428032e+00
   3_occ:  0.1213 0.1653   5.204313e+00   5.427934e+00
   4_bss:  0.1217 0.1656   5.207367e+00   5.429766e+00
   4_xyz:  0.1162 0.1606   5.172064e+00   5.398058e+00
   4_adp:  0.1150 0.1596   5.164401e+00   5.391814e+00
   4_occ:  0.1150 0.1596   5.164037e+00   5.391914e+00
   5_bss:  0.1150 0.1596   5.164075e+00   5.391947e+00
   5_xyz:  0.1089 0.1567   5.128327e+00   5.372460e+00
   5_adp:  0.1089 0.1561   5.127003e+00   5.371101e+00
   5_occ:  0.1088 0.1561   5.126983e+00   5.371517e+00
   5_bss:  0.1088 0.1562   5.127126e+00   5.371625e+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:  0.307  24.632  -2.770   2.227   1.596   0.000   0.000   0.000
   1_xyz:  0.307  24.632  -2.770   2.227   1.596   0.000   0.000   0.000
   1_adp:  0.307  24.632  -2.770   2.227   1.596   0.000   0.000   0.000
   1_occ:  0.307  24.632  -2.770   2.227   1.596   0.000   0.000   0.000
   2_bss:  0.326  50.001  -2.879   0.068  -0.571   0.000  -0.000  -0.000
   2_xyz:  0.326  50.001  -2.879   0.068  -0.571   0.000  -0.000  -0.000
   2_adp:  0.326  50.001  -2.879   0.068  -0.571   0.000  -0.000  -0.000
   2_occ:  0.326  50.001  -2.879   0.068  -0.571   0.000  -0.000  -0.000
   3_bss:  0.322  47.674  -2.805  -0.939  -1.378  -0.000  -0.000  -0.000
   3_xyz:  0.322  47.674  -2.805  -0.939  -1.378  -0.000  -0.000  -0.000
   3_adp:  0.322  47.674  -2.805  -0.939  -1.378  -0.000  -0.000  -0.000
   3_occ:  0.322  47.674  -2.805  -0.939  -1.378  -0.000  -0.000  -0.000
   4_bss:  0.324  48.175  -2.795  -1.455  -1.650  -0.000  -0.000  -0.000
   4_xyz:  0.324  48.175  -2.795  -1.455  -1.650  -0.000  -0.000  -0.000
   4_adp:  0.324  48.175  -2.795  -1.455  -1.650  -0.000  -0.000  -0.000
   4_occ:  0.324  48.175  -2.795  -1.455  -1.650  -0.000  -0.000  -0.000
   5_bss:  0.325  48.174  -2.683  -1.501  -1.626  -0.000  -0.000  -0.000
   5_xyz:  0.325  48.174  -2.683  -1.501  -1.626  -0.000  -0.000  -0.000
   5_adp:  0.325  48.174  -2.683  -1.501  -1.626  -0.000  -0.000  -0.000
   5_occ:  0.325  48.174  -2.683  -1.501  -1.626  -0.000  -0.000  -0.000
   5_bss:  0.327  48.127  -2.496  -1.398  -1.449  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  51.007 0.5078  0.6752    56365.893
   1_bss:  49.585 0.5238  0.7048    52169.871
   1_xyz:  31.234 0.7444  0.9535    24159.503
   1_adp:  32.664 0.7274  0.9373    25996.813
   1_occ:  32.665 0.7273  0.9367    25981.240
   2_bss:  32.323 0.7311  0.8961    25580.841
   2_xyz:  22.592 0.8350  0.9825    13249.480
   2_adp:  19.939 0.8622  0.9920    11005.484
   2_occ:  19.940 0.8622  0.9919    10999.969
   3_bss:  19.788 0.8634  0.9729    10805.981
   3_xyz:  15.996 0.8975  0.9916     7435.753
   3_adp:  15.035 0.9063  0.9908     6918.206
   3_occ:  15.031 0.9063  0.9906     6915.989
   4_bss:  15.056 0.9062  0.9813     6970.617
   4_xyz:  14.326 0.9124  0.9826     6465.415
   4_adp:  14.151 0.9139  0.9781     6408.470
   4_occ:  14.149 0.9140  0.9780     6407.698
   5_bss:  14.148 0.9140  0.9792     6409.589
   5_xyz:  13.771 0.9168  0.9810     6173.539
   5_adp:  13.727 0.9173  0.9769     6157.385
   5_occ:  13.731 0.9172  0.9768     6161.195
   5_bss:  13.733 0.9172  0.9807     6163.215
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.8239e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.8239e-01
   1_xyz:   1.377  0.011  0.087 15.818  0.005  4.112   1.0529e-01
   1_adp:   1.377  0.011  0.087 15.818  0.005  4.112   1.0529e-01
   1_occ:   1.377  0.011  0.087 15.818  0.005  4.112   1.0529e-01
   2_bss:   1.377  0.011  0.087 15.818  0.005  4.112   1.0529e-01
   2_xyz:   1.106  0.007  0.074 14.523  0.005  4.117   6.6122e-02
   2_adp:   1.106  0.007  0.074 14.523  0.005  4.117   6.6122e-02
   2_occ:   1.106  0.007  0.074 14.523  0.005  4.117   6.6122e-02
   3_bss:   1.106  0.007  0.074 14.523  0.005  4.117   6.6122e-02
   3_xyz:   1.043  0.007  0.071 14.555  0.004  4.109   6.1768e-02
   3_adp:   1.043  0.007  0.071 14.555  0.004  4.109   6.1768e-02
   3_occ:   1.043  0.007  0.071 14.555  0.004  4.109   6.1768e-02
   4_bss:   1.043  0.007  0.071 14.555  0.004  4.109   6.1768e-02
   4_xyz:   0.933  0.005  0.067 14.367  0.004  4.111   5.1394e-02
   4_adp:   0.933  0.005  0.067 14.367  0.004  4.111   5.1394e-02
   4_occ:   0.933  0.005  0.067 14.367  0.004  4.111   5.1394e-02
   5_bss:   0.933  0.005  0.067 14.367  0.004  4.111   5.1394e-02
   5_xyz:   1.069  0.008  0.077 14.678  0.004  4.112   6.5381e-02
   5_adp:   1.069  0.008  0.077 14.678  0.004  4.112   6.5381e-02
   5_occ:   1.069  0.008  0.077 14.678  0.004  4.112   6.5381e-02
   5_bss:   1.069  0.008  0.077 14.678  0.004  4.112   6.5381e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.616   2.4018e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.616   2.4018e-01
   1_xyz:   8.707  0.082  0.420 88.750  0.028  2.198   8.4433e-02
   1_adp:   8.707  0.082  0.420 88.750  0.028  2.198   8.4433e-02
   1_occ:   8.707  0.082  0.420 88.750  0.028  2.198   8.4433e-02
   2_bss:   8.707  0.082  0.420 88.750  0.028  2.198   8.4433e-02
   2_xyz:   7.912  0.049  0.250 82.358  0.048  2.321   6.8373e-02
   2_adp:   7.912  0.049  0.250 82.358  0.048  2.321   6.8373e-02
   2_occ:   7.912  0.049  0.250 82.358  0.048  2.321   6.8373e-02
   3_bss:   7.912  0.049  0.250 82.358  0.048  2.321   6.8373e-02
   3_xyz:   7.431  0.050  0.239 80.249  0.034  2.309   4.8049e-02
   3_adp:   7.431  0.050  0.239 80.249  0.034  2.309   4.8049e-02
   3_occ:   7.431  0.050  0.239 80.249  0.034  2.309   4.8049e-02
   4_bss:   7.431  0.050  0.239 80.249  0.034  2.309   4.8049e-02
   4_xyz:   6.586  0.031  0.228 82.433  0.032  2.400   3.5298e-02
   4_adp:   6.586  0.031  0.228 82.433  0.032  2.400   3.5298e-02
   4_occ:   6.586  0.031  0.228 82.433  0.032  2.400   3.5298e-02
   5_bss:   6.586  0.031  0.228 82.433  0.032  2.400   3.5298e-02
   5_xyz:   7.634  0.042  0.252 81.642  0.036  2.279   5.1766e-02
   5_adp:   7.634  0.042  0.252 81.642  0.036  2.279   5.1766e-02
   5_occ:   7.634  0.042  0.252 81.642  0.036  2.279   5.1766e-02
   5_bss:   7.634  0.042  0.252 81.642  0.036  2.279   5.1766e-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:  68.31   0.00  17.79  57.71   0.00  13.92  68.31   2.83  38.88
   1_occ:  68.31   0.00  17.79  57.71   0.00  13.92  68.31   2.83  38.88
   2_bss:  68.31   0.00  17.79  57.71   0.00  13.92  68.31   2.83  38.88
   2_xyz:  68.31   0.00  17.79  57.71   0.00  13.92  68.31   2.83  38.88
   2_adp:  79.49   0.49  17.44  79.49   0.49  13.29  74.08   5.81  40.08
   2_occ:  79.49   0.49  17.44  79.49   0.49  13.29  74.08   5.81  40.08
   3_bss:  79.49   0.49  17.44  79.49   0.49  13.29  74.08   5.81  40.08
   3_xyz:  79.49   0.49  17.44  79.49   0.49  13.29  74.08   5.81  40.08
   3_adp:  89.52   0.00  17.37  89.52   1.22  13.02  81.10   0.00  41.06
   3_occ:  89.52   0.00  17.37  89.52   1.22  13.02  81.10   0.00  41.06
   4_bss:  89.52   0.00  17.37  89.52   1.22  13.02  81.10   0.00  41.06
   4_xyz:  89.52   0.00  17.37  89.52   1.22  13.02  81.10   0.00  41.06
   4_adp:  91.97   1.54  17.04  91.97   1.54  12.83  83.23   1.66  39.98
   4_occ:  91.97   1.54  17.04  91.97   1.54  12.83  83.23   1.66  39.98
   5_bss:  91.97   1.54  17.04  91.97   1.54  12.83  83.23   1.66  39.98
   5_xyz:  91.97   1.54  17.04  91.97   1.54  12.83  83.23   1.66  39.98
   5_adp:  92.69   1.35  16.71  92.69   1.35  12.64  83.66   3.76  38.92
   5_occ:  92.69   1.35  16.71  92.69   1.35  12.64  83.66   3.76  38.92
   5_bss:  92.65   1.30  16.67  92.65   1.30  12.59  83.61   3.71  38.87
------------------------------------------------------------------------
 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:    2.055    0.026    0.413
   1_adp:    2.055    0.026    0.413
   1_occ:    2.055    0.026    0.413
   2_bss:    2.055    0.026    0.413
   2_xyz:    1.326    0.061    0.533
   2_adp:    1.326    0.061    0.533
   2_occ:    1.326    0.061    0.533
   3_bss:    1.326    0.061    0.533
   3_xyz:    1.324    0.054    0.615
   3_adp:    1.324    0.054    0.615
   3_occ:    1.324    0.054    0.615
   4_bss:    1.324    0.054    0.615
   4_xyz:    1.493    0.069    0.640
   4_adp:    1.493    0.069    0.640
   4_occ:    1.493    0.069    0.640
   5_bss:    1.493    0.069    0.640
   5_xyz:    1.409    0.080    0.656
   5_adp:    1.409    0.080    0.656
   5_occ:    1.409    0.080    0.656
   5_bss:    1.409    0.080    0.656
------------------------------------------------------------------------

CPU time actual refinement: 340.39


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_452/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_452/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_452/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_452/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_452/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 340.23 
  Macro-tasks:
    bulk solvent and scale       = 43.40  
    individual site refinement   = 142.07 
    weights calculation          = 29.25  
    collect and process          = 6.42   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 221.23 
  Micro-tasks:
    mask                            = 1.79   
    f_calc                          = 108.14 
    alpha_beta                      = 7.90   
    target                          = 1.10   
    gradients_wrt_atomic_parameters = 118.05 
    fmodel                         = 6.76   
    r_factors                      = 0.39   
    phase_errors                   = 10.75  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 255.17 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.747 micro seconds
Total CPU time: 5.90 minutes
from_scatterers_fft:    660 calls, 107.77 s
gradients_fft:          605 calls, 103.92 s

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

# Date 2008-01-16 Time 04:51:21 PST -0800 (1200487881.19 s)
Start R-work = 0.4305, R-free = 0.4264 (no bulk solvent and anisotropic scale)
Final R-work = 0.1326, R-free = 0.1765 (no bulk solvent and anisotropic scale)

Start R-work = 0.4206, R-free = 0.4157
Final R-work = 0.1088, R-free = 0.1562