# Date 2008-01-16 Time 04:55:50 PST -0800 (1200488150.30 s)
#phil __OFF__

Command line arguments: "../521.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 17174
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 521

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 46.4607, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.4607, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.919 1.98157
Completeness in resolution range: 0.978227
Completeness with d_max=infinity: 0.975159

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9190
                             d_min =   1.9816

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.4607, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.919 1.98157
Completeness in resolution range: 0.978227
Completeness with d_max=infinity: 0.975159

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9194 -  4.2396 [2102/2126]  1892   210  10.0%
  bin  2:  4.2396 -  3.3779 [2027/2047]  1823   204  10.1%
  bin  3:  3.3779 -  2.9547 [1993/2012]  1794   199  10.0%
  bin  4:  2.9547 -  2.6863 [1962/1992]  1765   197  10.0%
  bin  5:  2.6863 -  2.4947 [1977/1996]  1782   195   9.9%
  bin  6:  2.4947 -  2.3482 [1958/1983]  1758   200  10.2%
  bin  7:  2.3482 -  2.2310 [1940/1968]  1748   192   9.9%
  bin  8:  2.2310 -  2.1342 [1932/1968]  1739   193  10.0%
  bin  9:  2.1342 -  2.0522 [1917/1959]  1726   191  10.0%
  bin 10:  2.0522 -  1.9816 [1781/1974]  1603   178  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_521/model_refine_data.mtz


========================== Anomalous scatterer groups =========================

All atoms refined with f_prime=0 and f_double_prime=0.

========================== Set up restraints manager ==========================

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 22
        2.42 -     3.04: 2222
        3.04 -     3.66: 4733
        3.66 -     4.28: 9155
        4.28 -     4.90: 12431
  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  52 " - " O   HOH Z 183 "  2.092 3.040 -x+1,y+1/2,-z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z  70 " - " O   HOH Z 302 "  2.218 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 302 " - " O   HOH Z  70 "  2.218 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 28558 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_521/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_521/model_refine_001.geo

CPU time processing inputs: 9.22


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 46.4607 85.95805 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: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2926   r_free= 0.2922   ksol= 0.00   Bsol= 0.00   scale= 0.992    |
|                                                                             |
| 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:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.963770                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9194 -  4.7283 0.99   1374  152 0.2753 0.2686      6.3186      6.2703|
|  2:  4.7283 -  3.7730 0.99   1303  146 0.2297 0.2182      6.3391      6.2866|
|  3:  3.7730 -  3.3020 0.99   1287  144 0.2431 0.2390       6.241        6.33|
|  4:  3.3020 -  3.0028 0.99   1284  143 0.2586 0.2886      6.1262      6.1963|
|  5:  3.0028 -  2.7890 0.99   1267  138 0.2915 0.2706      6.0182      5.9253|
|  6:  2.7890 -  2.6255 0.99   1272  143 0.2963 0.3153      5.9553      5.9184|
|  7:  2.6255 -  2.4947 0.99   1269  139 0.3080 0.2807      5.9167      5.8175|
|  8:  2.4947 -  2.3865 0.98   1248  141 0.3123 0.3357      5.8928      5.9698|
|  9:  2.3865 -  2.2950 0.98   1256  138 0.3142 0.3311      5.8445      5.8111|
| 10:  2.2950 -  2.2161 1.00   1236  141 0.3240 0.3132      5.8297      5.7502|
| 11:  2.2161 -  2.1470 0.97   1255  135 0.3363 0.3207      5.7946      5.8186|
| 12:  2.1470 -  2.0858 0.98   1245  140 0.3394 0.3443      5.7773      5.7643|
| 13:  2.0858 -  2.0310 0.99   1243  136 0.3422 0.3332      5.6634      5.6658|
| 14:  2.0310 -  1.9816 0.86   1091  123 0.3562 0.3287      5.6719      5.4806|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9194 -  4.7283  1374   152  0.80  25.14   0.87     0.82      39526.68|
|  2:  4.7283 -  3.7730  1303   146  0.86  20.14   0.99     0.94      39161.52|
|  3:  3.7730 -  3.3020  1287   144  0.84  22.52   1.02     0.99      36436.54|
|  4:  3.3020 -  3.0028  1284   143  0.82  24.64   1.02     0.99      31585.51|
|  5:  3.0028 -  2.7890  1267   138  0.79  27.70   1.01     0.97      25173.79|
|  6:  2.7890 -  2.6255  1272   143  0.79  27.99   1.01     0.98      21552.31|
|  7:  2.6255 -  2.4947  1269   139  0.77  29.09   1.02     0.98      19760.82|
|  8:  2.4947 -  2.3865  1248   141  0.77  29.57   1.04     0.98      19325.23|
|  9:  2.3865 -  2.2950  1256   138  0.77  30.01   1.05     0.97      18093.42|
| 10:  2.2950 -  2.2161  1236   141  0.75  31.33   1.07     0.99      17221.28|
| 11:  2.2161 -  2.1470  1255   135  0.73  32.82   1.06     1.00      16638.25|
| 12:  2.1470 -  2.0858  1245   140  0.74  32.86   1.09     0.99      15494.71|
| 13:  2.0858 -  2.0310  1243   136  0.72  33.80   1.07     0.97      13340.51|
| 14:  2.0310 -  1.9816  1091   123  0.75  31.31   1.08     0.96      10200.21|
|alpha:            min =        0.82 max =            1.00 mean =         0.97|
|beta:             min =    10200.21 max =        39526.68 mean =     23436.43|
|figures of merit: min =        0.00 max =            1.00 mean =         0.78|
|phase err.(work): min =        0.00 max =           89.98 mean =        28.40|
|phase err.(test): min =        0.00 max =           89.81 mean =        28.47|
|-----------------------------------------------------------------------------|

============================== 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 = 4.646146              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.495   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.538060              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.124   (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:        2 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.115 -  2.424:       20 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.424 -  2.734:      212 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.734 -  3.043:     2010 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.043 -  3.353:     1874 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.353 -  3.662:     2859 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.662 -  3.972:     4702 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.972 -  4.281:     4453 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.281 -  4.591:     5660 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.591 -  4.900:     6771 |
|-----------------------------------------------------------------------------|
|-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 |        0.161 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.806 |       0.176 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.676)------------------------------------------|
|    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: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2926   r_free= 0.2922   ksol= 0.00   Bsol= 0.00   scale= 0.992    |
|                                                                             |
| 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:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.963770                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2760   r_free= 0.2737   ksol= 0.33   Bsol= 36.68   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.90,0.33,-1.45,0.00,-0.00,-0.00); trace/3= -1.34                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.937121                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.146042              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.502   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.278074              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.074   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2760      final r-factor (work) = 0.1499          |
| start r-factor (free) = 0.2737      final r-factor (free) = 0.1729          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.5078 = 4.15 * 0.50 * 5.9559 + 1.00 * 0.1611                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.6544 = 4.15 * 0.50 * 5.5914 + 1.00 * 0.0632                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1499      final r-factor (work) = 0.1368          |
| start r-factor (free) = 0.1729      final r-factor (free) = 0.1783          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5608 = 0.28 * 1.00 * 5.5914 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4758 = 0.28 * 1.00 * 5.2794 + 1.00 * 0.0077                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.676)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.62    68.18   16.91    None  None   None       |
|    all(noH): 2823   0      0.62    68.18   16.91    None  None   None       |
|    Sol.    : 438    0      7.51    68.18   38.37    None  None   None       |
|    Mac.    : 2385   0      0.62    65.34   12.97    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:     0.618 -   7.375:  337   |   5:    34.401 -  41.158:  114        |
|      1:     7.375 -  14.131: 1405   |   6:    41.158 -  47.914:   94        |
|      2:    14.131 -  20.888:  472   |   7:    47.914 -  54.671:   81        |
|      3:    20.888 -  27.644:  161   |   8:    54.671 -  61.427:   52        |
|      4:    27.644 -  34.401:   96   |   9:    61.427 -  68.184:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1368 r_free = 0.1783             target_work(ml) = 5.292         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1365 r_free = 0.1784             target_work(ml) = 5.290         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1365   r_free= 0.1784   ksol= 0.33   Bsol= 36.68   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.90,0.33,-1.45,0.00,-0.00,-0.00); trace/3= -1.34                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.290194                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1352   r_free= 0.1751   ksol= 0.32   Bsol= 42.10   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.10,-2.05,-1.78,-0.00,-0.00,-0.00); trace/3= -2.31                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.280186                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.180589              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.273  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.126921              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 119.601  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1352      final r-factor (work) = 0.1153          |
| start r-factor (free) = 0.1751      final r-factor (free) = 0.1561          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.8310 = 2.18 * 0.50 * 5.2902 + 1.00 * 0.0632                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7305 = 2.18 * 0.50 * 5.2051 + 1.00 * 0.0554                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1153      final r-factor (work) = 0.1134          |
| start r-factor (free) = 0.1561      final r-factor (free) = 0.1520          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6684 = 0.13 * 1.00 * 5.2051 + 1.00 * 0.0077                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6587 = 0.13 * 1.00 * 5.1381 + 1.00 * 0.0066                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.676)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.14    69.82   16.68    None  None   None       |
|    all(noH): 2823   0      2.14    69.82   16.68    None  None   None       |
|    Sol.    : 438    0      6.95    69.82   37.27    None  None   None       |
|    Mac.    : 2385   0      2.14    65.52   12.90    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:     2.138 -   8.906:  656   |   5:    35.978 -  42.746:  119        |
|      1:     8.906 -  15.674: 1264   |   6:    42.746 -  49.514:   85        |
|      2:    15.674 -  22.442:  364   |   7:    49.514 -  56.282:   75        |
|      3:    22.442 -  29.210:  124   |   8:    56.282 -  63.050:   22        |
|      4:    29.210 -  35.978:  106   |   9:    63.050 -  69.818:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1134 r_free = 0.1520             target_work(ml) = 5.126         |
| occupancies: max = 1.00  min = 0.22   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1133 r_free = 0.1520             target_work(ml) = 5.125         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1520   ksol= 0.32   Bsol= 42.10   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-3.10,-2.05,-1.78,-0.00,-0.00,-0.00); trace/3= -2.31                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.125476                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1132   r_free= 0.1519   ksol= 0.32   Bsol= 42.10   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.91,-2.43,-1.54,-0.00,-0.00,-0.00); trace/3= -2.30                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.123864                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.933342              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 143.579  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.605481              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.828  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1132      final r-factor (work) = 0.1090          |
| start r-factor (free) = 0.1519      final r-factor (free) = 0.1497          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0205 = 1.93 * 0.50 * 5.1370 + 1.00 * 0.0547                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9935 = 1.93 * 0.50 * 5.1067 + 1.00 * 0.0571                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1090      final r-factor (work) = 0.1070          |
| start r-factor (free) = 0.1497      final r-factor (free) = 0.1505          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.2052 = 1.61 * 1.00 * 5.1067 + 1.00 * 0.0066                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.1825 = 1.61 * 1.00 * 5.0911 + 1.00 * 0.0087                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.676)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.88    81.72   17.12    None  None   None       |
|    all(noH): 2823   0      0.88    81.72   17.12    None  None   None       |
|    Sol.    : 438    0      6.58    78.07   39.62    None  None   None       |
|    Mac.    : 2385   0      0.88    81.72   12.98    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 -   8.965:  762   |   5:    41.301 -  49.385:  109        |
|      1:     8.965 -  17.049: 1270   |   6:    49.385 -  57.470:   77        |
|      2:    17.049 -  25.133:  297   |   7:    57.470 -  65.554:   49        |
|      3:    25.133 -  33.217:  126   |   8:    65.554 -  73.638:   23        |
|      4:    33.217 -  41.301:  105   |   9:    73.638 -  81.722:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1070 r_free = 0.1505             target_work(ml) = 5.096         |
| occupancies: max = 1.00  min = 0.14   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1069 r_free = 0.1506             target_work(ml) = 5.096         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1069   r_free= 0.1506   ksol= 0.32   Bsol= 42.10   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.91,-2.43,-1.54,-0.00,-0.00,-0.00); trace/3= -2.30                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.096343                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1068   r_free= 0.1509   ksol= 0.32   Bsol= 43.34   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.71,-2.42,-1.39,-0.00,-0.00,-0.00); trace/3= -2.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.096415                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.952694              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 151.643  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.472178              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 118.361  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1068      final r-factor (work) = 0.1059          |
| start r-factor (free) = 0.1509      final r-factor (free) = 0.1516          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0275 = 1.95 * 0.50 * 5.0909 + 1.00 * 0.0571                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0274 = 1.95 * 0.50 * 5.0923 + 1.00 * 0.0556                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1059      final r-factor (work) = 0.1058          |
| start r-factor (free) = 0.1516      final r-factor (free) = 0.1519          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4132 = 0.47 * 1.00 * 5.0923 + 1.00 * 0.0087                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4139 = 0.47 * 1.00 * 5.0941 + 1.00 * 0.0086                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.676)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.80    83.60   16.85    None  None   None       |
|    all(noH): 2823   0      0.80    83.60   16.85    None  None   None       |
|    Sol.    : 438    0      6.42    79.64   38.91    None  None   None       |
|    Mac.    : 2385   0      0.80    83.60   12.80    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:     0.801 -   9.081:  829   |   5:    42.199 -  50.479:  101        |
|      1:     9.081 -  17.360: 1238   |   6:    50.479 -  58.758:   77        |
|      2:    17.360 -  25.640:  274   |   7:    58.758 -  67.038:   34        |
|      3:    25.640 -  33.919:  132   |   8:    67.038 -  75.317:   17        |
|      4:    33.919 -  42.199:  117   |   9:    75.317 -  83.597:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1058 r_free = 0.1519             target_work(ml) = 5.096         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1057 r_free = 0.1519             target_work(ml) = 5.096         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1057   r_free= 0.1519   ksol= 0.32   Bsol= 43.34   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.71,-2.42,-1.39,-0.00,-0.00,-0.00); trace/3= -2.17                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.096215                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1056   r_free= 0.1519   ksol= 0.32   Bsol= 43.34   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.49,-2.25,-1.16,-0.00,-0.00,-0.00); trace/3= -1.97                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.096288                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.032999              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 160.352  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.550712              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.133  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1056      final r-factor (work) = 0.1050          |
| start r-factor (free) = 0.1519      final r-factor (free) = 0.1529          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2348 = 2.03 * 0.50 * 5.0952 + 1.00 * 0.0556                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2339 = 2.03 * 0.50 * 5.0936 + 1.00 * 0.0563                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1050      final r-factor (work) = 0.1050          |
| start r-factor (free) = 0.1529      final r-factor (free) = 0.1528          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8137 = 0.55 * 1.00 * 5.0936 + 1.00 * 0.0086                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8146 = 0.55 * 1.00 * 5.0951 + 1.00 * 0.0087                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.676)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.79    83.92   16.69    None  None   None       |
|    all(noH): 2823   0      0.79    83.92   16.69    None  None   None       |
|    Sol.    : 438    0      6.26    79.74   38.79    None  None   None       |
|    Mac.    : 2385   0      0.79    83.92   12.63    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:     0.787 -   9.100:  877   |   5:    42.352 -  50.665:  104        |
|      1:     9.100 -  17.413: 1203   |   6:    50.665 -  58.978:   74        |
|      2:    17.413 -  25.726:  263   |   7:    58.978 -  67.292:   32        |
|      3:    25.726 -  34.039:  135   |   8:    67.292 -  75.605:   17        |
|      4:    34.039 -  42.352:  114   |   9:    75.605 -  83.918:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1050 r_free = 0.1528             target_work(ml) = 5.095         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1050 r_free = 0.1528             target_work(ml) = 5.095         |
| occupancies: max = 1.00  min = 0.07   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1050   r_free= 0.1528   ksol= 0.32   Bsol= 43.34   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.49,-2.25,-1.16,-0.00,-0.00,-0.00); trace/3= -1.97                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.095413                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9194 -  4.7283 0.99   1374  152 0.0969 0.1260      5.3614      5.5027|
|  2:  4.7283 -  3.7730 0.99   1303  146 0.0822 0.1119      5.4141      5.6257|
|  3:  3.7730 -  3.3020 0.99   1287  144 0.1012 0.1498      5.4486      5.8393|
|  4:  3.3020 -  3.0028 0.99   1284  143 0.1145 0.1511      5.4189      5.5638|
|  5:  3.0028 -  2.7890 0.99   1267  138 0.1215 0.1695      5.2814       5.519|
|  6:  2.7890 -  2.6255 0.99   1272  143 0.1130 0.1762      5.1721      5.4294|
|  7:  2.6255 -  2.4947 0.99   1269  139 0.1178 0.1540       5.111      5.3182|
|  8:  2.4947 -  2.3865 0.98   1248  141 0.1080 0.1691      5.0177      5.3327|
|  9:  2.3865 -  2.2950 0.98   1256  138 0.1067 0.1620      4.9712      5.1969|
| 10:  2.2950 -  2.2161 1.00   1236  141 0.1023 0.1705      4.9132      5.2325|
| 11:  2.2161 -  2.1470 0.97   1255  135 0.1069 0.1592      4.8964      5.1861|
| 12:  2.1470 -  2.0858 0.98   1245  140 0.1059 0.1683      4.8418      5.2148|
| 13:  2.0858 -  2.0310 0.99   1243  136 0.1019 0.1586      4.7445      5.0102|
| 14:  2.0310 -  1.9816 0.86   1091  123 0.0962 0.1746      4.6154      4.9219|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9194 -  4.7283  1374   152  0.94   9.04   0.98     0.95       6868.59|
|  2:  4.7283 -  3.7730  1303   146  0.95   7.72   1.02     1.01       8800.73|
|  3:  3.7730 -  3.3020  1287   144  0.94  10.79   1.03     1.02       9933.34|
|  4:  3.3020 -  3.0028  1284   143  0.92  12.94   1.01     1.00       9822.09|
|  5:  3.0028 -  2.7890  1267   138  0.91  14.97   1.00     0.97       7801.47|
|  6:  2.7890 -  2.6255  1272   143  0.91  15.31   0.99     0.96       6663.14|
|  7:  2.6255 -  2.4947  1269   139  0.91  15.00   0.99     0.96       5690.43|
|  8:  2.4947 -  2.3865  1248   141  0.92  13.81   0.99     0.97       4773.29|
|  9:  2.3865 -  2.2950  1256   138  0.92  14.25   1.01     0.98       4489.07|
| 10:  2.2950 -  2.2161  1236   141  0.91  14.26   1.00     0.96       3989.22|
| 11:  2.2161 -  2.1470  1255   135  0.90  15.55   1.00     0.97       4102.89|
| 12:  2.1470 -  2.0858  1245   140  0.92  14.61   1.01     0.99       3689.23|
| 13:  2.0858 -  2.0310  1243   136  0.92  14.58   1.00     0.99       3092.53|
| 14:  2.0310 -  1.9816  1091   123  0.92  13.54   0.98     0.95       2331.06|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2331.06 max =         9933.34 mean =      5929.50|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.96 mean =        13.26|
|phase err.(test): min =        0.00 max =           89.53 mean =        12.83|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1050   r_free= 0.1528   ksol= 0.32   Bsol= 43.31   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.28,-2.08,-0.95,-0.00,-0.00,-0.00); trace/3= -1.77                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.095477                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 14.92 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1050   r_free= 0.1528   ksol= 0.32   Bsol= 43.31   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.28,-2.08,-0.95,-0.00,-0.00,-0.00); trace/3= -1.77                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.095477                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9194 -  4.7283 0.99   1374  152 0.0970 0.1262      5.3624       5.504|
|  2:  4.7283 -  3.7730 0.99   1303  146 0.0822 0.1118      5.4146      5.6256|
|  3:  3.7730 -  3.3020 0.99   1287  144 0.1012 0.1499      5.4486      5.8397|
|  4:  3.3020 -  3.0028 0.99   1284  143 0.1145 0.1511      5.4188      5.5639|
|  5:  3.0028 -  2.7890 0.99   1267  138 0.1215 0.1695      5.2813      5.5187|
|  6:  2.7890 -  2.6255 0.99   1272  143 0.1130 0.1762      5.1719      5.4291|
|  7:  2.6255 -  2.4947 0.99   1269  139 0.1179 0.1541       5.111      5.3184|
|  8:  2.4947 -  2.3865 0.98   1248  141 0.1080 0.1691      5.0177      5.3326|
|  9:  2.3865 -  2.2950 0.98   1256  138 0.1067 0.1620      4.9712      5.1967|
| 10:  2.2950 -  2.2161 1.00   1236  141 0.1023 0.1706      4.9133      5.2332|
| 11:  2.2161 -  2.1470 0.97   1255  135 0.1069 0.1592      4.8965      5.1861|
| 12:  2.1470 -  2.0858 0.98   1245  140 0.1058 0.1683      4.8417      5.2148|
| 13:  2.0858 -  2.0310 0.99   1243  136 0.1019 0.1586      4.7443      5.0099|
| 14:  2.0310 -  1.9816 0.86   1091  123 0.0963 0.1745      4.6152      4.9215|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9194 -  4.7283  1374   152  0.94   9.05   0.98     0.95       6885.31|
|  2:  4.7283 -  3.7730  1303   146  0.95   7.73   1.02     1.01       8811.46|
|  3:  3.7730 -  3.3020  1287   144  0.94  10.79   1.03     1.02       9934.02|
|  4:  3.3020 -  3.0028  1284   143  0.92  12.94   1.01     1.00       9819.67|
|  5:  3.0028 -  2.7890  1267   138  0.91  14.97   1.00     0.98       7797.25|
|  6:  2.7890 -  2.6255  1272   143  0.91  15.31   1.00     0.97       6660.62|
|  7:  2.6255 -  2.4947  1269   139  0.91  15.00   0.99     0.97       5689.72|
|  8:  2.4947 -  2.3865  1248   141  0.92  13.81   1.00     0.98       4772.26|
|  9:  2.3865 -  2.2950  1256   138  0.92  14.25   1.01     0.99       4490.20|
| 10:  2.2950 -  2.2161  1236   141  0.91  14.26   1.00     0.96       3989.48|
| 11:  2.2161 -  2.1470  1255   135  0.90  15.56   1.00     0.97       4104.44|
| 12:  2.1470 -  2.0858  1245   140  0.92  14.61   1.02     1.00       3688.41|
| 13:  2.0858 -  2.0310  1243   136  0.92  14.57   1.01     1.00       3090.89|
| 14:  2.0310 -  1.9816  1091   123  0.92  13.53   0.99     0.96       2328.85|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2328.85 max =         9934.02 mean =      5930.76|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.96 mean =        13.26|
|phase err.(test): min =        0.00 max =           89.53 mean =        12.84|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.676)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.76    83.89   16.67    None  None   None       |
|    all(noH): 2823   0      0.76    83.89   16.67    None  None   None       |
|    Sol.    : 438    0      6.23    79.71   38.76    None  None   None       |
|    Mac.    : 2385   0      0.76    83.89   12.61    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:     0.761 -   9.074:  877   |   5:    42.326 -  50.639:  104        |
|      1:     9.074 -  17.387: 1203   |   6:    50.639 -  58.952:   74        |
|      2:    17.387 -  25.700:  263   |   7:    58.952 -  67.265:   32        |
|      3:    25.700 -  34.013:  135   |   8:    67.265 -  75.578:   17        |
|      4:    34.013 -  42.326:  114   |   9:    75.578 -  83.891:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 294         
Filter by distance & map next to the model:
   mapped sites are within: 0.472 - 4.626
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 291 from: 294
   mapped sites are within: 0.704 - 4.626

peak=    5.899 closest distance to " NE2 GLN A  11 " =    1.171
peak=    5.489 closest distance to " O   HOH Z 144 " =    1.766
peak=    5.484 closest distance to " O   HOH Z 126 " =    1.923
peak=    5.427 closest distance to " CG  PRO A  54 " =    1.266
peak=    5.248 closest distance to " CB  ARG A 275 " =    0.920
peak=    5.125 closest distance to " NH2 ARG A  56 " =    2.125
peak=    5.101 closest distance to " CG  PRO A 213 " =    1.240
peak=    4.963 closest distance to " CB  GLN A 223 " =    1.472
peak=    4.870 closest distance to " CB  GLN A 183 " =    1.222
peak=    4.836 closest distance to " CB  SER A  63 " =    1.170
peak=    4.785 closest distance to " O   HOH Z 232 " =    2.386
peak=    4.657 closest distance to " CB  PRO A  54 " =    0.947
peak=    4.578 closest distance to " C   PRO A 198 " =    1.434
peak=    4.556 closest distance to " O   HOH Z 209 " =    2.269
peak=    4.550 closest distance to " O   HOH Z 427 " =    2.864
peak=    4.526 closest distance to " O   HOH Z 303 " =    2.152
peak=    4.498 closest distance to " O   HOH Z  15 " =    2.342
peak=    4.480 closest distance to " O   HOH Z  78 " =    1.742
peak=    4.473 closest distance to " O   HOH Z 369 " =    2.118
peak=    4.462 closest distance to " CB  ARG A  79 " =    1.340
peak=    4.441 closest distance to " CB  GLU A 152 " =    1.255
peak=    4.436 closest distance to " CG2 VAL A 257 " =    0.882
peak=    4.427 closest distance to " ND2 ASN A 187 " =    1.493
peak=    4.401 closest distance to " O   HOH Z 203 " =    1.775
peak=    4.375 closest distance to " O   HOH Z 236 " =    2.026
peak=    4.334 closest distance to " CA  TYR A  30 " =    0.903
peak=    4.314 closest distance to " O   HOH Z 234 " =    3.647
peak=    4.289 closest distance to " CB  ASN A 148 " =    1.395
peak=    4.267 closest distance to " O   HOH Z 272 " =    1.818
peak=    4.260 closest distance to " CB  VAL A 265 " =    1.315
peak=    4.216 closest distance to " CG  PRO A 243 " =    1.087
peak=    4.215 closest distance to " NZ  LYS A 117 " =    3.216
peak=    4.201 closest distance to " O   HOH Z  61 " =    1.639
peak=    4.196 closest distance to " O   HOH Z 193 " =    1.769
peak=    4.157 closest distance to " OG ASER A 258 " =    3.096
peak=    4.131 closest distance to " O   HOH Z 158 " =    3.048
peak=    4.130 closest distance to " O   HOH Z 298 " =    1.873
peak=    4.115 closest distance to " OD1 ASN A  69 " =    2.585
peak=    4.111 closest distance to " CB  SER A   3 " =    1.292
peak=    4.103 closest distance to " CG  PRO A 198 " =    1.284
peak=    4.097 closest distance to " O   HOH Z 250 " =    1.474
peak=    4.057 closest distance to " O   HOH Z 346 " =    1.711
peak=    4.049 closest distance to " O   HOH Z 419 " =    2.086
peak=    4.037 closest distance to " CB  ARG A 190 " =    1.669
peak=    4.027 closest distance to " O   HOH Z  66 " =    2.146
peak=    4.022 closest distance to " CD  ARG A  66 " =    2.418
peak=    4.008 closest distance to " O   HOH Z   9 " =    2.037
peak=    3.999 closest distance to " CA  ASN A 215 " =    1.088
peak=    3.998 closest distance to " O   HOH Z 144 " =    2.227
peak=    3.977 closest distance to " CG1 ILE A  33 " =    1.246
peak=    3.963 closest distance to " O   SER A  87 " =    2.126
peak=    3.961 closest distance to " O   HOH Z  78 " =    2.111
peak=    3.933 closest distance to " O   HOH Z 344 " =    3.182
peak=    3.918 closest distance to " O   HOH Z 132 " =    2.364
peak=    3.914 closest distance to " CD2 TRP A 179 " =    1.342
peak=    3.912 closest distance to " O   HOH Z   1 " =    1.993
peak=    3.904 closest distance to " O   HOH Z 407 " =    2.315
peak=    3.898 closest distance to " O   HOH Z 402 " =    1.410
peak=    3.894 closest distance to " O   HOH Z 425 " =    2.091
peak=    3.885 closest distance to " CD BLYS A 290 " =    1.230
peak=    3.881 closest distance to " CB  TYR A 169 " =    0.756
peak=    3.864 closest distance to " O   HOH Z 389 " =    1.852
peak=    3.862 closest distance to " O   HOH Z 403 " =    1.675
peak=    3.854 closest distance to " CB  LEU A 228 " =    1.091
peak=    3.839 closest distance to " CB  GLU A 128 " =    1.012
peak=    3.837 closest distance to " O   HOH Z  44 " =    1.732
peak=    3.835 closest distance to " CE  LYS A  76 " =    0.817
peak=    3.826 closest distance to " O   HOH Z 189 " =    2.150
peak=    3.817 closest distance to " O   HOH Z 245 " =    1.294
peak=    3.815 closest distance to " O   HOH Z 371 " =    1.678
peak=    3.782 closest distance to " O   HOH Z  43 " =    1.784
peak=    3.778 closest distance to " CB  ASP A 140 " =    0.932
peak=    3.778 closest distance to " CB  TRP A 266 " =    1.045
peak=    3.771 closest distance to " CB  VAL A 202 " =    1.595
peak=    3.768 closest distance to " O   HOH Z  40 " =    1.588
peak=    3.745 closest distance to " O   HOH Z 392 " =    3.133
peak=    3.744 closest distance to " OG BSER A 164 " =    2.260
peak=    3.743 closest distance to " O   HOH Z  93 " =    2.427
peak=    3.725 closest distance to " O   HOH Z 368 " =    3.606
peak=    3.720 closest distance to " CB  ARG A 139 " =    0.973
peak=    3.710 closest distance to " O   HOH Z 327 " =    1.586
peak=    3.702 closest distance to " O   HOH Z 371 " =    3.083
peak=    3.699 closest distance to " O   HOH Z  61 " =    1.486
peak=    3.698 closest distance to " O   HOH Z 368 " =    2.015
peak=    3.688 closest distance to " CZ  PHE A 218 " =    1.020
peak=    3.684 closest distance to " O   HOH Z  64 " =    2.341
peak=    3.681 closest distance to " O   HOH Z 128 " =    2.172
peak=    3.654 closest distance to " O   HOH Z  59 " =    1.709
peak=    3.644 closest distance to " O   HOH Z 248 " =    1.543
peak=    3.643 closest distance to " CD  ARG A 159 " =    0.744
peak=    3.643 closest distance to " O   HOH Z  10 " =    1.839
peak=    3.637 closest distance to " O   HOH Z 423 " =    1.867
peak=    3.636 closest distance to " CB  TRP A 179 " =    1.331
peak=    3.628 closest distance to " CG2 ILE A 120 " =    1.213
peak=    3.627 closest distance to " O   HOH Z 193 " =    1.629
peak=    3.626 closest distance to " CB  SER A 212 " =    1.062
peak=    3.615 closest distance to " NH2BARG A 145 " =    2.052
peak=    3.610 closest distance to " O   HOH Z 417 " =    3.095
peak=    3.599 closest distance to " O   HOH Z 305 " =    3.576
peak=    3.599 closest distance to " O   HOH Z 133 " =    2.571
peak=    3.592 closest distance to " CB  THR A 157 " =    1.104
peak=    3.584 closest distance to " CB  ALA A  34 " =    1.135
peak=    3.582 closest distance to " O   HOH Z 180 " =    2.180
peak=    3.573 closest distance to " OD2 ASP A 286 " =    2.763
peak=    3.573 closest distance to " CB  TYR A 116 " =    0.799
peak=    3.570 closest distance to " O   HOH Z 219 " =    2.230
peak=    3.566 closest distance to " CB  TYR A 169 " =    0.805
peak=    3.565 closest distance to " NH1AARG A 145 " =    1.164
peak=    3.565 closest distance to " N   PHE A 130 " =    1.273
peak=    3.560 closest distance to " O   HOH Z 353 " =    2.649
peak=    3.558 closest distance to " O   HOH Z 172 " =    3.098
peak=    3.547 closest distance to " O   HOH Z  21 " =    1.752
peak=    3.546 closest distance to " O   HOH Z 214 " =    2.090
peak=    3.545 closest distance to " O   HOH Z 207 " =    1.756
peak=    3.544 closest distance to " O   HOH Z 291 " =    1.569
peak=    3.537 closest distance to " O   HOH Z 173 " =    1.860
peak=    3.535 closest distance to " NH1BARG A 145 " =    1.245
peak=    3.534 closest distance to " CB  GLU A 277 " =    3.520
peak=    3.520 closest distance to " CD  ARG A  66 " =    2.369
peak=    3.518 closest distance to " CB  SER A 216 " =    0.802
peak=    3.516 closest distance to " NE2 GLN A  73 " =    3.726
peak=    3.514 closest distance to " O  BHOH Z 338 " =    2.353
peak=    3.514 closest distance to " O   HOH Z 280 " =    3.045
peak=    3.513 closest distance to " O   HOH Z   6 " =    2.089
peak=    3.508 closest distance to " O   HOH Z   3 " =    1.911
peak=    3.506 closest distance to " CB  SER A  62 " =    1.238
peak=    3.506 closest distance to " CD1 ILE A 106 " =    0.835
peak=    3.502 closest distance to " O   HOH Z  19 " =    2.557
peak=    3.498 closest distance to " O   HOH Z 128 " =    2.096
peak=    3.496 closest distance to " O   HOH Z 357 " =    1.831
peak=    3.489 closest distance to " O   HOH Z   1 " =    1.652
peak=    3.486 closest distance to " ND1 HIS A  86 " =    1.804
peak=    3.485 closest distance to " O   HOH Z 261 " =    2.232
peak=    3.480 closest distance to " O   HOH Z  97 " =    1.989
peak=    3.476 closest distance to " CB  GLN A  89 " =    1.419
peak=    3.466 closest distance to " O   HOH Z 141 " =    1.666
peak=    3.466 closest distance to " O   HOH Z 435 " =    1.914
peak=    3.463 closest distance to " O   HOH Z 406 " =    1.589
peak=    3.463 closest distance to " CB  ALA A 291 " =    1.343
peak=    3.461 closest distance to " CG  LYS A  76 " =    0.980
peak=    3.459 closest distance to " O   HOH Z 437 " =    1.448
peak=    3.459 closest distance to " CB  SER A  26 " =    1.584
peak=    3.455 closest distance to " CG  LEU A 167 " =    1.228
peak=    3.450 closest distance to " O   HOH Z 337 " =    3.628
peak=    3.443 closest distance to " CA  THR A 221 " =    1.005
peak=    3.443 closest distance to " O   HOH Z 345 " =    3.352
peak=    3.442 closest distance to " CD2 LEU A 255 " =    1.454
peak=    3.442 closest distance to " CA  MET A  40 " =    1.093
peak=    3.440 closest distance to " O   MET A 105 " =    1.828
peak=    3.438 closest distance to " O   HOH Z 298 " =    2.547
peak=    3.435 closest distance to " O   HOH Z  88 " =    2.562
peak=    3.430 closest distance to " CB  LYS A 117 " =    1.222
peak=    3.430 closest distance to " O   HOH Z  89 " =    2.134
peak=    3.428 closest distance to " N   ARG A 156 " =    1.268
peak=    3.428 closest distance to " CA  ALA A  21 " =    1.103
peak=    3.426 closest distance to " O   HOH Z  40 " =    1.958
peak=    3.422 closest distance to " CA  PHE A 283 " =    1.244
peak=    3.421 closest distance to " CA  ALA A 291 " =    0.852
peak=    3.418 closest distance to " O   HOH Z 234 " =    1.816
peak=    3.417 closest distance to " O   HOH Z 286 " =    2.287
peak=    3.416 closest distance to " O   HOH Z 203 " =    1.208
peak=    3.415 closest distance to " O   HOH Z 193 " =    1.939
peak=    3.413 closest distance to " O   HOH Z 147 " =    1.741
peak=    3.406 closest distance to " O   HOH Z  85 " =    2.259
peak=    3.397 closest distance to " CG  MET A 113 " =    1.142
peak=    3.397 closest distance to " CG2 THR A 221 " =    1.159
peak=    3.394 closest distance to " CA  ALA A 233 " =    1.077
peak=    3.393 closest distance to " O   HOH Z 426 " =    1.864
peak=    3.391 closest distance to " O   HOH Z 380 " =    1.931
peak=    3.385 closest distance to " CA  THR A 264 " =    0.865
peak=    3.380 closest distance to " O   HOH Z 433 " =    1.800
peak=    3.377 closest distance to " OD1BASN A 224 " =    2.327
peak=    3.372 closest distance to " CD2 LEU A 297 " =    0.901
peak=    3.370 closest distance to " N   ASN A  39 " =    1.198
peak=    3.366 closest distance to " CG1BVAL A  72 " =    1.481
peak=    3.364 closest distance to " O   HOH Z 405 " =    1.048
peak=    3.360 closest distance to " CB  ILE A 120 " =    1.297
peak=    3.359 closest distance to " O   HOH Z 148 " =    3.318
peak=    3.354 closest distance to " O   HOH Z 329 " =    3.832
peak=    3.351 closest distance to " CB  ALA A   1 " =    4.626
peak=    3.349 closest distance to " O   HOH Z 213 " =    1.703
peak=    3.344 closest distance to " O   HOH Z 271 " =    2.330
peak=    3.333 closest distance to " CA  ALA A  84 " =    1.270
peak=    3.328 closest distance to " CB  ASN A 142 " =    0.993
peak=    3.326 closest distance to " CB  GLN A  88 " =    1.182
peak=    3.322 closest distance to " O   HOH Z 313 " =    1.888
peak=    3.315 closest distance to " O   HOH Z 213 " =    1.847
peak=    3.314 closest distance to " CB  HIS A 108 " =    0.808
peak=    3.313 closest distance to " CB  SER A 273 " =    0.847
peak=    3.313 closest distance to " N   TYR A 116 " =    1.530
peak=    3.311 closest distance to " CA  ALA A  43 " =    1.253
peak=    3.307 closest distance to " CA  ARG A  36 " =    0.980
peak=    3.305 closest distance to " O   HOH Z 391 " =    2.888
peak=    3.305 closest distance to " O   HOH Z 359 " =    1.403
peak=    3.304 closest distance to " CB  ASN A  39 " =    0.853
peak=    3.301 closest distance to " O   HOH Z 325 " =    3.801
peak=    3.298 closest distance to " CA  ASP A 162 " =    1.071
peak=    3.292 closest distance to " CA  SER A  87 " =    1.013
peak=    3.290 closest distance to " CG2 ILE A  20 " =    1.453
peak=    3.286 closest distance to " O   HOH Z  96 " =    2.174
peak=    3.286 closest distance to " CG AARG A 275 " =    1.026
peak=    3.284 closest distance to " CA  ALA A 158 " =    1.219
peak=    3.283 closest distance to " CB  VAL A 126 " =    1.066
peak=    3.281 closest distance to " CD1 LEU A 300 " =    1.303
peak=    3.278 closest distance to " CD  LYS A 166 " =    1.237
peak=    3.277 closest distance to " CG1 VAL A 153 " =    0.921
peak=    3.276 closest distance to " O   HOH Z 365 " =    2.877
peak=    3.276 closest distance to " CB  THR A  31 " =    1.726
peak=    3.276 closest distance to " OG1 THR A 294 " =    2.418
peak=    3.265 closest distance to " CD  ARG A 269 " =    0.963
peak=    3.259 closest distance to " O   HOH Z  66 " =    2.110
peak=    3.255 closest distance to " O   HOH Z 257 " =    2.201
peak=    3.252 closest distance to " CD1 ILE A 263 " =    1.353
peak=    3.251 closest distance to " CA  ALA A  51 " =    0.897
peak=    3.250 closest distance to " O   HOH Z 273 " =    2.682
peak=    3.248 closest distance to " CB  ALA A   9 " =    1.551
peak=    3.247 closest distance to " O   HOH Z 409 " =    2.686
peak=    3.244 closest distance to " CD  PRO A 243 " =    1.536
peak=    3.243 closest distance to " O   HOH Z 265 " =    2.448
peak=    3.242 closest distance to " OG  SER A  62 " =    2.837
peak=    3.237 closest distance to " CG2 VAL A 197 " =    1.120
peak=    3.236 closest distance to " CB  ASN A 110 " =    1.108
peak=    3.236 closest distance to " O   HOH Z  44 " =    3.039
peak=    3.236 closest distance to " CG  GLN A  89 " =    1.506
peak=    3.233 closest distance to " O   HOH Z 175 " =    2.193
peak=    3.228 closest distance to " O   HOH Z  71 " =    2.267
peak=    3.226 closest distance to " O   HOH Z 279 " =    2.151
peak=    3.224 closest distance to " O   HOH Z 411 " =    3.796
peak=    3.223 closest distance to " CE AMET A  47 " =    1.377
peak=    3.216 closest distance to " O   HOH Z 336 " =    1.941
peak=    3.214 closest distance to " CB  LEU A 255 " =    0.807
peak=    3.207 closest distance to " OG BSER A 134 " =    2.862
peak=    3.205 closest distance to " O   HOH Z 185 " =    1.809
peak=    3.204 closest distance to " CA  LYS A 117 " =    1.218
peak=    3.202 closest distance to " CA  SER A 146 " =    1.745
peak=    3.202 closest distance to " CB  ASN A 224 " =    0.962
peak=    3.201 closest distance to " CB  ALA A 248 " =    1.348
peak=    3.201 closest distance to " CG  MET A 185 " =    1.183
peak=    3.195 closest distance to " CA  ARG A 195 " =    1.153
peak=    3.191 closest distance to " O   HOH Z 291 " =    1.828
peak=    3.189 closest distance to " CA  ALA A 248 " =    1.220
peak=    3.189 closest distance to " CB  THR A 294 " =    1.668
peak=    3.188 closest distance to " N   ASN A 127 " =    1.235
peak=    3.187 closest distance to " O   HOH Z 285 " =    2.760
peak=    3.186 closest distance to " O   HOH Z  88 " =    2.396
peak=    3.185 closest distance to " O   HOH Z 422 " =    2.634
peak=    3.181 closest distance to " O   HOH Z 128 " =    2.033
peak=    3.180 closest distance to " CB  SER A  62 " =    0.842
peak=    3.178 closest distance to " CB  SER A 141 " =    1.018
peak=    3.177 closest distance to " O   HOH Z 153 " =    1.602
peak=    3.175 closest distance to " O   HOH Z 411 " =    1.705
peak=    3.175 closest distance to " CD  ARG A  36 " =    1.014
peak=    3.174 closest distance to " O   ALA A   1 " =    1.666
peak=    3.174 closest distance to " CB  GLN A 278 " =    0.824
peak=    3.173 closest distance to " CG  ARG A 159 " =    0.792
peak=    3.167 closest distance to " NZ  LYS A  76 " =    1.547
peak=    3.166 closest distance to " N   GLN A 278 " =    1.171
peak=    3.164 closest distance to " CA  MET A 105 " =    0.961
peak=    3.160 closest distance to " O   HOH Z 163 " =    1.599
peak=    3.155 closest distance to " O   HOH Z 236 " =    1.450
peak=    3.153 closest distance to " O   HOH Z 183 " =    1.315
peak=    3.152 closest distance to " NH1 ARG A 138 " =    1.137
peak=    3.148 closest distance to " OG  SER A  22 " =    2.714
peak=    3.143 closest distance to " CB  THR A 235 " =    1.052
peak=    3.142 closest distance to " CB  ALA A 114 " =    1.447
peak=    3.138 closest distance to " CA  ASN A 217 " =    1.207
peak=    3.137 closest distance to " O   HOH Z 295 " =    1.545
peak=    3.135 closest distance to " CA  ARG A 102 " =    1.048
peak=    3.125 closest distance to " CA  GLY A  80 " =    0.704
peak=    3.114 closest distance to " OG  SER A 206 " =    1.298
peak=    3.114 closest distance to " O   HOH Z 303 " =    1.652
peak=    3.096 closest distance to " CA  LYS A 290 " =    1.312
peak=    3.092 closest distance to " O   HOH Z  49 " =    2.113
peak=    3.090 closest distance to " O   HOH Z 261 " =    1.459
peak=    3.086 closest distance to " O   THR A 220 " =    1.335
peak=    3.086 closest distance to " ND2 ASN A 249 " =    0.869
peak=    3.077 closest distance to " CB  MET A  47 " =    1.190
peak=    3.077 closest distance to " CB  ASN A 215 " =    1.086
peak=    3.068 closest distance to " CB  LYS A 290 " =    1.148
peak=    3.063 closest distance to " O   HOH Z  88 " =    3.119
peak=    3.061 closest distance to " ND1 HIS A  81 " =    1.613
peak=    3.057 closest distance to " O   HOH Z 124 " =    2.122
peak=    3.057 closest distance to " O  BHOH Z  74 " =    1.346
peak=    3.055 closest distance to " O   HOH Z 423 " =    2.909
peak=    3.049 closest distance to " CB  ARG A 138 " =    0.901
peak=    3.049 closest distance to " CD1AILE A 234 " =    0.890
peak=    3.045 closest distance to " O   HOH Z 152 " =    1.743
peak=    3.039 closest distance to " O   HOH Z 342 " =    0.773
peak=    3.038 closest distance to " CB  GLU A  46 " =    1.087
peak=    3.037 closest distance to " OG BSER A  99 " =    2.181
peak=    3.019 closest distance to " CA  ALA A 299 " =    0.943

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 200         
Filter by distance & map next to the model:
   mapped sites are within: 0.780 - 5.976
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 200 from: 200
   mapped sites are within: 0.780 - 5.976

peak=   -4.730 closest distance to " CB  PRO A 243 " =    2.613
peak=   -4.627 closest distance to " O   HOH Z 266 " =    4.853
peak=   -4.554 closest distance to " CD  ARG A 156 " =    2.005
peak=   -4.492 closest distance to " CG  GLN A 223 " =    1.849
peak=   -4.356 closest distance to " OG BSER A 134 " =    1.234
peak=   -4.345 closest distance to " C   HIS A 108 " =    1.126
peak=   -4.298 closest distance to " O   HOH Z 377 " =    2.057
peak=   -4.268 closest distance to " O   VAL A  67 " =    2.670
peak=   -4.173 closest distance to " O   VAL A  67 " =    2.832
peak=   -4.156 closest distance to " O   HOH Z 290 " =    1.173
peak=   -4.131 closest distance to " SG  CYS A 254 " =    3.464
peak=   -4.119 closest distance to " O   HOH Z 231 " =    2.262
peak=   -4.103 closest distance to " CG1 VAL A 112 " =    2.833
peak=   -4.071 closest distance to " ND2 ASN A  45 " =    1.674
peak=   -4.028 closest distance to " CE  MET A 105 " =    2.306
peak=   -4.014 closest distance to " O   HOH Z 313 " =    1.888
peak=   -3.983 closest distance to " CD  ARG A 139 " =    1.527
peak=   -3.977 closest distance to " O   HOH Z 389 " =    1.878
peak=   -3.973 closest distance to " O   PRO A 198 " =    1.266
peak=   -3.970 closest distance to " O   HOH Z 435 " =    2.777
peak=   -3.945 closest distance to " O   HOH Z 372 " =    2.361
peak=   -3.945 closest distance to " CD  GLN A  58 " =    1.079
peak=   -3.938 closest distance to " CE2 PHE A 218 " =    2.428
peak=   -3.913 closest distance to " O   HOH Z 198 " =    1.934
peak=   -3.852 closest distance to " CZ3 TRP A 179 " =    1.181
peak=   -3.830 closest distance to " CB  ALA A 291 " =    2.203
peak=   -3.828 closest distance to " CB  ASN A  39 " =    2.238
peak=   -3.825 closest distance to " CB  ALA A 161 " =    2.461
peak=   -3.811 closest distance to " O   HOH Z 185 " =    2.219
peak=   -3.796 closest distance to " CD1 PHE A  59 " =    1.888
peak=   -3.791 closest distance to " CE2 TYR A  30 " =    2.790
peak=   -3.787 closest distance to " O   HOH Z 407 " =    2.972
peak=   -3.781 closest distance to " OD1 ASN A 187 " =    1.606
peak=   -3.775 closest distance to " OXT GLY A 302 " =    2.814
peak=   -3.766 closest distance to " ND2 ASN A  45 " =    1.082
peak=   -3.761 closest distance to " O   SER A 135 " =    1.455
peak=   -3.751 closest distance to " CD2 PHE A 192 " =    1.980
peak=   -3.750 closest distance to " N   GLN A  58 " =    1.682
peak=   -3.742 closest distance to " CB  ALA A 291 " =    2.238
peak=   -3.738 closest distance to " N   ALA A  43 " =    2.543
peak=   -3.731 closest distance to " CG  PHE A 283 " =    2.629
peak=   -3.726 closest distance to " O   HOH Z 114 " =    3.006
peak=   -3.719 closest distance to " O   HOH Z 351 " =    1.500
peak=   -3.719 closest distance to " O   ARG A 145 " =    1.520
peak=   -3.707 closest distance to " OD1 ASP A 171 " =    1.605
peak=   -3.694 closest distance to " CB  ALA A 248 " =    2.069
peak=   -3.668 closest distance to " CG  ASP A 231 " =    0.780
peak=   -3.660 closest distance to " O   HOH Z 211 " =    1.714
peak=   -3.660 closest distance to " O   HOH Z 198 " =    1.492
peak=   -3.656 closest distance to " OG  SER A  97 " =    2.143
peak=   -3.656 closest distance to " CZ  PHE A  59 " =    1.480
peak=   -3.654 closest distance to " CZ  TYR A 169 " =    1.717
peak=   -3.633 closest distance to " CB  TYR A  15 " =    2.158
peak=   -3.626 closest distance to " O   PRO A 163 " =    1.994
peak=   -3.620 closest distance to " CA  GLY A 203 " =    2.263
peak=   -3.614 closest distance to " O   HOH Z  43 " =    1.781
peak=   -3.587 closest distance to " O   HOH Z 126 " =    1.867
peak=   -3.586 closest distance to " O   ALA A 161 " =    1.576
peak=   -3.583 closest distance to " O   HOH Z 395 " =    5.162
peak=   -3.569 closest distance to " O   PRO A 198 " =    1.246
peak=   -3.568 closest distance to " O   HOH Z  13 " =    1.525
peak=   -3.568 closest distance to " O   HOH Z 362 " =    5.976
peak=   -3.560 closest distance to " CB  PHE A 208 " =    2.185
peak=   -3.557 closest distance to " O   HOH Z 102 " =    1.525
peak=   -3.556 closest distance to " OD2 ASP A 191 " =    1.405
peak=   -3.556 closest distance to " OD1 ASN A 148 " =    1.593
peak=   -3.545 closest distance to " O   HOH Z 353 " =    2.160
peak=   -3.545 closest distance to " CB  ALA A 248 " =    2.331
peak=   -3.540 closest distance to " OD2 ASP A 171 " =    2.354
peak=   -3.535 closest distance to " N   ALA A 248 " =    1.629
peak=   -3.522 closest distance to " ND2 ASN A 187 " =    1.513
peak=   -3.519 closest distance to " N   ASP A 286 " =    2.345
peak=   -3.509 closest distance to " CD2 TYR A 247 " =    2.523
peak=   -3.505 closest distance to " CA  GLY A 133 " =    1.964
peak=   -3.494 closest distance to " ND2 ASN A 249 " =    2.085
peak=   -3.488 closest distance to " C   ALA A 158 " =    1.323
peak=   -3.483 closest distance to " CG2 ILE A 263 " =    2.237
peak=   -3.481 closest distance to " CA  GLY A  98 " =    1.862
peak=   -3.480 closest distance to " C   LEU A 143 " =    1.066
peak=   -3.478 closest distance to " O   HOH Z 298 " =    1.287
peak=   -3.478 closest distance to " CG2 THR A 178 " =    2.245
peak=   -3.460 closest distance to " CD1 LEU A 228 " =    2.128
peak=   -3.458 closest distance to " NH2BARG A 275 " =    1.834
peak=   -3.457 closest distance to " NH2AARG A 275 " =    5.197
peak=   -3.453 closest distance to " O   HOH Z  63 " =    1.685
peak=   -3.452 closest distance to " O   HOH Z 385 " =    1.953
peak=   -3.450 closest distance to " O   HOH Z 196 " =    2.140
peak=   -3.425 closest distance to " O   HOH Z  60 " =    2.255
peak=   -3.412 closest distance to " O   VAL A 189 " =    2.562
peak=   -3.411 closest distance to " OG BSER A 134 " =    1.674
peak=   -3.411 closest distance to " NH1 ARG A 195 " =    2.581
peak=   -3.401 closest distance to " O   PHE A 218 " =    1.563
peak=   -3.393 closest distance to " O   HOH Z  10 " =    1.453
peak=   -3.389 closest distance to " O   HOH Z 263 " =    2.937
peak=   -3.386 closest distance to " CG1 VAL A 230 " =    2.010
peak=   -3.384 closest distance to " NH2 ARG A  79 " =    1.989
peak=   -3.378 closest distance to " O   HOH Z 339 " =    1.847
peak=   -3.373 closest distance to " O   SER A  95 " =    1.473
peak=   -3.367 closest distance to " N   THR A 157 " =    1.469
peak=   -3.364 closest distance to " OXT GLY A 302 " =    3.456
peak=   -3.362 closest distance to " CG1 VAL A 268 " =    2.417
peak=   -3.359 closest distance to " O   PRO A 198 " =    1.617
peak=   -3.340 closest distance to " O   HOH Z 244 " =    2.060
peak=   -3.335 closest distance to " O   HOH Z 359 " =    3.318
peak=   -3.328 closest distance to " O   HOH Z  11 " =    1.848
peak=   -3.323 closest distance to " OD2 ASP A  50 " =    1.598
peak=   -3.318 closest distance to " CB  PRO A 163 " =    2.497
peak=   -3.318 closest distance to " CB  ASP A 132 " =    2.239
peak=   -3.317 closest distance to " O   VAL A 189 " =    1.626
peak=   -3.312 closest distance to " O   HOH Z 165 " =    2.122
peak=   -3.311 closest distance to " O   HOH Z  38 " =    1.635
peak=   -3.311 closest distance to " O   VAL A 174 " =    2.140
peak=   -3.305 closest distance to " NE2 GLN A 278 " =    1.706
peak=   -3.302 closest distance to " O   ALA A 292 " =    1.983
peak=   -3.300 closest distance to " SG ACYS A 201 " =    1.805
peak=   -3.295 closest distance to " CG  GLU A 152 " =    1.149
peak=   -3.287 closest distance to " O   ALA A 180 " =    1.240
peak=   -3.285 closest distance to " O   SER A 146 " =    1.094
peak=   -3.285 closest distance to " O   HOH Z 131 " =    4.102
peak=   -3.284 closest distance to " NE  ARG A  36 " =    1.925
peak=   -3.280 closest distance to " CB  ASP A 286 " =    2.130
peak=   -3.280 closest distance to " CD2 LEU A 237 " =    2.725
peak=   -3.279 closest distance to " N   SER A 212 " =    1.958
peak=   -3.276 closest distance to " O   HOH Z 394 " =    1.425
peak=   -3.275 closest distance to " CB  ASP A 286 " =    1.752
peak=   -3.273 closest distance to " C   MET A 188 " =    1.438
peak=   -3.272 closest distance to " O   ALA A  51 " =    1.356
peak=   -3.272 closest distance to " O   HOH Z 322 " =    1.706
peak=   -3.272 closest distance to " O   HOH Z 311 " =    3.589
peak=   -3.269 closest distance to " O   HOH Z 123 " =    2.311
peak=   -3.268 closest distance to " OD1 ASP A 191 " =    1.496
peak=   -3.262 closest distance to " OE1 GLN A 223 " =    1.922
peak=   -3.259 closest distance to " CD2 PHE A 225 " =    1.186
peak=   -3.257 closest distance to " OH  TYR A 214 " =    1.234
peak=   -3.253 closest distance to " O   GLY A  80 " =    2.434
peak=   -3.249 closest distance to " OD1 ASP A 191 " =    1.793
peak=   -3.247 closest distance to " CD1 LEU A 101 " =    2.258
peak=   -3.242 closest distance to " CA  GLY A 241 " =    2.204
peak=   -3.240 closest distance to " O   ALA A  10 " =    1.637
peak=   -3.240 closest distance to " O   HOH Z 421 " =    3.006
peak=   -3.234 closest distance to " O   HOH Z  93 " =    2.105
peak=   -3.232 closest distance to " CD1 LEU A 297 " =    2.462
peak=   -3.231 closest distance to " O   HOH Z 111 " =    2.349
peak=   -3.225 closest distance to " OD1 ASN A 176 " =    1.330
peak=   -3.223 closest distance to " O   MET A  40 " =    2.736
peak=   -3.223 closest distance to " OG  SER A  62 " =    1.605
peak=   -3.222 closest distance to " O   ILE A 106 " =    2.044
peak=   -3.222 closest distance to " CG  GLU A 277 " =    1.277
peak=   -3.219 closest distance to " O   HOH Z 266 " =    4.662
peak=   -3.213 closest distance to " O   TRP A  70 " =    1.497
peak=   -3.207 closest distance to " CB  ASP A 132 " =    2.360
peak=   -3.206 closest distance to " OD1AASN A 224 " =    1.807
peak=   -3.203 closest distance to " CB  ALA A   7 " =    2.088
peak=   -3.202 closest distance to " O   SER A  22 " =    2.378
peak=   -3.197 closest distance to " N   PHE A  59 " =    2.167
peak=   -3.192 closest distance to " OE2 GLU A 152 " =    1.158
peak=   -3.191 closest distance to " C   PRO A  90 " =    1.516
peak=   -3.190 closest distance to " O   HOH Z  24 " =    1.381
peak=   -3.189 closest distance to " OE1 GLN A  88 " =    1.173
peak=   -3.185 closest distance to " CA  ASP A 298 " =    1.075
peak=   -3.184 closest distance to " CB  TRP A  85 " =    2.497
peak=   -3.183 closest distance to " CG1 VAL A  78 " =    3.131
peak=   -3.181 closest distance to " NH2 ARG A  79 " =    1.614
peak=   -3.179 closest distance to " CB  GLN A  11 " =    1.803
peak=   -3.179 closest distance to " CD2 PHE A  61 " =    2.596
peak=   -3.178 closest distance to " CA  GLY A 241 " =    3.215
peak=   -3.177 closest distance to " O   HOH Z 137 " =    1.415
peak=   -3.164 closest distance to " O   HOH Z 265 " =    2.089
peak=   -3.163 closest distance to " OG  SER A  87 " =    1.264
peak=   -3.161 closest distance to " CB  ALA A 244 " =    2.077
peak=   -3.159 closest distance to " O   ALA A 180 " =    1.041
peak=   -3.150 closest distance to " CG  TRP A 266 " =    1.939
peak=   -3.147 closest distance to " O   HOH Z 281 " =    2.722
peak=   -3.141 closest distance to " CA  TRP A 274 " =    1.469
peak=   -3.141 closest distance to " O   HOH Z  91 " =    1.636
peak=   -3.140 closest distance to " O   HOH Z 166 " =    1.495
peak=   -3.140 closest distance to " OG1 THR A 246 " =    1.378
peak=   -3.135 closest distance to " O   ASN A 249 " =    1.417
peak=   -3.133 closest distance to " O   HOH Z  73 " =    2.386
peak=   -3.132 closest distance to " CG  ARG A 269 " =    2.560
peak=   -3.126 closest distance to " CD  GLN A 223 " =    1.350
peak=   -3.121 closest distance to " O   HOH Z 295 " =    1.585
peak=   -3.117 closest distance to " O   HOH Z   6 " =    1.503
peak=   -3.110 closest distance to " O   HOH Z 149 " =    2.304
peak=   -3.108 closest distance to " CG  GLU A   2 " =    1.985
peak=   -3.104 closest distance to " CG1 VAL A 197 " =    2.125
peak=   -3.097 closest distance to " CB  CYS A 201 " =    2.618
peak=   -3.093 closest distance to " O   HOH Z 250 " =    1.408
peak=   -3.091 closest distance to " CG1 VAL A 250 " =    2.615
peak=   -3.077 closest distance to " O   HOH Z 377 " =    0.879
peak=   -3.077 closest distance to " OD1 ASP A 200 " =    1.385
peak=   -3.075 closest distance to " O   HOH Z  51 " =    1.343
peak=   -3.072 closest distance to " OG  SER A 206 " =    1.719
peak=   -3.069 closest distance to " O   HOH Z 234 " =    3.993
peak=   -3.069 closest distance to " O   HOH Z 283 " =    5.578
peak=   -3.068 closest distance to " CH2 TRP A 179 " =    2.098
peak=   -3.068 closest distance to " CG2 VAL A 189 " =    1.980
peak=   -3.051 closest distance to " C   LYS A  76 " =    1.727
peak=   -3.048 closest distance to " O   HOH Z 137 " =    1.490
peak=   -3.044 closest distance to " O   LYS A 289 " =    2.957

================= 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    :  0.2926 0.2922   5.963770e+00   5.938145e+00
   1_bss:  0.2760 0.2737   5.937121e+00   5.899803e+00
   1_xyz:  0.1499 0.1729   5.348362e+00   5.463364e+00
   1_adp:  0.1368 0.1783   5.291876e+00   5.495609e+00
   1_occ:  0.1365 0.1784   5.290194e+00   5.494368e+00
   2_bss:  0.1352 0.1751   5.280186e+00   5.480753e+00
   2_xyz:  0.1153 0.1561   5.145507e+00   5.370559e+00
   2_adp:  0.1134 0.1520   5.125803e+00   5.347137e+00
   2_occ:  0.1133 0.1520   5.125476e+00   5.347359e+00
   3_bss:  0.1132 0.1519   5.123864e+00   5.346166e+00
   3_xyz:  0.1090 0.1497   5.101282e+00   5.336021e+00
   3_adp:  0.1070 0.1505   5.096303e+00   5.342400e+00
   3_occ:  0.1069 0.1506   5.096343e+00   5.342691e+00
   4_bss:  0.1068 0.1509   5.096415e+00   5.343425e+00
   4_xyz:  0.1059 0.1516   5.095589e+00   5.350280e+00
   4_adp:  0.1058 0.1519   5.096144e+00   5.352239e+00
   4_occ:  0.1057 0.1519   5.096215e+00   5.352496e+00
   5_bss:  0.1056 0.1519   5.096288e+00   5.352565e+00
   5_xyz:  0.1050 0.1529   5.096192e+00   5.357807e+00
   5_adp:  0.1050 0.1528   5.095331e+00   5.357360e+00
   5_occ:  0.1050 0.1528   5.095413e+00   5.357518e+00
   5_bss:  0.1050 0.1528   5.095477e+00   5.357585e+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:  0.331  36.685  -2.901   0.327  -1.448   0.000  -0.000  -0.000
   1_xyz:  0.331  36.685  -2.901   0.327  -1.448   0.000  -0.000  -0.000
   1_adp:  0.331  36.685  -2.901   0.327  -1.448   0.000  -0.000  -0.000
   1_occ:  0.331  36.685  -2.901   0.327  -1.448   0.000  -0.000  -0.000
   2_bss:  0.321  42.096  -3.100  -2.046  -1.777  -0.000  -0.000  -0.000
   2_xyz:  0.321  42.096  -3.100  -2.046  -1.777  -0.000  -0.000  -0.000
   2_adp:  0.321  42.096  -3.100  -2.046  -1.777  -0.000  -0.000  -0.000
   2_occ:  0.321  42.096  -3.100  -2.046  -1.777  -0.000  -0.000  -0.000
   3_bss:  0.322  42.096  -2.912  -2.433  -1.541  -0.000  -0.000  -0.000
   3_xyz:  0.322  42.096  -2.912  -2.433  -1.541  -0.000  -0.000  -0.000
   3_adp:  0.322  42.096  -2.912  -2.433  -1.541  -0.000  -0.000  -0.000
   3_occ:  0.322  42.096  -2.912  -2.433  -1.541  -0.000  -0.000  -0.000
   4_bss:  0.319  43.338  -2.711  -2.420  -1.388  -0.000  -0.000  -0.000
   4_xyz:  0.319  43.338  -2.711  -2.420  -1.388  -0.000  -0.000  -0.000
   4_adp:  0.319  43.338  -2.711  -2.420  -1.388  -0.000  -0.000  -0.000
   4_occ:  0.319  43.338  -2.711  -2.420  -1.388  -0.000  -0.000  -0.000
   5_bss:  0.319  43.338  -2.491  -2.249  -1.157  -0.000  -0.000  -0.000
   5_xyz:  0.319  43.338  -2.491  -2.249  -1.157  -0.000  -0.000  -0.000
   5_adp:  0.319  43.338  -2.491  -2.249  -1.157  -0.000  -0.000  -0.000
   5_occ:  0.319  43.338  -2.491  -2.249  -1.157  -0.000  -0.000  -0.000
   5_bss:  0.319  43.311  -2.280  -2.082  -0.954  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  28.403 0.7796  0.9660    23437.160
   1_bss:  26.955 0.7929  0.9330    19935.265
   1_xyz:  15.370 0.9046  1.0110     7522.151
   1_adp:  16.093 0.8980  1.0101     7934.704
   1_occ:  16.061 0.8982  1.0100     7899.959
   2_bss:  15.694 0.9013  0.9786     7634.817
   2_xyz:  13.596 0.9180  0.9844     6059.656
   2_adp:  13.136 0.9216  0.9832     5828.745
   2_occ:  13.138 0.9216  0.9830     5824.349
   3_bss:  13.103 0.9218  0.9841     5811.049
   3_xyz:  12.868 0.9239  0.9847     5687.523
   3_adp:  12.977 0.9231  0.9783     5724.404
   3_occ:  12.981 0.9231  0.9782     5728.089
   4_bss:  13.000 0.9230  0.9829     5745.387
   4_xyz:  13.097 0.9223  0.9822     5836.286
   4_adp:  13.141 0.9219  0.9761     5856.519
   4_occ:  13.146 0.9219  0.9760     5859.333
   5_bss:  13.147 0.9219  0.9835     5860.651
   5_xyz:  13.231 0.9212  0.9834     5939.336
   5_adp:  13.215 0.9214  0.9772     5927.610
   5_occ:  13.219 0.9213  0.9771     5929.560
   5_bss:  13.220 0.9213  0.9832     5930.818
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.6111e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.6111e-01
   1_xyz:   1.016  0.007  0.073 15.299  0.004  4.105   6.3176e-02
   1_adp:   1.016  0.007  0.073 15.299  0.004  4.105   6.3176e-02
   1_occ:   1.016  0.007  0.073 15.299  0.004  4.105   6.3176e-02
   2_bss:   1.016  0.007  0.073 15.299  0.004  4.105   6.3176e-02
   2_xyz:   0.948  0.006  0.072 14.981  0.004  4.103   5.5390e-02
   2_adp:   0.948  0.006  0.072 14.981  0.004  4.103   5.5390e-02
   2_occ:   0.948  0.006  0.072 14.981  0.004  4.103   5.5390e-02
   3_bss:   0.948  0.006  0.072 14.981  0.004  4.103   5.5390e-02
   3_xyz:   0.961  0.006  0.074 14.942  0.004  4.115   5.7056e-02
   3_adp:   0.961  0.006  0.074 14.942  0.004  4.115   5.7056e-02
   3_occ:   0.961  0.006  0.074 14.942  0.004  4.115   5.7056e-02
   4_bss:   0.961  0.006  0.074 14.942  0.004  4.115   5.7056e-02
   4_xyz:   0.944  0.006  0.073 14.877  0.004  4.115   5.5552e-02
   4_adp:   0.944  0.006  0.073 14.877  0.004  4.115   5.5552e-02
   4_occ:   0.944  0.006  0.073 14.877  0.004  4.115   5.5552e-02
   5_bss:   0.944  0.006  0.073 14.877  0.004  4.115   5.5552e-02
   5_xyz:   0.951  0.006  0.073 14.843  0.004  4.115   5.6282e-02
   5_adp:   0.951  0.006  0.073 14.843  0.004  4.115   5.6282e-02
   5_occ:   0.951  0.006  0.073 14.843  0.004  4.115   5.6282e-02
   5_bss:   0.951  0.006  0.073 14.843  0.004  4.115   5.6282e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.806   2.3909e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.806   2.3909e-01
   1_xyz:   6.996  0.045  0.283 85.576  0.043  2.232   7.6070e-02
   1_adp:   6.996  0.045  0.283 85.576  0.043  2.232   7.6070e-02
   1_occ:   6.996  0.045  0.283 85.576  0.043  2.232   7.6070e-02
   2_bss:   6.996  0.045  0.283 85.576  0.043  2.232   7.6070e-02
   2_xyz:   6.766  0.039  0.217 83.923  0.029  2.344   3.9911e-02
   2_adp:   6.766  0.039  0.217 83.923  0.029  2.344   3.9911e-02
   2_occ:   6.766  0.039  0.217 83.923  0.029  2.344   3.9911e-02
   3_bss:   6.766  0.039  0.217 83.923  0.029  2.344   3.9911e-02
   3_xyz:   6.157  0.038  0.237 84.825  0.031  2.304   4.2178e-02
   3_adp:   6.157  0.038  0.237 84.825  0.031  2.304   4.2178e-02
   3_occ:   6.157  0.038  0.237 84.825  0.031  2.304   4.2178e-02
   4_bss:   6.157  0.038  0.237 84.825  0.031  2.304   4.2178e-02
   4_xyz:   6.089  0.040  0.224 83.224  0.033  2.321   3.9979e-02
   4_adp:   6.089  0.040  0.224 83.224  0.033  2.321   3.9979e-02
   4_occ:   6.089  0.040  0.224 83.224  0.033  2.321   3.9979e-02
   5_bss:   6.089  0.040  0.224 83.224  0.033  2.321   3.9979e-02
   5_xyz:   6.156  0.041  0.240 83.981  0.033  2.304   3.9729e-02
   5_adp:   6.156  0.041  0.240 83.981  0.033  2.304   3.9729e-02
   5_occ:   6.156  0.041  0.240 83.981  0.033  2.304   3.9729e-02
   5_bss:   6.156  0.041  0.240 83.981  0.033  2.304   3.9729e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_bss:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_xyz:  63.06   5.09  16.02  49.51   5.09  12.19  63.06   6.19  36.87
   1_adp:  68.18   0.62  16.91  65.34   0.62  12.97  68.18   7.51  38.37
   1_occ:  68.18   0.62  16.91  65.34   0.62  12.97  68.18   7.51  38.37
   2_bss:  68.18   0.62  16.91  65.34   0.62  12.97  68.18   7.51  38.37
   2_xyz:  68.18   0.62  16.91  65.34   0.62  12.97  68.18   7.51  38.37
   2_adp:  69.82   2.14  16.68  65.52   2.14  12.90  69.82   6.95  37.27
   2_occ:  69.82   2.14  16.68  65.52   2.14  12.90  69.82   6.95  37.27
   3_bss:  69.82   2.14  16.68  65.52   2.14  12.90  69.82   6.95  37.27
   3_xyz:  69.82   2.14  16.68  65.52   2.14  12.90  69.82   6.95  37.27
   3_adp:  81.72   0.88  17.12  81.72   0.88  12.98  78.07   6.58  39.62
   3_occ:  81.72   0.88  17.12  81.72   0.88  12.98  78.07   6.58  39.62
   4_bss:  81.72   0.88  17.12  81.72   0.88  12.98  78.07   6.58  39.62
   4_xyz:  81.72   0.88  17.12  81.72   0.88  12.98  78.07   6.58  39.62
   4_adp:  83.60   0.80  16.85  83.60   0.80  12.80  79.64   6.42  38.91
   4_occ:  83.60   0.80  16.85  83.60   0.80  12.80  79.64   6.42  38.91
   5_bss:  83.60   0.80  16.85  83.60   0.80  12.80  79.64   6.42  38.91
   5_xyz:  83.60   0.80  16.85  83.60   0.80  12.80  79.64   6.42  38.91
   5_adp:  83.92   0.79  16.69  83.92   0.79  12.63  79.74   6.26  38.79
   5_occ:  83.92   0.79  16.69  83.92   0.79  12.63  79.74   6.26  38.79
   5_bss:  83.89   0.76  16.67  83.89   0.76  12.61  79.71   6.23  38.76
------------------------------------------------------------------------
 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:    0.734    0.014    0.294
   1_adp:    0.734    0.014    0.294
   1_occ:    0.734    0.014    0.294
   2_bss:    0.734    0.014    0.294
   2_xyz:    0.725    0.023    0.322
   2_adp:    0.725    0.023    0.322
   2_occ:    0.725    0.023    0.322
   3_bss:    0.725    0.023    0.322
   3_xyz:    0.859    0.021    0.343
   3_adp:    0.859    0.021    0.343
   3_occ:    0.859    0.021    0.343
   4_bss:    0.859    0.021    0.343
   4_xyz:    0.989    0.028    0.351
   4_adp:    0.989    0.028    0.351
   4_occ:    0.989    0.028    0.351
   5_bss:    0.989    0.028    0.351
   5_xyz:    1.102    0.019    0.356
   5_adp:    1.102    0.019    0.356
   5_occ:    1.102    0.019    0.356
   5_bss:    1.102    0.019    0.356
------------------------------------------------------------------------

CPU time actual refinement: 325.53


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_521/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_521/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_521/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_521/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_521/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 325.37 
  Macro-tasks:
    bulk solvent and scale       = 36.32  
    individual site refinement   = 138.10 
    weights calculation          = 29.88  
    collect and process          = 6.64   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 211.04 
  Micro-tasks:
    mask                            = 1.18   
    f_calc                          = 103.34 
    alpha_beta                      = 8.08   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 113.49 
    fmodel                         = 6.57   
    r_factors                      = 0.16   
    phase_errors                   = 11.30  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 245.53 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 4.548 micro seconds
Total CPU time: 5.65 minutes
from_scatterers_fft:    657 calls, 102.99 s
gradients_fft:          602 calls,  99.22 s

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

# Date 2008-01-16 Time 05:01:28 PST -0800 (1200488488.77 s)
Start R-work = 0.2926, R-free = 0.2922 (no bulk solvent and anisotropic scale)
Final R-work = 0.1295, R-free = 0.1724 (no bulk solvent and anisotropic scale)

Start R-work = 0.2760, R-free = 0.2737
Final R-work = 0.1050, R-free = 0.1528