# Date 2008-01-16 Time 05:12:50 PST -0800 (1200489170.21 s)
#phil __OFF__

Command line arguments: "../639.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 28216
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 639

-------------------------------------------------------------------------------
  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: (70.25, 46.4607, 84.6622, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.4607, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9109 1.96109
Completeness in resolution range: 0.9586
Completeness with d_max=infinity: 0.955701

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9109
                             d_min =   1.9611

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: (70.25, 46.4607, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9109 1.96109
Completeness in resolution range: 0.9586
Completeness with d_max=infinity: 0.955701

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9113 -  4.1966 [2140/2169]  1929   211   9.9%
  bin  2:  4.1966 -  3.3433 [2055/2071]  1847   208  10.1%
  bin  3:  3.3433 -  2.9243 [2037/2056]  1831   206  10.1%
  bin  4:  2.9243 -  2.6586 [2028/2058]  1828   200   9.9%
  bin  5:  2.6586 -  2.4689 [2002/2021]  1806   196   9.8%
  bin  6:  2.4689 -  2.3240 [1997/2022]  1790   207  10.4%
  bin  7:  2.3240 -  2.2080 [1961/1995]  1767   194   9.9%
  bin  8:  2.2080 -  2.1121 [1992/2022]  1793   199  10.0%
  bin  9:  2.1121 -  2.0310 [1982/2024]  1783   199  10.0%
  bin 10:  2.0310 -  1.9611 [1395/1997]  1256   139  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_639/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: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 35
        2.42 -     3.04: 2245
        3.04 -     3.66: 4793
        3.66 -     4.28: 9132
        4.28 -     4.90: 12511
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.908 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.910 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.912 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.965 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28711 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_639/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_639/model_refine_001.geo

CPU time processing inputs: 9.13


============================ 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 = 70.25 46.4607 84.6622 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3837   r_free= 0.3814   ksol= 0.00   Bsol= 0.00   scale= 0.955    |
|                                                                             |
| 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:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.165904                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9113 -  4.6808 0.99   1388  155 0.3186 0.3147      6.4306      6.4125|
|  2:  4.6808 -  3.7345 0.99   1347  146 0.3136 0.2941      6.6039      6.5501|
|  3:  3.7345 -  3.2681 0.99   1316  147 0.3441 0.3628      6.4998      6.6525|
|  4:  3.2681 -  2.9719 0.99   1313  153 0.3462 0.3696      6.3724      6.3573|
|  5:  2.9719 -  2.7603 0.99   1296  140 0.3939 0.3598      6.2418      6.1901|
|  6:  2.7603 -  2.5985 0.99   1290  145 0.4092 0.4373      6.1625      6.1859|
|  7:  2.5985 -  2.4689 0.99   1291  135 0.4069 0.3777      6.1364      6.1099|
|  8:  2.4689 -  2.3619 0.98   1265  150 0.4214 0.4112      6.0916      6.0745|
|  9:  2.3619 -  2.2713 0.98   1271  142 0.4226 0.3841       6.048      5.9749|
| 10:  2.2713 -  2.1932 0.99   1287  137 0.4290 0.4548      6.0048      6.0561|
| 11:  2.1932 -  2.1248 0.99   1281  143 0.4505 0.4698      5.9807      6.0419|
| 12:  2.1248 -  2.0642 0.97   1248  139 0.4439 0.4347      5.9091      5.9436|
| 13:  2.0642 -  2.0100 0.99   1269  142 0.4411 0.4381      5.8168       5.756|
| 14:  2.0100 -  1.9611 0.59    768   85 0.4816 0.4417      5.8119      5.7143|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9113 -  4.6808  1388   155  0.76  28.65   0.86     0.79      50237.17|
|  2:  4.6808 -  3.7345  1347   146  0.79  26.80   0.96     0.90      66601.18|
|  3:  3.7345 -  3.2681  1316   147  0.73  32.89   0.98     0.92      69878.39|
|  4:  3.2681 -  2.9719  1313   153  0.68  37.32   1.00     0.89      63293.54|
|  5:  2.9719 -  2.7603  1296   140  0.62  42.10   0.95     0.83      51746.88|
|  6:  2.7603 -  2.5985  1290   145  0.60  44.15   0.96     0.81      45915.67|
|  7:  2.5985 -  2.4689  1291   135  0.60  43.70   0.99     0.81      41345.60|
|  8:  2.4689 -  2.3619  1265   150  0.59  45.14   0.96     0.81      37533.36|
|  9:  2.3619 -  2.2713  1271   142  0.60  44.47   1.00     0.81      33845.69|
| 10:  2.2713 -  2.1932  1287   137  0.56  47.50   1.01     0.80      33425.33|
| 11:  2.1932 -  2.1248  1281   143  0.53  49.75   1.02     0.77      32803.13|
| 12:  2.1248 -  2.0642  1248   139  0.53  50.01   1.03     0.79      31166.18|
| 13:  2.0642 -  2.0100  1269   142  0.51  51.14   1.02     0.76      26076.67|
| 14:  2.0100 -  1.9611   768    85  0.54  49.14   0.97     0.72      20767.02|
|alpha:            min =        0.72 max =            0.92 mean =         0.82|
|beta:             min =    20767.02 max =        69878.39 mean =     44109.49|
|figures of merit: min =        0.00 max =            1.00 mean =         0.62|
|phase err.(work): min =        0.00 max =           89.99 mean =        41.95|
|phase err.(test): min =        0.00 max =           89.94 mean =        42.13|
|-----------------------------------------------------------------------------|

============================== 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 = 4.344817              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.696   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.151155              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.578   (deg)                 |
|-----------------------------------------------------------------------------|


        ----------Initial model statistics (before refinement)----------       

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.007:  1367 |   0.001 -   0.989:  1519 |  1.806 -  2.115:       12 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       23 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      217 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2028 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1903 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2890 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4697 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4435 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5709 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6802 |
|-----------------------------------------------------------------------------|
|-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 |   4.109    4.900  1.806 |       0.295 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.571)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3837   r_free= 0.3814   ksol= 0.00   Bsol= 0.00   scale= 0.955    |
|                                                                             |
| 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:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.165904                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3693   r_free= 0.3660   ksol= 0.33   Bsol= 30.87   scale= 0.972   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.15,-0.35,2.33,-0.00,0.00,0.00); trace/3= -0.39                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.155144                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.477934              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.677   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.572479              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 88.562   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3693      final r-factor (work) = 0.2485          |
| start r-factor (free) = 0.3660      final r-factor (free) = 0.2744          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.8648 = 3.48 * 0.50 * 6.1509 + 1.00 * 0.1685                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.3993 = 3.48 * 0.50 * 5.9337 + 1.00 * 0.0809                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2485      final r-factor (work) = 0.2283          |
| start r-factor (free) = 0.2744      final r-factor (free) = 0.2811          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4029 = 0.57 * 1.00 * 5.9337 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3050 = 0.57 * 1.00 * 5.7530 + 1.00 * 0.0116                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.571)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.19   17.56    None  None   None       |
|    all(noH): 2823   0      0.00    82.19   17.56    None  None   None       |
|    Sol.    : 438    0      3.40    78.93   39.40    None  None   None       |
|    Mac.    : 2385   0      0.00    82.19   13.55    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 -   8.220:  649   |   5:    41.097 -  49.317:  122        |
|      1:     8.220 -  16.439: 1157   |   6:    49.317 -  57.536:   66        |
|      2:    16.439 -  24.658:  453   |   7:    57.536 -  65.756:   44        |
|      3:    24.658 -  32.878:  175   |   8:    65.756 -  73.975:   19        |
|      4:    32.878 -  41.097:  134   |   9:    73.975 -  82.194:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2283 r_free = 0.2811             target_work(ml) = 5.763         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2280 r_free = 0.2815             target_work(ml) = 5.763         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2280   r_free= 0.2815   ksol= 0.33   Bsol= 30.87   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.15,-0.35,2.33,-0.00,0.00,0.00); trace/3= -0.39                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.762849                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2262   r_free= 0.2795   ksol= 0.33   Bsol= 39.61   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.71,-1.84,-0.37,-0.00,-0.00,-0.00); trace/3= -1.64                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.758685                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.240738              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.724   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.186577              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.685  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2262      final r-factor (work) = 0.1659          |
| start r-factor (free) = 0.2795      final r-factor (free) = 0.2149          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5292 = 2.24 * 0.50 * 5.7555 + 1.00 * 0.0809                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3644 = 2.24 * 0.50 * 5.6340 + 1.00 * 0.0522                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1659      final r-factor (work) = 0.1558          |
| start r-factor (free) = 0.2149      final r-factor (free) = 0.2016          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0627 = 0.19 * 1.00 * 5.6340 + 1.00 * 0.0115                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0254 = 0.19 * 1.00 * 5.4566 + 1.00 * 0.0073                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.571)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.30    79.48   17.06    None  None   None       |
|    all(noH): 2823   0      1.30    79.48   17.06    None  None   None       |
|    Sol.    : 438    0      5.79    73.55   38.44    None  None   None       |
|    Mac.    : 2385   0      1.30    79.48   13.13    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.304 -   9.121:  769   |   5:    40.390 -  48.207:  115        |
|      1:     9.121 -  16.938: 1197   |   6:    48.207 -  56.024:   83        |
|      2:    16.938 -  24.755:  332   |   7:    56.024 -  63.841:   32        |
|      3:    24.755 -  32.573:  132   |   8:    63.841 -  71.658:   13        |
|      4:    32.573 -  40.390:  146   |   9:    71.658 -  79.475:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1558 r_free = 0.2016             target_work(ml) = 5.425         |
| occupancies: max = 1.00  min = 0.06   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1556 r_free = 0.2015             target_work(ml) = 5.424         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1556   r_free= 0.2015   ksol= 0.33   Bsol= 39.61   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.71,-1.84,-0.37,-0.00,-0.00,-0.00); trace/3= -1.64                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.424043                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1557   r_free= 0.2011   ksol= 0.33   Bsol= 39.61   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.49,-2.28,-1.18,-0.00,-0.00,-0.00); trace/3= -1.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.421645                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.225933              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.736  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.552674              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.722  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1557      final r-factor (work) = 0.1261          |
| start r-factor (free) = 0.2011      final r-factor (free) = 0.1658          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1245 = 2.23 * 0.50 * 5.4559 + 1.00 * 0.0522                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9800 = 2.23 * 0.50 * 5.3272 + 1.00 * 0.0510                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1261      final r-factor (work) = 0.1194          |
| start r-factor (free) = 0.1658      final r-factor (free) = 0.1618          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9515 = 0.55 * 1.00 * 5.3272 + 1.00 * 0.0073                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8807 = 0.55 * 1.00 * 5.1966 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.571)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.88    87.08   17.30    None  None   None       |
|    all(noH): 2823   0      0.88    87.08   17.30    None  None   None       |
|    Sol.    : 438    0      4.27    75.94   40.69    None  None   None       |
|    Mac.    : 2385   0      0.88    87.08   13.01    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:     0.880 -   9.499:  879   |   5:    43.978 -  52.598:  111        |
|      1:     9.499 -  18.119: 1204   |   6:    52.598 -  61.218:   76        |
|      2:    18.119 -  26.739:  258   |   7:    61.218 -  69.838:   31        |
|      3:    26.739 -  35.359:  128   |   8:    69.838 -  78.458:   15        |
|      4:    35.359 -  43.978:  119   |   9:    78.458 -  87.077:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1194 r_free = 0.1618             target_work(ml) = 5.181         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1194 r_free = 0.1617             target_work(ml) = 5.181         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1194   r_free= 0.1617   ksol= 0.33   Bsol= 39.61   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.49,-2.28,-1.18,-0.00,-0.00,-0.00); trace/3= -1.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.180897                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1198   r_free= 0.1620   ksol= 0.32   Bsol= 40.66   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.59,-2.48,-1.65,-0.00,-0.00,-0.00); trace/3= -2.24                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.182411                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.143850              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 129.677  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.359781              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.593  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1198      final r-factor (work) = 0.1108          |
| start r-factor (free) = 0.1620      final r-factor (free) = 0.1549          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6233 = 2.14 * 0.50 * 5.1985 + 1.00 * 0.0510                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5740 = 2.14 * 0.50 * 5.1469 + 1.00 * 0.0569                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1108      final r-factor (work) = 0.1093          |
| start r-factor (free) = 0.1549      final r-factor (free) = 0.1541          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8604 = 0.36 * 1.00 * 5.1469 + 1.00 * 0.0087                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8505 = 0.36 * 1.00 * 5.1200 + 1.00 * 0.0084                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.571)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.13    88.54   17.07    None  None   None       |
|    all(noH): 2823   0      1.13    88.54   17.07    None  None   None       |
|    Sol.    : 438    0      4.98    78.33   39.96    None  None   None       |
|    Mac.    : 2385   0      1.13    88.54   12.87    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:     1.134 -   9.875:  999   |   5:    44.839 -  53.580:  110        |
|      1:     9.875 -  18.616: 1129   |   6:    53.580 -  62.321:   58        |
|      2:    18.616 -  27.357:  234   |   7:    62.321 -  71.062:   28        |
|      3:    27.357 -  36.098:  129   |   8:    71.062 -  79.803:   12        |
|      4:    36.098 -  44.839:  122   |   9:    79.803 -  88.543:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1093 r_free = 0.1541             target_work(ml) = 5.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1092 r_free = 0.1540             target_work(ml) = 5.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1092   r_free= 0.1540   ksol= 0.32   Bsol= 40.66   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.59,-2.48,-1.65,-0.00,-0.00,-0.00); trace/3= -2.24                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.116891                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1092   r_free= 0.1541   ksol= 0.32   Bsol= 40.66   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.44,-2.38,-1.63,-0.00,-0.00,-0.00); trace/3= -2.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.116954                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.528881              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 155.672  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.676000              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.031  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1092      final r-factor (work) = 0.1061          |
| start r-factor (free) = 0.1541      final r-factor (free) = 0.1534          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5305 = 2.53 * 0.50 * 5.1201 + 1.00 * 0.0565                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5158 = 2.53 * 0.50 * 5.1051 + 1.00 * 0.0607                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1061      final r-factor (work) = 0.1056          |
| start r-factor (free) = 0.1534      final r-factor (free) = 0.1545          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 18.7747 = 3.68 * 1.00 * 5.1051 + 1.00 * 0.0084                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 18.7535 = 3.68 * 1.00 * 5.0991 + 1.00 * 0.0094                              |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.571)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.68   17.06    None  None   None       |
|    all(noH): 2823   0      0.00    95.68   17.06    None  None   None       |
|    Sol.    : 438    0      6.12    82.67   40.23    None  None   None       |
|    Mac.    : 2385   0      0.00    95.68   12.81    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.569:  964   |   5:    47.842 -  57.411:  100        |
|      1:     9.569 -  19.137: 1184   |   6:    57.411 -  66.979:   53        |
|      2:    19.137 -  28.705:  232   |   7:    66.979 -  76.548:   22        |
|      3:    28.705 -  38.274:  143   |   8:    76.548 -  86.116:    8        |
|      4:    38.274 -  47.842:  115   |   9:    86.116 -  95.684:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1056 r_free = 0.1545             target_work(ml) = 5.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1055 r_free = 0.1544             target_work(ml) = 5.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1055   r_free= 0.1544   ksol= 0.32   Bsol= 40.66   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.44,-2.38,-1.63,-0.00,-0.00,-0.00); trace/3= -2.15                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.104683                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9113 -  4.6808 0.99   1388  155 0.0947 0.1232      5.3448      5.5032|
|  2:  4.6808 -  3.7345 0.99   1347  146 0.0819 0.1116      5.4022      5.6112|
|  3:  3.7345 -  3.2681 0.99   1316  147 0.1023 0.1517      5.4454      5.8519|
|  4:  3.2681 -  2.9719 0.99   1313  153 0.1154 0.1514      5.4249      5.5632|
|  5:  2.9719 -  2.7603 0.99   1296  140 0.1230 0.1718      5.2724      5.5086|
|  6:  2.7603 -  2.5985 0.99   1290  145 0.1106 0.1640      5.1443      5.3741|
|  7:  2.5985 -  2.4689 0.99   1291  135 0.1161 0.1549      5.1092      5.3361|
|  8:  2.4689 -  2.3619 0.98   1265  150 0.1071 0.1690      5.0041      5.2952|
|  9:  2.3619 -  2.2713 0.98   1271  142 0.1103 0.1786      5.0006       5.334|
| 10:  2.2713 -  2.1932 0.99   1287  137 0.1035 0.1727      4.9212      5.1611|
| 11:  2.1932 -  2.1248 0.99   1281  143 0.1087 0.1799      4.9205      5.3125|
| 12:  2.1248 -  2.0642 0.97   1248  139 0.1032 0.1535      4.8381      5.0438|
| 13:  2.0642 -  2.0100 0.99   1269  142 0.1066 0.1785      4.7538      5.0614|
| 14:  2.0100 -  1.9611 0.59    768   85 0.1004 0.1565      4.6262      4.8904|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9113 -  4.6808  1388   155  0.94   8.43   0.98     0.96       6421.94|
|  2:  4.6808 -  3.7345  1347   146  0.96   7.55   1.03     1.02       8517.82|
|  3:  3.7345 -  3.2681  1316   147  0.93  11.18   1.04     1.03       9958.35|
|  4:  3.2681 -  2.9719  1313   153  0.92  13.23   1.01     1.00       9998.21|
|  5:  2.9719 -  2.7603  1296   140  0.90  15.24   1.00     0.97       7617.95|
|  6:  2.7603 -  2.5985  1290   145  0.91  15.02   0.99     0.96       6384.35|
|  7:  2.5985 -  2.4689  1291   135  0.91  14.43   0.99     0.96       5550.24|
|  8:  2.4689 -  2.3619  1265   150  0.91  14.56   0.99     0.97       4850.17|
|  9:  2.3619 -  2.2713  1271   142  0.92  14.53   1.01     0.99       4739.41|
| 10:  2.2713 -  2.1932  1287   137  0.91  15.07   1.00     0.96       4162.51|
| 11:  2.1932 -  2.1248  1281   143  0.90  16.36   1.00     0.98       4364.63|
| 12:  2.1248 -  2.0642  1248   139  0.92  14.28   1.00     0.98       3735.24|
| 13:  2.0642 -  2.0100  1269   142  0.90  15.89   1.01     1.00       3190.60|
| 14:  2.0100 -  1.9611   768    85  0.92  14.10   0.99     0.96       2382.03|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     2382.03 max =         9998.21 mean =      5986.47|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.91 mean =        13.49|
|phase err.(test): min =        0.00 max =           88.97 mean =        13.12|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1054   r_free= 0.1544   ksol= 0.32   Bsol= 42.48   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.24,-2.22,-1.48,-0.00,-0.00,-0.00); trace/3= -1.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.104710                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.91 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1054   r_free= 0.1544   ksol= 0.32   Bsol= 42.48   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.24,-2.22,-1.48,-0.00,-0.00,-0.00); trace/3= -1.98                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.104710                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9113 -  4.6808 0.99   1388  155 0.0949 0.1235      5.3471      5.5066|
|  2:  4.6808 -  3.7345 0.99   1347  146 0.0820 0.1117      5.4038      5.6116|
|  3:  3.7345 -  3.2681 0.99   1316  147 0.1024 0.1517      5.4459      5.8525|
|  4:  3.2681 -  2.9719 0.99   1313  153 0.1154 0.1514      5.4247       5.563|
|  5:  2.9719 -  2.7603 0.99   1296  140 0.1229 0.1716      5.2717      5.5072|
|  6:  2.7603 -  2.5985 0.99   1290  145 0.1105 0.1640      5.1437      5.3739|
|  7:  2.5985 -  2.4689 0.99   1291  135 0.1161 0.1548      5.1088      5.3359|
|  8:  2.4689 -  2.3619 0.98   1265  150 0.1071 0.1687      5.0037      5.2939|
|  9:  2.3619 -  2.2713 0.98   1271  142 0.1103 0.1788      5.0003      5.3347|
| 10:  2.2713 -  2.1932 0.99   1287  137 0.1035 0.1725       4.921        5.16|
| 11:  2.1932 -  2.1248 0.99   1281  143 0.1086 0.1797      4.9201      5.3121|
| 12:  2.1248 -  2.0642 0.97   1248  139 0.1032 0.1534      4.8376      5.0436|
| 13:  2.0642 -  2.0100 0.99   1269  142 0.1066 0.1784      4.7534      5.0603|
| 14:  2.0100 -  1.9611 0.59    768   85 0.1003 0.1564      4.6258      4.8904|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9113 -  4.6808  1388   155  0.94   8.47   0.99     0.96       6469.98|
|  2:  4.6808 -  3.7345  1347   146  0.96   7.57   1.03     1.02       8550.27|
|  3:  3.7345 -  3.2681  1316   147  0.93  11.19   1.04     1.03       9967.21|
|  4:  3.2681 -  2.9719  1313   153  0.92  13.23   1.02     1.00       9991.31|
|  5:  2.9719 -  2.7603  1296   140  0.90  15.24   1.00     0.98       7610.87|
|  6:  2.7603 -  2.5985  1290   145  0.91  15.01   0.99     0.97       6375.79|
|  7:  2.5985 -  2.4689  1291   135  0.91  14.43   1.00     0.96       5542.56|
|  8:  2.4689 -  2.3619  1265   150  0.91  14.55   1.00     0.98       4844.90|
|  9:  2.3619 -  2.2713  1271   142  0.92  14.53   1.02     1.00       4736.28|
| 10:  2.2713 -  2.1932  1287   137  0.91  15.06   1.00     0.97       4159.88|
| 11:  2.1932 -  2.1248  1281   143  0.90  16.35   1.01     0.99       4360.66|
| 12:  2.1248 -  2.0642  1248   139  0.92  14.27   1.01     0.99       3729.07|
| 13:  2.0642 -  2.0100  1269   142  0.90  15.88   1.02     1.01       3186.90|
| 14:  2.0100 -  1.9611   768    85  0.92  14.10   1.00     0.97       2380.79|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2380.79 max =         9991.31 mean =      5989.32|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.93 mean =        13.49|
|phase err.(test): min =        0.00 max =           89.01 mean =        13.12|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.571)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.69   17.06    None  None   None       |
|    all(noH): 2823   0      0.00    95.69   17.06    None  None   None       |
|    Sol.    : 438    0      6.12    82.67   40.23    None  None   None       |
|    Mac.    : 2385   0      0.00    95.69   12.81    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.571:  964   |   5:    47.845 -  57.414:  100        |
|      1:     9.571 -  19.140: 1184   |   6:    57.414 -  66.982:   53        |
|      2:    19.140 -  28.708:  232   |   7:    66.982 -  76.551:   22        |
|      3:    28.708 -  38.277:  143   |   8:    76.551 -  86.119:    8        |
|      4:    38.277 -  47.845:  115   |   9:    86.119 -  95.687:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 289         
Filter by distance & map next to the model:
   mapped sites are within: 0.415 - 4.525
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 286 from: 289
   mapped sites are within: 0.722 - 4.525

peak=    6.056 closest distance to " NE2 GLN A  11 " =    1.170
peak=    5.830 closest distance to " O   HOH Z 126 " =    1.988
peak=    5.768 closest distance to " NH2 ARG A  56 " =    2.154
peak=    5.412 closest distance to " O   HOH Z 144 " =    1.703
peak=    5.245 closest distance to " CG  PRO A  54 " =    1.134
peak=    5.086 closest distance to " CB  GLN A 183 " =    1.240
peak=    5.002 closest distance to " O   HOH Z 193 " =    1.824
peak=    4.986 closest distance to " CB  GLN A 223 " =    1.472
peak=    4.923 closest distance to " CB  SER A  63 " =    1.175
peak=    4.912 closest distance to " O   HOH Z 232 " =    2.327
peak=    4.868 closest distance to " CB  ARG A 275 " =    0.896
peak=    4.677 closest distance to " C   PRO A 198 " =    1.474
peak=    4.619 closest distance to " O   HOH Z  78 " =    1.794
peak=    4.613 closest distance to " CG  PRO A 213 " =    1.203
peak=    4.558 closest distance to " O   HOH Z 427 " =    2.722
peak=    4.489 closest distance to " CB  SER A   3 " =    1.358
peak=    4.482 closest distance to " OD1 ASN A  69 " =    2.604
peak=    4.473 closest distance to " O   HOH Z   9 " =    2.328
peak=    4.440 closest distance to " CB  ASN A 148 " =    1.393
peak=    4.417 closest distance to " O   HOH Z 236 " =    2.131
peak=    4.405 closest distance to " CB  GLU A 128 " =    1.083
peak=    4.383 closest distance to " CB  GLU A 152 " =    1.251
peak=    4.311 closest distance to " O   HOH Z 298 " =    1.856
peak=    4.291 closest distance to " OD2 ASP A 286 " =    2.720
peak=    4.268 closest distance to " O   HOH Z 272 " =    1.791
peak=    4.258 closest distance to " O   HOH Z 234 " =    3.621
peak=    4.247 closest distance to " OG BSER A 164 " =    2.297
peak=    4.230 closest distance to " CB  LEU A 228 " =    1.086
peak=    4.205 closest distance to " CB  TYR A 169 " =    0.852
peak=    4.196 closest distance to " CA  TYR A  30 " =    0.953
peak=    4.192 closest distance to " O   HOH Z 369 " =    2.102
peak=    4.188 closest distance to " CB  ARG A  79 " =    1.446
peak=    4.185 closest distance to " ND2 ASN A 187 " =    1.436
peak=    4.151 closest distance to " NZ  LYS A 117 " =    3.188
peak=    4.140 closest distance to " CB  PRO A  54 " =    0.948
peak=    4.131 closest distance to " CB  VAL A 265 " =    1.324
peak=    4.102 closest distance to " O   HOH Z 108 " =    1.318
peak=    4.091 closest distance to " O   HOH Z  10 " =    1.857
peak=    4.087 closest distance to " O   HOH Z 316 " =    2.992
peak=    4.087 closest distance to " O   HOH Z 207 " =    1.837
peak=    4.068 closest distance to " O   HOH Z 368 " =    1.916
peak=    4.053 closest distance to " CG1 ILE A  33 " =    1.219
peak=    4.052 closest distance to " O   HOH Z 425 " =    2.019
peak=    4.032 closest distance to " O   HOH Z  59 " =    1.793
peak=    4.025 closest distance to " O   HOH Z 128 " =    2.108
peak=    4.025 closest distance to " O   HOH Z 368 " =    3.648
peak=    3.994 closest distance to " O   HOH Z 203 " =    1.824
peak=    3.989 closest distance to " O   HOH Z 209 " =    2.282
peak=    3.984 closest distance to " O   HOH Z  44 " =    1.871
peak=    3.963 closest distance to " CB  TRP A 179 " =    1.311
peak=    3.961 closest distance to " O   HOH Z  61 " =    1.593
peak=    3.961 closest distance to " O   HOH Z 158 " =    3.030
peak=    3.940 closest distance to " O   HOH Z   1 " =    1.785
peak=    3.934 closest distance to " O   HOH Z 344 " =    3.064
peak=    3.933 closest distance to " CG  ARG A  66 " =    2.462
peak=    3.919 closest distance to " O   HOH Z 371 " =    3.145
peak=    3.918 closest distance to " CB  ARG A 139 " =    0.987
peak=    3.918 closest distance to " NH1BARG A 145 " =    1.337
peak=    3.912 closest distance to " CA  ALA A  21 " =    1.127
peak=    3.912 closest distance to " CG2 VAL A 257 " =    0.881
peak=    3.909 closest distance to " CG  PRO A  90 " =    1.045
peak=    3.906 closest distance to " CA  THR A 264 " =    0.845
peak=    3.905 closest distance to " O   HOH Z 284 " =    2.896
peak=    3.900 closest distance to " O   HOH Z 263 " =    2.256
peak=    3.895 closest distance to " O   HOH Z 303 " =    2.125
peak=    3.883 closest distance to " O   HOH Z   9 " =    2.030
peak=    3.882 closest distance to " O   MET A 105 " =    1.808
peak=    3.874 closest distance to " CB  TRP A 266 " =    1.015
peak=    3.870 closest distance to " CD BLYS A 290 " =    1.193
peak=    3.868 closest distance to " O   HOH Z 132 " =    2.195
peak=    3.866 closest distance to " O   HOH Z 144 " =    2.299
peak=    3.852 closest distance to " CA  ASN A 215 " =    1.220
peak=    3.837 closest distance to " O   SER A  87 " =    2.249
peak=    3.832 closest distance to " O   HOH Z 141 " =    1.704
peak=    3.792 closest distance to " O   HOH Z   6 " =    2.005
peak=    3.783 closest distance to " O   HOH Z  66 " =    2.086
peak=    3.783 closest distance to " O   HOH Z 124 " =    1.364
peak=    3.772 closest distance to " O   HOH Z 425 " =    1.259
peak=    3.770 closest distance to " CG  PRO A 198 " =    1.235
peak=    3.767 closest distance to " O   HOH Z 327 " =    1.624
peak=    3.766 closest distance to " O   HOH Z 193 " =    2.000
peak=    3.739 closest distance to " O   HOH Z  88 " =    3.086
peak=    3.735 closest distance to " O   HOH Z  97 " =    1.964
peak=    3.735 closest distance to " CE  LYS A  76 " =    0.881
peak=    3.734 closest distance to " O   HOH Z   3 " =    1.906
peak=    3.733 closest distance to " O   HOH Z  61 " =    1.677
peak=    3.725 closest distance to " O   HOH Z 389 " =    3.179
peak=    3.715 closest distance to " O   HOH Z 250 " =    1.346
peak=    3.712 closest distance to " O   HOH Z  93 " =    2.194
peak=    3.702 closest distance to " O   HOH Z 346 " =    1.766
peak=    3.697 closest distance to " O   HOH Z 234 " =    3.753
peak=    3.690 closest distance to " O   HOH Z 407 " =    2.243
peak=    3.679 closest distance to " O   HOH Z 180 " =    2.195
peak=    3.675 closest distance to " O   HOH Z 108 " =    1.991
peak=    3.672 closest distance to " O   HOH Z 261 " =    1.994
peak=    3.666 closest distance to " O   HOH Z 189 " =    1.748
peak=    3.663 closest distance to " O   HOH Z  21 " =    1.657
peak=    3.661 closest distance to " O   HOH Z   1 " =    1.663
peak=    3.655 closest distance to " NH1AARG A 145 " =    1.098
peak=    3.650 closest distance to " OD1BASN A 224 " =    2.234
peak=    3.649 closest distance to " O   HOH Z 219 " =    2.176
peak=    3.638 closest distance to " O   HOH Z 423 " =    2.662
peak=    3.629 closest distance to " CG  PRO A 280 " =    0.722
peak=    3.626 closest distance to " O   HOH Z 411 " =    3.813
peak=    3.622 closest distance to " O   HOH Z 214 " =    2.035
peak=    3.617 closest distance to " O   HOH Z 380 " =    1.961
peak=    3.615 closest distance to " CD2 LEU A 297 " =    0.916
peak=    3.609 closest distance to " CA  MET A  40 " =    1.072
peak=    3.606 closest distance to " O   HOH Z 134 " =    1.230
peak=    3.603 closest distance to " O   HOH Z 426 " =    1.587
peak=    3.597 closest distance to " O   HOH Z 260 " =    1.152
peak=    3.596 closest distance to " O   HOH Z 353 " =    2.637
peak=    3.593 closest distance to " O   HOH Z 371 " =    1.598
peak=    3.593 closest distance to " CD2 LEU A 255 " =    1.424
peak=    3.592 closest distance to " O   HOH Z  40 " =    2.024
peak=    3.587 closest distance to " CB  SER A 216 " =    0.780
peak=    3.583 closest distance to " O   HOH Z 147 " =    1.687
peak=    3.556 closest distance to " O   HOH Z 227 " =    1.715
peak=    3.553 closest distance to " O   HOH Z 227 " =    2.191
peak=    3.547 closest distance to " O   HOH Z 389 " =    1.749
peak=    3.544 closest distance to " O   HOH Z  73 " =    1.574
peak=    3.534 closest distance to " CE AMET A  47 " =    1.314
peak=    3.518 closest distance to " ND1 HIS A  86 " =    1.798
peak=    3.512 closest distance to " CG1BVAL A  72 " =    1.409
peak=    3.509 closest distance to " O   HOH Z 366 " =    3.044
peak=    3.504 closest distance to " CG2 THR A 221 " =    1.167
peak=    3.502 closest distance to " CB  ARG A 190 " =    1.646
peak=    3.501 closest distance to " NH2AARG A 275 " =    3.707
peak=    3.498 closest distance to " OG  SER A  22 " =    2.781
peak=    3.495 closest distance to " O   HOH Z 163 " =    1.771
peak=    3.493 closest distance to " N   PHE A 130 " =    1.284
peak=    3.483 closest distance to " O   HOH Z  40 " =    2.267
peak=    3.477 closest distance to " NH2BARG A 145 " =    1.963
peak=    3.475 closest distance to " CD2 TRP A 179 " =    1.404
peak=    3.469 closest distance to " CG  LEU A 167 " =    1.200
peak=    3.469 closest distance to " O   HOH Z 236 " =    1.538
peak=    3.468 closest distance to " O   HOH Z 211 " =    2.507
peak=    3.466 closest distance to " CB  SER A  26 " =    1.568
peak=    3.466 closest distance to " CB  LYS A 117 " =    1.143
peak=    3.458 closest distance to " O   HOH Z 279 " =    2.176
peak=    3.442 closest distance to " CG2BVAL A  41 " =    0.906
peak=    3.436 closest distance to " O   HOH Z 271 " =    2.305
peak=    3.429 closest distance to " O   HOH Z 402 " =    1.380
peak=    3.422 closest distance to " O   HOH Z 172 " =    3.417
peak=    3.421 closest distance to " O   HOH Z 437 " =    1.620
peak=    3.421 closest distance to " O   HOH Z 419 " =    1.954
peak=    3.417 closest distance to " OG BSER A  99 " =    2.195
peak=    3.417 closest distance to " O   HOH Z 135 " =    1.619
peak=    3.416 closest distance to " O   HOH Z 291 " =    1.535
peak=    3.410 closest distance to " CB  VAL A 126 " =    1.197
peak=    3.408 closest distance to " O   HOH Z 371 " =    3.323
peak=    3.407 closest distance to " CD1 LEU A 300 " =    1.267
peak=    3.405 closest distance to " CB  GLN A  88 " =    1.269
peak=    3.399 closest distance to " CD  ARG A 159 " =    0.762
peak=    3.398 closest distance to " O   HOH Z 409 " =    2.554
peak=    3.397 closest distance to " O   HOH Z 281 " =    4.525
peak=    3.387 closest distance to " CE2 TRP A 179 " =    1.556
peak=    3.384 closest distance to " N   ARG A 156 " =    1.245
peak=    3.383 closest distance to " O   HOH Z 295 " =    1.501
peak=    3.381 closest distance to " O   HOH Z  71 " =    1.069
peak=    3.379 closest distance to " CB  GLU A 277 " =    3.482
peak=    3.378 closest distance to " OG  SER A  62 " =    2.961
peak=    3.377 closest distance to " N   ASN A  39 " =    1.271
peak=    3.375 closest distance to " CA  THR A 221 " =    0.962
peak=    3.372 closest distance to " CE1 TYR A 186 " =    1.256
peak=    3.369 closest distance to " O   HOH Z 368 " =    2.627
peak=    3.367 closest distance to " CB  ASN A 285 " =    0.938
peak=    3.366 closest distance to " CG  PRO A 243 " =    1.118
peak=    3.362 closest distance to " O   HOH Z 403 " =    1.668
peak=    3.359 closest distance to " O   HOH Z 286 " =    2.449
peak=    3.357 closest distance to " CB  ALA A 291 " =    1.420
peak=    3.354 closest distance to " CA  ALA A 233 " =    1.147
peak=    3.350 closest distance to " O   HOH Z 329 " =    3.598
peak=    3.346 closest distance to " O   HOH Z  43 " =    2.018
peak=    3.346 closest distance to " O   HOH Z 218 " =    2.259
peak=    3.346 closest distance to " CB  LEU A 143 " =    1.104
peak=    3.342 closest distance to " CD  PRO A 243 " =    1.564
peak=    3.341 closest distance to " O   ALA A 165 " =    1.369
peak=    3.339 closest distance to " O   HOH Z  49 " =    2.014
peak=    3.337 closest distance to " O   HOH Z 234 " =    1.825
peak=    3.337 closest distance to " NH2 ARG A 156 " =    1.221
peak=    3.336 closest distance to " O   HOH Z 261 " =    2.084
peak=    3.331 closest distance to " CB  LEU A 255 " =    0.764
peak=    3.324 closest distance to " CB  ASP A 140 " =    0.917
peak=    3.323 closest distance to " O   HOH Z 128 " =    2.145
peak=    3.322 closest distance to " CB  VAL A 202 " =    1.655
peak=    3.316 closest distance to " O   HOH Z 245 " =    1.268
peak=    3.313 closest distance to " CB  SER A  62 " =    1.278
peak=    3.304 closest distance to " O   HOH Z 345 " =    3.442
peak=    3.303 closest distance to " CG  GLU A 277 " =    2.057
peak=    3.302 closest distance to " O   HOH Z 133 " =    2.559
peak=    3.299 closest distance to " CD  LYS A 166 " =    1.220
peak=    3.298 closest distance to " O   HOH Z 291 " =    1.805
peak=    3.297 closest distance to " CG  GLN A  89 " =    1.420
peak=    3.293 closest distance to " O   HOH Z 374 " =    2.532
peak=    3.293 closest distance to " O   HOH Z 193 " =    1.600
peak=    3.283 closest distance to " CG2 ILE A 120 " =    1.155
peak=    3.283 closest distance to " CB  SER A 141 " =    1.046
peak=    3.281 closest distance to " O   HOH Z  53 " =    2.503
peak=    3.276 closest distance to " O   HOH Z 106 " =    2.325
peak=    3.273 closest distance to " O   HOH Z 286 " =    2.215
peak=    3.272 closest distance to " CB  ALA A 233 " =    1.348
peak=    3.270 closest distance to " O   HOH Z 290 " =    0.957
peak=    3.269 closest distance to " N   GLN A 278 " =    1.031
peak=    3.266 closest distance to " O   HOH Z 217 " =    1.467
peak=    3.264 closest distance to " CA  ASN A 176 " =    1.233
peak=    3.260 closest distance to " CG  MET A 185 " =    1.218
peak=    3.258 closest distance to " O   HOH Z 128 " =    2.083
peak=    3.258 closest distance to " CA  ASP A 162 " =    1.094
peak=    3.257 closest distance to " O   HOH Z 336 " =    1.804
peak=    3.254 closest distance to " O   HOH Z 433 " =    1.837
peak=    3.248 closest distance to " O   HOH Z 326 " =    1.389
peak=    3.244 closest distance to " OE2 GLU A  53 " =    2.121
peak=    3.238 closest distance to " O   ALA A   1 " =    1.646
peak=    3.236 closest distance to " O   HOH Z 273 " =    2.757
peak=    3.236 closest distance to " CB  THR A 157 " =    1.030
peak=    3.232 closest distance to " CB  ASN A 215 " =    1.086
peak=    3.230 closest distance to " CG  MET A 185 " =    1.080
peak=    3.229 closest distance to " O   HOH Z 287 " =    1.795
peak=    3.225 closest distance to " O   HOH Z 153 " =    1.630
peak=    3.222 closest distance to " CG1 VAL A 202 " =    1.977
peak=    3.221 closest distance to " NH2 ARG A 219 " =    1.865
peak=    3.220 closest distance to " CG  GLN A  77 " =    2.117
peak=    3.219 closest distance to " O   HOH Z 125 " =    2.209
peak=    3.218 closest distance to " CA  LYS A 290 " =    1.344
peak=    3.217 closest distance to " CB  ALA A  21 " =    1.808
peak=    3.216 closest distance to " CG  ARG A 269 " =    1.288
peak=    3.213 closest distance to " O   HOH Z 248 " =    1.645
peak=    3.210 closest distance to " CB  SER A 212 " =    0.949
peak=    3.210 closest distance to " CE BMET A  47 " =    1.533
peak=    3.205 closest distance to " CB  GLU A 152 " =    1.373
peak=    3.204 closest distance to " CB  ASN A 110 " =    1.127
peak=    3.197 closest distance to " O   HOH Z 266 " =    2.958
peak=    3.195 closest distance to " O   HOH Z 261 " =    1.430
peak=    3.195 closest distance to " CB  MET A  47 " =    1.160
peak=    3.194 closest distance to " O   HOH Z 411 " =    1.741
peak=    3.193 closest distance to " O   HOH Z 173 " =    1.860
peak=    3.192 closest distance to " O   HOH Z  10 " =    2.436
peak=    3.189 closest distance to " O   HOH Z 391 " =    2.986
peak=    3.187 closest distance to " O   HOH Z 299 " =    4.298
peak=    3.185 closest distance to " O   HOH Z 116 " =    1.724
peak=    3.183 closest distance to " CA  ASP A 140 " =    1.108
peak=    3.179 closest distance to " O  BHOH Z 338 " =    2.348
peak=    3.179 closest distance to " CB  TYR A 116 " =    0.834
peak=    3.177 closest distance to " CA  ALA A  51 " =    0.979
peak=    3.171 closest distance to " N   ASN A 127 " =    1.234
peak=    3.170 closest distance to " CG1 ILE A 151 " =    0.856
peak=    3.169 closest distance to " NH2AARG A 190 " =    1.168
peak=    3.166 closest distance to " CG  MET A 113 " =    1.178
peak=    3.164 closest distance to " CB  ALA A 248 " =    1.387
peak=    3.163 closest distance to " CB  ARG A 259 " =    1.908
peak=    3.160 closest distance to " O   HOH Z 305 " =    3.533
peak=    3.159 closest distance to " O   HOH Z 357 " =    1.798
peak=    3.156 closest distance to " O   GLY A  57 " =    2.573
peak=    3.150 closest distance to " O   HOH Z  48 " =    1.340
peak=    3.148 closest distance to " O   HOH Z 175 " =    2.117
peak=    3.143 closest distance to " CG  GLN A  88 " =    1.009
peak=    3.143 closest distance to " O   HOH Z 438 " =    1.777
peak=    3.139 closest distance to " CG2 VAL A  67 " =    1.038
peak=    3.135 closest distance to " O   HOH Z 133 " =    1.425
peak=    3.134 closest distance to " O   HOH Z 422 " =    2.672
peak=    3.134 closest distance to " O   HOH Z 188 " =    1.979
peak=    3.131 closest distance to " CB  THR A  31 " =    1.804
peak=    3.129 closest distance to " CD2 HIS A  81 " =    1.080
peak=    3.127 closest distance to " NZ  LYS A 119 " =    1.198
peak=    3.126 closest distance to " O   SER A  26 " =    1.607
peak=    3.125 closest distance to " CB  VAL A 268 " =    0.822
peak=    3.118 closest distance to " CD1 LEU A 228 " =    1.576
peak=    3.115 closest distance to " O   HOH Z  83 " =    1.916
peak=    3.114 closest distance to " CA  VAL A  41 " =    0.927
peak=    3.112 closest distance to " CA  ALA A 158 " =    1.164
peak=    3.108 closest distance to " O   HOH Z 403 " =    1.300
peak=    3.108 closest distance to " CB  ASN A  39 " =    0.857
peak=    3.106 closest distance to " O   HOH Z 115 " =    2.010
peak=    3.097 closest distance to " O   HOH Z 379 " =    1.891
peak=    3.092 closest distance to " O   HOH Z 151 " =    1.399
peak=    3.088 closest distance to " ND1 HIS A  81 " =    1.566
peak=    3.086 closest distance to " O   HOH Z  71 " =    1.833
peak=    3.084 closest distance to " CA  ARG A 195 " =    1.228
peak=    3.081 closest distance to " CB  ILE A 120 " =    1.344
peak=    3.080 closest distance to " CA  ALA A 299 " =    0.932
peak=    3.074 closest distance to " CZ  PHE A 218 " =    0.967
peak=    3.072 closest distance to " O   GLY A 229 " =    1.639
peak=    3.018 closest distance to " OG1 THR A 246 " =    3.178
peak=    3.015 closest distance to " O  BHOH Z  74 " =    1.357
peak=    3.009 closest distance to " O   HOH Z 271 " =    2.536

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 193         
Filter by distance & map next to the model:
   mapped sites are within: 0.617 - 5.239
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 191 from: 193
   mapped sites are within: 0.775 - 5.239

peak=   -4.737 closest distance to " O   HOH Z 266 " =    4.382
peak=   -4.573 closest distance to " CD  ARG A 156 " =    1.982
peak=   -4.531 closest distance to " O   HOH Z 377 " =    2.099
peak=   -4.437 closest distance to " CB  PRO A 243 " =    2.542
peak=   -4.338 closest distance to " C   HIS A 108 " =    1.082
peak=   -4.330 closest distance to " SG  CYS A 254 " =    3.268
peak=   -4.303 closest distance to " O   HOH Z 198 " =    2.023
peak=   -4.290 closest distance to " O   VAL A  67 " =    2.684
peak=   -4.164 closest distance to " CG  GLN A 223 " =    2.011
peak=   -4.122 closest distance to " O   HOH Z 372 " =    2.429
peak=   -4.070 closest distance to " N   GLN A  58 " =    1.638
peak=   -4.049 closest distance to " O   HOH Z  13 " =    1.379
peak=   -4.013 closest distance to " O   PRO A 198 " =    1.332
peak=   -3.989 closest distance to " O   HOH Z 435 " =    2.718
peak=   -3.977 closest distance to " CB  TYR A  15 " =    2.179
peak=   -3.948 closest distance to " CZ  PHE A  59 " =    1.562
peak=   -3.928 closest distance to " O   HOH Z 185 " =    2.056
peak=   -3.926 closest distance to " CG1 VAL A 112 " =    2.848
peak=   -3.923 closest distance to " O   HOH Z 389 " =    1.878
peak=   -3.922 closest distance to " CA  GLY A  98 " =    1.891
peak=   -3.919 closest distance to " CZ  TYR A 169 " =    1.684
peak=   -3.903 closest distance to " CD1 PHE A  59 " =    1.866
peak=   -3.897 closest distance to " CE2 PHE A 218 " =    2.526
peak=   -3.887 closest distance to " O   HOH Z 231 " =    2.031
peak=   -3.870 closest distance to " O   HOH Z 407 " =    3.075
peak=   -3.861 closest distance to " NH1 ARG A 195 " =    2.582
peak=   -3.858 closest distance to " O   HOH Z 388 " =    1.972
peak=   -3.854 closest distance to " OG BSER A 134 " =    1.221
peak=   -3.850 closest distance to " O   ALA A 161 " =    1.594
peak=   -3.849 closest distance to " N   ALA A 248 " =    1.563
peak=   -3.847 closest distance to " O   PRO A 163 " =    1.936
peak=   -3.845 closest distance to " O   HOH Z  43 " =    1.678
peak=   -3.814 closest distance to " OXT GLY A 302 " =    2.766
peak=   -3.811 closest distance to " O   VAL A  67 " =    2.819
peak=   -3.810 closest distance to " O   HOH Z 126 " =    1.800
peak=   -3.803 closest distance to " O   HOH Z  47 " =    1.537
peak=   -3.801 closest distance to " CB  ASN A  39 " =    2.206
peak=   -3.785 closest distance to " CA  GLY A 203 " =    2.214
peak=   -3.771 closest distance to " O   HOH Z 290 " =    1.154
peak=   -3.766 closest distance to " CE2 TYR A  30 " =    2.846
peak=   -3.762 closest distance to " CD1 LEU A 228 " =    2.170
peak=   -3.761 closest distance to " CD  ARG A 139 " =    1.492
peak=   -3.751 closest distance to " CZ3 TRP A 179 " =    1.197
peak=   -3.746 closest distance to " CE  MET A 105 " =    2.183
peak=   -3.740 closest distance to " CG  PHE A 283 " =    2.676
peak=   -3.738 closest distance to " OD1 ASP A 191 " =    1.859
peak=   -3.734 closest distance to " CB  ALA A 161 " =    2.562
peak=   -3.723 closest distance to " N   ALA A  43 " =    2.390
peak=   -3.715 closest distance to " ND2 ASN A  45 " =    0.973
peak=   -3.714 closest distance to " O   HOH Z  52 " =    1.484
peak=   -3.711 closest distance to " O   SER A 135 " =    1.496
peak=   -3.690 closest distance to " O   VAL A 153 " =    2.343
peak=   -3.681 closest distance to " O   HOH Z 102 " =    1.654
peak=   -3.678 closest distance to " CE3 TRP A 274 " =    2.324
peak=   -3.675 closest distance to " O   HOH Z 385 " =    2.000
peak=   -3.674 closest distance to " O   HOH Z  11 " =    1.859
peak=   -3.672 closest distance to " O   HOH Z  24 " =    1.291
peak=   -3.667 closest distance to " OG  SER A  97 " =    2.026
peak=   -3.658 closest distance to " O   HOH Z 152 " =    5.107
peak=   -3.640 closest distance to " N   HIS A 115 " =    1.895
peak=   -3.639 closest distance to " CB  ALA A 291 " =    2.466
peak=   -3.619 closest distance to " N   ASP A 286 " =    2.379
peak=   -3.618 closest distance to " O   HOH Z  93 " =    1.906
peak=   -3.610 closest distance to " CB  ALA A 291 " =    2.162
peak=   -3.604 closest distance to " O   HOH Z 385 " =    1.885
peak=   -3.599 closest distance to " O   HOH Z 351 " =    1.561
peak=   -3.597 closest distance to " O   HOH Z 198 " =    1.474
peak=   -3.596 closest distance to " C   ALA A 158 " =    1.259
peak=   -3.595 closest distance to " O   HOH Z  90 " =    2.648
peak=   -3.574 closest distance to " O   HOH Z 313 " =    1.991
peak=   -3.574 closest distance to " CG  ASP A 231 " =    0.775
peak=   -3.573 closest distance to " OD1 ASN A 187 " =    1.579
peak=   -3.562 closest distance to " CA  SER A 146 " =    2.306
peak=   -3.558 closest distance to " OD1 ASN A 148 " =    1.641
peak=   -3.553 closest distance to " OH  TYR A 214 " =    1.264
peak=   -3.541 closest distance to " O   PRO A 198 " =    1.316
peak=   -3.536 closest distance to " O   MET A  40 " =    2.685
peak=   -3.536 closest distance to " O   HOH Z 353 " =    2.101
peak=   -3.523 closest distance to " CB  ASP A 149 " =    2.002
peak=   -3.517 closest distance to " O   HOH Z  88 " =    1.988
peak=   -3.511 closest distance to " O   HOH Z 114 " =    2.838
peak=   -3.510 closest distance to " ND2 ASN A  45 " =    1.605
peak=   -3.507 closest distance to " O   HOH Z 166 " =    1.319
peak=   -3.495 closest distance to " O   HOH Z   3 " =    2.024
peak=   -3.489 closest distance to " O   HOH Z 263 " =    2.845
peak=   -3.486 closest distance to " NH2 ARG A  79 " =    1.885
peak=   -3.484 closest distance to " CB  PRO A 163 " =    2.502
peak=   -3.483 closest distance to " CD1 LEU A 101 " =    2.355
peak=   -3.479 closest distance to " OD1 ASP A 191 " =    1.400
peak=   -3.477 closest distance to " CB  CYS A 201 " =    2.577
peak=   -3.475 closest distance to " O   ALA A  51 " =    1.286
peak=   -3.471 closest distance to " CB  ASP A 132 " =    2.309
peak=   -3.457 closest distance to " CD2 LEU A 300 " =    2.821
peak=   -3.449 closest distance to " OD1 ASP A 171 " =    1.572
peak=   -3.449 closest distance to " O   PHE A 218 " =    1.583
peak=   -3.441 closest distance to " O   HOH Z 298 " =    1.263
peak=   -3.419 closest distance to " CG  PRO A 163 " =    2.564
peak=   -3.418 closest distance to " OD2 ASP A 171 " =    2.235
peak=   -3.409 closest distance to " NH2BARG A 275 " =    1.885
peak=   -3.401 closest distance to " O   SER A 210 " =    1.959
peak=   -3.401 closest distance to " CB  ALA A 248 " =    2.330
peak=   -3.399 closest distance to " CB  ILE A  33 " =    2.897
peak=   -3.396 closest distance to " OD2 ASP A 191 " =    1.431
peak=   -3.388 closest distance to " O   TRP A  70 " =    1.494
peak=   -3.382 closest distance to " CB  ALA A 248 " =    1.950
peak=   -3.375 closest distance to " CG2 VAL A 189 " =    1.996
peak=   -3.372 closest distance to " O   HOH Z  11 " =    2.018
peak=   -3.372 closest distance to " CA  GLY A 133 " =    1.989
peak=   -3.369 closest distance to " OXT GLY A 302 " =    3.525
peak=   -3.362 closest distance to " CE3 TRP A 123 " =    1.301
peak=   -3.350 closest distance to " N   SER A 276 " =    1.162
peak=   -3.338 closest distance to " O   VAL A 174 " =    2.068
peak=   -3.332 closest distance to " O   HOH Z  88 " =    2.372
peak=   -3.327 closest distance to " O   SER A 146 " =    0.974
peak=   -3.317 closest distance to " N   GLN A 122 " =    1.403
peak=   -3.315 closest distance to " O   ASN A 249 " =    1.459
peak=   -3.313 closest distance to " CB  ALA A  43 " =    2.367
peak=   -3.312 closest distance to " SG ACYS A 201 " =    2.029
peak=   -3.311 closest distance to " OD1 ASN A 176 " =    1.242
peak=   -3.308 closest distance to " CB  ALA A  51 " =    1.853
peak=   -3.308 closest distance to " O   HOH Z 103 " =    1.755
peak=   -3.305 closest distance to " C   LEU A 143 " =    1.108
peak=   -3.303 closest distance to " O   HOH Z 311 " =    3.558
peak=   -3.302 closest distance to " OE1 GLN A 223 " =    1.893
peak=   -3.299 closest distance to " O   HOH Z  63 " =    1.519
peak=   -3.285 closest distance to " O   HOH Z 211 " =    1.554
peak=   -3.280 closest distance to " O   PRO A 243 " =    2.545
peak=   -3.280 closest distance to " CB  ALA A 131 " =    1.958
peak=   -3.280 closest distance to " O   HOH Z 345 " =    1.933
peak=   -3.278 closest distance to " OG  SER A  62 " =    1.555
peak=   -3.275 closest distance to " O   HOH Z 143 " =    2.454
peak=   -3.272 closest distance to " CD  LYS A 289 " =    2.409
peak=   -3.271 closest distance to " CG2 ILE A 263 " =    2.289
peak=   -3.266 closest distance to " CA  ASP A 298 " =    1.005
peak=   -3.252 closest distance to " O   HOH Z 137 " =    1.389
peak=   -3.250 closest distance to " O   HOH Z 423 " =    1.111
peak=   -3.247 closest distance to " C   GLN A 205 " =    1.902
peak=   -3.245 closest distance to " O   HOH Z  38 " =    1.688
peak=   -3.245 closest distance to " CD  ARG A  36 " =    1.881
peak=   -3.244 closest distance to " O   SER A  22 " =    2.394
peak=   -3.237 closest distance to " CG1 VAL A 197 " =    2.179
peak=   -3.222 closest distance to " NH1 ARG A  36 " =    2.006
peak=   -3.218 closest distance to " CD2 LEU A 237 " =    2.729
peak=   -3.215 closest distance to " NH2AARG A 275 " =    5.239
peak=   -3.210 closest distance to " O   VAL A 189 " =    2.467
peak=   -3.210 closest distance to " OD2 ASP A  50 " =    1.477
peak=   -3.208 closest distance to " O   HOH Z 435 " =    2.940
peak=   -3.204 closest distance to " O   HOH Z 317 " =    2.424
peak=   -3.203 closest distance to " OD2 ASP A 270 " =    1.511
peak=   -3.202 closest distance to " O   HOH Z  60 " =    2.040
peak=   -3.201 closest distance to " O   HOH Z 111 " =    2.512
peak=   -3.201 closest distance to " CE  MET A  93 " =    1.190
peak=   -3.199 closest distance to " O   HOH Z  71 " =    2.348
peak=   -3.199 closest distance to " O   TRP A  92 " =    1.616
peak=   -3.198 closest distance to " O   HOH Z 281 " =    2.778
peak=   -3.198 closest distance to " NH1AARG A 275 " =    1.744
peak=   -3.197 closest distance to " O   GLN A 240 " =    1.835
peak=   -3.193 closest distance to " OG ASER A 134 " =    1.025
peak=   -3.190 closest distance to " CB  ASP A 286 " =    2.372
peak=   -3.180 closest distance to " N   GLN A  77 " =    1.597
peak=   -3.179 closest distance to " ND2 ASN A 252 " =    1.575
peak=   -3.174 closest distance to " O   HOH Z 348 " =    1.725
peak=   -3.169 closest distance to " O   HOH Z 166 " =    2.118
peak=   -3.169 closest distance to " O   LYS A 117 " =    1.612
peak=   -3.167 closest distance to " O   HOH Z  10 " =    1.420
peak=   -3.163 closest distance to " O   HOH Z 275 " =    1.494
peak=   -3.162 closest distance to " CE  LYS A  76 " =    2.921
peak=   -3.159 closest distance to " C   TRP A 274 " =    1.503
peak=   -3.159 closest distance to " CB  ASP A  27 " =    2.414
peak=   -3.157 closest distance to " O   HOH Z 359 " =    3.150
peak=   -3.154 closest distance to " CD  GLU A 152 " =    2.479
peak=   -3.154 closest distance to " NE2 GLN A  88 " =    1.956
peak=   -3.153 closest distance to " CG  GLN A  88 " =    0.826
peak=   -3.150 closest distance to " O   HOH Z 326 " =    1.624
peak=   -3.149 closest distance to " NZ  LYS A 119 " =    3.385
peak=   -3.149 closest distance to " O   HOH Z  97 " =    1.750
peak=   -3.128 closest distance to " O   HOH Z 168 " =    1.718
peak=   -3.127 closest distance to " O   HOH Z 193 " =    1.830
peak=   -3.125 closest distance to " C   MET A 188 " =    1.463
peak=   -3.122 closest distance to " O   PRO A 198 " =    1.628
peak=   -3.111 closest distance to " OG BSER A 134 " =    1.604
peak=   -3.102 closest distance to " O   HOH Z 120 " =    2.197
peak=   -3.101 closest distance to " O   HOH Z 213 " =    1.247
peak=   -3.096 closest distance to " CB  TRP A  85 " =    2.532
peak=   -3.084 closest distance to " CG  ASN A 301 " =    1.931
peak=   -3.083 closest distance to " CG  GLU A 152 " =    1.306
peak=   -3.078 closest distance to " O   HOH Z 137 " =    1.540
peak=   -3.071 closest distance to " O   HOH Z 210 " =    1.172
peak=   -3.065 closest distance to " O   HOH Z 361 " =    3.391
peak=   -3.060 closest distance to " O   HOH Z 298 " =    2.474
peak=   -3.053 closest distance to " O   HOH Z 385 " =    1.580

================= 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    :  0.3837 0.3814   6.165904e+00   6.162206e+00
   1_bss:  0.3693 0.3660   6.155144e+00   6.133834e+00
   1_xyz:  0.2485 0.2744   5.812765e+00   5.899435e+00
   1_adp:  0.2283 0.2811   5.763470e+00   5.923147e+00
   1_occ:  0.2280 0.2815   5.762849e+00   5.923349e+00
   2_bss:  0.2262 0.2795   5.758685e+00   5.920021e+00
   2_xyz:  0.1659 0.2149   5.481110e+00   5.676463e+00
   2_adp:  0.1558 0.2016   5.424961e+00   5.617051e+00
   2_occ:  0.1556 0.2015   5.424043e+00   5.616151e+00
   3_bss:  0.1557 0.2011   5.421645e+00   5.614323e+00
   3_xyz:  0.1261 0.1658   5.223018e+00   5.436755e+00
   3_adp:  0.1194 0.1618   5.181487e+00   5.404833e+00
   3_occ:  0.1194 0.1617   5.180897e+00   5.404259e+00
   4_bss:  0.1198 0.1620   5.182411e+00   5.404741e+00
   4_xyz:  0.1108 0.1549   5.125121e+00   5.366357e+00
   4_adp:  0.1093 0.1541   5.117269e+00   5.360186e+00
   4_occ:  0.1092 0.1540   5.116891e+00   5.359871e+00
   5_bss:  0.1092 0.1541   5.116954e+00   5.359977e+00
   5_xyz:  0.1061 0.1534   5.102547e+00   5.356053e+00
   5_adp:  0.1056 0.1545   5.104675e+00   5.364036e+00
   5_occ:  0.1055 0.1544   5.104683e+00   5.364166e+00
   5_bss:  0.1054 0.1544   5.104710e+00   5.364112e+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:  0.333  30.867  -3.148  -0.347   2.332  -0.000   0.000   0.000
   1_xyz:  0.333  30.867  -3.148  -0.347   2.332  -0.000   0.000   0.000
   1_adp:  0.333  30.867  -3.148  -0.347   2.332  -0.000   0.000   0.000
   1_occ:  0.333  30.867  -3.148  -0.347   2.332  -0.000   0.000   0.000
   2_bss:  0.327  39.606  -2.708  -1.842  -0.373  -0.000  -0.000  -0.000
   2_xyz:  0.327  39.606  -2.708  -1.842  -0.373  -0.000  -0.000  -0.000
   2_adp:  0.327  39.606  -2.708  -1.842  -0.373  -0.000  -0.000  -0.000
   2_occ:  0.327  39.606  -2.708  -1.842  -0.373  -0.000  -0.000  -0.000
   3_bss:  0.327  39.606  -2.488  -2.277  -1.185  -0.000  -0.000  -0.000
   3_xyz:  0.327  39.606  -2.488  -2.277  -1.185  -0.000  -0.000  -0.000
   3_adp:  0.327  39.606  -2.488  -2.277  -1.185  -0.000  -0.000  -0.000
   3_occ:  0.327  39.606  -2.488  -2.277  -1.185  -0.000  -0.000  -0.000
   4_bss:  0.318  40.659  -2.586  -2.483  -1.655  -0.000  -0.000  -0.000
   4_xyz:  0.318  40.659  -2.586  -2.483  -1.655  -0.000  -0.000  -0.000
   4_adp:  0.318  40.659  -2.586  -2.483  -1.655  -0.000  -0.000  -0.000
   4_occ:  0.318  40.659  -2.586  -2.483  -1.655  -0.000  -0.000  -0.000
   5_bss:  0.320  40.659  -2.439  -2.383  -1.630  -0.000  -0.000  -0.000
   5_xyz:  0.320  40.659  -2.439  -2.383  -1.630  -0.000  -0.000  -0.000
   5_adp:  0.320  40.659  -2.439  -2.383  -1.630  -0.000  -0.000  -0.000
   5_occ:  0.320  40.659  -2.439  -2.383  -1.630  -0.000  -0.000  -0.000
   5_bss:  0.324  42.476  -2.236  -2.221  -1.483  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  41.969 0.6214  0.8186    44111.859
   1_bss:  40.259 0.6396  0.8306    39485.964
   1_xyz:  27.622 0.7849  0.9709    20178.919
   1_adp:  28.884 0.7700  0.9584    21344.939
   1_occ:  28.933 0.7695  0.9576    21389.390
   2_bss:  28.623 0.7726  0.9206    21063.104
   2_xyz:  20.945 0.8523  0.9832    11839.792
   2_adp:  19.054 0.8713  0.9914    10379.420
   2_occ:  19.035 0.8715  0.9911    10347.359
   3_bss:  18.953 0.8722  0.9796    10289.085
   3_xyz:  15.023 0.9061  0.9968     6955.062
   3_adp:  14.358 0.9119  0.9954     6583.191
   3_occ:  14.340 0.9121  0.9954     6573.583
   4_bss:  14.339 0.9121  0.9858     6586.770
   4_xyz:  13.558 0.9183  0.9880     6001.720
   4_adp:  13.399 0.9198  0.9844     5949.917
   4_occ:  13.389 0.9198  0.9843     5941.960
   5_bss:  13.393 0.9198  0.9876     5945.746
   5_xyz:  13.318 0.9204  0.9875     5923.577
   5_adp:  13.449 0.9195  0.9815     5986.263
   5_occ:  13.450 0.9195  0.9814     5987.298
   5_bss:  13.451 0.9195  0.9878     5990.153
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.109   1.6848e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.109   1.6848e-01
   1_xyz:   1.185  0.009  0.073 15.278  0.005  4.106   8.0896e-02
   1_adp:   1.185  0.009  0.073 15.278  0.005  4.106   8.0896e-02
   1_occ:   1.185  0.009  0.073 15.278  0.005  4.106   8.0896e-02
   2_bss:   1.185  0.009  0.073 15.278  0.005  4.106   8.0896e-02
   2_xyz:   0.953  0.005  0.067 14.133  0.004  4.113   5.2237e-02
   2_adp:   0.953  0.005  0.067 14.133  0.004  4.113   5.2237e-02
   2_occ:   0.953  0.005  0.067 14.133  0.004  4.113   5.2237e-02
   3_bss:   0.953  0.005  0.067 14.133  0.004  4.113   5.2237e-02
   3_xyz:   0.929  0.005  0.066 14.284  0.004  4.110   5.0962e-02
   3_adp:   0.929  0.005  0.066 14.284  0.004  4.110   5.0962e-02
   3_occ:   0.929  0.005  0.066 14.284  0.004  4.110   5.0962e-02
   4_bss:   0.929  0.005  0.066 14.284  0.004  4.110   5.0962e-02
   4_xyz:   0.980  0.006  0.072 14.607  0.004  4.109   5.6928e-02
   4_adp:   0.980  0.006  0.072 14.607  0.004  4.109   5.6928e-02
   4_occ:   0.980  0.006  0.072 14.607  0.004  4.109   5.6928e-02
   5_bss:   0.980  0.006  0.072 14.607  0.004  4.109   5.6928e-02
   5_xyz:   1.023  0.007  0.074 14.651  0.004  4.108   6.0685e-02
   5_adp:   1.023  0.007  0.074 14.651  0.004  4.108   6.0685e-02
   5_occ:   1.023  0.007  0.074 14.651  0.004  4.108   6.0685e-02
   5_bss:   1.023  0.007  0.074 14.651  0.004  4.108   6.0685e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.3835e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.3835e-01
   1_xyz:   8.897  0.048  0.313 86.735  0.031  2.235   8.2029e-02
   1_adp:   8.897  0.048  0.313 86.735  0.031  2.235   8.2029e-02
   1_occ:   8.897  0.048  0.313 86.735  0.031  2.235   8.2029e-02
   2_bss:   8.897  0.048  0.313 86.735  0.031  2.235   8.2029e-02
   2_xyz:   6.648  0.037  0.220 82.578  0.032  2.419   4.4076e-02
   2_adp:   6.648  0.037  0.220 82.578  0.032  2.419   4.4076e-02
   2_occ:   6.648  0.037  0.220 82.578  0.032  2.419   4.4076e-02
   3_bss:   6.648  0.037  0.220 82.578  0.032  2.419   4.4076e-02
   3_xyz:   6.535  0.036  0.265 85.278  0.031  2.355   3.6225e-02
   3_adp:   6.535  0.036  0.265 85.278  0.031  2.355   3.6225e-02
   3_occ:   6.535  0.036  0.265 85.278  0.031  2.355   3.6225e-02
   4_bss:   6.535  0.036  0.265 85.278  0.031  2.355   3.6225e-02
   4_xyz:   6.504  0.031  0.220 84.081  0.039  2.293   4.1225e-02
   4_adp:   6.504  0.031  0.220 84.081  0.039  2.293   4.1225e-02
   4_occ:   6.504  0.031  0.220 84.081  0.039  2.293   4.1225e-02
   5_bss:   6.504  0.031  0.220 84.081  0.039  2.293   4.1225e-02
   5_xyz:   6.417  0.037  0.232 83.511  0.036  2.250   4.6602e-02
   5_adp:   6.417  0.037  0.232 83.511  0.036  2.250   4.6602e-02
   5_occ:   6.417  0.037  0.232 83.511  0.036  2.250   4.6602e-02
   5_bss:   6.417  0.037  0.232 83.511  0.036  2.250   4.6602e-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:  82.19   0.00  17.56  82.19   0.00  13.55  78.93   3.40  39.40
   1_occ:  82.19   0.00  17.56  82.19   0.00  13.55  78.93   3.40  39.40
   2_bss:  82.19   0.00  17.56  82.19   0.00  13.55  78.93   3.40  39.40
   2_xyz:  82.19   0.00  17.56  82.19   0.00  13.55  78.93   3.40  39.40
   2_adp:  79.48   1.30  17.06  79.48   1.30  13.13  73.55   5.79  38.44
   2_occ:  79.48   1.30  17.06  79.48   1.30  13.13  73.55   5.79  38.44
   3_bss:  79.48   1.30  17.06  79.48   1.30  13.13  73.55   5.79  38.44
   3_xyz:  79.48   1.30  17.06  79.48   1.30  13.13  73.55   5.79  38.44
   3_adp:  87.08   0.88  17.30  87.08   0.88  13.01  75.94   4.27  40.69
   3_occ:  87.08   0.88  17.30  87.08   0.88  13.01  75.94   4.27  40.69
   4_bss:  87.08   0.88  17.30  87.08   0.88  13.01  75.94   4.27  40.69
   4_xyz:  87.08   0.88  17.30  87.08   0.88  13.01  75.94   4.27  40.69
   4_adp:  88.54   1.13  17.07  88.54   1.13  12.87  78.33   4.98  39.96
   4_occ:  88.54   1.13  17.07  88.54   1.13  12.87  78.33   4.98  39.96
   5_bss:  88.54   1.13  17.07  88.54   1.13  12.87  78.33   4.98  39.96
   5_xyz:  88.54   1.13  17.07  88.54   1.13  12.87  78.33   4.98  39.96
   5_adp:  95.68   0.00  17.06  95.68   0.00  12.81  82.67   6.12  40.23
   5_occ:  95.68   0.00  17.06  95.68   0.00  12.81  82.67   6.12  40.23
   5_bss:  95.69   0.00  17.06  95.69   0.00  12.81  82.67   6.12  40.23
------------------------------------------------------------------------
 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:    1.715    0.013    0.293
   1_adp:    1.715    0.013    0.293
   1_occ:    1.715    0.013    0.293
   2_bss:    1.715    0.013    0.293
   2_xyz:    1.088    0.019    0.402
   2_adp:    1.088    0.019    0.402
   2_occ:    1.088    0.019    0.402
   3_bss:    1.088    0.019    0.402
   3_xyz:    1.041    0.027    0.481
   3_adp:    1.041    0.027    0.481
   3_occ:    1.041    0.027    0.481
   4_bss:    1.041    0.027    0.481
   4_xyz:    1.149    0.056    0.510
   4_adp:    1.149    0.056    0.510
   4_occ:    1.149    0.056    0.510
   5_bss:    1.149    0.056    0.510
   5_xyz:    1.120    0.043    0.523
   5_adp:    1.120    0.043    0.523
   5_occ:    1.120    0.043    0.523
   5_bss:    1.120    0.043    0.523
------------------------------------------------------------------------

CPU time actual refinement: 333.12


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_639/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_639/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_639/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_639/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_639/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 332.96 
  Macro-tasks:
    bulk solvent and scale       = 37.35  
    individual site refinement   = 143.85 
    weights calculation          = 29.66  
    collect and process          = 6.65   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 217.64 
  Micro-tasks:
    mask                            = 1.79   
    f_calc                          = 106.18 
    alpha_beta                      = 8.20   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 116.49 
    fmodel                         = 6.67   
    r_factors                      = 0.19   
    phase_errors                   = 10.99  
    foms                           = 0.34   
    TOTAL for micro-tasks          = 252.03 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.647 micro seconds
Total CPU time: 5.77 minutes
from_scatterers_fft:    655 calls, 105.89 s
gradients_fft:          600 calls, 102.21 s

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

# Date 2008-01-16 Time 05:18:35 PST -0800 (1200489515.58 s)
Start R-work = 0.3837, R-free = 0.3814 (no bulk solvent and anisotropic scale)
Final R-work = 0.1308, R-free = 0.1744 (no bulk solvent and anisotropic scale)

Start R-work = 0.3693, R-free = 0.3660
Final R-work = 0.1054, R-free = 0.1544