# Date 2008-01-16 Time 06:23:07 PST -0800 (1200493387.37 s)
#phil __OFF__

Command line arguments: "../1121.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 3102
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1121

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.655, 46.2261, 88.5498, 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: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 46.2261, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3141 1.97406
Completeness in resolution range: 0.920709
Completeness with d_max=infinity: 0.918077

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.3141
                             d_min =   1.9741

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.655, 46.2261, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.3141 1.97406
Completeness in resolution range: 0.920709
Completeness with d_max=infinity: 0.918077

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.3145 -  4.2260 [2226/2252]  2004   222  10.0%
  bin  2:  4.2260 -  3.3660 [2158/2178]  1945   213   9.9%
  bin  3:  3.3660 -  2.9440 [2108/2127]  1893   215  10.2%
  bin  4:  2.9440 -  2.6763 [2091/2121]  1876   215  10.3%
  bin  5:  2.6763 -  2.4854 [2107/2126]  1903   204   9.7%
  bin  6:  2.4854 -  2.3394 [2071/2096]  1862   209  10.1%
  bin  7:  2.3394 -  2.2226 [2066/2094]  1855   211  10.2%
  bin  8:  2.2226 -  2.1261 [2055/2091]  1850   205  10.0%
  bin  9:  2.1261 -  2.0445 [2043/2091]  1849   194   9.5%
  bin 10:  2.0445 -  1.9741 [ 664/2100]   593    71  10.7%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1121/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:
        1.81 -     2.42: 28
        2.42 -     3.04: 2177
        3.04 -     3.66: 4646
        3.66 -     4.28: 8918
        4.28 -     4.90: 12180
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 324 " - " O   HOH Z 374 "  2.089 3.040 -x,y-1/2,-z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.091 3.040 x,y+1,z
  " O   HOH Z  61 " - " O   HOH Z 246 "  2.148 3.040 x,y+1,z
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  ... (remaining 27944 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_1121/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1121/model_refine_001.geo

CPU time processing inputs: 9.17


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.655 46.22605 88.54975 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4799   r_free= 0.4775   ksol= 0.00   Bsol= 0.00   scale= 0.872    |
|                                                                             |
| 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:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.288140                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3145 -  4.7144 0.99   1448  161 0.3817 0.3553      6.5887      6.5142|
|  2:  4.7144 -  3.7602 0.99   1391  154 0.4149 0.4140      6.8447        6.82|
|  3:  3.7602 -  3.2903 0.99   1372  153 0.4427 0.4102      6.6546       6.637|
|  4:  3.2903 -  2.9919 0.99   1362  154 0.4754 0.5069      6.5206      6.5157|
|  5:  2.9919 -  2.7788 0.99   1352  146 0.5197 0.4978       6.366      6.3981|
|  6:  2.7788 -  2.6158 0.99   1347  153 0.5018 0.5173      6.2635      6.2206|
|  7:  2.6158 -  2.4854 0.99   1349  148 0.5230 0.4825       6.233      6.1755|
|  8:  2.4854 -  2.3776 0.98   1321  149 0.5409 0.5630      6.1787      6.1592|
|  9:  2.3776 -  2.2864 0.98   1328  147 0.5356 0.5359      6.1348      6.1885|
| 10:  2.2864 -  2.2077 1.00   1337  154 0.5377 0.5285      6.0606       6.057|
| 11:  2.2077 -  2.1389 0.98   1322  143 0.5175 0.5263      6.0335      6.0499|
| 12:  2.1389 -  2.0779 0.98   1315  140 0.5399 0.5408      5.9305      5.9324|
| 13:  2.0779 -  2.0233 0.84   1130  126 0.5299 0.5455      5.8857      5.8091|
| 14:  2.0233 -  1.9741 0.19    256   31 0.5269 0.5029       5.849      5.8968|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.3145 -  4.7144  1448   161  0.73  31.23   0.81     0.77      62370.55|
|  2:  4.7144 -  3.7602  1391   154  0.72  33.24   0.89     0.83     101680.35|
|  3:  3.7602 -  3.2903  1372   153  0.58  45.41   0.89     0.77     114636.22|
|  4:  3.2903 -  2.9919  1362   154  0.46  54.81   0.87     0.64     110527.61|
|  5:  2.9919 -  2.7788  1352   146  0.37  62.30   0.85     0.53      88382.52|
|  6:  2.7788 -  2.6158  1347   153  0.33  65.37   0.88     0.46      76707.41|
|  7:  2.6158 -  2.4854  1349   148  0.32  65.80   0.89     0.45      68263.26|
|  8:  2.4854 -  2.3776  1321   149  0.29  67.97   0.86     0.43      62318.44|
|  9:  2.3776 -  2.2864  1328   147  0.30  67.42   0.89     0.45      58490.86|
| 10:  2.2864 -  2.2077  1337   154  0.29  68.23   0.89     0.44      51614.62|
| 11:  2.2077 -  2.1389  1322   143  0.28  68.93   0.92     0.43      50798.12|
| 12:  2.1389 -  2.0779  1315   140  0.25  71.45   0.88     0.40      45844.42|
| 13:  2.0779 -  2.0233  1130   126  0.22  73.45   0.90     0.37      41587.30|
| 14:  2.0233 -  1.9741   256    31  0.26  71.17   0.93     0.36      33525.56|
|alpha:            min =        0.36 max =            0.83 mean =         0.54|
|beta:             min =    33525.56 max =       114636.22 mean =     71837.70|
|figures of merit: min =        0.00 max =            1.00 mean =         0.40|
|phase err.(work): min =        0.00 max =           89.99 mean =        59.35|
|phase err.(test): min =        0.00 max =           90.00 mean =        59.28|
|-----------------------------------------------------------------------------|

============================== 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 = 19.048447             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.054   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.292303              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.545   (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 |  1.806 -  2.115:        3 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       25 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      195 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     1982 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1846 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2800 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4580 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4338 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5553 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6627 |
|-----------------------------------------------------------------------------|
|-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 |        0.166 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.806 |       0.204 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.169)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.97 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4799   r_free= 0.4775   ksol= 0.00   Bsol= 0.00   scale= 0.872    |
|                                                                             |
| 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:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.288140                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4727   r_free= 0.4736   ksol= 0.32   Bsol= 73.71   scale= 0.917   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.30,-0.62,3.58,-0.00,0.00,0.00); trace/3= 0.89                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.284757                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.083774             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 89.865   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.441040              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.122   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4727      final r-factor (work) = 0.3334          |
| start r-factor (free) = 0.4736      final r-factor (free) = 0.3688          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 50.6576 = 16.08 * 0.50 * 6.2786 + 1.00 * 0.1658                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 49.6646 = 16.08 * 0.50 * 6.1557 + 1.00 * 0.1614                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3334      final r-factor (work) = 0.3075          |
| start r-factor (free) = 0.3688      final r-factor (free) = 0.3724          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.8772 = 1.44 * 1.00 * 6.1557 + 1.00 * 0.0066                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.7070 = 1.44 * 1.00 * 6.0001 + 1.00 * 0.0606                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 8      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.169)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    112.74  17.26    None  None   None       |
|    all(noH): 2823   0      0.00    112.74  17.26    None  None   None       |
|    Sol.    : 438    0      0.69    63.77   38.79    None  None   None       |
|    Mac.    : 2385   0      0.00    112.74  13.31    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 -  11.274: 1086   |   5:    56.369 -  67.642:   30        |
|      1:    11.274 -  22.547: 1056   |   6:    67.642 -  78.916:    0        |
|      2:    22.547 -  33.821:  327   |   7:    78.916 -  90.190:    0        |
|      3:    33.821 -  45.095:  193   |   8:    90.190 - 101.463:    0        |
|      4:    45.095 -  56.369:  130   |   9:   101.463 - 112.737:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3075 r_free = 0.3724             target_work(ml) = 6.007         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3069 r_free = 0.3724             target_work(ml) = 6.007         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3069   r_free= 0.3724   ksol= 0.32   Bsol= 73.71   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.30,-0.62,3.58,-0.00,0.00,0.00); trace/3= 0.89                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.006654                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3063   r_free= 0.3717   ksol= 0.36   Bsol= 85.56   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.73,-1.24,2.18,-0.00,0.00,0.00); trace/3= 0.07                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.008443                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.942989              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.418   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.956751              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.154   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3063      final r-factor (work) = 0.2288          |
| start r-factor (free) = 0.3717      final r-factor (free) = 0.2842          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.9962 = 5.94 * 0.50 * 6.0020 + 1.00 * 0.1612                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.6366 = 5.94 * 0.50 * 5.9097 + 1.00 * 0.0759                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2288      final r-factor (work) = 0.2069          |
| start r-factor (free) = 0.2842      final r-factor (free) = 0.2779          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7192 = 0.96 * 1.00 * 5.9097 + 1.00 * 0.0650                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.4793 = 0.96 * 1.00 * 5.7100 + 1.00 * 0.0162                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.169)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.25   18.75    None  None   None       |
|    all(noH): 2823   0      0.00    99.25   18.75    None  None   None       |
|    Sol.    : 438    0      1.94    99.25   45.76    None  None   None       |
|    Mac.    : 2385   0      0.00    80.55   13.79    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.925: 1019   |   5:    49.623 -  59.547:  122        |
|      1:     9.925 -  19.849:  979   |   6:    59.547 -  69.472:   87        |
|      2:    19.849 -  29.774:  315   |   7:    69.472 -  79.396:   28        |
|      3:    29.774 -  39.698:  141   |   8:    79.396 -  89.321:    8        |
|      4:    39.698 -  49.623:  122   |   9:    89.321 -  99.246:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2069 r_free = 0.2779             target_work(ml) = 5.699         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2068 r_free = 0.2778             target_work(ml) = 5.699         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2068   r_free= 0.2778   ksol= 0.36   Bsol= 85.56   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.73,-1.24,2.18,-0.00,0.00,0.00); trace/3= 0.07                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.698692                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2071   r_free= 0.2786   ksol= 0.35   Bsol= 89.82   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.00,-1.45,1.20,-0.00,0.00,0.00); trace/3= -0.42                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.699835                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.094395              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.356   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.606465              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.638  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2071      final r-factor (work) = 0.1610          |
| start r-factor (free) = 0.2786      final r-factor (free) = 0.2221          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.6223 = 5.09 * 0.50 * 5.7108 + 1.00 * 0.0759                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.3450 = 5.09 * 0.50 * 5.6030 + 1.00 * 0.0731                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1610      final r-factor (work) = 0.1477          |
| start r-factor (free) = 0.2221      final r-factor (free) = 0.2059          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.0172 = 1.61 * 1.00 * 5.6030 + 1.00 * 0.0162                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.7511 = 1.61 * 1.00 * 5.4377 + 1.00 * 0.0156                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.169)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.70  18.85    None  None   None       |
|    all(noH): 2823   0      0.00    106.70  18.85    None  None   None       |
|    Sol.    : 438    0      0.00    106.70  49.79    None  None   None       |
|    Mac.    : 2385   0      0.00    88.93   13.17    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 -  10.670: 1236   |   5:    53.350 -  64.019:   84        |
|      1:    10.670 -  21.340:  929   |   6:    64.019 -  74.689:   91        |
|      2:    21.340 -  32.010:  211   |   7:    74.689 -  85.359:   43        |
|      3:    32.010 -  42.680:  107   |   8:    85.359 -  96.029:   17        |
|      4:    42.680 -  53.350:  101   |   9:    96.029 - 106.699:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1477 r_free = 0.2059             target_work(ml) = 5.398         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1476 r_free = 0.2058             target_work(ml) = 5.398         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1476   r_free= 0.2058   ksol= 0.35   Bsol= 89.82   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.00,-1.45,1.20,-0.00,0.00,0.00); trace/3= -0.42                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.397765                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1480   r_free= 0.2056   ksol= 0.34   Bsol= 87.50   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.40,-1.93,0.37,-0.00,0.00,0.00); trace/3= -0.99                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.396830                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.374243              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.266  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.726250              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 113.371  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1480      final r-factor (work) = 0.1363          |
| start r-factor (free) = 0.2056      final r-factor (free) = 0.1911          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5322 = 2.37 * 0.50 * 5.4408 + 1.00 * 0.0732                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4289 = 2.37 * 0.50 * 5.3662 + 1.00 * 0.0586                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1363      final r-factor (work) = 0.1327          |
| start r-factor (free) = 0.1911      final r-factor (free) = 0.1872          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.2790 = 1.73 * 1.00 * 5.3662 + 1.00 * 0.0155                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.1875 = 1.73 * 1.00 * 5.3135 + 1.00 * 0.0150                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.169)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    116.77  18.53    None  None   None       |
|    all(noH): 2823   0      0.00    116.77  18.53    None  None   None       |
|    Sol.    : 438    0      0.00    116.77  49.36    None  None   None       |
|    Mac.    : 2385   0      0.00    97.98   12.86    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 -  11.677: 1449   |   5:    58.383 -  70.060:   76        |
|      1:    11.677 -  23.353:  808   |   6:    70.060 -  81.737:   71        |
|      2:    23.353 -  35.030:  176   |   7:    81.737 -  93.414:   24        |
|      3:    35.030 -  46.707:  104   |   8:    93.414 - 105.090:   13        |
|      4:    46.707 -  58.383:   98   |   9:   105.090 - 116.767:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1327 r_free = 0.1872             target_work(ml) = 5.302         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1326 r_free = 0.1872             target_work(ml) = 5.302         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1326   r_free= 0.1872   ksol= 0.34   Bsol= 87.50   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.40,-1.93,0.37,-0.00,0.00,0.00); trace/3= -0.99                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.301722                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1326   r_free= 0.1872   ksol= 0.33   Bsol= 79.54   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.40,-1.93,0.37,-0.00,0.00,0.00); trace/3= -0.99                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.301618                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.449319              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 141.325  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.078318              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.177  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1326      final r-factor (work) = 0.1250          |
| start r-factor (free) = 0.1872      final r-factor (free) = 0.1783          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5654 = 2.45 * 0.50 * 5.3132 + 1.00 * 0.0586                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5289 = 2.45 * 0.50 * 5.2781 + 1.00 * 0.0650                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1250      final r-factor (work) = 0.1232          |
| start r-factor (free) = 0.1783      final r-factor (free) = 0.1756          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7063 = 1.08 * 1.00 * 5.2781 + 1.00 * 0.0149                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6727 = 1.08 * 1.00 * 5.2479 + 1.00 * 0.0137                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.169)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    123.66  18.02    None  None   None       |
|    all(noH): 2823   0      0.00    123.66  18.02    None  None   None       |
|    Sol.    : 438    0      1.21    123.66  47.39    None  None   None       |
|    Mac.    : 2385   0      0.00    99.82   12.62    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  12.366: 1585   |   5:    61.831 -  74.197:   75        |
|      1:    12.366 -  24.732:  718   |   6:    74.197 -  86.563:   40        |
|      2:    24.732 -  37.099:  172   |   7:    86.563 -  98.929:   19        |
|      3:    37.099 -  49.465:  115   |   8:    98.929 - 111.296:    9        |
|      4:    49.465 -  61.831:   88   |   9:   111.296 - 123.662:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1232 r_free = 0.1756             target_work(ml) = 5.240         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1231 r_free = 0.1756             target_work(ml) = 5.240         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1231   r_free= 0.1756   ksol= 0.33   Bsol= 79.54   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.40,-1.93,0.37,-0.00,0.00,0.00); trace/3= -0.99                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.239843                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3145 -  4.7144 0.99   1448  161 0.0948 0.1388      5.3803      5.6184|
|  2:  4.7144 -  3.7602 0.99   1391  154 0.0835 0.1154      5.4476      5.6598|
|  3:  3.7602 -  3.2903 0.99   1372  153 0.1139 0.1681       5.531      5.8704|
|  4:  3.2903 -  2.9919 0.99   1362  154 0.1398 0.1926      5.5487      5.7144|
|  5:  2.9919 -  2.7788 0.99   1352  146 0.1506 0.1974      5.4279      5.6733|
|  6:  2.7788 -  2.6158 0.99   1347  153 0.1443 0.2060      5.3143      5.5381|
|  7:  2.6158 -  2.4854 0.99   1349  148 0.1417 0.1785      5.2663      5.4014|
|  8:  2.4854 -  2.3776 0.98   1321  149 0.1373 0.1979      5.1842      5.4488|
|  9:  2.3776 -  2.2864 0.98   1328  147 0.1358 0.2121      5.1524      5.4328|
| 10:  2.2864 -  2.2077 1.00   1337  154 0.1237 0.1755      5.0132      5.2431|
| 11:  2.2077 -  2.1389 0.98   1322  143 0.1246 0.1903      5.0125      5.3801|
| 12:  2.1389 -  2.0779 0.98   1315  140 0.1307 0.2124      4.9633      5.2217|
| 13:  2.0779 -  2.0233 0.84   1130  126 0.1232 0.1765      4.8727      5.0695|
| 14:  2.0233 -  1.9741 0.19    256   31 0.1035 0.1704      4.7279      5.0817|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.3145 -  4.7144  1448   161  0.94   9.39   0.96     0.94       7719.05|
|  2:  4.7144 -  3.7602  1391   154  0.95   8.49   1.01     0.99       9792.35|
|  3:  3.7602 -  3.2903  1372   153  0.92  12.68   1.03     1.03      11898.37|
|  4:  3.2903 -  2.9919  1362   154  0.90  16.37   1.01     0.99      12706.57|
|  5:  2.9919 -  2.7788  1352   146  0.88  17.86   1.00     0.98      10199.52|
|  6:  2.7788 -  2.6158  1347   153  0.88  18.51   0.99     0.97       8547.39|
|  7:  2.6158 -  2.4854  1349   148  0.89  17.41   0.99     0.96       7614.80|
|  8:  2.4854 -  2.3776  1321   149  0.88  18.09   1.00     0.97       6691.63|
|  9:  2.3776 -  2.2864  1328   147  0.88  18.19   0.99     0.94       6265.81|
| 10:  2.2864 -  2.2077  1337   154  0.89  17.31   0.99     0.97       5061.17|
| 11:  2.2077 -  2.1389  1322   143  0.89  17.55   0.98     0.92       4943.14|
| 12:  2.1389 -  2.0779  1315   140  0.89  18.10   0.99     0.99       4746.12|
| 13:  2.0779 -  2.0233  1130   126  0.88  19.21   0.98     0.96       4199.29|
| 14:  2.0233 -  1.9741   256    31  0.92  14.70   0.97     0.94       3061.57|
|alpha:            min =        0.92 max =            1.03 mean =         0.97|
|beta:             min =     3061.57 max =        12706.57 mean =      7727.57|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.83 mean =        15.96|
|phase err.(test): min =        0.00 max =           89.31 mean =        15.41|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1235   r_free= 0.1753   ksol= 0.33   Bsol= 78.92   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.26,-1.89,0.36,-0.00,0.00,0.00); trace/3= -0.93                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.238347                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.31 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1235   r_free= 0.1753   ksol= 0.33   Bsol= 78.92   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.26,-1.89,0.36,-0.00,0.00,0.00); trace/3= -0.93                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.238347                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.3145 -  4.7144 0.99   1448  161 0.0958 0.1348      5.3635      5.5907|
|  2:  4.7144 -  3.7602 0.99   1391  154 0.0843 0.1158      5.4447      5.6646|
|  3:  3.7602 -  3.2903 0.99   1372  153 0.1144 0.1678      5.5334      5.8664|
|  4:  3.2903 -  2.9919 0.99   1362  154 0.1400 0.1932      5.5492      5.7178|
|  5:  2.9919 -  2.7788 0.99   1352  146 0.1506 0.1975      5.4281      5.6708|
|  6:  2.7788 -  2.6158 0.99   1347  153 0.1442 0.2062      5.3142      5.5386|
|  7:  2.6158 -  2.4854 0.99   1349  148 0.1417 0.1786      5.2664      5.4017|
|  8:  2.4854 -  2.3776 0.98   1321  149 0.1372 0.1979      5.1841      5.4483|
|  9:  2.3776 -  2.2864 0.98   1328  147 0.1357 0.2120      5.1522      5.4333|
| 10:  2.2864 -  2.2077 1.00   1337  154 0.1236 0.1752      5.0129      5.2425|
| 11:  2.2077 -  2.1389 0.98   1322  143 0.1246 0.1898      5.0122       5.379|
| 12:  2.1389 -  2.0779 0.98   1315  140 0.1307 0.2127      4.9627      5.2219|
| 13:  2.0779 -  2.0233 0.84   1130  126 0.1232 0.1764      4.8725      5.0692|
| 14:  2.0233 -  1.9741 0.19    256   31 0.1035 0.1704      4.7277       5.081|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.3145 -  4.7144  1448   161  0.94   9.00   0.96     0.94       7106.71|
|  2:  4.7144 -  3.7602  1391   154  0.95   8.31   1.01     0.99       9488.19|
|  3:  3.7602 -  3.2903  1372   153  0.92  12.70   1.03     1.03      11925.25|
|  4:  3.2903 -  2.9919  1362   154  0.90  16.40   1.02     0.99      12712.43|
|  5:  2.9919 -  2.7788  1352   146  0.88  17.87   1.00     0.99      10206.45|
|  6:  2.7788 -  2.6158  1347   153  0.88  18.51   0.99     0.97       8545.65|
|  7:  2.6158 -  2.4854  1349   148  0.89  17.41   1.00     0.96       7617.39|
|  8:  2.4854 -  2.3776  1321   149  0.88  18.09   1.00     0.97       6691.60|
|  9:  2.3776 -  2.2864  1328   147  0.88  18.20   1.00     0.94       6270.54|
| 10:  2.2864 -  2.2077  1337   154  0.89  17.30   1.00     0.97       5058.27|
| 11:  2.2077 -  2.1389  1322   143  0.89  17.54   0.98     0.92       4938.08|
| 12:  2.1389 -  2.0779  1315   140  0.89  18.08   0.99     0.99       4738.59|
| 13:  2.0779 -  2.0233  1130   126  0.88  19.21   0.98     0.96       4197.31|
| 14:  2.0233 -  1.9741   256    31  0.92  14.70   0.97     0.94       3060.08|
|alpha:            min =        0.92 max =            1.03 mean =         0.97|
|beta:             min =     3060.08 max =        12712.43 mean =      7655.47|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.78 mean =        15.91|
|phase err.(test): min =        0.00 max =           89.19 mean =        15.34|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.169)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    123.66  18.02    None  None   None       |
|    all(noH): 2823   0      0.00    123.66  18.02    None  None   None       |
|    Sol.    : 438    0      1.21    123.66  47.39    None  None   None       |
|    Mac.    : 2385   0      0.00    99.83   12.62    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -  12.369: 1585   |   5:    61.834 -  74.200:   75        |
|      1:    12.369 -  24.735:  718   |   6:    74.200 -  86.566:   40        |
|      2:    24.735 -  37.102:  172   |   7:    86.566 -  98.932:   19        |
|      3:    37.102 -  49.468:  115   |   8:    98.932 - 111.298:    9        |
|      4:    49.468 -  61.834:   88   |   9:   111.298 - 123.665:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 321         
Filter by distance & map next to the model:
   mapped sites are within: 0.692 - 4.237
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 319 from: 321
   mapped sites are within: 0.704 - 4.237

peak=    6.556 closest distance to " O   HOH Z 103 " =    1.047
peak=    6.390 closest distance to " O   HOH Z 222 " =    1.519
peak=    5.834 closest distance to " NE2 GLN A  11 " =    1.248
peak=    5.376 closest distance to " CG  PRO A  54 " =    1.358
peak=    5.232 closest distance to " O   HOH Z 144 " =    2.106
peak=    5.099 closest distance to " CB  GLN A 223 " =    1.553
peak=    5.085 closest distance to " CB  SER A  63 " =    1.325
peak=    5.054 closest distance to " O   HOH Z   7 " =    1.658
peak=    5.033 closest distance to " O   HOH Z 417 " =    1.959
peak=    4.895 closest distance to " O   HOH Z  63 " =    1.577
peak=    4.832 closest distance to " O   HOH Z 423 " =    2.249
peak=    4.822 closest distance to " O   HOH Z  69 " =    1.160
peak=    4.761 closest distance to " O   HOH Z 287 " =    2.076
peak=    4.695 closest distance to " O   HOH Z   9 " =    1.774
peak=    4.672 closest distance to " O   HOH Z 207 " =    0.892
peak=    4.655 closest distance to " O   HOH Z 232 " =    2.144
peak=    4.642 closest distance to " CB  ASN A 148 " =    1.525
peak=    4.595 closest distance to " O   HOH Z 183 " =    1.659
peak=    4.534 closest distance to " CG  PRO A  90 " =    1.415
peak=    4.524 closest distance to " O   HOH Z 369 " =    2.105
peak=    4.472 closest distance to " CB  PRO A  54 " =    1.072
peak=    4.448 closest distance to " O   HOH Z  49 " =    1.250
peak=    4.444 closest distance to " O   HOH Z 427 " =    2.520
peak=    4.363 closest distance to " CZ3 TRP A 266 " =    1.146
peak=    4.353 closest distance to " CG  PRO A 213 " =    1.363
peak=    4.343 closest distance to " CG  PRO A 198 " =    1.261
peak=    4.330 closest distance to " O   HOH Z 105 " =    0.895
peak=    4.329 closest distance to " O   HOH Z 126 " =    1.583
peak=    4.324 closest distance to " CA  TYR A  30 " =    1.088
peak=    4.316 closest distance to " O   HOH Z 425 " =    1.515
peak=    4.295 closest distance to " CG2 THR A 221 " =    1.051
peak=    4.284 closest distance to " CZ  PHE A 218 " =    1.132
peak=    4.277 closest distance to " CA  ARG A 195 " =    1.410
peak=    4.276 closest distance to " O   HOH Z 380 " =    1.757
peak=    4.246 closest distance to " CB  ASP A 124 " =    0.880
peak=    4.241 closest distance to " CB  ARG A 190 " =    1.513
peak=    4.223 closest distance to " O   HOH Z 126 " =    2.210
peak=    4.212 closest distance to " CG  LEU A 167 " =    1.269
peak=    4.179 closest distance to " NH1AARG A 145 " =    1.288
peak=    4.113 closest distance to " O   HOH Z 290 " =    1.132
peak=    4.099 closest distance to " CB  SER A 212 " =    1.298
peak=    4.096 closest distance to " O   HOH Z 211 " =    1.372
peak=    4.095 closest distance to " CD  ARG A 159 " =    0.835
peak=    4.091 closest distance to " O   HOH Z 182 " =    1.121
peak=    4.073 closest distance to " O   HOH Z 316 " =    3.056
peak=    4.051 closest distance to " CD2 TRP A 179 " =    1.234
peak=    4.039 closest distance to " O   HOH Z 298 " =    2.326
peak=    4.003 closest distance to " O   HOH Z 403 " =    1.546
peak=    4.000 closest distance to " O   PRO A 198 " =    1.285
peak=    3.995 closest distance to " CA  ARG A 156 " =    1.074
peak=    3.991 closest distance to " CB  ASP A 132 " =    4.103
peak=    3.988 closest distance to " O   HOH Z 437 " =    1.423
peak=    3.983 closest distance to " CA  ALA A 160 " =    0.969
peak=    3.982 closest distance to " NH2 ARG A  56 " =    1.121
peak=    3.978 closest distance to " O   HOH Z 394 " =    1.763
peak=    3.963 closest distance to " O   HOH Z 295 " =    1.322
peak=    3.954 closest distance to " ND2 ASN A 187 " =    1.509
peak=    3.952 closest distance to " CA  ALA A  51 " =    1.046
peak=    3.941 closest distance to " CB  SER A 216 " =    1.089
peak=    3.930 closest distance to " CB  ARG A 275 " =    1.044
peak=    3.929 closest distance to " CA  VAL A 125 " =    1.184
peak=    3.887 closest distance to " O   HOH Z 362 " =    2.207
peak=    3.885 closest distance to " CG  PRO A 243 " =    1.062
peak=    3.880 closest distance to " O   HOH Z 218 " =    1.679
peak=    3.852 closest distance to " O   HOH Z 214 " =    2.413
peak=    3.849 closest distance to " O   HOH Z 180 " =    2.149
peak=    3.842 closest distance to " O   HOH Z 422 " =    2.745
peak=    3.840 closest distance to " O   HOH Z 406 " =    1.629
peak=    3.837 closest distance to " CA  ALA A 160 " =    1.420
peak=    3.827 closest distance to " CA  ASN A 127 " =    1.153
peak=    3.826 closest distance to " CB  LEU A 228 " =    1.142
peak=    3.822 closest distance to " NZ  LYS A 119 " =    2.764
peak=    3.813 closest distance to " O   HOH Z  58 " =    1.712
peak=    3.807 closest distance to " CE  LYS A  76 " =    0.915
peak=    3.803 closest distance to " O   TYR A 116 " =    1.268
peak=    3.781 closest distance to " CD1 ILE A  33 " =    1.796
peak=    3.780 closest distance to " N   ASN A 127 " =    1.427
peak=    3.772 closest distance to " O   HOH Z 193 " =    1.673
peak=    3.759 closest distance to " CB  TRP A 266 " =    1.068
peak=    3.757 closest distance to " CB  VAL A 265 " =    1.348
peak=    3.751 closest distance to " O   HOH Z 303 " =    2.280
peak=    3.751 closest distance to " O   HOH Z  61 " =    1.667
peak=    3.747 closest distance to " OE1 GLN A 240 " =    1.548
peak=    3.735 closest distance to " NZ  LYS A 117 " =    2.869
peak=    3.726 closest distance to " O   HOH Z 112 " =    0.813
peak=    3.722 closest distance to " NE2 HIS A 207 " =    1.088
peak=    3.717 closest distance to " CB  SER A 210 " =    0.942
peak=    3.691 closest distance to " ND2BASN A 224 " =    0.878
peak=    3.681 closest distance to " CA  ALA A 158 " =    1.149
peak=    3.677 closest distance to " O   HOH Z 352 " =    1.814
peak=    3.674 closest distance to " OG  SER A  62 " =    3.108
peak=    3.674 closest distance to " O   HOH Z 411 " =    3.488
peak=    3.669 closest distance to " CD  ARG A 269 " =    0.952
peak=    3.668 closest distance to " CB  PRO A  90 " =    1.117
peak=    3.667 closest distance to " O   HOH Z 240 " =    1.898
peak=    3.665 closest distance to " CA  ILE A 234 " =    1.140
peak=    3.661 closest distance to " CB  SER A   3 " =    1.576
peak=    3.653 closest distance to " CA  MET A 105 " =    0.950
peak=    3.649 closest distance to " O  BHOH Z  74 " =    1.226
peak=    3.641 closest distance to " CB  SER A  62 " =    0.857
peak=    3.639 closest distance to " O   THR A 182 " =    1.448
peak=    3.637 closest distance to " O   HOH Z 273 " =    1.142
peak=    3.632 closest distance to " O   HOH Z 216 " =    3.938
peak=    3.631 closest distance to " CE3 TRP A  85 " =    0.947
peak=    3.625 closest distance to " CB  SER A 276 " =    1.076
peak=    3.624 closest distance to " O   HOH Z 167 " =    1.774
peak=    3.620 closest distance to " CB  ASN A  39 " =    0.939
peak=    3.618 closest distance to " CA  ASN A  74 " =    1.312
peak=    3.616 closest distance to " O   HOH Z 145 " =    1.840
peak=    3.610 closest distance to " CB  GLU A 277 " =    3.768
peak=    3.609 closest distance to " O   HOH Z   1 " =    1.692
peak=    3.604 closest distance to " CB  ASN A 142 " =    0.870
peak=    3.602 closest distance to " OG  SER A  62 " =    2.883
peak=    3.599 closest distance to " CB  VAL A 202 " =    1.550
peak=    3.592 closest distance to " CA  GLU A  46 " =    0.875
peak=    3.590 closest distance to " CB  GLN A 183 " =    1.278
peak=    3.586 closest distance to " O   HOH Z 258 " =    2.016
peak=    3.580 closest distance to " O   HOH Z 359 " =    1.470
peak=    3.572 closest distance to " O   HOH Z 193 " =    2.182
peak=    3.572 closest distance to " CB  TYR A 169 " =    0.704
peak=    3.572 closest distance to " CA  ARG A 102 " =    1.070
peak=    3.563 closest distance to " CD  LYS A  76 " =    1.891
peak=    3.558 closest distance to " CA  THR A 264 " =    0.887
peak=    3.554 closest distance to " O   HOH Z 368 " =    1.840
peak=    3.550 closest distance to " O   HOH Z 272 " =    1.798
peak=    3.548 closest distance to " N   TYR A  15 " =    0.994
peak=    3.547 closest distance to " CD BLYS A 290 " =    0.928
peak=    3.546 closest distance to " CZ  PHE A  38 " =    1.296
peak=    3.540 closest distance to " O   HOH Z 111 " =    1.745
peak=    3.537 closest distance to " O   HOH Z  61 " =    1.633
peak=    3.534 closest distance to " CB  GLU A 152 " =    1.131
peak=    3.532 closest distance to " N   SER A 271 " =    1.027
peak=    3.531 closest distance to " CG2 VAL A 257 " =    0.804
peak=    3.527 closest distance to " OD2 ASP A 286 " =    3.246
peak=    3.524 closest distance to " O   HOH Z 325 " =    2.278
peak=    3.520 closest distance to " O   HOH Z  80 " =    1.681
peak=    3.520 closest distance to " CD1 LEU A 300 " =    1.119
peak=    3.517 closest distance to " CA  ASP A 124 " =    0.817
peak=    3.515 closest distance to " NH2AARG A 190 " =    1.919
peak=    3.511 closest distance to " CZ3 TRP A 266 " =    0.957
peak=    3.510 closest distance to " O   PRO A 198 " =    1.583
peak=    3.506 closest distance to " O   HOH Z 188 " =    2.610
peak=    3.503 closest distance to " CA  LEU A 101 " =    1.194
peak=    3.500 closest distance to " O   HOH Z 394 " =    3.957
peak=    3.494 closest distance to " N   CYS A 260 " =    0.883
peak=    3.492 closest distance to " CE3 TRP A 150 " =    1.124
peak=    3.489 closest distance to " ND2 ASN A 249 " =    0.832
peak=    3.487 closest distance to " CB  ALA A  43 " =    0.881
peak=    3.482 closest distance to " OE2 GLU A  53 " =    1.500
peak=    3.482 closest distance to " O   HOH Z 154 " =    2.109
peak=    3.476 closest distance to " O   HOH Z 298 " =    2.608
peak=    3.475 closest distance to " CB  GLU A 128 " =    0.962
peak=    3.474 closest distance to " CA  GLU A 152 " =    1.041
peak=    3.471 closest distance to " O   HOH Z 434 " =    1.440
peak=    3.470 closest distance to " O   HOH Z 329 " =    4.237
peak=    3.469 closest distance to " O   HOH Z  78 " =    1.567
peak=    3.466 closest distance to " NE2 GLN A  55 " =    0.908
peak=    3.464 closest distance to " CA  ARG A  36 " =    1.172
peak=    3.463 closest distance to " CA  ARG A 139 " =    1.110
peak=    3.461 closest distance to " CA  TYR A 116 " =    1.352
peak=    3.461 closest distance to " O   HOH Z 124 " =    1.886
peak=    3.460 closest distance to " O   ASN A 209 " =    1.484
peak=    3.454 closest distance to " O   HOH Z 414 " =    1.170
peak=    3.451 closest distance to " CB  ASP A 140 " =    0.847
peak=    3.449 closest distance to " CB  LEU A 237 " =    0.850
peak=    3.448 closest distance to " O   HOH Z  90 " =    2.341
peak=    3.446 closest distance to " O   SER A  87 " =    2.433
peak=    3.443 closest distance to " O   HOH Z 285 " =    2.143
peak=    3.438 closest distance to " O   HOH Z 122 " =    1.961
peak=    3.428 closest distance to " O   ASN A  74 " =    1.381
peak=    3.423 closest distance to " O   HOH Z 369 " =    1.717
peak=    3.420 closest distance to " O   HOH Z 195 " =    1.259
peak=    3.416 closest distance to " CE2 TYR A 186 " =    0.844
peak=    3.410 closest distance to " O   MET A 105 " =    1.751
peak=    3.407 closest distance to " CB  ALA A  10 " =    0.929
peak=    3.404 closest distance to " CB  THR A  82 " =    1.197
peak=    3.399 closest distance to " CA  ARG A 159 " =    1.381
peak=    3.399 closest distance to " O   HOH Z 184 " =    1.673
peak=    3.399 closest distance to " O   HOH Z  28 " =    1.462
peak=    3.399 closest distance to " NH1 ARG A 138 " =    1.021
peak=    3.394 closest distance to " CE1 PHE A 218 " =    1.081
peak=    3.394 closest distance to " OG BSER A  99 " =    2.317
peak=    3.391 closest distance to " O   HOH Z 368 " =    3.775
peak=    3.386 closest distance to " CD  ARG A 195 " =    3.502
peak=    3.386 closest distance to " O   HOH Z 132 " =    2.490
peak=    3.384 closest distance to " O   THR A 220 " =    1.447
peak=    3.381 closest distance to " O   HOH Z 251 " =    1.570
peak=    3.380 closest distance to " N   VAL A 296 " =    1.826
peak=    3.379 closest distance to " O   HOH Z 298 " =    4.147
peak=    3.379 closest distance to " OG  SER A 135 " =    1.275
peak=    3.372 closest distance to " O   HOH Z 128 " =    2.262
peak=    3.372 closest distance to " CB  SER A  97 " =    1.106
peak=    3.371 closest distance to " CG2 THR A  29 " =    1.531
peak=    3.367 closest distance to " O   HOH Z 189 " =    3.499
peak=    3.365 closest distance to " CG2 ILE A  20 " =    1.465
peak=    3.363 closest distance to " CB  MET A  40 " =    0.794
peak=    3.358 closest distance to " O   HOH Z 112 " =    1.080
peak=    3.353 closest distance to " O   HOH Z  60 " =    1.338
peak=    3.352 closest distance to " O   ALA A 165 " =    1.513
peak=    3.346 closest distance to " CG1 VAL A 153 " =    1.065
peak=    3.345 closest distance to " CG1 ILE A  33 " =    1.146
peak=    3.341 closest distance to " O   HOH Z 213 " =    2.094
peak=    3.337 closest distance to " O   HOH Z 365 " =    2.770
peak=    3.336 closest distance to " O   HOH Z   2 " =    1.533
peak=    3.333 closest distance to " ND1 HIS A  81 " =    1.977
peak=    3.333 closest distance to " CB  ASP A 171 " =    0.779
peak=    3.331 closest distance to " CB  ALA A 114 " =    0.755
peak=    3.327 closest distance to " CB  TYR A 169 " =    0.903
peak=    3.327 closest distance to " CA  SER A  87 " =    1.062
peak=    3.325 closest distance to " O   HOH Z 346 " =    1.739
peak=    3.325 closest distance to " O   HOH Z  53 " =    2.386
peak=    3.322 closest distance to " CB  LYS A 117 " =    1.217
peak=    3.322 closest distance to " CB  ASN A 187 " =    1.029
peak=    3.321 closest distance to " CD  ARG A  66 " =    2.012
peak=    3.317 closest distance to " CA  ILE A 106 " =    0.868
peak=    3.308 closest distance to " CG2 ILE A  20 " =    1.480
peak=    3.306 closest distance to " CG AARG A 275 " =    1.371
peak=    3.304 closest distance to " CG2 VAL A 197 " =    1.184
peak=    3.304 closest distance to " CA  ILE A 263 " =    1.048
peak=    3.303 closest distance to " OH  TYR A 186 " =    1.164
peak=    3.303 closest distance to " CB  LEU A 300 " =    0.915
peak=    3.299 closest distance to " O   HOH Z 153 " =    1.499
peak=    3.296 closest distance to " O   HOH Z   3 " =    2.106
peak=    3.295 closest distance to " O   HOH Z 419 " =    1.919
peak=    3.295 closest distance to " O   HOH Z  40 " =    2.003
peak=    3.295 closest distance to " CB  ARG A  79 " =    0.997
peak=    3.290 closest distance to " O   HOH Z 373 " =    1.580
peak=    3.288 closest distance to " OG BSER A 134 " =    2.790
peak=    3.281 closest distance to " CD  ARG A  66 " =    2.015
peak=    3.280 closest distance to " O   HOH Z 367 " =    2.809
peak=    3.279 closest distance to " O   HOH Z 201 " =    1.612
peak=    3.278 closest distance to " CG  MET A 113 " =    1.580
peak=    3.274 closest distance to " CG  ARG A 138 " =    1.253
peak=    3.274 closest distance to " O   HOH Z 395 " =    3.154
peak=    3.271 closest distance to " CA  ALA A 129 " =    1.232
peak=    3.271 closest distance to " O   THR A 294 " =    1.076
peak=    3.270 closest distance to " OD2 ASP A  65 " =    3.112
peak=    3.265 closest distance to " CB  ARG A 138 " =    0.978
peak=    3.264 closest distance to " CG1 ILE A 151 " =    1.061
peak=    3.263 closest distance to " NE1 TRP A 274 " =    0.871
peak=    3.258 closest distance to " O   HOH Z 393 " =    1.311
peak=    3.255 closest distance to " CG  GLU A  37 " =    0.991
peak=    3.254 closest distance to " NE2 GLN A  73 " =    1.570
peak=    3.253 closest distance to " O   HOH Z 188 " =    1.500
peak=    3.249 closest distance to " O   HOH Z 385 " =    3.893
peak=    3.247 closest distance to " CG  PHE A 204 " =    0.865
peak=    3.245 closest distance to " O   HOH Z 222 " =    2.265
peak=    3.240 closest distance to " CE3 TRP A 274 " =    1.445
peak=    3.239 closest distance to " O   HOH Z 145 " =    1.529
peak=    3.239 closest distance to " O   HOH Z 207 " =    2.312
peak=    3.238 closest distance to " N   GLU A 152 " =    1.489
peak=    3.237 closest distance to " CA  SER A  95 " =    0.963
peak=    3.236 closest distance to " CD2 PHE A  59 " =    1.855
peak=    3.235 closest distance to " CG  GLN A  58 " =    1.133
peak=    3.234 closest distance to " O   HOH Z 265 " =    1.924
peak=    3.229 closest distance to " CB  ALA A 104 " =    0.746
peak=    3.227 closest distance to " O   HOH Z 327 " =    1.589
peak=    3.224 closest distance to " NE AARG A 275 " =    1.624
peak=    3.221 closest distance to " O   HOH Z  26 " =    1.160
peak=    3.220 closest distance to " O   HOH Z 357 " =    2.362
peak=    3.219 closest distance to " O   HOH Z   7 " =    3.535
peak=    3.218 closest distance to " O   HOH Z 148 " =    3.624
peak=    3.217 closest distance to " O   HOH Z  21 " =    1.783
peak=    3.212 closest distance to " CG1 ILE A 120 " =    1.430
peak=    3.208 closest distance to " O   HOH Z 390 " =    1.275
peak=    3.205 closest distance to " O   HOH Z  97 " =    1.419
peak=    3.200 closest distance to " O   HOH Z 402 " =    1.454
peak=    3.197 closest distance to " CB  GLN A  88 " =    1.436
peak=    3.197 closest distance to " CA  TRP A  92 " =    1.177
peak=    3.196 closest distance to " CB  ALA A 114 " =    1.081
peak=    3.194 closest distance to " CB  ASP A 253 " =    0.969
peak=    3.193 closest distance to " O   HOH Z 405 " =    1.602
peak=    3.192 closest distance to " O   HOH Z 302 " =    1.703
peak=    3.191 closest distance to " NZ  LYS A 166 " =    0.897
peak=    3.191 closest distance to " O   HOH Z 438 " =    1.942
peak=    3.187 closest distance to " O   HOH Z 234 " =    3.849
peak=    3.185 closest distance to " CB  ARG A 156 " =    1.097
peak=    3.181 closest distance to " O   HOH Z 116 " =    3.368
peak=    3.179 closest distance to " CG  GLN A 144 " =    0.931
peak=    3.178 closest distance to " O   THR A 251 " =    1.219
peak=    3.178 closest distance to " O   HOH Z 391 " =    2.889
peak=    3.178 closest distance to " O   HOH Z 282 " =    1.791
peak=    3.176 closest distance to " CB  ASP A 191 " =    1.345
peak=    3.171 closest distance to " O   HOH Z 171 " =    2.718
peak=    3.170 closest distance to " CD  LYS A 166 " =    1.409
peak=    3.170 closest distance to " CB  LEU A 143 " =    1.159
peak=    3.170 closest distance to " CB  PRO A 243 " =    1.222
peak=    3.167 closest distance to " NH1 ARG A  66 " =    1.883
peak=    3.166 closest distance to " O   HOH Z 280 " =    3.101
peak=    3.160 closest distance to " O   HOH Z 271 " =    3.072
peak=    3.146 closest distance to " CD1 LEU A 167 " =    1.180
peak=    3.142 closest distance to " CA  GLY A  35 " =    1.008
peak=    3.142 closest distance to " CB  TRP A 179 " =    1.478
peak=    3.136 closest distance to " O   HOH Z 218 " =    1.634
peak=    3.135 closest distance to " CA  GLY A 241 " =    0.866
peak=    3.134 closest distance to " O   HOH Z 213 " =    2.696
peak=    3.129 closest distance to " N   GLU A   2 " =    1.528
peak=    3.126 closest distance to " O   HOH Z  59 " =    1.773
peak=    3.126 closest distance to " N   PHE A 130 " =    1.255
peak=    3.125 closest distance to " CZ3 TRP A 177 " =    1.083
peak=    3.121 closest distance to " O   HOH Z   1 " =    1.736
peak=    3.119 closest distance to " CB  GLU A  46 " =    0.943
peak=    3.118 closest distance to " O   HOH Z  68 " =    2.022
peak=    3.118 closest distance to " O   HOH Z 392 " =    1.215
peak=    3.115 closest distance to " O   HOH Z 188 " =    2.427
peak=    3.111 closest distance to " CB  LYS A 193 " =    0.947
peak=    3.103 closest distance to " CB  ALA A 299 " =    0.922
peak=    3.102 closest distance to " O   HOH Z 130 " =    3.507
peak=    3.102 closest distance to " CA  ALA A 184 " =    1.218
peak=    3.094 closest distance to " CG2 ILE A 151 " =    0.948
peak=    3.092 closest distance to " O   HOH Z 172 " =    2.718
peak=    3.088 closest distance to " CA  ALA A 180 " =    1.255
peak=    3.087 closest distance to " CB  GLU A 236 " =    1.397
peak=    3.076 closest distance to " CA  ALA A 100 " =    1.075
peak=    3.074 closest distance to " CA  ASP A 162 " =    1.021
peak=    3.072 closest distance to " CG  GLU A 277 " =    1.933
peak=    3.071 closest distance to " O   HOH Z 421 " =    3.017
peak=    3.031 closest distance to " O   HOH Z 225 " =    1.742
peak=    3.016 closest distance to " O   HOH Z 116 " =    1.848

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 237         
Filter by distance & map next to the model:
   mapped sites are within: 0.550 - 5.597
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 236 from: 237
   mapped sites are within: 0.702 - 5.597

peak=   -4.864 closest distance to " O   HOH Z 103 " =    0.823
peak=   -4.690 closest distance to " O   PRO A 198 " =    1.319
peak=   -4.675 closest distance to " O   HOH Z 377 " =    1.912
peak=   -4.495 closest distance to " CB  PRO A 243 " =    2.604
peak=   -4.451 closest distance to " CD  ARG A  14 " =    3.420
peak=   -4.260 closest distance to " CG2 ILE A  49 " =    2.857
peak=   -4.174 closest distance to " CD  ARG A 156 " =    2.052
peak=   -4.166 closest distance to " CG  GLN A 223 " =    2.480
peak=   -4.148 closest distance to " CB  ASP A  27 " =    2.530
peak=   -4.120 closest distance to " O   HOH Z 103 " =    0.702
peak=   -4.085 closest distance to " O   HOH Z  52 " =    1.427
peak=   -4.066 closest distance to " O   HOH Z 216 " =    1.229
peak=   -4.035 closest distance to " CA  GLY A  98 " =    1.901
peak=   -3.997 closest distance to " CG1 VAL A 250 " =    2.587
peak=   -3.978 closest distance to " CD2 LEU A 143 " =    2.557
peak=   -3.972 closest distance to " CG  MET A 105 " =    0.996
peak=   -3.942 closest distance to " CD1 TYR A 247 " =    2.765
peak=   -3.938 closest distance to " CG  GLN A  88 " =    0.921
peak=   -3.928 closest distance to " NZ  LYS A 166 " =    1.199
peak=   -3.925 closest distance to " CD2 TYR A 293 " =    1.888
peak=   -3.923 closest distance to " O   PRO A 163 " =    1.925
peak=   -3.901 closest distance to " O   HOH Z  73 " =    1.911
peak=   -3.900 closest distance to " O   HOH Z  32 " =    1.663
peak=   -3.899 closest distance to " OE1 GLN A  88 " =    1.070
peak=   -3.856 closest distance to " CA  GLY A 241 " =    2.339
peak=   -3.838 closest distance to " O   HOH Z 111 " =    1.669
peak=   -3.817 closest distance to " CG2 THR A 178 " =    2.269
peak=   -3.797 closest distance to " OG BSER A 134 " =    1.516
peak=   -3.776 closest distance to " O   HOH Z 407 " =    3.309
peak=   -3.769 closest distance to " O   HOH Z 316 " =    1.920
peak=   -3.767 closest distance to " O   HOH Z 131 " =    3.958
peak=   -3.766 closest distance to " O   HOH Z 275 " =    1.817
peak=   -3.759 closest distance to " O   SER A  22 " =    2.879
peak=   -3.755 closest distance to " CZ3 TRP A 179 " =    1.187
peak=   -3.741 closest distance to " OG  SER A  97 " =    2.180
peak=   -3.719 closest distance to " CB  ALA A  43 " =    2.679
peak=   -3.715 closest distance to " CG1BVAL A  41 " =    2.737
peak=   -3.709 closest distance to " CE2 TYR A  30 " =    2.613
peak=   -3.680 closest distance to " O   HOH Z 351 " =    1.698
peak=   -3.676 closest distance to " CG  GLN A  55 " =    1.202
peak=   -3.671 closest distance to " O   ALA A  10 " =    1.633
peak=   -3.668 closest distance to " N   ALA A  43 " =    2.376
peak=   -3.662 closest distance to " O   HOH Z 231 " =    2.147
peak=   -3.655 closest distance to " CB  PRO A  54 " =    2.497
peak=   -3.643 closest distance to " CB  ALA A 291 " =    2.307
peak=   -3.635 closest distance to " O   HOH Z 389 " =    2.183
peak=   -3.632 closest distance to " NH2AARG A 275 " =    5.597
peak=   -3.629 closest distance to " O   SER A 135 " =    1.452
peak=   -3.611 closest distance to " CB  ALA A 160 " =    2.174
peak=   -3.610 closest distance to " O   HOH Z 313 " =    1.624
peak=   -3.593 closest distance to " CG1 VAL A 112 " =    2.652
peak=   -3.580 closest distance to " CB  TRP A  85 " =    2.429
peak=   -3.576 closest distance to " O   HOH Z 298 " =    2.439
peak=   -3.572 closest distance to " OG  SER A  87 " =    1.425
peak=   -3.572 closest distance to " O   ILE A  49 " =    1.691
peak=   -3.565 closest distance to " O   HOH Z 231 " =    0.828
peak=   -3.561 closest distance to " O   GLU A 152 " =    1.392
peak=   -3.558 closest distance to " O   HOH Z 185 " =    2.223
peak=   -3.556 closest distance to " O   HOH Z 198 " =    1.903
peak=   -3.553 closest distance to " O   HOH Z  39 " =    0.764
peak=   -3.551 closest distance to " O   HOH Z  69 " =    1.801
peak=   -3.536 closest distance to " CD  GLN A  58 " =    1.232
peak=   -3.535 closest distance to " C   HIS A 108 " =    1.134
peak=   -3.533 closest distance to " CB  ALA A   7 " =    2.006
peak=   -3.518 closest distance to " O   HOH Z 318 " =    1.747
peak=   -3.514 closest distance to " O   HOH Z 189 " =    2.825
peak=   -3.508 closest distance to " CD1 TRP A 179 " =    1.109
peak=   -3.499 closest distance to " CB  ALA A 158 " =    1.609
peak=   -3.496 closest distance to " O   HOH Z  11 " =    1.659
peak=   -3.495 closest distance to " CB  ALA A   9 " =    2.466
peak=   -3.495 closest distance to " O   HOH Z 337 " =    1.427
peak=   -3.482 closest distance to " N   THR A 157 " =    1.627
peak=   -3.463 closest distance to " CB  HIS A  86 " =    1.124
peak=   -3.463 closest distance to " CG1 VAL A  78 " =    2.590
peak=   -3.462 closest distance to " O   HOH Z  60 " =    1.524
peak=   -3.451 closest distance to " O   HOH Z 115 " =    1.576
peak=   -3.448 closest distance to " O   HOH Z  65 " =    1.563
peak=   -3.446 closest distance to " CA  GLY A 133 " =    1.912
peak=   -3.445 closest distance to " CD2 TYR A 116 " =    2.168
peak=   -3.443 closest distance to " O   VAL A 125 " =    2.345
peak=   -3.436 closest distance to " CB  ALA A 100 " =    2.141
peak=   -3.435 closest distance to " O   HOH Z 426 " =    1.632
peak=   -3.426 closest distance to " O   HOH Z 368 " =    1.557
peak=   -3.424 closest distance to " O   ARG A  56 " =    4.386
peak=   -3.422 closest distance to " O   HOH Z 134 " =    1.859
peak=   -3.418 closest distance to " O   HOH Z  68 " =    1.527
peak=   -3.414 closest distance to " O   HOH Z 275 " =    1.633
peak=   -3.407 closest distance to " C   ASN A 285 " =    2.412
peak=   -3.394 closest distance to " CB  ALA A 227 " =    2.418
peak=   -3.393 closest distance to " CG  LEU A  83 " =    2.230
peak=   -3.392 closest distance to " CB  ASP A 132 " =    2.356
peak=   -3.389 closest distance to " CE1 PHE A  16 " =    2.758
peak=   -3.385 closest distance to " O   HOH Z 278 " =    1.191
peak=   -3.383 closest distance to " O   HOH Z 105 " =    1.273
peak=   -3.382 closest distance to " O   PHE A 218 " =    1.445
peak=   -3.378 closest distance to " OG  SER A 245 " =    1.479
peak=   -3.377 closest distance to " O   HOH Z 281 " =    2.923
peak=   -3.374 closest distance to " N   ASP A 132 " =    1.904
peak=   -3.371 closest distance to " O   SER A 210 " =    1.872
peak=   -3.361 closest distance to " CA  GLY A 241 " =    3.023
peak=   -3.355 closest distance to " NE2 GLN A  55 " =    1.271
peak=   -3.353 closest distance to " O   TYR A 186 " =    1.789
peak=   -3.353 closest distance to " CB  GLN A  11 " =    1.627
peak=   -3.346 closest distance to " ND2 ASN A 187 " =    1.563
peak=   -3.346 closest distance to " O   HOH Z 364 " =    2.264
peak=   -3.344 closest distance to " OD1 ASN A  60 " =    0.894
peak=   -3.344 closest distance to " CD1 LEU A 101 " =    2.306
peak=   -3.343 closest distance to " O   HOH Z  69 " =    1.772
peak=   -3.343 closest distance to " O   ASP A 253 " =    1.777
peak=   -3.342 closest distance to " C   LEU A 143 " =    1.254
peak=   -3.341 closest distance to " CE BMET A  47 " =    1.584
peak=   -3.336 closest distance to " O   HOH Z 412 " =    4.510
peak=   -3.335 closest distance to " O   HOH Z 128 " =    2.577
peak=   -3.330 closest distance to " O   HOH Z 166 " =    2.289
peak=   -3.329 closest distance to " CD  LYS A 166 " =    2.555
peak=   -3.327 closest distance to " SG BCYS A 201 " =    2.113
peak=   -3.326 closest distance to " CD  LYS A 289 " =    2.276
peak=   -3.319 closest distance to " O   HOH Z 364 " =    1.530
peak=   -3.319 closest distance to " N   ARG A 159 " =    2.054
peak=   -3.316 closest distance to " CB  PRO A 163 " =    2.485
peak=   -3.313 closest distance to " O   HOH Z 166 " =    1.273
peak=   -3.311 closest distance to " O   SER A 141 " =    1.829
peak=   -3.311 closest distance to " CA  GLY A 203 " =    2.444
peak=   -3.310 closest distance to " CB  ALA A  10 " =    2.265
peak=   -3.309 closest distance to " CD  GLN A  88 " =    1.293
peak=   -3.309 closest distance to " CZ2 TRP A 274 " =    0.981
peak=   -3.306 closest distance to " O   HOH Z 394 " =    1.566
peak=   -3.302 closest distance to " O   GLY A 211 " =    1.193
peak=   -3.302 closest distance to " OD1 ASP A 171 " =    1.602
peak=   -3.301 closest distance to " CB  ALA A 131 " =    1.999
peak=   -3.300 closest distance to " CA  HIS A 207 " =    1.096
peak=   -3.298 closest distance to " CG1 VAL A 112 " =    2.763
peak=   -3.291 closest distance to " CG  LEU A 167 " =    1.005
peak=   -3.289 closest distance to " CG  GLU A  53 " =    1.325
peak=   -3.288 closest distance to " O   HOH Z 174 " =    2.526
peak=   -3.286 closest distance to " O   HOH Z 259 " =    4.327
peak=   -3.284 closest distance to " O   GLY A  80 " =    2.441
peak=   -3.284 closest distance to " N   ASP A 270 " =    1.359
peak=   -3.282 closest distance to " ND2 ASN A  60 " =    3.889
peak=   -3.280 closest distance to " CG2 ILE A 151 " =    2.525
peak=   -3.279 closest distance to " O   HOH Z 308 " =    2.111
peak=   -3.277 closest distance to " O   HOH Z 145 " =    1.277
peak=   -3.277 closest distance to " O   HOH Z  53 " =    1.638
peak=   -3.275 closest distance to " O   HOH Z  10 " =    1.620
peak=   -3.275 closest distance to " CB  ASN A  39 " =    2.378
peak=   -3.275 closest distance to " OH  TYR A 247 " =    1.712
peak=   -3.269 closest distance to " OD1 ASN A 148 " =    1.471
peak=   -3.266 closest distance to " O   HOH Z 359 " =    3.122
peak=   -3.262 closest distance to " O   HOH Z 421 " =    3.063
peak=   -3.260 closest distance to " N   ASP A 171 " =    2.465
peak=   -3.256 closest distance to " O   HOH Z 286 " =    1.640
peak=   -3.253 closest distance to " O   GLY A  17 " =    1.168
peak=   -3.251 closest distance to " NE2 GLN A 240 " =    1.429
peak=   -3.250 closest distance to " CG  TRP A 266 " =    1.689
peak=   -3.248 closest distance to " CG  MET A 188 " =    1.298
peak=   -3.246 closest distance to " N   LEU A 282 " =    2.154
peak=   -3.244 closest distance to " OG ASER A 134 " =    1.312
peak=   -3.243 closest distance to " O   HOH Z 102 " =    1.653
peak=   -3.242 closest distance to " C   LEU A 222 " =    1.080
peak=   -3.240 closest distance to " CD2 PHE A  61 " =    2.095
peak=   -3.239 closest distance to " O   PRO A 243 " =    2.470
peak=   -3.234 closest distance to " NH2 ARG A  79 " =    2.184
peak=   -3.228 closest distance to " CB  PHE A 130 " =    1.194
peak=   -3.228 closest distance to " C   PHE A  59 " =    1.177
peak=   -3.225 closest distance to " O   HOH Z 219 " =    4.219
peak=   -3.223 closest distance to " O   HOH Z 380 " =    5.338
peak=   -3.223 closest distance to " ND2 ASN A 285 " =    2.071
peak=   -3.221 closest distance to " OD2 ASP A 171 " =    1.721
peak=   -3.219 closest distance to " CZ  PHE A 130 " =    1.071
peak=   -3.217 closest distance to " O   ASP A 162 " =    2.266
peak=   -3.211 closest distance to " OH  TYR A 172 " =    1.900
peak=   -3.211 closest distance to " CA  ASN A 110 " =    0.972
peak=   -3.211 closest distance to " O   HOH Z 252 " =    3.887
peak=   -3.210 closest distance to " O   ALA A   7 " =    1.406
peak=   -3.206 closest distance to " O   HOH Z 193 " =    1.268
peak=   -3.203 closest distance to " O   HOH Z 114 " =    1.492
peak=   -3.203 closest distance to " CD2 TYR A 172 " =    2.208
peak=   -3.200 closest distance to " OE2 GLU A 152 " =    2.243
peak=   -3.196 closest distance to " ND2 ASN A 249 " =    2.085
peak=   -3.195 closest distance to " CB  ALA A 291 " =    2.037
peak=   -3.195 closest distance to " O   HOH Z  37 " =    1.799
peak=   -3.194 closest distance to " CD2 PHE A 225 " =    1.111
peak=   -3.191 closest distance to " O   HOH Z   9 " =    2.003
peak=   -3.189 closest distance to " O   HOH Z 163 " =    1.740
peak=   -3.184 closest distance to " CA  GLY A 241 " =    3.178
peak=   -3.183 closest distance to " CE3 TRP A  70 " =    1.715
peak=   -3.183 closest distance to " CG1 VAL A 125 " =    1.778
peak=   -3.180 closest distance to " O   ARG A  56 " =    1.912
peak=   -3.173 closest distance to " ND2 ASN A 173 " =    1.913
peak=   -3.172 closest distance to " CG2BVAL A  41 " =    1.226
peak=   -3.170 closest distance to " O   HOH Z 348 " =    2.115
peak=   -3.167 closest distance to " O   ASP A  27 " =    1.819
peak=   -3.161 closest distance to " CG  LEU A 282 " =    2.383
peak=   -3.160 closest distance to " O   HOH Z 357 " =    1.976
peak=   -3.159 closest distance to " O   HOH Z 259 " =    1.063
peak=   -3.155 closest distance to " O   ALA A  84 " =    1.691
peak=   -3.155 closest distance to " O   HOH Z 276 " =    1.214
peak=   -3.155 closest distance to " O   HOH Z 139 " =    3.994
peak=   -3.154 closest distance to " O   HOH Z 277 " =    1.649
peak=   -3.154 closest distance to " CB  ASP A  50 " =    2.531
peak=   -3.151 closest distance to " O   HOH Z  22 " =    2.057
peak=   -3.149 closest distance to " CB  VAL A 189 " =    2.411
peak=   -3.140 closest distance to " CZ  PHE A  16 " =    2.387
peak=   -3.136 closest distance to " CA  ASP A 298 " =    1.113
peak=   -3.133 closest distance to " O   HOH Z 290 " =    0.837
peak=   -3.127 closest distance to " CB  CYS A 254 " =    2.123
peak=   -3.125 closest distance to " CA  GLY A  57 " =    2.063
peak=   -3.123 closest distance to " O   HOH Z 198 " =    2.044
peak=   -3.122 closest distance to " OD2 ASP A 270 " =    1.141
peak=   -3.121 closest distance to " CE2 TRP A  70 " =    2.417
peak=   -3.117 closest distance to " O   HOH Z 201 " =    1.791
peak=   -3.117 closest distance to " SD  MET A 105 " =    2.618
peak=   -3.117 closest distance to " O   HOH Z  28 " =    1.406
peak=   -3.116 closest distance to " O   HOH Z 389 " =    1.569
peak=   -3.112 closest distance to " CE  LYS A  76 " =    2.876
peak=   -3.112 closest distance to " N   ASP A 191 " =    1.127
peak=   -3.110 closest distance to " CD1 LEU A 297 " =    2.623
peak=   -3.101 closest distance to " O   HOH Z 100 " =    1.502
peak=   -3.099 closest distance to " O   VAL A  67 " =    2.711
peak=   -3.094 closest distance to " CE3 TRP A 150 " =    2.275
peak=   -3.090 closest distance to " O   HOH Z 118 " =    1.380
peak=   -3.085 closest distance to " O   HOH Z   1 " =    1.307
peak=   -3.085 closest distance to " CG1 VAL A 112 " =    3.072
peak=   -3.084 closest distance to " O   HOH Z 108 " =    1.262
peak=   -3.082 closest distance to " CE3 TRP A 274 " =    2.541
peak=   -3.072 closest distance to " OE2 GLU A 152 " =    1.281
peak=   -3.071 closest distance to " O   HOH Z  26 " =    1.003
peak=   -3.070 closest distance to " O   GLN A 240 " =    2.032
peak=   -3.069 closest distance to " O   ARG A 145 " =    1.308
peak=   -3.063 closest distance to " O   TRP A  70 " =    1.453
peak=   -3.061 closest distance to " O   HOH Z 139 " =    1.065
peak=   -3.055 closest distance to " O   HOH Z  51 " =    1.529
peak=   -3.048 closest distance to " O   VAL A 189 " =    1.692
peak=   -3.044 closest distance to " OE1 GLU A 236 " =    1.162
peak=   -3.042 closest distance to " OG BSER A 134 " =    1.937
peak=   -3.026 closest distance to " CD  GLN A  55 " =    1.238

================= 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    :  0.4799 0.4775   6.288140e+00   6.272797e+00
   1_bss:  0.4727 0.4736   6.284757e+00   6.269109e+00
   1_xyz:  0.3334 0.3688   6.046876e+00   6.114914e+00
   1_adp:  0.3075 0.3724   6.007249e+00   6.126463e+00
   1_occ:  0.3069 0.3724   6.006654e+00   6.126517e+00
   2_bss:  0.3063 0.3717   6.008443e+00   6.127082e+00
   2_xyz:  0.2288 0.2842   5.756682e+00   5.921994e+00
   2_adp:  0.2069 0.2779   5.698929e+00   5.898509e+00
   2_occ:  0.2068 0.2778   5.698692e+00   5.899128e+00
   3_bss:  0.2071 0.2786   5.699835e+00   5.900257e+00
   3_xyz:  0.1610 0.2221   5.472294e+00   5.706028e+00
   3_adp:  0.1477 0.2059   5.397928e+00   5.633123e+00
   3_occ:  0.1476 0.2058   5.397765e+00   5.633373e+00
   4_bss:  0.1480 0.2056   5.396830e+00   5.631087e+00
   4_xyz:  0.1363 0.1911   5.323618e+00   5.560131e+00
   4_adp:  0.1327 0.1872   5.301780e+00   5.537292e+00
   4_occ:  0.1326 0.1872   5.301722e+00   5.537508e+00
   5_bss:  0.1326 0.1872   5.301618e+00   5.537353e+00
   5_xyz:  0.1250 0.1783   5.252390e+00   5.496873e+00
   5_adp:  0.1232 0.1756   5.239879e+00   5.484284e+00
   5_occ:  0.1231 0.1756   5.239843e+00   5.484430e+00
   5_bss:  0.1235 0.1753   5.238347e+00   5.482217e+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:  0.316  73.710  -0.300  -0.620   3.576  -0.000   0.000   0.000
   1_xyz:  0.316  73.710  -0.300  -0.620   3.576  -0.000   0.000   0.000
   1_adp:  0.316  73.710  -0.300  -0.620   3.576  -0.000   0.000   0.000
   1_occ:  0.316  73.710  -0.300  -0.620   3.576  -0.000   0.000   0.000
   2_bss:  0.356  85.557  -0.728  -1.236   2.175  -0.000   0.000   0.000
   2_xyz:  0.356  85.557  -0.728  -1.236   2.175  -0.000   0.000   0.000
   2_adp:  0.356  85.557  -0.728  -1.236   2.175  -0.000   0.000   0.000
   2_occ:  0.356  85.557  -0.728  -1.236   2.175  -0.000   0.000   0.000
   3_bss:  0.347  89.818  -1.004  -1.453   1.204  -0.000   0.000   0.000
   3_xyz:  0.347  89.818  -1.004  -1.453   1.204  -0.000   0.000   0.000
   3_adp:  0.347  89.818  -1.004  -1.453   1.204  -0.000   0.000   0.000
   3_occ:  0.347  89.818  -1.004  -1.453   1.204  -0.000   0.000   0.000
   4_bss:  0.338  87.495  -1.405  -1.934   0.371  -0.000   0.000   0.000
   4_xyz:  0.338  87.495  -1.405  -1.934   0.371  -0.000   0.000   0.000
   4_adp:  0.338  87.495  -1.405  -1.934   0.371  -0.000   0.000   0.000
   4_occ:  0.338  87.495  -1.405  -1.934   0.371  -0.000   0.000   0.000
   5_bss:  0.329  79.543  -1.405  -1.934   0.371  -0.000   0.000   0.000
   5_xyz:  0.329  79.543  -1.405  -1.934   0.371  -0.000   0.000   0.000
   5_adp:  0.329  79.543  -1.405  -1.934   0.371  -0.000   0.000   0.000
   5_occ:  0.329  79.543  -1.405  -1.934   0.371  -0.000   0.000   0.000
   5_bss:  0.328  78.924  -1.259  -1.892   0.364  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  59.341 0.4010  0.5389    71841.164
   1_bss:  58.734 0.4082  0.5740    70893.426
   1_xyz:  39.891 0.6444  0.8585    38140.691
   1_adp:  41.120 0.6287  0.8331    39826.050
   1_occ:  41.180 0.6279  0.8314    39838.705
   2_bss:  41.144 0.6284  0.8106    39925.474
   2_xyz:  29.051 0.7671  0.9451    21063.704
   2_adp:  28.002 0.7788  0.9469    20104.317
   2_occ:  28.018 0.7786  0.9463    20117.694
   3_bss:  28.035 0.7785  0.9300    20192.039
   3_xyz:  21.724 0.8436  0.9816    12537.516
   3_adp:  19.759 0.8634  0.9853    10897.716
   3_occ:  19.765 0.8634  0.9851    10895.990
   4_bss:  19.691 0.8640  0.9663    10826.402
   4_xyz:  17.839 0.8816  0.9725     9156.037
   4_adp:  17.283 0.8870  0.9665     8799.107
   4_occ:  17.286 0.8870  0.9664     8798.106
   5_bss:  17.286 0.8869  0.9663     8795.705
   5_xyz:  16.273 0.8959  0.9731     7934.763
   5_adp:  15.899 0.8994  0.9689     7725.808
   5_occ:  15.904 0.8993  0.9688     7727.903
   5_bss:  15.857 0.8996  0.9710     7655.804
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.6584e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.6584e-01
   1_xyz:   1.663  0.014  0.115 16.736  0.007  4.112   1.6139e-01
   1_adp:   1.663  0.014  0.115 16.736  0.007  4.112   1.6139e-01
   1_occ:   1.663  0.014  0.115 16.736  0.007  4.112   1.6139e-01
   2_bss:   1.663  0.014  0.115 16.736  0.007  4.112   1.6139e-01
   2_xyz:   1.165  0.008  0.083 14.725  0.005  4.110   7.5861e-02
   2_adp:   1.165  0.008  0.083 14.725  0.005  4.110   7.5861e-02
   2_occ:   1.165  0.008  0.083 14.725  0.005  4.110   7.5861e-02
   3_bss:   1.165  0.008  0.083 14.725  0.005  4.110   7.5861e-02
   3_xyz:   1.104  0.009  0.078 14.826  0.004  4.126   7.3107e-02
   3_adp:   1.104  0.009  0.078 14.826  0.004  4.126   7.3107e-02
   3_occ:   1.104  0.009  0.078 14.826  0.004  4.126   7.3107e-02
   4_bss:   1.104  0.009  0.078 14.826  0.004  4.126   7.3107e-02
   4_xyz:   0.989  0.008  0.074 14.482  0.004  4.126   5.8558e-02
   4_adp:   0.989  0.008  0.074 14.482  0.004  4.126   5.8558e-02
   4_occ:   0.989  0.008  0.074 14.482  0.004  4.126   5.8558e-02
   5_bss:   0.989  0.008  0.074 14.482  0.004  4.126   5.8558e-02
   5_xyz:   1.062  0.009  0.078 14.518  0.004  4.133   6.5048e-02
   5_adp:   1.062  0.009  0.078 14.518  0.004  4.133   6.5048e-02
   5_occ:   1.062  0.009  0.078 14.518  0.004  4.133   6.5048e-02
   5_bss:   1.062  0.009  0.078 14.518  0.004  4.133   6.5048e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.4329e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.4329e-01
   1_xyz:   9.904  0.088  0.390 82.065  0.046  1.950   1.2021e-01
   1_adp:   9.904  0.088  0.390 82.065  0.046  1.950   1.2021e-01
   1_occ:   9.904  0.088  0.390 82.065  0.046  1.950   1.2021e-01
   2_bss:   9.904  0.088  0.390 82.065  0.046  1.950   1.2021e-01
   2_xyz:   7.612  0.052  0.265 77.544  0.047  2.230   9.4490e-02
   2_adp:   7.612  0.052  0.265 77.544  0.047  2.230   9.4490e-02
   2_occ:   7.612  0.052  0.265 77.544  0.047  2.230   9.4490e-02
   3_bss:   7.612  0.052  0.265 77.544  0.047  2.230   9.4490e-02
   3_xyz:   8.527  0.049  0.267 81.995  0.037  2.220   9.3030e-02
   3_adp:   8.527  0.049  0.267 81.995  0.037  2.220   9.3030e-02
   3_occ:   8.527  0.049  0.267 81.995  0.037  2.220   9.3030e-02
   4_bss:   8.527  0.049  0.267 81.995  0.037  2.220   9.3030e-02
   4_xyz:   8.619  0.047  0.265 80.930  0.040  2.394   3.7503e-02
   4_adp:   8.619  0.047  0.265 80.930  0.040  2.394   3.7503e-02
   4_occ:   8.619  0.047  0.265 80.930  0.040  2.394   3.7503e-02
   5_bss:   8.619  0.047  0.265 80.930  0.040  2.394   3.7503e-02
   5_xyz:   8.570  0.051  0.241 82.117  0.038  2.353   4.2718e-02
   5_adp:   8.570  0.051  0.241 82.117  0.038  2.353   4.2718e-02
   5_occ:   8.570  0.051  0.241 82.117  0.038  2.353   4.2718e-02
   5_bss:   8.570  0.051  0.241 82.117  0.038  2.353   4.2718e-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: 112.74   0.00  17.26 112.74   0.00  13.31  63.77   0.69  38.79
   1_occ: 112.74   0.00  17.26 112.74   0.00  13.31  63.77   0.69  38.79
   2_bss: 112.74   0.00  17.26 112.74   0.00  13.31  63.77   0.69  38.79
   2_xyz: 112.74   0.00  17.26 112.74   0.00  13.31  63.77   0.69  38.79
   2_adp:  99.25   0.00  18.75  80.55   0.00  13.79  99.25   1.94  45.76
   2_occ:  99.25   0.00  18.75  80.55   0.00  13.79  99.25   1.94  45.76
   3_bss:  99.25   0.00  18.75  80.55   0.00  13.79  99.25   1.94  45.76
   3_xyz:  99.25   0.00  18.75  80.55   0.00  13.79  99.25   1.94  45.76
   3_adp: 106.70   0.00  18.85  88.93   0.00  13.17 106.70   0.00  49.79
   3_occ: 106.70   0.00  18.85  88.93   0.00  13.17 106.70   0.00  49.79
   4_bss: 106.70   0.00  18.85  88.93   0.00  13.17 106.70   0.00  49.79
   4_xyz: 106.70   0.00  18.85  88.93   0.00  13.17 106.70   0.00  49.79
   4_adp: 116.77   0.00  18.53  97.98   0.00  12.86 116.77   0.00  49.36
   4_occ: 116.77   0.00  18.53  97.98   0.00  12.86 116.77   0.00  49.36
   5_bss: 116.77   0.00  18.53  97.98   0.00  12.86 116.77   0.00  49.36
   5_xyz: 116.77   0.00  18.53  97.98   0.00  12.86 116.77   0.00  49.36
   5_adp: 123.66   0.00  18.02  99.82   0.00  12.62 123.66   1.21  47.39
   5_occ: 123.66   0.00  18.02  99.82   0.00  12.62 123.66   1.21  47.39
   5_bss: 123.66   0.00  18.02  99.83   0.00  12.62 123.66   1.21  47.39
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.478    0.020    0.490
   1_adp:    1.478    0.020    0.490
   1_occ:    1.478    0.020    0.490
   2_bss:    1.478    0.020    0.490
   2_xyz:    1.359    0.040    0.600
   2_adp:    1.359    0.040    0.600
   2_occ:    1.359    0.040    0.600
   3_bss:    1.359    0.040    0.600
   3_xyz:    1.303    0.043    0.727
   3_adp:    1.303    0.043    0.727
   3_occ:    1.303    0.043    0.727
   4_bss:    1.303    0.043    0.727
   4_xyz:    1.465    0.038    0.751
   4_adp:    1.465    0.038    0.751
   4_occ:    1.465    0.038    0.751
   5_bss:    1.465    0.038    0.751
   5_xyz:    1.532    0.040    0.777
   5_adp:    1.532    0.040    0.777
   5_occ:    1.532    0.040    0.777
   5_bss:    1.532    0.040    0.777
------------------------------------------------------------------------

CPU time actual refinement: 362.26


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1121/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_1121/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1121/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1121/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1121/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 362.10 
  Macro-tasks:
    bulk solvent and scale       = 61.60  
    individual site refinement   = 139.68 
    weights calculation          = 31.15  
    collect and process          = 6.57   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 239.12 
  Micro-tasks:
    mask                            = 2.47   
    f_calc                          = 109.91 
    alpha_beta                      = 8.23   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 117.00 
    fmodel                         = 9.86   
    r_factors                      = 0.38   
    phase_errors                   = 10.75  
    foms                           = 0.21   
    TOTAL for micro-tasks          = 259.98 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.154 micro seconds
Total CPU time: 6.26 minutes
from_scatterers_fft:    612 calls, 109.49 s
gradients_fft:          557 calls, 104.37 s

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

# Date 2008-01-16 Time 06:29:22 PST -0800 (1200493762.76 s)
Start R-work = 0.4799, R-free = 0.4775 (no bulk solvent and anisotropic scale)
Final R-work = 0.1418, R-free = 0.1913 (no bulk solvent and anisotropic scale)

Start R-work = 0.4727, R-free = 0.4736
Final R-work = 0.1235, R-free = 0.1753