# Date 2008-01-16 Time 04:02:23 PST -0800 (1200484943.39 s)
#phil __OFF__

Command line arguments: "../146.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 10322
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 146

-------------------------------------------------------------------------------
  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: (68.845, 46.2261, 85.5261, 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: (68.845, 46.2261, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7343 1.96057
Completeness in resolution range: 0.972304
Completeness with d_max=infinity: 0.969225

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7343
                             d_min =   1.9606

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: (68.845, 46.2261, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7343 1.96057
Completeness in resolution range: 0.972304
Completeness with d_max=infinity: 0.969225

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7347 -  4.1945 [2119/2144]  1905   214  10.1%
  bin  2:  4.1945 -  3.3421 [2035/2053]  1834   201   9.9%
  bin  3:  3.3421 -  2.9234 [2008/2027]  1809   199   9.9%
  bin  4:  2.9234 -  2.6578 [1983/2013]  1778   205  10.3%
  bin  5:  2.6578 -  2.4682 [1983/2002]  1787   196   9.9%
  bin  6:  2.4682 -  2.3233 [1966/1991]  1772   194   9.9%
  bin  7:  2.3233 -  2.2073 [1950/1978]  1755   195  10.0%
  bin  8:  2.2073 -  2.1115 [1950/1986]  1755   195  10.0%
  bin  9:  2.1115 -  2.0305 [1931/1973]  1736   195  10.1%
  bin 10:  2.0305 -  1.9606 [1664/1980]  1499   165   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_146/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:
        1.23 -     1.96: 12
        1.96 -     2.70: 190
        2.70 -     3.43: 4639
        3.43 -     4.17: 9606
        4.17 -     4.90: 14580
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.228 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.303 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.668 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 112 " - " O   HOH Z 408 "  1.781 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.804 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 29022 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_146/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_146/model_refine_001.geo

CPU time processing inputs: 9.07


============================ 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 = 68.845 46.22605 85.5261 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 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4327   r_free= 0.4301   ksol= 0.00   Bsol= 0.00   scale= 0.936    |
|                                                                             |
| 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:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.229792                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7347 -  4.6780 0.99   1380  153 0.3451 0.3377      6.4857      6.4695|
|  2:  4.6780 -  3.7329 0.99   1313  149 0.3558 0.3382      6.6891      6.6713|
|  3:  3.7329 -  3.2669 0.99   1304  145 0.4000 0.3919      6.6165      6.6867|
|  4:  3.2669 -  2.9709 0.99   1291  136 0.4084 0.4298       6.461      6.4973|
|  5:  2.9709 -  2.7594 0.99   1269  145 0.4517 0.4118      6.3147      6.2789|
|  6:  2.7594 -  2.5977 0.99   1276  144 0.4626 0.4547      6.2497      6.1848|
|  7:  2.5977 -  2.4682 0.99   1280  143 0.4606 0.4700      6.1989      6.1428|
|  8:  2.4682 -  2.3612 0.98   1263  135 0.4819 0.4891      6.1583      6.1998|
|  9:  2.3612 -  2.2707 0.98   1251  143 0.4858 0.4862      6.0976      6.1046|
| 10:  2.2707 -  2.1926 0.99   1266  136 0.4943 0.5159      6.0952      6.0843|
| 11:  2.1926 -  2.1242 0.98   1259  142 0.4771 0.5142      6.0057      6.0474|
| 12:  2.1242 -  2.0637 0.97   1228  139 0.4959 0.4754      5.9704      6.0008|
| 13:  2.0637 -  2.0095 1.00   1264  137 0.4842 0.4645       5.872      5.8267|
| 14:  2.0095 -  1.9606 0.78    986  112 0.5017 0.4886      5.8509       5.774|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7347 -  4.6780  1380   153  0.72  32.06   0.85     0.77      62143.83|
|  2:  4.6780 -  3.7329  1313   149  0.75  31.07   0.95     0.86      86873.16|
|  3:  3.7329 -  3.2669  1304   145  0.66  38.54   0.97     0.85      93366.04|
|  4:  3.2669 -  2.9709  1291   136  0.59  44.52   0.97     0.80      84512.71|
|  5:  2.9709 -  2.7594  1269   145  0.53  49.80   0.93     0.74      66619.81|
|  6:  2.7594 -  2.5977  1276   144  0.53  49.87   0.92     0.73      56924.41|
|  7:  2.5977 -  2.4682  1280   143  0.50  51.99   0.95     0.70      53275.58|
|  8:  2.4682 -  2.3612  1263   135  0.47  54.51   0.96     0.67      50666.47|
|  9:  2.3612 -  2.2707  1251   143  0.45  56.21   0.94     0.65      47753.18|
| 10:  2.2707 -  2.1926  1266   136  0.45  55.94   0.99     0.66      42880.77|
| 11:  2.1926 -  2.1242  1259   142  0.44  56.75   0.99     0.67      40242.29|
| 12:  2.1242 -  2.0637  1228   139  0.45  56.42   0.99     0.68      35880.98|
| 13:  2.0637 -  2.0095  1264   137  0.45  56.35   1.01     0.68      30619.49|
| 14:  2.0095 -  1.9606   986   112  0.50  52.21   0.97     0.69      23119.07|
|alpha:            min =        0.65 max =            0.86 mean =         0.73|
|beta:             min =    23119.07 max =        93366.04 mean =     56170.75|
|figures of merit: min =        0.00 max =            1.00 mean =         0.54|
|phase err.(work): min =        0.00 max =           89.99 mean =        48.76|
|phase err.(test): min =        0.00 max =           89.69 mean =        48.64|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.107272              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.502   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.638276              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.531   (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 |  1.228 -  1.595:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.595 -  1.962:       10 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  1.962 -  2.329:       34 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.329 -  2.697:      156 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.697 -  3.064:     2263 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.064 -  3.431:     2376 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.431 -  3.798:     4169 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.798 -  4.166:     5437 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.166 -  4.533:     6536 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.533 -  4.900:     8044 |
|-----------------------------------------------------------------------------|
|-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 |        0.198 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.107    4.900  1.228 |       0.762 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.347)------------------------------------------|
|    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 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4327   r_free= 0.4301   ksol= 0.00   Bsol= 0.00   scale= 0.936    |
|                                                                             |
| 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:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.229792                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4226   r_free= 0.4193   ksol= 0.33   Bsol= 13.54   scale= 0.963   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.40,1.43,-0.72,0.00,-0.00,-0.00); trace/3= 0.10                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.219850                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.837026              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.318   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.896701              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.324   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4226      final r-factor (work) = 0.2763          |
| start r-factor (free) = 0.4193      final r-factor (free) = 0.3097          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.3508 = 5.84 * 0.50 * 6.2198 + 1.00 * 0.1983                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.7228 = 5.84 * 0.50 * 6.0354 + 1.00 * 0.1085                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2763      final r-factor (work) = 0.2504          |
| start r-factor (free) = 0.3097      final r-factor (free) = 0.3175          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4179 = 0.90 * 1.00 * 6.0354 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2447 = 0.90 * 1.00 * 5.8323 + 1.00 * 0.0149                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.347)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.85   18.36    None  None   None       |
|    all(noH): 2823   0      0.00    88.85   18.36    None  None   None       |
|    Sol.    : 438    0      2.94    88.85   40.55    None  None   None       |
|    Mac.    : 2385   0      0.00    85.35   14.28    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 -   8.885:  806   |   5:    44.427 -  53.312:  115        |
|      1:     8.885 -  17.771:  992   |   6:    53.312 -  62.198:   62        |
|      2:    17.771 -  26.656:  449   |   7:    62.198 -  71.083:   43        |
|      3:    26.656 -  35.542:  195   |   8:    71.083 -  79.968:   12        |
|      4:    35.542 -  44.427:  147   |   9:    79.968 -  88.854:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2504 r_free = 0.3175             target_work(ml) = 5.847         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2502 r_free = 0.3179             target_work(ml) = 5.847         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2502   r_free= 0.3179   ksol= 0.33   Bsol= 13.54   scale= 1.044   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.40,1.43,-0.72,0.00,-0.00,-0.00); trace/3= 0.10                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.847058                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2465   r_free= 0.3161   ksol= 0.32   Bsol= 28.80   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.04,-0.69,-1.12,-0.00,-0.00,-0.00); trace/3= -1.28                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.837780                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.400191              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.374   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.195324              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.769  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2465      final r-factor (work) = 0.1838          |
| start r-factor (free) = 0.3161      final r-factor (free) = 0.2358          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0222 = 3.40 * 0.50 * 5.8314 + 1.00 * 0.1083                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7834 = 3.40 * 0.50 * 5.7200 + 1.00 * 0.0588                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1838      final r-factor (work) = 0.1697          |
| start r-factor (free) = 0.2358      final r-factor (free) = 0.2183          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1320 = 0.20 * 1.00 * 5.7200 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0875 = 0.20 * 1.00 * 5.5281 + 1.00 * 0.0077                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.347)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.50    83.48   17.30    None  None   None       |
|    all(noH): 2823   0      1.50    83.48   17.30    None  None   None       |
|    Sol.    : 438    0      5.87    81.87   38.91    None  None   None       |
|    Mac.    : 2385   0      1.50    83.48   13.33    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:     1.501 -   9.699:  897   |   5:    42.493 -  50.691:  115        |
|      1:     9.699 -  17.898: 1120   |   6:    50.691 -  58.890:   74        |
|      2:    17.898 -  26.096:  303   |   7:    58.890 -  67.088:   28        |
|      3:    26.096 -  34.294:  137   |   8:    67.088 -  75.286:    9        |
|      4:    34.294 -  42.493:  138   |   9:    75.286 -  83.485:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1697 r_free = 0.2183             target_work(ml) = 5.495         |
| occupancies: max = 1.00  min = 0.16   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1693 r_free = 0.2179             target_work(ml) = 5.494         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1693   r_free= 0.2179   ksol= 0.32   Bsol= 28.80   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.04,-0.69,-1.12,-0.00,-0.00,-0.00); trace/3= -1.28                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.493515                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1694   r_free= 0.2165   ksol= 0.31   Bsol= 33.66   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.53,-1.75,-1.18,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.489676                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.643831              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.062  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.425763              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.088  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1694      final r-factor (work) = 0.1315          |
| start r-factor (free) = 0.2165      final r-factor (free) = 0.1749          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.3671 = 2.64 * 0.50 * 5.5286 + 1.00 * 0.0588                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1598 = 2.64 * 0.50 * 5.3728 + 1.00 * 0.0575                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1315      final r-factor (work) = 0.1230          |
| start r-factor (free) = 0.1749      final r-factor (free) = 0.1690          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2953 = 0.43 * 1.00 * 5.3728 + 1.00 * 0.0077                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2356 = 0.43 * 1.00 * 5.2305 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.347)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.27    90.05   17.45    None  None   None       |
|    all(noH): 2823   0      0.27    90.05   17.45    None  None   None       |
|    Sol.    : 438    0      3.00    85.94   41.39    None  None   None       |
|    Mac.    : 2385   0      0.27    90.05   13.05    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:     0.271 -   9.249:  822   |   5:    45.161 -  54.139:   99        |
|      1:     9.249 -  18.227: 1259   |   6:    54.139 -  63.117:   77        |
|      2:    18.227 -  27.205:  270   |   7:    63.117 -  72.095:   34        |
|      3:    27.205 -  36.183:  124   |   8:    72.095 -  81.073:    8        |
|      4:    36.183 -  45.161:  125   |   9:    81.073 -  90.051:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1230 r_free = 0.1690             target_work(ml) = 5.211         |
| occupancies: max = 1.00  min = 0.08   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1229 r_free = 0.1689             target_work(ml) = 5.210         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1229   r_free= 0.1689   ksol= 0.31   Bsol= 33.66   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.53,-1.75,-1.18,-0.00,-0.00,-0.00); trace/3= -1.82                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.210305                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1231   r_free= 0.1679   ksol= 0.32   Bsol= 37.54   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,-2.33,-1.45,-0.00,-0.00,-0.00); trace/3= -2.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.209069                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.636984              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.758  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.192412              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.717  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1231      final r-factor (work) = 0.1118          |
| start r-factor (free) = 0.1679      final r-factor (free) = 0.1595          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9576 = 2.64 * 0.50 * 5.2333 + 1.00 * 0.0575                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8738 = 2.64 * 0.50 * 5.1677 + 1.00 * 0.0602                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1118      final r-factor (work) = 0.1108          |
| start r-factor (free) = 0.1595      final r-factor (free) = 0.1561          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0029 = 0.19 * 1.00 * 5.1677 + 1.00 * 0.0086                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9957 = 0.19 * 1.00 * 5.1362 + 1.00 * 0.0074                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.347)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.31    89.80   16.93    None  None   None       |
|    all(noH): 2823   0      1.31    89.80   16.93    None  None   None       |
|    Sol.    : 438    0      4.33    83.56   39.20    None  None   None       |
|    Mac.    : 2385   0      1.31    89.80   12.85    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:     1.309 -  10.158: 1046   |   5:    45.555 -  54.404:   87        |
|      1:    10.158 -  19.007: 1118   |   6:    54.404 -  63.253:   67        |
|      2:    19.007 -  27.856:  222   |   7:    63.253 -  72.102:   20        |
|      3:    27.856 -  36.705:  125   |   8:    72.102 -  80.951:    6        |
|      4:    36.705 -  45.555:  127   |   9:    80.951 -  89.800:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1108 r_free = 0.1561             target_work(ml) = 5.125         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1106 r_free = 0.1561             target_work(ml) = 5.125         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1106   r_free= 0.1561   ksol= 0.32   Bsol= 37.54   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.92,-2.33,-1.45,-0.00,-0.00,-0.00); trace/3= -2.23                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.124550                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1106   r_free= 0.1562   ksol= 0.32   Bsol= 37.54   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.90,-2.36,-1.34,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.124588                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.281681              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 149.995  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.795843              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.046  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1106      final r-factor (work) = 0.1080          |
| start r-factor (free) = 0.1562      final r-factor (free) = 0.1546          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9192 = 2.28 * 0.50 * 5.1359 + 1.00 * 0.0599                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8924 = 2.28 * 0.50 * 5.1139 + 1.00 * 0.0582                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1080      final r-factor (work) = 0.1070          |
| start r-factor (free) = 0.1546      final r-factor (free) = 0.1559          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.1914 = 1.80 * 1.00 * 5.1139 + 1.00 * 0.0075                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.1730 = 1.80 * 1.00 * 5.1030 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.347)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.35    92.89   17.01    None  None   None       |
|    all(noH): 2823   0      0.35    92.89   17.01    None  None   None       |
|    Sol.    : 438    0      5.79    85.03   40.06    None  None   None       |
|    Mac.    : 2385   0      0.35    92.89   12.78    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.350 -   9.604:  975   |   5:    46.619 -  55.873:  103        |
|      1:     9.604 -  18.858: 1171   |   6:    55.873 -  65.127:   54        |
|      2:    18.858 -  28.112:  229   |   7:    65.127 -  74.381:   23        |
|      3:    28.112 -  37.365:  138   |   8:    74.381 -  83.635:    6        |
|      4:    37.365 -  46.619:  119   |   9:    83.635 -  92.889:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1070 r_free = 0.1559             target_work(ml) = 5.109         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1069 r_free = 0.1559             target_work(ml) = 5.109         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1069   r_free= 0.1559   ksol= 0.32   Bsol= 37.54   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.90,-2.36,-1.34,-0.00,-0.00,-0.00); trace/3= -2.20                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.108559                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7347 -  4.6780 0.99   1380  153 0.0980 0.1237      5.3683      5.5232|
|  2:  4.6780 -  3.7329 0.99   1313  149 0.0826 0.1153      5.4254      5.6306|
|  3:  3.7329 -  3.2669 0.99   1304  145 0.1038 0.1546       5.466      5.8571|
|  4:  3.2669 -  2.9709 0.99   1291  136 0.1149 0.1535      5.4114      5.5622|
|  5:  2.9709 -  2.7594 0.99   1269  145 0.1224 0.1679       5.275      5.4866|
|  6:  2.7594 -  2.5977 0.99   1276  144 0.1127 0.1761        5.16      5.3886|
|  7:  2.5977 -  2.4682 0.99   1280  143 0.1166 0.1591       5.111       5.349|
|  8:  2.4682 -  2.3612 0.98   1263  135 0.1123 0.1660      5.0463      5.3311|
|  9:  2.3612 -  2.2707 0.98   1251  143 0.1108 0.1752      4.9911        5.27|
| 10:  2.2707 -  2.1926 0.99   1266  136 0.1052 0.1750      4.9282      5.1825|
| 11:  2.1926 -  2.1242 0.98   1259  142 0.1088 0.1722      4.9114       5.219|
| 12:  2.1242 -  2.0637 0.97   1228  139 0.1083 0.1586      4.8534       5.186|
| 13:  2.0637 -  2.0095 1.00   1264  137 0.1046 0.1743      4.7605      5.0395|
| 14:  2.0095 -  1.9606 0.78    986  112 0.0988 0.1756      4.6459      4.9415|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7347 -  4.6780  1380   153  0.94   8.98   0.99     0.96       6968.64|
|  2:  4.6780 -  3.7329  1313   149  0.95   7.89   1.03     1.02       9057.50|
|  3:  3.7329 -  3.2669  1304   145  0.94  11.07   1.04     1.03      10253.52|
|  4:  3.2669 -  2.9709  1291   136  0.93  12.64   1.02     1.01       9457.71|
|  5:  2.9709 -  2.7594  1269   145  0.91  14.88   1.01     0.98       7586.10|
|  6:  2.7594 -  2.5977  1276   144  0.91  14.87   0.99     0.96       6428.68|
|  7:  2.5977 -  2.4682  1280   143  0.91  15.17   0.99     0.95       5724.38|
|  8:  2.4682 -  2.3612  1263   135  0.91  14.39   1.00     0.98       5023.67|
|  9:  2.3612 -  2.2707  1251   143  0.91  14.70   1.02     0.99       4724.57|
| 10:  2.2707 -  2.1926  1266   136  0.90  15.23   1.00     0.97       4180.35|
| 11:  2.1926 -  2.1242  1259   142  0.91  15.50   1.01     0.97       4214.31|
| 12:  2.1242 -  2.0637  1228   139  0.91  15.12   1.02     1.01       3801.18|
| 13:  2.0637 -  2.0095  1264   137  0.91  15.18   1.01     1.00       3212.04|
| 14:  2.0095 -  1.9606   986   112  0.92  14.10   0.99     0.96       2511.77|
|alpha:            min =        0.95 max =            1.03 mean =         0.99|
|beta:             min =     2511.77 max =        10253.52 mean =      6029.76|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.80 mean =        13.49|
|phase err.(test): min =        0.00 max =           89.97 mean =        13.18|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1069   r_free= 0.1559   ksol= 0.32   Bsol= 40.03   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.75,-2.25,-1.18,-0.00,-0.00,-0.00); trace/3= -2.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.108180                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.73 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1069   r_free= 0.1559   ksol= 0.32   Bsol= 40.03   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.75,-2.25,-1.18,-0.00,-0.00,-0.00); trace/3= -2.06                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.108180                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7347 -  4.6780 0.99   1380  153 0.0981 0.1238      5.3683      5.5231|
|  2:  4.6780 -  3.7329 0.99   1313  149 0.0828 0.1154       5.427      5.6315|
|  3:  3.7329 -  3.2669 0.99   1304  145 0.1040 0.1547      5.4669      5.8584|
|  4:  3.2669 -  2.9709 0.99   1291  136 0.1149 0.1534      5.4113      5.5614|
|  5:  2.9709 -  2.7594 0.99   1269  145 0.1224 0.1676      5.2742      5.4855|
|  6:  2.7594 -  2.5977 0.99   1276  144 0.1125 0.1758       5.159       5.387|
|  7:  2.5977 -  2.4682 0.99   1280  143 0.1165 0.1589      5.1098      5.3478|
|  8:  2.4682 -  2.3612 0.98   1263  135 0.1122 0.1658      5.0452      5.3297|
|  9:  2.3612 -  2.2707 0.98   1251  143 0.1107 0.1753      4.9904      5.2702|
| 10:  2.2707 -  2.1926 0.99   1266  136 0.1051 0.1748      4.9279      5.1817|
| 11:  2.1926 -  2.1242 0.98   1259  142 0.1087 0.1721      4.9109      5.2183|
| 12:  2.1242 -  2.0637 0.97   1228  139 0.1082 0.1586      4.8528      5.1855|
| 13:  2.0637 -  2.0095 1.00   1264  137 0.1047 0.1741        4.76      5.0388|
| 14:  2.0095 -  1.9606 0.78    986  112 0.0987 0.1754      4.6449        4.94|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7347 -  4.6780  1380   153  0.94   8.98   0.99     0.96       6970.33|
|  2:  4.6780 -  3.7329  1313   149  0.95   7.90   1.03     1.02       9068.84|
|  3:  3.7329 -  3.2669  1304   145  0.94  11.08   1.04     1.04      10266.91|
|  4:  3.2669 -  2.9709  1291   136  0.93  12.63   1.02     1.01       9451.81|
|  5:  2.9709 -  2.7594  1269   145  0.91  14.86   1.01     0.99       7571.77|
|  6:  2.7594 -  2.5977  1276   144  0.91  14.85   0.99     0.97       6414.32|
|  7:  2.5977 -  2.4682  1280   143  0.91  15.14   0.99     0.96       5704.37|
|  8:  2.4682 -  2.3612  1263   135  0.91  14.37   1.01     0.99       5011.13|
|  9:  2.3612 -  2.2707  1251   143  0.91  14.70   1.02     1.00       4717.86|
| 10:  2.2707 -  2.1926  1266   136  0.90  15.22   1.01     0.97       4179.26|
| 11:  2.1926 -  2.1242  1259   142  0.91  15.48   1.01     0.98       4208.35|
| 12:  2.1242 -  2.0637  1228   139  0.91  15.11   1.03     1.02       3795.78|
| 13:  2.0637 -  2.0095  1264   137  0.91  15.16   1.02     1.01       3205.72|
| 14:  2.0095 -  1.9606   986   112  0.92  14.08   1.00     0.97       2505.51|
|alpha:            min =        0.96 max =            1.04 mean =         0.99|
|beta:             min =     2505.51 max =        10266.91 mean =      6024.71|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.48|
|phase err.(test): min =        0.00 max =           89.81 mean =        13.17|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.347)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.34    92.88   17.00    None  None   None       |
|    all(noH): 2823   0      0.34    92.88   17.00    None  None   None       |
|    Sol.    : 438    0      5.78    85.02   40.05    None  None   None       |
|    Mac.    : 2385   0      0.34    92.88   12.77    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.340 -   9.593:  975   |   5:    46.609 -  55.863:  103        |
|      1:     9.593 -  18.847: 1171   |   6:    55.863 -  65.117:   54        |
|      2:    18.847 -  28.101:  229   |   7:    65.117 -  74.371:   23        |
|      3:    28.101 -  37.355:  138   |   8:    74.371 -  83.625:    6        |
|      4:    37.355 -  46.609:  119   |   9:    83.625 -  92.879:    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)= 291         
Filter by distance & map next to the model:
   mapped sites are within: 0.536 - 4.040
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 287 from: 291
   mapped sites are within: 0.748 - 4.040

peak=    6.505 closest distance to " O   HOH Z 142 " =    1.947
peak=    6.287 closest distance to " NE2 GLN A  11 " =    1.179
peak=    5.884 closest distance to " O   HOH Z 126 " =    1.965
peak=    5.862 closest distance to " O   HOH Z 236 " =    1.480
peak=    5.556 closest distance to " CB  ARG A 275 " =    0.923
peak=    5.302 closest distance to " CG  PRO A  54 " =    1.224
peak=    5.247 closest distance to " NH2 ARG A  56 " =    2.077
peak=    4.960 closest distance to " CG  PRO A 213 " =    1.263
peak=    4.914 closest distance to " O   HOH Z 427 " =    2.601
peak=    4.863 closest distance to " O   HOH Z 193 " =    1.687
peak=    4.858 closest distance to " O   HOH Z  78 " =    1.692
peak=    4.799 closest distance to " O   HOH Z 369 " =    2.208
peak=    4.764 closest distance to " CB  SER A  63 " =    1.150
peak=    4.742 closest distance to " O   HOH Z 272 " =    1.849
peak=    4.704 closest distance to " O   HOH Z 209 " =    2.201
peak=    4.667 closest distance to " O   HOH Z 371 " =    1.873
peak=    4.576 closest distance to " CB  GLN A 183 " =    1.207
peak=    4.545 closest distance to " CB  GLN A 223 " =    1.554
peak=    4.477 closest distance to " CB  GLU A 152 " =    1.271
peak=    4.447 closest distance to " C   PRO A 198 " =    1.441
peak=    4.446 closest distance to " OG BSER A 164 " =    2.181
peak=    4.430 closest distance to " O   HOH Z 232 " =    2.397
peak=    4.429 closest distance to " O   HOH Z 375 " =    1.019
peak=    4.417 closest distance to " O   HOH Z 287 " =    1.755
peak=    4.409 closest distance to " CB  ARG A  79 " =    1.322
peak=    4.366 closest distance to " CG2 VAL A 257 " =    0.868
peak=    4.338 closest distance to " O   HOH Z 316 " =    2.952
peak=    4.332 closest distance to " NZ  LYS A 117 " =    2.995
peak=    4.329 closest distance to " O   HOH Z 203 " =    1.698
peak=    4.310 closest distance to " CG  ARG A  66 " =    2.410
peak=    4.297 closest distance to " O   HOH Z 425 " =    2.053
peak=    4.272 closest distance to " O   HOH Z 124 " =    1.346
peak=    4.256 closest distance to " CB  ASN A 148 " =    1.415
peak=    4.252 closest distance to " O   SER A  87 " =    2.240
peak=    4.235 closest distance to " O   HOH Z 112 " =    1.206
peak=    4.209 closest distance to " O   HOH Z 327 " =    1.665
peak=    4.197 closest distance to " O   HOH Z 213 " =    1.632
peak=    4.195 closest distance to " O   HOH Z  44 " =    1.821
peak=    4.192 closest distance to " O   HOH Z 128 " =    2.000
peak=    4.173 closest distance to " CA  TYR A  30 " =    0.933
peak=    4.173 closest distance to " O   HOH Z 403 " =    1.732
peak=    4.132 closest distance to " O   HOH Z 407 " =    2.333
peak=    4.132 closest distance to " O   HOH Z 303 " =    2.199
peak=    4.129 closest distance to " O   HOH Z 419 " =    2.044
peak=    4.119 closest distance to " O   HOH Z   9 " =    2.306
peak=    4.116 closest distance to " O   HOH Z 289 " =    1.645
peak=    4.104 closest distance to " CB  PRO A  54 " =    0.953
peak=    4.101 closest distance to " CB  SER A   3 " =    1.250
peak=    4.094 closest distance to " O   HOH Z 189 " =    1.862
peak=    4.091 closest distance to " O   HOH Z 298 " =    1.851
peak=    4.070 closest distance to " O   HOH Z 132 " =    2.049
peak=    4.050 closest distance to " O   HOH Z 417 " =    1.208
peak=    4.046 closest distance to " O   HOH Z 368 " =    3.559
peak=    4.039 closest distance to " O   HOH Z  61 " =    1.691
peak=    4.037 closest distance to " O   HOH Z   1 " =    1.846
peak=    4.019 closest distance to " O   HOH Z   6 " =    2.109
peak=    3.993 closest distance to " CB  SER A  26 " =    1.620
peak=    3.974 closest distance to " O   HOH Z 344 " =    3.179
peak=    3.969 closest distance to " O   HOH Z 245 " =    1.326
peak=    3.938 closest distance to " O   HOH Z  93 " =    2.022
peak=    3.934 closest distance to " CB  VAL A 265 " =    1.270
peak=    3.931 closest distance to " O   HOH Z 368 " =    2.013
peak=    3.931 closest distance to " CD2 TRP A 179 " =    1.367
peak=    3.912 closest distance to " O   HOH Z 250 " =    1.513
peak=    3.911 closest distance to " ND2 ASN A 187 " =    1.421
peak=    3.906 closest distance to " CG1 ILE A  33 " =    1.259
peak=    3.886 closest distance to " CD2 LEU A 297 " =    1.010
peak=    3.886 closest distance to " O   HOH Z 402 " =    1.391
peak=    3.878 closest distance to " CB  ARG A 190 " =    1.647
peak=    3.876 closest distance to " CG  PRO A 198 " =    1.252
peak=    3.874 closest distance to " O   HOH Z 234 " =    3.446
peak=    3.861 closest distance to " CB  GLU A 128 " =    1.055
peak=    3.858 closest distance to " O   HOH Z  59 " =    1.555
peak=    3.857 closest distance to " O   HOH Z  61 " =    1.434
peak=    3.855 closest distance to " O   HOH Z  66 " =    2.117
peak=    3.840 closest distance to " O   HOH Z 423 " =    2.456
peak=    3.835 closest distance to " O   HOH Z  92 " =    1.155
peak=    3.807 closest distance to " O   HOH Z   3 " =    1.984
peak=    3.791 closest distance to " O   HOH Z   1 " =    1.488
peak=    3.789 closest distance to " O   HOH Z 144 " =    2.035
peak=    3.756 closest distance to " CG  PRO A 243 " =    1.144
peak=    3.729 closest distance to " O   HOH Z 128 " =    1.994
peak=    3.719 closest distance to " O   HOH Z 380 " =    1.632
peak=    3.717 closest distance to " O   HOH Z 286 " =    2.304
peak=    3.716 closest distance to " CB  TRP A 179 " =    1.240
peak=    3.694 closest distance to " CG AARG A 275 " =    1.021
peak=    3.690 closest distance to " O   HOH Z 193 " =    1.994
peak=    3.689 closest distance to " CG  MET A 185 " =    1.240
peak=    3.682 closest distance to " O   HOH Z 357 " =    1.792
peak=    3.681 closest distance to " O   HOH Z 423 " =    1.340
peak=    3.677 closest distance to " CB  ARG A 139 " =    1.074
peak=    3.675 closest distance to " CA  ALA A  84 " =    1.296
peak=    3.664 closest distance to " OD1 ASN A  69 " =    2.601
peak=    3.661 closest distance to " O   HOH Z  54 " =    1.689
peak=    3.653 closest distance to " CE  LYS A  76 " =    0.781
peak=    3.651 closest distance to " O   HOH Z 112 " =    2.315
peak=    3.645 closest distance to " OD1 ASN A 148 " =    1.691
peak=    3.645 closest distance to " CB  LEU A 228 " =    1.076
peak=    3.639 closest distance to " OG BSER A  99 " =    2.354
peak=    3.637 closest distance to " O   HOH Z 392 " =    2.918
peak=    3.626 closest distance to " O   HOH Z 158 " =    2.854
peak=    3.625 closest distance to " CG  PRO A  90 " =    1.127
peak=    3.618 closest distance to " NH1BARG A 145 " =    1.363
peak=    3.614 closest distance to " O   HOH Z 371 " =    3.084
peak=    3.612 closest distance to " O   HOH Z  97 " =    1.965
peak=    3.610 closest distance to " O   HOH Z 415 " =    3.526
peak=    3.609 closest distance to " C   ALA A 299 " =    0.975
peak=    3.608 closest distance to " CB  GLU A 277 " =    3.459
peak=    3.605 closest distance to " NH1AARG A 145 " =    1.212
peak=    3.603 closest distance to " O   HOH Z  10 " =    1.785
peak=    3.596 closest distance to " CE AMET A  47 " =    1.303
peak=    3.576 closest distance to " O   HOH Z 207 " =    1.654
peak=    3.576 closest distance to " O   HOH Z 305 " =    3.391
peak=    3.576 closest distance to " CG2 ILE A 120 " =    1.063
peak=    3.572 closest distance to " CB  THR A  31 " =    1.682
peak=    3.570 closest distance to " O   HOH Z 146 " =    1.688
peak=    3.569 closest distance to " CB  TYR A 169 " =    0.955
peak=    3.558 closest distance to " O   HOH Z 147 " =    1.701
peak=    3.555 closest distance to " O   HOH Z 175 " =    2.075
peak=    3.554 closest distance to " CB  TRP A 266 " =    1.135
peak=    3.520 closest distance to " O   HOH Z 261 " =    2.271
peak=    3.520 closest distance to " O  BHOH Z 338 " =    2.358
peak=    3.510 closest distance to " CA  ASN A 215 " =    1.059
peak=    3.507 closest distance to " O   HOH Z  88 " =    2.439
peak=    3.506 closest distance to " CB  ALA A 114 " =    1.409
peak=    3.503 closest distance to " O   HOH Z 425 " =    1.274
peak=    3.499 closest distance to " NZ  LYS A 119 " =    2.771
peak=    3.496 closest distance to " O   HOH Z 389 " =    1.626
peak=    3.496 closest distance to " O   HOH Z 257 " =    2.092
peak=    3.496 closest distance to " O   HOH Z  40 " =    1.903
peak=    3.492 closest distance to " OE2 GLU A  53 " =    2.082
peak=    3.488 closest distance to " N   PHE A 130 " =    1.241
peak=    3.487 closest distance to " O   HOH Z 426 " =    1.844
peak=    3.482 closest distance to " O   HOH Z 411 " =    3.680
peak=    3.480 closest distance to " O   HOH Z 336 " =    1.788
peak=    3.478 closest distance to " NE2 GLN A  73 " =    3.594
peak=    3.473 closest distance to " CA  ALA A 233 " =    0.893
peak=    3.470 closest distance to " CG  GLN A  77 " =    2.258
peak=    3.459 closest distance to " CB  ILE A 120 " =    1.360
peak=    3.459 closest distance to " OG  SER A  62 " =    2.812
peak=    3.458 closest distance to " O   HOH Z 234 " =    1.898
peak=    3.455 closest distance to " O   HOH Z 313 " =    1.639
peak=    3.454 closest distance to " CB  THR A 157 " =    1.082
peak=    3.452 closest distance to " CB  VAL A 202 " =    1.567
peak=    3.448 closest distance to " O   ALA A   1 " =    1.599
peak=    3.447 closest distance to " O   HOH Z 346 " =    1.438
peak=    3.442 closest distance to " O   HOH Z  88 " =    2.351
peak=    3.438 closest distance to " O   HOH Z 244 " =    1.681
peak=    3.435 closest distance to " NH2BARG A 145 " =    2.088
peak=    3.434 closest distance to " O   HOH Z 222 " =    2.361
peak=    3.431 closest distance to " O   HOH Z  43 " =    1.799
peak=    3.429 closest distance to " CA  ALA A  21 " =    1.091
peak=    3.425 closest distance to " O  BHOH Z  74 " =    1.424
peak=    3.423 closest distance to " CA  ASP A 162 " =    1.040
peak=    3.422 closest distance to " O   HOH Z 284 " =    2.721
peak=    3.418 closest distance to " O   HOH Z 153 " =    1.607
peak=    3.411 closest distance to " O   HOH Z 283 " =    2.255
peak=    3.408 closest distance to " NH1 ARG A  14 " =    1.236
peak=    3.401 closest distance to " CB  ALA A  34 " =    1.146
peak=    3.399 closest distance to " O   HOH Z 365 " =    2.683
peak=    3.396 closest distance to " O   HOH Z 337 " =    3.397
peak=    3.396 closest distance to " CB  VAL A 126 " =    1.126
peak=    3.394 closest distance to " CG  GLU A 277 " =    1.999
peak=    3.393 closest distance to " OD2 ASP A 286 " =    2.561
peak=    3.391 closest distance to " CB  GLN A  89 " =    1.402
peak=    3.385 closest distance to " CA  SER A 146 " =    1.793
peak=    3.378 closest distance to " N   ASN A  39 " =    1.165
peak=    3.370 closest distance to " CA  PHE A 283 " =    1.261
peak=    3.370 closest distance to " O   HOH Z 106 " =    2.624
peak=    3.359 closest distance to " O   HOH Z 362 " =    2.524
peak=    3.356 closest distance to " O   HOH Z  94 " =    1.909
peak=    3.354 closest distance to " N   ARG A 156 " =    1.284
peak=    3.353 closest distance to " CB  ASN A 110 " =    1.050
peak=    3.351 closest distance to " O   HOH Z 302 " =    1.582
peak=    3.348 closest distance to " CD BLYS A 290 " =    1.219
peak=    3.339 closest distance to " O   HOH Z 217 " =    2.305
peak=    3.339 closest distance to " O   HOH Z 272 " =    2.077
peak=    3.337 closest distance to " O   HOH Z 126 " =    1.453
peak=    3.336 closest distance to " CB  THR A 279 " =    1.686
peak=    3.332 closest distance to " O   HOH Z 173 " =    2.133
peak=    3.332 closest distance to " O   HOH Z 189 " =    2.297
peak=    3.327 closest distance to " CB  LYS A 117 " =    1.168
peak=    3.324 closest distance to " N   GLU A   2 " =    1.410
peak=    3.323 closest distance to " OD1BASN A 224 " =    2.183
peak=    3.322 closest distance to " CG2 THR A 221 " =    1.091
peak=    3.320 closest distance to " CB  SER A 273 " =    0.820
peak=    3.319 closest distance to " O   HOH Z 437 " =    1.673
peak=    3.318 closest distance to " CG2 THR A 294 " =    1.572
peak=    3.317 closest distance to " O   HOH Z 345 " =    3.225
peak=    3.311 closest distance to " O   HOH Z  47 " =    1.445
peak=    3.310 closest distance to " CB  ALA A  21 " =    1.909
peak=    3.308 closest distance to " O   HOH Z 433 " =    1.830
peak=    3.308 closest distance to " CB  LEU A 300 " =    0.936
peak=    3.308 closest distance to " N   ASP A 162 " =    1.213
peak=    3.307 closest distance to " OG  SER A  22 " =    2.610
peak=    3.307 closest distance to " O   HOH Z  85 " =    2.266
peak=    3.302 closest distance to " O   HOH Z 180 " =    2.258
peak=    3.301 closest distance to " O   HOH Z 132 " =    1.146
peak=    3.293 closest distance to " CB  MET A 188 " =    1.555
peak=    3.292 closest distance to " CA  THR A 264 " =    0.806
peak=    3.286 closest distance to " CG2BVAL A  41 " =    0.761
peak=    3.284 closest distance to " O   HOH Z 214 " =    2.322
peak=    3.284 closest distance to " CG1 ILE A 151 " =    0.987
peak=    3.281 closest distance to " CB  ASN A  39 " =    0.829
peak=    3.280 closest distance to " CD  LYS A 166 " =    1.251
peak=    3.277 closest distance to " CB  ALA A 291 " =    1.367
peak=    3.276 closest distance to " O   HOH Z 298 " =    2.573
peak=    3.275 closest distance to " O   HOH Z 172 " =    3.090
peak=    3.270 closest distance to " CB  SER A  62 " =    1.394
peak=    3.268 closest distance to " O   HOH Z 422 " =    2.536
peak=    3.267 closest distance to " O   HOH Z 109 " =    2.420
peak=    3.263 closest distance to " O   HOH Z  71 " =    1.863
peak=    3.262 closest distance to " CB  TYR A 169 " =    0.868
peak=    3.258 closest distance to " ND1 HIS A  86 " =    1.837
peak=    3.258 closest distance to " O   HOH Z 218 " =    2.114
peak=    3.255 closest distance to " O   HOH Z 227 " =    1.808
peak=    3.249 closest distance to " O   HOH Z 406 " =    1.592
peak=    3.248 closest distance to " CD1 ILE A  49 " =    1.478
peak=    3.245 closest distance to " CA  MET A  40 " =    1.111
peak=    3.244 closest distance to " O   ASN A  74 " =    1.573
peak=    3.243 closest distance to " O   HOH Z  43 " =    2.641
peak=    3.241 closest distance to " O   HOH Z 251 " =    1.654
peak=    3.239 closest distance to " N   TYR A 116 " =    1.562
peak=    3.238 closest distance to " OE1 GLN A  11 " =    2.044
peak=    3.236 closest distance to " O   HOH Z   2 " =    1.435
peak=    3.235 closest distance to " O   HOH Z 213 " =    1.841
peak=    3.234 closest distance to " O   HOH Z 423 " =    1.859
peak=    3.233 closest distance to " O   HOH Z  88 " =    2.945
peak=    3.221 closest distance to " CE  LYS A 119 " =    1.264
peak=    3.217 closest distance to " O   HOH Z  59 " =    1.884
peak=    3.216 closest distance to " CG  MET A 113 " =    0.925
peak=    3.216 closest distance to " O   HOH Z  24 " =    1.560
peak=    3.210 closest distance to " O   HOH Z 108 " =    2.116
peak=    3.205 closest distance to " CG1BVAL A  72 " =    1.330
peak=    3.204 closest distance to " CA  ILE A 234 " =    1.046
peak=    3.203 closest distance to " O   HOH Z 432 " =    1.746
peak=    3.201 closest distance to " O   HOH Z 388 " =    1.938
peak=    3.201 closest distance to " NH1 ARG A 138 " =    1.175
peak=    3.196 closest distance to " O   HOH Z 313 " =    1.884
peak=    3.190 closest distance to " CZ  PHE A 218 " =    0.999
peak=    3.190 closest distance to " CB  HIS A 108 " =    0.830
peak=    3.185 closest distance to " O   GLY A 147 " =    1.579
peak=    3.182 closest distance to " CD  PRO A 243 " =    1.556
peak=    3.178 closest distance to " CA  LEU A 300 " =    0.953
peak=    3.178 closest distance to " O   HOH Z 271 " =    1.963
peak=    3.175 closest distance to " O   HOH Z 291 " =    1.496
peak=    3.172 closest distance to " CB  PRO A 163 " =    4.040
peak=    3.171 closest distance to " O   HOH Z  63 " =    1.446
peak=    3.169 closest distance to " O   HOH Z  49 " =    2.068
peak=    3.167 closest distance to " CD1 ILE A 239 " =    1.244
peak=    3.166 closest distance to " N   GLN A 278 " =    1.080
peak=    3.160 closest distance to " O   HOH Z  89 " =    2.095
peak=    3.156 closest distance to " CB  ASP A 140 " =    0.910
peak=    3.153 closest distance to " CG2 VAL A 197 " =    1.021
peak=    3.149 closest distance to " CB  GLN A  88 " =    1.271
peak=    3.144 closest distance to " O   HOH Z 194 " =    1.807
peak=    3.141 closest distance to " O   HOH Z 188 " =    2.446
peak=    3.141 closest distance to " O   HOH Z  20 " =    3.665
peak=    3.141 closest distance to " O   HOH Z  80 " =    1.945
peak=    3.134 closest distance to " CB  LYS A 290 " =    1.282
peak=    3.133 closest distance to " O   HOH Z 248 " =    1.571
peak=    3.131 closest distance to " O   HOH Z 265 " =    2.149
peak=    3.128 closest distance to " O   HOH Z 128 " =    1.552
peak=    3.127 closest distance to " O   ASP A 124 " =    1.299
peak=    3.127 closest distance to " O   HOH Z 329 " =    3.699
peak=    3.125 closest distance to " CA  ALA A 291 " =    0.829
peak=    3.124 closest distance to " O   HOH Z  47 " =    1.677
peak=    3.124 closest distance to " CB  TYR A 116 " =    0.831
peak=    3.124 closest distance to " CB  SER A 216 " =    0.748
peak=    3.122 closest distance to " CB  ASP A 171 " =    1.409
peak=    3.121 closest distance to " CA  MET A 105 " =    0.899
peak=    3.117 closest distance to " O   HOH Z 291 " =    1.738
peak=    3.114 closest distance to " CG1BVAL A  72 " =    1.247
peak=    3.111 closest distance to " CB  GLN A 278 " =    0.819
peak=    3.105 closest distance to " CA  ARG A 195 " =    1.241
peak=    3.099 closest distance to " CE  LYS A 166 " =    1.834
peak=    3.091 closest distance to " O   HOH Z 163 " =    1.695
peak=    3.088 closest distance to " O   HOH Z 421 " =    1.841
peak=    3.084 closest distance to " CD2 HIS A  81 " =    1.021
peak=    3.076 closest distance to " CA  ALA A 158 " =    1.195
peak=    3.075 closest distance to " O   HOH Z 266 " =    3.155
peak=    3.072 closest distance to " CD1 ILE A 106 " =    0.865
peak=    3.071 closest distance to " CB  ALA A 248 " =    1.532
peak=    3.065 closest distance to " CB  LEU A 255 " =    0.761
peak=    3.032 closest distance to " OD1 ASP A 231 " =    1.946
peak=    3.022 closest distance to " O   HOH Z  66 " =    1.921
peak=    3.009 closest distance to " O   HOH Z 305 " =    3.046

                           ----------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: 0.750 - 5.905
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 204 from: 205
   mapped sites are within: 0.750 - 5.905

peak=   -4.574 closest distance to " C   HIS A 108 " =    1.131
peak=   -4.573 closest distance to " O   HOH Z 266 " =    4.692
peak=   -4.477 closest distance to " CA  VAL A  67 " =    2.833
peak=   -4.331 closest distance to " CD  ARG A 156 " =    2.064
peak=   -4.318 closest distance to " OG BSER A 134 " =    1.356
peak=   -4.313 closest distance to " N   GLN A  58 " =    1.670
peak=   -4.253 closest distance to " CB  PRO A 243 " =    2.585
peak=   -4.222 closest distance to " O   HOH Z 377 " =    2.145
peak=   -4.215 closest distance to " OD2 ASP A 191 " =    1.374
peak=   -4.185 closest distance to " O   HOH Z 372 " =    2.461
peak=   -4.143 closest distance to " CD1 LEU A 255 " =    2.862
peak=   -4.129 closest distance to " O   PRO A 198 " =    1.310
peak=   -4.107 closest distance to " OD2 ASP A 171 " =    2.136
peak=   -4.073 closest distance to " CD  ARG A  14 " =    3.248
peak=   -4.071 closest distance to " O   HOH Z 290 " =    1.154
peak=   -4.052 closest distance to " O   ALA A 161 " =    1.596
peak=   -4.020 closest distance to " CG  PHE A 283 " =    2.582
peak=   -4.017 closest distance to " CG  GLN A 223 " =    1.796
peak=   -4.015 closest distance to " OG  SER A   3 " =    1.646
peak=   -3.970 closest distance to " O   VAL A  67 " =    2.644
peak=   -3.961 closest distance to " CG1 VAL A 112 " =    2.833
peak=   -3.960 closest distance to " ND2 ASN A  45 " =    1.025
peak=   -3.937 closest distance to " O   HOH Z 198 " =    1.773
peak=   -3.925 closest distance to " CE  MET A 105 " =    2.316
peak=   -3.923 closest distance to " CZ  PHE A  59 " =    1.394
peak=   -3.908 closest distance to " O   HOH Z 351 " =    1.563
peak=   -3.897 closest distance to " OXT GLY A 302 " =    2.766
peak=   -3.880 closest distance to " CB  ASN A  39 " =    2.263
peak=   -3.820 closest distance to " O   HOH Z 102 " =    1.601
peak=   -3.820 closest distance to " OD1 ASP A 191 " =    1.860
peak=   -3.816 closest distance to " O   SER A 135 " =    1.468
peak=   -3.814 closest distance to " N   HIS A 115 " =    2.186
peak=   -3.813 closest distance to " CZ  TYR A 169 " =    1.788
peak=   -3.803 closest distance to " OD1 ASP A 191 " =    1.448
peak=   -3.799 closest distance to " CB  ALA A 291 " =    2.371
peak=   -3.793 closest distance to " CG  GLN A  58 " =    1.121
peak=   -3.792 closest distance to " O   HOH Z  24 " =    1.257
peak=   -3.771 closest distance to " O   ARG A 145 " =    1.546
peak=   -3.760 closest distance to " O   SER A 146 " =    0.983
peak=   -3.755 closest distance to " O   HOH Z 429 " =    1.987
peak=   -3.745 closest distance to " CB  PHE A 192 " =    1.859
peak=   -3.745 closest distance to " O   VAL A 189 " =    2.538
peak=   -3.728 closest distance to " O   HOH Z 389 " =    1.868
peak=   -3.714 closest distance to " O   HOH Z  52 " =    1.162
peak=   -3.690 closest distance to " O   HOH Z 313 " =    1.807
peak=   -3.689 closest distance to " O   PHE A 218 " =    1.538
peak=   -3.680 closest distance to " CB  TYR A  15 " =    2.135
peak=   -3.677 closest distance to " N   ALA A 248 " =    1.618
peak=   -3.650 closest distance to " O   HOH Z 231 " =    2.301
peak=   -3.649 closest distance to " O   HOH Z 407 " =    2.753
peak=   -3.639 closest distance to " CA  GLY A  98 " =    1.861
peak=   -3.634 closest distance to " CG1 VAL A 230 " =    1.890
peak=   -3.630 closest distance to " O   HOH Z 131 " =    4.003
peak=   -3.629 closest distance to " CD1 LEU A 101 " =    2.272
peak=   -3.622 closest distance to " O   HOH Z  52 " =    1.779
peak=   -3.608 closest distance to " O   PRO A 198 " =    1.284
peak=   -3.606 closest distance to " O   HOH Z  13 " =    1.488
peak=   -3.585 closest distance to " O   HOH Z 185 " =    2.072
peak=   -3.577 closest distance to " ND2 ASN A  39 " =    1.325
peak=   -3.577 closest distance to " CD1 PHE A  59 " =    1.983
peak=   -3.571 closest distance to " OD1 ASP A 171 " =    1.593
peak=   -3.570 closest distance to " O   HOH Z 114 " =    3.019
peak=   -3.555 closest distance to " CG  PRO A 243 " =    1.579
peak=   -3.554 closest distance to " CD  ARG A 139 " =    1.488
peak=   -3.552 closest distance to " CB  ALA A 291 " =    2.118
peak=   -3.546 closest distance to " O   HOH Z 134 " =    3.045
peak=   -3.544 closest distance to " O   ALA A  51 " =    1.187
peak=   -3.543 closest distance to " O   HOH Z 263 " =    2.936
peak=   -3.542 closest distance to " CE2 TYR A  30 " =    2.739
peak=   -3.540 closest distance to " CB  ILE A  33 " =    2.904
peak=   -3.538 closest distance to " CG  ASP A 231 " =    0.750
peak=   -3.531 closest distance to " CG2 THR A 178 " =    2.300
peak=   -3.524 closest distance to " O   HOH Z 385 " =    1.828
peak=   -3.522 closest distance to " CE1 TYR A 169 " =    2.399
peak=   -3.516 closest distance to " N   ASP A 286 " =    2.214
peak=   -3.513 closest distance to " O   SER A  95 " =    1.380
peak=   -3.508 closest distance to " O   HOH Z  37 " =    1.670
peak=   -3.507 closest distance to " CD1 LEU A 228 " =    1.995
peak=   -3.507 closest distance to " CB  ALA A 244 " =    2.003
peak=   -3.502 closest distance to " O   HOH Z  43 " =    1.899
peak=   -3.489 closest distance to " O   HOH Z 298 " =    1.241
peak=   -3.480 closest distance to " O   HOH Z  90 " =    2.314
peak=   -3.476 closest distance to " O   ALA A  34 " =    2.361
peak=   -3.476 closest distance to " CB  PRO A 163 " =    2.482
peak=   -3.475 closest distance to " CA  GLY A 203 " =    2.192
peak=   -3.474 closest distance to " NH1 ARG A 195 " =    2.634
peak=   -3.474 closest distance to " CD1 ILE A 239 " =    2.523
peak=   -3.467 closest distance to " O   HOH Z 265 " =    1.849
peak=   -3.467 closest distance to " O   HOH Z  11 " =    1.774
peak=   -3.467 closest distance to " CB  ASP A 132 " =    2.355
peak=   -3.463 closest distance to " O   HOH Z 126 " =    1.897
peak=   -3.462 closest distance to " O   HOH Z 256 " =    1.358
peak=   -3.461 closest distance to " N   ALA A  43 " =    2.348
peak=   -3.458 closest distance to " ND2 ASN A 187 " =    1.576
peak=   -3.455 closest distance to " CD  LYS A 289 " =    2.384
peak=   -3.446 closest distance to " O   PRO A 163 " =    1.871
peak=   -3.437 closest distance to " O   HOH Z 362 " =    5.905
peak=   -3.429 closest distance to " O   HOH Z 165 " =    2.160
peak=   -3.426 closest distance to " O   HOH Z  63 " =    1.770
peak=   -3.425 closest distance to " N   GLN A 122 " =    1.405
peak=   -3.422 closest distance to " O   HOH Z 148 " =    1.810
peak=   -3.420 closest distance to " O   HOH Z 137 " =    1.362
peak=   -3.411 closest distance to " CZ3 TRP A 179 " =    1.266
peak=   -3.406 closest distance to " OD1 ASN A 148 " =    1.554
peak=   -3.404 closest distance to " O   TRP A  70 " =    1.418
peak=   -3.403 closest distance to " CA  ASP A 298 " =    1.086
peak=   -3.400 closest distance to " O   HOH Z 423 " =    2.207
peak=   -3.397 closest distance to " CD2 LEU A 237 " =    2.570
peak=   -3.388 closest distance to " CB  PHE A 208 " =    2.190
peak=   -3.387 closest distance to " OE2 GLU A 152 " =    1.200
peak=   -3.386 closest distance to " O   HOH Z 211 " =    1.605
peak=   -3.382 closest distance to " CA  GLY A 133 " =    1.914
peak=   -3.372 closest distance to " O   HOH Z 388 " =    2.097
peak=   -3.371 closest distance to " O   HOH Z 250 " =    1.384
peak=   -3.364 closest distance to " O   SER A  22 " =    2.171
peak=   -3.364 closest distance to " O   GLN A  89 " =    1.547
peak=   -3.363 closest distance to " CZ2 TRP A 274 " =    0.941
peak=   -3.360 closest distance to " O   HOH Z 395 " =    5.130
peak=   -3.359 closest distance to " CG2 VAL A 296 " =    1.900
peak=   -3.357 closest distance to " O   HOH Z 345 " =    1.781
peak=   -3.354 closest distance to " O   HOH Z  60 " =    1.765
peak=   -3.351 closest distance to " N   PRO A 163 " =    1.565
peak=   -3.345 closest distance to " NH2 ARG A  79 " =    2.024
peak=   -3.342 closest distance to " C   ALA A 158 " =    1.315
peak=   -3.337 closest distance to " C   ASP A 231 " =    2.483
peak=   -3.335 closest distance to " NE2 GLN A 278 " =    1.734
peak=   -3.333 closest distance to " N   GLN A  77 " =    1.664
peak=   -3.330 closest distance to " O   HOH Z 191 " =    5.557
peak=   -3.322 closest distance to " CD2 PHE A 225 " =    1.178
peak=   -3.321 closest distance to " OG  SER A  97 " =    2.093
peak=   -3.312 closest distance to " O   HOH Z 213 " =    1.336
peak=   -3.306 closest distance to " CB  ALA A 248 " =    2.245
peak=   -3.304 closest distance to " CG2 ILE A 263 " =    2.225
peak=   -3.303 closest distance to " OG  SER A  87 " =    1.339
peak=   -3.300 closest distance to " CD  ARG A  36 " =    1.881
peak=   -3.299 closest distance to " O   HOH Z 266 " =    4.463
peak=   -3.293 closest distance to " CB  ASP A 286 " =    2.109
peak=   -3.290 closest distance to " NH1 ARG A  36 " =    1.997
peak=   -3.289 closest distance to " NH1AARG A 275 " =    1.760
peak=   -3.286 closest distance to " O   HOH Z 198 " =    1.528
peak=   -3.281 closest distance to " CA  GLY A  57 " =    2.116
peak=   -3.280 closest distance to " OG1 THR A 178 " =    1.189
peak=   -3.278 closest distance to " CB  ALA A   7 " =    2.030
peak=   -3.276 closest distance to " O   ASN A 170 " =    1.888
peak=   -3.266 closest distance to " N   SER A 212 " =    1.987
peak=   -3.266 closest distance to " N   PHE A  59 " =    1.847
peak=   -3.263 closest distance to " O   HOH Z 326 " =    1.522
peak=   -3.260 closest distance to " O   SER A   3 " =    1.061
peak=   -3.254 closest distance to " O   HOH Z 137 " =    1.515
peak=   -3.244 closest distance to " CG  GLU A   2 " =    1.993
peak=   -3.242 closest distance to " O   HOH Z 218 " =    3.222
peak=   -3.239 closest distance to " O   ASN A 249 " =    1.409
peak=   -3.231 closest distance to " CE3 TRP A 274 " =    2.245
peak=   -3.224 closest distance to " CE3 TRP A 123 " =    1.273
peak=   -3.220 closest distance to " OD2 ASP A  50 " =    1.415
peak=   -3.220 closest distance to " O   HOH Z 166 " =    1.371
peak=   -3.216 closest distance to " O   HOH Z 385 " =    1.883
peak=   -3.214 closest distance to " O   MET A  40 " =    2.638
peak=   -3.212 closest distance to " O   HOH Z 147 " =    1.382
peak=   -3.211 closest distance to " O   HOH Z 337 " =    1.530
peak=   -3.211 closest distance to " CG1 VAL A 125 " =    2.340
peak=   -3.209 closest distance to " O   ASP A 162 " =    2.144
peak=   -3.205 closest distance to " O   ASN A 187 " =    1.444
peak=   -3.205 closest distance to " CG2 VAL A 189 " =    1.997
peak=   -3.203 closest distance to " CA  TRP A  70 " =    2.350
peak=   -3.201 closest distance to " N   ASN A 127 " =    1.508
peak=   -3.199 closest distance to " OE1 GLN A 183 " =    1.269
peak=   -3.193 closest distance to " O   HOH Z 193 " =    1.949
peak=   -3.193 closest distance to " O   HOH Z 134 " =    3.550
peak=   -3.190 closest distance to " CG1 VAL A  78 " =    2.805
peak=   -3.190 closest distance to " CB  SER A 210 " =    1.293
peak=   -3.187 closest distance to " CE2 PHE A 218 " =    2.370
peak=   -3.186 closest distance to " C   LEU A 143 " =    1.055
peak=   -3.185 closest distance to " CE  LYS A  76 " =    2.805
peak=   -3.179 closest distance to " O   HOH Z 377 " =    0.968
peak=   -3.168 closest distance to " O   HOH Z 243 " =    1.944
peak=   -3.164 closest distance to " CE  MET A 105 " =    2.015
peak=   -3.156 closest distance to " CD2 TYR A 293 " =    1.949
peak=   -3.154 closest distance to " OG  SER A  97 " =    1.574
peak=   -3.151 closest distance to " O   HOH Z 438 " =    1.166
peak=   -3.150 closest distance to " O   HOH Z 352 " =    1.521
peak=   -3.146 closest distance to " OG  SER A 245 " =    1.274
peak=   -3.144 closest distance to " O   HOH Z 158 " =    2.095
peak=   -3.135 closest distance to " O   VAL A 174 " =    2.134
peak=   -3.132 closest distance to " CB  ALA A  51 " =    1.836
peak=   -3.129 closest distance to " O   ALA A 180 " =    1.057
peak=   -3.128 closest distance to " CD  GLN A  88 " =    0.917
peak=   -3.123 closest distance to " CG  GLU A 152 " =    1.039
peak=   -3.118 closest distance to " O   HOH Z 414 " =    1.828
peak=   -3.116 closest distance to " CG1 VAL A 197 " =    2.062
peak=   -3.111 closest distance to " O   HOH Z 298 " =    2.402
peak=   -3.109 closest distance to " O   HOH Z   6 " =    1.532
peak=   -3.107 closest distance to " O   HOH Z  60 " =    2.060
peak=   -3.100 closest distance to " CB  ASP A 132 " =    2.269
peak=   -3.098 closest distance to " O   HOH Z 427 " =    1.482
peak=   -3.097 closest distance to " OE1 GLU A 277 " =    2.006
peak=   -3.096 closest distance to " SG ACYS A 201 " =    1.859
peak=   -3.093 closest distance to " O   HOH Z 119 " =    2.271
peak=   -3.087 closest distance to " O   HOH Z 236 " =    2.051
peak=   -3.077 closest distance to " O   HOH Z 389 " =    4.811
peak=   -3.056 closest distance to " NH1 ARG A  56 " =    2.515
peak=   -3.053 closest distance to " O   HOH Z 281 " =    2.782
peak=   -3.035 closest distance to " O   HOH Z 198 " =    1.719
peak=   -3.030 closest distance to " CA  GLY A  57 " =    2.094

================= 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    :  0.4327 0.4301   6.229792e+00   6.223434e+00
   1_bss:  0.4226 0.4193   6.219850e+00   6.201866e+00
   1_xyz:  0.2763 0.3097   5.900494e+00   5.971625e+00
   1_adp:  0.2504 0.3175   5.847316e+00   6.002982e+00
   1_occ:  0.2502 0.3179   5.847058e+00   6.003695e+00
   2_bss:  0.2465 0.3161   5.837780e+00   5.997679e+00
   2_xyz:  0.1838 0.2358   5.563621e+00   5.757897e+00
   2_adp:  0.1697 0.2183   5.495004e+00   5.687889e+00
   2_occ:  0.1693 0.2179   5.493515e+00   5.686376e+00
   3_bss:  0.1694 0.2165   5.489676e+00   5.680137e+00
   3_xyz:  0.1315 0.1749   5.263083e+00   5.476940e+00
   3_adp:  0.1230 0.1690   5.210935e+00   5.438419e+00
   3_occ:  0.1229 0.1689   5.210305e+00   5.437594e+00
   4_bss:  0.1231 0.1679   5.209069e+00   5.435246e+00
   4_xyz:  0.1118 0.1595   5.139012e+00   5.384637e+00
   4_adp:  0.1108 0.1561   5.124939e+00   5.365986e+00
   4_occ:  0.1106 0.1561   5.124550e+00   5.365688e+00
   5_bss:  0.1106 0.1562   5.124588e+00   5.365693e+00
   5_xyz:  0.1080 0.1546   5.108402e+00   5.357039e+00
   5_adp:  0.1070 0.1559   5.108761e+00   5.365289e+00
   5_occ:  0.1069 0.1559   5.108559e+00   5.365038e+00
   5_bss:  0.1069 0.1559   5.108180e+00   5.364497e+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:  0.330  13.543  -0.400   1.426  -0.718   0.000  -0.000  -0.000
   1_xyz:  0.330  13.543  -0.400   1.426  -0.718   0.000  -0.000  -0.000
   1_adp:  0.330  13.543  -0.400   1.426  -0.718   0.000  -0.000  -0.000
   1_occ:  0.330  13.543  -0.400   1.426  -0.718   0.000  -0.000  -0.000
   2_bss:  0.320  28.805  -2.037  -0.692  -1.123  -0.000  -0.000  -0.000
   2_xyz:  0.320  28.805  -2.037  -0.692  -1.123  -0.000  -0.000  -0.000
   2_adp:  0.320  28.805  -2.037  -0.692  -1.123  -0.000  -0.000  -0.000
   2_occ:  0.320  28.805  -2.037  -0.692  -1.123  -0.000  -0.000  -0.000
   3_bss:  0.314  33.664  -2.529  -1.755  -1.175  -0.000  -0.000  -0.000
   3_xyz:  0.314  33.664  -2.529  -1.755  -1.175  -0.000  -0.000  -0.000
   3_adp:  0.314  33.664  -2.529  -1.755  -1.175  -0.000  -0.000  -0.000
   3_occ:  0.314  33.664  -2.529  -1.755  -1.175  -0.000  -0.000  -0.000
   4_bss:  0.315  37.541  -2.917  -2.326  -1.451  -0.000  -0.000  -0.000
   4_xyz:  0.315  37.541  -2.917  -2.326  -1.451  -0.000  -0.000  -0.000
   4_adp:  0.315  37.541  -2.917  -2.326  -1.451  -0.000  -0.000  -0.000
   4_occ:  0.315  37.541  -2.917  -2.326  -1.451  -0.000  -0.000  -0.000
   5_bss:  0.320  37.541  -2.901  -2.364  -1.345  -0.000  -0.000  -0.000
   5_xyz:  0.320  37.541  -2.901  -2.364  -1.345  -0.000  -0.000  -0.000
   5_adp:  0.320  37.541  -2.901  -2.364  -1.345  -0.000  -0.000  -0.000
   5_occ:  0.320  37.541  -2.901  -2.364  -1.345  -0.000  -0.000  -0.000
   5_bss:  0.321  40.029  -2.749  -2.248  -1.179  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  48.745 0.5379  0.7272    56166.021
   1_bss:  47.548 0.5508  0.7455    52054.160
   1_xyz:  30.586 0.7528  0.9668    24671.958
   1_adp:  32.184 0.7339  0.9470    26567.864
   1_occ:  32.223 0.7335  0.9459    26614.199
   2_bss:  31.881 0.7368  0.9067    25947.884
   2_xyz:  22.743 0.8346  0.9931    13895.677
   2_adp:  20.441 0.8584  1.0073    11931.548
   2_occ:  20.407 0.8587  1.0071    11874.396
   3_bss:  20.182 0.8605  0.9891    11600.883
   3_xyz:  15.967 0.8981  1.0071     7555.853
   3_adp:  15.087 0.9058  1.0058     7040.532
   3_occ:  15.076 0.9059  1.0058     7021.502
   4_bss:  15.003 0.9065  0.9911     6970.126
   4_xyz:  13.956 0.9150  0.9945     6209.776
   4_adp:  13.533 0.9186  0.9925     6037.397
   4_occ:  13.528 0.9186  0.9924     6025.900
   5_bss:  13.529 0.9186  0.9935     6027.980
   5_xyz:  13.318 0.9205  0.9930     5952.543
   5_adp:  13.460 0.9195  0.9867     6033.591
   5_occ:  13.458 0.9195  0.9866     6029.312
   5_bss:  13.446 0.9196  0.9918     6024.266
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.107   1.9833e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.107   1.9833e-01
   1_xyz:   1.397  0.011  0.089 15.017  0.006  4.103   1.0847e-01
   1_adp:   1.397  0.011  0.089 15.017  0.006  4.103   1.0847e-01
   1_occ:   1.397  0.011  0.089 15.017  0.006  4.103   1.0847e-01
   2_bss:   1.397  0.011  0.089 15.017  0.006  4.103   1.0847e-01
   2_xyz:   1.030  0.006  0.072 14.095  0.004  4.107   5.8764e-02
   2_adp:   1.030  0.006  0.072 14.095  0.004  4.107   5.8764e-02
   2_occ:   1.030  0.006  0.072 14.095  0.004  4.107   5.8764e-02
   3_bss:   1.030  0.006  0.072 14.095  0.004  4.107   5.8764e-02
   3_xyz:   0.983  0.006  0.067 14.507  0.004  4.107   5.7496e-02
   3_adp:   0.983  0.006  0.067 14.507  0.004  4.107   5.7496e-02
   3_occ:   0.983  0.006  0.067 14.507  0.004  4.107   5.7496e-02
   4_bss:   0.983  0.006  0.067 14.507  0.004  4.107   5.7496e-02
   4_xyz:   1.021  0.006  0.072 14.711  0.004  4.108   6.0193e-02
   4_adp:   1.021  0.006  0.072 14.711  0.004  4.108   6.0193e-02
   4_occ:   1.021  0.006  0.072 14.711  0.004  4.108   6.0193e-02
   5_bss:   1.021  0.006  0.072 14.711  0.004  4.108   6.0193e-02
   5_xyz:   1.000  0.006  0.071 14.655  0.004  4.108   5.8213e-02
   5_adp:   1.000  0.006  0.071 14.655  0.004  4.108   5.8213e-02
   5_occ:   1.000  0.006  0.071 14.655  0.004  4.108   5.8213e-02
   5_bss:   1.000  0.006  0.071 14.655  0.004  4.108   5.8213e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.228   2.3818e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.228   2.3818e-01
   1_xyz:   9.362  0.055  0.326 89.142  0.059  1.974   7.7993e-02
   1_adp:   9.362  0.055  0.326 89.142  0.059  1.974   7.7993e-02
   1_occ:   9.362  0.055  0.326 89.142  0.059  1.974   7.7993e-02
   2_bss:   9.362  0.055  0.326 89.142  0.059  1.974   7.7993e-02
   2_xyz:   6.734  0.039  0.220 77.607  0.038  2.374   6.2005e-02
   2_adp:   6.734  0.039  0.220 77.607  0.038  2.374   6.2005e-02
   2_occ:   6.734  0.039  0.220 77.607  0.038  2.374   6.2005e-02
   3_bss:   6.734  0.039  0.220 77.607  0.038  2.374   6.2005e-02
   3_xyz:   7.619  0.045  0.196 83.464  0.029  2.335   8.4392e-02
   3_adp:   7.619  0.045  0.196 83.464  0.029  2.335   8.4392e-02
   3_occ:   7.619  0.045  0.196 83.464  0.029  2.335   8.4392e-02
   4_bss:   7.619  0.045  0.196 83.464  0.029  2.335   8.4392e-02
   4_xyz:   6.920  0.032  0.218 83.865  0.044  2.274   4.4451e-02
   4_adp:   6.920  0.032  0.218 83.865  0.044  2.274   4.4451e-02
   4_occ:   6.920  0.032  0.218 83.865  0.044  2.274   4.4451e-02
   5_bss:   6.920  0.032  0.218 83.865  0.044  2.274   4.4451e-02
   5_xyz:   7.026  0.031  0.225 84.559  0.041  2.268   4.2278e-02
   5_adp:   7.026  0.031  0.225 84.559  0.041  2.268   4.2278e-02
   5_occ:   7.026  0.031  0.225 84.559  0.041  2.268   4.2278e-02
   5_bss:   7.026  0.031  0.225 84.559  0.041  2.268   4.2278e-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:  88.85   0.00  18.36  85.35   0.00  14.28  88.85   2.94  40.55
   1_occ:  88.85   0.00  18.36  85.35   0.00  14.28  88.85   2.94  40.55
   2_bss:  88.85   0.00  18.36  85.35   0.00  14.28  88.85   2.94  40.55
   2_xyz:  88.85   0.00  18.36  85.35   0.00  14.28  88.85   2.94  40.55
   2_adp:  83.48   1.50  17.30  83.48   1.50  13.33  81.87   5.87  38.91
   2_occ:  83.48   1.50  17.30  83.48   1.50  13.33  81.87   5.87  38.91
   3_bss:  83.48   1.50  17.30  83.48   1.50  13.33  81.87   5.87  38.91
   3_xyz:  83.48   1.50  17.30  83.48   1.50  13.33  81.87   5.87  38.91
   3_adp:  90.05   0.27  17.45  90.05   0.27  13.05  85.94   3.00  41.39
   3_occ:  90.05   0.27  17.45  90.05   0.27  13.05  85.94   3.00  41.39
   4_bss:  90.05   0.27  17.45  90.05   0.27  13.05  85.94   3.00  41.39
   4_xyz:  90.05   0.27  17.45  90.05   0.27  13.05  85.94   3.00  41.39
   4_adp:  89.80   1.31  16.93  89.80   1.31  12.85  83.56   4.33  39.20
   4_occ:  89.80   1.31  16.93  89.80   1.31  12.85  83.56   4.33  39.20
   5_bss:  89.80   1.31  16.93  89.80   1.31  12.85  83.56   4.33  39.20
   5_xyz:  89.80   1.31  16.93  89.80   1.31  12.85  83.56   4.33  39.20
   5_adp:  92.89   0.35  17.01  92.89   0.35  12.78  85.03   5.79  40.06
   5_occ:  92.89   0.35  17.01  92.89   0.35  12.78  85.03   5.79  40.06
   5_bss:  92.88   0.34  17.00  92.88   0.34  12.77  85.02   5.78  40.05
------------------------------------------------------------------------
 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:    2.371    0.011    0.383
   1_adp:    2.371    0.011    0.383
   1_occ:    2.371    0.011    0.383
   2_bss:    2.371    0.011    0.383
   2_xyz:    2.160    0.030    0.496
   2_adp:    2.160    0.030    0.496
   2_occ:    2.160    0.030    0.496
   3_bss:    2.160    0.030    0.496
   3_xyz:    1.898    0.070    0.595
   3_adp:    1.898    0.070    0.595
   3_occ:    1.898    0.070    0.595
   4_bss:    1.898    0.070    0.595
   4_xyz:    1.540    0.076    0.621
   4_adp:    1.540    0.076    0.621
   4_occ:    1.540    0.076    0.621
   5_bss:    1.540    0.076    0.621
   5_xyz:    1.286    0.069    0.635
   5_adp:    1.286    0.069    0.635
   5_occ:    1.286    0.069    0.635
   5_bss:    1.286    0.069    0.635
------------------------------------------------------------------------

CPU time actual refinement: 321.79


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_146/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_146/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_146/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_146/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_146/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 321.65 
  Macro-tasks:
    bulk solvent and scale       = 42.55  
    individual site refinement   = 126.54 
    weights calculation          = 29.60  
    collect and process          = 6.57   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 205.35 
  Micro-tasks:
    mask                            = 1.76   
    f_calc                          = 100.01 
    alpha_beta                      = 8.40   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 107.38 
    fmodel                         = 6.85   
    r_factors                      = 0.26   
    phase_errors                   = 10.81  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 236.91 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.623 micro seconds
Total CPU time: 5.58 minutes
from_scatterers_fft:    627 calls, 99.81 s
gradients_fft:          572 calls, 94.71 s

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

# Date 2008-01-16 Time 04:07:57 PST -0800 (1200485277.34 s)
Start R-work = 0.4327, R-free = 0.4301 (no bulk solvent and anisotropic scale)
Final R-work = 0.1330, R-free = 0.1760 (no bulk solvent and anisotropic scale)

Start R-work = 0.4226, R-free = 0.4193
Final R-work = 0.1069, R-free = 0.1559