# Date 2008-01-16 Time 05:59:46 PST -0800 (1200491986.31 s)
#phil __OFF__

Command line arguments: "../967.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 20661
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 967

-------------------------------------------------------------------------------
  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: (70.9525, 48.1033, 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: 3.28, 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: (70.9525, 48.1033, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2039 2.02066
Completeness in resolution range: 0.959211
Completeness with d_max=infinity: 0.956214

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2039
                             d_min =   2.0207

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: (70.9525, 48.1033, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2039 2.02066
Completeness in resolution range: 0.959211
Completeness with d_max=infinity: 0.956214

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2043 -  4.3232 [2156/2183]  1939   217  10.1%
  bin  2:  4.3232 -  3.4445 [2047/2063]  1844   203   9.9%
  bin  3:  3.4445 -  3.0130 [2043/2062]  1839   204  10.0%
  bin  4:  3.0130 -  2.7393 [2010/2040]  1810   200  10.0%
  bin  5:  2.7393 -  2.5439 [1993/2012]  1788   205  10.3%
  bin  6:  2.5439 -  2.3945 [2005/2041]  1810   195   9.7%
  bin  7:  2.3945 -  2.2750 [1983/2016]  1784   199  10.0%
  bin  8:  2.2750 -  2.1763 [1978/2012]  1777   201  10.2%
  bin  9:  2.1763 -  2.0927 [1950/1978]  1752   198  10.2%
  bin 10:  2.0927 -  2.0207 [1424/2015]  1287   137   9.6%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_967/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: 0.15 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:
        1.76 -     2.39: 15
        2.39 -     3.02: 1975
        3.02 -     3.64: 4476
        3.64 -     4.27: 8837
        4.27 -     4.90: 12228
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.762 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.842 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.873 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.873 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 27526 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_967/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_967/model_refine_001.geo

CPU time processing inputs: 9.23


============================ 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 = 70.9525 48.10325 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: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4913   r_free= 0.4831   ksol= 0.00   Bsol= 0.00   scale= 0.849    |
|                                                                             |
| 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:   0.82 A                  |
| x-ray target function (ml) for work reflections: 6.299064                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2043 -  4.8215 0.99   1395  154 0.3957 0.3879      6.5984      6.5654|
|  2:  4.8215 -  3.8474 0.99   1338  151 0.4460 0.4754      6.9081      6.9488|
|  3:  3.8474 -  3.3671 0.99   1321  148 0.4792 0.4280      6.7315      6.6496|
|  4:  3.3671 -  3.0620 0.99   1297  135 0.4848 0.4838      6.5619      6.5054|
|  5:  3.0620 -  2.8440 0.99   1298  148 0.5154 0.4614      6.3882        6.41|
|  6:  2.8440 -  2.6773 0.99   1302  147 0.5187 0.5361      6.2837      6.2138|
|  7:  2.6773 -  2.5439 0.99   1269  146 0.5225 0.4860      6.2617      6.1669|
|  8:  2.5439 -  2.4336 0.98   1306  138 0.5192 0.4880      6.1933      6.1971|
|  9:  2.4336 -  2.3403 0.98   1272  145 0.5255 0.5356      6.1124      6.1634|
| 10:  2.3403 -  2.2598 0.98   1257  136 0.5417 0.5032      6.1224      6.1241|
| 11:  2.2598 -  2.1893 1.00   1278  147 0.5345 0.5488      6.0396      6.0829|
| 12:  2.1893 -  2.1269 0.97   1279  136 0.5272 0.5573      5.9706      6.0302|
| 13:  2.1269 -  2.0711 0.98   1252  142 0.5287 0.5587      5.8983      5.8397|
| 14:  2.0711 -  2.0207 0.60    766   86 0.5154 0.5057      5.8528      5.7585|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2043 -  4.8215  1395   154  0.68  35.74   0.80     0.72      77581.45|
|  2:  4.8215 -  3.8474  1338   151  0.68  36.86   0.86     0.76     116110.31|
|  3:  3.8474 -  3.3671  1321   148  0.57  45.96   0.85     0.73     121854.63|
|  4:  3.3671 -  3.0620  1297   135  0.47  53.93   0.85     0.62     110317.35|
|  5:  3.0620 -  2.8440  1298   148  0.39  60.74   0.85     0.53      84353.31|
|  6:  2.8440 -  2.6773  1302   147  0.35  63.75   0.83     0.47      74653.19|
|  7:  2.6773 -  2.5439  1269   146  0.33  65.47   0.87     0.44      67619.28|
|  8:  2.5439 -  2.4336  1306   138  0.30  67.83   0.87     0.41      64404.78|
|  9:  2.4336 -  2.3403  1272   145  0.26  70.68   0.87     0.38      61600.72|
| 10:  2.3403 -  2.2598  1257   136  0.29  68.52   0.88     0.41      54251.79|
| 11:  2.2598 -  2.1893  1278   147  0.27  70.12   0.89     0.40      51049.96|
| 12:  2.1893 -  2.1269  1279   136  0.27  69.98   0.88     0.39      46176.98|
| 13:  2.1269 -  2.0711  1252   142  0.24  71.81   0.87     0.36      40862.13|
| 14:  2.0711 -  2.0207   766    86  0.28  69.22   0.91     0.37      31466.63|
|alpha:            min =        0.36 max =            0.76 mean =         0.50|
|beta:             min =    31466.63 max =       121854.63 mean =     73191.12|
|figures of merit: min =        0.00 max =            1.00 mean =         0.39|
|phase err.(work): min =        0.00 max =           89.99 mean =        60.21|
|phase err.(test): min =        0.00 max =           89.92 mean =        60.49|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.028764             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.117   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.819092              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.882   (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 |  1.762 -  2.076:        7 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.076 -  2.389:        8 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.389 -  2.703:      108 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.703 -  3.017:     1867 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.017 -  3.331:     1820 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.331 -  3.645:     2656 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.645 -  3.958:     4595 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.958 -  4.272:     4242 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.272 -  4.586:     5532 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.586 -  4.900:     6696 |
|-----------------------------------------------------------------------------|
|-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 |        0.168 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.762 |       0.211 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.551)------------------------------------------|
|    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: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4913   r_free= 0.4831   ksol= 0.00   Bsol= 0.00   scale= 0.849    |
|                                                                             |
| 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:   0.82 A                  |
| x-ray target function (ml) for work reflections: 6.299064                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4836   r_free= 0.4764   ksol= 0.27   Bsol= 35.94   scale= 0.895   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.12,3.13,3.22,0.00,0.00,0.00); trace/3= 1.08                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.294442                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.013805             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.664   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.629599              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.437   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4836      final r-factor (work) = 0.4150          |
| start r-factor (free) = 0.4764      final r-factor (free) = 0.4450          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.6720 = 10.01 * 0.50 * 6.2920 + 1.00 * 0.1683                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.2629 = 10.01 * 0.50 * 6.2178 + 1.00 * 0.1311                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4150      final r-factor (work) = 0.3813          |
| start r-factor (free) = 0.4450      final r-factor (free) = 0.4500          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.1385 = 1.63 * 1.00 * 6.2178 + 1.00 * 0.0060                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.0657 = 1.63 * 1.00 * 6.1620 + 1.00 * 0.0242                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.551)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    111.71  19.79    None  None   None       |
|    all(noH): 2823   0      0.00    111.71  19.79    None  None   None       |
|    Sol.    : 438    0      0.00    111.71  36.21    None  None   None       |
|    Mac.    : 2385   0      0.00    88.84   16.78    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.171:  961   |   5:    55.856 -  67.028:   59        |
|      1:    11.171 -  22.343:  894   |   6:    67.028 -  78.199:   33        |
|      2:    22.343 -  33.514:  512   |   7:    78.199 -  89.370:   16        |
|      3:    33.514 -  44.685:  240   |   8:    89.370 - 100.541:    1        |
|      4:    44.685 -  55.856:  106   |   9:   100.541 - 111.713:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3813 r_free = 0.4500             target_work(ml) = 6.165         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3807 r_free = 0.4490             target_work(ml) = 6.165         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3807   r_free= 0.4490   ksol= 0.27   Bsol= 35.94   scale= 0.966   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.12,3.13,3.22,0.00,0.00,0.00); trace/3= 1.08                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.164927                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3804   r_free= 0.4472   ksol= 0.28   Bsol= 64.49   scale= 0.977   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.79,2.47,2.55,0.00,0.00,0.00); trace/3= 1.41                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.167740                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.468648             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.551   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.158714              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.046  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3804      final r-factor (work) = 0.3207          |
| start r-factor (free) = 0.4472      final r-factor (free) = 0.3909          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 41.6460 = 13.47 * 0.50 * 6.1647 + 1.00 * 0.1311                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 41.2425 = 13.47 * 0.50 * 6.1059 + 1.00 * 0.1236                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3207      final r-factor (work) = 0.3015          |
| start r-factor (free) = 0.3909      final r-factor (free) = 0.3771          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.0993 = 1.16 * 1.00 * 6.1059 + 1.00 * 0.0244                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.9932 = 1.16 * 1.00 * 6.0147 + 1.00 * 0.0239                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.551)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    119.60  19.23    None  None   None       |
|    all(noH): 2823   0      0.00    119.60  19.23    None  None   None       |
|    Sol.    : 438    0      0.00    119.60  38.65    None  None   None       |
|    Mac.    : 2385   0      0.00    94.85   15.66    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 -  11.960: 1135   |   5:    59.801 -  71.762:   62        |
|      1:    11.960 -  23.921:  897   |   6:    71.762 -  83.722:   17        |
|      2:    23.921 -  35.881:  408   |   7:    83.722 -  95.682:   13        |
|      3:    35.881 -  47.841:  191   |   8:    95.682 - 107.642:    1        |
|      4:    47.841 -  59.801:   97   |   9:   107.642 - 119.603:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3015 r_free = 0.3771             target_work(ml) = 6.003         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       16 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3012 r_free = 0.3775             target_work(ml) = 6.003         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3012   r_free= 0.3775   ksol= 0.28   Bsol= 64.49   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.79,2.47,2.55,0.00,0.00,0.00); trace/3= 1.41                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.002602                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3012   r_free= 0.3770   ksol= 0.32   Bsol= 75.46   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.15,2.13,1.95,0.00,0.00,0.00); trace/3= 1.31                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.003115                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.804768              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.043   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.653712              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.064  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3012      final r-factor (work) = 0.2645          |
| start r-factor (free) = 0.3770      final r-factor (free) = 0.3316          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.5814 = 5.80 * 0.50 * 6.0150 + 1.00 * 0.1236                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.3484 = 5.80 * 0.50 * 5.9533 + 1.00 * 0.0696                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2645      final r-factor (work) = 0.2540          |
| start r-factor (free) = 0.3316      final r-factor (free) = 0.3150          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9127 = 0.65 * 1.00 * 5.9533 + 1.00 * 0.0210                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8628 = 0.65 * 1.00 * 5.8746 + 1.00 * 0.0224                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.551)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    116.17  18.00    None  None   None       |
|    all(noH): 2823   0      0.00    116.17  18.00    None  None   None       |
|    Sol.    : 438    0      0.00    116.17  40.21    None  None   None       |
|    Mac.    : 2385   0      0.00    93.89   13.92    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.617: 1297   |   5:    58.084 -  69.701:   63        |
|      1:    11.617 -  23.234:  843   |   6:    69.701 -  81.318:   28        |
|      2:    23.234 -  34.851:  307   |   7:    81.318 -  92.935:   14        |
|      3:    34.851 -  46.467:  173   |   8:    92.935 - 104.552:    2        |
|      4:    46.467 -  58.084:   94   |   9:   104.552 - 116.168:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2540 r_free = 0.3150             target_work(ml) = 5.857         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2537 r_free = 0.3154             target_work(ml) = 5.857         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2537   r_free= 0.3154   ksol= 0.32   Bsol= 75.46   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.15,2.13,1.95,0.00,0.00,0.00); trace/3= 1.31                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.856823                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2538   r_free= 0.3154   ksol= 0.33   Bsol= 87.15   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.76,1.25,1.23,0.00,0.00,0.00); trace/3= 0.57                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.857821                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.348546              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.740  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.587312              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.960   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2538      final r-factor (work) = 0.1951          |
| start r-factor (free) = 0.3154      final r-factor (free) = 0.2423          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.6562 = 7.35 * 0.50 * 5.8750 + 1.00 * 0.0699                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.2425 = 7.35 * 0.50 * 5.7546 + 1.00 * 0.0986                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1951      final r-factor (work) = 0.1733          |
| start r-factor (free) = 0.2423      final r-factor (free) = 0.2260          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3988 = 0.59 * 1.00 * 5.7546 + 1.00 * 0.0190                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2894 = 0.59 * 1.00 * 5.5526 + 1.00 * 0.0283                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.551)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    112.97  17.62    None  None   None       |
|    all(noH): 2823   0      0.00    112.97  17.62    None  None   None       |
|    Sol.    : 438    0      3.88    112.97  45.23    None  None   None       |
|    Mac.    : 2385   0      0.00    96.21   12.55    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 -  11.298: 1448   |   5:    56.487 -  67.785:   93        |
|      1:    11.298 -  22.595:  761   |   6:    67.785 -  79.082:   43        |
|      2:    22.595 -  33.893:  204   |   7:    79.082 -  90.380:   18        |
|      3:    33.893 -  45.190:  128   |   8:    90.380 - 101.677:    8        |
|      4:    45.190 -  56.487:  117   |   9:   101.677 - 112.975:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1733 r_free = 0.2260             target_work(ml) = 5.522         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1730 r_free = 0.2261             target_work(ml) = 5.521         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1730   r_free= 0.2261   ksol= 0.33   Bsol= 87.15   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.76,1.25,1.23,0.00,0.00,0.00); trace/3= 0.57                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.521193                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1731   r_free= 0.2258   ksol= 0.34   Bsol= 84.29   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.91,0.49,1.01,0.00,0.00,0.00); trace/3= 0.20                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.519685                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.580500              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.918  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.259828              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.508   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1731      final r-factor (work) = 0.1504          |
| start r-factor (free) = 0.2258      final r-factor (free) = 0.2008          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0390 = 3.58 * 0.50 * 5.5526 + 1.00 * 0.0986                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8549 = 3.58 * 0.50 * 5.4629 + 1.00 * 0.0749                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1504      final r-factor (work) = 0.1464          |
| start r-factor (free) = 0.2008      final r-factor (free) = 0.1951          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4370 = 0.26 * 1.00 * 5.4629 + 1.00 * 0.0176                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4129 = 0.26 * 1.00 * 5.3907 + 1.00 * 0.0123                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.551)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.16  16.79    None  None   None       |
|    all(noH): 2823   0      0.00    109.16  16.79    None  None   None       |
|    Sol.    : 438    0      3.75    109.16  43.61    None  None   None       |
|    Mac.    : 2385   0      0.00    94.69   11.87    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 -  10.916: 1484   |   5:    54.581 -  65.497:   81        |
|      1:    10.916 -  21.832:  768   |   6:    65.497 -  76.413:   44        |
|      2:    21.832 -  32.749:  178   |   7:    76.413 -  87.330:   19        |
|      3:    32.749 -  43.665:  123   |   8:    87.330 -  98.246:    7        |
|      4:    43.665 -  54.581:  116   |   9:    98.246 - 109.162:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1464 r_free = 0.1951             target_work(ml) = 5.373         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1462 r_free = 0.1949             target_work(ml) = 5.373         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1462   r_free= 0.1949   ksol= 0.34   Bsol= 84.29   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.91,0.49,1.01,0.00,0.00,0.00); trace/3= 0.20                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.372751                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2043 -  4.8215 0.99   1395  154 0.1086 0.1441      5.4846      5.6605|
|  2:  4.8215 -  3.8474 0.99   1338  151 0.1006 0.1226      5.5879      5.7806|
|  3:  3.8474 -  3.3671 0.99   1321  148 0.1327 0.1853      5.6811       6.035|
|  4:  3.3671 -  3.0620 0.99   1297  135 0.1545 0.2019      5.6625      5.8189|
|  5:  3.0620 -  2.8440 0.99   1298  148 0.1814 0.2030      5.5884      5.6919|
|  6:  2.8440 -  2.6773 0.99   1302  147 0.1661 0.2567      5.4529      5.6912|
|  7:  2.6773 -  2.5439 0.99   1269  146 0.1688 0.2159      5.4321      5.5966|
|  8:  2.5439 -  2.4336 0.98   1306  138 0.1680 0.2237      5.3696      5.6128|
|  9:  2.4336 -  2.3403 0.98   1272  145 0.1669 0.2369      5.3074      5.5403|
| 10:  2.3403 -  2.2598 0.98   1257  136 0.1597 0.1955       5.231      5.3571|
| 11:  2.2598 -  2.1893 1.00   1278  147 0.1524 0.2350      5.1652      5.4809|
| 12:  2.1893 -  2.1269 0.97   1279  136 0.1490 0.1983       5.074      5.3534|
| 13:  2.1269 -  2.0711 0.98   1252  142 0.1525 0.2031       5.017       5.189|
| 14:  2.0711 -  2.0207 0.60    766   86 0.1544 0.2108      4.9438      5.1637|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2043 -  4.8215  1395   154  0.93  11.06   0.95     0.92       9437.10|
|  2:  4.8215 -  3.8474  1338   151  0.94  10.30   1.00     0.97      12264.36|
|  3:  3.8474 -  3.3671  1321   148  0.91  14.56   1.02     1.01      15517.65|
|  4:  3.3671 -  3.0620  1297   135  0.89  17.62   1.00     0.97      15643.81|
|  5:  3.0620 -  2.8440  1298   148  0.85  21.16   1.00     0.97      13578.31|
|  6:  2.8440 -  2.6773  1302   147  0.86  20.63   0.97     0.93      10940.85|
|  7:  2.6773 -  2.5439  1269   146  0.86  21.12   1.00     0.95      10669.87|
|  8:  2.5439 -  2.4336  1306   138  0.85  21.31   0.99     0.94       9459.92|
|  9:  2.4336 -  2.3403  1272   145  0.85  22.15   0.99     0.92       8771.41|
| 10:  2.3403 -  2.2598  1257   136  0.85  20.97   0.99     0.93       7005.18|
| 11:  2.2598 -  2.1893  1278   147  0.87  20.24   0.98     0.92       6520.91|
| 12:  2.1893 -  2.1269  1279   136  0.88  19.13   1.00     0.98       5661.66|
| 13:  2.1269 -  2.0711  1252   142  0.87  20.06   0.97     0.94       5007.40|
| 14:  2.0711 -  2.0207   766    86  0.87  19.58   0.94     0.90       4127.63|
|alpha:            min =        0.90 max =            1.01 mean =         0.95|
|beta:             min =     4127.63 max =        15643.81 mean =      9818.29|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.91 mean =        18.45|
|phase err.(test): min =        0.00 max =           89.51 mean =        17.61|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1467   r_free= 0.1948   ksol= 0.33   Bsol= 81.67   scale= 0.983   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.00,0.09,0.90,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.373508                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.02 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1467   r_free= 0.1948   ksol= 0.33   Bsol= 81.67   scale= 0.983   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.00,0.09,0.90,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.373508                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2043 -  4.8215 0.99   1395  154 0.1098 0.1443      5.4899      5.6607|
|  2:  4.8215 -  3.8474 0.99   1338  151 0.1014 0.1220      5.5922      5.7761|
|  3:  3.8474 -  3.3671 0.99   1321  148 0.1332 0.1841      5.6813      6.0327|
|  4:  3.3671 -  3.0620 0.99   1297  135 0.1549 0.2024      5.6637      5.8204|
|  5:  3.0620 -  2.8440 0.99   1298  148 0.1817 0.2037      5.5899      5.6942|
|  6:  2.8440 -  2.6773 0.99   1302  147 0.1660 0.2561      5.4524      5.6892|
|  7:  2.6773 -  2.5439 0.99   1269  146 0.1689 0.2161      5.4317      5.5968|
|  8:  2.5439 -  2.4336 0.98   1306  138 0.1680 0.2238      5.3693      5.6134|
|  9:  2.4336 -  2.3403 0.98   1272  145 0.1668 0.2372      5.3071      5.5406|
| 10:  2.3403 -  2.2598 0.98   1257  136 0.1596 0.1963       5.231      5.3582|
| 11:  2.2598 -  2.1893 1.00   1278  147 0.1523 0.2348      5.1645      5.4791|
| 12:  2.1893 -  2.1269 0.97   1279  136 0.1488 0.1986       5.074      5.3548|
| 13:  2.1269 -  2.0711 0.98   1252  142 0.1525 0.2028      5.0167      5.1886|
| 14:  2.0711 -  2.0207 0.60    766   86 0.1546 0.2099      4.9437      5.1627|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.2043 -  4.8215  1395   154  0.93  11.13   0.95     0.92       9511.77|
|  2:  4.8215 -  3.8474  1338   151  0.94  10.28   1.00     0.97      12215.56|
|  3:  3.8474 -  3.3671  1321   148  0.91  14.51   1.02     1.01      15420.11|
|  4:  3.3671 -  3.0620  1297   135  0.89  17.65   1.00     0.97      15656.53|
|  5:  3.0620 -  2.8440  1298   148  0.85  21.17   1.00     0.96      13599.24|
|  6:  2.8440 -  2.6773  1302   147  0.86  20.63   0.97     0.93      10942.21|
|  7:  2.6773 -  2.5439  1269   146  0.86  21.09   0.99     0.95      10656.97|
|  8:  2.5439 -  2.4336  1306   138  0.85  21.31   0.98     0.93       9458.64|
|  9:  2.4336 -  2.3403  1272   145  0.85  22.14   0.99     0.91       8773.78|
| 10:  2.3403 -  2.2598  1257   136  0.85  20.97   0.98     0.92       7007.67|
| 11:  2.2598 -  2.1893  1278   147  0.87  20.24   0.97     0.91       6522.87|
| 12:  2.1893 -  2.1269  1279   136  0.88  19.13   0.99     0.97       5664.92|
| 13:  2.1269 -  2.0711  1252   142  0.87  20.05   0.96     0.94       5003.35|
| 14:  2.0711 -  2.0207   766    86  0.87  19.55   0.93     0.89       4114.11|
|alpha:            min =        0.89 max =            1.01 mean =         0.94|
|beta:             min =     4114.11 max =        15656.53 mean =      9814.59|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.83 mean =        18.45|
|phase err.(test): min =        0.00 max =           89.96 mean =        17.59|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.551)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.02    109.18  16.81    None  None   None       |
|    all(noH): 2823   0      0.02    109.18  16.81    None  None   None       |
|    Sol.    : 438    0      3.77    109.18  43.63    None  None   None       |
|    Mac.    : 2385   0      0.02    94.70   11.89    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:     0.016 -  10.932: 1484   |   5:    54.597 -  65.513:   81        |
|      1:    10.932 -  21.848:  768   |   6:    65.513 -  76.429:   44        |
|      2:    21.848 -  32.764:  178   |   7:    76.429 -  87.345:   19        |
|      3:    32.764 -  43.681:  123   |   8:    87.345 -  98.262:    7        |
|      4:    43.681 -  54.597:  116   |   9:    98.262 - 109.178:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 336         
Filter by distance & map next to the model:
   mapped sites are within: 0.181 - 5.268
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 329 from: 336
   mapped sites are within: 0.734 - 5.268

peak=    9.380 closest distance to " O  BHOH Z  74 " =    1.236
peak=    8.491 closest distance to " O   HOH Z 400 " =    1.024
peak=    6.921 closest distance to " O   HOH Z 203 " =    1.123
peak=    6.894 closest distance to " O   HOH Z  41 " =    1.365
peak=    6.878 closest distance to " O   HOH Z 138 " =    1.223
peak=    5.906 closest distance to " O   GLN A  11 " =    1.064
peak=    5.635 closest distance to " O   HOH Z 117 " =    1.621
peak=    5.434 closest distance to " O   HOH Z  54 " =    1.525
peak=    5.304 closest distance to " OD1 ASN A  69 " =    1.081
peak=    5.188 closest distance to " OD1 ASN A 301 " =    1.027
peak=    5.153 closest distance to " O   HOH Z 210 " =    1.712
peak=    4.921 closest distance to " O   HOH Z 159 " =    1.151
peak=    4.909 closest distance to " O   HOH Z  69 " =    1.768
peak=    4.888 closest distance to " O   HOH Z  82 " =    1.036
peak=    4.879 closest distance to " CB  ASN A  39 " =    0.824
peak=    4.819 closest distance to " CG AARG A 275 " =    1.165
peak=    4.818 closest distance to " NH2AARG A 145 " =    1.266
peak=    4.758 closest distance to " O   HOH Z 248 " =    1.577
peak=    4.731 closest distance to " CG1 ILE A 120 " =    1.137
peak=    4.710 closest distance to " CB  SER A  63 " =    1.276
peak=    4.684 closest distance to " CG  PRO A  54 " =    1.430
peak=    4.668 closest distance to " OH  TYR A  68 " =    1.011
peak=    4.647 closest distance to " CG  GLN A  77 " =    0.841
peak=    4.521 closest distance to " O   HOH Z  49 " =    1.593
peak=    4.492 closest distance to " O   HOH Z 422 " =    1.191
peak=    4.476 closest distance to " N   SER A 164 " =    0.969
peak=    4.473 closest distance to " O   HOH Z 425 " =    1.765
peak=    4.435 closest distance to " CZ  PHE A 218 " =    1.142
peak=    4.353 closest distance to " O   HOH Z 147 " =    1.487
peak=    4.322 closest distance to " CA  GLN A  11 " =    1.326
peak=    4.314 closest distance to " NH1AARG A 145 " =    1.421
peak=    4.312 closest distance to " NH1 ARG A 269 " =    0.852
peak=    4.295 closest distance to " O   HOH Z  65 " =    1.137
peak=    4.291 closest distance to " CA  ALA A 100 " =    1.057
peak=    4.285 closest distance to " CB  TRP A 179 " =    1.456
peak=    4.267 closest distance to " CB  GLU A  37 " =    1.092
peak=    4.261 closest distance to " CG  GLN A  11 " =    1.003
peak=    4.249 closest distance to " NE2 GLN A  11 " =    1.271
peak=    4.225 closest distance to " O   PRO A 198 " =    1.620
peak=    4.218 closest distance to " CD2 TRP A 179 " =    1.222
peak=    4.217 closest distance to " NH1BARG A 102 " =    0.951
peak=    4.205 closest distance to " O   HOH Z 222 " =    1.073
peak=    4.203 closest distance to " CG2 VAL A 197 " =    1.271
peak=    4.162 closest distance to " CE1 HIS A 115 " =    1.083
peak=    4.131 closest distance to " O   HOH Z 412 " =    3.418
peak=    4.083 closest distance to " ND2 ASN A 301 " =    1.007
peak=    4.082 closest distance to " CD2 TYR A  68 " =    0.930
peak=    4.081 closest distance to " O   HOH Z 139 " =    1.388
peak=    4.069 closest distance to " CA  TYR A  30 " =    0.955
peak=    4.054 closest distance to " O   HOH Z 174 " =    2.000
peak=    4.039 closest distance to " ND2 ASN A  69 " =    1.491
peak=    4.018 closest distance to " O   HOH Z 113 " =    1.940
peak=    4.014 closest distance to " CB  VAL A 202 " =    1.362
peak=    4.008 closest distance to " CB  GLN A 223 " =    1.472
peak=    4.002 closest distance to " CG2BVAL A  41 " =    1.014
peak=    3.994 closest distance to " N   SER A 271 " =    1.115
peak=    3.992 closest distance to " O   HOH Z 134 " =    2.006
peak=    3.983 closest distance to " O   HOH Z 394 " =    1.573
peak=    3.977 closest distance to " O   HOH Z 234 " =    4.026
peak=    3.974 closest distance to " O   HOH Z 362 " =    3.049
peak=    3.957 closest distance to " N   TYR A 116 " =    1.870
peak=    3.955 closest distance to " CB  SER A  62 " =    0.952
peak=    3.934 closest distance to " O  BHOH Z 338 " =    0.955
peak=    3.930 closest distance to " O   HOH Z 426 " =    1.307
peak=    3.922 closest distance to " O   HOH Z 377 " =    1.534
peak=    3.911 closest distance to " CG  PRO A  90 " =    1.403
peak=    3.903 closest distance to " O   HOH Z 369 " =    1.158
peak=    3.890 closest distance to " CZ  PHE A  38 " =    1.143
peak=    3.883 closest distance to " NE2 GLN A  77 " =    3.078
peak=    3.875 closest distance to " CB  GLU A 128 " =    0.956
peak=    3.867 closest distance to " NH2 ARG A  56 " =    1.309
peak=    3.864 closest distance to " O   HOH Z  85 " =    2.015
peak=    3.852 closest distance to " O   HOH Z 261 " =    2.112
peak=    3.837 closest distance to " O   HOH Z 176 " =    1.869
peak=    3.835 closest distance to " O   HOH Z 431 " =    1.244
peak=    3.834 closest distance to " CG2AVAL A 121 " =    1.796
peak=    3.832 closest distance to " O   SER A  87 " =    2.314
peak=    3.829 closest distance to " CB  GLN A 183 " =    1.171
peak=    3.825 closest distance to " O   SER A   3 " =    1.022
peak=    3.813 closest distance to " OE1 GLN A  88 " =    1.029
peak=    3.805 closest distance to " N   ALA A   1 " =    2.261
peak=    3.799 closest distance to " O   HOH Z 272 " =    1.392
peak=    3.796 closest distance to " CZ3 TRP A 266 " =    1.113
peak=    3.795 closest distance to " O   HOH Z 107 " =    0.981
peak=    3.793 closest distance to " O   HOH Z 395 " =    1.644
peak=    3.767 closest distance to " O   HOH Z 149 " =    2.062
peak=    3.766 closest distance to " O   THR A 251 " =    1.155
peak=    3.761 closest distance to " CB  LEU A  83 " =    0.744
peak=    3.745 closest distance to " CB  GLN A  88 " =    1.239
peak=    3.741 closest distance to " O   HOH Z  54 " =    1.430
peak=    3.738 closest distance to " CB  ASN A 187 " =    1.135
peak=    3.729 closest distance to " CB  MET A  40 " =    0.989
peak=    3.727 closest distance to " O   HOH Z 250 " =    1.298
peak=    3.727 closest distance to " CB  ARG A 275 " =    0.869
peak=    3.719 closest distance to " NH2 ARG A 156 " =    1.121
peak=    3.718 closest distance to " CG  PRO A 243 " =    1.190
peak=    3.718 closest distance to " CB  TRP A 266 " =    0.917
peak=    3.716 closest distance to " CD1 ILE A 120 " =    1.061
peak=    3.712 closest distance to " CB  ARG A 190 " =    1.876
peak=    3.694 closest distance to " CD  ARG A 269 " =    0.768
peak=    3.688 closest distance to " O   HOH Z 214 " =    1.996
peak=    3.685 closest distance to " CB  MET A  47 " =    0.988
peak=    3.684 closest distance to " O   HOH Z  67 " =    1.143
peak=    3.678 closest distance to " O   HOH Z  18 " =    2.287
peak=    3.678 closest distance to " O   HOH Z 369 " =    2.159
peak=    3.677 closest distance to " O   HOH Z 343 " =    2.426
peak=    3.673 closest distance to " O   HOH Z  27 " =    1.198
peak=    3.671 closest distance to " CD  ARG A  66 " =    2.647
peak=    3.668 closest distance to " O   HOH Z 365 " =    2.128
peak=    3.668 closest distance to " O   HOH Z 200 " =    1.889
peak=    3.666 closest distance to " O   HOH Z 346 " =    1.675
peak=    3.664 closest distance to " O   HOH Z 144 " =    2.161
peak=    3.639 closest distance to " CA  CYS A 260 " =    1.005
peak=    3.633 closest distance to " CG1AVAL A 121 " =    0.838
peak=    3.633 closest distance to " O   HOH Z 196 " =    1.610
peak=    3.625 closest distance to " N   TYR A  15 " =    0.879
peak=    3.623 closest distance to " CA  ARG A 195 " =    1.189
peak=    3.622 closest distance to " O   HOH Z 404 " =    1.678
peak=    3.613 closest distance to " O   HOH Z 421 " =    1.452
peak=    3.612 closest distance to " CB  PRO A  54 " =    0.884
peak=    3.603 closest distance to " O   ASP A 200 " =    1.767
peak=    3.595 closest distance to " O   HOH Z 415 " =    1.271
peak=    3.594 closest distance to " OG BSER A  99 " =    2.954
peak=    3.590 closest distance to " CB  ALA A 256 " =    1.423
peak=    3.589 closest distance to " O   HOH Z 221 " =    1.273
peak=    3.586 closest distance to " O   HOH Z  76 " =    1.323
peak=    3.578 closest distance to " CD  LYS A 166 " =    1.830
peak=    3.568 closest distance to " CG  LYS A  76 " =    1.161
peak=    3.564 closest distance to " CD  LYS A  76 " =    1.779
peak=    3.564 closest distance to " ND2 ASN A 249 " =    2.081
peak=    3.550 closest distance to " O   HOH Z 359 " =    1.589
peak=    3.549 closest distance to " O   HOH Z  53 " =    1.471
peak=    3.546 closest distance to " O   HOH Z  47 " =    2.289
peak=    3.544 closest distance to " CA  GLU A 152 " =    1.013
peak=    3.542 closest distance to " O   HOH Z 146 " =    1.785
peak=    3.524 closest distance to " O   HOH Z 301 " =    1.644
peak=    3.524 closest distance to " CG2 THR A  42 " =    0.832
peak=    3.513 closest distance to " CB  THR A  52 " =    0.907
peak=    3.508 closest distance to " CB  PHE A 283 " =    0.874
peak=    3.503 closest distance to " O   HOH Z  38 " =    2.324
peak=    3.503 closest distance to " O   HOH Z 437 " =    1.767
peak=    3.499 closest distance to " CG1 VAL A 153 " =    1.154
peak=    3.497 closest distance to " CB  ALA A 248 " =    1.475
peak=    3.488 closest distance to " CB  GLU A  46 " =    1.052
peak=    3.487 closest distance to " O   HOH Z  88 " =    3.335
peak=    3.483 closest distance to " CA  GLY A 196 " =    0.887
peak=    3.482 closest distance to " CA  ILE A 106 " =    0.818
peak=    3.477 closest distance to " O   HOH Z 418 " =    2.036
peak=    3.476 closest distance to " O   HOH Z  50 " =    3.617
peak=    3.476 closest distance to " CG2 VAL A 268 " =    1.111
peak=    3.473 closest distance to " CD1 LEU A  96 " =    0.734
peak=    3.463 closest distance to " CG2 THR A 221 " =    1.025
peak=    3.461 closest distance to " O   HOH Z  56 " =    1.558
peak=    3.458 closest distance to " O   HOH Z 358 " =    1.470
peak=    3.455 closest distance to " CG  GLU A  37 " =    1.070
peak=    3.454 closest distance to " NH1 ARG A  14 " =    1.124
peak=    3.447 closest distance to " OE1 GLU A   2 " =    1.256
peak=    3.447 closest distance to " O   HOH Z 417 " =    2.998
peak=    3.446 closest distance to " CB  ALA A 299 " =    0.814
peak=    3.437 closest distance to " O   HOH Z 298 " =    2.159
peak=    3.435 closest distance to " CG  PRO A 198 " =    1.390
peak=    3.434 closest distance to " CB  TYR A 116 " =    1.276
peak=    3.433 closest distance to " CA  GLN A 223 " =    0.890
peak=    3.429 closest distance to " CA  ALA A 154 " =    1.036
peak=    3.429 closest distance to " OE1 GLN A  58 " =    0.976
peak=    3.428 closest distance to " N   THR A  52 " =    1.250
peak=    3.427 closest distance to " CB  SER A 210 " =    0.981
peak=    3.423 closest distance to " O   HOH Z 199 " =    1.594
peak=    3.419 closest distance to " CB  GLU A   2 " =    1.005
peak=    3.417 closest distance to " CB  LEU A 101 " =    1.199
peak=    3.417 closest distance to " CA  TRP A 274 " =    0.933
peak=    3.409 closest distance to " CA  PRO A 198 " =    1.134
peak=    3.409 closest distance to " O   HOH Z 188 " =    3.120
peak=    3.405 closest distance to " CB  SER A  26 " =    0.806
peak=    3.400 closest distance to " O   HOH Z 279 " =    1.020
peak=    3.393 closest distance to " OD2 ASP A  50 " =    1.328
peak=    3.390 closest distance to " O   HOH Z 213 " =    1.718
peak=    3.383 closest distance to " CB  ASN A 285 " =    0.794
peak=    3.383 closest distance to " CB  ASP A 124 " =    0.886
peak=    3.383 closest distance to " CA  SER A  62 " =    0.867
peak=    3.381 closest distance to " CG1 ILE A  33 " =    1.254
peak=    3.379 closest distance to " CA  ASP A 124 " =    0.907
peak=    3.378 closest distance to " O   HOH Z 197 " =    5.268
peak=    3.376 closest distance to " CB  ALA A   1 " =    1.152
peak=    3.375 closest distance to " CG  ARG A 138 " =    1.446
peak=    3.374 closest distance to " O   HOH Z 126 " =    1.568
peak=    3.373 closest distance to " O   HOH Z  63 " =    1.425
peak=    3.365 closest distance to " O   ALA A 165 " =    1.394
peak=    3.364 closest distance to " CB  ASN A  45 " =    1.026
peak=    3.363 closest distance to " CA  SER A  87 " =    0.918
peak=    3.362 closest distance to " CB  GLU A 152 " =    1.134
peak=    3.360 closest distance to " O   HOH Z 303 " =    2.365
peak=    3.360 closest distance to " CB  VAL A 296 " =    1.480
peak=    3.360 closest distance to " O   HOH Z  73 " =    2.468
peak=    3.356 closest distance to " CB  GLU A 236 " =    1.311
peak=    3.355 closest distance to " NH1 ARG A  36 " =    1.401
peak=    3.353 closest distance to " O   HOH Z  38 " =    1.547
peak=    3.353 closest distance to " O   HOH Z 403 " =    1.561
peak=    3.353 closest distance to " O   HOH Z 132 " =    3.404
peak=    3.352 closest distance to " CG  GLN A  77 " =    1.345
peak=    3.352 closest distance to " CD  PRO A  54 " =    1.040
peak=    3.350 closest distance to " O   HOH Z 193 " =    2.015
peak=    3.348 closest distance to " NE2 GLN A 278 " =    2.567
peak=    3.347 closest distance to " CB  SER A  62 " =    1.023
peak=    3.346 closest distance to " CB  SER A 288 " =    1.091
peak=    3.344 closest distance to " CA  ASP A 162 " =    0.919
peak=    3.339 closest distance to " O   HOH Z 428 " =    1.088
peak=    3.338 closest distance to " CB  ASN A 148 " =    1.537
peak=    3.337 closest distance to " O   HOH Z 192 " =    1.316
peak=    3.335 closest distance to " O   HOH Z 343 " =    1.560
peak=    3.334 closest distance to " O   HOH Z 371 " =    2.000
peak=    3.334 closest distance to " O   THR A 182 " =    1.404
peak=    3.333 closest distance to " OG  SER A  62 " =    2.875
peak=    3.331 closest distance to " O   HOH Z 287 " =    1.733
peak=    3.327 closest distance to " CB  PRO A  90 " =    1.116
peak=    3.325 closest distance to " O   HOH Z 133 " =    3.026
peak=    3.323 closest distance to " CB  GLU A 277 " =    3.893
peak=    3.323 closest distance to " CE  LYS A  76 " =    0.891
peak=    3.322 closest distance to " CD1 LEU A 300 " =    1.091
peak=    3.319 closest distance to " CB  SER A 141 " =    1.188
peak=    3.316 closest distance to " O   HOH Z 128 " =    1.368
peak=    3.315 closest distance to " O   HOH Z 232 " =    2.564
peak=    3.314 closest distance to " CB  ALA A 291 " =    1.205
peak=    3.312 closest distance to " CD  ARG A  36 " =    0.971
peak=    3.308 closest distance to " O   HOH Z 406 " =    1.741
peak=    3.304 closest distance to " O   HOH Z 223 " =    1.207
peak=    3.304 closest distance to " CG2 VAL A 126 " =    1.087
peak=    3.301 closest distance to " O   HOH Z  44 " =    1.890
peak=    3.295 closest distance to " CB  ASN A 142 " =    0.907
peak=    3.292 closest distance to " O   GLU A   2 " =    1.792
peak=    3.287 closest distance to " CD  ARG A 159 " =    0.829
peak=    3.287 closest distance to " CB  GLN A  89 " =    1.278
peak=    3.286 closest distance to " CB  LYS A 289 " =    1.282
peak=    3.286 closest distance to " O   HOH Z 427 " =    3.338
peak=    3.283 closest distance to " O   HOH Z  80 " =    2.194
peak=    3.283 closest distance to " CB  VAL A 265 " =    1.316
peak=    3.282 closest distance to " O   HOH Z 411 " =    2.548
peak=    3.281 closest distance to " O   HOH Z  21 " =    1.697
peak=    3.279 closest distance to " N   VAL A 265 " =    1.050
peak=    3.278 closest distance to " O   HOH Z  96 " =    1.989
peak=    3.275 closest distance to " O   HOH Z   1 " =    2.744
peak=    3.269 closest distance to " O   HOH Z 163 " =    2.203
peak=    3.266 closest distance to " N   TYR A 247 " =    1.226
peak=    3.260 closest distance to " O   HOH Z 251 " =    1.768
peak=    3.256 closest distance to " OH  TYR A 116 " =    1.289
peak=    3.253 closest distance to " CA  ALA A 295 " =    1.002
peak=    3.252 closest distance to " CA  ARG A 156 " =    1.078
peak=    3.248 closest distance to " CB  ALA A 100 " =    1.367
peak=    3.247 closest distance to " CB  MET A 105 " =    1.077
peak=    3.246 closest distance to " NZ  LYS A  76 " =    0.955
peak=    3.242 closest distance to " CA  ALA A  51 " =    0.957
peak=    3.238 closest distance to " CB  ALA A 114 " =    0.793
peak=    3.235 closest distance to " O   HOH Z  43 " =    2.019
peak=    3.232 closest distance to " CD ALYS A 290 " =    1.120
peak=    3.232 closest distance to " CB  GLN A 194 " =    0.970
peak=    3.229 closest distance to " O   HOH Z 368 " =    4.187
peak=    3.229 closest distance to " O   HOH Z 379 " =    3.478
peak=    3.224 closest distance to " O   ASP A 124 " =    1.171
peak=    3.223 closest distance to " O   HOH Z 344 " =    1.867
peak=    3.221 closest distance to " CA  GLY A 267 " =    1.144
peak=    3.218 closest distance to " O   HOH Z 284 " =    3.019
peak=    3.211 closest distance to " C   GLN A  88 " =    1.677
peak=    3.210 closest distance to " CB  ARG A  79 " =    0.844
peak=    3.209 closest distance to " O   HOH Z 316 " =    3.084
peak=    3.201 closest distance to " ND2 ASN A  45 " =    1.195
peak=    3.200 closest distance to " O   HOH Z  44 " =    1.773
peak=    3.198 closest distance to " O   HOH Z 294 " =    1.707
peak=    3.196 closest distance to " CB  PHE A  61 " =    0.760
peak=    3.194 closest distance to " O   HOH Z 144 " =    1.513
peak=    3.191 closest distance to " CA  ARG A  36 " =    1.035
peak=    3.189 closest distance to " CE1 TYR A 186 " =    1.355
peak=    3.184 closest distance to " OG  SER A  62 " =    2.956
peak=    3.182 closest distance to " CA  THR A 246 " =    1.047
peak=    3.180 closest distance to " O   HOH Z   7 " =    1.623
peak=    3.179 closest distance to " OH  TYR A 293 " =    1.047
peak=    3.177 closest distance to " O   HOH Z 214 " =    2.453
peak=    3.175 closest distance to " O   ASN A 301 " =    1.488
peak=    3.174 closest distance to " NH2AARG A 190 " =    1.989
peak=    3.172 closest distance to " CA  ARG A 139 " =    1.373
peak=    3.172 closest distance to " CG ALYS A 290 " =    1.191
peak=    3.172 closest distance to " CA  GLY A   6 " =    0.819
peak=    3.170 closest distance to " CA  ALA A 160 " =    1.102
peak=    3.168 closest distance to " CA  ASN A 249 " =    1.257
peak=    3.154 closest distance to " CB  ARG A 156 " =    1.016
peak=    3.150 closest distance to " CB  TYR A 172 " =    0.941
peak=    3.150 closest distance to " O   HOH Z 207 " =    1.440
peak=    3.149 closest distance to " CE3 TRP A  85 " =    1.220
peak=    3.148 closest distance to " O   HOH Z 365 " =    1.323
peak=    3.148 closest distance to " CB  ASP A 191 " =    1.118
peak=    3.148 closest distance to " CD  ARG A  24 " =    1.288
peak=    3.140 closest distance to " CG  ARG A 269 " =    1.611
peak=    3.135 closest distance to " CB  PRO A 243 " =    1.293
peak=    3.133 closest distance to " OG1 THR A 221 " =    1.770
peak=    3.133 closest distance to " O   HOH Z  40 " =    1.672
peak=    3.133 closest distance to " CB  PRO A 198 " =    1.099
peak=    3.124 closest distance to " CA  ALA A 291 " =    0.877
peak=    3.123 closest distance to " CB  ALA A 104 " =    0.962
peak=    3.121 closest distance to " OG1 THR A  82 " =    1.039
peak=    3.118 closest distance to " CB  ARG A 269 " =    1.783
peak=    3.116 closest distance to " CA  HIS A 115 " =    1.071
peak=    3.111 closest distance to " CE1 TYR A 247 " =    1.175
peak=    3.107 closest distance to " CB  ASP A 140 " =    0.870
peak=    3.104 closest distance to " O   HOH Z 435 " =    2.558
peak=    3.100 closest distance to " O   HOH Z 409 " =    3.178
peak=    3.100 closest distance to " OE2 GLU A   2 " =    2.085
peak=    3.099 closest distance to " O   HOH Z 141 " =    1.501
peak=    3.098 closest distance to " CG1 VAL A 257 " =    1.284
peak=    3.098 closest distance to " CA  ALA A  21 " =    1.503
peak=    3.097 closest distance to " N   LYS A 166 " =    0.870
peak=    3.096 closest distance to " N   ASP A 132 " =    1.036
peak=    3.094 closest distance to " OE1 GLN A  58 " =    3.717
peak=    3.093 closest distance to " CA  ALA A 227 " =    1.245
peak=    3.089 closest distance to " CA  ALA A 248 " =    1.383
peak=    3.088 closest distance to " CB  TYR A 247 " =    0.918
peak=    3.086 closest distance to " O   HOH Z 193 " =    1.762
peak=    3.079 closest distance to " O   HOH Z 313 " =    1.923
peak=    3.079 closest distance to " CB  ASN A 301 " =    0.974
peak=    3.070 closest distance to " O   HOH Z 339 " =    2.276
peak=    3.069 closest distance to " O   HOH Z  63 " =    2.090
peak=    3.062 closest distance to " O   HOH Z  44 " =    1.661
peak=    3.061 closest distance to " CZ3 TRP A 274 " =    4.559
peak=    3.060 closest distance to " O   HOH Z 258 " =    2.152
peak=    3.059 closest distance to " O   HOH Z 327 " =    2.314
peak=    3.047 closest distance to " ND2BASN A 224 " =    0.811
peak=    3.045 closest distance to " NH2AARG A 190 " =    1.249
peak=    3.042 closest distance to " O   HOH Z  73 " =    2.017
peak=    3.038 closest distance to " CA  SER A  32 " =    1.598
peak=    3.033 closest distance to " OD1 ASN A 252 " =    1.221
peak=    3.033 closest distance to " NE2 GLN A  58 " =    5.237

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 228         
Filter by distance & map next to the model:
   mapped sites are within: 0.481 - 5.824
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 221 from: 228
   mapped sites are within: 0.714 - 5.824

peak=   -4.789 closest distance to " CD  GLN A 223 " =    1.347
peak=   -4.413 closest distance to " O   HOH Z 418 " =    1.059
peak=   -4.366 closest distance to " O   HOH Z 114 " =    0.963
peak=   -4.226 closest distance to " O   HOH Z 411 " =    5.385
peak=   -4.152 closest distance to " CB  PRO A 243 " =    2.920
peak=   -4.112 closest distance to " N   ALA A  43 " =    2.773
peak=   -4.108 closest distance to " CD1 PHE A  59 " =    2.042
peak=   -4.074 closest distance to " O   HOH Z 166 " =    1.289
peak=   -4.028 closest distance to " CG  ARG A 269 " =    2.475
peak=   -4.003 closest distance to " O   HOH Z 203 " =    0.955
peak=   -3.996 closest distance to " OD2 ASP A 171 " =    1.879
peak=   -3.983 closest distance to " CD  ARG A  14 " =    3.346
peak=   -3.956 closest distance to " CE2 PHE A  61 " =    2.784
peak=   -3.953 closest distance to " O   SER A   3 " =    0.909
peak=   -3.936 closest distance to " O   HOH Z 221 " =    0.863
peak=   -3.917 closest distance to " O   HOH Z 128 " =    2.870
peak=   -3.917 closest distance to " O   GLN A  11 " =    1.006
peak=   -3.914 closest distance to " CG  GLN A  11 " =    1.058
peak=   -3.903 closest distance to " O   HOH Z   7 " =    1.086
peak=   -3.896 closest distance to " O   PRO A 198 " =    1.281
peak=   -3.885 closest distance to " O   HOH Z 400 " =    1.253
peak=   -3.868 closest distance to " O   HOH Z   5 " =    1.665
peak=   -3.865 closest distance to " O   HOH Z 211 " =    0.889
peak=   -3.844 closest distance to " CG  PRO A 243 " =    1.717
peak=   -3.842 closest distance to " CZ  TYR A  68 " =    1.098
peak=   -3.812 closest distance to " O   HOH Z 259 " =    0.758
peak=   -3.783 closest distance to " N   ILE A 120 " =    1.051
peak=   -3.766 closest distance to " CA  TRP A 274 " =    0.938
peak=   -3.763 closest distance to " CG2 ILE A  20 " =    2.516
peak=   -3.745 closest distance to " O   HOH Z 156 " =    3.581
peak=   -3.738 closest distance to " O   HOH Z 222 " =    0.979
peak=   -3.735 closest distance to " N   ARG A 275 " =    1.146
peak=   -3.734 closest distance to " O   SER A 210 " =    1.908
peak=   -3.730 closest distance to " OD1 ASN A 301 " =    0.908
peak=   -3.714 closest distance to " O   HOH Z  65 " =    1.868
peak=   -3.713 closest distance to " CZ  ARG A 259 " =    0.831
peak=   -3.708 closest distance to " CG2 VAL A 189 " =    2.277
peak=   -3.698 closest distance to " O   HOH Z  37 " =    1.468
peak=   -3.692 closest distance to " O   HOH Z   7 " =    1.359
peak=   -3.677 closest distance to " CA  SER A 164 " =    1.994
peak=   -3.677 closest distance to " CB  ALA A 291 " =    2.509
peak=   -3.672 closest distance to " O   ASN A  69 " =    1.209
peak=   -3.668 closest distance to " O   HOH Z 155 " =    2.148
peak=   -3.660 closest distance to " O   VAL A 174 " =    2.142
peak=   -3.653 closest distance to " CG  LEU A  83 " =    1.870
peak=   -3.648 closest distance to " O   HOH Z  54 " =    1.538
peak=   -3.647 closest distance to " C   ASN A 285 " =    2.293
peak=   -3.641 closest distance to " CD2 HIS A 115 " =    1.106
peak=   -3.640 closest distance to " O   HOH Z 109 " =    3.863
peak=   -3.637 closest distance to " OD1 ASN A 148 " =    1.252
peak=   -3.624 closest distance to " CD  GLN A  88 " =    0.960
peak=   -3.624 closest distance to " CG  GLN A  58 " =    1.193
peak=   -3.618 closest distance to " CZ  TYR A 169 " =    1.878
peak=   -3.618 closest distance to " CA  GLU A 277 " =    1.137
peak=   -3.614 closest distance to " CA  GLY A 241 " =    2.316
peak=   -3.611 closest distance to " CG2BVAL A 121 " =    1.314
peak=   -3.606 closest distance to " CD2 LEU A 237 " =    2.629
peak=   -3.602 closest distance to " CD  GLN A 223 " =    0.737
peak=   -3.593 closest distance to " O   HOH Z  19 " =    2.211
peak=   -3.577 closest distance to " CE3 TRP A 274 " =    2.060
peak=   -3.575 closest distance to " OE1 GLN A  88 " =    1.047
peak=   -3.567 closest distance to " O   HOH Z 133 " =    1.620
peak=   -3.566 closest distance to " O   HOH Z 394 " =    1.678
peak=   -3.565 closest distance to " O   HOH Z  55 " =    1.640
peak=   -3.543 closest distance to " ND2 ASN A  60 " =    1.353
peak=   -3.536 closest distance to " N   GLN A  11 " =    1.230
peak=   -3.523 closest distance to " O   HOH Z 185 " =    2.602
peak=   -3.522 closest distance to " OD1 ASP A 171 " =    1.513
peak=   -3.522 closest distance to " NE2 GLN A 194 " =    2.315
peak=   -3.515 closest distance to " CG  MET A 105 " =    0.903
peak=   -3.503 closest distance to " SD  MET A  40 " =    2.093
peak=   -3.503 closest distance to " O   HOH Z 166 " =    2.348
peak=   -3.501 closest distance to " O   HOH Z  41 " =    2.650
peak=   -3.498 closest distance to " O   HOH Z 400 " =    1.121
peak=   -3.495 closest distance to " O   HOH Z 134 " =    2.424
peak=   -3.493 closest distance to " O   HOH Z 250 " =    2.023
peak=   -3.488 closest distance to " CA  GLY A 229 " =    2.488
peak=   -3.488 closest distance to " N   SER A 134 " =    1.163
peak=   -3.484 closest distance to " CG  GLU A  53 " =    1.463
peak=   -3.478 closest distance to " CD1 ILE A 263 " =    2.040
peak=   -3.478 closest distance to " O   HOH Z 198 " =    1.386
peak=   -3.474 closest distance to " O   HOH Z 216 " =    0.714
peak=   -3.468 closest distance to " O   HOH Z  67 " =    1.438
peak=   -3.466 closest distance to " O   HOH Z 278 " =    0.897
peak=   -3.462 closest distance to " CB  PRO A 280 " =    2.171
peak=   -3.461 closest distance to " SD  MET A 105 " =    2.412
peak=   -3.461 closest distance to " ND2 ASN A  74 " =    1.070
peak=   -3.455 closest distance to " O   VAL A  67 " =    2.871
peak=   -3.454 closest distance to " O   HOH Z 155 " =    1.598
peak=   -3.451 closest distance to " CD  ARG A  36 " =    0.955
peak=   -3.449 closest distance to " OD1 ASN A  39 " =    0.964
peak=   -3.443 closest distance to " CG  ARG A 259 " =    1.577
peak=   -3.442 closest distance to " O   HOH Z 184 " =    1.709
peak=   -3.442 closest distance to " O   HOH Z 186 " =    3.885
peak=   -3.431 closest distance to " CG1 VAL A 112 " =    2.583
peak=   -3.428 closest distance to " O   HOH Z 340 " =    1.381
peak=   -3.426 closest distance to " OXT GLY A 302 " =    3.220
peak=   -3.425 closest distance to " SD  MET A  93 " =    1.689
peak=   -3.421 closest distance to " CD  GLN A  77 " =    1.014
peak=   -3.417 closest distance to " CG  GLN A 103 " =    2.285
peak=   -3.406 closest distance to " O   HOH Z 152 " =    1.534
peak=   -3.404 closest distance to " O   HOH Z 122 " =    1.151
peak=   -3.399 closest distance to " O   HOH Z  52 " =    1.898
peak=   -3.399 closest distance to " O   HOH Z  88 " =    2.840
peak=   -3.387 closest distance to " O   VAL A 189 " =    2.627
peak=   -3.386 closest distance to " O   HOH Z 407 " =    0.831
peak=   -3.382 closest distance to " O   HOH Z  40 " =    3.056
peak=   -3.375 closest distance to " O   HOH Z 225 " =    1.447
peak=   -3.372 closest distance to " CG  TYR A 169 " =    2.228
peak=   -3.371 closest distance to " CD1 LEU A 167 " =    1.997
peak=   -3.369 closest distance to " CD  GLN A  11 " =    0.766
peak=   -3.369 closest distance to " CD2 PHE A  61 " =    2.038
peak=   -3.368 closest distance to " N   GLN A  58 " =    1.747
peak=   -3.367 closest distance to " CB  SER A 146 " =    2.159
peak=   -3.340 closest distance to " CD1 PHE A 130 " =    2.372
peak=   -3.337 closest distance to " O   HOH Z 196 " =    1.497
peak=   -3.336 closest distance to " CD  GLU A 236 " =    1.075
peak=   -3.335 closest distance to " O   HOH Z  65 " =    0.914
peak=   -3.322 closest distance to " N   ALA A 242 " =    1.549
peak=   -3.321 closest distance to " CA  VAL A 197 " =    0.976
peak=   -3.319 closest distance to " O   GLY A 262 " =    2.477
peak=   -3.311 closest distance to " O   HOH Z 119 " =    4.811
peak=   -3.304 closest distance to " O   HOH Z 251 " =    4.516
peak=   -3.303 closest distance to " O   ARG A  79 " =    1.187
peak=   -3.303 closest distance to " O   ALA A   7 " =    1.535
peak=   -3.302 closest distance to " O   HOH Z 380 " =    4.480
peak=   -3.302 closest distance to " CG2 ILE A  49 " =    2.698
peak=   -3.298 closest distance to " OD1 ASN A  69 " =    0.968
peak=   -3.295 closest distance to " O   HOH Z 137 " =    1.417
peak=   -3.295 closest distance to " O   HOH Z 207 " =    1.387
peak=   -3.293 closest distance to " O   ASP A 171 " =    1.006
peak=   -3.293 closest distance to " O   HOH Z   6 " =    1.210
peak=   -3.290 closest distance to " O   HOH Z 191 " =    5.824
peak=   -3.290 closest distance to " OE1 GLN A  58 " =    1.880
peak=   -3.281 closest distance to " CG1 VAL A 112 " =    2.689
peak=   -3.277 closest distance to " O   MET A 113 " =    1.326
peak=   -3.275 closest distance to " NH2 ARG A  79 " =    1.903
peak=   -3.275 closest distance to " O   GLY A  17 " =    1.172
peak=   -3.274 closest distance to " OE1 GLN A  88 " =    1.476
peak=   -3.274 closest distance to " CD2 TYR A 293 " =    1.832
peak=   -3.268 closest distance to " N   ASP A 191 " =    1.388
peak=   -3.262 closest distance to " O   HOH Z 103 " =    2.353
peak=   -3.261 closest distance to " O   HOH Z 401 " =    1.283
peak=   -3.255 closest distance to " O   HOH Z  53 " =    2.070
peak=   -3.255 closest distance to " CB  ASP A 286 " =    2.039
peak=   -3.250 closest distance to " CE  MET A  93 " =    2.009
peak=   -3.242 closest distance to " CG  ASP A 231 " =    0.770
peak=   -3.242 closest distance to " O   HOH Z   9 " =    0.727
peak=   -3.238 closest distance to " ND2BASN A 224 " =    1.639
peak=   -3.236 closest distance to " O   HOH Z  11 " =    1.776
peak=   -3.234 closest distance to " O   HOH Z 422 " =    0.844
peak=   -3.232 closest distance to " O   HOH Z 368 " =    2.025
peak=   -3.230 closest distance to " O   HOH Z 174 " =    1.605
peak=   -3.228 closest distance to " O   HOH Z 211 " =    1.489
peak=   -3.228 closest distance to " O   HOH Z 411 " =    1.127
peak=   -3.227 closest distance to " O   HOH Z 287 " =    1.643
peak=   -3.223 closest distance to " O   HOH Z  48 " =    1.022
peak=   -3.218 closest distance to " OG  SER A 276 " =    0.952
peak=   -3.218 closest distance to " O   ARG A 275 " =    2.110
peak=   -3.217 closest distance to " CB  PRO A  54 " =    2.666
peak=   -3.215 closest distance to " O   HOH Z 424 " =    2.924
peak=   -3.213 closest distance to " O   HOH Z 164 " =    2.535
peak=   -3.213 closest distance to " O   HOH Z  83 " =    1.556
peak=   -3.208 closest distance to " NH2 ARG A 259 " =    2.398
peak=   -3.199 closest distance to " O   HOH Z  60 " =    1.813
peak=   -3.198 closest distance to " C   VAL A 265 " =    0.921
peak=   -3.197 closest distance to " ND2 ASN A  45 " =    1.629
peak=   -3.195 closest distance to " O   HOH Z  94 " =    3.709
peak=   -3.195 closest distance to " O   HOH Z  64 " =    1.978
peak=   -3.194 closest distance to " NH2 ARG A  36 " =    1.250
peak=   -3.193 closest distance to " O   HOH Z 371 " =    0.862
peak=   -3.193 closest distance to " CD2 TYR A  30 " =    2.795
peak=   -3.189 closest distance to " OG  SER A  63 " =    1.079
peak=   -3.189 closest distance to " O   HOH Z 189 " =    1.843
peak=   -3.186 closest distance to " OG  SER A  62 " =    4.507
peak=   -3.186 closest distance to " O   SER A 276 " =    1.885
peak=   -3.183 closest distance to " O   ASN A 127 " =    2.134
peak=   -3.181 closest distance to " C   LYS A  76 " =    1.828
peak=   -3.181 closest distance to " OG1 THR A  82 " =    2.310
peak=   -3.179 closest distance to " O   HOH Z 192 " =    2.010
peak=   -3.179 closest distance to " C   LEU A 101 " =    1.134
peak=   -3.177 closest distance to " NE2 GLN A  88 " =    0.963
peak=   -3.176 closest distance to " O   HOH Z 193 " =    1.589
peak=   -3.174 closest distance to " O   HOH Z  38 " =    0.786
peak=   -3.173 closest distance to " O   HOH Z  90 " =    3.274
peak=   -3.167 closest distance to " O   MET A  47 " =    2.312
peak=   -3.167 closest distance to " O   HOH Z  60 " =    1.451
peak=   -3.166 closest distance to " O   HOH Z 130 " =    1.327
peak=   -3.162 closest distance to " O   HOH Z 345 " =    3.162
peak=   -3.157 closest distance to " CE3 TRP A 150 " =    1.583
peak=   -3.156 closest distance to " NH2 ARG A  66 " =    2.097
peak=   -3.155 closest distance to " O   HOH Z  99 " =    1.279
peak=   -3.154 closest distance to " O   HOH Z  32 " =    2.204
peak=   -3.154 closest distance to " CG  TRP A 266 " =    1.812
peak=   -3.154 closest distance to " O   HOH Z 132 " =    0.882
peak=   -3.151 closest distance to " CG  PRO A 163 " =    1.855
peak=   -3.151 closest distance to " CD  ARG A  79 " =    1.167
peak=   -3.150 closest distance to " CG2BVAL A  41 " =    1.425
peak=   -3.144 closest distance to " O   HOH Z 384 " =    1.876
peak=   -3.140 closest distance to " O   VAL A 121 " =    0.926
peak=   -3.135 closest distance to " OG BSER A 210 " =    2.478
peak=   -3.134 closest distance to " O   HOH Z 403 " =    0.946
peak=   -3.132 closest distance to " O   HOH Z 298 " =    3.065
peak=   -3.128 closest distance to " O   HOH Z 331 " =    0.937
peak=   -3.126 closest distance to " OG BSER A 164 " =    1.407
peak=   -3.121 closest distance to " OD1 ASN A 173 " =    1.518
peak=   -3.108 closest distance to " O   ALA A   1 " =    2.226
peak=   -3.106 closest distance to " O   HOH Z 137 " =    1.409
peak=   -3.105 closest distance to " OE1 GLU A  44 " =    0.833
peak=   -3.101 closest distance to " O   HOH Z 203 " =    1.249
peak=   -3.098 closest distance to " CD  LYS A 289 " =    2.224
peak=   -3.094 closest distance to " CE1 PHE A 225 " =    2.568
peak=   -3.091 closest distance to " CH2 TRP A 150 " =    1.095
peak=   -3.090 closest distance to " OD1 ASP A 272 " =    1.527
peak=   -3.086 closest distance to " CD1 ILE A 151 " =    2.530
peak=   -3.062 closest distance to " CB  ALA A  43 " =    2.854
peak=   -3.054 closest distance to " O   HOH Z 287 " =    1.534
peak=   -3.048 closest distance to " O   HOH Z 428 " =    1.362
peak=   -3.044 closest distance to " CG  ARG A 259 " =    2.443
peak=   -3.040 closest distance to " O   HOH Z 154 " =    1.155
peak=   -2.988 closest distance to " CA  ASN A  39 " =    1.365

================= 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    :  0.4913 0.4831   6.299064e+00   6.281628e+00
   1_bss:  0.4836 0.4764   6.294442e+00   6.274898e+00
   1_xyz:  0.4150 0.4450   6.202928e+00   6.232013e+00
   1_adp:  0.3813 0.4500   6.165439e+00   6.237697e+00
   1_occ:  0.3807 0.4490   6.164927e+00   6.237912e+00
   2_bss:  0.3804 0.4472   6.167740e+00   6.239407e+00
   2_xyz:  0.3207 0.3909   6.036222e+00   6.157615e+00
   2_adp:  0.3015 0.3771   6.003340e+00   6.138966e+00
   2_occ:  0.3012 0.3775   6.002602e+00   6.138723e+00
   3_bss:  0.3012 0.3770   6.003115e+00   6.138444e+00
   3_xyz:  0.2645 0.3316   5.891434e+00   6.047804e+00
   3_adp:  0.2540 0.3150   5.857017e+00   6.015232e+00
   3_occ:  0.2537 0.3154   5.856823e+00   6.015390e+00
   4_bss:  0.2538 0.3154   5.857821e+00   6.015869e+00
   4_xyz:  0.1951 0.2423   5.606973e+00   5.788217e+00
   4_adp:  0.1733 0.2260   5.521982e+00   5.725094e+00
   4_occ:  0.1730 0.2261   5.521193e+00   5.724939e+00
   5_bss:  0.1731 0.2258   5.519685e+00   5.722780e+00
   5_xyz:  0.1504 0.2008   5.401670e+00   5.617266e+00
   5_adp:  0.1464 0.1951   5.373477e+00   5.585113e+00
   5_occ:  0.1462 0.1949   5.372751e+00   5.584772e+00
   5_bss:  0.1467 0.1948   5.373508e+00   5.584442e+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:  0.268  35.940  -3.116   3.135   3.224   0.000   0.000   0.000
   1_xyz:  0.268  35.940  -3.116   3.135   3.224   0.000   0.000   0.000
   1_adp:  0.268  35.940  -3.116   3.135   3.224   0.000   0.000   0.000
   1_occ:  0.268  35.940  -3.116   3.135   3.224   0.000   0.000   0.000
   2_bss:  0.278  64.492  -0.788   2.465   2.546   0.000   0.000   0.000
   2_xyz:  0.278  64.492  -0.788   2.465   2.546   0.000   0.000   0.000
   2_adp:  0.278  64.492  -0.788   2.465   2.546   0.000   0.000   0.000
   2_occ:  0.278  64.492  -0.788   2.465   2.546   0.000   0.000   0.000
   3_bss:  0.324  75.465  -0.154   2.125   1.955   0.000   0.000   0.000
   3_xyz:  0.324  75.465  -0.154   2.125   1.955   0.000   0.000   0.000
   3_adp:  0.324  75.465  -0.154   2.125   1.955   0.000   0.000   0.000
   3_occ:  0.324  75.465  -0.154   2.125   1.955   0.000   0.000   0.000
   4_bss:  0.333  87.153  -0.758   1.249   1.232   0.000   0.000   0.000
   4_xyz:  0.333  87.153  -0.758   1.249   1.232   0.000   0.000   0.000
   4_adp:  0.333  87.153  -0.758   1.249   1.232   0.000   0.000   0.000
   4_occ:  0.333  87.153  -0.758   1.249   1.232   0.000   0.000   0.000
   5_bss:  0.335  84.290  -0.906   0.493   1.008   0.000   0.000   0.000
   5_xyz:  0.335  84.290  -0.906   0.493   1.008   0.000   0.000   0.000
   5_adp:  0.335  84.290  -0.906   0.493   1.008   0.000   0.000   0.000
   5_occ:  0.335  84.290  -0.906   0.493   1.008   0.000   0.000   0.000
   5_bss:  0.330  81.671  -0.995   0.090   0.905   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  60.235 0.3904  0.5041    73183.365
   1_bss:  58.507 0.4121  0.5580    70655.885
   1_xyz:  53.142 0.4796  0.6379    59282.990
   1_adp:  53.814 0.4710  0.6287    60879.444
   1_occ:  53.843 0.4706  0.6278    61008.913
   2_bss:  53.768 0.4717  0.6378    61110.836
   2_xyz:  44.173 0.5914  0.7940    43828.612
   2_adp:  42.164 0.6161  0.8031    40808.094
   2_occ:  42.146 0.6162  0.8029    40713.581
   3_bss:  42.069 0.6172  0.8026    40646.817
   3_xyz:  35.679 0.6934  0.8901    30837.918
   3_adp:  33.281 0.7217  0.8959    27886.250
   3_occ:  33.290 0.7216  0.8952    27888.261
   4_bss:  33.267 0.7219  0.8735    27897.942
   4_xyz:  24.459 0.8168  0.9517    15320.844
   4_adp:  22.332 0.8389  0.9487    13341.752
   4_occ:  22.323 0.8390  0.9488    13336.030
   5_bss:  22.241 0.8397  0.9370    13210.044
   5_xyz:  19.343 0.8681  0.9530    10422.914
   5_adp:  18.382 0.8774  0.9485     9830.429
   5_occ:  18.364 0.8776  0.9485     9817.267
   5_bss:  18.360 0.8776  0.9427     9813.549
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6832e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6832e-01
   1_xyz:   1.548  0.012  0.098 15.791  0.006  4.112   1.3109e-01
   1_adp:   1.548  0.012  0.098 15.791  0.006  4.112   1.3109e-01
   1_occ:   1.548  0.012  0.098 15.791  0.006  4.112   1.3109e-01
   2_bss:   1.548  0.012  0.098 15.791  0.006  4.112   1.3109e-01
   2_xyz:   1.504  0.011  0.103 15.534  0.006  4.116   1.2364e-01
   2_adp:   1.504  0.011  0.103 15.534  0.006  4.116   1.2364e-01
   2_occ:   1.504  0.011  0.103 15.534  0.006  4.116   1.2364e-01
   3_bss:   1.504  0.011  0.103 15.534  0.006  4.116   1.2364e-01
   3_xyz:   1.109  0.007  0.073 14.802  0.004  4.127   6.9572e-02
   3_adp:   1.109  0.007  0.073 14.802  0.004  4.127   6.9572e-02
   3_occ:   1.109  0.007  0.073 14.802  0.004  4.127   6.9572e-02
   4_bss:   1.109  0.007  0.073 14.802  0.004  4.127   6.9572e-02
   4_xyz:   1.317  0.011  0.093 14.861  0.004  4.112   9.8552e-02
   4_adp:   1.317  0.011  0.093 14.861  0.004  4.112   9.8552e-02
   4_occ:   1.317  0.011  0.093 14.861  0.004  4.112   9.8552e-02
   5_bss:   1.317  0.011  0.093 14.861  0.004  4.112   9.8552e-02
   5_xyz:   1.108  0.010  0.078 14.581  0.004  4.125   7.4890e-02
   5_adp:   1.108  0.010  0.078 14.581  0.004  4.125   7.4890e-02
   5_occ:   1.108  0.010  0.078 14.581  0.004  4.125   7.4890e-02
   5_bss:   1.108  0.010  0.078 14.581  0.004  4.125   7.4890e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.762   2.4634e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.762   2.4634e-01
   1_xyz:  11.003  0.083  0.329 83.220  0.049  2.057   1.3516e-01
   1_adp:  11.003  0.083  0.329 83.220  0.049  2.057   1.3516e-01
   1_occ:  11.003  0.083  0.329 83.220  0.049  2.057   1.3516e-01
   2_bss:  11.003  0.083  0.329 83.220  0.049  2.057   1.3516e-01
   2_xyz:  10.193  0.056  0.384 86.454  0.036  2.170   1.3699e-01
   2_adp:  10.193  0.056  0.384 86.454  0.036  2.170   1.3699e-01
   2_occ:  10.193  0.056  0.384 86.454  0.036  2.170   1.3699e-01
   3_bss:  10.193  0.056  0.384 86.454  0.036  2.170   1.3699e-01
   3_xyz:   8.898  0.043  0.294 85.660  0.040  2.270   6.0534e-02
   3_adp:   8.898  0.043  0.294 85.660  0.040  2.270   6.0534e-02
   3_occ:   8.898  0.043  0.294 85.660  0.040  2.270   6.0534e-02
   4_bss:   8.898  0.043  0.294 85.660  0.040  2.270   6.0534e-02
   4_xyz:   8.654  0.063  0.240 86.355  0.041  2.126   7.5253e-02
   4_adp:   8.654  0.063  0.240 86.355  0.041  2.126   7.5253e-02
   4_occ:   8.654  0.063  0.240 86.355  0.041  2.126   7.5253e-02
   5_bss:   8.654  0.063  0.240 86.355  0.041  2.126   7.5253e-02
   5_xyz:   8.011  0.051  0.247 85.278  0.042  2.240   5.7580e-02
   5_adp:   8.011  0.051  0.247 85.278  0.042  2.240   5.7580e-02
   5_occ:   8.011  0.051  0.247 85.278  0.042  2.240   5.7580e-02
   5_bss:   8.011  0.051  0.247 85.278  0.042  2.240   5.7580e-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: 111.71   0.00  19.79  88.84   0.00  16.78 111.71   0.00  36.21
   1_occ: 111.71   0.00  19.79  88.84   0.00  16.78 111.71   0.00  36.21
   2_bss: 111.71   0.00  19.79  88.84   0.00  16.78 111.71   0.00  36.21
   2_xyz: 111.71   0.00  19.79  88.84   0.00  16.78 111.71   0.00  36.21
   2_adp: 119.60   0.00  19.23  94.85   0.00  15.66 119.60   0.00  38.65
   2_occ: 119.60   0.00  19.23  94.85   0.00  15.66 119.60   0.00  38.65
   3_bss: 119.60   0.00  19.23  94.85   0.00  15.66 119.60   0.00  38.65
   3_xyz: 119.60   0.00  19.23  94.85   0.00  15.66 119.60   0.00  38.65
   3_adp: 116.17   0.00  18.00  93.89   0.00  13.92 116.17   0.00  40.21
   3_occ: 116.17   0.00  18.00  93.89   0.00  13.92 116.17   0.00  40.21
   4_bss: 116.17   0.00  18.00  93.89   0.00  13.92 116.17   0.00  40.21
   4_xyz: 116.17   0.00  18.00  93.89   0.00  13.92 116.17   0.00  40.21
   4_adp: 112.97   0.00  17.62  96.21   0.00  12.55 112.97   3.88  45.23
   4_occ: 112.97   0.00  17.62  96.21   0.00  12.55 112.97   3.88  45.23
   5_bss: 112.97   0.00  17.62  96.21   0.00  12.55 112.97   3.88  45.23
   5_xyz: 112.97   0.00  17.62  96.21   0.00  12.55 112.97   3.88  45.23
   5_adp: 109.16   0.00  16.79  94.69   0.00  11.87 109.16   3.75  43.61
   5_occ: 109.16   0.00  16.79  94.69   0.00  11.87 109.16   3.75  43.61
   5_bss: 109.18   0.02  16.81  94.70   0.02  11.89 109.18   3.77  43.63
------------------------------------------------------------------------
 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:    1.765    0.024    0.311
   1_adp:    1.765    0.024    0.311
   1_occ:    1.765    0.024    0.311
   2_bss:    1.765    0.024    0.311
   2_xyz:    1.579    0.047    0.569
   2_adp:    1.579    0.047    0.569
   2_occ:    1.579    0.047    0.569
   3_bss:    1.579    0.047    0.569
   3_xyz:    1.586    0.036    0.675
   3_adp:    1.586    0.036    0.675
   3_occ:    1.586    0.036    0.675
   4_bss:    1.586    0.036    0.675
   4_xyz:    1.722    0.061    0.857
   4_adp:    1.722    0.061    0.857
   4_occ:    1.722    0.061    0.857
   5_bss:    1.722    0.061    0.857
   5_xyz:    1.795    0.165    0.900
   5_adp:    1.795    0.165    0.900
   5_occ:    1.795    0.165    0.900
   5_bss:    1.795    0.165    0.900
------------------------------------------------------------------------

CPU time actual refinement: 363.82


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_967/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_967/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_967/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_967/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_967/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 363.67 
  Macro-tasks:
    bulk solvent and scale       = 52.38  
    individual site refinement   = 151.42 
    weights calculation          = 29.50  
    collect and process          = 6.41   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 239.83 
  Micro-tasks:
    mask                            = 2.93   
    f_calc                          = 113.81 
    alpha_beta                      = 8.27   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 124.36 
    fmodel                         = 8.99   
    r_factors                      = 0.34   
    phase_errors                   = 10.05  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 270.16 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 5.081 micro seconds
Total CPU time: 6.29 minutes
from_scatterers_fft:    662 calls, 113.44 s
gradients_fft:          608 calls, 110.80 s

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

# Date 2008-01-16 Time 06:06:04 PST -0800 (1200492364.52 s)
Start R-work = 0.4913, R-free = 0.4831 (no bulk solvent and anisotropic scale)
Final R-work = 0.1618, R-free = 0.2082 (no bulk solvent and anisotropic scale)

Start R-work = 0.4836, R-free = 0.4764
Final R-work = 0.1467, R-free = 0.1948