# Date 2008-01-16 Time 04:28:29 PST -0800 (1200486509.57 s)
#phil __OFF__

Command line arguments: "../333.param" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 19818
JOB_ID = 5159
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 333

-------------------------------------------------------------------------------
  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: (69.1963, 47.6339, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.6339, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.885 1.97061
Completeness in resolution range: 0.953839
Completeness with d_max=infinity: 0.950876

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8850
                             d_min =   1.9706

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: (69.1963, 47.6339, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.885 1.97061
Completeness in resolution range: 0.953839
Completeness with d_max=infinity: 0.950876

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8855 -  4.2164 [2162/2190]  1946   216  10.0%
  bin  2:  4.2164 -  3.3593 [2065/2088]  1858   207  10.0%
  bin  3:  3.3593 -  2.9384 [2046/2071]  1841   205  10.0%
  bin  4:  2.9384 -  2.6714 [2024/2040]  1822   202  10.0%
  bin  5:  2.6714 -  2.4809 [2004/2042]  1798   206  10.3%
  bin  6:  2.4809 -  2.3352 [2003/2036]  1811   192   9.6%
  bin  7:  2.3352 -  2.2187 [1983/2020]  1784   199  10.0%
  bin  8:  2.2187 -  2.1224 [1986/2028]  1787   199  10.0%
  bin  9:  2.1224 -  2.0409 [1975/2014]  1779   196   9.9%
  bin 10:  2.0409 -  1.9706 [1341/2008]  1204   137  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_333/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:
        1.55 -     2.22: 17
        2.22 -     2.89: 1340
        2.89 -     3.56: 4520
        3.56 -     4.23: 9224
        4.23 -     4.90: 13367
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.551 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.785 3.040 -x+1,y+1/2,-z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.798 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 109 " - " O   HOH Z 417 "  1.851 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28463 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_333/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_333/model_refine_001.geo

CPU time processing inputs: 9.35


============================ 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 = 69.19625 47.63395 85.5261 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: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4019   r_free= 0.3966   ksol= 0.00   Bsol= 0.00   scale= 0.940    |
|                                                                             |
| 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:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.193345                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8855 -  4.7026 0.99   1398  158 0.3246 0.3404      6.4493      6.4974|
|  2:  4.7026 -  3.7523 0.99   1350  148 0.3290 0.3203      6.6405      6.6311|
|  3:  3.7523 -  3.2838 0.99   1318  149 0.3525 0.3389      6.5261      6.5391|
|  4:  3.2838 -  2.9862 0.99   1321  136 0.3749 0.3591       6.386       6.317|
|  5:  2.9862 -  2.7736 0.98   1296  147 0.4134 0.3750      6.2708       6.217|
|  6:  2.7736 -  2.6110 0.99   1293  144 0.4303 0.4076      6.1955      6.0821|
|  7:  2.6110 -  2.4809 0.99   1289  154 0.4304 0.3931      6.1743      6.0691|
|  8:  2.4809 -  2.3733 0.99   1311  132 0.4423 0.4819      6.1127      6.1441|
|  9:  2.3733 -  2.2823 0.99   1273  149 0.4731 0.4640      6.0714      6.1242|
| 10:  2.2823 -  2.2038 0.98   1270  139 0.4557 0.4955      6.0607      6.0675|
| 11:  2.2038 -  2.1351 0.98   1274  146 0.4590 0.4446      5.9865      6.0239|
| 12:  2.1351 -  2.0742 1.00   1286  142 0.4665 0.4624      5.9233      5.9604|
| 13:  2.0742 -  2.0198 0.96   1272  130 0.4812 0.4920       5.862      5.8477|
| 14:  2.0198 -  1.9706 0.54    679   85 0.4724 0.4616      5.7941      5.6922|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8855 -  4.7026  1398   158  0.73  31.47   0.85     0.74      59302.44|
|  2:  4.7026 -  3.7523  1350   148  0.78  28.08   0.95     0.87      70366.99|
|  3:  3.7523 -  3.2838  1318   149  0.73  32.59   0.97     0.91      69107.02|
|  4:  3.2838 -  2.9862  1321   136  0.69  36.07   0.96     0.89      58292.57|
|  5:  2.9862 -  2.7736  1296   147  0.65  39.97   0.93     0.86      47081.11|
|  6:  2.7736 -  2.6110  1293   144  0.63  41.82   0.96     0.83      41237.08|
|  7:  2.6110 -  2.4809  1289   154  0.62  42.14   0.96     0.81      39066.35|
|  8:  2.4809 -  2.3733  1311   132  0.56  47.60   0.97     0.76      40957.78|
|  9:  2.3733 -  2.2823  1273   149  0.51  51.76   0.95     0.71      40910.03|
| 10:  2.2823 -  2.2038  1270   139  0.48  54.01   1.00     0.67      40713.85|
| 11:  2.2038 -  2.1351  1274   146  0.47  54.95   0.98     0.68      37969.02|
| 12:  2.1351 -  2.0742  1286   142  0.46  55.71   0.99     0.70      35394.31|
| 13:  2.0742 -  2.0198  1272   130  0.47  54.96   0.97     0.70      29790.72|
| 14:  2.0198 -  1.9706   679    85  0.48  53.52   0.98     0.67      23512.25|
|alpha:            min =        0.67 max =            0.91 mean =         0.77|
|beta:             min =    23512.25 max =        70366.99 mean =     46279.63|
|figures of merit: min =        0.00 max =            1.00 mean =         0.59|
|phase err.(work): min =        0.00 max =           89.98 mean =        44.10|
|phase err.(test): min =        0.00 max =           89.72 mean =        44.18|
|-----------------------------------------------------------------------------|

============================== 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 = 5.146838              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 91.024   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.201390              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.297   (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 |  1.551 -  1.886:        5 |
| 0.007 - 0.014:   729 |   0.989 -   1.976:   994 |  1.886 -  2.221:       12 |
| 0.014 - 0.021:   262 |   1.976 -   2.963:   470 |  2.221 -  2.556:       45 |
| 0.021 - 0.028:    63 |   2.963 -   3.950:   196 |  2.556 -  2.891:     1295 |
| 0.028 - 0.035:    15 |   3.950 -   4.938:    66 |  2.891 -  3.226:     1919 |
| 0.035 - 0.042:     0 |   4.938 -   5.925:    29 |  3.226 -  3.561:     2601 |
| 0.042 - 0.049:     2 |   5.925 -   6.912:    16 |  3.561 -  3.895:     4672 |
| 0.049 - 0.056:     0 |   6.912 -   7.899:     2 |  3.895 -  4.230:     4552 |
| 0.056 - 0.063:     0 |   7.899 -   8.887:     3 |  4.230 -  4.565:     6062 |
| 0.063 - 0.070:     1 |   8.887 -   9.874:     4 |  4.565 -  4.900:     7305 |
|-----------------------------------------------------------------------------|
|-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 |        0.176 |
| 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  1.551 |       0.387 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.729)------------------------------------------|
|    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: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4019   r_free= 0.3966   ksol= 0.00   Bsol= 0.00   scale= 0.940    |
|                                                                             |
| 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:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.193345                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3924   r_free= 0.3845   ksol= 0.30   Bsol= 24.85   scale= 0.965   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.57,2.64,-0.70,0.00,-0.00,-0.00); trace/3= 0.12                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.180261                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.615796              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 90.765   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.644706              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.052   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3924      final r-factor (work) = 0.2612          |
| start r-factor (free) = 0.3845      final r-factor (free) = 0.2823          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.4468 = 4.62 * 0.50 * 6.1835 + 1.00 * 0.1759                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.8795 = 4.62 * 0.50 * 5.9751 + 1.00 * 0.0896                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2612      final r-factor (work) = 0.2373          |
| start r-factor (free) = 0.2823      final r-factor (free) = 0.2942          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8582 = 0.64 * 1.00 * 5.9751 + 1.00 * 0.0060                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7464 = 0.64 * 1.00 * 5.7877 + 1.00 * 0.0150                               |
|-----------------------------------------------------------------------------|
| number of iterations = 10      |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.729)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    67.04   17.55    None  None   None       |
|    all(noH): 2823   0      0.00    67.04   17.55    None  None   None       |
|    Sol.    : 438    0      3.67    67.04   37.98    None  None   None       |
|    Mac.    : 2385   0      0.00    61.67   13.80    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.704:  482   |   5:    33.521 -  40.225:  136        |
|      1:     6.704 -  13.408:  957   |   6:    40.225 -  46.929:   88        |
|      2:    13.408 -  20.113:  551   |   7:    46.929 -  53.633:   95        |
|      3:    20.113 -  26.817:  287   |   8:    53.633 -  60.337:   51        |
|      4:    26.817 -  33.521:  160   |   9:    60.337 -  67.042:   16        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2373 r_free = 0.2942             target_work(ml) = 5.802         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2368 r_free = 0.2949             target_work(ml) = 5.801         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2368   r_free= 0.2949   ksol= 0.30   Bsol= 24.85   scale= 1.029   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.57,2.64,-0.70,0.00,-0.00,-0.00); trace/3= 0.12                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.801057                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2354   r_free= 0.2924   ksol= 0.32   Bsol= 42.76   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.59,0.31,-1.26,0.00,-0.00,-0.00); trace/3= -1.18                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.797170                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.904199              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.881   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.243518              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 104.266  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2354      final r-factor (work) = 0.1725          |
| start r-factor (free) = 0.2924      final r-factor (free) = 0.2182          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.4976 = 2.90 * 0.50 * 5.7903 + 1.00 * 0.0896                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2940 = 2.90 * 0.50 * 5.6723 + 1.00 * 0.0573                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1725      final r-factor (work) = 0.1619          |
| start r-factor (free) = 0.2182      final r-factor (free) = 0.2022          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3986 = 0.24 * 1.00 * 5.6723 + 1.00 * 0.0173                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3435 = 0.24 * 1.00 * 5.4838 + 1.00 * 0.0081                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.729)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.29    70.62   16.96    None  None   None       |
|    all(noH): 2823   0      1.29    70.62   16.96    None  None   None       |
|    Sol.    : 438    0      5.14    68.73   37.74    None  None   None       |
|    Mac.    : 2385   0      1.29    70.62   13.15    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.285 -   8.219:  610   |   5:    35.954 -  42.888:  128        |
|      1:     8.219 -  15.153: 1203   |   6:    42.888 -  49.822:   82        |
|      2:    15.153 -  22.087:  405   |   7:    49.822 -  56.756:   72        |
|      3:    22.087 -  29.021:  165   |   8:    56.756 -  63.690:   36        |
|      4:    29.021 -  35.954:  109   |   9:    63.690 -  70.623:   13        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1619 r_free = 0.2022             target_work(ml) = 5.453         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1617 r_free = 0.2022             target_work(ml) = 5.453         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1617   r_free= 0.2022   ksol= 0.32   Bsol= 42.76   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.59,0.31,-1.26,0.00,-0.00,-0.00); trace/3= -1.18                         |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.452517                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1619   r_free= 0.2017   ksol= 0.32   Bsol= 45.45   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.75,-0.81,-1.35,-0.00,-0.00,-0.00); trace/3= -1.64                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.451497                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.763460              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.946  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.805709              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.705  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1619      final r-factor (work) = 0.1274          |
| start r-factor (free) = 0.2017      final r-factor (free) = 0.1687          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6359 = 2.76 * 0.50 * 5.4849 + 1.00 * 0.0571                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4396 = 2.76 * 0.50 * 5.3417 + 1.00 * 0.0588                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1274      final r-factor (work) = 0.1209          |
| start r-factor (free) = 0.1687      final r-factor (free) = 0.1654          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3119 = 0.81 * 1.00 * 5.3417 + 1.00 * 0.0081                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2133 = 0.81 * 1.00 * 5.2177 + 1.00 * 0.0094                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.729)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.72   17.10    None  None   None       |
|    all(noH): 2823   0      0.00    80.72   17.10    None  None   None       |
|    Sol.    : 438    0      0.00    70.19   39.99    None  None   None       |
|    Mac.    : 2385   0      1.36    80.72   12.90    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.072:  612   |   5:    40.361 -  48.434:  114        |
|      1:     8.072 -  16.145: 1338   |   6:    48.434 -  56.506:   93        |
|      2:    16.145 -  24.217:  344   |   7:    56.506 -  64.578:   56        |
|      3:    24.217 -  32.289:  130   |   8:    64.578 -  72.651:   23        |
|      4:    32.289 -  40.361:  110   |   9:    72.651 -  80.723:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1209 r_free = 0.1654             target_work(ml) = 5.205         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1209 r_free = 0.1654             target_work(ml) = 5.205         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1209   r_free= 0.1654   ksol= 0.32   Bsol= 45.45   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.75,-0.81,-1.35,-0.00,-0.00,-0.00); trace/3= -1.64                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.204549                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1214   r_free= 0.1652   ksol= 0.32   Bsol= 48.94   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.75,-1.27,-1.33,-0.00,-0.00,-0.00); trace/3= -1.78                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.206126                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.290746              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 134.188  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.664789              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.434   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1214      final r-factor (work) = 0.1129          |
| start r-factor (free) = 0.1652      final r-factor (free) = 0.1593          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0370 = 2.29 * 0.50 * 5.2194 + 1.00 * 0.0588                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9886 = 2.29 * 0.50 * 5.1760 + 1.00 * 0.0601                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1129      final r-factor (work) = 0.1114          |
| start r-factor (free) = 0.1593      final r-factor (free) = 0.1587          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4502 = 0.66 * 1.00 * 5.1760 + 1.00 * 0.0093                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4317 = 0.66 * 1.00 * 5.1480 + 1.00 * 0.0094                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.729)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.47   16.90    None  None   None       |
|    all(noH): 2823   0      0.00    88.47   16.90    None  None   None       |
|    Sol.    : 438    0      0.00    76.97   39.89    None  None   None       |
|    Mac.    : 2385   0      1.07    88.47   12.68    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 -   8.847:  824   |   5:    44.235 -  53.081:  109        |
|      1:     8.847 -  17.694: 1248   |   6:    53.081 -  61.928:   82        |
|      2:    17.694 -  26.541:  271   |   7:    61.928 -  70.775:   28        |
|      3:    26.541 -  35.388:  138   |   8:    70.775 -  79.622:   11        |
|      4:    35.388 -  44.235:  109   |   9:    79.622 -  88.469:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1114 r_free = 0.1587             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1114 r_free = 0.1588             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1114   r_free= 0.1588   ksol= 0.32   Bsol= 48.94   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.75,-1.27,-1.33,-0.00,-0.00,-0.00); trace/3= -1.78                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.144786                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1113   r_free= 0.1588   ksol= 0.32   Bsol= 48.53   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,-1.25,-1.13,-0.00,-0.00,-0.00); trace/3= -1.65                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.144938                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.477702              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 154.115  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.215529              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 125.578  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1113      final r-factor (work) = 0.1122          |
| start r-factor (free) = 0.1588      final r-factor (free) = 0.1586          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8640 = 1.48 * 0.50 * 5.1483 + 1.00 * 0.0601                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8557 = 1.48 * 0.50 * 5.1505 + 1.00 * 0.0503                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1122      final r-factor (work) = 0.1118          |
| start r-factor (free) = 0.1586      final r-factor (free) = 0.1592          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2699 = 1.22 * 1.00 * 5.1505 + 1.00 * 0.0094                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2675 = 1.22 * 1.00 * 5.1480 + 1.00 * 0.0100                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.729)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.42    99.09   16.85    None  None   None       |
|    all(noH): 2823   0      0.42    99.09   16.85    None  None   None       |
|    Sol.    : 438    0      1.68    88.77   40.05    None  None   None       |
|    Mac.    : 2385   0      0.42    99.09   12.58    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:     0.419 -  10.286: 1193   |   5:    49.752 -  59.619:   92        |
|      1:    10.286 -  20.152: 1015   |   6:    59.619 -  69.486:   52        |
|      2:    20.152 -  30.019:  197   |   7:    69.486 -  79.353:    7        |
|      3:    30.019 -  39.886:  127   |   8:    79.353 -  89.219:    8        |
|      4:    39.886 -  49.752:  128   |   9:    89.219 -  99.086:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1118 r_free = 0.1592             target_work(ml) = 5.151         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1117 r_free = 0.1592             target_work(ml) = 5.150         |
| occupancies: max = 1.00  min = 0.05   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1117   r_free= 0.1592   ksol= 0.32   Bsol= 48.53   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.55,-1.25,-1.13,-0.00,-0.00,-0.00); trace/3= -1.65                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.150394                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8855 -  4.7026 0.99   1398  158 0.0974 0.1292      5.3659      5.5422|
|  2:  4.7026 -  3.7523 0.99   1350  148 0.0836 0.1055      5.4174      5.5981|
|  3:  3.7523 -  3.2838 0.99   1318  149 0.1039 0.1503       5.457      5.8334|
|  4:  3.2838 -  2.9862 0.99   1321  136 0.1220 0.1598      5.4514      5.6275|
|  5:  2.9862 -  2.7736 0.98   1296  147 0.1314 0.1716      5.3282      5.5033|
|  6:  2.7736 -  2.6110 0.99   1293  144 0.1272 0.1979      5.2375      5.4837|
|  7:  2.6110 -  2.4809 0.99   1289  154 0.1189 0.1634      5.1435      5.3612|
|  8:  2.4809 -  2.3733 0.99   1311  132 0.1194 0.1771      5.0903      5.3374|
|  9:  2.3733 -  2.2823 0.99   1273  149 0.1179 0.1896      5.0285      5.3393|
| 10:  2.2823 -  2.2038 0.98   1270  139 0.1131 0.1760      4.9841       5.181|
| 11:  2.2038 -  2.1351 0.98   1274  146 0.1164 0.1800      4.9375      5.2619|
| 12:  2.1351 -  2.0742 1.00   1286  142 0.1101 0.1696      4.8663       5.151|
| 13:  2.0742 -  2.0198 0.96   1272  130 0.1148 0.1771      4.8118      5.0843|
| 14:  2.0198 -  1.9706 0.54    679   85 0.1112 0.1811      4.7302      4.9632|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8855 -  4.7026  1398   158  0.94   8.87   0.98     0.95       6820.54|
|  2:  4.7026 -  3.7523  1350   148  0.95   7.82   1.02     1.00       8651.48|
|  3:  3.7523 -  3.2838  1318   149  0.94  10.90   1.03     1.02       9962.46|
|  4:  3.2838 -  2.9862  1321   136  0.92  13.65   1.01     1.00      10279.24|
|  5:  2.9862 -  2.7736  1296   147  0.90  16.10   1.00     0.98       8390.03|
|  6:  2.7736 -  2.6110  1293   144  0.90  16.43   0.98     0.95       7318.10|
|  7:  2.6110 -  2.4809  1289   154  0.91  15.05   0.99     0.96       5963.45|
|  8:  2.4809 -  2.3733  1311   132  0.91  15.37   1.00     0.97       5593.90|
|  9:  2.3733 -  2.2823  1273   149  0.90  15.96   1.00     0.96       5007.51|
| 10:  2.2823 -  2.2038  1270   139  0.90  15.96   0.99     0.95       4687.10|
| 11:  2.2038 -  2.1351  1274   146  0.91  15.76   0.99     0.95       4283.89|
| 12:  2.1351 -  2.0742  1286   142  0.91  15.36   1.00     0.99       3895.17|
| 13:  2.0742 -  2.0198  1272   130  0.90  16.61   0.99     0.99       3541.50|
| 14:  2.0198 -  1.9706   679    85  0.90  15.97   0.97     0.92       2934.26|
|alpha:            min =        0.92 max =            1.02 mean =         0.97|
|beta:             min =     2934.26 max =        10279.24 mean =      6385.22|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.77 mean =        14.15|
|phase err.(test): min =        0.00 max =           89.28 mean =        13.76|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1117   r_free= 0.1592   ksol= 0.32   Bsol= 48.65   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.36,-1.12,-0.94,-0.00,-0.00,-0.00); trace/3= -1.47                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.150481                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1117   r_free= 0.1592   ksol= 0.32   Bsol= 48.65   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-2.36,-1.12,-0.94,-0.00,-0.00,-0.00); trace/3= -1.47                       |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.150481                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8855 -  4.7026 0.99   1398  158 0.0975 0.1293      5.3665      5.5435|
|  2:  4.7026 -  3.7523 0.99   1350  148 0.0837 0.1055       5.418      5.5984|
|  3:  3.7523 -  3.2838 0.99   1318  149 0.1039 0.1503      5.4572      5.8338|
|  4:  3.2838 -  2.9862 0.99   1321  136 0.1220 0.1598      5.4513      5.6275|
|  5:  2.9862 -  2.7736 0.98   1296  147 0.1314 0.1716       5.328       5.503|
|  6:  2.7736 -  2.6110 0.99   1293  144 0.1272 0.1978      5.2372       5.483|
|  7:  2.6110 -  2.4809 0.99   1289  154 0.1189 0.1635      5.1433      5.3613|
|  8:  2.4809 -  2.3733 0.99   1311  132 0.1194 0.1771      5.0904      5.3373|
|  9:  2.3733 -  2.2823 0.99   1273  149 0.1179 0.1896      5.0286      5.3395|
| 10:  2.2823 -  2.2038 0.98   1270  139 0.1131 0.1761      4.9844      5.1813|
| 11:  2.2038 -  2.1351 0.98   1274  146 0.1163 0.1799      4.9376      5.2621|
| 12:  2.1351 -  2.0742 1.00   1286  142 0.1101 0.1698      4.8663      5.1514|
| 13:  2.0742 -  2.0198 0.96   1272  130 0.1148 0.1770      4.8118      5.0838|
| 14:  2.0198 -  1.9706 0.54    679   85 0.1112 0.1811      4.7301      4.9629|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8855 -  4.7026  1398   158  0.94   8.89   0.98     0.95       6829.17|
|  2:  4.7026 -  3.7523  1350   148  0.95   7.83   1.02     1.00       8660.71|
|  3:  3.7523 -  3.2838  1318   149  0.94  10.90   1.03     1.03       9969.10|
|  4:  3.2838 -  2.9862  1321   136  0.92  13.65   1.02     1.01      10280.18|
|  5:  2.9862 -  2.7736  1296   147  0.90  16.10   1.00     0.98       8383.48|
|  6:  2.7736 -  2.6110  1293   144  0.90  16.42   0.99     0.95       7312.35|
|  7:  2.6110 -  2.4809  1289   154  0.91  15.05   0.99     0.96       5960.15|
|  8:  2.4809 -  2.3733  1311   132  0.91  15.37   1.00     0.97       5594.05|
|  9:  2.3733 -  2.2823  1273   149  0.90  15.97   1.00     0.97       5009.61|
| 10:  2.2823 -  2.2038  1270   139  0.90  15.96   1.00     0.96       4688.32|
| 11:  2.2038 -  2.1351  1274   146  0.91  15.77   1.00     0.96       4284.85|
| 12:  2.1351 -  2.0742  1286   142  0.91  15.36   1.01     1.00       3895.03|
| 13:  2.0742 -  2.0198  1272   130  0.90  16.61   1.00     1.00       3539.75|
| 14:  2.0198 -  1.9706   679    85  0.90  15.97   0.98     0.93       2931.26|
|alpha:            min =        0.93 max =            1.03 mean =         0.98|
|beta:             min =     2931.26 max =        10280.18 mean =      6386.10|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.80 mean =        14.15|
|phase err.(test): min =        0.00 max =           89.28 mean =        13.76|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.729)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.41    99.07   16.83    None  None   None       |
|    all(noH): 2823   0      0.41    99.07   16.83    None  None   None       |
|    Sol.    : 438    0      1.66    88.76   40.04    None  None   None       |
|    Mac.    : 2385   0      0.41    99.07   12.57    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:     0.406 -  10.273: 1193   |   5:    49.740 -  59.606:   92        |
|      1:    10.273 -  20.140: 1015   |   6:    59.606 -  69.473:   52        |
|      2:    20.140 -  30.006:  197   |   7:    69.473 -  79.340:    7        |
|      3:    30.006 -  39.873:  127   |   8:    79.340 -  89.206:    8        |
|      4:    39.873 -  49.740:  128   |   9:    89.206 -  99.073:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 292         
Filter by distance & map next to the model:
   mapped sites are within: 0.536 - 4.437
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 290 from: 292
   mapped sites are within: 0.704 - 4.437

peak=    5.733 closest distance to " CB  ARG A 275 " =    0.929
peak=    5.503 closest distance to " CB  GLN A 223 " =    1.372
peak=    5.439 closest distance to " NH2 ARG A  56 " =    2.302
peak=    5.424 closest distance to " CG  PRO A  54 " =    1.296
peak=    5.115 closest distance to " CG  PRO A 213 " =    1.287
peak=    5.081 closest distance to " CA  TYR A  30 " =    0.940
peak=    5.007 closest distance to " CG  PRO A  90 " =    1.197
peak=    4.839 closest distance to " CG  PRO A 198 " =    1.241
peak=    4.760 closest distance to " CB  SER A  63 " =    1.144
peak=    4.712 closest distance to " O   HOH Z  97 " =    1.941
peak=    4.645 closest distance to " CB  GLN A 183 " =    1.293
peak=    4.631 closest distance to " O   HOH Z 234 " =    3.742
peak=    4.605 closest distance to " O   HOH Z 402 " =    1.484
peak=    4.592 closest distance to " O   HOH Z 403 " =    1.807
peak=    4.575 closest distance to " O   HOH Z 193 " =    1.715
peak=    4.535 closest distance to " O  BHOH Z  74 " =    1.234
peak=    4.528 closest distance to " O   HOH Z 298 " =    1.871
peak=    4.481 closest distance to " CB  PRO A  54 " =    0.945
peak=    4.478 closest distance to " O   HOH Z 232 " =    2.364
peak=    4.464 closest distance to " O   HOH Z 209 " =    2.232
peak=    4.441 closest distance to " O   HOH Z 142 " =    1.612
peak=    4.435 closest distance to " C   PRO A 198 " =    1.497
peak=    4.383 closest distance to " O   SER A  87 " =    2.232
peak=    4.374 closest distance to " O   HOH Z  15 " =    2.245
peak=    4.344 closest distance to " CG  PRO A 243 " =    1.139
peak=    4.328 closest distance to " CB  GLU A 128 " =    1.133
peak=    4.319 closest distance to " NZ  LYS A 117 " =    3.059
peak=    4.294 closest distance to " O   HOH Z 389 " =    1.905
peak=    4.287 closest distance to " CB  ARG A 190 " =    1.732
peak=    4.284 closest distance to " CD  ARG A 269 " =    1.041
peak=    4.268 closest distance to " O   HOH Z 102 " =    1.310
peak=    4.263 closest distance to " O   HOH Z  59 " =    2.238
peak=    4.255 closest distance to " NH2BARG A 145 " =    2.119
peak=    4.250 closest distance to " CG1 ILE A  33 " =    1.284
peak=    4.242 closest distance to " CB  GLU A 152 " =    1.161
peak=    4.238 closest distance to " O   HOH Z 272 " =    1.857
peak=    4.209 closest distance to " O   HOH Z 126 " =    1.857
peak=    4.177 closest distance to " CA  ALA A  21 " =    1.228
peak=    4.158 closest distance to " O   HOH Z  44 " =    2.057
peak=    4.154 closest distance to " O   HOH Z 124 " =    1.333
peak=    4.145 closest distance to " CB  TYR A 169 " =    0.810
peak=    4.138 closest distance to " CG  ARG A  66 " =    1.023
peak=    4.133 closest distance to " CB  GLU A 277 " =    3.571
peak=    4.131 closest distance to " O   HOH Z 368 " =    2.071
peak=    4.129 closest distance to " O   HOH Z 203 " =    1.800
peak=    4.088 closest distance to " CG  ARG A  66 " =    2.763
peak=    4.082 closest distance to " O   HOH Z  43 " =    2.247
peak=    4.077 closest distance to " O   HOH Z 247 " =    1.374
peak=    4.050 closest distance to " CA  ASN A 176 " =    1.156
peak=    4.043 closest distance to " CB  SER A   3 " =    1.217
peak=    4.026 closest distance to " CB  ASN A 148 " =    1.413
peak=    4.011 closest distance to " CB  ARG A  79 " =    1.304
peak=    4.010 closest distance to " O   HOH Z 346 " =    1.598
peak=    4.009 closest distance to " O   HOH Z 189 " =    1.950
peak=    4.006 closest distance to " O   HOH Z 134 " =    1.385
peak=    4.002 closest distance to " O   HOH Z  78 " =    1.716
peak=    3.999 closest distance to " CB  TRP A 179 " =    1.175
peak=    3.983 closest distance to " CD2 TRP A 179 " =    1.426
peak=    3.980 closest distance to " O   HOH Z  80 " =    1.713
peak=    3.974 closest distance to " O   HOH Z 369 " =    2.453
peak=    3.965 closest distance to " O   HOH Z 227 " =    1.740
peak=    3.959 closest distance to " O   HOH Z 426 " =    1.509
peak=    3.949 closest distance to " O   HOH Z 284 " =    2.844
peak=    3.948 closest distance to " NE2 GLN A  11 " =    0.978
peak=    3.911 closest distance to " O   HOH Z 287 " =    1.951
peak=    3.911 closest distance to " CA  ARG A 195 " =    1.284
peak=    3.897 closest distance to " O   HOH Z 279 " =    2.099
peak=    3.895 closest distance to " O   HOH Z  40 " =    1.932
peak=    3.886 closest distance to " CA  ARG A  36 " =    1.032
peak=    3.886 closest distance to " O   HOH Z 128 " =    2.215
peak=    3.885 closest distance to " O   HOH Z 128 " =    1.929
peak=    3.885 closest distance to " O   HOH Z 132 " =    2.419
peak=    3.880 closest distance to " O   HOH Z 406 " =    1.595
peak=    3.863 closest distance to " ND2 ASN A 187 " =    1.552
peak=    3.863 closest distance to " O   HOH Z 261 " =    1.673
peak=    3.862 closest distance to " O   HOH Z  63 " =    1.953
peak=    3.861 closest distance to " O   HOH Z  97 " =    2.404
peak=    3.858 closest distance to " O   HOH Z 345 " =    2.723
peak=    3.853 closest distance to " O   HOH Z 357 " =    1.919
peak=    3.853 closest distance to " CB  SER A  62 " =    0.866
peak=    3.848 closest distance to " N   ASN A  39 " =    1.265
peak=    3.843 closest distance to " O   HOH Z 421 " =    1.857
peak=    3.842 closest distance to " O   HOH Z 245 " =    1.355
peak=    3.839 closest distance to " O   HOH Z 345 " =    1.673
peak=    3.836 closest distance to " O   HOH Z 316 " =    2.903
peak=    3.826 closest distance to " CG  GLN A  58 " =    2.531
peak=    3.818 closest distance to " O   HOH Z 423 " =    1.942
peak=    3.815 closest distance to " CB  LEU A 228 " =    1.122
peak=    3.813 closest distance to " O   HOH Z 411 " =    3.595
peak=    3.789 closest distance to " O   HOH Z  61 " =    1.596
peak=    3.781 closest distance to " CG2BVAL A  41 " =    0.827
peak=    3.772 closest distance to " CG2 ILE A 120 " =    1.211
peak=    3.772 closest distance to " O   HOH Z 303 " =    2.076
peak=    3.761 closest distance to " O   HOH Z 371 " =    3.259
peak=    3.746 closest distance to " O   HOH Z 214 " =    2.372
peak=    3.745 closest distance to " O   HOH Z  49 " =    2.274
peak=    3.736 closest distance to " O   HOH Z 327 " =    1.636
peak=    3.736 closest distance to " O   HOH Z 427 " =    2.832
peak=    3.732 closest distance to " O   HOH Z 132 " =    2.575
peak=    3.726 closest distance to " CA  ALA A  84 " =    1.182
peak=    3.724 closest distance to " O   HOH Z  21 " =    1.796
peak=    3.711 closest distance to " O   HOH Z 250 " =    1.448
peak=    3.709 closest distance to " OD2 ASP A 286 " =    2.778
peak=    3.709 closest distance to " O   HOH Z 173 " =    2.117
peak=    3.703 closest distance to " O   HOH Z  54 " =    1.706
peak=    3.702 closest distance to " OE1 GLU A   2 " =    2.221
peak=    3.690 closest distance to " CB  VAL A 265 " =    1.194
peak=    3.688 closest distance to " CA  THR A 221 " =    0.977
peak=    3.687 closest distance to " O   HOH Z 147 " =    1.777
peak=    3.683 closest distance to " CA  ALA A  51 " =    0.937
peak=    3.681 closest distance to " CB  SER A 141 " =    1.006
peak=    3.680 closest distance to " CG2 ILE A  20 " =    1.409
peak=    3.678 closest distance to " O   HOH Z 158 " =    2.953
peak=    3.668 closest distance to " CA  ASP A 140 " =    1.114
peak=    3.668 closest distance to " CD1 LEU A  96 " =    0.798
peak=    3.666 closest distance to " O   HOH Z 183 " =    1.465
peak=    3.666 closest distance to " OD1 ASN A  69 " =    2.503
peak=    3.662 closest distance to " O   HOH Z  85 " =    1.477
peak=    3.660 closest distance to " NZ  LYS A 119 " =    1.492
peak=    3.644 closest distance to " CA  LYS A 117 " =    1.283
peak=    3.642 closest distance to " CD2 LEU A 297 " =    0.900
peak=    3.637 closest distance to " CB  ALA A 248 " =    1.431
peak=    3.632 closest distance to " CG2 VAL A 257 " =    0.836
peak=    3.625 closest distance to " CG1BVAL A  72 " =    1.677
peak=    3.623 closest distance to " O   HOH Z 344 " =    3.001
peak=    3.614 closest distance to " CB  TRP A 266 " =    0.982
peak=    3.612 closest distance to " CZ  PHE A 218 " =    1.049
peak=    3.605 closest distance to " OD2 ASP A 298 " =    3.912
peak=    3.601 closest distance to " O   HOH Z 108 " =    2.581
peak=    3.598 closest distance to " CA  ALA A 160 " =    0.830
peak=    3.594 closest distance to " CE  LYS A 119 " =    1.148
peak=    3.586 closest distance to " O   HOH Z 402 " =    2.880
peak=    3.584 closest distance to " CD  ARG A 159 " =    0.803
peak=    3.579 closest distance to " NH2AARG A 145 " =    2.270
peak=    3.572 closest distance to " O   HOH Z 365 " =    2.725
peak=    3.558 closest distance to " CB  MET A  47 " =    1.015
peak=    3.551 closest distance to " O   HOH Z 291 " =    1.378
peak=    3.533 closest distance to " NH2 ARG A 156 " =    1.129
peak=    3.531 closest distance to " O   HOH Z  68 " =    1.874
peak=    3.529 closest distance to " O   HOH Z 337 " =    3.651
peak=    3.526 closest distance to " CB  VAL A 202 " =    1.503
peak=    3.523 closest distance to " O   HOH Z 383 " =    2.125
peak=    3.522 closest distance to " O   HOH Z  66 " =    2.150
peak=    3.519 closest distance to " O   HOH Z 427 " =    3.049
peak=    3.518 closest distance to " OG  SER A  62 " =    2.816
peak=    3.513 closest distance to " CB  PRO A 198 " =    1.085
peak=    3.498 closest distance to " CG2 VAL A  78 " =    0.849
peak=    3.498 closest distance to " CB  ASN A 148 " =    1.962
peak=    3.496 closest distance to " CG AARG A 275 " =    1.098
peak=    3.493 closest distance to " O   HOH Z 374 " =    2.580
peak=    3.493 closest distance to " O   HOH Z 298 " =    2.279
peak=    3.491 closest distance to " O   HOH Z 261 " =    2.014
peak=    3.489 closest distance to " O   HOH Z 408 " =    1.523
peak=    3.482 closest distance to " O   HOH Z 361 " =    3.572
peak=    3.480 closest distance to " CZ  PHE A  38 " =    1.346
peak=    3.479 closest distance to " CG2 VAL A 197 " =    1.151
peak=    3.478 closest distance to " CB  ASN A  39 " =    0.832
peak=    3.476 closest distance to " O   HOH Z 185 " =    1.711
peak=    3.471 closest distance to " CA  ASN A 215 " =    1.087
peak=    3.470 closest distance to " O   HOH Z 257 " =    2.279
peak=    3.467 closest distance to " CA  ASP A 162 " =    1.188
peak=    3.460 closest distance to " OG1 THR A 294 " =    2.338
peak=    3.456 closest distance to " O   THR A 220 " =    1.150
peak=    3.455 closest distance to " O   SER A  26 " =    1.638
peak=    3.448 closest distance to " CB  ALA A 291 " =    1.222
peak=    3.438 closest distance to " O   HOH Z  19 " =    1.584
peak=    3.431 closest distance to " O   HOH Z 380 " =    2.034
peak=    3.431 closest distance to " CE  LYS A  76 " =    0.857
peak=    3.428 closest distance to " CB  TYR A 169 " =    0.865
peak=    3.427 closest distance to " O   HOH Z 419 " =    1.504
peak=    3.427 closest distance to " CB  ARG A 269 " =    0.740
peak=    3.426 closest distance to " O   HOH Z 417 " =    3.036
peak=    3.421 closest distance to " CA  ASP A 124 " =    0.704
peak=    3.418 closest distance to " O   HOH Z 336 " =    1.667
peak=    3.418 closest distance to " O   HOH Z 265 " =    2.245
peak=    3.416 closest distance to " CA  ARG A 275 " =    1.908
peak=    3.407 closest distance to " OG BSER A 164 " =    2.369
peak=    3.400 closest distance to " O   HOH Z 392 " =    2.525
peak=    3.395 closest distance to " CE1 HIS A 108 " =    1.168
peak=    3.386 closest distance to " CD  LYS A 166 " =    1.345
peak=    3.385 closest distance to " O   HOH Z 163 " =    1.479
peak=    3.373 closest distance to " CA  ARG A  66 " =    0.989
peak=    3.372 closest distance to " N   TYR A 116 " =    1.573
peak=    3.368 closest distance to " O   HOH Z 299 " =    4.437
peak=    3.361 closest distance to " CB  SER A  26 " =    1.694
peak=    3.360 closest distance to " O   HOH Z 250 " =    1.730
peak=    3.358 closest distance to " NE2 GLN A  77 " =    3.189
peak=    3.357 closest distance to " O   HOH Z 126 " =    1.557
peak=    3.354 closest distance to " CG2AVAL A 121 " =    2.118
peak=    3.353 closest distance to " O   ASN A  74 " =    1.658
peak=    3.344 closest distance to " CB  ASN A 285 " =    0.963
peak=    3.339 closest distance to " NH1AARG A 145 " =    1.201
peak=    3.334 closest distance to " O   HOH Z 305 " =    3.661
peak=    3.331 closest distance to " O   HOH Z 414 " =    1.619
peak=    3.327 closest distance to " CG2 THR A 221 " =    1.154
peak=    3.325 closest distance to " CB  THR A  31 " =    1.751
peak=    3.318 closest distance to " O   HOH Z 313 " =    1.795
peak=    3.316 closest distance to " N   HIS A 108 " =    1.863
peak=    3.315 closest distance to " CA  GLY A  80 " =    1.088
peak=    3.308 closest distance to " N   TRP A 150 " =    1.163
peak=    3.299 closest distance to " O   HOH Z 234 " =    1.787
peak=    3.298 closest distance to " O   HOH Z 375 " =    2.224
peak=    3.297 closest distance to " O   HOH Z  35 " =    2.327
peak=    3.296 closest distance to " CA  ALA A 291 " =    0.810
peak=    3.290 closest distance to " CA  MET A  40 " =    1.063
peak=    3.270 closest distance to " O   ALA A 165 " =    1.394
peak=    3.265 closest distance to " CB  ILE A 120 " =    1.283
peak=    3.264 closest distance to " O   HOH Z 334 " =    1.459
peak=    3.264 closest distance to " C   SER A  32 " =    1.092
peak=    3.260 closest distance to " O   ALA A 242 " =    1.056
peak=    3.256 closest distance to " CB  GLN A 278 " =    0.872
peak=    3.255 closest distance to " O   HOH Z 423 " =    3.439
peak=    3.255 closest distance to " CG  ARG A 219 " =    1.233
peak=    3.253 closest distance to " CA  VAL A  41 " =    0.949
peak=    3.252 closest distance to " OE1 GLN A  11 " =    1.850
peak=    3.252 closest distance to " O   HOH Z 435 " =    1.814
peak=    3.250 closest distance to " CB  ASP A 140 " =    1.007
peak=    3.248 closest distance to " CZ2 TRP A 179 " =    1.720
peak=    3.245 closest distance to " CD BLYS A 290 " =    1.112
peak=    3.243 closest distance to " CA  MET A 105 " =    1.092
peak=    3.241 closest distance to " O   HOH Z 193 " =    2.160
peak=    3.239 closest distance to " CA  VAL A 125 " =    1.249
peak=    3.239 closest distance to " CG2 VAL A 202 " =    1.172
peak=    3.238 closest distance to " CD  GLN A 194 " =    1.568
peak=    3.238 closest distance to " CE1 TYR A 186 " =    1.321
peak=    3.236 closest distance to " O   ILE A  33 " =    1.325
peak=    3.235 closest distance to " CG  LEU A 167 " =    1.136
peak=    3.229 closest distance to " O   HOH Z 148 " =    3.183
peak=    3.226 closest distance to " O   HOH Z 273 " =    2.867
peak=    3.222 closest distance to " O   HOH Z 367 " =    3.596
peak=    3.221 closest distance to " CA  ASP A 191 " =    1.207
peak=    3.219 closest distance to " O   HOH Z 267 " =    1.942
peak=    3.217 closest distance to " O   HOH Z 438 " =    1.996
peak=    3.213 closest distance to " CD  PRO A  54 " =    1.191
peak=    3.210 closest distance to " CG1 VAL A 153 " =    0.980
peak=    3.199 closest distance to " CB  PHE A  16 " =    1.012
peak=    3.198 closest distance to " CG  MET A 185 " =    1.185
peak=    3.197 closest distance to " OH  TYR A 116 " =    1.077
peak=    3.194 closest distance to " O   THR A 251 " =    1.179
peak=    3.191 closest distance to " O   HOH Z  88 " =    3.258
peak=    3.189 closest distance to " O   HOH Z 359 " =    1.402
peak=    3.188 closest distance to " O   HOH Z   1 " =    2.266
peak=    3.188 closest distance to " CB  SER A 273 " =    0.850
peak=    3.188 closest distance to " CB  PRO A 163 " =    3.966
peak=    3.184 closest distance to " CB  ASN A 215 " =    1.132
peak=    3.182 closest distance to " O   HOH Z 156 " =    2.625
peak=    3.180 closest distance to " O   HOH Z 358 " =    2.073
peak=    3.180 closest distance to " O   HOH Z 409 " =    3.398
peak=    3.179 closest distance to " O   HOH Z 152 " =    1.915
peak=    3.174 closest distance to " O   HOH Z 422 " =    2.675
peak=    3.174 closest distance to " CB  THR A 157 " =    1.057
peak=    3.164 closest distance to " NZ  LYS A 117 " =    2.242
peak=    3.162 closest distance to " O   HOH Z  48 " =    1.677
peak=    3.162 closest distance to " O   HOH Z  63 " =    2.178
peak=    3.161 closest distance to " CA  ASP A 191 " =    0.898
peak=    3.161 closest distance to " NH2 ARG A 219 " =    1.917
peak=    3.156 closest distance to " OG BSER A 212 " =    2.743
peak=    3.155 closest distance to " CA  LEU A  83 " =    1.324
peak=    3.153 closest distance to " CA  SER A  32 " =    1.572
peak=    3.153 closest distance to " O   HOH Z 135 " =    1.793
peak=    3.145 closest distance to " O   HOH Z 123 " =    2.148
peak=    3.145 closest distance to " O   HOH Z 281 " =    4.421
peak=    3.145 closest distance to " CB  LYS A 289 " =    0.995
peak=    3.145 closest distance to " CB  ARG A  79 " =    0.793
peak=    3.143 closest distance to " O   HOH Z  20 " =    1.296
peak=    3.138 closest distance to " CB  GLN A 103 " =    0.830
peak=    3.132 closest distance to " CA  ASN A 217 " =    1.244
peak=    3.132 closest distance to " CA  VAL A 126 " =    1.201
peak=    3.125 closest distance to " CD1 LEU A 300 " =    1.270
peak=    3.119 closest distance to " CB  ALA A   9 " =    1.558
peak=    3.118 closest distance to " CD2 LEU A 255 " =    1.164
peak=    3.114 closest distance to " O   HOH Z 211 " =    2.859
peak=    3.113 closest distance to " CA  GLU A 152 " =    0.852
peak=    3.107 closest distance to " O   ASP A 238 " =    0.729
peak=    3.097 closest distance to " CG1 VAL A 174 " =    1.295
peak=    3.094 closest distance to " CB  ALA A  71 " =    1.285
peak=    3.093 closest distance to " CB  TYR A 116 " =    0.818
peak=    3.092 closest distance to " CB  GLU A  46 " =    1.020
peak=    3.091 closest distance to " N   ARG A 156 " =    1.418
peak=    3.091 closest distance to " CD  LYS A 119 " =    1.341
peak=    3.085 closest distance to " CA  SER A  87 " =    1.009
peak=    3.065 closest distance to " O   HOH Z 189 " =    2.524
peak=    3.061 closest distance to " CB  ALA A 114 " =    1.005
peak=    3.060 closest distance to " O   HOH Z 394 " =    1.602
peak=    3.059 closest distance to " CB  PRO A 243 " =    1.276
peak=    3.054 closest distance to " CG1 ILE A 120 " =    1.145
peak=    3.054 closest distance to " O   GLY A 147 " =    1.299
peak=    3.049 closest distance to " CD1AILE A 234 " =    0.894
peak=    3.048 closest distance to " O   HOH Z  30 " =    2.068
peak=    3.024 closest distance to " NZ  LYS A 166 " =    2.698

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 202         
Filter by distance & map next to the model:
   mapped sites are within: 0.892 - 5.875
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 200 from: 202
   mapped sites are within: 0.892 - 5.875

peak=   -4.928 closest distance to " O   HOH Z 266 " =    4.556
peak=   -4.486 closest distance to " C   HIS A 108 " =    1.076
peak=   -4.346 closest distance to " OXT GLY A 302 " =    2.842
peak=   -4.345 closest distance to " CD  ARG A 156 " =    2.090
peak=   -4.261 closest distance to " O   HOH Z 165 " =    1.923
peak=   -4.200 closest distance to " CD1 LEU A 101 " =    2.452
peak=   -4.199 closest distance to " O   HOH Z  13 " =    1.674
peak=   -4.187 closest distance to " CD  GLN A  58 " =    1.181
peak=   -4.160 closest distance to " O   VAL A  67 " =    2.760
peak=   -4.102 closest distance to " SG  CYS A 254 " =    3.288
peak=   -4.081 closest distance to " O   HOH Z 372 " =    2.337
peak=   -4.022 closest distance to " O   ILE A 109 " =    2.574
peak=   -4.017 closest distance to " O   HOH Z 353 " =    2.217
peak=   -4.013 closest distance to " O   PRO A 163 " =    2.040
peak=   -4.008 closest distance to " O   HOH Z 377 " =    1.906
peak=   -3.997 closest distance to " CA  VAL A  67 " =    2.912
peak=   -3.995 closest distance to " OG BSER A 134 " =    1.285
peak=   -3.927 closest distance to " CB  PHE A 192 " =    1.996
peak=   -3.893 closest distance to " ND2 ASN A  45 " =    0.977
peak=   -3.871 closest distance to " O   HOH Z 198 " =    1.910
peak=   -3.840 closest distance to " CD1 PHE A 130 " =    2.351
peak=   -3.828 closest distance to " N   ALA A 248 " =    1.717
peak=   -3.819 closest distance to " O   HOH Z 407 " =    2.921
peak=   -3.818 closest distance to " O   PHE A 218 " =    1.525
peak=   -3.814 closest distance to " O   PRO A 198 " =    1.269
peak=   -3.812 closest distance to " O   ALA A 256 " =    1.515
peak=   -3.811 closest distance to " CE2 TYR A  30 " =    2.782
peak=   -3.805 closest distance to " OE1 GLN A 223 " =    2.121
peak=   -3.794 closest distance to " CB  PRO A 243 " =    2.659
peak=   -3.780 closest distance to " CA  ASP A 298 " =    1.055
peak=   -3.769 closest distance to " C   THR A 279 " =    1.180
peak=   -3.766 closest distance to " O   ALA A  34 " =    2.238
peak=   -3.754 closest distance to " OD2 ASP A 171 " =    2.425
peak=   -3.742 closest distance to " CG  ASP A 132 " =    2.312
peak=   -3.724 closest distance to " O   HOH Z  10 " =    1.601
peak=   -3.719 closest distance to " N   GLN A  58 " =    1.678
peak=   -3.719 closest distance to " O   HOH Z 292 " =    4.513
peak=   -3.715 closest distance to " O   HOH Z  11 " =    1.925
peak=   -3.707 closest distance to " CA  TYR A  68 " =    2.994
peak=   -3.697 closest distance to " CD1 LEU A  25 " =    2.455
peak=   -3.683 closest distance to " O   HOH Z 166 " =    1.910
peak=   -3.672 closest distance to " CZ  TYR A 169 " =    1.826
peak=   -3.671 closest distance to " O   HOH Z 351 " =    1.484
peak=   -3.662 closest distance to " OG  SER A  97 " =    2.157
peak=   -3.651 closest distance to " NE2 GLN A  88 " =    1.714
peak=   -3.645 closest distance to " OG  SER A   3 " =    1.644
peak=   -3.642 closest distance to " O   TRP A  92 " =    1.845
peak=   -3.637 closest distance to " O   HOH Z 150 " =    2.285
peak=   -3.634 closest distance to " O   HOH Z 234 " =    4.120
peak=   -3.633 closest distance to " N   ALA A  43 " =    2.601
peak=   -3.628 closest distance to " CG  GLN A  58 " =    1.019
peak=   -3.625 closest distance to " O   SER A 210 " =    1.924
peak=   -3.610 closest distance to " O   HOH Z 102 " =    1.595
peak=   -3.607 closest distance to " ND2 ASN A 187 " =    1.516
peak=   -3.598 closest distance to " CG1 VAL A 112 " =    2.746
peak=   -3.589 closest distance to " CD  ARG A 139 " =    1.579
peak=   -3.581 closest distance to " O   HOH Z 126 " =    1.911
peak=   -3.565 closest distance to " O   HOH Z 196 " =    1.903
peak=   -3.565 closest distance to " CD2 LEU A 237 " =    2.214
peak=   -3.562 closest distance to " O   ALA A 160 " =    1.525
peak=   -3.552 closest distance to " CH2 TRP A 179 " =    1.323
peak=   -3.552 closest distance to " CG  GLU A  53 " =    1.302
peak=   -3.549 closest distance to " OD1 ASN A  39 " =    2.216
peak=   -3.541 closest distance to " CB  PHE A 208 " =    2.278
peak=   -3.536 closest distance to " CD1 TYR A 247 " =    2.482
peak=   -3.529 closest distance to " O   GLY A  80 " =    2.388
peak=   -3.510 closest distance to " CD1 PHE A  59 " =    1.932
peak=   -3.504 closest distance to " O   HOH Z 290 " =    1.025
peak=   -3.500 closest distance to " CB  ALA A 291 " =    2.318
peak=   -3.500 closest distance to " O   GLN A  11 " =    1.301
peak=   -3.500 closest distance to " O   HOH Z  71 " =    1.650
peak=   -3.496 closest distance to " CD1 LEU A 228 " =    2.124
peak=   -3.494 closest distance to " CE3 TRP A 150 " =    2.127
peak=   -3.493 closest distance to " O   HOH Z 369 " =    2.279
peak=   -3.490 closest distance to " N   THR A  52 " =    1.686
peak=   -3.477 closest distance to " NH1 ARG A  66 " =    1.112
peak=   -3.475 closest distance to " OD2 ASP A 191 " =    1.437
peak=   -3.467 closest distance to " NH2 ARG A  66 " =    5.246
peak=   -3.467 closest distance to " CG  ASP A 231 " =    0.892
peak=   -3.466 closest distance to " CD  ARG A 195 " =    5.050
peak=   -3.466 closest distance to " O   HOH Z 114 " =    3.461
peak=   -3.453 closest distance to " O   HOH Z 166 " =    1.752
peak=   -3.448 closest distance to " ND2 ASN A  69 " =    1.608
peak=   -3.447 closest distance to " CB  ALA A 248 " =    1.969
peak=   -3.440 closest distance to " NH1 ARG A 195 " =    2.616
peak=   -3.435 closest distance to " OD1 ASP A 191 " =    1.419
peak=   -3.431 closest distance to " O   HOH Z 418 " =    1.349
peak=   -3.428 closest distance to " CG1AVAL A  41 " =    2.566
peak=   -3.423 closest distance to " O   HOH Z 377 " =    1.791
peak=   -3.417 closest distance to " O   HOH Z 422 " =    1.445
peak=   -3.408 closest distance to " CE  MET A 105 " =    2.120
peak=   -3.402 closest distance to " CA  GLY A 133 " =    1.852
peak=   -3.400 closest distance to " CD  LYS A 289 " =    2.405
peak=   -3.399 closest distance to " O   HOH Z 414 " =    1.547
peak=   -3.398 closest distance to " N   ALA A 226 " =    1.888
peak=   -3.398 closest distance to " O   HOH Z 427 " =    1.414
peak=   -3.395 closest distance to " O   LEU A 167 " =    1.612
peak=   -3.394 closest distance to " CG2 ILE A 263 " =    2.257
peak=   -3.392 closest distance to " CB  ASP A 286 " =    1.928
peak=   -3.387 closest distance to " O   HOH Z 301 " =    2.242
peak=   -3.383 closest distance to " O  BHOH Z 338 " =    1.302
peak=   -3.381 closest distance to " ND2 ASN A  39 " =    1.226
peak=   -3.380 closest distance to " O   HOH Z 171 " =    2.090
peak=   -3.374 closest distance to " CG  GLN A 223 " =    1.440
peak=   -3.373 closest distance to " CG  PRO A 243 " =    1.685
peak=   -3.371 closest distance to " O   HOH Z 389 " =    1.706
peak=   -3.363 closest distance to " OG BSER A 134 " =    1.744
peak=   -3.362 closest distance to " O   VAL A 174 " =    2.083
peak=   -3.356 closest distance to " N   THR A 235 " =    1.330
peak=   -3.355 closest distance to " O   HOH Z  52 " =    1.468
peak=   -3.351 closest distance to " OD1 ASN A 148 " =    1.567
peak=   -3.342 closest distance to " OG BSER A 210 " =    2.085
peak=   -3.342 closest distance to " C   ASN A 285 " =    2.290
peak=   -3.340 closest distance to " O   SER A   3 " =    1.081
peak=   -3.337 closest distance to " CZ  PHE A  59 " =    1.612
peak=   -3.336 closest distance to " CE  LYS A 166 " =    2.881
peak=   -3.330 closest distance to " NH2 ARG A  79 " =    2.097
peak=   -3.326 closest distance to " O   HOH Z  15 " =    1.545
peak=   -3.324 closest distance to " O   ASN A 187 " =    1.476
peak=   -3.323 closest distance to " NE1 TRP A 266 " =    2.351
peak=   -3.312 closest distance to " O   HOH Z 250 " =    1.371
peak=   -3.307 closest distance to " C   SER A 206 " =    1.622
peak=   -3.305 closest distance to " NE2 GLN A  88 " =    1.094
peak=   -3.304 closest distance to " O   ALA A   1 " =    1.864
peak=   -3.297 closest distance to " CA  GLY A 203 " =    2.232
peak=   -3.289 closest distance to " O   SER A 135 " =    1.535
peak=   -3.288 closest distance to " CD2 LEU A 300 " =    2.787
peak=   -3.288 closest distance to " NE2 GLN A 194 " =    1.760
peak=   -3.286 closest distance to " N   VAL A 189 " =    1.655
peak=   -3.285 closest distance to " O   ALA A 161 " =    1.471
peak=   -3.282 closest distance to " O   HOH Z 283 " =    1.927
peak=   -3.280 closest distance to " O   HOH Z 111 " =    3.733
peak=   -3.278 closest distance to " O   MET A  40 " =    2.594
peak=   -3.278 closest distance to " O   VAL A 189 " =    2.511
peak=   -3.278 closest distance to " O   HOH Z 185 " =    2.377
peak=   -3.271 closest distance to " O   GLY A  75 " =    1.790
peak=   -3.269 closest distance to " CD  PRO A 198 " =    1.253
peak=   -3.264 closest distance to " N   ALA A 248 " =    2.459
peak=   -3.264 closest distance to " O   HOH Z 423 " =    2.331
peak=   -3.262 closest distance to " CD1 ILE A 239 " =    2.183
peak=   -3.259 closest distance to " CG2 VAL A 189 " =    2.206
peak=   -3.257 closest distance to " N   SER A 276 " =    1.423
peak=   -3.256 closest distance to " CG  GLU A 277 " =    1.226
peak=   -3.254 closest distance to " O   HOH Z 360 " =    2.526
peak=   -3.248 closest distance to " O   ASN A  45 " =    1.822
peak=   -3.238 closest distance to " CG1 VAL A 125 " =    2.327
peak=   -3.235 closest distance to " O   SER A  26 " =    1.349
peak=   -3.230 closest distance to " C   ALA A 158 " =    1.314
peak=   -3.229 closest distance to " O   HOH Z 311 " =    3.551
peak=   -3.226 closest distance to " C   LEU A 143 " =    1.054
peak=   -3.225 closest distance to " CZ  PHE A 130 " =    0.915
peak=   -3.223 closest distance to " O   HOH Z 265 " =    2.191
peak=   -3.222 closest distance to " O   HOH Z 377 " =    1.667
peak=   -3.222 closest distance to " O   PRO A 198 " =    1.286
peak=   -3.220 closest distance to " CB  ALA A 248 " =    2.225
peak=   -3.217 closest distance to " O   ALA A  10 " =    1.786
peak=   -3.216 closest distance to " OE2 GLU A   2 " =    1.601
peak=   -3.216 closest distance to " O   HOH Z  11 " =    1.808
peak=   -3.205 closest distance to " OG  SER A  62 " =    1.493
peak=   -3.197 closest distance to " CA  GLY A 241 " =    2.332
peak=   -3.197 closest distance to " CB  PHE A  16 " =    2.580
peak=   -3.192 closest distance to " OE1 GLN A 183 " =    1.516
peak=   -3.191 closest distance to " O   HOH Z  43 " =    1.663
peak=   -3.191 closest distance to " O   HOH Z 191 " =    5.875
peak=   -3.190 closest distance to " O   HOH Z 252 " =    3.324
peak=   -3.186 closest distance to " O   HOH Z 213 " =    1.493
peak=   -3.184 closest distance to " O   HOH Z 111 " =    3.475
peak=   -3.180 closest distance to " O   HOH Z 280 " =    2.359
peak=   -3.179 closest distance to " O   GLY A  80 " =    2.577
peak=   -3.178 closest distance to " NH2 ARG A  66 " =    1.795
peak=   -3.171 closest distance to " O   GLY A 196 " =    0.988
peak=   -3.168 closest distance to " O   HOH Z  61 " =    1.591
peak=   -3.168 closest distance to " O   HOH Z 145 " =    2.020
peak=   -3.161 closest distance to " CB  GLN A  11 " =    1.721
peak=   -3.159 closest distance to " O   HOH Z 326 " =    1.731
peak=   -3.159 closest distance to " O   HOH Z 297 " =    2.838
peak=   -3.151 closest distance to " OG ASER A 134 " =    1.319
peak=   -3.148 closest distance to " O   HOH Z 287 " =    2.234
peak=   -3.142 closest distance to " OD1 ASP A 171 " =    1.443
peak=   -3.137 closest distance to " O   HOH Z   9 " =    1.984
peak=   -3.129 closest distance to " O   HOH Z   6 " =    1.773
peak=   -3.121 closest distance to " CE  MET A  93 " =    1.159
peak=   -3.121 closest distance to " OD1 ASP A 200 " =    1.345
peak=   -3.121 closest distance to " O   HOH Z 361 " =    3.398
peak=   -3.116 closest distance to " OH  TYR A 169 " =    0.995
peak=   -3.114 closest distance to " CG2 THR A 178 " =    2.152
peak=   -3.111 closest distance to " O   HOH Z  41 " =    2.240
peak=   -3.108 closest distance to " OG  SER A  26 " =    1.300
peak=   -3.098 closest distance to " O   GLU A 152 " =    1.482
peak=   -3.091 closest distance to " CG  PHE A 283 " =    2.537
peak=   -3.090 closest distance to " O   VAL A 189 " =    1.901
peak=   -3.087 closest distance to " CG  LYS A 119 " =    2.901
peak=   -3.078 closest distance to " O   HOH Z 174 " =    3.723
peak=   -3.076 closest distance to " O   HOH Z 392 " =    1.497
peak=   -3.072 closest distance to " CE1 TYR A 169 " =    2.200
peak=   -3.072 closest distance to " CB  PRO A 213 " =    1.553
peak=   -3.067 closest distance to " OD2 ASP A 171 " =    1.739
peak=   -3.042 closest distance to " O   HOH Z 193 " =    1.766
peak=   -3.032 closest distance to " O   HOH Z  91 " =    2.224
peak=   -3.017 closest distance to " CB  TRP A  85 " =    2.419

================= 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    :  0.4019 0.3966   6.193345e+00   6.177941e+00
   1_bss:  0.3924 0.3845   6.180261e+00   6.157097e+00
   1_xyz:  0.2612 0.2823   5.853424e+00   5.919021e+00
   1_adp:  0.2373 0.2942   5.801590e+00   5.951752e+00
   1_occ:  0.2368 0.2949   5.801057e+00   5.952256e+00
   2_bss:  0.2354 0.2924   5.797170e+00   5.948066e+00
   2_xyz:  0.1725 0.2182   5.514085e+00   5.697784e+00
   2_adp:  0.1619 0.2022   5.452936e+00   5.629982e+00
   2_occ:  0.1617 0.2022   5.452517e+00   5.629695e+00
   3_bss:  0.1619 0.2017   5.451497e+00   5.625640e+00
   3_xyz:  0.1274 0.1687   5.243030e+00   5.455183e+00
   3_adp:  0.1209 0.1654   5.204663e+00   5.429195e+00
   3_occ:  0.1209 0.1654   5.204549e+00   5.429004e+00
   4_bss:  0.1214 0.1652   5.206126e+00   5.429063e+00
   4_xyz:  0.1129 0.1593   5.155144e+00   5.394574e+00
   4_adp:  0.1114 0.1587   5.144852e+00   5.388348e+00
   4_occ:  0.1114 0.1588   5.144786e+00   5.388616e+00
   5_bss:  0.1113 0.1588   5.144938e+00   5.388770e+00
   5_xyz:  0.1122 0.1586   5.150681e+00   5.389977e+00
   5_adp:  0.1118 0.1592   5.150514e+00   5.393387e+00
   5_occ:  0.1117 0.1592   5.150394e+00   5.393432e+00
   5_bss:  0.1117 0.1592   5.150481e+00   5.393533e+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:  0.300  24.850  -1.569   2.643  -0.705   0.000  -0.000  -0.000
   1_xyz:  0.300  24.850  -1.569   2.643  -0.705   0.000  -0.000  -0.000
   1_adp:  0.300  24.850  -1.569   2.643  -0.705   0.000  -0.000  -0.000
   1_occ:  0.300  24.850  -1.569   2.643  -0.705   0.000  -0.000  -0.000
   2_bss:  0.315  42.759  -2.594   0.309  -1.259   0.000  -0.000  -0.000
   2_xyz:  0.315  42.759  -2.594   0.309  -1.259   0.000  -0.000  -0.000
   2_adp:  0.315  42.759  -2.594   0.309  -1.259   0.000  -0.000  -0.000
   2_occ:  0.315  42.759  -2.594   0.309  -1.259   0.000  -0.000  -0.000
   3_bss:  0.319  45.450  -2.749  -0.813  -1.354  -0.000  -0.000  -0.000
   3_xyz:  0.319  45.450  -2.749  -0.813  -1.354  -0.000  -0.000  -0.000
   3_adp:  0.319  45.450  -2.749  -0.813  -1.354  -0.000  -0.000  -0.000
   3_occ:  0.319  45.450  -2.749  -0.813  -1.354  -0.000  -0.000  -0.000
   4_bss:  0.322  48.937  -2.748  -1.267  -1.328  -0.000  -0.000  -0.000
   4_xyz:  0.322  48.937  -2.748  -1.267  -1.328  -0.000  -0.000  -0.000
   4_adp:  0.322  48.937  -2.748  -1.267  -1.328  -0.000  -0.000  -0.000
   4_occ:  0.322  48.937  -2.748  -1.267  -1.328  -0.000  -0.000  -0.000
   5_bss:  0.323  48.532  -2.555  -1.248  -1.134  -0.000  -0.000  -0.000
   5_xyz:  0.323  48.532  -2.555  -1.248  -1.134  -0.000  -0.000  -0.000
   5_adp:  0.323  48.532  -2.555  -1.248  -1.134  -0.000  -0.000  -0.000
   5_occ:  0.323  48.532  -2.555  -1.248  -1.134  -0.000  -0.000  -0.000
   5_bss:  0.323  48.655  -2.365  -1.121  -0.936  -0.000  -0.000  -0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  44.108 0.5948  0.7748    46270.665
   1_bss:  42.951 0.6070  0.7935    42651.780
   1_xyz:  28.859 0.7712  0.9602    21169.354
   1_adp:  30.495 0.7522  0.9392    23040.414
   1_occ:  30.534 0.7518  0.9384    23073.073
   2_bss:  30.192 0.7554  0.9029    22608.689
   2_xyz:  21.572 0.8456  0.9763    12196.778
   2_adp:  19.528 0.8663  0.9815    10510.479
   2_occ:  19.535 0.8663  0.9811    10504.980
   3_bss:  19.417 0.8673  0.9668    10374.189
   3_xyz:  15.674 0.9006  0.9864     7224.312
   3_adp:  15.040 0.9063  0.9827     6907.887
   3_occ:  15.043 0.9063  0.9825     6904.374
   4_bss:  15.020 0.9065  0.9777     6894.890
   4_xyz:  14.262 0.9128  0.9798     6425.698
   4_adp:  14.096 0.9143  0.9738     6363.379
   4_occ:  14.098 0.9143  0.9737     6364.245
   5_bss:  14.101 0.9142  0.9787     6367.197
   5_xyz:  14.066 0.9146  0.9789     6340.895
   5_adp:  14.109 0.9143  0.9722     6383.315
   5_occ:  14.108 0.9143  0.9721     6383.267
   5_bss:  14.111 0.9143  0.9778     6384.147
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :   1.822  0.010  0.101 15.968  0.009  4.111   1.7590e-01
   1_bss:   1.822  0.010  0.101 15.968  0.009  4.111   1.7590e-01
   1_xyz:   1.287  0.010  0.077 15.314  0.005  4.108   8.9558e-02
   1_adp:   1.287  0.010  0.077 15.314  0.005  4.108   8.9558e-02
   1_occ:   1.287  0.010  0.077 15.314  0.005  4.108   8.9558e-02
   2_bss:   1.287  0.010  0.077 15.314  0.005  4.108   8.9558e-02
   2_xyz:   1.003  0.007  0.066 14.355  0.004  4.117   5.7294e-02
   2_adp:   1.003  0.007  0.066 14.355  0.004  4.117   5.7294e-02
   2_occ:   1.003  0.007  0.066 14.355  0.004  4.117   5.7294e-02
   3_bss:   1.003  0.007  0.066 14.355  0.004  4.117   5.7294e-02
   3_xyz:   1.011  0.007  0.070 14.637  0.004  4.117   5.8827e-02
   3_adp:   1.011  0.007  0.070 14.637  0.004  4.117   5.8827e-02
   3_occ:   1.011  0.007  0.070 14.637  0.004  4.117   5.8827e-02
   4_bss:   1.011  0.007  0.070 14.637  0.004  4.117   5.8827e-02
   4_xyz:   1.018  0.007  0.074 14.707  0.004  4.110   6.0134e-02
   4_adp:   1.018  0.007  0.074 14.707  0.004  4.110   6.0134e-02
   4_occ:   1.018  0.007  0.074 14.707  0.004  4.110   6.0134e-02
   5_bss:   1.018  0.007  0.074 14.707  0.004  4.110   6.0134e-02
   5_xyz:   0.913  0.006  0.068 14.393  0.004  4.110   5.0291e-02
   5_adp:   0.913  0.006  0.068 14.393  0.004  4.110   5.0291e-02
   5_occ:   0.913  0.006  0.068 14.393  0.004  4.110   5.0291e-02
   5_bss:   0.913  0.006  0.068 14.393  0.004  4.110   5.0291e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :   9.874  0.070  0.314 85.889  0.055  1.551   2.4045e-01
   1_bss:   9.874  0.070  0.314 85.889  0.055  1.551   2.4045e-01
   1_xyz:   8.586  0.061  0.381 86.970  0.027  2.139   8.7820e-02
   1_adp:   8.586  0.061  0.381 86.970  0.027  2.139   8.7820e-02
   1_occ:   8.586  0.061  0.381 86.970  0.027  2.139   8.7820e-02
   2_bss:   8.586  0.061  0.381 86.970  0.027  2.139   8.7820e-02
   2_xyz:   7.453  0.037  0.190 81.561  0.033  2.265   6.0208e-02
   2_adp:   7.453  0.037  0.190 81.561  0.033  2.265   6.0208e-02
   2_occ:   7.453  0.037  0.190 81.561  0.033  2.265   6.0208e-02
   3_bss:   7.453  0.037  0.190 81.561  0.033  2.265   6.0208e-02
   3_xyz:   7.565  0.046  0.236 80.908  0.038  2.304   4.1899e-02
   3_adp:   7.565  0.046  0.236 80.908  0.038  2.304   4.1899e-02
   3_occ:   7.565  0.046  0.236 80.908  0.038  2.304   4.1899e-02
   4_bss:   7.565  0.046  0.236 80.908  0.038  2.304   4.1899e-02
   4_xyz:   7.228  0.044  0.232 82.908  0.038  2.345   4.2263e-02
   4_adp:   7.228  0.044  0.232 82.908  0.038  2.345   4.2263e-02
   4_occ:   7.228  0.044  0.232 82.908  0.038  2.345   4.2263e-02
   5_bss:   7.228  0.044  0.232 82.908  0.038  2.345   4.2263e-02
   5_xyz:   6.713  0.043  0.228 81.512  0.033  2.387   3.0962e-02
   5_adp:   6.713  0.043  0.228 81.512  0.033  2.387   3.0962e-02
   5_occ:   6.713  0.043  0.228 81.512  0.033  2.387   3.0962e-02
   5_bss:   6.713  0.043  0.228 81.512  0.033  2.387   3.0962e-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:  67.04   0.00  17.55  61.67   0.00  13.80  67.04   3.67  37.98
   1_occ:  67.04   0.00  17.55  61.67   0.00  13.80  67.04   3.67  37.98
   2_bss:  67.04   0.00  17.55  61.67   0.00  13.80  67.04   3.67  37.98
   2_xyz:  67.04   0.00  17.55  61.67   0.00  13.80  67.04   3.67  37.98
   2_adp:  70.62   1.29  16.96  70.62   1.29  13.15  68.73   5.14  37.74
   2_occ:  70.62   1.29  16.96  70.62   1.29  13.15  68.73   5.14  37.74
   3_bss:  70.62   1.29  16.96  70.62   1.29  13.15  68.73   5.14  37.74
   3_xyz:  70.62   1.29  16.96  70.62   1.29  13.15  68.73   5.14  37.74
   3_adp:  80.72   0.00  17.10  80.72   1.36  12.90  70.19   0.00  39.99
   3_occ:  80.72   0.00  17.10  80.72   1.36  12.90  70.19   0.00  39.99
   4_bss:  80.72   0.00  17.10  80.72   1.36  12.90  70.19   0.00  39.99
   4_xyz:  80.72   0.00  17.10  80.72   1.36  12.90  70.19   0.00  39.99
   4_adp:  88.47   0.00  16.90  88.47   1.07  12.68  76.97   0.00  39.89
   4_occ:  88.47   0.00  16.90  88.47   1.07  12.68  76.97   0.00  39.89
   5_bss:  88.47   0.00  16.90  88.47   1.07  12.68  76.97   0.00  39.89
   5_xyz:  88.47   0.00  16.90  88.47   1.07  12.68  76.97   0.00  39.89
   5_adp:  99.09   0.42  16.85  99.09   0.42  12.58  88.77   1.68  40.05
   5_occ:  99.09   0.42  16.85  99.09   0.42  12.58  88.77   1.68  40.05
   5_bss:  99.07   0.41  16.83  99.07   0.41  12.57  88.76   1.66  40.04
------------------------------------------------------------------------
 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:    1.827    0.028    0.326
   1_adp:    1.827    0.028    0.326
   1_occ:    1.827    0.028    0.326
   2_bss:    1.827    0.028    0.326
   2_xyz:    1.199    0.011    0.445
   2_adp:    1.199    0.011    0.445
   2_occ:    1.199    0.011    0.445
   3_bss:    1.199    0.011    0.445
   3_xyz:    1.153    0.060    0.539
   3_adp:    1.153    0.060    0.539
   3_occ:    1.153    0.060    0.539
   4_bss:    1.153    0.060    0.539
   4_xyz:    1.293    0.029    0.572
   4_adp:    1.293    0.029    0.572
   4_occ:    1.293    0.029    0.572
   5_bss:    1.293    0.029    0.572
   5_xyz:    1.303    0.055    0.580
   5_adp:    1.303    0.055    0.580
   5_occ:    1.303    0.055    0.580
   5_bss:    1.303    0.055    0.580
------------------------------------------------------------------------

CPU time actual refinement: 347.50


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_333/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_333/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_333/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_333/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/noshake/run_333/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 347.35 
  Macro-tasks:
    bulk solvent and scale       = 44.47  
    individual site refinement   = 143.48 
    weights calculation          = 30.27  
    collect and process          = 6.66   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 225.01 
  Micro-tasks:
    mask                            = 1.88   
    f_calc                          = 110.34 
    alpha_beta                      = 8.32   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 119.11 
    fmodel                         = 7.39   
    r_factors                      = 0.29   
    phase_errors                   = 10.62  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 259.38 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.865 micro seconds
Total CPU time: 6.02 minutes
from_scatterers_fft:    653 calls, 109.96 s
gradients_fft:          598 calls, 105.35 s

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

# Date 2008-01-16 Time 04:34:29 PST -0800 (1200486869.43 s)
Start R-work = 0.4019, R-free = 0.3966 (no bulk solvent and anisotropic scale)
Final R-work = 0.1338, R-free = 0.1771 (no bulk solvent and anisotropic scale)

Start R-work = 0.3924, R-free = 0.3845
Final R-work = 0.1117, R-free = 0.1592