# Date 2008-01-16 Time 04:49:25 PST -0800 (1200487765.19 s)
#phil __OFF__

Command line arguments: "../477.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 13774
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 477

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.5475, 48.1033, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 48.1033, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.023 1.98063
Completeness in resolution range: 0.949724
Completeness with d_max=infinity: 0.946832

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0230
                             d_min =   1.9806

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.5475, 48.1033, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.023 1.98063
Completeness in resolution range: 0.949724
Completeness with d_max=infinity: 0.946832

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0234 -  4.2382 [2168/2197]  1952   216  10.0%
  bin  2:  4.2382 -  3.3765 [2080/2103]  1873   207  10.0%
  bin  3:  3.3765 -  2.9534 [2062/2087]  1850   212  10.3%
  bin  4:  2.9534 -  2.6851 [2022/2038]  1827   195   9.6%
  bin  5:  2.6851 -  2.4935 [2005/2049]  1795   210  10.5%
  bin  6:  2.4935 -  2.3471 [2021/2049]  1831   190   9.4%
  bin  7:  2.3471 -  2.2299 [2006/2042]  1799   207  10.3%
  bin  8:  2.2299 -  2.1332 [1979/2021]  1787   192   9.7%
  bin  9:  2.1332 -  2.0513 [1981/2027]  1780   201  10.1%
  bin 10:  2.0513 -  1.9806 [1265/2013]  1136   129  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_477/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:
        1.78 -     2.40: 25
        2.40 -     3.03: 2098
        3.03 -     3.65: 4634
        3.65 -     4.28: 9041
        4.28 -     4.90: 12404
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.780 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  18 " - " O   HOH Z 102 "  1.833 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.857 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.879 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 28197 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_477/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_477/model_refine_001.geo

CPU time processing inputs: 9.07


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.5475 48.10325 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4292   r_free= 0.4140   ksol= 0.00   Bsol= 0.00   scale= 0.909    |
|                                                                             |
| 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:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.248920                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0234 -  4.7271 0.99   1405  158 0.3554 0.3927      6.5346      6.5817|
|  2:  4.7271 -  3.7716 0.99   1350  151 0.3775 0.3756       6.795      6.7776|
|  3:  3.7716 -  3.3006 0.99   1330  146 0.3962 0.3681      6.6408      6.6068|
|  4:  3.3006 -  3.0015 0.99   1322  137 0.4098 0.3611      6.4699      6.3515|
|  5:  3.0015 -  2.7878 0.98   1306  150 0.4613 0.4069      6.3545      6.3122|
|  6:  2.7878 -  2.6243 0.99   1303  147 0.4598 0.4140      6.2539      6.0915|
|  7:  2.6243 -  2.4935 0.98   1281  151 0.4614 0.4018      6.2296      6.1061|
|  8:  2.4935 -  2.3854 0.99   1313  133 0.4562 0.4789      6.1385      6.1468|
|  9:  2.3854 -  2.2939 0.99   1296  148 0.4788 0.4643      6.0885      6.1312|
| 10:  2.2939 -  2.2150 0.98   1275  143 0.4633 0.4683      6.0854      6.0748|
| 11:  2.2150 -  2.1460 0.97   1282  148 0.4763 0.4444      6.0087      5.9643|
| 12:  2.1460 -  2.0848 0.99   1273  142 0.4677 0.4645      5.9293      5.9761|
| 13:  2.0848 -  2.0300 0.94   1258  129 0.4670 0.4558      5.8422       5.839|
| 14:  2.0300 -  1.9806 0.50    636   76 0.4533 0.4743      5.8032      5.6785|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0234 -  4.7271  1405   158  0.68  36.02   0.83     0.71      76753.94|
|  2:  4.7271 -  3.7716  1350   151  0.73  32.38   0.92     0.82      90668.05|
|  3:  3.7716 -  3.3006  1330   146  0.68  37.18   0.93     0.85      88593.42|
|  4:  3.3006 -  3.0015  1322   137  0.64  40.31   0.93     0.83      70555.17|
|  5:  3.0015 -  2.7878  1306   150  0.58  45.38   0.90     0.79      57106.28|
|  6:  2.7878 -  2.6243  1303   147  0.57  46.48   0.91     0.74      47402.32|
|  7:  2.6243 -  2.4935  1281   151  0.55  47.66   0.94     0.73      46088.19|
|  8:  2.4935 -  2.3854  1313   133  0.52  50.95   0.94     0.70      44827.26|
|  9:  2.3854 -  2.2939  1296   148  0.50  52.42   0.92     0.71      42701.66|
| 10:  2.2939 -  2.2150  1275   143  0.52  50.80   0.96     0.71      37714.79|
| 11:  2.2150 -  2.1460  1282   148  0.52  50.82   0.95     0.76      34180.35|
| 12:  2.1460 -  2.0848  1273   142  0.51  51.79   0.98     0.74      32109.68|
| 13:  2.0848 -  2.0300  1258   129  0.47  54.78   0.96     0.69      29256.10|
| 14:  2.0300 -  1.9806   636    76  0.42  58.65   1.00     0.58      26334.55|
|alpha:            min =        0.58 max =            0.85 mean =         0.74|
|beta:             min =    26334.55 max =        90668.05 mean =     53162.96|
|figures of merit: min =        0.00 max =            1.00 mean =         0.57|
|phase err.(work): min =        0.00 max =           89.96 mean =        46.22|
|phase err.(test): min =        0.00 max =           89.84 mean =        46.11|
|-----------------------------------------------------------------------------|

============================== 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 = 6.328406              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.547   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.284528              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.359   (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 |  1.780 -  2.092:       12 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  2.092 -  2.404:       13 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.404 -  2.716:      151 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.716 -  3.028:     1947 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  3.028 -  3.340:     1873 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.340 -  3.652:     2761 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.652 -  3.964:     4673 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.964 -  4.276:     4368 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.276 -  4.588:     5633 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.588 -  4.900:     6771 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.010    0.070  0.000 |       0.254 |              |
|     angle |     3299 |   1.822    9.874  0.001 |       1.000 |              |
| chirality |      348 |   0.101    0.314  0.000 |       0.257 |        0.170 |
| planarity |      436 |   0.009    0.055  0.000 |       0.973 |              |
|  dihedral |      870 |  15.968   85.889  0.013 |       1.071 |              |
| nonbonded |     2439 |   4.111    4.900  1.780 |       0.289 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.941)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      5.09    63.06   16.02    None  None   None       |
|    all(noH): 2823   0      5.09    63.06   16.02    None  None   None       |
|    Sol.    : 438    0      6.19    63.06   36.87    None  None   None       |
|    Mac.    : 2385   0      5.09    49.51   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     5.090 -  10.887: 1254   |   5:    34.075 -  39.872:   81        |
|      1:    10.887 -  16.684:  844   |   6:    39.872 -  45.669:   78        |
|      2:    16.684 -  22.481:  225   |   7:    45.669 -  51.466:   64        |
|      3:    22.481 -  28.278:  122   |   8:    51.466 -  57.263:   37        |
|      4:    28.278 -  34.075:   94   |   9:    57.263 -  63.060:   24        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

|--(resolution: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4292   r_free= 0.4140   ksol= 0.00   Bsol= 0.00   scale= 0.909    |
|                                                                             |
| 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:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.248920                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4175   r_free= 0.3986   ksol= 0.29   Bsol= 26.70   scale= 0.936   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.85,5.74,-1.78,0.00,-0.00,-0.00); trace/3= 0.37                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.235298                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.847011              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.096   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.745524              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.197   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4175      final r-factor (work) = 0.3464          |
| start r-factor (free) = 0.3986      final r-factor (free) = 0.3696          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.4010 = 5.85 * 0.50 * 6.2359 + 1.00 * 0.1705                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.9861 = 5.85 * 0.50 * 6.1198 + 1.00 * 0.0947                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3464      final r-factor (work) = 0.3212          |
| start r-factor (free) = 0.3696      final r-factor (free) = 0.3733          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5685 = 0.75 * 1.00 * 6.1198 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5491 = 0.75 * 1.00 * 6.0608 + 1.00 * 0.0306                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.941)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    94.80   17.38    None  None   None       |
|    all(noH): 2823   0      0.00    94.80   17.38    None  None   None       |
|    Sol.    : 438    0      2.53    68.85   35.27    None  None   None       |
|    Mac.    : 2385   0      0.00    94.80   14.09    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 -   9.480:  887   |   5:    47.398 -  56.878:   81        |
|      1:     9.480 -  18.959:  955   |   6:    56.878 -  66.357:   23        |
|      2:    18.959 -  28.439:  508   |   7:    66.357 -  75.837:    1        |
|      3:    28.439 -  37.919:  235   |   8:    75.837 -  85.317:    0        |
|      4:    37.919 -  47.398:  132   |   9:    85.317 -  94.796:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3212 r_free = 0.3733             target_work(ml) = 6.061         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3207 r_free = 0.3729             target_work(ml) = 6.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3207   r_free= 0.3729   ksol= 0.29   Bsol= 26.70   scale= 0.983   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.85,5.74,-1.78,0.00,-0.00,-0.00); trace/3= 0.37                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.059842                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3203   r_free= 0.3715   ksol= 0.28   Bsol= 38.32   scale= 0.980   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.39,3.33,-0.91,0.00,-0.00,-0.00); trace/3= 0.01                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.061463                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.536529             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.835  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.549423              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.941   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3203      final r-factor (work) = 0.2439          |
| start r-factor (free) = 0.3715      final r-factor (free) = 0.2904          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.0325 = 10.54 * 0.50 * 6.0623 + 1.00 * 0.0947                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.4147 = 10.54 * 0.50 * 5.9380 + 1.00 * 0.1318                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2439      final r-factor (work) = 0.2196          |
| start r-factor (free) = 0.2904      final r-factor (free) = 0.2797          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3064 = 0.55 * 1.00 * 5.9380 + 1.00 * 0.0440                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1760 = 0.55 * 1.00 * 5.7587 + 1.00 * 0.0121                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.941)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.46   17.44    None  None   None       |
|    all(noH): 2823   0      0.00    80.46   17.44    None  None   None       |
|    Sol.    : 438    0      1.80    80.46   38.25    None  None   None       |
|    Mac.    : 2385   0      0.00    79.28   13.62    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.046:  775   |   5:    40.231 -  48.277:  115        |
|      1:     8.046 -  16.092: 1009   |   6:    48.277 -  56.323:   85        |
|      2:    16.092 -  24.139:  415   |   7:    56.323 -  64.370:   46        |
|      3:    24.139 -  32.185:  213   |   8:    64.370 -  72.416:   21        |
|      4:    32.185 -  40.231:  132   |   9:    72.416 -  80.462:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2196 r_free = 0.2797             target_work(ml) = 5.742         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2193 r_free = 0.2797             target_work(ml) = 5.741         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2193   r_free= 0.2797   ksol= 0.28   Bsol= 38.32   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.39,3.33,-0.91,0.00,-0.00,-0.00); trace/3= 0.01                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.741444                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2183   r_free= 0.2771   ksol= 0.32   Bsol= 55.78   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.79,1.22,-0.57,0.00,-0.00,-0.00); trace/3= -0.38                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.738157                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.237673              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.629   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.513456              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 150.691  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2183      final r-factor (work) = 0.1783          |
| start r-factor (free) = 0.2771      final r-factor (free) = 0.2247          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4532 = 3.24 * 0.50 * 5.7580 + 1.00 * 0.1318                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2101 = 3.24 * 0.50 * 5.6539 + 1.00 * 0.0573                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1783      final r-factor (work) = 0.1669          |
| start r-factor (free) = 0.2247      final r-factor (free) = 0.2128          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9152 = 0.51 * 1.00 * 5.6539 + 1.00 * 0.0121                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8635 = 0.51 * 1.00 * 5.5103 + 1.00 * 0.0342                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.941)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.92   17.50    None  None   None       |
|    all(noH): 2823   0      0.00    92.92   17.50    None  None   None       |
|    Sol.    : 438    0      5.05    91.21   41.70    None  None   None       |
|    Mac.    : 2385   0      0.00    92.92   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 -   9.292: 1026   |   5:    46.458 -  55.749:  102        |
|      1:     9.292 -  18.583: 1034   |   6:    55.749 -  65.041:   67        |
|      2:    18.583 -  27.875:  273   |   7:    65.041 -  74.332:   30        |
|      3:    27.875 -  37.166:  141   |   8:    74.332 -  83.624:   19        |
|      4:    37.166 -  46.458:  122   |   9:    83.624 -  92.915:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1669 r_free = 0.2128             target_work(ml) = 5.489         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1667 r_free = 0.2130             target_work(ml) = 5.489         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1667   r_free= 0.2130   ksol= 0.32   Bsol= 55.78   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.79,1.22,-0.57,0.00,-0.00,-0.00); trace/3= -0.38                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.488931                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1671   r_free= 0.2128   ksol= 0.32   Bsol= 61.93   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,0.17,-0.82,0.00,-0.00,-0.00); trace/3= -0.93                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.489438                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.028291              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.362  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.005994              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.250   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1671      final r-factor (work) = 0.1403          |
| start r-factor (free) = 0.2128      final r-factor (free) = 0.1842          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6485 = 2.03 * 0.50 * 5.5132 + 1.00 * 0.0573                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5428 = 2.03 * 0.50 * 5.4083 + 1.00 * 0.0580                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1403      final r-factor (work) = 0.1331          |
| start r-factor (free) = 0.1842      final r-factor (free) = 0.1813          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.8625 = 2.01 * 1.00 * 5.4083 + 1.00 * 0.0134                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.6539 = 2.01 * 1.00 * 5.3042 + 1.00 * 0.0137                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.941)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    113.29  17.77    None  None   None       |
|    all(noH): 2823   0      0.00    113.29  17.77    None  None   None       |
|    Sol.    : 438    0      4.32    109.96  45.17    None  None   None       |
|    Mac.    : 2385   0      0.00    113.29  12.74    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.329: 1435   |   5:    56.645 -  67.974:   85        |
|      1:    11.329 -  22.658:  823   |   6:    67.974 -  79.303:   45        |
|      2:    22.658 -  33.987:  165   |   7:    79.303 -  90.632:   23        |
|      3:    33.987 -  45.316:  129   |   8:    90.632 - 101.961:   10        |
|      4:    45.316 -  56.645:  102   |   9:   101.961 - 113.291:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1331 r_free = 0.1813             target_work(ml) = 5.292         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1331 r_free = 0.1812             target_work(ml) = 5.292         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1331   r_free= 0.1812   ksol= 0.32   Bsol= 61.93   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.15,0.17,-0.82,0.00,-0.00,-0.00); trace/3= -0.93                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.291785                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1334   r_free= 0.1813   ksol= 0.33   Bsol= 64.79   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.07,-0.24,-0.60,-0.00,-0.00,-0.00); trace/3= -0.97                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.293550                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.986004              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 116.738  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.201125              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.537  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1334      final r-factor (work) = 0.1242          |
| start r-factor (free) = 0.1813      final r-factor (free) = 0.1733          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3265 = 1.99 * 0.50 * 5.3056 + 1.00 * 0.0580                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2807 = 1.99 * 0.50 * 5.2611 + 1.00 * 0.0564                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1242      final r-factor (work) = 0.1239          |
| start r-factor (free) = 0.1733      final r-factor (free) = 0.1692          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0718 = 0.20 * 1.00 * 5.2611 + 1.00 * 0.0136                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0653 = 0.20 * 1.00 * 5.2385 + 1.00 * 0.0117                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.941)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.28  16.81    None  None   None       |
|    all(noH): 2823   0      0.00    109.28  16.81    None  None   None       |
|    Sol.    : 438    0      4.43    103.37  41.56    None  None   None       |
|    Mac.    : 2385   0      0.00    109.28  12.26    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 -  10.928: 1404   |   5:    54.638 -  65.566:   75        |
|      1:    10.928 -  21.855:  873   |   6:    65.566 -  76.494:   38        |
|      2:    21.855 -  32.783:  176   |   7:    76.494 -  87.421:   11        |
|      3:    32.783 -  43.711:  127   |   8:    87.421 -  98.349:    8        |
|      4:    43.711 -  54.638:  106   |   9:    98.349 - 109.276:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1239 r_free = 0.1692             target_work(ml) = 5.225         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1238 r_free = 0.1691             target_work(ml) = 5.225         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1238   r_free= 0.1691   ksol= 0.33   Bsol= 64.79   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.07,-0.24,-0.60,-0.00,-0.00,-0.00); trace/3= -0.97                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.224561                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0234 -  4.7271 0.99   1405  158 0.0978 0.1302      5.3678      5.5581|
|  2:  4.7271 -  3.7716 0.99   1350  151 0.0880 0.1102       5.461      5.6772|
|  3:  3.7716 -  3.3006 0.99   1330  146 0.1146 0.1661      5.5467      5.8964|
|  4:  3.3006 -  3.0015 0.99   1322  137 0.1384 0.1816      5.5405      5.7093|
|  5:  3.0015 -  2.7878 0.98   1306  150 0.1511 0.1797      5.4338      5.5688|
|  6:  2.7878 -  2.6243 0.99   1303  147 0.1464 0.2219       5.341      5.5566|
|  7:  2.6243 -  2.4935 0.98   1281  151 0.1332 0.1793      5.2509      5.4535|
|  8:  2.4935 -  2.3854 0.99   1313  133 0.1352 0.1906      5.1901       5.418|
|  9:  2.3854 -  2.2939 0.99   1296  148 0.1297 0.1930      5.0982      5.3985|
| 10:  2.2939 -  2.2150 0.98   1275  143 0.1302 0.1733      5.0742      5.2458|
| 11:  2.2150 -  2.1460 0.97   1282  148 0.1313 0.1916      4.9915      5.2757|
| 12:  2.1460 -  2.0848 0.99   1273  142 0.1252 0.1688      4.9347      5.1614|
| 13:  2.0848 -  2.0300 0.94   1258  129 0.1299 0.1917      4.8658       5.134|
| 14:  2.0300 -  1.9806 0.50    636   76 0.1192 0.1913      4.7443      4.9693|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0234 -  4.7271  1405   158  0.94   9.04   0.97     0.94       6883.76|
|  2:  4.7271 -  3.7716  1350   151  0.95   8.53   1.01     1.00       9649.66|
|  3:  3.7716 -  3.3006  1330   146  0.93  12.45   1.02     1.01      11950.23|
|  4:  3.3006 -  3.0015  1322   137  0.91  15.33   1.01     0.99      11900.67|
|  5:  3.0015 -  2.7878  1306   150  0.88  17.81   1.00     0.98      10104.45|
|  6:  2.7878 -  2.6243  1303   147  0.88  18.21   0.98     0.94       8645.84|
|  7:  2.6243 -  2.4935  1281   151  0.89  16.89   0.99     0.95       7341.75|
|  8:  2.4935 -  2.3854  1313   133  0.89  17.35   1.00     0.96       6755.82|
|  9:  2.3854 -  2.2939  1296   148  0.89  17.63   1.00     0.95       5777.41|
| 10:  2.2939 -  2.2150  1275   143  0.89  17.33   0.99     0.95       5403.57|
| 11:  2.2150 -  2.1460  1282   148  0.89  17.24   0.99     0.96       4668.80|
| 12:  2.1460 -  2.0848  1273   142  0.90  16.35   0.99     0.97       4229.38|
| 13:  2.0848 -  2.0300  1258   129  0.89  17.17   0.98     0.99       3684.86|
| 14:  2.0300 -  1.9806   636    76  0.90  16.28   0.97     0.93       2958.45|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2958.45 max =        11950.23 mean =      7335.56|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.98 mean =        15.44|
|phase err.(test): min =        0.00 max =           89.54 mean =        14.94|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1238   r_free= 0.1691   ksol= 0.32   Bsol= 60.07   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.00,-0.42,-0.51,-0.00,-0.00,-0.00); trace/3= -0.97                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.224664                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1238   r_free= 0.1691   ksol= 0.32   Bsol= 60.07   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.00,-0.42,-0.51,-0.00,-0.00,-0.00); trace/3= -0.97                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.224664                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0234 -  4.7271 0.99   1405  158 0.0977 0.1304      5.3677       5.557|
|  2:  4.7271 -  3.7716 0.99   1350  151 0.0877 0.1102      5.4586      5.6743|
|  3:  3.7716 -  3.3006 0.99   1330  146 0.1147 0.1659      5.5459      5.8964|
|  4:  3.3006 -  3.0015 0.99   1322  137 0.1385 0.1820      5.5411      5.7098|
|  5:  3.0015 -  2.7878 0.98   1306  150 0.1513 0.1800      5.4347      5.5693|
|  6:  2.7878 -  2.6243 0.99   1303  147 0.1463 0.2214      5.3408      5.5557|
|  7:  2.6243 -  2.4935 0.98   1281  151 0.1333 0.1797      5.2513      5.4535|
|  8:  2.4935 -  2.3854 0.99   1313  133 0.1351 0.1909      5.1908      5.4195|
|  9:  2.3854 -  2.2939 0.99   1296  148 0.1296 0.1930      5.0985         5.4|
| 10:  2.2939 -  2.2150 0.98   1275  143 0.1301 0.1738      5.0749       5.248|
| 11:  2.2150 -  2.1460 0.97   1282  148 0.1312 0.1917      4.9919      5.2758|
| 12:  2.1460 -  2.0848 0.99   1273  142 0.1252 0.1691      4.9347      5.1621|
| 13:  2.0848 -  2.0300 0.94   1258  129 0.1302 0.1914      4.8669      5.1331|
| 14:  2.0300 -  1.9806 0.50    636   76 0.1192 0.1913       4.744      4.9688|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0234 -  4.7271  1405   158  0.94   9.05   0.97     0.94       6891.02|
|  2:  4.7271 -  3.7716  1350   151  0.95   8.52   1.01     1.00       9619.04|
|  3:  3.7716 -  3.3006  1330   146  0.93  12.43   1.02     1.01      11906.46|
|  4:  3.3006 -  3.0015  1322   137  0.91  15.34   1.01     0.99      11915.18|
|  5:  3.0015 -  2.7878  1306   150  0.88  17.80   1.00     0.98      10103.36|
|  6:  2.7878 -  2.6243  1303   147  0.88  18.20   0.98     0.94       8644.71|
|  7:  2.6243 -  2.4935  1281   151  0.89  16.89   0.99     0.95       7344.90|
|  8:  2.4935 -  2.3854  1313   133  0.89  17.37   1.00     0.96       6772.88|
|  9:  2.3854 -  2.2939  1296   148  0.89  17.66   1.00     0.95       5797.17|
| 10:  2.2939 -  2.2150  1275   143  0.89  17.35   0.99     0.95       5414.47|
| 11:  2.2150 -  2.1460  1282   148  0.89  17.26   0.99     0.96       4677.99|
| 12:  2.1460 -  2.0848  1273   142  0.90  16.35   0.99     0.97       4235.24|
| 13:  2.0848 -  2.0300  1258   129  0.89  17.16   0.98     0.99       3683.66|
| 14:  2.0300 -  1.9806   636    76  0.90  16.28   0.97     0.93       2952.68|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2952.68 max =        11915.18 mean =      7335.95|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.91 mean =        15.45|
|phase err.(test): min =        0.00 max =           89.62 mean =        14.94|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.941)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    109.28  16.81    None  None   None       |
|    all(noH): 2823   0      0.00    109.28  16.81    None  None   None       |
|    Sol.    : 438    0      4.43    103.38  41.56    None  None   None       |
|    Mac.    : 2385   0      0.00    109.28  12.27    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 -  10.931: 1404   |   5:    54.641 -  65.569:   75        |
|      1:    10.931 -  21.858:  873   |   6:    65.569 -  76.497:   38        |
|      2:    21.858 -  32.786:  176   |   7:    76.497 -  87.424:   11        |
|      3:    32.786 -  43.714:  127   |   8:    87.424 -  98.352:    8        |
|      4:    43.714 -  54.641:  106   |   9:    98.352 - 109.279:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 349         
Filter by distance & map next to the model:
   mapped sites are within: 0.574 - 5.507
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 346 from: 349
   mapped sites are within: 0.725 - 5.507

peak=   11.528 closest distance to " O  BHOH Z  74 " =    1.033
peak=    5.685 closest distance to " O   HOH Z 210 " =    1.359
peak=    5.184 closest distance to " CB  SER A  63 " =    1.144
peak=    5.108 closest distance to " O   HOH Z 113 " =    2.388
peak=    4.819 closest distance to " CB  GLN A 223 " =    1.349
peak=    4.797 closest distance to " CA  TYR A  30 " =    0.946
peak=    4.779 closest distance to " O   HOH Z 433 " =    1.855
peak=    4.761 closest distance to " O   HOH Z 422 " =    0.910
peak=    4.730 closest distance to " CG  PRO A  90 " =    1.261
peak=    4.703 closest distance to " CG  PRO A 213 " =    1.341
peak=    4.703 closest distance to " O   HOH Z 134 " =    1.975
peak=    4.676 closest distance to " O   PRO A 198 " =    1.536
peak=    4.648 closest distance to " CG  PRO A 198 " =    1.266
peak=    4.633 closest distance to " CG  PRO A 280 " =    0.779
peak=    4.627 closest distance to " CB  ARG A 275 " =    0.807
peak=    4.589 closest distance to " O   HOH Z 403 " =    1.923
peak=    4.582 closest distance to " O   HOH Z  49 " =    1.221
peak=    4.562 closest distance to " O   HOH Z 124 " =    1.313
peak=    4.495 closest distance to " O   HOH Z  80 " =    2.028
peak=    4.484 closest distance to " O   HOH Z 102 " =    1.380
peak=    4.410 closest distance to " CB  GLN A 183 " =    1.276
peak=    4.403 closest distance to " O   HOH Z  15 " =    2.151
peak=    4.400 closest distance to " O   HOH Z 189 " =    2.233
peak=    4.384 closest distance to " CB  SER A 141 " =    1.062
peak=    4.374 closest distance to " O   HOH Z 209 " =    2.309
peak=    4.372 closest distance to " CB  ARG A 190 " =    1.831
peak=    4.365 closest distance to " O   HOH Z  63 " =    2.318
peak=    4.352 closest distance to " O   HOH Z 357 " =    2.128
peak=    4.281 closest distance to " O   HOH Z 154 " =    1.584
peak=    4.262 closest distance to " CD2 TRP A 179 " =    1.319
peak=    4.262 closest distance to " O   HOH Z 126 " =    1.607
peak=    4.248 closest distance to " O   HOH Z  44 " =    2.015
peak=    4.243 closest distance to " O   HOH Z   7 " =    0.990
peak=    4.222 closest distance to " O   HOH Z 402 " =    1.706
peak=    4.218 closest distance to " O   HOH Z 389 " =    2.073
peak=    4.215 closest distance to " O   HOH Z 130 " =    2.554
peak=    4.196 closest distance to " O   HOH Z 214 " =    1.439
peak=    4.188 closest distance to " O   HOH Z  61 " =    1.625
peak=    4.174 closest distance to " O   HOH Z  20 " =    1.723
peak=    4.169 closest distance to " O   HOH Z 247 " =    1.543
peak=    4.167 closest distance to " O   HOH Z 130 " =    1.182
peak=    4.164 closest distance to " O   HOH Z 132 " =    2.335
peak=    4.157 closest distance to " O   HOH Z 234 " =    3.682
peak=    4.151 closest distance to " O   HOH Z  39 " =    1.553
peak=    4.133 closest distance to " O   GLY A  23 " =    2.409
peak=    4.132 closest distance to " CB  SER A  62 " =    0.800
peak=    4.110 closest distance to " O   HOH Z 203 " =    1.912
peak=    4.101 closest distance to " CB  ARG A  79 " =    1.292
peak=    4.099 closest distance to " O   HOH Z 425 " =    1.549
peak=    4.075 closest distance to " O   HOH Z 406 " =    1.635
peak=    4.072 closest distance to " O   HOH Z  97 " =    1.926
peak=    4.069 closest distance to " O   HOH Z 196 " =    1.484
peak=    4.060 closest distance to " O   HOH Z 120 " =    1.006
peak=    4.030 closest distance to " CG1 ILE A  33 " =    1.240
peak=    4.028 closest distance to " O   HOH Z 339 " =    1.458
peak=    4.028 closest distance to " NE2 GLN A  11 " =    1.040
peak=    4.023 closest distance to " O   HOH Z 412 " =    3.418
peak=    4.002 closest distance to " CG  ARG A  66 " =    0.948
peak=    3.996 closest distance to " CB  TRP A 266 " =    1.046
peak=    3.993 closest distance to " O   HOH Z 128 " =    2.044
peak=    3.990 closest distance to " O   HOH Z  40 " =    1.900
peak=    3.988 closest distance to " CA  ALA A  51 " =    0.981
peak=    3.940 closest distance to " NH2BARG A 145 " =    2.129
peak=    3.938 closest distance to " O   HOH Z  59 " =    2.346
peak=    3.932 closest distance to " O   HOH Z 232 " =    2.427
peak=    3.930 closest distance to " CB  GLU A 277 " =    3.711
peak=    3.928 closest distance to " O   HOH Z 414 " =    1.721
peak=    3.918 closest distance to " O  BHOH Z 338 " =    0.967
peak=    3.915 closest distance to " CB  LEU A 228 " =    1.174
peak=    3.910 closest distance to " O   SER A  87 " =    2.214
peak=    3.906 closest distance to " O   HOH Z  43 " =    1.612
peak=    3.901 closest distance to " O   HOH Z 336 " =    1.710
peak=    3.895 closest distance to " CB  GLU A 128 " =    1.154
peak=    3.892 closest distance to " CB  TRP A 179 " =    1.149
peak=    3.871 closest distance to " CG2BVAL A  41 " =    0.904
peak=    3.857 closest distance to " O   HOH Z 361 " =    3.339
peak=    3.853 closest distance to " O   HOH Z 132 " =    2.654
peak=    3.846 closest distance to " O   HOH Z 298 " =    1.934
peak=    3.841 closest distance to " O   HOH Z 423 " =    1.810
peak=    3.832 closest distance to " CG2 THR A 220 " =    0.793
peak=    3.806 closest distance to " CB  ASN A 148 " =    1.315
peak=    3.787 closest distance to " O   THR A 251 " =    1.295
peak=    3.785 closest distance to " O   HOH Z  11 " =    1.295
peak=    3.778 closest distance to " CG2 VAL A 197 " =    1.148
peak=    3.774 closest distance to " N   ASN A  39 " =    1.309
peak=    3.773 closest distance to " O   HOH Z 272 " =    1.229
peak=    3.772 closest distance to " O   HOH Z 431 " =    1.290
peak=    3.771 closest distance to " NH2 ARG A 156 " =    1.195
peak=    3.768 closest distance to " O   HOH Z 437 " =    1.888
peak=    3.764 closest distance to " CD  ARG A 195 " =    1.054
peak=    3.763 closest distance to " CD  LYS A 166 " =    1.557
peak=    3.759 closest distance to " NZ  LYS A 117 " =    2.970
peak=    3.753 closest distance to " O   HOH Z 371 " =    3.280
peak=    3.746 closest distance to " ND2 ASN A 187 " =    1.595
peak=    3.733 closest distance to " N   TRP A 150 " =    1.091
peak=    3.731 closest distance to " CB  ASN A  39 " =    0.850
peak=    3.722 closest distance to " O   HOH Z 365 " =    1.413
peak=    3.721 closest distance to " O   HOH Z 245 " =    1.399
peak=    3.709 closest distance to " OE1 GLN A  11 " =    2.049
peak=    3.705 closest distance to " O   HOH Z 377 " =    1.298
peak=    3.705 closest distance to " O   HOH Z 417 " =    2.958
peak=    3.697 closest distance to " O   HOH Z 163 " =    1.623
peak=    3.694 closest distance to " CA  LEU A  83 " =    1.421
peak=    3.694 closest distance to " CG2 ILE A  20 " =    1.401
peak=    3.685 closest distance to " O   HOH Z 193 " =    1.783
peak=    3.683 closest distance to " O   HOH Z 394 " =    1.594
peak=    3.663 closest distance to " CB  SER A   3 " =    1.299
peak=    3.658 closest distance to " NE2 GLN A  77 " =    3.246
peak=    3.657 closest distance to " CD  ARG A 159 " =    0.843
peak=    3.651 closest distance to " CA  ALA A  21 " =    1.333
peak=    3.650 closest distance to " CG AARG A 275 " =    1.023
peak=    3.648 closest distance to " O   HOH Z  21 " =    1.849
peak=    3.648 closest distance to " O   HOH Z 265 " =    2.086
peak=    3.647 closest distance to " CE1 HIS A 108 " =    1.118
peak=    3.638 closest distance to " OE1 GLN A  58 " =    3.367
peak=    3.637 closest distance to " O   HOH Z 418 " =    1.850
peak=    3.636 closest distance to " CB  GLU A 152 " =    1.175
peak=    3.634 closest distance to " O   HOH Z 346 " =    1.654
peak=    3.631 closest distance to " CB  VAL A 202 " =    1.496
peak=    3.625 closest distance to " CB  PHE A 283 " =    0.880
peak=    3.619 closest distance to " O   HOH Z 435 " =    1.827
peak=    3.616 closest distance to " CB  MET A 105 " =    1.070
peak=    3.601 closest distance to " O   HOH Z 369 " =    2.085
peak=    3.600 closest distance to " O   HOH Z 380 " =    1.784
peak=    3.598 closest distance to " O   HOH Z 345 " =    1.734
peak=    3.595 closest distance to " CB  TYR A 169 " =    0.778
peak=    3.584 closest distance to " O   HOH Z 236 " =    1.472
peak=    3.584 closest distance to " CZ3 TRP A 266 " =    0.979
peak=    3.582 closest distance to " CA  GLU A 152 " =    0.910
peak=    3.580 closest distance to " O   HOH Z  54 " =    1.699
peak=    3.574 closest distance to " CG2 THR A 221 " =    1.192
peak=    3.570 closest distance to " CA  ARG A 195 " =    1.118
peak=    3.570 closest distance to " O   ASN A  74 " =    1.586
peak=    3.567 closest distance to " CD  ARG A 269 " =    1.043
peak=    3.566 closest distance to " O   HOH Z 428 " =    1.117
peak=    3.558 closest distance to " CB  ASN A 285 " =    0.909
peak=    3.556 closest distance to " CG  PRO A 243 " =    1.178
peak=    3.551 closest distance to " CA  GLN A  88 " =    1.227
peak=    3.545 closest distance to " CG2 VAL A  78 " =    0.936
peak=    3.544 closest distance to " O   HOH Z 395 " =    1.465
peak=    3.543 closest distance to " CA  ASN A 176 " =    1.226
peak=    3.542 closest distance to " CB  PRO A 243 " =    1.236
peak=    3.542 closest distance to " O   HOH Z 257 " =    2.235
peak=    3.541 closest distance to " CA  ASP A 162 " =    1.182
peak=    3.535 closest distance to " O   HOH Z 403 " =    1.569
peak=    3.534 closest distance to " O   HOH Z 334 " =    1.591
peak=    3.533 closest distance to " O   HOH Z 303 " =    2.249
peak=    3.527 closest distance to " CA  ASP A 191 " =    0.870
peak=    3.525 closest distance to " CZ  PHE A 218 " =    1.105
peak=    3.514 closest distance to " O   GLY A  91 " =    1.181
peak=    3.502 closest distance to " O   HOH Z 345 " =    2.662
peak=    3.501 closest distance to " O   HOH Z 150 " =    1.675
peak=    3.498 closest distance to " O   HOH Z 423 " =    3.278
peak=    3.496 closest distance to " O   HOH Z 358 " =    1.412
peak=    3.494 closest distance to " NZ  LYS A 117 " =    2.103
peak=    3.493 closest distance to " O   HOH Z 271 " =    2.313
peak=    3.492 closest distance to " OE1 GLU A   2 " =    1.589
peak=    3.489 closest distance to " O   HOH Z  67 " =    2.147
peak=    3.486 closest distance to " CB  ARG A  79 " =    0.730
peak=    3.484 closest distance to " N   SER A 164 " =    0.953
peak=    3.483 closest distance to " CD1 LEU A 300 " =    1.202
peak=    3.483 closest distance to " O   HOH Z  48 " =    2.457
peak=    3.480 closest distance to " O   HOH Z 409 " =    3.566
peak=    3.474 closest distance to " O   HOH Z 291 " =    1.410
peak=    3.473 closest distance to " CB  PHE A  16 " =    1.146
peak=    3.469 closest distance to " O   HOH Z 279 " =    2.022
peak=    3.467 closest distance to " CA  VAL A  41 " =    0.860
peak=    3.462 closest distance to " CB  PRO A 198 " =    0.961
peak=    3.461 closest distance to " CD1 LEU A 222 " =    0.756
peak=    3.460 closest distance to " CA  GLY A 196 " =    0.948
peak=    3.458 closest distance to " O   HOH Z 250 " =    1.888
peak=    3.458 closest distance to " O   HOH Z  22 " =    2.675
peak=    3.458 closest distance to " O   ASP A 124 " =    1.794
peak=    3.451 closest distance to " CG  GLN A  11 " =    1.164
peak=    3.450 closest distance to " O   HOH Z 250 " =    1.466
peak=    3.447 closest distance to " O   HOH Z 162 " =    2.403
peak=    3.447 closest distance to " O   HOH Z 214 " =    2.244
peak=    3.444 closest distance to " O   HOH Z  88 " =    3.433
peak=    3.443 closest distance to " O   HOH Z 386 " =    2.245
peak=    3.442 closest distance to " OG  SER A  62 " =    2.889
peak=    3.439 closest distance to " O   HOH Z  35 " =    1.975
peak=    3.433 closest distance to " CD  PRO A  54 " =    0.862
peak=    3.428 closest distance to " O   HOH Z 261 " =    1.977
peak=    3.423 closest distance to " CG2 THR A  42 " =    0.851
peak=    3.419 closest distance to " O   HOH Z 375 " =    1.840
peak=    3.417 closest distance to " CB  SER A  26 " =    1.771
peak=    3.413 closest distance to " O   HOH Z 408 " =    1.775
peak=    3.411 closest distance to " C   ILE A 106 " =    1.796
peak=    3.408 closest distance to " O   HOH Z 109 " =    2.099
peak=    3.403 closest distance to " CA  GLY A  80 " =    0.962
peak=    3.402 closest distance to " CG1BVAL A  72 " =    1.759
peak=    3.400 closest distance to " O   HOH Z 128 " =    1.499
peak=    3.400 closest distance to " O   ALA A 165 " =    1.303
peak=    3.399 closest distance to " NH1 ARG A 269 " =    0.767
peak=    3.399 closest distance to " OG BSER A 210 " =    1.091
peak=    3.396 closest distance to " O   HOH Z 316 " =    2.834
peak=    3.394 closest distance to " CD2 LEU A 297 " =    0.809
peak=    3.388 closest distance to " O   ALA A 158 " =    1.179
peak=    3.385 closest distance to " CA  PRO A  90 " =    0.922
peak=    3.385 closest distance to " O   HOH Z 434 " =    3.081
peak=    3.382 closest distance to " CA  ASP A 191 " =    1.129
peak=    3.380 closest distance to " CB  MET A  40 " =    0.749
peak=    3.377 closest distance to " OD1 ASN A 301 " =    1.172
peak=    3.373 closest distance to " CD  ARG A 139 " =    1.294
peak=    3.371 closest distance to " O   HOH Z 156 " =    2.551
peak=    3.367 closest distance to " O   HOH Z 142 " =    1.334
peak=    3.366 closest distance to " CG2 THR A  29 " =    1.313
peak=    3.365 closest distance to " O   HOH Z  78 " =    1.719
peak=    3.365 closest distance to " O   HOH Z 365 " =    2.581
peak=    3.364 closest distance to " O   HOH Z 185 " =    1.692
peak=    3.364 closest distance to " CB  ASP A 140 " =    0.725
peak=    3.364 closest distance to " CA  ILE A 106 " =    0.748
peak=    3.363 closest distance to " O   HOH Z  90 " =    3.632
peak=    3.360 closest distance to " O   HOH Z 282 " =    2.181
peak=    3.359 closest distance to " CA  ALA A 100 " =    1.151
peak=    3.349 closest distance to " O   HOH Z 374 " =    2.611
peak=    3.348 closest distance to " CA  ALA A 160 " =    0.972
peak=    3.347 closest distance to " OG BSER A 164 " =    2.435
peak=    3.347 closest distance to " O   HOH Z 126 " =    1.961
peak=    3.339 closest distance to " O   HOH Z 272 " =    1.920
peak=    3.338 closest distance to " O   HOH Z 240 " =    2.310
peak=    3.335 closest distance to " O   HOH Z  30 " =    1.393
peak=    3.335 closest distance to " O   HOH Z 146 " =    1.452
peak=    3.335 closest distance to " CA  ILE A 263 " =    0.983
peak=    3.334 closest distance to " CB  GLN A  58 " =    0.927
peak=    3.332 closest distance to " O   HOH Z  66 " =    2.066
peak=    3.332 closest distance to " O   HOH Z 284 " =    2.932
peak=    3.328 closest distance to " CB  ALA A 248 " =    1.322
peak=    3.326 closest distance to " O   HOH Z 368 " =    1.885
peak=    3.326 closest distance to " O   HOH Z 344 " =    3.239
peak=    3.325 closest distance to " O   HOH Z 162 " =    1.327
peak=    3.324 closest distance to " OH  TYR A 116 " =    1.270
peak=    3.320 closest distance to " OG BSER A 212 " =    2.500
peak=    3.307 closest distance to " O   HOH Z 173 " =    2.268
peak=    3.305 closest distance to " CA  THR A 294 " =    1.658
peak=    3.301 closest distance to " O   HOH Z 438 " =    2.332
peak=    3.298 closest distance to " NE1 TRP A 274 " =    0.839
peak=    3.296 closest distance to " CG  ARG A 219 " =    1.268
peak=    3.295 closest distance to " O   HOH Z 301 " =    1.478
peak=    3.294 closest distance to " CG1 ILE A 120 " =    1.112
peak=    3.293 closest distance to " O   HOH Z 421 " =    2.048
peak=    3.292 closest distance to " O   HOH Z  48 " =    1.863
peak=    3.291 closest distance to " O   HOH Z 281 " =    4.543
peak=    3.291 closest distance to " O   HOH Z  40 " =    2.200
peak=    3.291 closest distance to " CA  ARG A  36 " =    1.049
peak=    3.290 closest distance to " CG2 ILE A 120 " =    1.122
peak=    3.290 closest distance to " CD  GLN A 194 " =    1.627
peak=    3.289 closest distance to " CA  SER A  12 " =    1.513
peak=    3.283 closest distance to " O   SER A  26 " =    1.604
peak=    3.282 closest distance to " O   HOH Z 358 " =    2.102
peak=    3.281 closest distance to " O   HOH Z 128 " =    1.908
peak=    3.278 closest distance to " O   GLN A  11 " =    0.914
peak=    3.274 closest distance to " O   HOH Z 415 " =    1.051
peak=    3.268 closest distance to " CB  PRO A  54 " =    1.087
peak=    3.268 closest distance to " CB  GLN A 194 " =    0.935
peak=    3.267 closest distance to " O   HOH Z   6 " =    1.270
peak=    3.266 closest distance to " O   HOH Z 299 " =    1.615
peak=    3.261 closest distance to " CE1 TYR A 186 " =    1.273
peak=    3.254 closest distance to " O   HOH Z 426 " =    1.365
peak=    3.252 closest distance to " O   HOH Z  48 " =    1.524
peak=    3.251 closest distance to " CB  GLU A 175 " =    1.298
peak=    3.250 closest distance to " CB  LEU A   5 " =    1.092
peak=    3.249 closest distance to " CB  SER A 210 " =    1.037
peak=    3.247 closest distance to " CZ  PHE A  38 " =    1.281
peak=    3.244 closest distance to " CE  LYS A 119 " =    1.099
peak=    3.241 closest distance to " NH1AARG A 275 " =    0.843
peak=    3.240 closest distance to " OD1 ASN A  69 " =    2.419
peak=    3.240 closest distance to " OG  SER A 245 " =    1.554
peak=    3.235 closest distance to " O   HOH Z 343 " =    2.510
peak=    3.235 closest distance to " CB  THR A  31 " =    1.635
peak=    3.234 closest distance to " O   HOH Z  88 " =    1.550
peak=    3.234 closest distance to " O   HOH Z 325 " =    3.892
peak=    3.233 closest distance to " O   HOH Z 123 " =    2.025
peak=    3.231 closest distance to " O   HOH Z 146 " =    1.248
peak=    3.229 closest distance to " CB  ALA A 100 " =    1.355
peak=    3.227 closest distance to " CG  GLN A 205 " =    1.047
peak=    3.226 closest distance to " CB  ASN A 142 " =    1.168
peak=    3.226 closest distance to " CB  ALA A  71 " =    1.272
peak=    3.222 closest distance to " O   HOH Z 420 " =    1.802
peak=    3.221 closest distance to " O   HOH Z 189 " =    2.704
peak=    3.221 closest distance to " O   HOH Z 327 " =    1.664
peak=    3.219 closest distance to " CA  ALA A 158 " =    1.134
peak=    3.218 closest distance to " O   HOH Z 298 " =    4.286
peak=    3.213 closest distance to " O   HOH Z 238 " =    5.507
peak=    3.207 closest distance to " O   HOH Z 139 " =    4.449
peak=    3.205 closest distance to " NH2AARG A 275 " =    2.549
peak=    3.201 closest distance to " N   ARG A 156 " =    1.421
peak=    3.195 closest distance to " CD  LYS A 119 " =    1.861
peak=    3.190 closest distance to " N   ILE A  33 " =    1.080
peak=    3.188 closest distance to " CD1 LEU A 228 " =    1.714
peak=    3.185 closest distance to " NH2AARG A 145 " =    2.308
peak=    3.184 closest distance to " CA  ALA A 291 " =    0.889
peak=    3.177 closest distance to " CZ3 TRP A  85 " =    1.029
peak=    3.173 closest distance to " O   HOH Z 219 " =    5.149
peak=    3.172 closest distance to " CB  ARG A 156 " =    0.959
peak=    3.171 closest distance to " CB  SER A  97 " =    1.699
peak=    3.170 closest distance to " OD1BASN A 224 " =    2.249
peak=    3.168 closest distance to " CG1 VAL A 153 " =    1.051
peak=    3.161 closest distance to " O   HOH Z 299 " =    2.159
peak=    3.160 closest distance to " O   HOH Z 280 " =    2.354
peak=    3.153 closest distance to " O   HOH Z 147 " =    1.771
peak=    3.151 closest distance to " SG ACYS A 201 " =    0.811
peak=    3.150 closest distance to " CG  GLU A  37 " =    0.965
peak=    3.150 closest distance to " CA  THR A 221 " =    1.631
peak=    3.146 closest distance to " ND1 HIS A  81 " =    1.480
peak=    3.145 closest distance to " O   CYS A 168 " =    1.517
peak=    3.139 closest distance to " CB  ALA A   9 " =    1.537
peak=    3.138 closest distance to " CA  THR A 246 " =    1.039
peak=    3.138 closest distance to " CB  ARG A 269 " =    1.126
peak=    3.133 closest distance to " CB  LEU A  83 " =    0.792
peak=    3.132 closest distance to " CA  ALA A  84 " =    1.039
peak=    3.131 closest distance to " CB  GLU A  46 " =    1.021
peak=    3.129 closest distance to " O   TYR A 116 " =    1.407
peak=    3.127 closest distance to " CG2AVAL A 121 " =    2.001
peak=    3.127 closest distance to " NE2 HIS A 115 " =    1.055
peak=    3.125 closest distance to " CA  VAL A 125 " =    1.191
peak=    3.124 closest distance to " O   HOH Z 126 " =    1.831
peak=    3.123 closest distance to " CB  TRP A 179 " =    1.912
peak=    3.123 closest distance to " CA  GLY A 241 " =    0.878
peak=    3.123 closest distance to " O   HOH Z 427 " =    3.133
peak=    3.121 closest distance to " O   HOH Z 255 " =    1.842
peak=    3.119 closest distance to " O   HOH Z 219 " =    1.947
peak=    3.118 closest distance to " CA  GLN A 223 " =    0.760
peak=    3.116 closest distance to " OD2 ASP A 298 " =    3.459
peak=    3.115 closest distance to " CG2 VAL A 257 " =    0.824
peak=    3.104 closest distance to " O   HOH Z 428 " =    1.718
peak=    3.104 closest distance to " O   HOH Z 298 " =    5.215
peak=    3.103 closest distance to " O   HOH Z 145 " =    2.231
peak=    3.102 closest distance to " O   HOH Z 109 " =    2.893
peak=    3.101 closest distance to " O   HOH Z 118 " =    0.892
peak=    3.096 closest distance to " OG BSER A 258 " =    3.061
peak=    3.085 closest distance to " CD  ARG A  36 " =    0.990
peak=    3.085 closest distance to " O   HOH Z  78 " =    1.939
peak=    3.080 closest distance to " CB  PRO A  90 " =    0.942
peak=    3.079 closest distance to " CA  SER A  87 " =    0.946
peak=    3.077 closest distance to " O   HOH Z 313 " =    1.716
peak=    3.075 closest distance to " CA  ASP A 124 " =    0.795
peak=    3.063 closest distance to " O   HOH Z 294 " =    1.610
peak=    3.062 closest distance to " CH2 TRP A 274 " =    1.885
peak=    3.054 closest distance to " CG2 THR A 294 " =    1.282
peak=    3.043 closest distance to " CA  ASP A 149 " =    1.155
peak=    3.038 closest distance to " CD AARG A 275 " =    1.360
peak=    3.036 closest distance to " O   HOH Z 152 " =    1.688
peak=    3.036 closest distance to " CA  LYS A 117 " =    1.307
peak=    3.024 closest distance to " O   HOH Z 132 " =    1.071
peak=    3.017 closest distance to " O   HOH Z  85 " =    1.868

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 216         
Filter by distance & map next to the model:
   mapped sites are within: 0.677 - 5.627
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 214 from: 216
   mapped sites are within: 0.708 - 5.627

peak=   -4.387 closest distance to " C   HIS A 108 " =    1.057
peak=   -4.384 closest distance to " C   THR A 279 " =    1.144
peak=   -4.366 closest distance to " O   HOH Z 266 " =    4.872
peak=   -4.325 closest distance to " CA  SER A 164 " =    2.125
peak=   -4.207 closest distance to " CG2 ILE A  49 " =    2.673
peak=   -4.165 closest distance to " CD1 LEU A 167 " =    2.116
peak=   -4.157 closest distance to " CD  GLN A  58 " =    1.214
peak=   -4.154 closest distance to " O   HOH Z 290 " =    0.934
peak=   -4.150 closest distance to " OXT GLY A 302 " =    2.798
peak=   -4.097 closest distance to " O   HOH Z 196 " =    1.740
peak=   -4.069 closest distance to " CE2 TYR A  30 " =    2.751
peak=   -4.068 closest distance to " CD  GLN A 223 " =    0.950
peak=   -4.039 closest distance to " CD  GLN A 223 " =    1.582
peak=   -3.959 closest distance to " CB  ASP A 162 " =    2.521
peak=   -3.917 closest distance to " CD1 PHE A  59 " =    1.977
peak=   -3.908 closest distance to " C   ASN A 285 " =    2.342
peak=   -3.902 closest distance to " O   HOH Z 155 " =    1.553
peak=   -3.882 closest distance to " CA  VAL A  67 " =    3.002
peak=   -3.868 closest distance to " CA  TYR A  68 " =    2.969
peak=   -3.829 closest distance to " SG  CYS A 254 " =    3.344
peak=   -3.825 closest distance to " OG  SER A  97 " =    2.211
peak=   -3.805 closest distance to " CD1 LEU A 101 " =    2.469
peak=   -3.775 closest distance to " CD  ARG A 156 " =    2.031
peak=   -3.743 closest distance to " O   HOH Z   7 " =    0.990
peak=   -3.743 closest distance to " O   HOH Z 407 " =    3.566
peak=   -3.741 closest distance to " NH2 ARG A  66 " =    1.613
peak=   -3.739 closest distance to " O   HOH Z  15 " =    1.606
peak=   -3.714 closest distance to " O   HOH Z 234 " =    4.119
peak=   -3.709 closest distance to " CG  PRO A 243 " =    1.626
peak=   -3.708 closest distance to " O   HOH Z 120 " =    0.913
peak=   -3.697 closest distance to " O   HOH Z 377 " =    0.999
peak=   -3.690 closest distance to " O   PRO A 198 " =    1.385
peak=   -3.678 closest distance to " O   HOH Z 348 " =    2.394
peak=   -3.673 closest distance to " O   ALA A  34 " =    2.274
peak=   -3.655 closest distance to " O   HOH Z 165 " =    2.010
peak=   -3.649 closest distance to " N   ALA A  43 " =    2.677
peak=   -3.640 closest distance to " CA  VAL A 197 " =    0.979
peak=   -3.639 closest distance to " CD  GLN A  88 " =    0.886
peak=   -3.636 closest distance to " O   HOH Z 351 " =    1.424
peak=   -3.634 closest distance to " O   HOH Z 233 " =    2.411
peak=   -3.625 closest distance to " O   HOH Z 422 " =    1.536
peak=   -3.620 closest distance to " O  BHOH Z 338 " =    1.193
peak=   -3.610 closest distance to " CD2 LEU A 237 " =    2.306
peak=   -3.591 closest distance to " CD1 TRP A 179 " =    1.017
peak=   -3.588 closest distance to " ND2 ASN A  60 " =    1.427
peak=   -3.582 closest distance to " CB  SER A 146 " =    2.152
peak=   -3.577 closest distance to " O   HOH Z  56 " =    0.990
peak=   -3.571 closest distance to " O   PHE A 218 " =    1.400
peak=   -3.571 closest distance to " O   HOH Z 392 " =    1.254
peak=   -3.566 closest distance to " OG BSER A 210 " =    2.443
peak=   -3.566 closest distance to " O   HOH Z 318 " =    1.595
peak=   -3.563 closest distance to " CG  GLU A  53 " =    1.353
peak=   -3.562 closest distance to " CA  SER A 276 " =    1.464
peak=   -3.546 closest distance to " O   HOH Z 407 " =    1.073
peak=   -3.541 closest distance to " O   HOH Z 196 " =    2.031
peak=   -3.538 closest distance to " O   HOH Z 196 " =    2.063
peak=   -3.530 closest distance to " O   VAL A 174 " =    2.035
peak=   -3.526 closest distance to " O   TRP A  92 " =    1.938
peak=   -3.525 closest distance to " O   HOH Z   5 " =    1.599
peak=   -3.518 closest distance to " O   HOH Z 423 " =    2.315
peak=   -3.515 closest distance to " CG2 THR A 221 " =    2.333
peak=   -3.514 closest distance to " O   HOH Z   6 " =    1.571
peak=   -3.511 closest distance to " CD2 LEU A 237 " =    2.611
peak=   -3.511 closest distance to " O   ASN A 187 " =    1.621
peak=   -3.508 closest distance to " CD  ARG A 195 " =    5.006
peak=   -3.494 closest distance to " CG2 VAL A 189 " =    2.191
peak=   -3.492 closest distance to " O   HOH Z 150 " =    1.045
peak=   -3.483 closest distance to " CA  GLY A 241 " =    2.246
peak=   -3.478 closest distance to " ND2 ASN A  45 " =    1.789
peak=   -3.478 closest distance to " O   HOH Z 197 " =    1.792
peak=   -3.474 closest distance to " C   GLY A 133 " =    1.236
peak=   -3.472 closest distance to " O   GLN A  11 " =    1.196
peak=   -3.469 closest distance to " C   SER A 206 " =    1.420
peak=   -3.468 closest distance to " OD1 ASN A 148 " =    1.476
peak=   -3.455 closest distance to " NH2 ARG A  66 " =    5.627
peak=   -3.454 closest distance to " O   HOH Z 151 " =    1.130
peak=   -3.454 closest distance to " OD1 ASP A 191 " =    1.494
peak=   -3.452 closest distance to " CB  ALA A 291 " =    2.480
peak=   -3.449 closest distance to " CB  ALA A  43 " =    2.527
peak=   -3.447 closest distance to " O   TYR A  15 " =    1.655
peak=   -3.446 closest distance to " O   SER A  95 " =    1.766
peak=   -3.445 closest distance to " CG  ASP A 231 " =    0.830
peak=   -3.445 closest distance to " CG1 VAL A 112 " =    2.597
peak=   -3.444 closest distance to " O   HOH Z 171 " =    2.366
peak=   -3.444 closest distance to " CH2 TRP A 150 " =    1.107
peak=   -3.438 closest distance to " NH2 ARG A  79 " =    2.146
peak=   -3.437 closest distance to " O   HOH Z  49 " =    0.836
peak=   -3.434 closest distance to " O   ALA A   1 " =    2.077
peak=   -3.430 closest distance to " CG  MET A 105 " =    0.952
peak=   -3.428 closest distance to " CD2 PHE A  59 " =    2.424
peak=   -3.425 closest distance to " O   HOH Z 210 " =    1.183
peak=   -3.421 closest distance to " CG  ARG A 219 " =    2.411
peak=   -3.420 closest distance to " ND2 ASN A  45 " =    1.076
peak=   -3.419 closest distance to " CD2 PHE A  61 " =    2.074
peak=   -3.415 closest distance to " O   HOH Z 377 " =    2.260
peak=   -3.414 closest distance to " O   HOH Z  71 " =    1.746
peak=   -3.409 closest distance to " CA  ASP A 298 " =    1.073
peak=   -3.408 closest distance to " O   HOH Z 418 " =    1.292
peak=   -3.402 closest distance to " O   HOH Z 114 " =    3.643
peak=   -3.397 closest distance to " CG  ARG A 269 " =    2.309
peak=   -3.396 closest distance to " N   LEU A 281 " =    1.937
peak=   -3.394 closest distance to " CB  ALA A  10 " =    2.103
peak=   -3.393 closest distance to " NE1 TRP A 177 " =    1.985
peak=   -3.389 closest distance to " CB  ALA A 248 " =    2.209
peak=   -3.374 closest distance to " O   ILE A 109 " =    2.575
peak=   -3.374 closest distance to " OD2 ASP A 171 " =    1.796
peak=   -3.371 closest distance to " O   HOH Z 150 " =    1.943
peak=   -3.362 closest distance to " O   HOH Z 150 " =    1.936
peak=   -3.354 closest distance to " O   HOH Z  52 " =    1.961
peak=   -3.352 closest distance to " O   ALA A  10 " =    1.865
peak=   -3.351 closest distance to " O   HOH Z 397 " =    1.152
peak=   -3.351 closest distance to " C   ALA A 158 " =    1.363
peak=   -3.343 closest distance to " CB  SER A 210 " =    1.118
peak=   -3.339 closest distance to " OG BSER A 210 " =    1.243
peak=   -3.337 closest distance to " O   HOH Z 139 " =    3.323
peak=   -3.334 closest distance to " O   ARG A  79 " =    0.919
peak=   -3.331 closest distance to " OG  SER A  63 " =    1.025
peak=   -3.320 closest distance to " O   HOH Z  37 " =    1.440
peak=   -3.318 closest distance to " SD  MET A 105 " =    2.411
peak=   -3.317 closest distance to " OG  SER A   3 " =    1.768
peak=   -3.311 closest distance to " N   ALA A 226 " =    1.936
peak=   -3.310 closest distance to " O   HOH Z 246 " =    1.177
peak=   -3.308 closest distance to " SG  CYS A 168 " =    1.004
peak=   -3.302 closest distance to " CD  GLN A  11 " =    1.268
peak=   -3.299 closest distance to " O   GLY A  80 " =    2.572
peak=   -3.290 closest distance to " CD2 PHE A 225 " =    1.409
peak=   -3.284 closest distance to " O   HOH Z 185 " =    2.459
peak=   -3.283 closest distance to " CD2 HIS A 115 " =    0.991
peak=   -3.280 closest distance to " CG2BVAL A  41 " =    1.931
peak=   -3.277 closest distance to " O   HOH Z 422 " =    1.257
peak=   -3.276 closest distance to " OD2 ASP A 171 " =    2.255
peak=   -3.275 closest distance to " O   HOH Z 424 " =    3.032
peak=   -3.269 closest distance to " O   HOH Z 369 " =    2.380
peak=   -3.267 closest distance to " CD  PRO A 213 " =    2.194
peak=   -3.266 closest distance to " N   THR A 220 " =    2.277
peak=   -3.258 closest distance to " OD1 ASP A 298 " =    2.025
peak=   -3.252 closest distance to " CE  MET A 105 " =    2.304
peak=   -3.252 closest distance to " CD  GLU A 236 " =    1.065
peak=   -3.250 closest distance to " CA  GLY A 133 " =    2.174
peak=   -3.247 closest distance to " OH  TYR A 169 " =    0.891
peak=   -3.246 closest distance to " O   HOH Z 368 " =    1.955
peak=   -3.242 closest distance to " NE1 TRP A 123 " =    1.369
peak=   -3.235 closest distance to " CE  MET A 105 " =    1.988
peak=   -3.233 closest distance to " CG  PRO A 198 " =    2.352
peak=   -3.231 closest distance to " O   HOH Z  41 " =    2.084
peak=   -3.230 closest distance to " CG  GLN A  58 " =    1.195
peak=   -3.228 closest distance to " O   SER A 146 " =    1.018
peak=   -3.228 closest distance to " C   ASN A 148 " =    1.719
peak=   -3.225 closest distance to " N   ALA A 248 " =    1.801
peak=   -3.222 closest distance to " O   HOH Z 222 " =    1.298
peak=   -3.221 closest distance to " O   HOH Z 396 " =    1.954
peak=   -3.219 closest distance to " O   ASP A 171 " =    1.055
peak=   -3.219 closest distance to " CG  ASP A 132 " =    2.333
peak=   -3.217 closest distance to " O   HOH Z 388 " =    1.911
peak=   -3.215 closest distance to " CE  MET A  93 " =    1.242
peak=   -3.215 closest distance to " OG1 THR A  82 " =    1.479
peak=   -3.214 closest distance to " O   SER A  26 " =    1.541
peak=   -3.214 closest distance to " O   LEU A 282 " =    2.202
peak=   -3.209 closest distance to " CE  LYS A 119 " =    2.055
peak=   -3.208 closest distance to " OG  SER A  87 " =    1.728
peak=   -3.207 closest distance to " ND2 ASN A  69 " =    1.543
peak=   -3.207 closest distance to " O   ALA A 256 " =    1.606
peak=   -3.202 closest distance to " OXT GLY A 302 " =    3.411
peak=   -3.201 closest distance to " CD  ARG A 139 " =    1.614
peak=   -3.199 closest distance to " O   HOH Z 221 " =    1.080
peak=   -3.197 closest distance to " O  BHOH Z  74 " =    1.031
peak=   -3.196 closest distance to " NH1 ARG A  66 " =    3.329
peak=   -3.196 closest distance to " NH2 ARG A  66 " =    1.557
peak=   -3.194 closest distance to " CG2 THR A   4 " =    1.834
peak=   -3.190 closest distance to " O   HOH Z 136 " =    2.017
peak=   -3.185 closest distance to " ND2 ASN A 187 " =    1.650
peak=   -3.183 closest distance to " O   HOH Z 135 " =    1.724
peak=   -3.180 closest distance to " O   SER A   3 " =    1.065
peak=   -3.180 closest distance to " O   HOH Z 339 " =    0.990
peak=   -3.179 closest distance to " OG  SER A 273 " =    2.192
peak=   -3.175 closest distance to " CG1 VAL A 197 " =    2.131
peak=   -3.170 closest distance to " O   HOH Z 176 " =    1.781
peak=   -3.170 closest distance to " O   HOH Z  93 " =    1.592
peak=   -3.168 closest distance to " NH2 ARG A 159 " =    2.452
peak=   -3.167 closest distance to " N   GLN A  58 " =    1.568
peak=   -3.167 closest distance to " O   HOH Z 428 " =    1.159
peak=   -3.166 closest distance to " O   HOH Z  29 " =    1.428
peak=   -3.161 closest distance to " CA  TRP A 274 " =    1.451
peak=   -3.154 closest distance to " O   HOH Z 426 " =    1.759
peak=   -3.153 closest distance to " O   HOH Z 283 " =    1.795
peak=   -3.147 closest distance to " CG2AVAL A  41 " =    2.858
peak=   -3.146 closest distance to " CZ  TYR A 169 " =    1.940
peak=   -3.138 closest distance to " CA  GLU A   2 " =    2.550
peak=   -3.138 closest distance to " N   ASP A 272 " =    1.215
peak=   -3.137 closest distance to " O   THR A  52 " =    1.873
peak=   -3.132 closest distance to " O   HOH Z 103 " =    1.850
peak=   -3.128 closest distance to " O   GLY A 196 " =    1.109
peak=   -3.122 closest distance to " O   HOH Z 380 " =    4.306
peak=   -3.122 closest distance to " CG2BVAL A  41 " =    1.417
peak=   -3.120 closest distance to " CG1 VAL A 112 " =    2.458
peak=   -3.119 closest distance to " O   HOH Z 174 " =    3.706
peak=   -3.113 closest distance to " O   HOH Z 313 " =    1.409
peak=   -3.110 closest distance to " CG  GLN A 103 " =    2.420
peak=   -3.109 closest distance to " OG ASER A 134 " =    1.277
peak=   -3.106 closest distance to " O   HOH Z 109 " =    3.475
peak=   -3.105 closest distance to " CE2 TRP A 274 " =    1.210
peak=   -3.098 closest distance to " O   HOH Z 252 " =    4.245
peak=   -3.093 closest distance to " O   ASP A 107 " =    1.521
peak=   -3.089 closest distance to " OE2 GLU A   2 " =    1.534
peak=   -3.088 closest distance to " CD  LYS A 289 " =    2.373
peak=   -3.085 closest distance to " O   HOH Z  39 " =    0.708
peak=   -3.064 closest distance to " O   HOH Z 384 " =    1.600
peak=   -3.061 closest distance to " OG BSER A 134 " =    1.374
peak=   -3.058 closest distance to " O   HOH Z 140 " =    1.211
peak=   -3.055 closest distance to " O   HOH Z 157 " =    3.552
peak=   -3.053 closest distance to " O   HOH Z  40 " =    2.872
peak=   -3.053 closest distance to " O   HOH Z 345 " =    3.007
peak=   -3.051 closest distance to " OD1 ASN A 176 " =    1.425
peak=   -3.034 closest distance to " CH2 TRP A 177 " =    1.961

================= 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    :  0.4292 0.4140   6.248920e+00   6.213440e+00
   1_bss:  0.4175 0.3986   6.235298e+00   6.197663e+00
   1_xyz:  0.3464 0.3696   6.109042e+00   6.144413e+00
   1_adp:  0.3212 0.3733   6.060622e+00   6.148390e+00
   1_occ:  0.3207 0.3729   6.059842e+00   6.148130e+00
   2_bss:  0.3203 0.3715   6.061463e+00   6.148952e+00
   2_xyz:  0.2439 0.2904   5.810419e+00   5.946756e+00
   2_adp:  0.2196 0.2797   5.742080e+00   5.914845e+00
   2_occ:  0.2193 0.2797   5.741444e+00   5.915030e+00
   3_bss:  0.2183 0.2771   5.738157e+00   5.910496e+00
   3_xyz:  0.1783 0.2247   5.542350e+00   5.728457e+00
   3_adp:  0.1669 0.2128   5.489067e+00   5.681832e+00
   3_occ:  0.1667 0.2130   5.488931e+00   5.682040e+00
   4_bss:  0.1671 0.2128   5.489438e+00   5.681689e+00
   4_xyz:  0.1403 0.1842   5.329489e+00   5.541112e+00
   4_adp:  0.1331 0.1813   5.292216e+00   5.516896e+00
   4_occ:  0.1331 0.1812   5.291785e+00   5.516502e+00
   5_bss:  0.1334 0.1813   5.293550e+00   5.516919e+00
   5_xyz:  0.1242 0.1733   5.237955e+00   5.474237e+00
   5_adp:  0.1239 0.1692   5.224974e+00   5.450549e+00
   5_occ:  0.1238 0.1691   5.224561e+00   5.450481e+00
   5_bss:  0.1238 0.1691   5.224664e+00   5.450525e+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:  0.294  26.699  -2.852   5.736  -1.776   0.000  -0.000  -0.000
   1_xyz:  0.294  26.699  -2.852   5.736  -1.776   0.000  -0.000  -0.000
   1_adp:  0.294  26.699  -2.852   5.736  -1.776   0.000  -0.000  -0.000
   1_occ:  0.294  26.699  -2.852   5.736  -1.776   0.000  -0.000  -0.000
   2_bss:  0.283  38.322  -2.387   3.325  -0.907   0.000  -0.000  -0.000
   2_xyz:  0.283  38.322  -2.387   3.325  -0.907   0.000  -0.000  -0.000
   2_adp:  0.283  38.322  -2.387   3.325  -0.907   0.000  -0.000  -0.000
   2_occ:  0.283  38.322  -2.387   3.325  -0.907   0.000  -0.000  -0.000
   3_bss:  0.318  55.781  -1.787   1.219  -0.573   0.000  -0.000  -0.000
   3_xyz:  0.318  55.781  -1.787   1.219  -0.573   0.000  -0.000  -0.000
   3_adp:  0.318  55.781  -1.787   1.219  -0.573   0.000  -0.000  -0.000
   3_occ:  0.318  55.781  -1.787   1.219  -0.573   0.000  -0.000  -0.000
   4_bss:  0.324  61.926  -2.151   0.166  -0.817   0.000  -0.000  -0.000
   4_xyz:  0.324  61.926  -2.151   0.166  -0.817   0.000  -0.000  -0.000
   4_adp:  0.324  61.926  -2.151   0.166  -0.817   0.000  -0.000  -0.000
   4_occ:  0.324  61.926  -2.151   0.166  -0.817   0.000  -0.000  -0.000
   5_bss:  0.327  64.795  -2.065  -0.241  -0.598  -0.000  -0.000  -0.000
   5_xyz:  0.327  64.795  -2.065  -0.241  -0.598  -0.000  -0.000  -0.000
   5_adp:  0.327  64.795  -2.065  -0.241  -0.598  -0.000  -0.000  -0.000
   5_occ:  0.327  64.795  -2.065  -0.241  -0.598  -0.000  -0.000  -0.000
   5_bss:  0.324  60.072  -1.996  -0.422  -0.506  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  46.209 0.5705  0.7447    53154.522
   1_bss:  45.123 0.5825  0.7655    49453.850
   1_xyz:  42.294 0.6151  0.7958    41674.622
   1_adp:  42.135 0.6170  0.7930    41572.464
   1_occ:  42.122 0.6170  0.7918    41446.356
   2_bss:  41.830 0.6207  0.7912    41194.857
   2_xyz:  31.122 0.7440  0.9246    23087.923
   2_adp:  29.293 0.7649  0.9273    21154.216
   2_occ:  29.283 0.7650  0.9272    21152.211
   3_bss:  28.972 0.7684  0.9210    20791.472
   3_xyz:  22.246 0.8394  0.9737    13079.867
   3_adp:  20.752 0.8548  0.9754    11889.139
   3_occ:  20.753 0.8548  0.9755    11903.015
   4_bss:  20.680 0.8555  0.9579    11845.416
   4_xyz:  17.437 0.8852  0.9736     8624.682
   4_adp:  16.804 0.8913  0.9668     8260.953
   4_occ:  16.790 0.8914  0.9668     8252.135
   5_bss:  16.781 0.8915  0.9660     8250.835
   5_xyz:  15.894 0.8992  0.9707     7610.316
   5_adp:  15.399 0.9036  0.9673     7335.733
   5_occ:  15.394 0.9036  0.9673     7333.659
   5_bss:  15.397 0.9036  0.9675     7334.044
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.7047e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.7047e-01
   1_xyz:   1.344  0.010  0.082 15.536  0.005  4.108   9.4666e-02
   1_adp:   1.344  0.010  0.082 15.536  0.005  4.108   9.4666e-02
   1_occ:   1.344  0.010  0.082 15.536  0.005  4.108   9.4666e-02
   2_bss:   1.344  0.010  0.082 15.536  0.005  4.108   9.4666e-02
   2_xyz:   1.512  0.012  0.097 15.958  0.006  4.113   1.3183e-01
   2_adp:   1.512  0.012  0.097 15.958  0.006  4.113   1.3183e-01
   2_occ:   1.512  0.012  0.097 15.958  0.006  4.113   1.3183e-01
   3_bss:   1.512  0.012  0.097 15.958  0.006  4.113   1.3183e-01
   3_xyz:   0.941  0.007  0.064 14.810  0.004  4.124   5.7311e-02
   3_adp:   0.941  0.007  0.064 14.810  0.004  4.124   5.7311e-02
   3_occ:   0.941  0.007  0.064 14.810  0.004  4.124   5.7311e-02
   4_bss:   0.941  0.007  0.064 14.810  0.004  4.124   5.7311e-02
   4_xyz:   1.001  0.006  0.072 14.548  0.004  4.120   5.8011e-02
   4_adp:   1.001  0.006  0.072 14.548  0.004  4.120   5.8011e-02
   4_occ:   1.001  0.006  0.072 14.548  0.004  4.120   5.8011e-02
   5_bss:   1.001  0.006  0.072 14.548  0.004  4.120   5.8011e-02
   5_xyz:   0.976  0.007  0.071 14.703  0.004  4.113   5.6410e-02
   5_adp:   0.976  0.007  0.071 14.703  0.004  4.113   5.6410e-02
   5_occ:   0.976  0.007  0.071 14.703  0.004  4.113   5.6410e-02
   5_bss:   0.976  0.007  0.071 14.703  0.004  4.113   5.6410e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.780   2.4191e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.780   2.4191e-01
   1_xyz:   8.371  0.054  0.442 85.986  0.052  2.153   9.0511e-02
   1_adp:   8.371  0.054  0.442 85.986  0.052  2.153   9.0511e-02
   1_occ:   8.371  0.054  0.442 85.986  0.052  2.153   9.0511e-02
   2_bss:   8.371  0.054  0.442 85.986  0.052  2.153   9.0511e-02
   2_xyz:   8.047  0.077  0.291 82.529  0.039  2.085   2.2479e-01
   2_adp:   8.047  0.077  0.291 82.529  0.039  2.085   2.2479e-01
   2_occ:   8.047  0.077  0.291 82.529  0.039  2.085   2.2479e-01
   3_bss:   8.047  0.077  0.291 82.529  0.039  2.085   2.2479e-01
   3_xyz:   7.473  0.039  0.241 89.252  0.039  2.228   5.4683e-02
   3_adp:   7.473  0.039  0.241 89.252  0.039  2.228   5.4683e-02
   3_occ:   7.473  0.039  0.241 89.252  0.039  2.228   5.4683e-02
   4_bss:   7.473  0.039  0.241 89.252  0.039  2.228   5.4683e-02
   4_xyz:   6.913  0.045  0.214 81.006  0.027  2.335   4.5158e-02
   4_adp:   6.913  0.045  0.214 81.006  0.027  2.335   4.5158e-02
   4_occ:   6.913  0.045  0.214 81.006  0.027  2.335   4.5158e-02
   5_bss:   6.913  0.045  0.214 81.006  0.027  2.335   4.5158e-02
   5_xyz:   7.089  0.041  0.223 81.225  0.029  2.404   3.5959e-02
   5_adp:   7.089  0.041  0.223 81.225  0.029  2.404   3.5959e-02
   5_occ:   7.089  0.041  0.223 81.225  0.029  2.404   3.5959e-02
   5_bss:   7.089  0.041  0.223 81.225  0.029  2.404   3.5959e-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:  94.80   0.00  17.38  94.80   0.00  14.09  68.85   2.53  35.27
   1_occ:  94.80   0.00  17.38  94.80   0.00  14.09  68.85   2.53  35.27
   2_bss:  94.80   0.00  17.38  94.80   0.00  14.09  68.85   2.53  35.27
   2_xyz:  94.80   0.00  17.38  94.80   0.00  14.09  68.85   2.53  35.27
   2_adp:  80.46   0.00  17.44  79.28   0.00  13.62  80.46   1.80  38.25
   2_occ:  80.46   0.00  17.44  79.28   0.00  13.62  80.46   1.80  38.25
   3_bss:  80.46   0.00  17.44  79.28   0.00  13.62  80.46   1.80  38.25
   3_xyz:  80.46   0.00  17.44  79.28   0.00  13.62  80.46   1.80  38.25
   3_adp:  92.92   0.00  17.50  92.92   0.00  13.06  91.21   5.05  41.70
   3_occ:  92.92   0.00  17.50  92.92   0.00  13.06  91.21   5.05  41.70
   4_bss:  92.92   0.00  17.50  92.92   0.00  13.06  91.21   5.05  41.70
   4_xyz:  92.92   0.00  17.50  92.92   0.00  13.06  91.21   5.05  41.70
   4_adp: 113.29   0.00  17.77 113.29   0.00  12.74 109.96   4.32  45.17
   4_occ: 113.29   0.00  17.77 113.29   0.00  12.74 109.96   4.32  45.17
   5_bss: 113.29   0.00  17.77 113.29   0.00  12.74 109.96   4.32  45.17
   5_xyz: 113.29   0.00  17.77 113.29   0.00  12.74 109.96   4.32  45.17
   5_adp: 109.28   0.00  16.81 109.28   0.00  12.26 103.37   4.43  41.56
   5_occ: 109.28   0.00  16.81 109.28   0.00  12.26 103.37   4.43  41.56
   5_bss: 109.28   0.00  16.81 109.28   0.00  12.27 103.38   4.43  41.56
------------------------------------------------------------------------
 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:    1.649    0.010    0.267
   1_adp:    1.649    0.010    0.267
   1_occ:    1.649    0.010    0.267
   2_bss:    1.649    0.010    0.267
   2_xyz:    1.604    0.065    0.592
   2_adp:    1.604    0.065    0.592
   2_occ:    1.604    0.065    0.592
   3_bss:    1.604    0.065    0.592
   3_xyz:    1.383    0.060    0.662
   3_adp:    1.383    0.060    0.662
   3_occ:    1.383    0.060    0.662
   4_bss:    1.383    0.060    0.662
   4_xyz:    1.517    0.064    0.738
   4_adp:    1.517    0.064    0.738
   4_occ:    1.517    0.064    0.738
   5_bss:    1.517    0.064    0.738
   5_xyz:    1.485    0.064    0.762
   5_adp:    1.485    0.064    0.762
   5_occ:    1.485    0.064    0.762
   5_bss:    1.485    0.064    0.762
------------------------------------------------------------------------

CPU time actual refinement: 349.69


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_477/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_477/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_477/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_477/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_477/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 349.54 
  Macro-tasks:
    bulk solvent and scale       = 38.19  
    individual site refinement   = 150.91 
    weights calculation          = 30.24  
    collect and process          = 6.55   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 226.02 
  Micro-tasks:
    mask                            = 2.39   
    f_calc                          = 113.29 
    alpha_beta                      = 8.10   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 123.29 
    fmodel                         = 6.83   
    r_factors                      = 0.11   
    phase_errors                   = 10.83  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 266.24 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.873 micro seconds
Total CPU time: 6.05 minutes
from_scatterers_fft:    662 calls, 112.79 s
gradients_fft:          607 calls, 109.06 s

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

# Date 2008-01-16 Time 04:55:27 PST -0800 (1200488127.81 s)
Start R-work = 0.4292, R-free = 0.4140 (no bulk solvent and anisotropic scale)
Final R-work = 0.1425, R-free = 0.1851 (no bulk solvent and anisotropic scale)

Start R-work = 0.4175, R-free = 0.3986
Final R-work = 0.1238, R-free = 0.1691