# Date 2008-01-16 Time 03:27:06 PST -0800 (1200482826.76 s)
#phil __OFF__

Command line arguments: "../1245.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 4182
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1245

-------------------------------------------------------------------------------
  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.modify_start_model.adp.set_b_iso = 10

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (72.0062, 46.4607, 85.0941, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (72.0062, 46.4607, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.199 1.97105
Completeness in resolution range: 0.944048
Completeness with d_max=infinity: 0.941281

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1990
                             d_min =   1.9711

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: (72.0062, 46.4607, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.199 1.97105
Completeness in resolution range: 0.944048
Completeness with d_max=infinity: 0.941281

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1995 -  4.2191 [2173/2199]  1960   213   9.8%
  bin  2:  4.2191 -  3.3607 [2099/2119]  1887   212  10.1%
  bin  3:  3.3607 -  2.9394 [2046/2065]  1838   208  10.2%
  bin  4:  2.9394 -  2.6722 [2056/2086]  1857   199   9.7%
  bin  5:  2.6722 -  2.4816 [2036/2055]  1832   204  10.0%
  bin  6:  2.4816 -  2.3358 [2032/2057]  1819   213  10.5%
  bin  7:  2.3358 -  2.2192 [2021/2049]  1820   201   9.9%
  bin  8:  2.2192 -  2.1229 [1995/2031]  1802   193   9.7%
  bin  9:  2.1229 -  2.0413 [1989/2043]  1794   195   9.8%
  bin 10:  2.0413 -  1.9711 [1142/2046]  1021   121  10.6%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1245/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:
        1.70 -     2.34: 20
        2.34 -     2.98: 1811
        2.98 -     3.62: 4591
        3.62 -     4.26: 9216
        4.26 -     4.90: 12749
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 107 " - " O   HOH Z 340 "  1.697 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 206 " - " O   HOH Z 341 "  1.879 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 208 " - " O   HOH Z 342 "  1.903 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.931 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28382 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 =====================

Setting all isotropic ADP = 10.000: selected atoms: all (2823)
Shaking sites (RMS = 0.500): selected atoms: all (2823)

==================== 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/trial/run_1245/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1245/model_refine_001.geo

CPU time processing inputs: 9.31


============================ 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 = 72.00625 46.4607 85.09415 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
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4888   r_free= 0.4754   ksol= 0.00   Bsol= 0.00   scale= 0.787    |
|                                                                             |
| 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:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.287741                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1995 -  4.7065 0.99   1412  160 0.4033 0.4294      6.5976      6.6193|
|  2:  4.7065 -  3.7542 0.99   1366  145 0.4141 0.4157      6.8159      6.8302|
|  3:  3.7542 -  3.2851 0.99   1316  147 0.4607 0.4287      6.6763      6.7058|
|  4:  3.2851 -  2.9872 0.99   1342  155 0.4718 0.4476      6.5387      6.5055|
|  5:  2.9872 -  2.7745 0.99   1324  144 0.5087 0.5299      6.3725      6.3689|
|  6:  2.7745 -  2.6118 0.99   1304  149 0.5194 0.5186      6.2824       6.275|
|  7:  2.6118 -  2.4816 0.99   1310  136 0.5395 0.4618      6.2708      6.1691|
|  8:  2.4816 -  2.3740 0.98   1294  151 0.5451 0.4895      6.1751      6.1927|
|  9:  2.3740 -  2.2829 0.98   1300  151 0.5199 0.4731      6.1308      6.0737|
| 10:  2.2829 -  2.2044 0.99   1287  140 0.5269 0.5217      6.0924      6.1016|
| 11:  2.2044 -  2.1356 0.98   1304  137 0.5359 0.5208      6.0567      6.0453|
| 12:  2.1356 -  2.0747 0.97   1267  151 0.5029 0.5579      5.9491       6.001|
| 13:  2.0747 -  2.0202 0.93   1211  136 0.5543 0.4873       5.884      5.8181|
| 14:  2.0202 -  1.9711 0.44    593   57 0.5598 0.5395      5.8328      5.8378|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1995 -  4.7065  1412   160  0.66  37.72   0.79     0.71      83808.38|
|  2:  4.7065 -  3.7542  1366   145  0.68  36.75   0.87     0.76     116521.77|
|  3:  3.7542 -  3.2851  1316   147  0.56  46.67   0.83     0.70     123831.38|
|  4:  3.2851 -  2.9872  1342   155  0.48  53.36   0.79     0.60     111250.33|
|  5:  2.9872 -  2.7745  1324   144  0.38  61.54   0.72     0.45      89452.88|
|  6:  2.7745 -  2.6118  1304   149  0.36  62.75   0.73     0.44      75875.25|
|  7:  2.6118 -  2.4816  1310   136  0.38  61.66   0.72     0.43      64225.41|
|  8:  2.4816 -  2.3740  1294   151  0.40  60.28   0.70     0.48      55986.65|
|  9:  2.3740 -  2.2829  1300   151  0.41  59.13   0.74     0.47      49380.23|
| 10:  2.2829 -  2.2044  1287   140  0.38  61.49   0.74     0.45      47412.72|
| 11:  2.2044 -  2.1356  1304   137  0.32  65.73   0.76     0.40      47355.15|
| 12:  2.1356 -  2.0747  1267   151  0.27  70.06   0.75     0.33      45929.59|
| 13:  2.0747 -  2.0202  1211   136  0.22  73.58   0.72     0.29      40963.75|
| 14:  2.0202 -  1.9711   593    57  0.23  72.87   0.69     0.27      34432.19|
|alpha:            min =        0.27 max =            0.76 mean =         0.50|
|beta:             min =    34432.19 max =       123831.38 mean =     72541.63|
|figures of merit: min =        0.00 max =            1.00 mean =         0.42|
|phase err.(work): min =        0.00 max =           89.99 mean =        57.93|
|phase err.(test): min =        0.00 max =           89.93 mean =        57.98|
|-----------------------------------------------------------------------------|

============================== 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 = 16.229259             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.557   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.312416              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.329   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       22 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      174 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      703 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1512 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2648 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3944 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5061 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6595 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7715 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.644 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.196 |       1.789 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.895)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

                ----------Modify initial isotropic ADP----------               

Randomizing
|-ADP statistics (Wilson B = 11.895)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     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:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4921   r_free= 0.4821   ksol= 0.00   Bsol= 0.00   scale= 0.758    |
|                                                                             |
| 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:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.289399                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4802   r_free= 0.4659   ksol= 0.30   Bsol= 20.00   scale= 0.961   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.89,7.09,6.79,0.00,0.00,0.00); trace/3= 7.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.284114                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.040864             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.820   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.083427              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.585   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4802      final r-factor (work) = 0.4049          |
| start r-factor (free) = 0.4659      final r-factor (free) = 0.4280          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 97.7564 = 14.04 * 0.50 * 6.2835 + 1.00 * 53.6437                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 43.7293 = 14.04 * 0.50 * 6.2074 + 1.00 * 0.1504                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4049      final r-factor (work) = 0.3609          |
| start r-factor (free) = 0.4280      final r-factor (free) = 0.4103          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.7397 = 1.08 * 1.00 * 6.2074 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.6609 = 1.08 * 1.00 * 6.1342 + 1.00 * 0.0149                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.895)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.32   13.74    None  None   None       |
|    all(noH): 2823   0      0.00    89.32   13.74    None  None   None       |
|    Sol.    : 438    0      0.00    75.33   26.96    None  None   None       |
|    Mac.    : 2385   0      0.00    89.32   11.31    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 -   8.932: 1274   |   5:    44.658 -  53.590:   57        |
|      1:     8.932 -  17.863:  770   |   6:    53.590 -  62.521:   18        |
|      2:    17.863 -  26.795:  397   |   7:    62.521 -  71.453:    9        |
|      3:    26.795 -  35.726:  203   |   8:    71.453 -  80.384:    4        |
|      4:    35.726 -  44.658:   88   |   9:    80.384 -  89.316:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3609 r_free = 0.4103             target_work(ml) = 6.115         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3603 r_free = 0.4109             target_work(ml) = 6.115         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3603   r_free= 0.4109   ksol= 0.30   Bsol= 20.00   scale= 1.078   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.89,7.09,6.79,0.00,0.00,0.00); trace/3= 7.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.114843                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3589   r_free= 0.4073   ksol= 0.33   Bsol= 42.78   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.41,3.82,4.49,0.00,0.00,0.00); trace/3= 4.57                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.115656                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.025707              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.982   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.547793              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.054  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3589      final r-factor (work) = 0.2716          |
| start r-factor (free) = 0.4073      final r-factor (free) = 0.3292          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.6180 = 6.03 * 0.50 * 6.1296 + 1.00 * 0.1504                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.1845 = 6.03 * 0.50 * 6.0075 + 1.00 * 0.0847                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2716      final r-factor (work) = 0.2504          |
| start r-factor (free) = 0.3292      final r-factor (free) = 0.3185          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3058 = 0.55 * 1.00 * 6.0075 + 1.00 * 0.0149                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2241 = 0.55 * 1.00 * 5.8633 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.895)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.50   13.77    None  None   None       |
|    all(noH): 2823   0      0.00    90.50   13.77    None  None   None       |
|    Sol.    : 438    0      0.00    77.84   32.74    None  None   None       |
|    Mac.    : 2385   0      0.00    90.50   10.29    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.051: 1375   |   5:    45.253 -  54.303:   59        |
|      1:     9.051 -  18.101:  743   |   6:    54.303 -  63.354:   22        |
|      2:    18.101 -  27.152:  289   |   7:    63.354 -  72.404:    8        |
|      3:    27.152 -  36.202:  179   |   8:    72.404 -  81.455:    2        |
|      4:    36.202 -  45.253:  143   |   9:    81.455 -  90.505:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2504 r_free = 0.3185             target_work(ml) = 5.845         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2501 r_free = 0.3183             target_work(ml) = 5.845         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2501   r_free= 0.3183   ksol= 0.33   Bsol= 42.78   scale= 1.052   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.41,3.82,4.49,0.00,0.00,0.00); trace/3= 4.57                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.844601                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2489   r_free= 0.3167   ksol= 0.34   Bsol= 54.16   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.41,1.93,3.01,0.00,0.00,0.00); trace/3= 2.78                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.844656                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.684157              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.690   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.734434              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.297  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2489      final r-factor (work) = 0.1824          |
| start r-factor (free) = 0.3167      final r-factor (free) = 0.2382          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.8223 = 4.68 * 0.50 * 5.8655 + 1.00 * 0.0847                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.4836 = 4.68 * 0.50 * 5.7274 + 1.00 * 0.0697                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1824      final r-factor (work) = 0.1644          |
| start r-factor (free) = 0.2382      final r-factor (free) = 0.2196          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2187 = 0.73 * 1.00 * 5.7274 + 1.00 * 0.0123                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0661 = 0.73 * 1.00 * 5.5187 + 1.00 * 0.0130                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.895)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.33   14.28    None  None   None       |
|    all(noH): 2823   0      0.00    92.33   14.28    None  None   None       |
|    Sol.    : 438    0      2.11    83.55   38.39    None  None   None       |
|    Mac.    : 2385   0      0.00    92.33   9.85     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.233: 1491   |   5:    46.164 -  55.396:  117        |
|      1:     9.233 -  18.466:  710   |   6:    55.396 -  64.629:   49        |
|      2:    18.466 -  27.698:  191   |   7:    64.629 -  73.862:   14        |
|      3:    27.698 -  36.931:  119   |   8:    73.862 -  83.094:    4        |
|      4:    36.931 -  46.164:  125   |   9:    83.094 -  92.327:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1644 r_free = 0.2196             target_work(ml) = 5.478         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1643 r_free = 0.2193             target_work(ml) = 5.477         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1643   r_free= 0.2193   ksol= 0.34   Bsol= 54.16   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.41,1.93,3.01,0.00,0.00,0.00); trace/3= 2.78                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.476844                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1642   r_free= 0.2190   ksol= 0.34   Bsol= 56.11   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.15,1.15,2.07,0.00,0.00,0.00); trace/3= 1.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.477515                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.610246              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.381  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.684831              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.056  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1642      final r-factor (work) = 0.1336          |
| start r-factor (free) = 0.2190      final r-factor (free) = 0.1863          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.8052 = 4.61 * 0.50 * 5.5249 + 1.00 * 0.0697                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.5154 = 4.61 * 0.50 * 5.3963 + 1.00 * 0.0762                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1336      final r-factor (work) = 0.1263          |
| start r-factor (free) = 0.1863      final r-factor (free) = 0.1775          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7084 = 0.68 * 1.00 * 5.3963 + 1.00 * 0.0128                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6272 = 0.68 * 1.00 * 5.2785 + 1.00 * 0.0124                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.895)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.87   14.32    None  None   None       |
|    all(noH): 2823   0      0.00    95.87   14.32    None  None   None       |
|    Sol.    : 438    0      2.97    89.01   39.42    None  None   None       |
|    Mac.    : 2385   0      0.00    95.87   9.71     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.587: 1595   |   5:    47.936 -  57.524:   92        |
|      1:     9.587 -  19.175:  660   |   6:    57.524 -  67.111:   50        |
|      2:    19.175 -  28.762:  164   |   7:    67.111 -  76.698:   17        |
|      3:    28.762 -  38.349:  128   |   8:    76.698 -  86.285:   11        |
|      4:    38.349 -  47.936:  102   |   9:    86.285 -  95.873:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1263 r_free = 0.1775             target_work(ml) = 5.252         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1262 r_free = 0.1771             target_work(ml) = 5.251         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1262   r_free= 0.1771   ksol= 0.34   Bsol= 56.11   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.15,1.15,2.07,0.00,0.00,0.00); trace/3= 1.79                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.250606                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1263   r_free= 0.1767   ksol= 0.33   Bsol= 54.37   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.66,0.85,1.75,0.00,0.00,0.00); trace/3= 1.42                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.250895                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.081447              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 141.108  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.115352              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.751  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1263      final r-factor (work) = 0.1178          |
| start r-factor (free) = 0.1767      final r-factor (free) = 0.1684          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.2109 = 3.08 * 0.50 * 5.2798 + 1.00 * 0.0762                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1246 = 3.08 * 0.50 * 5.2256 + 1.00 * 0.0733                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1178      final r-factor (work) = 0.1201          |
| start r-factor (free) = 0.1684      final r-factor (free) = 0.1657          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6151 = 0.12 * 1.00 * 5.2256 + 1.00 * 0.0123                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.6104 = 0.12 * 1.00 * 5.2111 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 18      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.895)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.65   13.34    None  None   None       |
|    all(noH): 2823   0      0.00    88.65   13.34    None  None   None       |
|    Sol.    : 438    0      3.64    84.47   34.36    None  None   None       |
|    Mac.    : 2385   0      0.00    88.65   9.48     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 -   8.865: 1486   |   5:    44.326 -  53.191:   78        |
|      1:     8.865 -  17.730:  776   |   6:    53.191 -  62.056:   33        |
|      2:    17.730 -  26.596:  175   |   7:    62.056 -  70.922:   14        |
|      3:    26.596 -  35.461:  149   |   8:    70.922 -  79.787:    4        |
|      4:    35.461 -  44.326:  104   |   9:    79.787 -  88.652:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1201 r_free = 0.1657             target_work(ml) = 5.201         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1198 r_free = 0.1652             target_work(ml) = 5.200         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1198   r_free= 0.1652   ksol= 0.33   Bsol= 54.37   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.66,0.85,1.75,0.00,0.00,0.00); trace/3= 1.42                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.199576                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1995 -  4.7065 0.99   1412  160 0.1025 0.1410      5.4224      5.6336|
|  2:  4.7065 -  3.7542 0.99   1366  145 0.0935 0.1149      5.5055      5.6677|
|  3:  3.7542 -  3.2851 0.99   1316  147 0.1128 0.1667      5.5287      5.9137|
|  4:  3.2851 -  2.9872 0.99   1342  155 0.1323 0.1585       5.517      5.6166|
|  5:  2.9872 -  2.7745 0.99   1324  144 0.1413 0.1826       5.372      5.5781|
|  6:  2.7745 -  2.6118 0.99   1304  149 0.1291 0.1882      5.2453      5.4937|
|  7:  2.6118 -  2.4816 0.99   1310  136 0.1340 0.1707      5.2188      5.3697|
|  8:  2.4816 -  2.3740 0.98   1294  151 0.1248 0.1836      5.1029      5.3988|
|  9:  2.3740 -  2.2829 0.98   1300  151 0.1274 0.1949      5.0911      5.3776|
| 10:  2.2829 -  2.2044 0.99   1287  140 0.1224 0.1820      5.0023      5.2137|
| 11:  2.2044 -  2.1356 0.98   1304  137 0.1238 0.1854      4.9909      5.3291|
| 12:  2.1356 -  2.0747 0.97   1267  151 0.1167 0.1625      4.9036      5.0914|
| 13:  2.0747 -  2.0202 0.93   1211  136 0.1290 0.1795      4.8428      5.0897|
| 14:  2.0202 -  1.9711 0.44    593   57 0.1097 0.1668      4.6842      4.9488|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1995 -  4.7065  1412   160  0.94   9.66   0.98     0.96       8176.74|
|  2:  4.7065 -  3.7542  1366   145  0.95   8.80   1.01     1.00      10175.90|
|  3:  3.7542 -  3.2851  1316   147  0.93  12.21   1.03     1.03      11574.84|
|  4:  3.2851 -  2.9872  1342   155  0.91  14.88   1.00     0.97      11474.33|
|  5:  2.9872 -  2.7745  1324   144  0.90  16.37   0.99     0.98       8715.54|
|  6:  2.7745 -  2.6118  1304   149  0.90  16.48   0.98     0.96       7425.90|
|  7:  2.6118 -  2.4816  1310   136  0.90  15.92   1.00     0.98       6630.66|
|  8:  2.4816 -  2.3740  1294   151  0.90  16.44   0.99     0.96       5661.16|
|  9:  2.3740 -  2.2829  1300   151  0.90  16.53   1.02     0.98       5508.92|
| 10:  2.2829 -  2.2044  1287   140  0.90  15.83   1.01     0.99       4650.32|
| 11:  2.2044 -  2.1356  1304   137  0.89  17.05   1.01     0.96       4635.51|
| 12:  2.1356 -  2.0747  1267   151  0.91  15.61   1.02     1.03       4130.26|
| 13:  2.0747 -  2.0202  1211   136  0.90  16.77   1.01     1.00       3528.64|
| 14:  2.0202 -  1.9711   593    57  0.90  15.64   1.00     0.97       2693.59|
|alpha:            min =        0.96 max =            1.03 mean =         0.98|
|beta:             min =     2693.59 max =        11574.84 mean =      7011.12|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.67 mean =        14.78|
|phase err.(test): min =        0.00 max =           88.72 mean =        14.22|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1197   r_free= 0.1650   ksol= 0.33   Bsol= 49.80   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.15,-0.53,0.38,-0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.199385                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1197   r_free= 0.1650   ksol= 0.33   Bsol= 49.80   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.15,-0.53,0.38,-0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.13 A                  |
| x-ray target function (ml) for work reflections: 5.199385                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1995 -  4.7065 0.99   1412  160 0.1021 0.1401       5.418      5.6269|
|  2:  4.7065 -  3.7542 0.99   1366  145 0.0930 0.1141      5.5003      5.6622|
|  3:  3.7542 -  3.2851 0.99   1316  147 0.1126 0.1664      5.5259       5.912|
|  4:  3.2851 -  2.9872 0.99   1342  155 0.1323 0.1583      5.5168      5.6168|
|  5:  2.9872 -  2.7745 0.99   1324  144 0.1416 0.1828      5.3732      5.5797|
|  6:  2.7745 -  2.6118 0.99   1304  149 0.1295 0.1887      5.2469      5.4952|
|  7:  2.6118 -  2.4816 0.99   1310  136 0.1339 0.1708      5.2196      5.3703|
|  8:  2.4816 -  2.3740 0.98   1294  151 0.1250 0.1838       5.104      5.4001|
|  9:  2.3740 -  2.2829 0.98   1300  151 0.1274 0.1951      5.0919      5.3783|
| 10:  2.2829 -  2.2044 0.99   1287  140 0.1227 0.1818      5.0038      5.2151|
| 11:  2.2044 -  2.1356 0.98   1304  137 0.1239 0.1857      4.9916      5.3299|
| 12:  2.1356 -  2.0747 0.97   1267  151 0.1169 0.1630      4.9053      5.0936|
| 13:  2.0747 -  2.0202 0.93   1211  136 0.1291 0.1797      4.8438      5.0902|
| 14:  2.0202 -  1.9711 0.44    593   57 0.1097 0.1671      4.6851      4.9506|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1995 -  4.7065  1412   160  0.94   9.59   0.98     0.96       8083.34|
|  2:  4.7065 -  3.7542  1366   145  0.95   8.76   1.01     1.00      10063.78|
|  3:  3.7542 -  3.2851  1316   147  0.93  12.14   1.02     1.02      11480.07|
|  4:  3.2851 -  2.9872  1342   155  0.91  14.88   1.00     0.97      11467.86|
|  5:  2.9872 -  2.7745  1324   144  0.90  16.39   0.99     0.97       8733.46|
|  6:  2.7745 -  2.6118  1304   149  0.90  16.51   0.98     0.95       7445.94|
|  7:  2.6118 -  2.4816  1310   136  0.90  15.94   0.99     0.97       6647.97|
|  8:  2.4816 -  2.3740  1294   151  0.90  16.46   0.98     0.95       5675.58|
|  9:  2.3740 -  2.2829  1300   151  0.90  16.55   1.01     0.97       5521.39|
| 10:  2.2829 -  2.2044  1287   140  0.90  15.84   1.00     0.98       4659.75|
| 11:  2.2044 -  2.1356  1304   137  0.89  17.07   0.99     0.95       4643.73|
| 12:  2.1356 -  2.0747  1267   151  0.91  15.64   1.01     1.02       4145.52|
| 13:  2.0747 -  2.0202  1211   136  0.90  16.80   1.00     0.99       3539.96|
| 14:  2.0202 -  1.9711   593    57  0.90  15.68   0.99     0.96       2700.45|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2700.45 max =        11480.07 mean =      6996.88|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.78 mean =        14.77|
|phase err.(test): min =        0.00 max =           88.83 mean =        14.22|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.895)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.21    89.86   14.55    None  None   None       |
|    all(noH): 2823   0      1.21    89.86   14.55    None  None   None       |
|    Sol.    : 438    0      4.84    85.67   35.57    None  None   None       |
|    Mac.    : 2385   0      1.21    89.86   10.69    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:     1.206 -  10.072: 1486   |   5:    45.532 -  54.398:   78        |
|      1:    10.072 -  18.937:  776   |   6:    54.398 -  63.263:   33        |
|      2:    18.937 -  27.802:  175   |   7:    63.263 -  72.128:   14        |
|      3:    27.802 -  36.667:  149   |   8:    72.128 -  80.993:    4        |
|      4:    36.667 -  45.532:  104   |   9:    80.993 -  89.858:    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)= 326         
Filter by distance & map next to the model:
   mapped sites are within: 0.577 - 5.506
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 319 from: 326
   mapped sites are within: 0.722 - 5.506

peak=   10.630 closest distance to " CB  VAL A 230 " =    1.450
peak=    7.219 closest distance to " CG2 VAL A 296 " =    1.135
peak=    6.906 closest distance to " CG  ARG A 138 " =    1.164
peak=    6.127 closest distance to " NH2 ARG A  56 " =    2.264
peak=    6.064 closest distance to " CD2 LEU A   5 " =    1.342
peak=    5.323 closest distance to " NE2 GLN A  11 " =    1.189
peak=    5.136 closest distance to " CG  LEU A   5 " =    1.228
peak=    5.100 closest distance to " CD1AILE A 234 " =    1.080
peak=    5.019 closest distance to " CG  LEU A 228 " =    1.240
peak=    4.970 closest distance to " CB  SER A  63 " =    1.307
peak=    4.969 closest distance to " NH1 ARG A 138 " =    1.064
peak=    4.941 closest distance to " O   HOH Z 186 " =    1.829
peak=    4.857 closest distance to " O   HOH Z 183 " =    1.575
peak=    4.840 closest distance to " O   HOH Z 102 " =    0.946
peak=    4.830 closest distance to " O   HOH Z 236 " =    1.932
peak=    4.813 closest distance to " CB  GLU A 152 " =    1.262
peak=    4.749 closest distance to " CB  GLN A 223 " =    1.412
peak=    4.725 closest distance to " O   PRO A 198 " =    1.565
peak=    4.720 closest distance to " O   HOH Z 232 " =    2.227
peak=    4.698 closest distance to " CB  GLN A 183 " =    1.117
peak=    4.657 closest distance to " CG  PRO A 213 " =    1.261
peak=    4.651 closest distance to " O   HOH Z 112 " =    1.579
peak=    4.624 closest distance to " O   HOH Z 193 " =    1.822
peak=    4.544 closest distance to " O   HOH Z   7 " =    1.356
peak=    4.500 closest distance to " CD2 LEU A 228 " =    1.210
peak=    4.476 closest distance to " O   HOH Z 278 " =    0.988
peak=    4.471 closest distance to " O   HOH Z 144 " =    1.610
peak=    4.460 closest distance to " O   HOH Z 368 " =    1.996
peak=    4.444 closest distance to " CD  ARG A 138 " =    1.162
peak=    4.430 closest distance to " OD2 ASP A 286 " =    2.915
peak=    4.420 closest distance to " CB  SER A   3 " =    1.517
peak=    4.411 closest distance to " NH1AARG A 145 " =    1.176
peak=    4.410 closest distance to " O   HOH Z 298 " =    1.835
peak=    4.396 closest distance to " CB  ASN A 148 " =    1.379
peak=    4.362 closest distance to " O   HOH Z 126 " =    1.957
peak=    4.322 closest distance to " O   HOH Z 425 " =    1.505
peak=    4.313 closest distance to " CB  VAL A 296 " =    1.187
peak=    4.288 closest distance to " O   HOH Z 316 " =    3.073
peak=    4.287 closest distance to " CG  PRO A 243 " =    1.156
peak=    4.241 closest distance to " O   HOH Z   9 " =    2.075
peak=    4.226 closest distance to " O   HOH Z  48 " =    1.680
peak=    4.181 closest distance to " NH1 ARG A  56 " =    1.055
peak=    4.164 closest distance to " O   HOH Z 193 " =    2.063
peak=    4.160 closest distance to " O   HOH Z 369 " =    1.936
peak=    4.156 closest distance to " O   HOH Z 303 " =    2.290
peak=    4.153 closest distance to " O   HOH Z 108 " =    1.470
peak=    4.147 closest distance to " O   HOH Z 132 " =    2.423
peak=    4.133 closest distance to " CE3 TRP A 274 " =    2.432
peak=    4.113 closest distance to " O   HOH Z  58 " =    1.917
peak=    4.107 closest distance to " O   HOH Z 126 " =    1.653
peak=    4.089 closest distance to " O   HOH Z 427 " =    3.060
peak=    4.084 closest distance to " CG  PRO A 198 " =    1.303
peak=    4.076 closest distance to " O   HOH Z   2 " =    1.815
peak=    4.062 closest distance to " CB  VAL A 230 " =    1.249
peak=    4.048 closest distance to " CB  ASN A  39 " =    0.811
peak=    4.044 closest distance to " ND2 ASN A 187 " =    1.576
peak=    4.012 closest distance to " CA  SER A  87 " =    0.867
peak=    3.991 closest distance to " OD1 ASN A  69 " =    2.639
peak=    3.988 closest distance to " NE AARG A 275 " =    1.430
peak=    3.988 closest distance to " O   HOH Z 271 " =    2.128
peak=    3.977 closest distance to " CD1 LEU A 300 " =    1.277
peak=    3.970 closest distance to " CA  ALA A  51 " =    1.042
peak=    3.969 closest distance to " CB  ARG A 275 " =    0.878
peak=    3.963 closest distance to " CG2 THR A 221 " =    1.093
peak=    3.953 closest distance to " O   HOH Z 217 " =    2.850
peak=    3.935 closest distance to " O   HOH Z 411 " =    3.606
peak=    3.928 closest distance to " O   HOH Z 222 " =    2.325
peak=    3.916 closest distance to " O   HOH Z 437 " =    2.265
peak=    3.912 closest distance to " O   HOH Z 184 " =    1.570
peak=    3.906 closest distance to " O   SER A  87 " =    2.347
peak=    3.889 closest distance to " NH2BARG A 102 " =    1.032
peak=    3.888 closest distance to " CB  LEU A 228 " =    1.189
peak=    3.887 closest distance to " O   HOH Z 234 " =    3.773
peak=    3.886 closest distance to " O   HOH Z 276 " =    1.351
peak=    3.883 closest distance to " CD ALYS A 290 " =    1.111
peak=    3.874 closest distance to " O   HOH Z 246 " =    1.522
peak=    3.872 closest distance to " O   HOH Z 334 " =    1.739
peak=    3.870 closest distance to " CB  GLU A 128 " =    1.033
peak=    3.867 closest distance to " CG  GLN A  88 " =    1.098
peak=    3.866 closest distance to " O   HOH Z 255 " =    1.677
peak=    3.842 closest distance to " CG  LEU A 167 " =    1.195
peak=    3.841 closest distance to " CB  MET A  40 " =    0.804
peak=    3.829 closest distance to " O   HOH Z  88 " =    3.273
peak=    3.827 closest distance to " CD2 LEU A 255 " =    1.634
peak=    3.818 closest distance to " O   HOH Z 281 " =    4.423
peak=    3.807 closest distance to " CB  VAL A 202 " =    1.462
peak=    3.806 closest distance to " O   HOH Z 410 " =    1.590
peak=    3.806 closest distance to " CG  PRO A 280 " =    0.815
peak=    3.804 closest distance to " CB  ASN A 148 " =    1.919
peak=    3.803 closest distance to " CB  ASN A 187 " =    1.025
peak=    3.796 closest distance to " O   HOH Z  55 " =    2.328
peak=    3.780 closest distance to " O   HOH Z 171 " =    3.922
peak=    3.778 closest distance to " CD1 ILE A  33 " =    1.686
peak=    3.772 closest distance to " CG BARG A 275 " =    1.542
peak=    3.771 closest distance to " O   HOH Z 263 " =    1.609
peak=    3.764 closest distance to " O   HOH Z  80 " =    1.585
peak=    3.761 closest distance to " CB  VAL A 265 " =    1.353
peak=    3.761 closest distance to " O   HOH Z  37 " =    1.268
peak=    3.751 closest distance to " ND1 HIS A  86 " =    1.606
peak=    3.742 closest distance to " O   HOH Z  61 " =    1.618
peak=    3.733 closest distance to " O   HOH Z 133 " =    2.557
peak=    3.731 closest distance to " N   PHE A 130 " =    1.354
peak=    3.712 closest distance to " O   HOH Z   3 " =    1.906
peak=    3.703 closest distance to " CB  TYR A 169 " =    0.793
peak=    3.703 closest distance to " O   HOH Z 346 " =    1.610
peak=    3.697 closest distance to " CB  ILE A 234 " =    0.990
peak=    3.696 closest distance to " O   ALA A 291 " =    1.649
peak=    3.693 closest distance to " O   HOH Z  21 " =    1.782
peak=    3.693 closest distance to " O   HOH Z 344 " =    1.230
peak=    3.679 closest distance to " O   HOH Z   9 " =    1.809
peak=    3.679 closest distance to " CZ  PHE A 192 " =    0.988
peak=    3.677 closest distance to " C   ALA A 299 " =    0.946
peak=    3.677 closest distance to " CA  LEU A 282 " =    1.129
peak=    3.676 closest distance to " CA  TYR A 186 " =    1.532
peak=    3.672 closest distance to " CB  TRP A 150 " =    1.502
peak=    3.669 closest distance to " CB  TRP A 266 " =    0.943
peak=    3.661 closest distance to " CB  ARG A  79 " =    1.509
peak=    3.653 closest distance to " O   HOH Z 371 " =    2.817
peak=    3.649 closest distance to " CB  ALA A 291 " =    1.358
peak=    3.649 closest distance to " O   HOH Z 272 " =    1.906
peak=    3.647 closest distance to " O   HOH Z 116 " =    1.653
peak=    3.635 closest distance to " O   HOH Z 145 " =    3.448
peak=    3.631 closest distance to " O   HOH Z 227 " =    1.723
peak=    3.629 closest distance to " CA  ALA A  21 " =    1.173
peak=    3.627 closest distance to " O   HOH Z  64 " =    2.193
peak=    3.611 closest distance to " CG1 ILE A  33 " =    1.318
peak=    3.610 closest distance to " CB  GLU A 236 " =    1.266
peak=    3.597 closest distance to " O   HOH Z 126 " =    1.842
peak=    3.596 closest distance to " C   GLU A 277 " =    1.444
peak=    3.595 closest distance to " CA  ALA A 154 " =    1.080
peak=    3.594 closest distance to " O   HOH Z 280 " =    3.112
peak=    3.589 closest distance to " O   HOH Z 313 " =    1.780
peak=    3.587 closest distance to " CB  GLU A 277 " =    3.546
peak=    3.587 closest distance to " CB  LEU A 143 " =    1.152
peak=    3.584 closest distance to " O   HOH Z 134 " =    1.525
peak=    3.573 closest distance to " O   HOH Z 260 " =    1.259
peak=    3.570 closest distance to " OH  TYR A 186 " =    0.987
peak=    3.566 closest distance to " O   HOH Z 273 " =    2.670
peak=    3.564 closest distance to " O   HOH Z 135 " =    1.954
peak=    3.556 closest distance to " CE  MET A  93 " =    1.499
peak=    3.555 closest distance to " CB  GLN A  88 " =    1.267
peak=    3.553 closest distance to " O   HOH Z  57 " =    1.362
peak=    3.553 closest distance to " O   HOH Z 282 " =    1.978
peak=    3.553 closest distance to " O   HOH Z 124 " =    1.392
peak=    3.551 closest distance to " O   HOH Z 189 " =    2.749
peak=    3.541 closest distance to " O   HOH Z 158 " =    2.718
peak=    3.532 closest distance to " O   HOH Z 128 " =    1.583
peak=    3.519 closest distance to " O   HOH Z 332 " =    1.572
peak=    3.517 closest distance to " CB  ASN A 142 " =    0.952
peak=    3.510 closest distance to " CA  TYR A  30 " =    0.982
peak=    3.509 closest distance to " CD  ARG A 159 " =    0.722
peak=    3.501 closest distance to " CA  THR A 221 " =    0.876
peak=    3.501 closest distance to " O   HOH Z 117 " =    1.818
peak=    3.500 closest distance to " O   HOH Z  40 " =    2.337
peak=    3.493 closest distance to " O   HOH Z 301 " =    1.797
peak=    3.489 closest distance to " O   HOH Z  68 " =    1.542
peak=    3.487 closest distance to " O   HOH Z 227 " =    2.058
peak=    3.483 closest distance to " OD1 ASN A 217 " =    1.657
peak=    3.482 closest distance to " O   HOH Z  98 " =    2.097
peak=    3.480 closest distance to " O   HOH Z 392 " =    1.333
peak=    3.475 closest distance to " CA  LYS A 117 " =    1.181
peak=    3.474 closest distance to " O   HOH Z 153 " =    1.829
peak=    3.467 closest distance to " O   HOH Z 193 " =    1.829
peak=    3.451 closest distance to " O   HOH Z  59 " =    2.092
peak=    3.449 closest distance to " O   HOH Z 403 " =    1.649
peak=    3.442 closest distance to " CB  MET A  47 " =    0.938
peak=    3.441 closest distance to " CA  ASN A 215 " =    1.272
peak=    3.437 closest distance to " NH2AARG A 190 " =    1.432
peak=    3.435 closest distance to " O   HOH Z  10 " =    1.817
peak=    3.432 closest distance to " O   HOH Z 115 " =    2.161
peak=    3.432 closest distance to " O   HOH Z 409 " =    2.653
peak=    3.429 closest distance to " NH2BARG A 145 " =    2.032
peak=    3.428 closest distance to " OG BSER A 134 " =    3.011
peak=    3.428 closest distance to " CA  ALA A 295 " =    0.997
peak=    3.426 closest distance to " O   MET A 105 " =    1.752
peak=    3.420 closest distance to " CB  SER A 210 " =    0.818
peak=    3.417 closest distance to " OE1 GLN A 240 " =    1.581
peak=    3.409 closest distance to " CA  ALA A 158 " =    1.120
peak=    3.409 closest distance to " CA  VAL A  41 " =    0.993
peak=    3.402 closest distance to " CA  MET A  40 " =    1.129
peak=    3.400 closest distance to " O   HOH Z   1 " =    1.786
peak=    3.399 closest distance to " CB  ALA A 114 " =    1.379
peak=    3.397 closest distance to " CG1 ILE A 151 " =    1.245
peak=    3.397 closest distance to " CA  GLY A 267 " =    1.036
peak=    3.395 closest distance to " CG1 VAL A 153 " =    0.969
peak=    3.394 closest distance to " O   HOH Z 327 " =    1.916
peak=    3.394 closest distance to " CD  ARG A  14 " =    1.242
peak=    3.393 closest distance to " CB  ALA A  34 " =    0.994
peak=    3.387 closest distance to " O   HOH Z 105 " =    1.556
peak=    3.386 closest distance to " N   ASN A  39 " =    1.109
peak=    3.386 closest distance to " CB  ALA A 104 " =    0.770
peak=    3.382 closest distance to " CG2AVAL A  72 " =    1.567
peak=    3.379 closest distance to " NH2BARG A 190 " =    1.668
peak=    3.378 closest distance to " O   HOH Z  78 " =    1.675
peak=    3.377 closest distance to " CB  ALA A   9 " =    1.565
peak=    3.374 closest distance to " CB  SER A 216 " =    0.821
peak=    3.372 closest distance to " O   HOH Z 357 " =    1.982
peak=    3.370 closest distance to " N   ARG A 156 " =    1.380
peak=    3.368 closest distance to " O   HOH Z 175 " =    3.562
peak=    3.367 closest distance to " O   HOH Z 175 " =    2.186
peak=    3.365 closest distance to " CB  LEU A 237 " =    0.888
peak=    3.361 closest distance to " O   HOH Z 248 " =    1.906
peak=    3.360 closest distance to " CA  ILE A 234 " =    0.922
peak=    3.358 closest distance to " O   HOH Z 209 " =    2.501
peak=    3.355 closest distance to " O   HOH Z  64 " =    2.081
peak=    3.355 closest distance to " CB  ARG A 139 " =    0.998
peak=    3.347 closest distance to " CZ3 TRP A 123 " =    1.357
peak=    3.346 closest distance to " ND2 ASN A 249 " =    1.808
peak=    3.340 closest distance to " O   HOH Z 251 " =    1.920
peak=    3.335 closest distance to " NH1BARG A 275 " =    1.471
peak=    3.330 closest distance to " O   HOH Z 344 " =    2.829
peak=    3.317 closest distance to " OG1 THR A 246 " =    3.321
peak=    3.316 closest distance to " O   HOH Z 261 " =    1.951
peak=    3.316 closest distance to " O   HOH Z 128 " =    1.927
peak=    3.316 closest distance to " O   HOH Z 355 " =    1.714
peak=    3.311 closest distance to " O   HOH Z 345 " =    3.402
peak=    3.309 closest distance to " CB  ALA A 161 " =    0.871
peak=    3.305 closest distance to " O   HOH Z  68 " =    2.017
peak=    3.305 closest distance to " CB  SER A 212 " =    1.195
peak=    3.302 closest distance to " CE1 TYR A 186 " =    1.335
peak=    3.300 closest distance to " CA  LYS A  48 " =    1.412
peak=    3.297 closest distance to " CG1 ILE A  49 " =    1.313
peak=    3.297 closest distance to " CB  LYS A 117 " =    1.196
peak=    3.290 closest distance to " O   HOH Z 216 " =    2.468
peak=    3.290 closest distance to " NH2 ARG A 219 " =    1.883
peak=    3.290 closest distance to " OE1 GLN A  58 " =    1.356
peak=    3.288 closest distance to " O   HOH Z   6 " =    2.112
peak=    3.288 closest distance to " CB  THR A 157 " =    1.106
peak=    3.288 closest distance to " CB  TRP A 179 " =    1.503
peak=    3.286 closest distance to " O   HOH Z 302 " =    1.837
peak=    3.285 closest distance to " NE2 GLN A  58 " =    5.506
peak=    3.284 closest distance to " CB  TYR A  30 " =    1.357
peak=    3.284 closest distance to " O   HOH Z 295 " =    1.569
peak=    3.282 closest distance to " NH1 ARG A  66 " =    1.633
peak=    3.277 closest distance to " CG  ARG A 159 " =    0.980
peak=    3.276 closest distance to " O   HOH Z 281 " =    1.743
peak=    3.276 closest distance to " O   HOH Z 244 " =    1.610
peak=    3.268 closest distance to " O   HOH Z 145 " =    1.704
peak=    3.266 closest distance to " O   HOH Z 407 " =    1.846
peak=    3.262 closest distance to " O   HOH Z  40 " =    2.079
peak=    3.261 closest distance to " O   HOH Z  61 " =    1.531
peak=    3.261 closest distance to " O   HOH Z 435 " =    2.129
peak=    3.261 closest distance to " CB  ILE A 120 " =    1.303
peak=    3.258 closest distance to " CA  ASP A 162 " =    0.961
peak=    3.255 closest distance to " CD2 LEU A 167 " =    0.781
peak=    3.253 closest distance to " O   HOH Z 388 " =    2.043
peak=    3.252 closest distance to " CG  LYS A 166 " =    1.357
peak=    3.251 closest distance to " CG AARG A 275 " =    1.134
peak=    3.250 closest distance to " O   HOH Z 371 " =    1.632
peak=    3.247 closest distance to " O   HOH Z 182 " =    1.452
peak=    3.246 closest distance to " CA  GLN A 223 " =    0.847
peak=    3.245 closest distance to " O   HOH Z 130 " =    2.189
peak=    3.243 closest distance to " CB  SER A  62 " =    1.230
peak=    3.242 closest distance to " CB  ALA A 248 " =    1.319
peak=    3.240 closest distance to " CG2 VAL A 257 " =    0.950
peak=    3.239 closest distance to " O   HOH Z  71 " =    1.333
peak=    3.237 closest distance to " O   HOH Z 280 " =    1.765
peak=    3.235 closest distance to " O   HOH Z 380 " =    1.714
peak=    3.233 closest distance to " O   GLY A  57 " =    2.589
peak=    3.228 closest distance to " O   HOH Z  59 " =    1.702
peak=    3.226 closest distance to " O   HOH Z  38 " =    1.916
peak=    3.225 closest distance to " O   HOH Z 109 " =    2.666
peak=    3.224 closest distance to " O   HOH Z 133 " =    1.775
peak=    3.223 closest distance to " O   PRO A 198 " =    1.315
peak=    3.221 closest distance to " O   HOH Z 345 " =    1.743
peak=    3.221 closest distance to " CG BARG A 102 " =    1.886
peak=    3.221 closest distance to " O   HOH Z 374 " =    2.585
peak=    3.217 closest distance to " O   HOH Z 350 " =    1.416
peak=    3.217 closest distance to " O   HOH Z  49 " =    2.414
peak=    3.212 closest distance to " O   HOH Z  59 " =    1.889
peak=    3.209 closest distance to " O   HOH Z 294 " =    1.565
peak=    3.203 closest distance to " O   HOH Z 148 " =    3.442
peak=    3.202 closest distance to " O   TYR A 116 " =    1.221
peak=    3.200 closest distance to " CB  VAL A 250 " =    1.070
peak=    3.199 closest distance to " O   HOH Z 141 " =    1.660
peak=    3.195 closest distance to " CA  ASN A  74 " =    1.099
peak=    3.194 closest distance to " CH2 TRP A 150 " =    1.014
peak=    3.186 closest distance to " CG  GLN A 144 " =    0.900
peak=    3.186 closest distance to " OG  SER A  62 " =    2.980
peak=    3.185 closest distance to " O   HOH Z  44 " =    1.610
peak=    3.181 closest distance to " CB  SER A 273 " =    0.887
peak=    3.179 closest distance to " O   HOH Z 303 " =    1.800
peak=    3.179 closest distance to " CE  LYS A  76 " =    0.951
peak=    3.178 closest distance to " O   HOH Z 189 " =    3.514
peak=    3.177 closest distance to " O   HOH Z 196 " =    1.376
peak=    3.170 closest distance to " O   HOH Z  88 " =    2.648
peak=    3.168 closest distance to " O   HOH Z  44 " =    2.330
peak=    3.166 closest distance to " OG BSER A 164 " =    2.231
peak=    3.162 closest distance to " O   HOH Z 148 " =    3.774
peak=    3.161 closest distance to " O   HOH Z 156 " =    2.782
peak=    3.156 closest distance to " O   HOH Z  88 " =    2.663
peak=    3.153 closest distance to " O   HOH Z 184 " =    2.366
peak=    3.151 closest distance to " N   ALA A   1 " =    1.980
peak=    3.150 closest distance to " O   HOH Z 180 " =    2.072
peak=    3.146 closest distance to " CD1 ILE A 263 " =    1.285
peak=    3.145 closest distance to " OG  SER A  22 " =    2.948
peak=    3.144 closest distance to " CG2 VAL A 189 " =    1.331
peak=    3.143 closest distance to " CG  PRO A  54 " =    1.120
peak=    3.142 closest distance to " O   HOH Z  63 " =    2.166
peak=    3.141 closest distance to " O   ASN A 209 " =    1.399
peak=    3.138 closest distance to " O   HOH Z 225 " =    1.806
peak=    3.137 closest distance to " O   ALA A   1 " =    1.582
peak=    3.133 closest distance to " CA  THR A 264 " =    0.840
peak=    3.132 closest distance to " O   HOH Z 419 " =    1.710
peak=    3.130 closest distance to " CA  GLU A 152 " =    1.043
peak=    3.118 closest distance to " O   HOH Z 328 " =    1.710
peak=    3.104 closest distance to " CD BARG A 102 " =    1.291
peak=    3.102 closest distance to " CA  ILE A  33 " =    1.593
peak=    3.101 closest distance to " CG1 VAL A 174 " =    0.947
peak=    3.093 closest distance to " O  BHOH Z 338 " =    2.419
peak=    3.092 closest distance to " O   HOH Z  53 " =    2.580
peak=    3.090 closest distance to " CA  LEU A 101 " =    1.520
peak=    3.090 closest distance to " CG2 VAL A 174 " =    1.340
peak=    3.089 closest distance to " O   HOH Z 171 " =    2.322
peak=    3.085 closest distance to " CB  ALA A 100 " =    1.410
peak=    3.079 closest distance to " CG  MET A 188 " =    1.511
peak=    3.079 closest distance to " CA  ASP A 140 " =    1.319
peak=    3.057 closest distance to " C   GLN A  88 " =    1.487
peak=    3.043 closest distance to " O   HOH Z  57 " =    1.691

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 205         
Filter by distance & map next to the model:
   mapped sites are within: 0.181 - 5.523
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 190 from: 205
   mapped sites are within: 0.701 - 5.523

peak=   -5.321 closest distance to " O   HOH Z 290 " =    0.946
peak=   -4.890 closest distance to " O   HOH Z 102 " =    1.134
peak=   -4.532 closest distance to " CD  ARG A  14 " =    3.122
peak=   -4.530 closest distance to " O   HOH Z 231 " =    1.245
peak=   -4.418 closest distance to " O   HOH Z 377 " =    1.199
peak=   -4.357 closest distance to " O   HOH Z  52 " =    1.164
peak=   -4.237 closest distance to " CG  ARG A 138 " =    0.952
peak=   -4.078 closest distance to " CG  LEU A 101 " =    2.583
peak=   -3.984 closest distance to " C   ALA A 158 " =    1.340
peak=   -3.963 closest distance to " CD  ARG A 138 " =    1.082
peak=   -3.946 closest distance to " CG1 VAL A 296 " =    1.358
peak=   -3.945 closest distance to " O   HOH Z 388 " =    2.038
peak=   -3.918 closest distance to " CB  PRO A 163 " =    2.566
peak=   -3.890 closest distance to " CD1 LEU A 228 " =    2.439
peak=   -3.844 closest distance to " CB  ASP A  27 " =    2.436
peak=   -3.820 closest distance to " CA  GLY A 241 " =    2.305
peak=   -3.818 closest distance to " CB  PRO A 243 " =    2.622
peak=   -3.815 closest distance to " CG1 VAL A 250 " =    2.695
peak=   -3.814 closest distance to " O   HOH Z 322 " =    0.739
peak=   -3.804 closest distance to " CD  LYS A 289 " =    2.557
peak=   -3.794 closest distance to " O   PRO A 163 " =    1.882
peak=   -3.793 closest distance to " CE1 TYR A 169 " =    2.596
peak=   -3.790 closest distance to " CG  ASP A 231 " =    0.771
peak=   -3.787 closest distance to " N   THR A 157 " =    1.534
peak=   -3.782 closest distance to " OE1 GLN A  88 " =    1.063
peak=   -3.740 closest distance to " O   GLY A  80 " =    2.518
peak=   -3.731 closest distance to " OG  SER A  87 " =    1.335
peak=   -3.726 closest distance to " CD2 LEU A   5 " =    0.957
peak=   -3.717 closest distance to " O   HOH Z 211 " =    1.530
peak=   -3.713 closest distance to " CD  GLU A 152 " =    0.701
peak=   -3.695 closest distance to " CB  TRP A  85 " =    2.553
peak=   -3.695 closest distance to " CB  ILE A 239 " =    2.086
peak=   -3.686 closest distance to " N   GLN A  58 " =    1.710
peak=   -3.686 closest distance to " CD  ARG A 156 " =    1.979
peak=   -3.660 closest distance to " CG  PRO A 163 " =    2.374
peak=   -3.649 closest distance to " C   ASN A 285 " =    2.508
peak=   -3.637 closest distance to " O   HOH Z 274 " =    2.789
peak=   -3.633 closest distance to " CZ3 TRP A 179 " =    1.138
peak=   -3.632 closest distance to " O   HOH Z  71 " =    1.057
peak=   -3.602 closest distance to " C   LEU A 222 " =    0.813
peak=   -3.596 closest distance to " O   PRO A 198 " =    1.347
peak=   -3.595 closest distance to " O   HOH Z 275 " =    1.618
peak=   -3.595 closest distance to " CD1 PHE A  59 " =    1.839
peak=   -3.591 closest distance to " CD1 LEU A 101 " =    2.716
peak=   -3.590 closest distance to " O   HOH Z 179 " =    2.182
peak=   -3.588 closest distance to " CD2 LEU A 237 " =    2.817
peak=   -3.588 closest distance to " NH2 ARG A  79 " =    1.917
peak=   -3.583 closest distance to " CG2 VAL A 296 " =    0.920
peak=   -3.576 closest distance to " CG  MET A 105 " =    1.051
peak=   -3.573 closest distance to " O   HOH Z 166 " =    1.314
peak=   -3.573 closest distance to " CB  TYR A 172 " =    2.355
peak=   -3.567 closest distance to " CG  GLN A 223 " =    2.045
peak=   -3.557 closest distance to " CD  GLN A  88 " =    0.760
peak=   -3.543 closest distance to " O   GLY A 211 " =    1.384
peak=   -3.543 closest distance to " CD  GLN A  88 " =    2.323
peak=   -3.528 closest distance to " O   HOH Z  98 " =    1.985
peak=   -3.528 closest distance to " OG1 THR A 178 " =    1.202
peak=   -3.520 closest distance to " O   HOH Z 389 " =    1.701
peak=   -3.517 closest distance to " OG BSER A 134 " =    1.377
peak=   -3.517 closest distance to " O   HOH Z 423 " =    0.918
peak=   -3.507 closest distance to " N   ALA A  43 " =    2.247
peak=   -3.499 closest distance to " CB  ALA A 248 " =    2.526
peak=   -3.492 closest distance to " NH2AARG A 275 " =    5.523
peak=   -3.486 closest distance to " CB  VAL A 296 " =    1.013
peak=   -3.479 closest distance to " O   HOH Z 435 " =    2.809
peak=   -3.465 closest distance to " O   HOH Z 266 " =    4.627
peak=   -3.465 closest distance to " O   HOH Z 168 " =    1.838
peak=   -3.464 closest distance to " O   HOH Z  43 " =    1.738
peak=   -3.462 closest distance to " O   GLY A 203 " =    2.512
peak=   -3.453 closest distance to " O   HOH Z 317 " =    2.264
peak=   -3.444 closest distance to " O   HOH Z 198 " =    0.702
peak=   -3.436 closest distance to " CE BMET A  47 " =    1.650
peak=   -3.433 closest distance to " CG  LEU A 228 " =    0.861
peak=   -3.416 closest distance to " CB  ASP A 132 " =    2.342
peak=   -3.414 closest distance to " C   GLN A 240 " =    2.292
peak=   -3.411 closest distance to " O   ALA A 161 " =    1.462
peak=   -3.406 closest distance to " O   HOH Z 281 " =    2.928
peak=   -3.403 closest distance to " CD1 TRP A 179 " =    0.769
peak=   -3.396 closest distance to " O   HOH Z 351 " =    1.410
peak=   -3.395 closest distance to " O   HOH Z 394 " =    1.452
peak=   -3.392 closest distance to " O   SER A  62 " =    2.323
peak=   -3.385 closest distance to " O   HOH Z 148 " =    2.170
peak=   -3.384 closest distance to " O   HOH Z  93 " =    0.981
peak=   -3.382 closest distance to " CB  ALA A  43 " =    2.394
peak=   -3.380 closest distance to " O   HOH Z  13 " =    1.196
peak=   -3.380 closest distance to " ND2 ASN A  45 " =    1.130
peak=   -3.372 closest distance to " CE2 TYR A  30 " =    2.922
peak=   -3.370 closest distance to " CG  TRP A 266 " =    1.609
peak=   -3.355 closest distance to " CD  GLN A  58 " =    0.879
peak=   -3.350 closest distance to " O   HOH Z 298 " =    1.246
peak=   -3.349 closest distance to " CG1 VAL A 296 " =    1.257
peak=   -3.348 closest distance to " O   HOH Z 371 " =    1.353
peak=   -3.339 closest distance to " O   SER A  22 " =    2.306
peak=   -3.337 closest distance to " OG  SER A  63 " =    1.041
peak=   -3.337 closest distance to " O   HOH Z  51 " =    0.931
peak=   -3.334 closest distance to " CG  PHE A 283 " =    2.629
peak=   -3.321 closest distance to " O   HOH Z 222 " =    1.129
peak=   -3.320 closest distance to " O   HOH Z 407 " =    3.252
peak=   -3.313 closest distance to " O   SER A  12 " =    1.527
peak=   -3.305 closest distance to " O   HOH Z  65 " =    1.197
peak=   -3.300 closest distance to " O   HOH Z  53 " =    1.548
peak=   -3.294 closest distance to " O   HOH Z 281 " =    4.963
peak=   -3.292 closest distance to " OG BSER A 134 " =    1.712
peak=   -3.292 closest distance to " O   HOH Z 128 " =    3.916
peak=   -3.288 closest distance to " NE2 GLN A 278 " =    0.942
peak=   -3.286 closest distance to " SG BCYS A 201 " =    2.277
peak=   -3.284 closest distance to " CB  CYS A 254 " =    2.153
peak=   -3.282 closest distance to " O   VAL A 197 " =    1.525
peak=   -3.281 closest distance to " CZ BARG A 275 " =    1.697
peak=   -3.275 closest distance to " O   HOH Z 100 " =    1.074
peak=   -3.275 closest distance to " OH  TYR A 214 " =    1.141
peak=   -3.274 closest distance to " O   PRO A 198 " =    1.183
peak=   -3.268 closest distance to " C   LYS A  76 " =    1.701
peak=   -3.265 closest distance to " O   HOH Z 353 " =    2.366
peak=   -3.265 closest distance to " CB  ASN A  39 " =    2.055
peak=   -3.264 closest distance to " O   GLY A 196 " =    1.238
peak=   -3.262 closest distance to " O   HOH Z 185 " =    2.223
peak=   -3.262 closest distance to " CG2 THR A   4 " =    2.093
peak=   -3.262 closest distance to " N   PHE A  59 " =    2.203
peak=   -3.257 closest distance to " O   SER A 135 " =    1.466
peak=   -3.257 closest distance to " CD2 PHE A  61 " =    1.837
peak=   -3.256 closest distance to " ND2 ASN A  60 " =    1.622
peak=   -3.253 closest distance to " O   HOH Z 278 " =    1.075
peak=   -3.248 closest distance to " O   HOH Z 198 " =    1.200
peak=   -3.245 closest distance to " CD2 PHE A 225 " =    2.758
peak=   -3.241 closest distance to " O   HOH Z 423 " =    2.260
peak=   -3.226 closest distance to " CB  ALA A 248 " =    1.881
peak=   -3.226 closest distance to " O   THR A  18 " =    1.663
peak=   -3.222 closest distance to " C   HIS A 108 " =    1.178
peak=   -3.221 closest distance to " O   HOH Z 436 " =    1.384
peak=   -3.219 closest distance to " NH1 ARG A  56 " =    2.402
peak=   -3.217 closest distance to " O   ILE A 109 " =    2.669
peak=   -3.216 closest distance to " O   HOH Z  98 " =    1.612
peak=   -3.215 closest distance to " CB  ALA A   9 " =    2.658
peak=   -3.208 closest distance to " C   MET A 188 " =    1.496
peak=   -3.208 closest distance to " O   HOH Z 390 " =    2.326
peak=   -3.203 closest distance to " O   HOH Z  60 " =    2.136
peak=   -3.199 closest distance to " CB  PRO A  54 " =    2.283
peak=   -3.199 closest distance to " O   HOH Z  38 " =    1.875
peak=   -3.198 closest distance to " O   HOH Z 241 " =    1.262
peak=   -3.196 closest distance to " O   HOH Z 350 " =    1.910
peak=   -3.195 closest distance to " O   HOH Z 147 " =    1.508
peak=   -3.191 closest distance to " O   HOH Z 389 " =    4.327
peak=   -3.186 closest distance to " C   VAL A 174 " =    1.798
peak=   -3.184 closest distance to " OG ASER A 134 " =    1.415
peak=   -3.183 closest distance to " O   ASP A 270 " =    1.720
peak=   -3.177 closest distance to " CG  GLU A 152 " =    2.018
peak=   -3.174 closest distance to " NH1AARG A 275 " =    1.869
peak=   -3.172 closest distance to " N   GLY A  23 " =    2.213
peak=   -3.172 closest distance to " O   HOH Z 170 " =    2.401
peak=   -3.172 closest distance to " CB  SER A  63 " =    3.274
peak=   -3.167 closest distance to " CG2BVAL A  41 " =    2.600
peak=   -3.161 closest distance to " CA  GLY A 241 " =    2.863
peak=   -3.161 closest distance to " CE  MET A 105 " =    2.195
peak=   -3.160 closest distance to " OG  SER A 206 " =    1.611
peak=   -3.155 closest distance to " CD  GLN A 223 " =    1.026
peak=   -3.154 closest distance to " O   ASP A 231 " =    2.527
peak=   -3.154 closest distance to " CE  LYS A  76 " =    2.805
peak=   -3.151 closest distance to " O   MET A  47 " =    2.638
peak=   -3.150 closest distance to " O   HOH Z 309 " =    2.319
peak=   -3.149 closest distance to " CG  ASN A  45 " =    1.757
peak=   -3.147 closest distance to " O   HOH Z 152 " =    5.038
peak=   -3.146 closest distance to " O   HOH Z  97 " =    1.506
peak=   -3.144 closest distance to " OE1 GLN A 278 " =    1.025
peak=   -3.143 closest distance to " CB  ALA A 244 " =    2.008
peak=   -3.138 closest distance to " O   HOH Z 359 " =    1.700
peak=   -3.136 closest distance to " O   HOH Z 282 " =    0.910
peak=   -3.126 closest distance to " CG  ASP A 200 " =    1.230
peak=   -3.126 closest distance to " CD1 ILE A 199 " =    2.589
peak=   -3.122 closest distance to " O   HOH Z 210 " =    0.796
peak=   -3.117 closest distance to " CB  ARG A  79 " =    2.542
peak=   -3.116 closest distance to " CA  ARG A 139 " =    0.956
peak=   -3.112 closest distance to " O   SER A  62 " =    1.726
peak=   -3.107 closest distance to " ND2 ASN A  60 " =    1.948
peak=   -3.101 closest distance to " OG  SER A  97 " =    2.314
peak=   -3.099 closest distance to " CG  ARG A 259 " =    2.560
peak=   -3.099 closest distance to " O   HOH Z 306 " =    3.019
peak=   -3.099 closest distance to " OG  SER A  26 " =    1.119
peak=   -3.090 closest distance to " CB  TYR A  15 " =    2.156
peak=   -3.090 closest distance to " O   HOH Z 140 " =    1.494
peak=   -3.088 closest distance to " O   HOH Z 385 " =    2.023
peak=   -3.079 closest distance to " N   ALA A 248 " =    2.408
peak=   -3.065 closest distance to " ND2 ASN A 249 " =    2.395
peak=   -3.063 closest distance to " CD1 LEU A 297 " =    2.654
peak=   -3.062 closest distance to " CB  ALA A 227 " =    2.397
peak=   -3.057 closest distance to " CE2 PHE A 218 " =    2.571
peak=   -3.055 closest distance to " CG2 THR A 178 " =    2.193
peak=   -3.048 closest distance to " O   HOH Z  99 " =    1.633
peak=   -3.045 closest distance to " O   HOH Z 392 " =    0.847
peak=   -3.037 closest distance to " O   HOH Z 426 " =    2.251

================= 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    :  0.4888 0.4754   6.287741e+00   6.278442e+00
   1_bss:  0.4802 0.4659   6.284114e+00   6.272837e+00
   1_xyz:  0.4049 0.4280   6.185754e+00   6.221185e+00
   1_adp:  0.3609 0.4103   6.115422e+00   6.197733e+00
   1_occ:  0.3603 0.4109   6.114843e+00   6.197628e+00
   2_bss:  0.3589 0.4073   6.115656e+00   6.197039e+00
   2_xyz:  0.2716 0.3292   5.898487e+00   6.046144e+00
   2_adp:  0.2504 0.3185   5.845133e+00   6.011521e+00
   2_occ:  0.2501 0.3183   5.844601e+00   6.011347e+00
   3_bss:  0.2489 0.3167   5.844656e+00   6.009971e+00
   3_xyz:  0.1824 0.2382   5.565591e+00   5.768976e+00
   3_adp:  0.1644 0.2196   5.477723e+00   5.695257e+00
   3_occ:  0.1643 0.2193   5.476844e+00   5.693941e+00
   4_bss:  0.1642 0.2190   5.477515e+00   5.693414e+00
   4_xyz:  0.1336 0.1863   5.300309e+00   5.542427e+00
   4_adp:  0.1263 0.1775   5.251773e+00   5.497404e+00
   4_occ:  0.1262 0.1771   5.250606e+00   5.495937e+00
   5_bss:  0.1263 0.1767   5.250895e+00   5.495507e+00
   5_xyz:  0.1178 0.1684   5.198534e+00   5.448642e+00
   5_adp:  0.1201 0.1657   5.201293e+00   5.436141e+00
   5_occ:  0.1198 0.1652   5.199576e+00   5.434151e+00
   5_bss:  0.1197 0.1650   5.199385e+00   5.433909e+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  20.000   8.892   7.087   6.785   0.000   0.000   0.000
   1_xyz:  0.300  20.000   8.892   7.087   6.785   0.000   0.000   0.000
   1_adp:  0.300  20.000   8.892   7.087   6.785   0.000   0.000   0.000
   1_occ:  0.300  20.000   8.892   7.087   6.785   0.000   0.000   0.000
   2_bss:  0.334  42.776   5.412   3.823   4.489   0.000   0.000   0.000
   2_xyz:  0.334  42.776   5.412   3.823   4.489   0.000   0.000   0.000
   2_adp:  0.334  42.776   5.412   3.823   4.489   0.000   0.000   0.000
   2_occ:  0.334  42.776   5.412   3.823   4.489   0.000   0.000   0.000
   3_bss:  0.344  54.160   3.406   1.932   3.013   0.000   0.000   0.000
   3_xyz:  0.344  54.160   3.406   1.932   3.013   0.000   0.000   0.000
   3_adp:  0.344  54.160   3.406   1.932   3.013   0.000   0.000   0.000
   3_occ:  0.344  54.160   3.406   1.932   3.013   0.000   0.000   0.000
   4_bss:  0.335  56.110   2.147   1.149   2.072   0.000   0.000   0.000
   4_xyz:  0.335  56.110   2.147   1.149   2.072   0.000   0.000   0.000
   4_adp:  0.335  56.110   2.147   1.149   2.072   0.000   0.000   0.000
   4_occ:  0.335  56.110   2.147   1.149   2.072   0.000   0.000   0.000
   5_bss:  0.332  54.372   1.660   0.850   1.754   0.000   0.000   0.000
   5_xyz:  0.332  54.372   1.660   0.850   1.754   0.000   0.000   0.000
   5_adp:  0.332  54.372   1.660   0.850   1.754   0.000   0.000   0.000
   5_occ:  0.332  54.372   1.660   0.850   1.754   0.000   0.000   0.000
   5_bss:  0.326  49.805   0.151  -0.528   0.378  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  57.938 0.4208  0.4978    72545.160
   1_bss:  58.252 0.4151  0.6056    70082.605
   1_xyz:  50.266 0.5159  0.7403    55150.812
   1_adp:  46.387 0.5646  0.8637    49826.466
   1_occ:  46.549 0.5625  0.8591    49957.993
   2_bss:  46.364 0.5646  0.7782    49692.580
   2_xyz:  35.293 0.6967  0.9305    30003.821
   2_adp:  33.345 0.7194  0.9522    27492.745
   2_occ:  33.337 0.7195  0.9523    27482.874
   3_bss:  33.194 0.7210  0.8955    27307.347
   3_xyz:  23.606 0.8254  0.9872    14832.176
   3_adp:  21.234 0.8499  1.0018    12552.411
   3_occ:  21.197 0.8502  1.0020    12503.616
   4_bss:  21.161 0.8505  0.9671    12487.051
   4_xyz:  17.426 0.8853  0.9874     8871.879
   4_adp:  16.276 0.8960  0.9901     8073.280
   4_occ:  16.237 0.8963  0.9901     8033.274
   5_bss:  16.237 0.8962  0.9767     8019.116
   5_xyz:  15.195 0.9053  0.9799     7196.369
   5_adp:  14.755 0.9094  0.9840     7049.585
   5_occ:  14.720 0.9096  0.9841     7012.256
   5_bss:  14.719 0.9096  0.9764     6998.037
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3644e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3644e+01
   1_xyz:   1.746  0.014  0.110 18.495  0.007  4.109   1.5041e-01
   1_adp:   1.746  0.014  0.110 18.495  0.007  4.109   1.5041e-01
   1_occ:   1.746  0.014  0.110 18.495  0.007  4.109   1.5041e-01
   2_bss:   1.746  0.014  0.110 18.495  0.007  4.109   1.5041e-01
   2_xyz:   1.147  0.009  0.075 16.532  0.005  4.108   8.4748e-02
   2_adp:   1.147  0.009  0.075 16.532  0.005  4.108   8.4748e-02
   2_occ:   1.147  0.009  0.075 16.532  0.005  4.108   8.4748e-02
   3_bss:   1.147  0.009  0.075 16.532  0.005  4.108   8.4748e-02
   3_xyz:   1.088  0.007  0.079 15.766  0.004  4.125   6.9661e-02
   3_adp:   1.088  0.007  0.079 15.766  0.004  4.125   6.9661e-02
   3_occ:   1.088  0.007  0.079 15.766  0.004  4.125   6.9661e-02
   4_bss:   1.088  0.007  0.079 15.766  0.004  4.125   6.9661e-02
   4_xyz:   1.124  0.009  0.085 15.845  0.004  4.110   7.6175e-02
   4_adp:   1.124  0.009  0.085 15.845  0.004  4.110   7.6175e-02
   4_occ:   1.124  0.009  0.085 15.845  0.004  4.110   7.6175e-02
   5_bss:   1.124  0.009  0.085 15.845  0.004  4.110   7.6175e-02
   5_xyz:   1.111  0.008  0.084 15.980  0.004  4.111   7.3318e-02
   5_adp:   1.111  0.008  0.084 15.980  0.004  4.111   7.3318e-02
   5_occ:   1.111  0.008  0.084 15.980  0.004  4.111   7.3318e-02
   5_bss:   1.111  0.008  0.084 15.980  0.004  4.111   7.3318e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9546e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9546e+00
   1_xyz:  14.414  0.173  0.490 86.592  0.046  2.162   1.0638e-01
   1_adp:  14.414  0.173  0.490 86.592  0.046  2.162   1.0638e-01
   1_occ:  14.414  0.173  0.490 86.592  0.046  2.162   1.0638e-01
   2_bss:  14.414  0.173  0.490 86.592  0.046  2.162   1.0638e-01
   2_xyz:   6.833  0.105  0.257 84.069  0.043  2.217   1.0109e-01
   2_adp:   6.833  0.105  0.257 84.069  0.043  2.217   1.0109e-01
   2_occ:   6.833  0.105  0.257 84.069  0.043  2.217   1.0109e-01
   3_bss:   6.833  0.105  0.257 84.069  0.043  2.217   1.0109e-01
   3_xyz:   8.792  0.064  0.303 88.090  0.046  2.321   5.5539e-02
   3_adp:   8.792  0.064  0.303 88.090  0.046  2.321   5.5539e-02
   3_occ:   8.792  0.064  0.303 88.090  0.046  2.321   5.5539e-02
   4_bss:   8.792  0.064  0.303 88.090  0.046  2.321   5.5539e-02
   4_xyz:   8.882  0.072  0.478 81.218  0.034  2.217   5.6620e-02
   4_adp:   8.882  0.072  0.478 81.218  0.034  2.217   5.6620e-02
   4_occ:   8.882  0.072  0.478 81.218  0.034  2.217   5.6620e-02
   5_bss:   8.882  0.072  0.478 81.218  0.034  2.217   5.6620e-02
   5_xyz:   9.272  0.062  0.541 84.034  0.031  2.302   5.5546e-02
   5_adp:   9.272  0.062  0.541 84.034  0.031  2.302   5.5546e-02
   5_occ:   9.272  0.062  0.541 84.034  0.031  2.302   5.5546e-02
   5_bss:   9.272  0.062  0.541 84.034  0.031  2.302   5.5546e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  89.32   0.00  13.74  89.32   0.00  11.31  75.33   0.00  26.96
   1_occ:  89.32   0.00  13.74  89.32   0.00  11.31  75.33   0.00  26.96
   2_bss:  89.32   0.00  13.74  89.32   0.00  11.31  75.33   0.00  26.96
   2_xyz:  89.32   0.00  13.74  89.32   0.00  11.31  75.33   0.00  26.96
   2_adp:  90.50   0.00  13.77  90.50   0.00  10.29  77.84   0.00  32.74
   2_occ:  90.50   0.00  13.77  90.50   0.00  10.29  77.84   0.00  32.74
   3_bss:  90.50   0.00  13.77  90.50   0.00  10.29  77.84   0.00  32.74
   3_xyz:  90.50   0.00  13.77  90.50   0.00  10.29  77.84   0.00  32.74
   3_adp:  92.33   0.00  14.28  92.33   0.00   9.85  83.55   2.11  38.39
   3_occ:  92.33   0.00  14.28  92.33   0.00   9.85  83.55   2.11  38.39
   4_bss:  92.33   0.00  14.28  92.33   0.00   9.85  83.55   2.11  38.39
   4_xyz:  92.33   0.00  14.28  92.33   0.00   9.85  83.55   2.11  38.39
   4_adp:  95.87   0.00  14.32  95.87   0.00   9.71  89.01   2.97  39.42
   4_occ:  95.87   0.00  14.32  95.87   0.00   9.71  89.01   2.97  39.42
   5_bss:  95.87   0.00  14.32  95.87   0.00   9.71  89.01   2.97  39.42
   5_xyz:  95.87   0.00  14.32  95.87   0.00   9.71  89.01   2.97  39.42
   5_adp:  88.65   0.00  13.34  88.65   0.00   9.48  84.47   3.64  34.36
   5_occ:  88.65   0.00  13.34  88.65   0.00   9.48  84.47   3.64  34.36
   5_bss:  89.86   1.21  14.55  89.86   1.21  10.69  85.67   4.84  35.57
------------------------------------------------------------------------
 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:    1.244    0.011    0.415
   1_adp:    1.244    0.011    0.415
   1_occ:    1.244    0.011    0.415
   2_bss:    1.244    0.011    0.415
   2_xyz:    1.526    0.017    0.580
   2_adp:    1.526    0.017    0.580
   2_occ:    1.526    0.017    0.580
   3_bss:    1.526    0.017    0.580
   3_xyz:    1.568    0.017    0.683
   3_adp:    1.568    0.017    0.683
   3_occ:    1.568    0.017    0.683
   4_bss:    1.568    0.017    0.683
   4_xyz:    1.893    0.022    0.746
   4_adp:    1.893    0.022    0.746
   4_occ:    1.893    0.022    0.746
   5_bss:    1.893    0.022    0.746
   5_xyz:    2.105    0.027    0.769
   5_adp:    2.105    0.027    0.769
   5_occ:    2.105    0.027    0.769
   5_bss:    2.105    0.027    0.769
------------------------------------------------------------------------

CPU time actual refinement: 354.24


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1245/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/trial/run_1245/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1245/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1245/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1245/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 354.08 
  Macro-tasks:
    bulk solvent and scale       = 40.94  
    individual site refinement   = 146.30 
    weights calculation          = 32.26  
    collect and process          = 6.48   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 226.11 
  Micro-tasks:
    mask                            = 2.45   
    f_calc                          = 113.32 
    alpha_beta                      = 8.20   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 122.18 
    fmodel                         = 7.52   
    r_factors                      = 0.19   
    phase_errors                   = 10.36  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 265.60 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.988 micro seconds
Total CPU time: 6.13 minutes
from_scatterers_fft:    653 calls, 112.97 s
gradients_fft:          598 calls, 108.85 s

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

# Date 2008-01-16 Time 03:33:14 PST -0800 (1200483194.83 s)
Start R-work = 0.4888, R-free = 0.4754 (no bulk solvent and anisotropic scale)
Final R-work = 0.1365, R-free = 0.1824 (no bulk solvent and anisotropic scale)

Start R-work = 0.4802, R-free = 0.4659
Final R-work = 0.1197, R-free = 0.1650