# Date 2008-01-16 Time 06:16:06 PST -0800 (1200492966.29 s)
#phil __OFF__

Command line arguments: "../1073.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 13596
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1073

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.3037, 47.8686, 86.822, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.8686, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1778 2.01117
Completeness in resolution range: 0.963599
Completeness with d_max=infinity: 0.960575

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1778
                             d_min =   2.0112

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.8686, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1778 2.01117
Completeness in resolution range: 0.963599
Completeness with d_max=infinity: 0.960575

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1782 -  4.3031 [2127/2154]  1915   212  10.0%
  bin  2:  4.3031 -  3.4284 [2044/2060]  1838   206  10.1%
  bin  3:  3.4284 -  2.9989 [2032/2051]  1827   205  10.1%
  bin  4:  2.9989 -  2.7264 [2006/2036]  1809   197   9.8%
  bin  5:  2.7264 -  2.5319 [1995/2014]  1798   197   9.9%
  bin  6:  2.5319 -  2.3833 [1965/2001]  1770   195   9.9%
  bin  7:  2.3833 -  2.2643 [1976/2009]  1776   200  10.1%
  bin  8:  2.2643 -  2.1660 [1967/2000]  1768   199  10.1%
  bin  9:  2.1660 -  2.0829 [1963/1992]  1770   193   9.8%
  bin 10:  2.0829 -  2.0112 [1514/2012]  1359   155  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1073/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:
        1.43 -     2.13: 6
        2.13 -     2.82: 831
        2.82 -     3.51: 4347
        3.51 -     4.21: 9116
        4.21 -     4.90: 13475
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.432 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 277 " - " O   HOH Z 343 "  1.920 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 343 " - " O   HOH Z 277 "  1.920 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.939 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 27770 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_1073/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1073/model_refine_001.geo

CPU time processing inputs: 9.05


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 47.8686 86.82195 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4184   r_free= 0.4018   ksol= 0.00   Bsol= 0.00   scale= 0.905    |
|                                                                             |
| 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:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.224051                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1782 -  4.7993 0.99   1380  154 0.3313 0.3481      6.4659       6.424|
|  2:  4.7993 -  3.8295 0.99   1346  146 0.3503 0.3583      6.7379      6.7422|
|  3:  3.8295 -  3.3514 0.99   1306  149 0.3822 0.3398       6.595       6.515|
|  4:  3.3514 -  3.0476 0.99   1295  143 0.4064 0.3752      6.4663      6.3849|
|  5:  3.0476 -  2.8307 0.99   1292  142 0.4411 0.4261      6.3184      6.3411|
|  6:  2.8307 -  2.6648 0.99   1288  144 0.4503 0.4150      6.2375      6.1424|
|  7:  2.6648 -  2.5319 0.99   1280  139 0.4494 0.3951      6.1865      6.1126|
|  8:  2.5319 -  2.4222 0.98   1274  147 0.4626 0.4275      6.1403      6.1138|
|  9:  2.4222 -  2.3293 0.98   1276  140 0.4659 0.4738      6.0761      6.1419|
| 10:  2.3293 -  2.2492 0.98   1244  138 0.4696 0.4340      6.0661      6.0191|
| 11:  2.2492 -  2.1791 1.00   1283  143 0.4707 0.4500      6.0219      6.0129|
| 12:  2.1791 -  2.1169 0.97   1243  136 0.4784 0.4915      5.9542      6.0067|
| 13:  2.1169 -  2.0613 0.98   1257  144 0.4735 0.4535        5.86      5.8075|
| 14:  2.0613 -  2.0112 0.67    866   94 0.4552 0.4631      5.7963      5.7789|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1782 -  4.7993  1380   154  0.74  30.88   0.84     0.77      58577.91|
|  2:  4.7993 -  3.8295  1346   146  0.77  28.77   0.92     0.84      74736.77|
|  3:  3.8295 -  3.3514  1306   149  0.70  35.17   0.92     0.84      78449.01|
|  4:  3.3514 -  3.0476  1295   143  0.65  39.67   0.91     0.79      70136.86|
|  5:  3.0476 -  2.8307  1292   142  0.57  46.35   0.91     0.74      57984.50|
|  6:  2.8307 -  2.6648  1288   144  0.57  46.53   0.91     0.73      48493.82|
|  7:  2.6648 -  2.5319  1280   139  0.56  47.33   0.93     0.72      43968.27|
|  8:  2.5319 -  2.4222  1274   147  0.53  49.77   0.93     0.72      42887.32|
|  9:  2.4222 -  2.3293  1276   140  0.51  51.40   0.92     0.69      41467.22|
| 10:  2.3293 -  2.2492  1244   138  0.49  52.76   0.95     0.68      39112.23|
| 11:  2.2492 -  2.1791  1283   143  0.49  53.14   0.94     0.68      36725.29|
| 12:  2.1791 -  2.1169  1243   136  0.47  54.57   0.95     0.68      35284.30|
| 13:  2.1169 -  2.0613  1257   144  0.45  56.09   0.92     0.65      30774.78|
| 14:  2.0613 -  2.0112   866    94  0.48  53.85   0.94     0.62      23605.96|
|alpha:            min =        0.62 max =            0.84 mean =         0.73|
|beta:             min =    23605.96 max =        78449.01 mean =     49613.16|
|figures of merit: min =        0.00 max =            1.00 mean =         0.57|
|phase err.(work): min =        0.00 max =           89.99 mean =        45.76|
|phase err.(test): min =        0.00 max =           89.91 mean =        45.75|
|-----------------------------------------------------------------------------|

============================== 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 = 10.096591             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.582   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.482119              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.198   (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 |  1.432 -  1.779:        1 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.779 -  2.125:        5 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.125 -  2.472:        8 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.472 -  2.819:      823 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.819 -  3.166:     2000 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.166 -  3.513:     2347 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.513 -  3.859:     4521 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.859 -  4.206:     4595 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.206 -  4.553:     6105 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.553 -  4.900:     7370 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.166 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.114    4.900  1.432 |       0.199 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.373)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4184   r_free= 0.4018   ksol= 0.00   Bsol= 0.00   scale= 0.905    |
|                                                                             |
| 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:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.224051                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4086   r_free= 0.3924   ksol= 0.30   Bsol= 50.00   scale= 0.945   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.06,4.57,-1.31,0.00,-0.00,-0.00); trace/3= 0.73                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.212967                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.010634              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.417   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.743861              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.034   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4086      final r-factor (work) = 0.2777          |
| start r-factor (free) = 0.3924      final r-factor (free) = 0.3042          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.1542 = 9.01 * 0.50 * 6.2122 + 1.00 * 0.1663                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.2078 = 9.01 * 0.50 * 6.0114 + 1.00 * 0.1245                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2777      final r-factor (work) = 0.2561          |
| start r-factor (free) = 0.3042      final r-factor (free) = 0.3071          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4782 = 0.74 * 1.00 * 6.0114 + 1.00 * 0.0066                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4112 = 0.74 * 1.00 * 5.8546 + 1.00 * 0.0562                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.373)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.51   16.85    None  None   None       |
|    all(noH): 2823   0      0.00    95.51   16.85    None  None   None       |
|    Sol.    : 438    0      3.15    68.15   37.78    None  None   None       |
|    Mac.    : 2385   0      0.00    95.51   13.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.551:  942   |   5:    47.756 -  57.307:   92        |
|      1:     9.551 -  19.102: 1046   |   6:    57.307 -  66.858:   28        |
|      2:    19.102 -  28.654:  389   |   7:    66.858 -  76.409:    1        |
|      3:    28.654 -  38.205:  181   |   8:    76.409 -  85.961:    0        |
|      4:    38.205 -  47.756:  143   |   9:    85.961 -  95.512:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2561 r_free = 0.3071             target_work(ml) = 5.856         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2558 r_free = 0.3065             target_work(ml) = 5.855         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2558   r_free= 0.3065   ksol= 0.30   Bsol= 50.00   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.06,4.57,-1.31,0.00,-0.00,-0.00); trace/3= 0.73                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.855214                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2542   r_free= 0.3045   ksol= 0.33   Bsol= 68.84   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.50,1.38,-0.84,0.00,-0.00,-0.00); trace/3= -0.32                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.852210                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.737352              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.638   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.774130              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.333   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2542      final r-factor (work) = 0.1848          |
| start r-factor (free) = 0.3045      final r-factor (free) = 0.2197          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.9920 = 4.74 * 0.50 * 5.8545 + 1.00 * 0.1245                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.6529 = 4.74 * 0.50 * 5.7234 + 1.00 * 0.0961                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1848      final r-factor (work) = 0.1632          |
| start r-factor (free) = 0.2197      final r-factor (free) = 0.2068          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5155 = 0.77 * 1.00 * 5.7234 + 1.00 * 0.0849                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2634 = 0.77 * 1.00 * 5.4902 + 1.00 * 0.0133                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.373)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.11   17.79    None  None   None       |
|    all(noH): 2823   0      0.00    97.11   17.79    None  None   None       |
|    Sol.    : 438    0      4.04    97.11   43.50    None  None   None       |
|    Mac.    : 2385   0      0.00    91.09   13.06    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.711: 1073   |   5:    48.555 -  58.267:   99        |
|      1:     9.711 -  19.422: 1036   |   6:    58.267 -  67.978:   80        |
|      2:    19.422 -  29.133:  251   |   7:    67.978 -  77.689:   34        |
|      3:    29.133 -  38.844:  135   |   8:    77.689 -  87.400:   18        |
|      4:    38.844 -  48.555:   94   |   9:    87.400 -  97.111:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1632 r_free = 0.2068             target_work(ml) = 5.462         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1630 r_free = 0.2068             target_work(ml) = 5.461         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1630   r_free= 0.2068   ksol= 0.33   Bsol= 68.84   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.50,1.38,-0.84,0.00,-0.00,-0.00); trace/3= -0.32                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.461400                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1627   r_free= 0.2071   ksol= 0.33   Bsol= 79.30   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.60,-0.13,-0.68,-0.00,-0.00,-0.00); trace/3= -0.80                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.459262                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.966998              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 92.705   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.783072              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.969  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1627      final r-factor (work) = 0.1323          |
| start r-factor (free) = 0.2071      final r-factor (free) = 0.1791          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.9860 = 3.97 * 0.50 * 5.4902 + 1.00 * 0.0961                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.7289 = 3.97 * 0.50 * 5.3691 + 1.00 * 0.0793                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1323      final r-factor (work) = 0.1260          |
| start r-factor (free) = 0.1791      final r-factor (free) = 0.1732          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2177 = 0.78 * 1.00 * 5.3691 + 1.00 * 0.0133                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1385 = 0.78 * 1.00 * 5.2688 + 1.00 * 0.0127                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.373)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.03  17.35    None  None   None       |
|    all(noH): 2823   0      0.00    104.03  17.35    None  None   None       |
|    Sol.    : 438    0      0.00    104.03  43.70    None  None   None       |
|    Mac.    : 2385   0      0.00    101.36  12.52    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.403: 1261   |   5:    52.014 -  62.416:   92        |
|      1:    10.403 -  20.806:  955   |   6:    62.416 -  72.819:   55        |
|      2:    20.806 -  31.208:  188   |   7:    72.819 -  83.222:   29        |
|      3:    31.208 -  41.611:  132   |   8:    83.222 -  93.625:    7        |
|      4:    41.611 -  52.014:   98   |   9:    93.625 - 104.027:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1260 r_free = 0.1732             target_work(ml) = 5.248         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1259 r_free = 0.1731             target_work(ml) = 5.247         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1259   r_free= 0.1731   ksol= 0.33   Bsol= 79.30   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.60,-0.13,-0.68,-0.00,-0.00,-0.00); trace/3= -0.80                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.247184                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1263   r_free= 0.1727   ksol= 0.33   Bsol= 77.34   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.35,-0.50,-0.28,-0.00,-0.00,-0.00); trace/3= -0.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.247936                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.965551              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 133.477  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.342349              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.333  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1263      final r-factor (work) = 0.1231          |
| start r-factor (free) = 0.1727      final r-factor (free) = 0.1702          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2584 = 1.97 * 0.50 * 5.2698 + 1.00 * 0.0793                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2105 = 1.97 * 0.50 * 5.2385 + 1.00 * 0.0622                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1231      final r-factor (work) = 0.1224          |
| start r-factor (free) = 0.1702      final r-factor (free) = 0.1678          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8059 = 0.34 * 1.00 * 5.2385 + 1.00 * 0.0125                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7996 = 0.34 * 1.00 * 5.2253 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.373)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.30  16.66    None  None   None       |
|    all(noH): 2823   0      0.00    102.30  16.66    None  None   None       |
|    Sol.    : 438    0      0.20    102.30  41.45    None  None   None       |
|    Mac.    : 2385   0      0.00    99.59   12.11    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.230: 1271   |   5:    51.151 -  61.381:   86        |
|      1:    10.230 -  20.460:  953   |   6:    61.381 -  71.611:   45        |
|      2:    20.460 -  30.690:  202   |   7:    71.611 -  81.841:   22        |
|      3:    30.690 -  40.920:  127   |   8:    81.841 -  92.071:    7        |
|      4:    40.920 -  51.151:  104   |   9:    92.071 - 102.301:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1224 r_free = 0.1678             target_work(ml) = 5.220         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1224 r_free = 0.1677             target_work(ml) = 5.220         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1224   r_free= 0.1677   ksol= 0.33   Bsol= 77.34   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.35,-0.50,-0.28,-0.00,-0.00,-0.00); trace/3= -0.71                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.220136                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1223   r_free= 0.1677   ksol= 0.32   Bsol= 70.16   scale= 0.990   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.25,-0.63,-0.12,-0.00,-0.00,-0.00); trace/3= -0.67                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.219962                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.951566              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 151.789  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.273106              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.241  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1223      final r-factor (work) = 0.1153          |
| start r-factor (free) = 0.1677      final r-factor (free) = 0.1648          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7731 = 2.95 * 0.50 * 5.2249 + 1.00 * 0.0622                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7452 = 2.95 * 0.50 * 5.1941 + 1.00 * 0.0798                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1153      final r-factor (work) = 0.1153          |
| start r-factor (free) = 0.1648      final r-factor (free) = 0.1636          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4292 = 0.27 * 1.00 * 5.1941 + 1.00 * 0.0106                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4240 = 0.27 * 1.00 * 5.1797 + 1.00 * 0.0094                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.373)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.90   16.01    None  None   None       |
|    all(noH): 2823   0      0.00    95.90   16.01    None  None   None       |
|    Sol.    : 438    0      1.94    95.03   39.16    None  None   None       |
|    Mac.    : 2385   0      0.00    95.90   11.76    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.590: 1197   |   5:    47.948 -  57.537:   91        |
|      1:     9.590 -  19.179: 1007   |   6:    57.537 -  67.127:   40        |
|      2:    19.179 -  28.769:  211   |   7:    67.127 -  76.716:   22        |
|      3:    28.769 -  38.358:  132   |   8:    76.716 -  86.306:    2        |
|      4:    38.358 -  47.948:  113   |   9:    86.306 -  95.895:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1153 r_free = 0.1636             target_work(ml) = 5.177         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1152 r_free = 0.1636             target_work(ml) = 5.177         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1152   r_free= 0.1636   ksol= 0.32   Bsol= 70.16   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.25,-0.63,-0.12,-0.00,-0.00,-0.00); trace/3= -0.67                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.177226                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1782 -  4.7993 0.99   1380  154 0.0999 0.1330      5.3943      5.5503|
|  2:  4.7993 -  3.8295 0.99   1346  146 0.0858 0.1089      5.4367      5.6268|
|  3:  3.8295 -  3.3514 0.99   1306  149 0.1052 0.1484      5.4735      5.8389|
|  4:  3.3514 -  3.0476 0.99   1295  143 0.1243 0.1635      5.4844      5.6414|
|  5:  3.0476 -  2.8307 0.99   1292  142 0.1433 0.1906      5.3941      5.6076|
|  6:  2.8307 -  2.6648 0.99   1288  144 0.1306 0.1948      5.2815      5.4952|
|  7:  2.6648 -  2.5319 0.99   1280  139 0.1300 0.1753      5.2106      5.4268|
|  8:  2.5319 -  2.4222 0.98   1274  147 0.1232 0.1776      5.1202      5.3695|
|  9:  2.4222 -  2.3293 0.98   1276  140 0.1205 0.1812      5.0608      5.3506|
| 10:  2.3293 -  2.2492 0.98   1244  138 0.1185 0.1862      5.0162       5.241|
| 11:  2.2492 -  2.1791 1.00   1283  143 0.1184 0.1830      4.9637      5.2788|
| 12:  2.1791 -  2.1169 0.97   1243  136 0.1158 0.1740       4.923      5.1956|
| 13:  2.1169 -  2.0613 0.98   1257  144 0.1176 0.1857      4.8183      5.1261|
| 14:  2.0613 -  2.0112 0.67    866   94 0.1097 0.1719      4.6829      4.9451|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1782 -  4.7993  1380   154  0.94   9.38   0.96     0.94       7572.05|
|  2:  4.7993 -  3.8295  1346   146  0.95   8.04   0.99     0.98       9044.31|
|  3:  3.8295 -  3.3514  1306   149  0.93  11.48   1.01     1.00      10518.11|
|  4:  3.3514 -  3.0476  1295   143  0.92  14.19   0.99     0.97      11002.31|
|  5:  3.0476 -  2.8307  1292   142  0.89  17.29   0.99     0.96       9476.38|
|  6:  2.8307 -  2.6648  1288   144  0.89  17.05   0.98     0.95       8069.49|
|  7:  2.6648 -  2.5319  1280   139  0.90  16.50   0.98     0.96       6899.08|
|  8:  2.5319 -  2.4222  1274   147  0.90  16.11   0.98     0.95       5912.54|
|  9:  2.4222 -  2.3293  1276   140  0.90  16.05   0.98     0.94       5252.32|
| 10:  2.3293 -  2.2492  1244   138  0.90  16.32   0.98     0.94       4848.01|
| 11:  2.2492 -  2.1791  1283   143  0.89  16.90   0.98     0.94       4542.39|
| 12:  2.1791 -  2.1169  1243   136  0.91  15.64   0.99     0.97       4286.78|
| 13:  2.1169 -  2.0613  1257   144  0.90  16.50   0.98     0.97       3548.43|
| 14:  2.0613 -  2.0112   866    94  0.91  14.82   0.95     0.91       2563.65|
|alpha:            min =        0.91 max =            1.00 mean =         0.96|
|beta:             min =     2563.65 max =        11002.31 mean =      6816.67|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.77 mean =        14.67|
|phase err.(test): min =        0.00 max =           89.04 mean =        14.07|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1152   r_free= 0.1635   ksol= 0.32   Bsol= 65.15   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.17,-0.66,-0.05,-0.00,-0.00,-0.00); trace/3= -0.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.177194                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1152   r_free= 0.1635   ksol= 0.32   Bsol= 65.15   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.17,-0.66,-0.05,-0.00,-0.00,-0.00); trace/3= -0.63                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.177194                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1782 -  4.7993 0.99   1380  154 0.0996 0.1331      5.3923      5.5484|
|  2:  4.7993 -  3.8295 0.99   1346  146 0.0856 0.1085      5.4341       5.623|
|  3:  3.8295 -  3.3514 0.99   1306  149 0.1052 0.1484      5.4723      5.8393|
|  4:  3.3514 -  3.0476 0.99   1295  143 0.1244 0.1634      5.4851      5.6413|
|  5:  3.0476 -  2.8307 0.99   1292  142 0.1435 0.1908      5.3953      5.6087|
|  6:  2.8307 -  2.6648 0.99   1288  144 0.1307 0.1948      5.2823      5.4954|
|  7:  2.6648 -  2.5319 0.99   1280  139 0.1301 0.1756      5.2113      5.4279|
|  8:  2.5319 -  2.4222 0.98   1274  147 0.1233 0.1777      5.1209      5.3699|
|  9:  2.4222 -  2.3293 0.98   1276  140 0.1204 0.1811      5.0612      5.3508|
| 10:  2.3293 -  2.2492 0.98   1244  138 0.1185 0.1865       5.017      5.2426|
| 11:  2.2492 -  2.1791 1.00   1283  143 0.1184 0.1829      4.9641      5.2787|
| 12:  2.1791 -  2.1169 0.97   1243  136 0.1158 0.1741      4.9233      5.1965|
| 13:  2.1169 -  2.0613 0.98   1257  144 0.1176 0.1858      4.8183      5.1262|
| 14:  2.0613 -  2.0112 0.67    866   94 0.1098 0.1717      4.6826       4.944|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1782 -  4.7993  1380   154  0.94   9.37   0.96     0.94       7548.81|
|  2:  4.7993 -  3.8295  1346   146  0.95   8.02   1.00     0.98       8999.47|
|  3:  3.8295 -  3.3514  1306   149  0.93  11.44   1.01     1.00      10475.84|
|  4:  3.3514 -  3.0476  1295   143  0.92  14.20   1.00     0.97      11010.11|
|  5:  3.0476 -  2.8307  1292   142  0.89  17.30   0.99     0.97       9489.69|
|  6:  2.8307 -  2.6648  1288   144  0.89  17.06   0.98     0.95       8080.49|
|  7:  2.6648 -  2.5319  1280   139  0.90  16.50   0.99     0.96       6906.35|
|  8:  2.5319 -  2.4222  1274   147  0.90  16.13   0.98     0.95       5921.04|
|  9:  2.4222 -  2.3293  1276   140  0.90  16.07   0.99     0.94       5262.08|
| 10:  2.3293 -  2.2492  1244   138  0.90  16.33   0.99     0.94       4856.32|
| 11:  2.2492 -  2.1791  1283   143  0.89  16.91   0.98     0.94       4548.17|
| 12:  2.1791 -  2.1169  1243   136  0.91  15.65   0.99     0.97       4291.68|
| 13:  2.1169 -  2.0613  1257   144  0.90  16.50   0.98     0.97       3547.25|
| 14:  2.0613 -  2.0112   866    94  0.91  14.81   0.95     0.92       2559.20|
|alpha:            min =        0.92 max =            1.00 mean =         0.96|
|beta:             min =     2559.20 max =        11010.11 mean =      6813.54|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.79 mean =        14.67|
|phase err.(test): min =        0.00 max =           89.15 mean =        14.07|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.373)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.90   16.01    None  None   None       |
|    all(noH): 2823   0      0.00    95.90   16.01    None  None   None       |
|    Sol.    : 438    0      1.95    95.03   39.17    None  None   None       |
|    Mac.    : 2385   0      0.00    95.90   11.76    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.003 -   9.593: 1197   |   5:    47.951 -  57.540:   91        |
|      1:     9.593 -  19.182: 1007   |   6:    57.540 -  67.130:   40        |
|      2:    19.182 -  28.772:  211   |   7:    67.130 -  76.719:   22        |
|      3:    28.772 -  38.361:  132   |   8:    76.719 -  86.309:    2        |
|      4:    38.361 -  47.951:  113   |   9:    86.309 -  95.898:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 327         
Filter by distance & map next to the model:
   mapped sites are within: 0.440 - 4.758
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 320 from: 327
   mapped sites are within: 0.726 - 4.758

peak=    6.000 closest distance to " O   HOH Z 111 " =    2.144
peak=    5.473 closest distance to " CB  GLN A 223 " =    1.394
peak=    5.080 closest distance to " CB  SER A  63 " =    1.298
peak=    5.061 closest distance to " O   HOH Z 210 " =    1.190
peak=    4.949 closest distance to " CG  PRO A  54 " =    1.331
peak=    4.855 closest distance to " O   HOH Z 232 " =    2.360
peak=    4.800 closest distance to " CB  ARG A 190 " =    1.704
peak=    4.714 closest distance to " CB  GLN A 183 " =    1.271
peak=    4.495 closest distance to " O   PRO A 198 " =    1.560
peak=    4.426 closest distance to " O   HOH Z 403 " =    1.775
peak=    4.409 closest distance to " CB  ARG A 275 " =    0.926
peak=    4.401 closest distance to " O   HOH Z 369 " =    2.055
peak=    4.367 closest distance to " O   HOH Z 298 " =    2.110
peak=    4.314 closest distance to " O   HOH Z 134 " =    1.688
peak=    4.302 closest distance to " O   HOH Z 234 " =    3.840
peak=    4.281 closest distance to " CB  GLU A 152 " =    1.139
peak=    4.257 closest distance to " CB  ARG A  79 " =    1.384
peak=    4.250 closest distance to " CB  PRO A  54 " =    0.856
peak=    4.246 closest distance to " CB  GLU A 128 " =    1.080
peak=    4.244 closest distance to " O   HOH Z 368 " =    2.195
peak=    4.242 closest distance to " CZ  PHE A 218 " =    1.128
peak=    4.233 closest distance to " O   HOH Z  44 " =    2.262
peak=    4.227 closest distance to " CD  LYS A 166 " =    1.321
peak=    4.226 closest distance to " CG  PRO A 213 " =    1.180
peak=    4.203 closest distance to " CA  TYR A  30 " =    0.923
peak=    4.197 closest distance to " O   HOH Z  15 " =    2.071
peak=    4.193 closest distance to " NH2 ARG A 156 " =    1.206
peak=    4.161 closest distance to " CA  ALA A  51 " =    0.987
peak=    4.150 closest distance to " CB  TRP A 266 " =    0.980
peak=    4.138 closest distance to " CB  GLU A 277 " =    3.753
peak=    4.117 closest distance to " CB  TYR A 169 " =    0.836
peak=    4.113 closest distance to " O   HOH Z 133 " =    2.403
peak=    4.111 closest distance to " O   HOH Z 265 " =    2.102
peak=    4.102 closest distance to " O   HOH Z 433 " =    1.545
peak=    4.085 closest distance to " O   HOH Z 271 " =    2.870
peak=    4.044 closest distance to " O   HOH Z  68 " =    2.059
peak=    4.038 closest distance to " CB  LEU A 228 " =    1.086
peak=    4.031 closest distance to " O   HOH Z  40 " =    1.825
peak=    4.026 closest distance to " CG1 ILE A  33 " =    1.214
peak=    4.007 closest distance to " CA  ASP A 191 " =    0.866
peak=    4.004 closest distance to " O   HOH Z 418 " =    1.602
peak=    3.992 closest distance to " O   HOH Z  21 " =    1.789
peak=    3.986 closest distance to " O   HOH Z 423 " =    1.887
peak=    3.961 closest distance to " O   HOH Z 126 " =    1.529
peak=    3.957 closest distance to " O   HOH Z 402 " =    1.539
peak=    3.956 closest distance to " CG2 THR A 221 " =    1.051
peak=    3.946 closest distance to " O   HOH Z 412 " =    3.654
peak=    3.943 closest distance to " CG  PRO A 198 " =    1.302
peak=    3.941 closest distance to " O   HOH Z 189 " =    2.649
peak=    3.932 closest distance to " CD  ARG A 269 " =    0.898
peak=    3.922 closest distance to " O   HOH Z 425 " =    1.414
peak=    3.917 closest distance to " O   HOH Z  80 " =    1.782
peak=    3.911 closest distance to " O   HOH Z 236 " =    1.985
peak=    3.904 closest distance to " O   HOH Z 214 " =    2.327
peak=    3.893 closest distance to " CB  VAL A 202 " =    1.556
peak=    3.889 closest distance to " O   HOH Z 128 " =    2.141
peak=    3.886 closest distance to " CB  ASP A 140 " =    0.894
peak=    3.875 closest distance to " C   ILE A 106 " =    1.881
peak=    3.871 closest distance to " CB  ASN A  39 " =    0.869
peak=    3.857 closest distance to " O   HOH Z 383 " =    2.187
peak=    3.821 closest distance to " CB  ASN A 148 " =    1.359
peak=    3.817 closest distance to " O   HOH Z  97 " =    2.049
peak=    3.802 closest distance to " OD1 ASN A  69 " =    2.557
peak=    3.800 closest distance to " O   HOH Z  20 " =    1.780
peak=    3.800 closest distance to " NE2 GLN A  11 " =    1.072
peak=    3.799 closest distance to " CD  ARG A  66 " =    2.569
peak=    3.795 closest distance to " O   HOH Z 303 " =    2.290
peak=    3.790 closest distance to " CD2 TRP A 179 " =    1.311
peak=    3.786 closest distance to " O   HOH Z  43 " =    1.891
peak=    3.785 closest distance to " O   SER A  87 " =    2.233
peak=    3.782 closest distance to " O   ALA A 165 " =    1.366
peak=    3.776 closest distance to " CD1 LEU A 300 " =    1.179
peak=    3.776 closest distance to " CB  SER A 141 " =    1.024
peak=    3.770 closest distance to " O   HOH Z 362 " =    3.443
peak=    3.766 closest distance to " CA  ALA A  21 " =    1.358
peak=    3.755 closest distance to " ND2 ASN A 187 " =    1.462
peak=    3.725 closest distance to " O   HOH Z 285 " =    3.012
peak=    3.719 closest distance to " CG2BVAL A  41 " =    0.884
peak=    3.716 closest distance to " O   HOH Z 193 " =    1.975
peak=    3.713 closest distance to " O   HOH Z  19 " =    1.935
peak=    3.706 closest distance to " O   HOH Z 374 " =    2.878
peak=    3.701 closest distance to " CG  PRO A 243 " =    1.137
peak=    3.695 closest distance to " O   HOH Z 406 " =    1.624
peak=    3.691 closest distance to " CA  ARG A 195 " =    1.190
peak=    3.688 closest distance to " N   ASN A  39 " =    1.295
peak=    3.685 closest distance to " O   HOH Z  63 " =    1.827
peak=    3.675 closest distance to " CB  ASN A 187 " =    1.038
peak=    3.671 closest distance to " O   THR A 251 " =    1.238
peak=    3.669 closest distance to " CB  ALA A 291 " =    1.297
peak=    3.668 closest distance to " CB  TYR A 116 " =    1.064
peak=    3.668 closest distance to " NH2BARG A 145 " =    2.082
peak=    3.667 closest distance to " CA  GLY A 241 " =    0.850
peak=    3.665 closest distance to " OD1 ASN A 217 " =    1.634
peak=    3.656 closest distance to " CA  GLU A 152 " =    0.925
peak=    3.656 closest distance to " CB  TRP A 179 " =    1.506
peak=    3.654 closest distance to " CB  MET A  40 " =    0.835
peak=    3.652 closest distance to " CB  ILE A 120 " =    1.340
peak=    3.648 closest distance to " CD1 ILE A 106 " =    0.883
peak=    3.645 closest distance to " O   HOH Z 158 " =    2.990
peak=    3.644 closest distance to " O   HOH Z 196 " =    1.227
peak=    3.639 closest distance to " O   HOH Z  30 " =    1.494
peak=    3.637 closest distance to " O   HOH Z 126 " =    2.045
peak=    3.635 closest distance to " OE1 GLN A  11 " =    2.038
peak=    3.628 closest distance to " O   HOH Z 174 " =    2.327
peak=    3.626 closest distance to " CG  GLU A  37 " =    0.933
peak=    3.617 closest distance to " CD  ARG A  66 " =    2.402
peak=    3.615 closest distance to " O   HOH Z 280 " =    2.990
peak=    3.614 closest distance to " CB  SER A   3 " =    1.384
peak=    3.614 closest distance to " ND2 ASN A 249 " =    2.047
peak=    3.599 closest distance to " O   ASN A  74 " =    1.385
peak=    3.590 closest distance to " CA  ARG A  36 " =    1.179
peak=    3.581 closest distance to " O   HOH Z 147 " =    1.820
peak=    3.578 closest distance to " CA  ALA A 160 " =    0.945
peak=    3.576 closest distance to " O   HOH Z 163 " =    1.687
peak=    3.573 closest distance to " O   HOH Z  61 " =    1.590
peak=    3.565 closest distance to " CD1 LEU A  96 " =    0.745
peak=    3.564 closest distance to " N   CYS A 260 " =    0.817
peak=    3.563 closest distance to " O   HOH Z 281 " =    4.758
peak=    3.561 closest distance to " O   ALA A 158 " =    1.243
peak=    3.558 closest distance to " CB  GLU A  46 " =    0.986
peak=    3.558 closest distance to " CD2 LEU A 297 " =    0.937
peak=    3.550 closest distance to " CA  LYS A 117 " =    1.231
peak=    3.547 closest distance to " O   HOH Z 432 " =    1.799
peak=    3.545 closest distance to " OD2 ASP A 298 " =    3.903
peak=    3.540 closest distance to " CA  ASP A 162 " =    1.186
peak=    3.536 closest distance to " CG AARG A 275 " =    1.133
peak=    3.536 closest distance to " CB  LEU A  83 " =    0.809
peak=    3.535 closest distance to " CA  THR A 221 " =    0.906
peak=    3.526 closest distance to " O   HOH Z 197 " =    1.937
peak=    3.515 closest distance to " O   HOH Z 357 " =    2.125
peak=    3.514 closest distance to " O   HOH Z 245 " =    1.375
peak=    3.512 closest distance to " CB  ALA A 100 " =    1.323
peak=    3.501 closest distance to " O   HOH Z 426 " =    1.545
peak=    3.499 closest distance to " CA  ILE A 106 " =    0.838
peak=    3.496 closest distance to " CA  ALA A 295 " =    1.105
peak=    3.492 closest distance to " CB  ASN A 142 " =    1.137
peak=    3.490 closest distance to " CD  ARG A 159 " =    0.821
peak=    3.489 closest distance to " O   HOH Z 394 " =    1.709
peak=    3.488 closest distance to " CE  LYS A  76 " =    0.815
peak=    3.482 closest distance to " CG2 ILE A  20 " =    1.396
peak=    3.479 closest distance to " O   HOH Z  47 " =    1.311
peak=    3.475 closest distance to " O   HOH Z 316 " =    3.123
peak=    3.475 closest distance to " O   HOH Z 132 " =    2.813
peak=    3.472 closest distance to " NZ  LYS A 117 " =    3.195
peak=    3.472 closest distance to " CB  GLN A 103 " =    0.912
peak=    3.471 closest distance to " O   HOH Z 130 " =    2.246
peak=    3.468 closest distance to " CA  ASN A 217 " =    1.320
peak=    3.465 closest distance to " CZ  PHE A 192 " =    0.946
peak=    3.465 closest distance to " O   HOH Z   1 " =    2.814
peak=    3.456 closest distance to " O   HOH Z  59 " =    2.557
peak=    3.451 closest distance to " O   HOH Z 403 " =    1.483
peak=    3.448 closest distance to " O   HOH Z 346 " =    1.503
peak=    3.447 closest distance to " CG1 VAL A 153 " =    1.023
peak=    3.446 closest distance to " CG2 VAL A 197 " =    1.161
peak=    3.446 closest distance to " O   HOH Z 352 " =    1.941
peak=    3.443 closest distance to " N   ASN A 127 " =    1.252
peak=    3.439 closest distance to " CA  GLN A  88 " =    1.283
peak=    3.438 closest distance to " O   HOH Z 109 " =    2.497
peak=    3.426 closest distance to " O   HOH Z 180 " =    2.184
peak=    3.420 closest distance to " O   HOH Z 421 " =    1.661
peak=    3.420 closest distance to " CA  SER A  87 " =    1.033
peak=    3.419 closest distance to " OG BSER A 164 " =    2.401
peak=    3.417 closest distance to " O   HOH Z 125 " =    3.767
peak=    3.406 closest distance to " CZ3 TRP A 266 " =    1.059
peak=    3.405 closest distance to " O   HOH Z  44 " =    1.797
peak=    3.403 closest distance to " CG2 ILE A 120 " =    0.950
peak=    3.402 closest distance to " O   HOH Z 391 " =    3.009
peak=    3.396 closest distance to " O   ASP A 124 " =    1.242
peak=    3.396 closest distance to " O   HOH Z 279 " =    2.281
peak=    3.396 closest distance to " O   HOH Z 345 " =    1.716
peak=    3.391 closest distance to " O   HOH Z 176 " =    1.671
peak=    3.383 closest distance to " CA  VAL A 125 " =    1.150
peak=    3.383 closest distance to " CB  VAL A 265 " =    1.276
peak=    3.383 closest distance to " O   HOH Z 128 " =    2.203
peak=    3.382 closest distance to " CA  GLU A  46 " =    0.819
peak=    3.381 closest distance to " O   HOH Z 295 " =    1.504
peak=    3.381 closest distance to " CB  PHE A 204 " =    0.860
peak=    3.374 closest distance to " O   HOH Z  88 " =    3.557
peak=    3.371 closest distance to " N   ASP A 132 " =    1.057
peak=    3.370 closest distance to " O  BHOH Z 338 " =    2.172
peak=    3.369 closest distance to " N   GLY A  98 " =    1.165
peak=    3.368 closest distance to " CA  ALA A  84 " =    1.318
peak=    3.368 closest distance to " CG  ARG A 219 " =    1.197
peak=    3.367 closest distance to " O   HOH Z 135 " =    1.930
peak=    3.365 closest distance to " O   HOH Z 344 " =    3.149
peak=    3.359 closest distance to " O  BHOH Z  74 " =    1.200
peak=    3.357 closest distance to " O   HOH Z 371 " =    2.950
peak=    3.354 closest distance to " CG  MET A 185 " =    1.177
peak=    3.353 closest distance to " CB  ASN A 148 " =    1.981
peak=    3.352 closest distance to " O   HOH Z 294 " =    1.524
peak=    3.348 closest distance to " O   HOH Z  66 " =    2.143
peak=    3.347 closest distance to " O   HOH Z 417 " =    3.234
peak=    3.341 closest distance to " O   HOH Z 261 " =    1.853
peak=    3.339 closest distance to " NH1AARG A 145 " =    1.286
peak=    3.336 closest distance to " O   HOH Z 427 " =    3.073
peak=    3.335 closest distance to " OG  SER A  22 " =    2.828
peak=    3.334 closest distance to " CZ  PHE A  38 " =    1.259
peak=    3.330 closest distance to " O   HOH Z 419 " =    3.000
peak=    3.330 closest distance to " O   HOH Z  10 " =    1.821
peak=    3.322 closest distance to " CE1 TYR A 186 " =    1.239
peak=    3.321 closest distance to " O   GLN A 278 " =    1.174
peak=    3.320 closest distance to " O   HOH Z  78 " =    1.660
peak=    3.320 closest distance to " O   HOH Z 272 " =    1.970
peak=    3.319 closest distance to " NE2 GLN A  77 " =    3.395
peak=    3.319 closest distance to " C   SER A  32 " =    1.055
peak=    3.318 closest distance to " O   HOH Z 141 " =    1.611
peak=    3.317 closest distance to " O   HOH Z 353 " =    2.802
peak=    3.317 closest distance to " CB  THR A 157 " =    1.168
peak=    3.315 closest distance to " O   HOH Z 171 " =    3.895
peak=    3.312 closest distance to " O   HOH Z 411 " =    1.713
peak=    3.310 closest distance to " O   HOH Z 386 " =    2.391
peak=    3.310 closest distance to " O   HOH Z 133 " =    3.372
peak=    3.309 closest distance to " O   HOH Z  88 " =    1.805
peak=    3.307 closest distance to " CG  GLN A  58 " =    2.726
peak=    3.306 closest distance to " O   TRP A 274 " =    1.801
peak=    3.306 closest distance to " CB  HIS A 108 " =    0.822
peak=    3.306 closest distance to " CG2AVAL A  72 " =    1.896
peak=    3.298 closest distance to " CD BLYS A 290 " =    1.055
peak=    3.297 closest distance to " OG  SER A 245 " =    1.654
peak=    3.295 closest distance to " CB  ALA A  71 " =    1.268
peak=    3.289 closest distance to " O   HOH Z 164 " =    3.456
peak=    3.286 closest distance to " C   TYR A 214 " =    1.467
peak=    3.285 closest distance to " O   HOH Z 305 " =    3.831
peak=    3.283 closest distance to " O   HOH Z 258 " =    2.149
peak=    3.283 closest distance to " CB  ALA A   9 " =    1.613
peak=    3.277 closest distance to " CA  ILE A  33 " =    1.529
peak=    3.276 closest distance to " O   HOH Z 148 " =    3.228
peak=    3.270 closest distance to " CG2 THR A 220 " =    0.787
peak=    3.268 closest distance to " OG BSER A 134 " =    2.865
peak=    3.268 closest distance to " CG2 THR A  29 " =    1.376
peak=    3.265 closest distance to " CB  MET A 113 " =    1.822
peak=    3.264 closest distance to " CB  ASN A 127 " =    0.953
peak=    3.262 closest distance to " O   HOH Z 227 " =    1.712
peak=    3.262 closest distance to " CB  GLN A  88 " =    1.229
peak=    3.261 closest distance to " O   HOH Z 291 " =    1.511
peak=    3.261 closest distance to " O   HOH Z 173 " =    2.210
peak=    3.255 closest distance to " NE2 HIS A 115 " =    1.014
peak=    3.255 closest distance to " CB  SER A 212 " =    1.197
peak=    3.253 closest distance to " CA  ASN A 252 " =    2.174
peak=    3.249 closest distance to " CZ2 TRP A 179 " =    1.819
peak=    3.249 closest distance to " CB  SER A  62 " =    0.852
peak=    3.246 closest distance to " CB  ALA A 104 " =    0.754
peak=    3.245 closest distance to " ND1 HIS A  81 " =    1.650
peak=    3.243 closest distance to " O   HOH Z  20 " =    1.862
peak=    3.243 closest distance to " CD  PRO A  54 " =    1.061
peak=    3.238 closest distance to " CA  SER A  32 " =    1.701
peak=    3.234 closest distance to " CA  ALA A 233 " =    1.642
peak=    3.233 closest distance to " NZ  LYS A  48 " =    1.314
peak=    3.232 closest distance to " O   HOH Z 419 " =    1.723
peak=    3.232 closest distance to " O   HOH Z 367 " =    2.238
peak=    3.231 closest distance to " O   HOH Z 199 " =    1.592
peak=    3.231 closest distance to " OG  SER A  28 " =    1.543
peak=    3.229 closest distance to " CA  ASP A 124 " =    0.755
peak=    3.223 closest distance to " CB  ASP A 298 " =    1.225
peak=    3.222 closest distance to " CB  ASN A 285 " =    0.882
peak=    3.221 closest distance to " N   VAL A 126 " =    1.493
peak=    3.221 closest distance to " O   HOH Z 247 " =    1.470
peak=    3.218 closest distance to " O   HOH Z 437 " =    1.359
peak=    3.218 closest distance to " O   HOH Z 282 " =    1.993
peak=    3.218 closest distance to " CG  LEU A 167 " =    1.140
peak=    3.215 closest distance to " CG  GLN A  89 " =    1.472
peak=    3.213 closest distance to " CD  ARG A 195 " =    0.929
peak=    3.213 closest distance to " O   HOH Z 248 " =    1.814
peak=    3.210 closest distance to " O   HOH Z 156 " =    2.653
peak=    3.208 closest distance to " CA  LEU A 282 " =    1.010
peak=    3.208 closest distance to " O   HOH Z  88 " =    2.821
peak=    3.203 closest distance to " O   HOH Z 387 " =    2.712
peak=    3.203 closest distance to " O   HOH Z 365 " =    2.925
peak=    3.203 closest distance to " CA  MET A 105 " =    1.010
peak=    3.200 closest distance to " O   HOH Z 299 " =    4.528
peak=    3.199 closest distance to " O   HOH Z 298 " =    2.526
peak=    3.195 closest distance to " O   HOH Z 134 " =    2.541
peak=    3.192 closest distance to " CB  ALA A 242 " =    0.831
peak=    3.192 closest distance to " O   GLU A   2 " =    1.545
peak=    3.189 closest distance to " O   ILE A  20 " =    2.284
peak=    3.188 closest distance to " O   THR A 220 " =    1.142
peak=    3.187 closest distance to " O   HOH Z  78 " =    1.977
peak=    3.181 closest distance to " CG2 ILE A 106 " =    0.945
peak=    3.179 closest distance to " N   ARG A 190 " =    1.004
peak=    3.178 closest distance to " O   HOH Z 128 " =    1.771
peak=    3.178 closest distance to " CB  MET A  47 " =    0.985
peak=    3.172 closest distance to " CG2 ILE A 151 " =    0.792
peak=    3.165 closest distance to " O   HOH Z 313 " =    1.770
peak=    3.163 closest distance to " NH2AARG A 275 " =    3.366
peak=    3.162 closest distance to " CB  GLN A  89 " =    1.111
peak=    3.160 closest distance to " CB  ARG A 139 " =    0.947
peak=    3.154 closest distance to " O   HOH Z 422 " =    2.494
peak=    3.154 closest distance to " O   HOH Z  46 " =    1.539
peak=    3.151 closest distance to " O   TYR A 116 " =    1.324
peak=    3.146 closest distance to " CA  THR A 221 " =    1.342
peak=    3.143 closest distance to " O   HOH Z 325 " =    2.185
peak=    3.140 closest distance to " O   HOH Z 197 " =    2.565
peak=    3.136 closest distance to " O   HOH Z 116 " =    1.763
peak=    3.133 closest distance to " CA  LEU A  83 " =    1.450
peak=    3.129 closest distance to " N   TYR A  15 " =    0.726
peak=    3.123 closest distance to " O   HOH Z 251 " =    1.611
peak=    3.122 closest distance to " OD2 ASP A 200 " =    1.259
peak=    3.117 closest distance to " CG1 ILE A  49 " =    1.544
peak=    3.115 closest distance to " O   HOH Z 336 " =    1.807
peak=    3.114 closest distance to " NZ  LYS A 117 " =    1.684
peak=    3.110 closest distance to " CA  ALA A 100 " =    1.077
peak=    3.106 closest distance to " CD2 LEU A 255 " =    1.528
peak=    3.100 closest distance to " CZ3 TRP A  85 " =    0.975
peak=    3.098 closest distance to " O   HOH Z 145 " =    2.456
peak=    3.094 closest distance to " OD2 ASP A 298 " =    3.646
peak=    3.091 closest distance to " CB  ALA A  43 " =    0.856
peak=    3.090 closest distance to " O   HOH Z 355 " =    1.814
peak=    3.087 closest distance to " NE2 GLN A  58 " =    4.070
peak=    3.087 closest distance to " N   ALA A 158 " =    1.442
peak=    3.081 closest distance to " CA  GLN A 223 " =    0.877
peak=    3.075 closest distance to " CB  SER A 216 " =    0.824
peak=    3.074 closest distance to " O   HOH Z 261 " =    1.660
peak=    3.065 closest distance to " CB  PRO A 163 " =    4.135
peak=    3.062 closest distance to " CD1AILE A 234 " =    0.855
peak=    3.058 closest distance to " O   HOH Z 327 " =    1.677
peak=    3.052 closest distance to " O   HOH Z  88 " =    3.308
peak=    3.046 closest distance to " CG  ARG A 159 " =    0.945
peak=    3.041 closest distance to " O   HOH Z 188 " =    2.447
peak=    3.041 closest distance to " CB  ASN A 215 " =    1.171
peak=    3.026 closest distance to " CA  THR A 264 " =    0.821

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 225         
Filter by distance & map next to the model:
   mapped sites are within: 0.632 - 5.951
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 224 from: 225
   mapped sites are within: 0.749 - 5.951

peak=   -4.578 closest distance to " O   HOH Z 266 " =    5.153
peak=   -4.446 closest distance to " CD  ARG A 156 " =    2.102
peak=   -4.382 closest distance to " CG1 VAL A 112 " =    2.597
peak=   -4.363 closest distance to " CG1 VAL A 250 " =    2.733
peak=   -4.272 closest distance to " O   HOH Z 196 " =    2.566
peak=   -4.226 closest distance to " O   HOH Z   5 " =    1.603
peak=   -4.223 closest distance to " O   HOH Z 210 " =    0.749
peak=   -4.207 closest distance to " O   VAL A  67 " =    2.666
peak=   -4.129 closest distance to " O   HOH Z 377 " =    1.070
peak=   -4.122 closest distance to " CD  GLN A 223 " =    1.332
peak=   -4.071 closest distance to " CD  GLN A  58 " =    0.982
peak=   -4.067 closest distance to " O   HOH Z 290 " =    1.058
peak=   -4.061 closest distance to " CB  PRO A 243 " =    2.697
peak=   -4.049 closest distance to " O   HOH Z 166 " =    1.620
peak=   -4.039 closest distance to " CE2 TYR A  30 " =    2.718
peak=   -4.032 closest distance to " O   HOH Z 231 " =    2.403
peak=   -4.025 closest distance to " OG  SER A  97 " =    2.220
peak=   -4.007 closest distance to " O   HOH Z 283 " =    2.284
peak=   -4.006 closest distance to " CD1 LEU A 101 " =    2.573
peak=   -3.991 closest distance to " O   PRO A 198 " =    1.303
peak=   -3.968 closest distance to " CH2 TRP A 179 " =    1.174
peak=   -3.952 closest distance to " C   ASN A 285 " =    2.461
peak=   -3.946 closest distance to " OXT GLY A 302 " =    2.977
peak=   -3.940 closest distance to " CD1 PHE A  59 " =    1.929
peak=   -3.927 closest distance to " N   ALA A  43 " =    2.692
peak=   -3.896 closest distance to " O   HOH Z  13 " =    1.678
peak=   -3.874 closest distance to " O   HOH Z 150 " =    1.068
peak=   -3.861 closest distance to " O   HOH Z 185 " =    2.477
peak=   -3.853 closest distance to " O   HOH Z 394 " =    1.513
peak=   -3.846 closest distance to " C   HIS A 108 " =    1.137
peak=   -3.838 closest distance to " O   PRO A 163 " =    2.182
peak=   -3.830 closest distance to " OD1 ASN A 148 " =    1.526
peak=   -3.816 closest distance to " O   HOH Z  52 " =    1.714
peak=   -3.812 closest distance to " ND2 ASN A  45 " =    1.926
peak=   -3.802 closest distance to " CG  ARG A  66 " =    2.510
peak=   -3.793 closest distance to " CB  ALA A 161 " =    2.675
peak=   -3.767 closest distance to " CB  ASP A 132 " =    2.405
peak=   -3.760 closest distance to " CD2 TYR A 293 " =    2.069
peak=   -3.755 closest distance to " C   SER A 206 " =    1.493
peak=   -3.734 closest distance to " CD  ARG A  14 " =    3.386
peak=   -3.729 closest distance to " O   HOH Z 234 " =    4.445
peak=   -3.729 closest distance to " O   HOH Z 292 " =    4.634
peak=   -3.714 closest distance to " CD  PRO A 213 " =    2.281
peak=   -3.705 closest distance to " CA  ASP A 298 " =    1.106
peak=   -3.696 closest distance to " O   HOH Z  19 " =    2.186
peak=   -3.682 closest distance to " CE2 PHE A  61 " =    2.568
peak=   -3.678 closest distance to " NH2 ARG A  66 " =    1.772
peak=   -3.669 closest distance to " CB  ALA A  10 " =    2.164
peak=   -3.653 closest distance to " CB  ALA A  43 " =    2.582
peak=   -3.636 closest distance to " NE2 GLN A 103 " =    1.809
peak=   -3.623 closest distance to " O   HOH Z  15 " =    1.479
peak=   -3.617 closest distance to " CB  PHE A 208 " =    2.322
peak=   -3.610 closest distance to " O   ALA A  34 " =    2.553
peak=   -3.607 closest distance to " O   SER A 210 " =    1.960
peak=   -3.607 closest distance to " CG1 VAL A 265 " =    2.399
peak=   -3.586 closest distance to " O   ALA A  10 " =    1.757
peak=   -3.586 closest distance to " O   HOH Z 353 " =    2.278
peak=   -3.584 closest distance to " O   HOH Z 150 " =    1.895
peak=   -3.572 closest distance to " O   HOH Z 252 " =    3.890
peak=   -3.568 closest distance to " O   HOH Z  71 " =    1.674
peak=   -3.565 closest distance to " CD  ARG A 139 " =    1.572
peak=   -3.564 closest distance to " O   HOH Z  38 " =    1.308
peak=   -3.550 closest distance to " CG  ASP A 231 " =    0.846
peak=   -3.545 closest distance to " CG  MET A 105 " =    0.899
peak=   -3.541 closest distance to " O   HOH Z 166 " =    1.875
peak=   -3.540 closest distance to " CD2 LEU A 300 " =    2.959
peak=   -3.528 closest distance to " CD  GLN A  88 " =    0.836
peak=   -3.528 closest distance to " ND2 ASN A 187 " =    1.684
peak=   -3.516 closest distance to " CH2 TRP A 177 " =    2.106
peak=   -3.500 closest distance to " O   HOH Z 200 " =    1.426
peak=   -3.498 closest distance to " OD1 ASP A 191 " =    1.693
peak=   -3.496 closest distance to " O   HOH Z 236 " =    1.472
peak=   -3.493 closest distance to " CA  GLY A 133 " =    2.354
peak=   -3.486 closest distance to " O   HOH Z 264 " =    1.820
peak=   -3.479 closest distance to " C   LEU A 143 " =    1.185
peak=   -3.478 closest distance to " O   HOH Z 426 " =    1.701
peak=   -3.472 closest distance to " O   HOH Z 351 " =    1.529
peak=   -3.470 closest distance to " OE1 GLN A 223 " =    2.123
peak=   -3.465 closest distance to " CB  ALA A 291 " =    2.237
peak=   -3.462 closest distance to " ND2 ASN A 249 " =    2.413
peak=   -3.454 closest distance to " C   ALA A 158 " =    1.381
peak=   -3.446 closest distance to " O   HOH Z 197 " =    2.109
peak=   -3.442 closest distance to " NH2AARG A 275 " =    5.431
peak=   -3.440 closest distance to " O   HOH Z 177 " =    1.777
peak=   -3.439 closest distance to " CA  GLY A 241 " =    2.358
peak=   -3.439 closest distance to " CG  LYS A 193 " =    2.661
peak=   -3.434 closest distance to " CG  GLU A  53 " =    1.569
peak=   -3.433 closest distance to " CD1 TRP A 179 " =    1.019
peak=   -3.431 closest distance to " CD1 ILE A 151 " =    2.442
peak=   -3.430 closest distance to " O   HOH Z 298 " =    2.660
peak=   -3.426 closest distance to " O   HOH Z 377 " =    2.083
peak=   -3.423 closest distance to " O   SER A 276 " =    1.709
peak=   -3.423 closest distance to " O   HOH Z 165 " =    1.882
peak=   -3.416 closest distance to " O   HOH Z 136 " =    2.060
peak=   -3.409 closest distance to " O   HOH Z   6 " =    1.487
peak=   -3.406 closest distance to " SG  CYS A 168 " =    1.135
peak=   -3.401 closest distance to " O   HOH Z 372 " =    2.565
peak=   -3.397 closest distance to " O   HOH Z 150 " =    2.076
peak=   -3.395 closest distance to " CG1 VAL A  78 " =    2.757
peak=   -3.394 closest distance to " O   HOH Z  90 " =    1.829
peak=   -3.391 closest distance to " O   HOH Z 111 " =    1.964
peak=   -3.390 closest distance to " CG  ARG A 269 " =    2.327
peak=   -3.379 closest distance to " CB  PRO A 163 " =    2.636
peak=   -3.377 closest distance to " O   HOH Z  49 " =    1.269
peak=   -3.374 closest distance to " O   HOH Z 407 " =    3.751
peak=   -3.374 closest distance to " C   ARG A  79 " =    2.626
peak=   -3.373 closest distance to " O   HOH Z 275 " =    1.540
peak=   -3.369 closest distance to " CA  GLY A 203 " =    2.268
peak=   -3.366 closest distance to " CG1 VAL A 112 " =    2.904
peak=   -3.364 closest distance to " CG2 VAL A 189 " =    2.209
peak=   -3.362 closest distance to " CD  GLN A 223 " =    0.896
peak=   -3.360 closest distance to " O   HOH Z 396 " =    1.863
peak=   -3.358 closest distance to " NE1 TRP A 266 " =    2.313
peak=   -3.355 closest distance to " NH2 ARG A 159 " =    2.400
peak=   -3.354 closest distance to " CG2BVAL A  41 " =    1.625
peak=   -3.349 closest distance to " CZ  PHE A  38 " =    1.966
peak=   -3.348 closest distance to " O   HOH Z 111 " =    1.467
peak=   -3.342 closest distance to " CE3 TRP A 150 " =    2.107
peak=   -3.340 closest distance to " CE BMET A  47 " =    2.157
peak=   -3.340 closest distance to " O   HOH Z 311 " =    3.865
peak=   -3.339 closest distance to " CD2 PHE A  61 " =    1.979
peak=   -3.337 closest distance to " C   ILE A 234 " =    1.235
peak=   -3.329 closest distance to " O   HOH Z 275 " =    1.879
peak=   -3.328 closest distance to " ND2 ASN A  45 " =    1.181
peak=   -3.328 closest distance to " CB  PHE A  16 " =    2.643
peak=   -3.327 closest distance to " O   VAL A  67 " =    2.964
peak=   -3.326 closest distance to " OG BSER A 210 " =    1.422
peak=   -3.324 closest distance to " CB  ALA A 291 " =    2.388
peak=   -3.321 closest distance to " N   SER A 276 " =    1.524
peak=   -3.318 closest distance to " CG1 VAL A 197 " =    2.326
peak=   -3.317 closest distance to " CA  GLY A 241 " =    3.143
peak=   -3.316 closest distance to " O   HOH Z 128 " =    2.566
peak=   -3.315 closest distance to " O   HOH Z  17 " =    1.442
peak=   -3.313 closest distance to " N   ASP A 171 " =    2.420
peak=   -3.312 closest distance to " O   HOH Z 241 " =    1.163
peak=   -3.312 closest distance to " CB  ALA A   9 " =    2.650
peak=   -3.307 closest distance to " CG  PRO A 243 " =    1.852
peak=   -3.305 closest distance to " CB  PHE A 192 " =    1.951
peak=   -3.304 closest distance to " O   HOH Z 106 " =    2.041
peak=   -3.302 closest distance to " O   HOH Z 313 " =    1.308
peak=   -3.300 closest distance to " OD2 ASP A 171 " =    1.947
peak=   -3.300 closest distance to " ND2 ASN A  60 " =    1.848
peak=   -3.299 closest distance to " NE2 GLN A 194 " =    1.948
peak=   -3.295 closest distance to " O   HOH Z  43 " =    1.404
peak=   -3.293 closest distance to " O   HOH Z 351 " =    1.446
peak=   -3.291 closest distance to " O   ALA A   1 " =    1.926
peak=   -3.288 closest distance to " CB  ASP A 286 " =    2.184
peak=   -3.285 closest distance to " O   GLY A 118 " =    2.270
peak=   -3.285 closest distance to " OG BSER A 210 " =    2.186
peak=   -3.281 closest distance to " OH  TYR A 247 " =    2.201
peak=   -3.281 closest distance to " C   THR A 279 " =    1.059
peak=   -3.280 closest distance to " O   ASN A 301 " =    1.357
peak=   -3.277 closest distance to " CD1 ILE A 263 " =    1.963
peak=   -3.276 closest distance to " O   HOH Z  58 " =    1.227
peak=   -3.271 closest distance to " CG1 VAL A 112 " =    2.871
peak=   -3.269 closest distance to " C   VAL A 121 " =    1.645
peak=   -3.267 closest distance to " CG  LYS A 166 " =    2.173
peak=   -3.265 closest distance to " NE2 GLN A  88 " =    1.073
peak=   -3.265 closest distance to " OH  TYR A 169 " =    0.975
peak=   -3.263 closest distance to " CD1 LEU A 228 " =    2.421
peak=   -3.260 closest distance to " CD2 PHE A 225 " =    1.320
peak=   -3.259 closest distance to " CG  PRO A 163 " =    2.379
peak=   -3.258 closest distance to " O   HOH Z 283 " =    5.951
peak=   -3.257 closest distance to " O   HOH Z 211 " =    1.584
peak=   -3.252 closest distance to " OG  SER A  62 " =    1.628
peak=   -3.247 closest distance to " CB  ALA A 114 " =    2.499
peak=   -3.246 closest distance to " O   HOH Z 368 " =    1.820
peak=   -3.246 closest distance to " O   HOH Z 117 " =    4.481
peak=   -3.242 closest distance to " CD2 PHE A  59 " =    2.529
peak=   -3.238 closest distance to " O   HOH Z 353 " =    2.240
peak=   -3.228 closest distance to " CB  TRP A  85 " =    2.492
peak=   -3.227 closest distance to " OG  SER A  26 " =    1.340
peak=   -3.226 closest distance to " O   HOH Z 156 " =    3.510
peak=   -3.223 closest distance to " O   HOH Z 193 " =    2.024
peak=   -3.219 closest distance to " NH2 ARG A  79 " =    1.635
peak=   -3.216 closest distance to " O   HOH Z  11 " =    1.890
peak=   -3.216 closest distance to " O   HOH Z 114 " =    1.463
peak=   -3.216 closest distance to " C   ASN A 187 " =    1.908
peak=   -3.214 closest distance to " O   SER A 271 " =    2.125
peak=   -3.211 closest distance to " N   SER A   3 " =    2.126
peak=   -3.203 closest distance to " O   ASP A  27 " =    2.093
peak=   -3.202 closest distance to " O   HOH Z 409 " =    4.638
peak=   -3.201 closest distance to " OD2 ASP A 171 " =    2.535
peak=   -3.194 closest distance to " N   ALA A 226 " =    2.122
peak=   -3.192 closest distance to " O   HOH Z  88 " =    2.449
peak=   -3.191 closest distance to " OG BSER A 134 " =    1.930
peak=   -3.188 closest distance to " O   HOH Z 414 " =    1.534
peak=   -3.187 closest distance to " O   PHE A 218 " =    1.512
peak=   -3.187 closest distance to " O   GLY A 211 " =    1.472
peak=   -3.183 closest distance to " OD1 ASP A 171 " =    1.586
peak=   -3.179 closest distance to " O   HOH Z  37 " =    1.958
peak=   -3.174 closest distance to " O   HOH Z 350 " =    1.968
peak=   -3.164 closest distance to " CB  SER A 146 " =    2.227
peak=   -3.164 closest distance to " OH  TYR A 247 " =    1.819
peak=   -3.162 closest distance to " CD1 TYR A 247 " =    2.164
peak=   -3.151 closest distance to " C   GLY A 262 " =    2.082
peak=   -3.146 closest distance to " C   GLY A  17 " =    1.307
peak=   -3.143 closest distance to " O   HOH Z 326 " =    5.047
peak=   -3.141 closest distance to " O   HOH Z 232 " =    1.628
peak=   -3.139 closest distance to " CG1 VAL A 125 " =    2.064
peak=   -3.136 closest distance to " CZ  TYR A 169 " =    1.814
peak=   -3.136 closest distance to " O   HOH Z 149 " =    2.016
peak=   -3.135 closest distance to " N   GLN A  58 " =    1.620
peak=   -3.131 closest distance to " O   VAL A 125 " =    2.241
peak=   -3.129 closest distance to " O   HOH Z 417 " =    2.733
peak=   -3.127 closest distance to " SD  MET A 188 " =    2.325
peak=   -3.126 closest distance to " CG  ASN A 301 " =    1.963
peak=   -3.126 closest distance to " CG  TRP A 266 " =    1.831
peak=   -3.109 closest distance to " O   HOH Z 371 " =    1.611
peak=   -3.108 closest distance to " O   HOH Z 259 " =    1.974
peak=   -3.102 closest distance to " CG  ARG A 219 " =    2.748
peak=   -3.099 closest distance to " O   LEU A 101 " =    2.872
peak=   -3.098 closest distance to " ND2 ASN A  60 " =    1.558
peak=   -3.097 closest distance to " O   HOH Z 422 " =    1.492
peak=   -3.096 closest distance to " O   HOH Z  90 " =    3.651
peak=   -3.093 closest distance to " N   GLY A  23 " =    2.234
peak=   -3.091 closest distance to " O   HOH Z  40 " =    2.220
peak=   -3.090 closest distance to " CG2 THR A 221 " =    2.290
peak=   -3.079 closest distance to " O   HOH Z 322 " =    1.412
peak=   -3.064 closest distance to " CE  MET A  93 " =    1.786
peak=   -3.060 closest distance to " CA  SER A  62 " =    2.492
peak=   -3.055 closest distance to " CD2 LEU A 237 " =    2.898
peak=   -3.018 closest distance to " O   HOH Z 174 " =    2.086
peak=   -3.004 closest distance to " NH2 ARG A  66 " =    1.499

================= 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    :  0.4184 0.4018   6.224051e+00   6.195771e+00
   1_bss:  0.4086 0.3924   6.212967e+00   6.180579e+00
   1_xyz:  0.2777 0.3042   5.908192e+00   5.982202e+00
   1_adp:  0.2561 0.3071   5.856293e+00   5.990553e+00
   1_occ:  0.2558 0.3065   5.855214e+00   5.989741e+00
   2_bss:  0.2542 0.3045   5.852210e+00   5.986960e+00
   2_xyz:  0.1848 0.2197   5.553271e+00   5.709970e+00
   2_adp:  0.1632 0.2068   5.462166e+00   5.652594e+00
   2_occ:  0.1630 0.2068   5.461400e+00   5.652070e+00
   3_bss:  0.1627 0.2071   5.459262e+00   5.649597e+00
   3_xyz:  0.1323 0.1791   5.290333e+00   5.517770e+00
   3_adp:  0.1260 0.1732   5.247583e+00   5.480697e+00
   3_occ:  0.1259 0.1731   5.247184e+00   5.480377e+00
   4_bss:  0.1263 0.1727   5.247936e+00   5.478910e+00
   4_xyz:  0.1231 0.1702   5.227572e+00   5.458170e+00
   4_adp:  0.1224 0.1678   5.220371e+00   5.449064e+00
   4_occ:  0.1224 0.1677   5.220136e+00   5.449254e+00
   5_bss:  0.1223 0.1677   5.219962e+00   5.448982e+00
   5_xyz:  0.1153 0.1648   5.179692e+00   5.425626e+00
   5_adp:  0.1153 0.1636   5.177402e+00   5.421502e+00
   5_occ:  0.1152 0.1636   5.177226e+00   5.421652e+00
   5_bss:  0.1152 0.1635   5.177194e+00   5.421591e+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:  0.298  50.001  -1.059   4.565  -1.308   0.000  -0.000  -0.000
   1_xyz:  0.298  50.001  -1.059   4.565  -1.308   0.000  -0.000  -0.000
   1_adp:  0.298  50.001  -1.059   4.565  -1.308   0.000  -0.000  -0.000
   1_occ:  0.298  50.001  -1.059   4.565  -1.308   0.000  -0.000  -0.000
   2_bss:  0.328  68.842  -1.497   1.376  -0.843   0.000  -0.000  -0.000
   2_xyz:  0.328  68.842  -1.497   1.376  -0.843   0.000  -0.000  -0.000
   2_adp:  0.328  68.842  -1.497   1.376  -0.843   0.000  -0.000  -0.000
   2_occ:  0.328  68.842  -1.497   1.376  -0.843   0.000  -0.000  -0.000
   3_bss:  0.331  79.300  -1.605  -0.126  -0.680  -0.000  -0.000  -0.000
   3_xyz:  0.331  79.300  -1.605  -0.126  -0.680  -0.000  -0.000  -0.000
   3_adp:  0.331  79.300  -1.605  -0.126  -0.680  -0.000  -0.000  -0.000
   3_occ:  0.331  79.300  -1.605  -0.126  -0.680  -0.000  -0.000  -0.000
   4_bss:  0.332  77.338  -1.349  -0.504  -0.282  -0.000  -0.000  -0.000
   4_xyz:  0.332  77.338  -1.349  -0.504  -0.282  -0.000  -0.000  -0.000
   4_adp:  0.332  77.338  -1.349  -0.504  -0.282  -0.000  -0.000  -0.000
   4_occ:  0.332  77.338  -1.349  -0.504  -0.282  -0.000  -0.000  -0.000
   5_bss:  0.325  70.159  -1.250  -0.634  -0.121  -0.000  -0.000  -0.000
   5_xyz:  0.325  70.159  -1.250  -0.634  -0.121  -0.000  -0.000  -0.000
   5_adp:  0.325  70.159  -1.250  -0.634  -0.121  -0.000  -0.000  -0.000
   5_occ:  0.325  70.159  -1.250  -0.634  -0.121  -0.000  -0.000  -0.000
   5_bss:  0.319  65.149  -1.174  -0.662  -0.050  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  45.762 0.5748  0.7285    49612.938
   1_bss:  45.074 0.5817  0.7576    46979.558
   1_xyz:  32.267 0.7330  0.9187    25448.612
   1_adp:  32.529 0.7297  0.9030    25825.220
   1_occ:  32.526 0.7296  0.9024    25758.991
   2_bss:  32.229 0.7330  0.8775    25474.259
   2_xyz:  22.114 0.8399  0.9659    12535.006
   2_adp:  20.221 0.8592  0.9653    11064.028
   2_occ:  20.204 0.8594  0.9654    11050.701
   3_bss:  20.107 0.8603  0.9504    10969.771
   3_xyz:  16.951 0.8895  0.9674     8169.700
   3_adp:  15.946 0.8988  0.9607     7648.096
   3_occ:  15.935 0.8989  0.9605     7644.522
   4_bss:  15.923 0.8990  0.9642     7629.662
   4_xyz:  15.431 0.9033  0.9664     7274.846
   4_adp:  15.180 0.9057  0.9590     7174.252
   4_occ:  15.182 0.9056  0.9589     7175.756
   5_bss:  15.179 0.9057  0.9605     7169.188
   5_xyz:  14.736 0.9091  0.9636     6838.370
   5_adp:  14.609 0.9103  0.9565     6813.819
   5_occ:  14.607 0.9103  0.9565     6816.558
   5_bss:  14.607 0.9103  0.9580     6813.434
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.114   1.6630e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.114   1.6630e-01
   1_xyz:   1.563  0.014  0.096 15.735  0.006  4.119   1.2453e-01
   1_adp:   1.563  0.014  0.096 15.735  0.006  4.119   1.2453e-01
   1_occ:   1.563  0.014  0.096 15.735  0.006  4.119   1.2453e-01
   2_bss:   1.563  0.014  0.096 15.735  0.006  4.119   1.2453e-01
   2_xyz:   1.231  0.011  0.081 14.844  0.005  4.114   9.6115e-02
   2_adp:   1.231  0.011  0.081 14.844  0.005  4.114   9.6115e-02
   2_occ:   1.231  0.011  0.081 14.844  0.005  4.114   9.6115e-02
   3_bss:   1.231  0.011  0.081 14.844  0.005  4.114   9.6115e-02
   3_xyz:   1.159  0.011  0.081 15.014  0.004  4.126   7.9339e-02
   3_adp:   1.159  0.011  0.081 15.014  0.004  4.126   7.9339e-02
   3_occ:   1.159  0.011  0.081 15.014  0.004  4.126   7.9339e-02
   4_bss:   1.159  0.011  0.081 15.014  0.004  4.126   7.9339e-02
   4_xyz:   1.014  0.008  0.074 14.782  0.004  4.117   6.2197e-02
   4_adp:   1.014  0.008  0.074 14.782  0.004  4.117   6.2197e-02
   4_occ:   1.014  0.008  0.074 14.782  0.004  4.117   6.2197e-02
   5_bss:   1.014  0.008  0.074 14.782  0.004  4.117   6.2197e-02
   5_xyz:   1.145  0.011  0.086 15.007  0.004  4.122   7.9775e-02
   5_adp:   1.145  0.011  0.086 15.007  0.004  4.122   7.9775e-02
   5_occ:   1.145  0.011  0.086 15.007  0.004  4.122   7.9775e-02
   5_bss:   1.145  0.011  0.086 15.007  0.004  4.122   7.9775e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.432   2.4474e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.432   2.4474e-01
   1_xyz:  11.075  0.103  0.332 88.730  0.037  2.056   1.0545e-01
   1_adp:  11.075  0.103  0.332 88.730  0.037  2.056   1.0545e-01
   1_occ:  11.075  0.103  0.332 88.730  0.037  2.056   1.0545e-01
   2_bss:  11.075  0.103  0.332 88.730  0.037  2.056   1.0545e-01
   2_xyz:   8.701  0.075  0.279 86.013  0.048  2.273   2.4630e-01
   2_adp:   8.701  0.075  0.279 86.013  0.048  2.273   2.4630e-01
   2_occ:   8.701  0.075  0.279 86.013  0.048  2.273   2.4630e-01
   3_bss:   8.701  0.075  0.279 86.013  0.048  2.273   2.4630e-01
   3_xyz:   8.329  0.068  0.243 81.709  0.044  2.218   5.9986e-02
   3_adp:   8.329  0.068  0.243 81.709  0.044  2.218   5.9986e-02
   3_occ:   8.329  0.068  0.243 81.709  0.044  2.218   5.9986e-02
   4_bss:   8.329  0.068  0.243 81.709  0.044  2.218   5.9986e-02
   4_xyz:   7.831  0.046  0.229 82.262  0.043  2.382   3.7961e-02
   4_adp:   7.831  0.046  0.229 82.262  0.043  2.382   3.7961e-02
   4_occ:   7.831  0.046  0.229 82.262  0.043  2.382   3.7961e-02
   5_bss:   7.831  0.046  0.229 82.262  0.043  2.382   3.7961e-02
   5_xyz:   8.435  0.049  0.285 81.918  0.040  2.309   5.7536e-02
   5_adp:   8.435  0.049  0.285 81.918  0.040  2.309   5.7536e-02
   5_occ:   8.435  0.049  0.285 81.918  0.040  2.309   5.7536e-02
   5_bss:   8.435  0.049  0.285 81.918  0.040  2.309   5.7536e-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:  95.51   0.00  16.85  95.51   0.00  13.00  68.15   3.15  37.78
   1_occ:  95.51   0.00  16.85  95.51   0.00  13.00  68.15   3.15  37.78
   2_bss:  95.51   0.00  16.85  95.51   0.00  13.00  68.15   3.15  37.78
   2_xyz:  95.51   0.00  16.85  95.51   0.00  13.00  68.15   3.15  37.78
   2_adp:  97.11   0.00  17.79  91.09   0.00  13.06  97.11   4.04  43.50
   2_occ:  97.11   0.00  17.79  91.09   0.00  13.06  97.11   4.04  43.50
   3_bss:  97.11   0.00  17.79  91.09   0.00  13.06  97.11   4.04  43.50
   3_xyz:  97.11   0.00  17.79  91.09   0.00  13.06  97.11   4.04  43.50
   3_adp: 104.03   0.00  17.35 101.36   0.00  12.52 104.03   0.00  43.70
   3_occ: 104.03   0.00  17.35 101.36   0.00  12.52 104.03   0.00  43.70
   4_bss: 104.03   0.00  17.35 101.36   0.00  12.52 104.03   0.00  43.70
   4_xyz: 104.03   0.00  17.35 101.36   0.00  12.52 104.03   0.00  43.70
   4_adp: 102.30   0.00  16.66  99.59   0.00  12.11 102.30   0.20  41.45
   4_occ: 102.30   0.00  16.66  99.59   0.00  12.11 102.30   0.20  41.45
   5_bss: 102.30   0.00  16.66  99.59   0.00  12.11 102.30   0.20  41.45
   5_xyz: 102.30   0.00  16.66  99.59   0.00  12.11 102.30   0.20  41.45
   5_adp:  95.90   0.00  16.01  95.90   0.00  11.76  95.03   1.94  39.16
   5_occ:  95.90   0.00  16.01  95.90   0.00  11.76  95.03   1.94  39.16
   5_bss:  95.90   0.00  16.01  95.90   0.00  11.76  95.03   1.95  39.17
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.566    0.018    0.440
   1_adp:    1.566    0.018    0.440
   1_occ:    1.566    0.018    0.440
   2_bss:    1.566    0.018    0.440
   2_xyz:    1.266    0.030    0.567
   2_adp:    1.266    0.030    0.567
   2_occ:    1.266    0.030    0.567
   3_bss:    1.266    0.030    0.567
   3_xyz:    1.333    0.054    0.644
   3_adp:    1.333    0.054    0.644
   3_occ:    1.333    0.054    0.644
   4_bss:    1.333    0.054    0.644
   4_xyz:    1.314    0.039    0.663
   4_adp:    1.314    0.039    0.663
   4_occ:    1.314    0.039    0.663
   5_bss:    1.314    0.039    0.663
   5_xyz:    1.336    0.142    0.683
   5_adp:    1.336    0.142    0.683
   5_occ:    1.336    0.142    0.683
   5_bss:    1.336    0.142    0.683
------------------------------------------------------------------------

CPU time actual refinement: 327.16


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1073/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_1073/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1073/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1073/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_1073/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 327.02 
  Macro-tasks:
    bulk solvent and scale       = 49.46  
    individual site refinement   = 127.96 
    weights calculation          = 28.56  
    collect and process          = 6.59   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 212.66 
  Micro-tasks:
    mask                            = 1.86   
    f_calc                          = 99.20  
    alpha_beta                      = 8.26   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 107.53 
    fmodel                         = 8.00   
    r_factors                      = 0.24   
    phase_errors                   = 11.06  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 237.62 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.678 micro seconds
Total CPU time: 5.67 minutes
from_scatterers_fft:    626 calls, 98.84 s
gradients_fft:          571 calls, 94.73 s

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

# Date 2008-01-16 Time 06:21:45 PST -0800 (1200493305.88 s)
Start R-work = 0.4184, R-free = 0.4018 (no bulk solvent and anisotropic scale)
Final R-work = 0.1327, R-free = 0.1782 (no bulk solvent and anisotropic scale)

Start R-work = 0.4086, R-free = 0.3924
Final R-work = 0.1152, R-free = 0.1635