# Date 2008-01-16 Time 00:57:34 PST -0800 (1200473854.13 s)
#phil __OFF__

Command line arguments: "../224.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 13037
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 224

-------------------------------------------------------------------------------
  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: (68.845, 47.8686, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.25, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 47.8686, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9586 1.96073
Completeness in resolution range: 0.934902
Completeness with d_max=infinity: 0.932099

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9586
                             d_min =   1.9607

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: (68.845, 47.8686, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9586 1.96073
Completeness in resolution range: 0.934902
Completeness with d_max=infinity: 0.932099

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9590 -  4.1961 [2207/2236]  1981   226  10.2%
  bin  2:  4.1961 -  3.3428 [2106/2129]  1897   209   9.9%
  bin  3:  3.3428 -  2.9238 [2074/2099]  1868   206   9.9%
  bin  4:  2.9238 -  2.6581 [2055/2072]  1850   205  10.0%
  bin  5:  2.6581 -  2.4685 [2056/2099]  1846   210  10.2%
  bin  6:  2.4685 -  2.3235 [2048/2076]  1853   195   9.5%
  bin  7:  2.3235 -  2.2076 [2023/2059]  1821   202  10.0%
  bin  8:  2.2076 -  2.1117 [2029/2071]  1831   198   9.8%
  bin  9:  2.1117 -  2.0306 [2004/2062]  1797   207  10.3%
  bin 10:  2.0306 -  1.9607 [ 987/2050]   886   101  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_224/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:
        1.19 -     1.93: 11
        1.93 -     2.67: 111
        2.67 -     3.42: 4472
        3.42 -     4.16: 9381
        4.16 -     4.90: 14491
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.188 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.430 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.545 3.040 -x+1,y+1/2,-z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.697 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  70 " - " O   HOH Z 296 "  1.712 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28461 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_224/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_224/model_refine_001.geo

CPU time processing inputs: 9.08


============================ 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 = 68.845 47.8686 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  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: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5004   r_free= 0.4839   ksol= 0.00   Bsol= 0.00   scale= 0.782    |
|                                                                             |
| 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:   0.81 A                  |
| x-ray target function (ml) for work reflections: 6.298707                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9590 -  4.6804 0.99   1428  159 0.4119 0.4136      6.6227      6.6684|
|  2:  4.6804 -  3.7340 0.99   1371  153 0.4289 0.4232      6.8313      6.8429|
|  3:  3.7340 -  3.2676 0.99   1362  148 0.4719 0.4375       6.703      6.7183|
|  4:  3.2676 -  2.9714 0.99   1322  144 0.4882 0.4442      6.5307      6.4662|
|  5:  2.9714 -  2.7599 0.99   1335  152 0.5378 0.5286      6.3806      6.4141|
|  6:  2.7599 -  2.5980 0.99   1330  150 0.5244 0.5092      6.2921       6.177|
|  7:  2.5980 -  2.4685 0.98   1294  150 0.5272 0.4969      6.2496      6.1992|
|  8:  2.4685 -  2.3615 0.98   1330  135 0.5366 0.5049      6.1865      6.1978|
|  9:  2.3615 -  2.2709 0.99   1313  151 0.5433 0.5630      6.1243      6.1694|
| 10:  2.2709 -  2.1928 0.98   1301  141 0.5407 0.5428      6.1152      6.1233|
| 11:  2.1928 -  2.1244 0.97   1305  146 0.5651 0.5452      6.0357      6.0337|
| 12:  2.1244 -  2.0639 0.98   1288  147 0.5382 0.4937      5.9529      5.9718|
| 13:  2.0639 -  2.0097 0.91   1188  132 0.5430 0.5498      5.8828      5.8581|
| 14:  2.0097 -  1.9607 0.35    463   51 0.5745 0.5084      5.8938      5.7029|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9590 -  4.6804  1428   159  0.63  40.05   0.79     0.65      90365.05|
|  2:  4.6804 -  3.7340  1371   153  0.65  39.47   0.87     0.71     124707.40|
|  3:  3.7340 -  3.2676  1362   148  0.55  47.96   0.82     0.67     127622.59|
|  4:  3.2676 -  2.9714  1322   144  0.48  53.16   0.79     0.58     104305.77|
|  5:  2.9714 -  2.7599  1335   152  0.38  61.48   0.71     0.47      87323.10|
|  6:  2.7599 -  2.5980  1330   150  0.34  64.41   0.71     0.39      75818.60|
|  7:  2.5980 -  2.4685  1294   150  0.30  67.45   0.73     0.35      70850.77|
|  8:  2.4685 -  2.3615  1330   135  0.30  67.29   0.71     0.36      62988.76|
|  9:  2.3615 -  2.2709  1313   151  0.30  67.43   0.72     0.38      58748.69|
| 10:  2.2709 -  2.1928  1301   141  0.29  68.00   0.74     0.35      52946.51|
| 11:  2.1928 -  2.1244  1305   146  0.26  70.72   0.73     0.34      51147.47|
| 12:  2.1244 -  2.0639  1288   147  0.24  72.03   0.74     0.33      47937.16|
| 13:  2.0639 -  2.0097  1188   132  0.26  70.39   0.73     0.35      40195.42|
| 14:  2.0097 -  1.9607   463    51  0.33  65.34   0.71     0.36      27912.02|
|alpha:            min =        0.33 max =            0.71 mean =         0.46|
|beta:             min =    27912.02 max =       127622.59 mean =     75994.71|
|figures of merit: min =        0.00 max =            1.00 mean =         0.39|
|phase err.(work): min =        0.00 max =           90.00 mean =        60.54|
|phase err.(test): min =        0.00 max =           89.98 mean =        60.53|
|-----------------------------------------------------------------------------|

============================== 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 = 18.404264             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.653   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.520780              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.788   (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 |  0.778 -  1.190:        1 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.190 -  1.602:        6 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.602 -  2.014:       39 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.014 -  2.427:      323 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.427 -  2.839:     1084 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.839 -  3.251:     2297 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.251 -  3.663:     3829 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.663 -  4.076:     5334 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.076 -  4.488:     7037 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.488 -  4.900:     8502 |
|-----------------------------------------------------------------------------|
|-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 |       53.584 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.088    4.900  0.778 |       2.590 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.732)------------------------------------------|
|    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 = 11.732)------------------------------------------|
|    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: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5052   r_free= 0.4902   ksol= 0.00   Bsol= 0.00   scale= 0.752    |
|                                                                             |
| 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:   0.83 A                  |
| x-ray target function (ml) for work reflections: 6.299394                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4928   r_free= 0.4791   ksol= 0.35   Bsol= 20.00   scale= 0.974   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.10,11.26,7.04,0.00,0.00,0.00); trace/3= 8.47                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.82 A                  |
| x-ray target function (ml) for work reflections: 6.291998                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 17.441715             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.988   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.572563              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.918   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4928      final r-factor (work) = 0.4181          |
| start r-factor (free) = 0.4791      final r-factor (free) = 0.4368          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 108.5029 = 17.44 * 0.50 * 6.2974 + 1.00 * 53.5845                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 54.4796 = 17.44 * 0.50 * 6.2284 + 1.00 * 0.1622                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4181      final r-factor (work) = 0.3728          |
| start r-factor (free) = 0.4368      final r-factor (free) = 0.4263          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.8093 = 1.57 * 1.00 * 6.2284 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.7122 = 1.57 * 1.00 * 6.1627 + 1.00 * 0.0210                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.732)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.54  15.10    None  None   None       |
|    all(noH): 2823   0      0.00    102.54  15.10    None  None   None       |
|    Sol.    : 438    0      0.00    102.54  26.60    None  None   None       |
|    Mac.    : 2385   0      0.00    72.90   12.99    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.254: 1317   |   5:    51.270 -  61.524:   36        |
|      1:    10.254 -  20.508:  744   |   6:    61.524 -  71.778:   16        |
|      2:    20.508 -  30.762:  404   |   7:    71.778 -  82.032:    8        |
|      3:    30.762 -  41.016:  208   |   8:    82.032 -  92.285:    2        |
|      4:    41.016 -  51.270:   87   |   9:    92.285 - 102.539:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3728 r_free = 0.4263             target_work(ml) = 6.147         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3722 r_free = 0.4254             target_work(ml) = 6.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3722   r_free= 0.4254   ksol= 0.35   Bsol= 20.00   scale= 1.106   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.10,11.26,7.04,0.00,0.00,0.00); trace/3= 8.47                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.145486                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3710   r_free= 0.4195   ksol= 0.30   Bsol= 20.00   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.85,7.01,4.44,0.00,0.00,0.00); trace/3= 5.10                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.146987                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.759243             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.337  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.571254              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.225  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3710      final r-factor (work) = 0.2866          |
| start r-factor (free) = 0.4195      final r-factor (free) = 0.3388          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 45.6121 = 14.76 * 0.50 * 6.1589 + 1.00 * 0.1614                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 44.7037 = 14.76 * 0.50 * 6.0412 + 1.00 * 0.1220                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2866      final r-factor (work) = 0.2598          |
| start r-factor (free) = 0.3388      final r-factor (free) = 0.3222          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4721 = 0.57 * 1.00 * 6.0412 + 1.00 * 0.0211                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3813 = 0.57 * 1.00 * 5.8933 + 1.00 * 0.0147                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.732)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.90   14.40    None  None   None       |
|    all(noH): 2823   0      0.00    97.90   14.40    None  None   None       |
|    Sol.    : 438    0      0.00    97.90   31.40    None  None   None       |
|    Mac.    : 2385   0      0.00    79.39   11.28    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 -   9.790: 1355   |   5:    48.952 -  58.743:   39        |
|      1:     9.790 -  19.581:  782   |   6:    58.743 -  68.533:   21        |
|      2:    19.581 -  29.371:  328   |   7:    68.533 -  78.323:   10        |
|      3:    29.371 -  39.162:  174   |   8:    78.323 -  88.114:    2        |
|      4:    39.162 -  48.952:  111   |   9:    88.114 -  97.904:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2598 r_free = 0.3222             target_work(ml) = 5.866         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2596 r_free = 0.3221             target_work(ml) = 5.865         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2596   r_free= 0.3221   ksol= 0.30   Bsol= 20.00   scale= 1.071   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.85,7.01,4.44,0.00,0.00,0.00); trace/3= 5.10                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.865430                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2559   r_free= 0.3194   ksol= 0.33   Bsol= 45.65   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.33,3.82,2.71,0.00,0.00,0.00); trace/3= 2.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.861593                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.089635              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.359  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.247328              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 108.528  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2559      final r-factor (work) = 0.1998          |
| start r-factor (free) = 0.3194      final r-factor (free) = 0.2480          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.1811 = 4.09 * 0.50 * 5.8974 + 1.00 * 0.1220                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.8649 = 4.09 * 0.50 * 5.7700 + 1.00 * 0.0663                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1998      final r-factor (work) = 0.1870          |
| start r-factor (free) = 0.2480      final r-factor (free) = 0.2277          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4489 = 0.25 * 1.00 * 5.7700 + 1.00 * 0.0218                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3964 = 0.25 * 1.00 * 5.6103 + 1.00 * 0.0088                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.732)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.95   14.12    None  None   None       |
|    all(noH): 2823   0      0.00    86.95   14.12    None  None   None       |
|    Sol.    : 438    0      3.54    86.95   34.40    None  None   None       |
|    Mac.    : 2385   0      0.00    78.68   10.39    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 -   8.695: 1323   |   5:    43.476 -  52.171:  102        |
|      1:     8.695 -  17.390:  829   |   6:    52.171 -  60.866:   34        |
|      2:    17.390 -  26.086:  244   |   7:    60.866 -  69.561:   13        |
|      3:    26.086 -  34.781:  145   |   8:    69.561 -  78.256:    8        |
|      4:    34.781 -  43.476:  123   |   9:    78.256 -  86.952:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1870 r_free = 0.2277             target_work(ml) = 5.577         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1868 r_free = 0.2279             target_work(ml) = 5.577         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1868   r_free= 0.2279   ksol= 0.33   Bsol= 45.65   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.33,3.82,2.71,0.00,0.00,0.00); trace/3= 2.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.577102                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1864   r_free= 0.2280   ksol= 0.32   Bsol= 44.88   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.08,2.34,1.74,0.00,0.00,0.00); trace/3= 1.39                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.577306                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.035051              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.601  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.266125              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.401  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1864      final r-factor (work) = 0.1493          |
| start r-factor (free) = 0.2280      final r-factor (free) = 0.1891          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7814 = 2.04 * 0.50 * 5.6166 + 1.00 * 0.0663                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6265 = 2.04 * 0.50 * 5.4721 + 1.00 * 0.0585                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1493      final r-factor (work) = 0.1413          |
| start r-factor (free) = 0.1891      final r-factor (free) = 0.1825          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4651 = 0.27 * 1.00 * 5.4721 + 1.00 * 0.0088                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4323 = 0.27 * 1.00 * 5.3464 + 1.00 * 0.0095                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.732)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.52   14.29    None  None   None       |
|    all(noH): 2823   0      0.00    81.52   14.29    None  None   None       |
|    Sol.    : 438    0      2.70    81.52   36.74    None  None   None       |
|    Mac.    : 2385   0      0.00    80.95   10.17    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 -   8.152: 1252   |   5:    40.762 -  48.914:  102        |
|      1:     8.152 -  16.305:  893   |   6:    48.914 -  57.067:   79        |
|      2:    16.305 -  24.457:  217   |   7:    57.067 -  65.219:   28        |
|      3:    24.457 -  32.609:  111   |   8:    65.219 -  73.371:    9        |
|      4:    32.609 -  40.762:  125   |   9:    73.371 -  81.524:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1413 r_free = 0.1825             target_work(ml) = 5.328         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1411 r_free = 0.1825             target_work(ml) = 5.328         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1411   r_free= 0.1825   ksol= 0.32   Bsol= 44.88   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.08,2.34,1.74,0.00,0.00,0.00); trace/3= 1.39                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.328120                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1413   r_free= 0.1832   ksol= 0.32   Bsol= 44.88   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.28,1.62,1.57,0.00,0.00,0.00); trace/3= 0.97                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.330833                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.802334              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.815  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.129061              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 156.121  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1413      final r-factor (work) = 0.1232          |
| start r-factor (free) = 0.1832      final r-factor (free) = 0.1677          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.5525 = 2.80 * 0.50 * 5.3484 + 1.00 * 0.0585                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4559 = 2.80 * 0.50 * 5.2707 + 1.00 * 0.0708                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1232      final r-factor (work) = 0.1191          |
| start r-factor (free) = 0.1677      final r-factor (free) = 0.1672          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.2311 = 2.13 * 1.00 * 5.2707 + 1.00 * 0.0094                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.1031 = 2.13 * 1.00 * 5.2091 + 1.00 * 0.0126                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.732)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.50   14.84    None  None   None       |
|    all(noH): 2823   0      0.00    93.50   14.84    None  None   None       |
|    Sol.    : 438    0      2.56    90.67   40.27    None  None   None       |
|    Mac.    : 2385   0      0.00    93.50   10.17    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 -   9.351: 1500   |   5:    46.752 -  56.103:   88        |
|      1:     9.351 -  18.701:  739   |   6:    56.103 -  65.453:   68        |
|      2:    18.701 -  28.051:  174   |   7:    65.453 -  74.804:   34        |
|      3:    28.051 -  37.402:  105   |   8:    74.804 -  84.154:   12        |
|      4:    37.402 -  46.752:   97   |   9:    84.154 -  93.504:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1191 r_free = 0.1672             target_work(ml) = 5.207         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1191 r_free = 0.1673             target_work(ml) = 5.207         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1191   r_free= 0.1673   ksol= 0.32   Bsol= 44.88   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.28,1.62,1.57,0.00,0.00,0.00); trace/3= 0.97                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.206903                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9590 -  4.6804 0.99   1428  159 0.0994 0.1360      5.4061      5.5786|
|  2:  4.6804 -  3.7340 0.99   1371  153 0.0861 0.1058      5.4581      5.6342|
|  3:  3.7340 -  3.2676 0.99   1362  148 0.1144 0.1615      5.5203      5.8991|
|  4:  3.2676 -  2.9714 0.99   1322  144 0.1314 0.1718      5.5099      5.6972|
|  5:  2.9714 -  2.7599 0.99   1335  152 0.1435 0.1761      5.3986      5.5433|
|  6:  2.7599 -  2.5980 0.99   1330  150 0.1376 0.2330      5.3052      5.6097|
|  7:  2.5980 -  2.4685 0.98   1294  150 0.1328 0.1644      5.2292      5.3765|
|  8:  2.4685 -  2.3615 0.98   1330  135 0.1258 0.1743      5.1364       5.362|
|  9:  2.3615 -  2.2709 0.99   1313  151 0.1263 0.2075      5.0786      5.4198|
| 10:  2.2709 -  2.1928 0.98   1301  141 0.1223 0.1782      5.0425      5.2525|
| 11:  2.1928 -  2.1244 0.97   1305  146 0.1194 0.1956      4.9811       5.282|
| 12:  2.1244 -  2.0639 0.98   1288  147 0.1221 0.1594      4.8979      5.1166|
| 13:  2.0639 -  2.0097 0.91   1188  132 0.1158 0.1831      4.8069       5.107|
| 14:  2.0097 -  1.9607 0.35    463   51 0.1066 0.1754       4.715       4.927|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9590 -  4.6804  1428   159  0.94   9.77   0.98     0.96       8006.82|
|  2:  4.6804 -  3.7340  1371   153  0.95   8.42   1.02     1.01       9695.37|
|  3:  3.7340 -  3.2676  1362   148  0.93  12.11   1.03     1.02      11232.54|
|  4:  3.2676 -  2.9714  1322   144  0.91  15.21   1.01     1.00      11693.54|
|  5:  2.9714 -  2.7599  1335   152  0.88  17.87   1.00     0.97       9931.02|
|  6:  2.7599 -  2.5980  1330   150  0.88  18.22   0.98     0.93       8446.25|
|  7:  2.5980 -  2.4685  1294   150  0.89  17.10   0.98     0.94       7114.94|
|  8:  2.4685 -  2.3615  1330   135  0.89  16.90   1.00     0.97       6333.77|
|  9:  2.3615 -  2.2709  1313   151  0.89  17.25   1.00     0.96       5675.13|
| 10:  2.2709 -  2.1928  1301   141  0.89  17.52   1.00     0.96       5401.48|
| 11:  2.1928 -  2.1244  1305   146  0.89  17.58   1.00     0.96       4934.70|
| 12:  2.1244 -  2.0639  1288   147  0.90  16.55   1.00     0.97       4109.97|
| 13:  2.0639 -  2.0097  1188   132  0.90  16.60   1.00     0.98       3512.66|
| 14:  2.0097 -  1.9607   463    51  0.90  16.00   0.97     0.93       2885.29|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2885.29 max =        11693.54 mean =      7335.61|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.99 mean =        15.41|
|phase err.(test): min =        0.00 max =           89.03 mean =        14.84|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1190   r_free= 0.1672   ksol= 0.32   Bsol= 52.54   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.16,0.52,0.63,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.206686                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.96 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1190   r_free= 0.1672   ksol= 0.32   Bsol= 52.54   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.16,0.52,0.63,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.206686                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9590 -  4.6804 0.99   1428  159 0.0996 0.1365      5.4073      5.5828|
|  2:  4.6804 -  3.7340 0.99   1371  153 0.0867 0.1062      5.4629      5.6393|
|  3:  3.7340 -  3.2676 0.99   1362  148 0.1145 0.1624      5.5232      5.9011|
|  4:  3.2676 -  2.9714 0.99   1322  144 0.1313 0.1715      5.5089      5.6974|
|  5:  2.9714 -  2.7599 0.99   1335  152 0.1431 0.1754      5.3963       5.541|
|  6:  2.7599 -  2.5980 0.99   1330  150 0.1372 0.2323      5.3031      5.6068|
|  7:  2.5980 -  2.4685 0.98   1294  150 0.1326 0.1647      5.2275      5.3766|
|  8:  2.4685 -  2.3615 0.98   1330  135 0.1255 0.1735      5.1353      5.3603|
|  9:  2.3615 -  2.2709 0.99   1313  151 0.1261 0.2078      5.0779      5.4193|
| 10:  2.2709 -  2.1928 0.98   1301  141 0.1220 0.1781      5.0413      5.2529|
| 11:  2.1928 -  2.1244 0.97   1305  146 0.1192 0.1953      4.9804      5.2809|
| 12:  2.1244 -  2.0639 0.98   1288  147 0.1221 0.1594      4.8977      5.1165|
| 13:  2.0639 -  2.0097 0.91   1188  132 0.1158 0.1825      4.8062       5.104|
| 14:  2.0097 -  1.9607 0.35    463   51 0.1064 0.1752      4.7132      4.9259|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9590 -  4.6804  1428   159  0.94   9.80   0.98     0.96       8032.58|
|  2:  4.6804 -  3.7340  1371   153  0.95   8.48   1.02     1.01       9787.18|
|  3:  3.7340 -  3.2676  1362   148  0.93  12.18   1.03     1.02      11348.52|
|  4:  3.2676 -  2.9714  1322   144  0.91  15.22   1.02     1.01      11691.34|
|  5:  2.9714 -  2.7599  1335   152  0.88  17.84   1.00     0.97       9888.54|
|  6:  2.7599 -  2.5980  1330   150  0.88  18.17   0.98     0.93       8409.89|
|  7:  2.5980 -  2.4685  1294   150  0.89  17.08   0.99     0.94       7097.92|
|  8:  2.4685 -  2.3615  1330   135  0.89  16.89   1.00     0.98       6323.76|
|  9:  2.3615 -  2.2709  1313   151  0.89  17.24   1.01     0.97       5670.72|
| 10:  2.2709 -  2.1928  1301   141  0.89  17.49   1.00     0.97       5385.47|
| 11:  2.1928 -  2.1244  1305   146  0.89  17.56   1.00     0.97       4924.36|
| 12:  2.1244 -  2.0639  1288   147  0.90  16.54   1.00     0.98       4107.26|
| 13:  2.0639 -  2.0097  1188   132  0.90  16.57   1.00     0.99       3501.66|
| 14:  2.0097 -  1.9607   463    51  0.90  15.95   0.98     0.94       2861.04|
|alpha:            min =        0.93 max =            1.02 mean =         0.98|
|beta:             min =     2861.04 max =        11691.34 mean =      7341.82|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.77 mean =        15.40|
|phase err.(test): min =        0.00 max =           89.01 mean =        14.84|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.732)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.07    94.58   15.91    None  None   None       |
|    all(noH): 2823   0      1.07    94.58   15.91    None  None   None       |
|    Sol.    : 438    0      3.63    91.74   41.34    None  None   None       |
|    Mac.    : 2385   0      1.07    94.58   11.24    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:     1.074 -  10.424: 1500   |   5:    47.826 -  57.176:   88        |
|      1:    10.424 -  19.775:  739   |   6:    57.176 -  66.527:   68        |
|      2:    19.775 -  29.125:  174   |   7:    66.527 -  75.877:   34        |
|      3:    29.125 -  38.475:  105   |   8:    75.877 -  85.228:   12        |
|      4:    38.475 -  47.826:   97   |   9:    85.228 -  94.578:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 317         
Filter by distance & map next to the model:
   mapped sites are within: 0.390 - 4.995
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 313 from: 317
   mapped sites are within: 0.737 - 4.995

peak=   10.058 closest distance to " CB  VAL A 230 " =    1.378
peak=    6.800 closest distance to " CD1AILE A 234 " =    1.332
peak=    6.242 closest distance to " O   HOH Z 120 " =    1.180
peak=    5.762 closest distance to " CB  VAL A 296 " =    1.076
peak=    5.601 closest distance to " O   HOH Z 402 " =    1.647
peak=    5.527 closest distance to " CG  LEU A   5 " =    1.261
peak=    5.497 closest distance to " O   HOH Z 403 " =    1.998
peak=    5.353 closest distance to " O   HOH Z 124 " =    1.634
peak=    5.040 closest distance to " NH2 ARG A  56 " =    2.292
peak=    4.958 closest distance to " O   HOH Z 128 " =    1.671
peak=    4.901 closest distance to " CA  TYR A  30 " =    0.963
peak=    4.900 closest distance to " O   HOH Z 193 " =    1.724
peak=    4.833 closest distance to " CB  VAL A 230 " =    1.168
peak=    4.822 closest distance to " CB  GLN A 183 " =    1.322
peak=    4.812 closest distance to " O   HOH Z 209 " =    2.281
peak=    4.810 closest distance to " CB  ARG A 275 " =    0.934
peak=    4.800 closest distance to " O   HOH Z 433 " =    1.716
peak=    4.792 closest distance to " CB  SER A  63 " =    1.191
peak=    4.737 closest distance to " CG  PRO A  54 " =    1.180
peak=    4.721 closest distance to " CG  LEU A 228 " =    1.122
peak=    4.689 closest distance to " O   HOH Z 102 " =    1.361
peak=    4.686 closest distance to " O   HOH Z 248 " =    1.576
peak=    4.684 closest distance to " O   HOH Z 154 " =    1.888
peak=    4.668 closest distance to " O   HOH Z  80 " =    2.121
peak=    4.658 closest distance to " O   HOH Z 142 " =    1.498
peak=    4.654 closest distance to " O   HOH Z  49 " =    1.357
peak=    4.643 closest distance to " O   HOH Z  85 " =    1.773
peak=    4.600 closest distance to " O   HOH Z 404 " =    1.240
peak=    4.579 closest distance to " O   HOH Z  43 " =    1.952
peak=    4.549 closest distance to " O   HOH Z 414 " =    2.324
peak=    4.518 closest distance to " CB  PRO A  54 " =    0.937
peak=    4.506 closest distance to " O   HOH Z 263 " =    1.541
peak=    4.469 closest distance to " O   HOH Z 126 " =    1.570
peak=    4.468 closest distance to " CB  GLN A 223 " =    1.418
peak=    4.461 closest distance to " O   HOH Z 357 " =    1.998
peak=    4.424 closest distance to " O   HOH Z 247 " =    1.337
peak=    4.418 closest distance to " NE2 GLN A  11 " =    0.982
peak=    4.413 closest distance to " O   HOH Z 327 " =    1.772
peak=    4.396 closest distance to " O   HOH Z 232 " =    2.370
peak=    4.346 closest distance to " O   HOH Z 130 " =    1.101
peak=    4.341 closest distance to " O   HOH Z  68 " =    1.983
peak=    4.339 closest distance to " O   HOH Z 272 " =    1.951
peak=    4.324 closest distance to " O   HOH Z 126 " =    2.500
peak=    4.322 closest distance to " O   HOH Z 116 " =    1.151
peak=    4.314 closest distance to " CG1 ILE A  33 " =    1.194
peak=    4.289 closest distance to " O   PRO A 198 " =    1.492
peak=    4.281 closest distance to " CG1 VAL A 296 " =    1.182
peak=    4.279 closest distance to " O   SER A  87 " =    2.310
peak=    4.273 closest distance to " CD2 LEU A 228 " =    1.190
peak=    4.273 closest distance to " CD2 TRP A 179 " =    1.438
peak=    4.265 closest distance to " O   GLY A  23 " =    2.356
peak=    4.253 closest distance to " CG  PRO A 213 " =    1.256
peak=    4.224 closest distance to " CD2 LEU A   5 " =    1.119
peak=    4.220 closest distance to " O   HOH Z 236 " =    1.371
peak=    4.219 closest distance to " CG2 VAL A 296 " =    1.043
peak=    4.215 closest distance to " O   HOH Z 130 " =    2.549
peak=    4.211 closest distance to " OE1 GLU A   2 " =    2.147
peak=    4.211 closest distance to " O   HOH Z  46 " =    1.179
peak=    4.201 closest distance to " CG  ARG A  66 " =    1.028
peak=    4.198 closest distance to " O   HOH Z 245 " =    1.467
peak=    4.122 closest distance to " CB  TRP A 179 " =    1.097
peak=    4.116 closest distance to " CG  PRO A 198 " =    1.203
peak=    4.112 closest distance to " O   HOH Z 394 " =    1.644
peak=    4.106 closest distance to " O   HOH Z 346 " =    1.633
peak=    4.098 closest distance to " O   HOH Z 134 " =    1.979
peak=    4.064 closest distance to " O   HOH Z 409 " =    3.305
peak=    4.050 closest distance to " CB  ASN A 148 " =    1.256
peak=    4.035 closest distance to " O   HOH Z 234 " =    3.417
peak=    4.033 closest distance to " O   HOH Z 431 " =    1.294
peak=    4.027 closest distance to " O   HOH Z 142 " =    2.277
peak=    3.996 closest distance to " O   HOH Z  47 " =    1.427
peak=    3.986 closest distance to " O   HOH Z 425 " =    1.437
peak=    3.981 closest distance to " O   HOH Z 345 " =    2.569
peak=    3.970 closest distance to " O   HOH Z 412 " =    3.475
peak=    3.956 closest distance to " O   HOH Z 395 " =    1.345
peak=    3.947 closest distance to " O   HOH Z 389 " =    1.955
peak=    3.921 closest distance to " O   ASP A 124 " =    1.508
peak=    3.913 closest distance to " O   HOH Z 406 " =    1.507
peak=    3.901 closest distance to " O   HOH Z 361 " =    2.763
peak=    3.898 closest distance to " O   HOH Z 156 " =    3.195
peak=    3.896 closest distance to " O   HOH Z  39 " =    1.318
peak=    3.893 closest distance to " CD  ARG A 159 " =    0.814
peak=    3.892 closest distance to " O   HOH Z  44 " =    2.126
peak=    3.889 closest distance to " O   HOH Z  11 " =    1.317
peak=    3.881 closest distance to " O   HOH Z 132 " =    2.595
peak=    3.877 closest distance to " O   HOH Z  48 " =    1.672
peak=    3.875 closest distance to " O   HOH Z 109 " =    1.455
peak=    3.874 closest distance to " O   HOH Z 406 " =    1.231
peak=    3.868 closest distance to " CG AARG A 275 " =    1.194
peak=    3.864 closest distance to " CB BVAL A  41 " =    1.076
peak=    3.849 closest distance to " O   HOH Z 369 " =    2.347
peak=    3.841 closest distance to " NZ  LYS A 117 " =    2.923
peak=    3.840 closest distance to " O   HOH Z 203 " =    1.731
peak=    3.829 closest distance to " CA  VAL A  41 " =    0.916
peak=    3.820 closest distance to " CB  SER A  26 " =    1.743
peak=    3.819 closest distance to " O   HOH Z 403 " =    1.455
peak=    3.819 closest distance to " CG2 ILE A  20 " =    1.363
peak=    3.816 closest distance to " CG  PRO A 243 " =    1.245
peak=    3.816 closest distance to " CG2 THR A 221 " =    1.163
peak=    3.811 closest distance to " O   HOH Z  40 " =    2.012
peak=    3.808 closest distance to " O   HOH Z 316 " =    2.499
peak=    3.787 closest distance to " CA  ALA A  51 " =    1.096
peak=    3.785 closest distance to " O   HOH Z 423 " =    1.829
peak=    3.782 closest distance to " CB  SER A   3 " =    1.324
peak=    3.768 closest distance to " NH2BARG A 145 " =    2.211
peak=    3.764 closest distance to " O   HOH Z 303 " =    2.411
peak=    3.747 closest distance to " O   HOH Z 408 " =    1.731
peak=    3.743 closest distance to " O   HOH Z 322 " =    2.207
peak=    3.726 closest distance to " O   HOH Z 265 " =    1.986
peak=    3.724 closest distance to " O   HOH Z 136 " =    1.235
peak=    3.721 closest distance to " O   HOH Z  88 " =    3.425
peak=    3.720 closest distance to " CB  PRO A 198 " =    1.134
peak=    3.716 closest distance to " O   HOH Z 146 " =    1.255
peak=    3.713 closest distance to " O   HOH Z  54 " =    1.196
peak=    3.710 closest distance to " N   ASN A  39 " =    1.332
peak=    3.710 closest distance to " NH2 ARG A 156 " =    1.138
peak=    3.698 closest distance to " O   HOH Z  97 " =    2.014
peak=    3.691 closest distance to " CD  LYS A 119 " =    1.783
peak=    3.690 closest distance to " O   HOH Z 366 " =    2.654
peak=    3.688 closest distance to " O   HOH Z 253 " =    1.361
peak=    3.684 closest distance to " O   HOH Z 146 " =    1.356
peak=    3.682 closest distance to " CB  ARG A  79 " =    1.395
peak=    3.672 closest distance to " O   HOH Z 423 " =    2.948
peak=    3.643 closest distance to " CD  LYS A 166 " =    1.558
peak=    3.633 closest distance to " O   HOH Z   4 " =    1.576
peak=    3.630 closest distance to " CE1 HIS A 108 " =    1.140
peak=    3.630 closest distance to " O   ALA A 165 " =    1.316
peak=    3.627 closest distance to " O   HOH Z 126 " =    1.815
peak=    3.623 closest distance to " OG  SER A  97 " =    2.805
peak=    3.620 closest distance to " O   HOH Z  97 " =    2.109
peak=    3.611 closest distance to " CB  GLU A 175 " =    1.303
peak=    3.604 closest distance to " CD  ARG A 269 " =    1.114
peak=    3.603 closest distance to " O   HOH Z 154 " =    2.191
peak=    3.599 closest distance to " O   HOH Z 417 " =    3.358
peak=    3.595 closest distance to " CB  ALA A 100 " =    1.242
peak=    3.595 closest distance to " O   HOH Z 388 " =    2.228
peak=    3.591 closest distance to " CA  ALA A  21 " =    1.240
peak=    3.582 closest distance to " OH  TYR A 116 " =    1.183
peak=    3.580 closest distance to " O   GLY A  91 " =    1.288
peak=    3.576 closest distance to " OG  SER A  62 " =    2.823
peak=    3.572 closest distance to " CE1 TYR A 186 " =    1.304
peak=    3.566 closest distance to " O   HOH Z 193 " =    2.071
peak=    3.563 closest distance to " CG  PRO A  90 " =    1.170
peak=    3.563 closest distance to " O   HOH Z 422 " =    2.649
peak=    3.554 closest distance to " O   HOH Z 250 " =    1.367
peak=    3.546 closest distance to " CD  LYS A  76 " =    1.927
peak=    3.541 closest distance to " CD2 LEU A 297 " =    1.013
peak=    3.540 closest distance to " O   HOH Z 284 " =    2.988
peak=    3.540 closest distance to " O   HOH Z 126 " =    1.597
peak=    3.536 closest distance to " CA  ARG A 195 " =    1.346
peak=    3.536 closest distance to " O   HOH Z 339 " =    1.172
peak=    3.535 closest distance to " CA  ALA A 295 " =    1.027
peak=    3.527 closest distance to " O   HOH Z 298 " =    4.995
peak=    3.522 closest distance to " O   HOH Z 403 " =    1.316
peak=    3.511 closest distance to " NH1AARG A 275 " =    1.056
peak=    3.508 closest distance to " O   HOH Z 427 " =    2.650
peak=    3.504 closest distance to " O   HOH Z 163 " =    1.384
peak=    3.503 closest distance to " CB  TRP A 266 " =    1.162
peak=    3.498 closest distance to " O   HOH Z 238 " =    1.064
peak=    3.498 closest distance to " O   HOH Z 298 " =    1.899
peak=    3.497 closest distance to " O   HOH Z 368 " =    2.172
peak=    3.493 closest distance to " CB  GLU A 152 " =    1.059
peak=    3.489 closest distance to " CB  THR A  31 " =    1.487
peak=    3.488 closest distance to " CG2 ILE A 120 " =    1.385
peak=    3.479 closest distance to " NZ  LYS A 117 " =    1.697
peak=    3.479 closest distance to " CA  ASN A 176 " =    1.231
peak=    3.471 closest distance to " OG BSER A 212 " =    2.615
peak=    3.467 closest distance to " CZ  PHE A  38 " =    1.222
peak=    3.465 closest distance to " O   HOH Z 214 " =    1.499
peak=    3.464 closest distance to " O   HOH Z 435 " =    1.948
peak=    3.463 closest distance to " O   HOH Z 412 " =    3.659
peak=    3.460 closest distance to " O   HOH Z 155 " =    2.964
peak=    3.460 closest distance to " OG BSER A 164 " =    2.102
peak=    3.459 closest distance to " O   HOH Z 227 " =    1.622
peak=    3.458 closest distance to " O   HOH Z 162 " =    2.045
peak=    3.455 closest distance to " CD1 LEU A   5 " =    1.443
peak=    3.455 closest distance to " O   HOH Z 332 " =    1.532
peak=    3.454 closest distance to " O   HOH Z  78 " =    1.597
peak=    3.453 closest distance to " CB  ARG A  79 " =    0.914
peak=    3.449 closest distance to " O   HOH Z 426 " =    1.462
peak=    3.448 closest distance to " CG1BVAL A  72 " =    1.805
peak=    3.443 closest distance to " CD  PRO A  54 " =    1.059
peak=    3.443 closest distance to " OG  SER A 245 " =    1.432
peak=    3.441 closest distance to " O   HOH Z 380 " =    1.653
peak=    3.432 closest distance to " O   HOH Z  15 " =    2.123
peak=    3.432 closest distance to " CB  VAL A 265 " =    1.348
peak=    3.431 closest distance to " O   HOH Z 313 " =    1.780
peak=    3.429 closest distance to " OE1 GLN A  11 " =    1.857
peak=    3.425 closest distance to " O   HOH Z 359 " =    1.471
peak=    3.422 closest distance to " O   HOH Z 271 " =    2.247
peak=    3.422 closest distance to " O   HOH Z 214 " =    2.698
peak=    3.418 closest distance to " O   HOH Z  54 " =    1.543
peak=    3.404 closest distance to " ND1 HIS A  81 " =    1.427
peak=    3.403 closest distance to " O   HOH Z 250 " =    1.630
peak=    3.396 closest distance to " CG2 VAL A 197 " =    1.126
peak=    3.396 closest distance to " CD  ARG A 195 " =    1.012
peak=    3.392 closest distance to " CB  VAL A 202 " =    1.425
peak=    3.392 closest distance to " CB  TYR A 169 " =    0.815
peak=    3.390 closest distance to " CE  LYS A 119 " =    1.052
peak=    3.382 closest distance to " OG1 THR A 294 " =    2.275
peak=    3.382 closest distance to " O   HOH Z 249 " =    1.062
peak=    3.375 closest distance to " CB  ARG A 190 " =    1.803
peak=    3.375 closest distance to " O   HOH Z 419 " =    1.750
peak=    3.372 closest distance to " CA  TRP A  85 " =    1.119
peak=    3.372 closest distance to " O   HOH Z 438 " =    2.278
peak=    3.372 closest distance to " NH1 ARG A  14 " =    1.150
peak=    3.370 closest distance to " CB  SER A 141 " =    1.109
peak=    3.369 closest distance to " CD1 LEU A  96 " =    0.770
peak=    3.365 closest distance to " O   HOH Z 334 " =    1.542
peak=    3.364 closest distance to " O   HOH Z 166 " =    1.579
peak=    3.360 closest distance to " OD1 ASN A  60 " =    1.679
peak=    3.357 closest distance to " CZ  PHE A 218 " =    1.222
peak=    3.354 closest distance to " O   HOH Z 421 " =    2.044
peak=    3.346 closest distance to " CA  ARG A  36 " =    0.967
peak=    3.345 closest distance to " CD1 LEU A 222 " =    0.737
peak=    3.324 closest distance to " O   HOH Z 336 " =    1.857
peak=    3.322 closest distance to " O   HOH Z 257 " =    2.218
peak=    3.322 closest distance to " CD1 LEU A 101 " =    1.258
peak=    3.320 closest distance to " CB  GLU A 128 " =    1.294
peak=    3.314 closest distance to " O   HOH Z 387 " =    2.813
peak=    3.313 closest distance to " O   HOH Z 112 " =    1.742
peak=    3.309 closest distance to " O   HOH Z  61 " =    1.524
peak=    3.308 closest distance to " O   ALA A 158 " =    1.163
peak=    3.305 closest distance to " O   HOH Z  66 " =    2.138
peak=    3.295 closest distance to " O   HOH Z 210 " =    1.058
peak=    3.288 closest distance to " CZ3 TRP A  85 " =    0.963
peak=    3.288 closest distance to " CG2AVAL A 121 " =    2.003
peak=    3.286 closest distance to " CA  ALA A 100 " =    1.093
peak=    3.284 closest distance to " CB  ASN A 285 " =    0.989
peak=    3.283 closest distance to " CB  THR A  52 " =    0.976
peak=    3.281 closest distance to " O   HOH Z 427 " =    3.048
peak=    3.281 closest distance to " CA  SER A  12 " =    1.477
peak=    3.281 closest distance to " ND2 ASN A 187 " =    1.677
peak=    3.279 closest distance to " CB  ALA A 256 " =    1.001
peak=    3.275 closest distance to " O   HOH Z 173 " =    2.339
peak=    3.274 closest distance to " O   HOH Z 280 " =    2.453
peak=    3.270 closest distance to " CG  ARG A 269 " =    1.213
peak=    3.269 closest distance to " CG2 THR A 220 " =    0.813
peak=    3.268 closest distance to " O   HOH Z 159 " =    1.027
peak=    3.267 closest distance to " O   HOH Z 345 " =    1.801
peak=    3.265 closest distance to " NE2 HIS A 115 " =    1.009
peak=    3.264 closest distance to " OG BSER A 210 " =    1.209
peak=    3.264 closest distance to " O   HOH Z  40 " =    2.574
peak=    3.262 closest distance to " CG1BVAL A 121 " =    1.243
peak=    3.261 closest distance to " CZ AARG A 102 " =    1.786
peak=    3.259 closest distance to " O   HOH Z 281 " =    4.289
peak=    3.258 closest distance to " O   HOH Z 189 " =    2.443
peak=    3.258 closest distance to " O   HOH Z 301 " =    1.875
peak=    3.258 closest distance to " O   HOH Z 313 " =    1.689
peak=    3.257 closest distance to " O   HOH Z 215 " =    1.508
peak=    3.257 closest distance to " N   ASP A 231 " =    1.578
peak=    3.255 closest distance to " O   HOH Z 273 " =    2.797
peak=    3.254 closest distance to " O   HOH Z 298 " =    2.169
peak=    3.254 closest distance to " CB  ARG A 139 " =    0.983
peak=    3.254 closest distance to " NH2 ARG A  79 " =    1.248
peak=    3.248 closest distance to " O   HOH Z 329 " =    3.838
peak=    3.246 closest distance to " O   HOH Z 271 " =    1.299
peak=    3.246 closest distance to " O   HOH Z 437 " =    2.528
peak=    3.241 closest distance to " O   HOH Z 130 " =    2.993
peak=    3.240 closest distance to " O   HOH Z  35 " =    2.088
peak=    3.235 closest distance to " O   HOH Z 374 " =    2.564
peak=    3.233 closest distance to " NE1 TRP A 274 " =    0.933
peak=    3.224 closest distance to " CB  TYR A 247 " =    0.993
peak=    3.223 closest distance to " O   HOH Z 147 " =    1.733
peak=    3.220 closest distance to " CB  MET A  47 " =    1.139
peak=    3.216 closest distance to " O   HOH Z 367 " =    3.258
peak=    3.214 closest distance to " CA  THR A  82 " =    1.500
peak=    3.213 closest distance to " CB  ALA A   9 " =    1.634
peak=    3.212 closest distance to " O   HOH Z  48 " =    1.552
peak=    3.205 closest distance to " O   HOH Z 183 " =    1.740
peak=    3.205 closest distance to " O   HOH Z   9 " =    2.508
peak=    3.205 closest distance to " O   HOH Z 130 " =    2.498
peak=    3.202 closest distance to " O   HOH Z 383 " =    2.111
peak=    3.198 closest distance to " O   HOH Z 279 " =    2.027
peak=    3.196 closest distance to " CB  ARG A 219 " =    1.457
peak=    3.193 closest distance to " NH2AARG A 275 " =    3.686
peak=    3.193 closest distance to " N   SER A 164 " =    0.964
peak=    3.189 closest distance to " N   GLU A  44 " =    1.338
peak=    3.188 closest distance to " O   HOH Z 123 " =    2.045
peak=    3.186 closest distance to " CD  GLN A 194 " =    1.538
peak=    3.177 closest distance to " O   HOH Z 420 " =    4.591
peak=    3.171 closest distance to " O   HOH Z 234 " =    1.879
peak=    3.169 closest distance to " NZ  LYS A 166 " =    2.952
peak=    3.159 closest distance to " O   HOH Z 120 " =    2.336
peak=    3.157 closest distance to " CB  ASP A 140 " =    0.912
peak=    3.155 closest distance to " CA  ASP A 162 " =    1.134
peak=    3.152 closest distance to " CA  VAL A 126 " =    1.125
peak=    3.149 closest distance to " O   HOH Z 425 " =    2.025
peak=    3.143 closest distance to " CB  THR A 235 " =    1.078
peak=    3.140 closest distance to " O   HOH Z 419 " =    2.277
peak=    3.140 closest distance to " CE BLYS A 290 " =    1.036
peak=    3.129 closest distance to " NH2BARG A 190 " =    1.657
peak=    3.122 closest distance to " CG2 ILE A 234 " =    1.003
peak=    3.120 closest distance to " CG2 THR A 294 " =    1.382
peak=    3.113 closest distance to " O   GLU A   2 " =    1.628
peak=    3.111 closest distance to " CZ2 TRP A 150 " =    1.023
peak=    3.110 closest distance to " O   HOH Z 185 " =    1.657
peak=    3.107 closest distance to " OG BSER A 258 " =    3.022
peak=    3.103 closest distance to " O   HOH Z 170 " =    1.577
peak=    3.099 closest distance to " N   SER A 135 " =    1.271
peak=    3.097 closest distance to " CB  ARG A 259 " =    1.917
peak=    3.091 closest distance to " CB  ASN A  39 " =    0.759
peak=    3.081 closest distance to " O   HOH Z 133 " =    2.883
peak=    3.079 closest distance to " CB  SER A  62 " =    0.902
peak=    3.078 closest distance to " O   HOH Z 287 " =    1.851
peak=    3.073 closest distance to " N   TYR A 247 " =    1.276
peak=    3.073 closest distance to " C   SER A  32 " =    1.092
peak=    3.067 closest distance to " CB  ALA A  71 " =    1.306
peak=    3.065 closest distance to " O   HOH Z 197 " =    2.304
peak=    3.060 closest distance to " CA  ALA A 129 " =    1.115
peak=    3.047 closest distance to " OG BSER A 164 " =    1.870
peak=    3.041 closest distance to " O   PHE A  61 " =    1.451
peak=    2.989 closest distance to " CG  ARG A  66 " =    2.933

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 196         
Filter by distance & map next to the model:
   mapped sites are within: 0.694 - 5.961
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 195 from: 196
   mapped sites are within: 0.795 - 5.961

peak=   -4.847 closest distance to " O   HOH Z 210 " =    0.797
peak=   -4.683 closest distance to " CG2 VAL A 230 " =    0.893
peak=   -4.590 closest distance to " O   HOH Z  13 " =    1.756
peak=   -4.583 closest distance to " CG2BVAL A  41 " =    2.684
peak=   -4.396 closest distance to " OXT GLY A 302 " =    2.819
peak=   -4.327 closest distance to " O   PRO A 163 " =    2.043
peak=   -4.314 closest distance to " O   HOH Z 266 " =    4.787
peak=   -4.261 closest distance to " CD  ARG A 156 " =    1.974
peak=   -4.219 closest distance to " CD  GLN A  58 " =    1.233
peak=   -4.189 closest distance to " O   HOH Z 422 " =    1.305
peak=   -4.146 closest distance to " OG BSER A 134 " =    1.408
peak=   -4.117 closest distance to " SG  CYS A 254 " =    3.196
peak=   -4.095 closest distance to " O   VAL A  67 " =    2.832
peak=   -4.058 closest distance to " C   HIS A 108 " =    1.188
peak=   -4.036 closest distance to " C   THR A 279 " =    1.158
peak=   -3.980 closest distance to " CE2 TYR A  30 " =    2.707
peak=   -3.953 closest distance to " O   HOH Z 166 " =    1.627
peak=   -3.936 closest distance to " O   HOH Z 109 " =    5.961
peak=   -3.916 closest distance to " CG1 VAL A 112 " =    2.520
peak=   -3.911 closest distance to " OG  SER A  97 " =    2.263
peak=   -3.894 closest distance to " O   HOH Z   6 " =    1.979
peak=   -3.884 closest distance to " OG BSER A 210 " =    1.317
peak=   -3.882 closest distance to " CD1 PHE A  59 " =    1.930
peak=   -3.880 closest distance to " O   HOH Z 120 " =    1.143
peak=   -3.872 closest distance to " CB  ALA A 248 " =    2.048
peak=   -3.872 closest distance to " CB  PHE A 208 " =    2.341
peak=   -3.860 closest distance to " CZ  TYR A 169 " =    1.737
peak=   -3.860 closest distance to " O   HOH Z 174 " =    1.939
peak=   -3.828 closest distance to " O   HOH Z 423 " =    2.175
peak=   -3.817 closest distance to " CD2 LEU A 237 " =    2.575
peak=   -3.813 closest distance to " CG  ARG A 219 " =    2.368
peak=   -3.811 closest distance to " CD1 LEU A 101 " =    2.493
peak=   -3.810 closest distance to " O   HOH Z 426 " =    1.663
peak=   -3.778 closest distance to " CB  SER A 210 " =    1.348
peak=   -3.767 closest distance to " O   MET A  40 " =    2.784
peak=   -3.757 closest distance to " CB  ALA A 248 " =    2.105
peak=   -3.752 closest distance to " OG  SER A   3 " =    1.635
peak=   -3.742 closest distance to " CB  ALA A 161 " =    2.503
peak=   -3.742 closest distance to " CG1 VAL A 296 " =    1.069
peak=   -3.730 closest distance to " CA  SER A 276 " =    1.461
peak=   -3.730 closest distance to " CG2 THR A 182 " =    2.280
peak=   -3.714 closest distance to " CA  ASP A 298 " =    1.011
peak=   -3.714 closest distance to " N   ALA A 226 " =    1.896
peak=   -3.692 closest distance to " O   PRO A 198 " =    1.358
peak=   -3.677 closest distance to " O   HOH Z  92 " =    1.526
peak=   -3.672 closest distance to " O   HOH Z 312 " =    1.508
peak=   -3.649 closest distance to " O  BHOH Z 338 " =    1.351
peak=   -3.641 closest distance to " O   PHE A 218 " =    1.526
peak=   -3.638 closest distance to " O   HOH Z 165 " =    1.940
peak=   -3.636 closest distance to " O   HOH Z 377 " =    2.167
peak=   -3.634 closest distance to " O   HOH Z 196 " =    1.899
peak=   -3.633 closest distance to " O   HOH Z 407 " =    3.113
peak=   -3.632 closest distance to " O   ASN A  45 " =    1.851
peak=   -3.630 closest distance to " CD2 TYR A 293 " =    1.870
peak=   -3.599 closest distance to " O   HOH Z 351 " =    1.610
peak=   -3.594 closest distance to " N   THR A 235 " =    1.291
peak=   -3.593 closest distance to " ND2 ASN A  39 " =    1.133
peak=   -3.590 closest distance to " ND2 ASN A  45 " =    1.129
peak=   -3.583 closest distance to " O   HOH Z 368 " =    1.891
peak=   -3.579 closest distance to " O   HOH Z 388 " =    1.981
peak=   -3.576 closest distance to " O   HOH Z 136 " =    2.383
peak=   -3.571 closest distance to " O   HOH Z  60 " =    2.259
peak=   -3.562 closest distance to " CG2 ILE A  49 " =    2.704
peak=   -3.557 closest distance to " O   TRP A  92 " =    2.037
peak=   -3.550 closest distance to " O   HOH Z  15 " =    1.509
peak=   -3.548 closest distance to " CD1 TYR A 247 " =    2.329
peak=   -3.545 closest distance to " O   SER A 273 " =    1.201
peak=   -3.541 closest distance to " O   HOH Z 119 " =    2.045
peak=   -3.529 closest distance to " CG2 VAL A 189 " =    2.043
peak=   -3.510 closest distance to " O   ARG A 219 " =    1.812
peak=   -3.503 closest distance to " O   HOH Z  78 " =    1.652
peak=   -3.499 closest distance to " O   HOH Z 166 " =    1.288
peak=   -3.492 closest distance to " O   HOH Z 126 " =    1.919
peak=   -3.491 closest distance to " ND2 ASN A  69 " =    1.641
peak=   -3.479 closest distance to " O   HOH Z  56 " =    1.622
peak=   -3.478 closest distance to " CD1 LEU A 167 " =    2.043
peak=   -3.476 closest distance to " O   ALA A   1 " =    2.044
peak=   -3.457 closest distance to " CD2 LEU A 167 " =    1.569
peak=   -3.455 closest distance to " O   HOH Z 151 " =    1.032
peak=   -3.454 closest distance to " O   HOH Z 171 " =    2.384
peak=   -3.452 closest distance to " CD2 PHE A 192 " =    2.067
peak=   -3.449 closest distance to " CD1 LEU A 228 " =    2.158
peak=   -3.448 closest distance to " O   HOH Z 145 " =    2.131
peak=   -3.444 closest distance to " O   HOH Z  71 " =    1.772
peak=   -3.441 closest distance to " O   HOH Z 340 " =    1.199
peak=   -3.436 closest distance to " CA  GLY A 203 " =    2.351
peak=   -3.434 closest distance to " CD1 PHE A 130 " =    2.282
peak=   -3.433 closest distance to " CG  PRO A 243 " =    1.623
peak=   -3.432 closest distance to " NH2 ARG A  66 " =    1.434
peak=   -3.423 closest distance to " OG  SER A  26 " =    1.300
peak=   -3.417 closest distance to " O   SER A 146 " =    1.067
peak=   -3.408 closest distance to " OD1 ASN A 148 " =    1.529
peak=   -3.391 closest distance to " CG  GLN A  11 " =    1.622
peak=   -3.391 closest distance to " OD1 ASN A 173 " =    1.662
peak=   -3.387 closest distance to " O   HOH Z 103 " =    1.841
peak=   -3.385 closest distance to " CD1 TRP A  70 " =    1.878
peak=   -3.384 closest distance to " CE  LYS A 166 " =    3.000
peak=   -3.383 closest distance to " CG  ASP A 231 " =    0.801
peak=   -3.382 closest distance to " OD1 ASN A 249 " =    2.437
peak=   -3.382 closest distance to " ND2 ASN A 187 " =    1.608
peak=   -3.374 closest distance to " O   HOH Z 191 " =    5.871
peak=   -3.371 closest distance to " O   HOH Z 345 " =    2.803
peak=   -3.362 closest distance to " CD1 TRP A 179 " =    1.265
peak=   -3.362 closest distance to " CD  ARG A 195 " =    5.154
peak=   -3.355 closest distance to " O   ALA A 256 " =    1.488
peak=   -3.352 closest distance to " O   HOH Z  97 " =    1.062
peak=   -3.352 closest distance to " OE2 GLU A   2 " =    1.720
peak=   -3.349 closest distance to " O   VAL A 174 " =    2.196
peak=   -3.345 closest distance to " O   TYR A  15 " =    1.755
peak=   -3.344 closest distance to " CA  GLY A 133 " =    1.993
peak=   -3.341 closest distance to " SG  CYS A 260 " =    2.533
peak=   -3.338 closest distance to " C   SER A 206 " =    1.575
peak=   -3.336 closest distance to " O   HOH Z 420 " =    5.096
peak=   -3.335 closest distance to " O   HOH Z 234 " =    3.847
peak=   -3.333 closest distance to " O   HOH Z 397 " =    1.176
peak=   -3.331 closest distance to " O   HOH Z 407 " =    1.539
peak=   -3.324 closest distance to " OG1 THR A  82 " =    1.306
peak=   -3.314 closest distance to " O   HOH Z 176 " =    1.747
peak=   -3.303 closest distance to " CA  VAL A 197 " =    0.931
peak=   -3.299 closest distance to " CD2 LEU A 300 " =    2.739
peak=   -3.298 closest distance to " CG1 VAL A  78 " =    2.596
peak=   -3.295 closest distance to " O   HOH Z 424 " =    2.888
peak=   -3.295 closest distance to " O   HOH Z 426 " =    2.293
peak=   -3.291 closest distance to " OD2 ASP A 171 " =    2.261
peak=   -3.290 closest distance to " N   GLN A  58 " =    1.692
peak=   -3.287 closest distance to " OD2 ASP A  50 " =    1.462
peak=   -3.286 closest distance to " O   HOH Z 124 " =    1.505
peak=   -3.284 closest distance to " O   HOH Z 131 " =    4.076
peak=   -3.283 closest distance to " O   ALA A  34 " =    2.227
peak=   -3.282 closest distance to " O   HOH Z 290 " =    1.021
peak=   -3.280 closest distance to " CE BMET A  47 " =    1.237
peak=   -3.276 closest distance to " CE3 TRP A 274 " =    2.275
peak=   -3.275 closest distance to " O   HOH Z  10 " =    1.566
peak=   -3.273 closest distance to " O   HOH Z 196 " =    2.268
peak=   -3.260 closest distance to " O   HOH Z 385 " =    3.693
peak=   -3.260 closest distance to " CG2 VAL A 296 " =    1.180
peak=   -3.256 closest distance to " O   HOH Z 285 " =    1.428
peak=   -3.251 closest distance to " OD2 ASP A 191 " =    1.612
peak=   -3.247 closest distance to " O   HOH Z  52 " =    2.375
peak=   -3.246 closest distance to " O   HOH Z 377 " =    1.912
peak=   -3.241 closest distance to " O   HOH Z 150 " =    1.869
peak=   -3.236 closest distance to " O   LEU A 101 " =    1.507
peak=   -3.234 closest distance to " O   HOH Z 200 " =    1.429
peak=   -3.229 closest distance to " O   HOH Z 252 " =    3.956
peak=   -3.223 closest distance to " NE2 GLN A 194 " =    1.782
peak=   -3.215 closest distance to " OE1 GLN A 223 " =    5.352
peak=   -3.215 closest distance to " O   HOH Z 193 " =    1.617
peak=   -3.213 closest distance to " CD2 TYR A 172 " =    1.986
peak=   -3.213 closest distance to " O   HOH Z  46 " =    0.795
peak=   -3.205 closest distance to " O   ASP A 171 " =    1.806
peak=   -3.205 closest distance to " OG1 THR A   4 " =    1.924
peak=   -3.202 closest distance to " O   HOH Z 139 " =    3.296
peak=   -3.202 closest distance to " NE2 GLN A  58 " =    2.408
peak=   -3.195 closest distance to " O   HOH Z 311 " =    3.576
peak=   -3.191 closest distance to " N   SER A   3 " =    2.336
peak=   -3.188 closest distance to " O   HOH Z 193 " =    1.461
peak=   -3.187 closest distance to " NH2 ARG A  66 " =    5.354
peak=   -3.186 closest distance to " CB  ALA A  43 " =    2.373
peak=   -3.178 closest distance to " CG  ARG A 269 " =    2.193
peak=   -3.177 closest distance to " OD1 ASN A  39 " =    2.239
peak=   -3.171 closest distance to " O   HOH Z 123 " =    2.304
peak=   -3.170 closest distance to " O   HOH Z 297 " =    2.801
peak=   -3.164 closest distance to " O   GLY A 241 " =    2.262
peak=   -3.161 closest distance to " O   HOH Z  64 " =    0.917
peak=   -3.161 closest distance to " O   HOH Z 313 " =    2.317
peak=   -3.156 closest distance to " CE1 HIS A  81 " =    1.398
peak=   -3.153 closest distance to " C   GLN A 144 " =    0.830
peak=   -3.151 closest distance to " CH2 TRP A 150 " =    1.044
peak=   -3.143 closest distance to " O   ILE A 234 " =    1.259
peak=   -3.138 closest distance to " C   ALA A 158 " =    1.295
peak=   -3.138 closest distance to " OG BSER A  99 " =    1.095
peak=   -3.137 closest distance to " O   HOH Z 353 " =    2.160
peak=   -3.135 closest distance to " O   HOH Z 177 " =    1.767
peak=   -3.133 closest distance to " CD2 PHE A  59 " =    2.483
peak=   -3.131 closest distance to " O   HOH Z 392 " =    1.736
peak=   -3.124 closest distance to " CD  ARG A 139 " =    1.566
peak=   -3.122 closest distance to " CH2 TRP A 179 " =    1.330
peak=   -3.122 closest distance to " O   ASP A 191 " =    1.937
peak=   -3.112 closest distance to " OXT GLY A 302 " =    3.373
peak=   -3.109 closest distance to " O   HOH Z  11 " =    1.690
peak=   -3.107 closest distance to " CD  GLN A  88 " =    0.854
peak=   -3.097 closest distance to " O   GLY A  80 " =    2.572
peak=   -3.094 closest distance to " OG BSER A 134 " =    1.659
peak=   -3.089 closest distance to " O   HOH Z 261 " =    1.342
peak=   -3.084 closest distance to " CG  ASP A 132 " =    2.305
peak=   -3.083 closest distance to " CD  PRO A 243 " =    1.894
peak=   -3.082 closest distance to " NE1 TRP A 266 " =    2.138
peak=   -3.081 closest distance to " O   HOH Z 396 " =    1.574
peak=   -3.077 closest distance to " O   HOH Z 351 " =    1.424
peak=   -3.073 closest distance to " O   HOH Z 371 " =    1.924
peak=   -3.068 closest distance to " O   HOH Z 227 " =    0.976
peak=   -3.066 closest distance to " CA  ASN A 110 " =    1.105
peak=   -3.055 closest distance to " O   HOH Z 110 " =    1.550
peak=   -3.055 closest distance to " O   HOH Z 425 " =    1.159
peak=   -3.010 closest distance to " CG  GLN A 223 " =    1.299

================= 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    :  0.5004 0.4839   6.298707e+00   6.288212e+00
   1_bss:  0.4928 0.4791   6.291998e+00   6.283886e+00
   1_xyz:  0.4181 0.4368   6.210300e+00   6.235802e+00
   1_adp:  0.3728 0.4263   6.146763e+00   6.220754e+00
   1_occ:  0.3722 0.4254   6.145486e+00   6.220394e+00
   2_bss:  0.3710 0.4195   6.146987e+00   6.220202e+00
   2_xyz:  0.2866 0.3388   5.932476e+00   6.073208e+00
   2_adp:  0.2598 0.3222   5.866144e+00   6.023298e+00
   2_occ:  0.2596 0.3221   5.865430e+00   6.022903e+00
   3_bss:  0.2559 0.3194   5.861593e+00   6.018541e+00
   3_xyz:  0.1998 0.2480   5.640803e+00   5.814708e+00
   3_adp:  0.1870 0.2277   5.577369e+00   5.740372e+00
   3_occ:  0.1868 0.2279   5.577102e+00   5.741006e+00
   4_bss:  0.1864 0.2280   5.577306e+00   5.740548e+00
   4_xyz:  0.1493 0.1891   5.373388e+00   5.565670e+00
   4_adp:  0.1413 0.1825   5.328421e+00   5.529272e+00
   4_occ:  0.1411 0.1825   5.328120e+00   5.529294e+00
   5_bss:  0.1413 0.1832   5.330833e+00   5.531734e+00
   5_xyz:  0.1232 0.1677   5.224309e+00   5.448727e+00
   5_adp:  0.1191 0.1672   5.207021e+00   5.443857e+00
   5_occ:  0.1191 0.1673   5.206903e+00   5.443890e+00
   5_bss:  0.1190 0.1672   5.206686e+00   5.443955e+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:  0.350  20.000   7.100  11.263   7.038   0.000   0.000   0.000
   1_xyz:  0.350  20.000   7.100  11.263   7.038   0.000   0.000   0.000
   1_adp:  0.350  20.000   7.100  11.263   7.038   0.000   0.000   0.000
   1_occ:  0.350  20.000   7.100  11.263   7.038   0.000   0.000   0.000
   2_bss:  0.298  20.000   3.853   7.006   4.437   0.000   0.000   0.000
   2_xyz:  0.298  20.000   3.853   7.006   4.437   0.000   0.000   0.000
   2_adp:  0.298  20.000   3.853   7.006   4.437   0.000   0.000   0.000
   2_occ:  0.298  20.000   3.853   7.006   4.437   0.000   0.000   0.000
   3_bss:  0.326  45.645   1.328   3.818   2.707   0.000   0.000   0.000
   3_xyz:  0.326  45.645   1.328   3.818   2.707   0.000   0.000   0.000
   3_adp:  0.326  45.645   1.328   3.818   2.707   0.000   0.000   0.000
   3_occ:  0.326  45.645   1.328   3.818   2.707   0.000   0.000   0.000
   4_bss:  0.325  44.884   0.075   2.344   1.736   0.000   0.000   0.000
   4_xyz:  0.325  44.884   0.075   2.344   1.736   0.000   0.000   0.000
   4_adp:  0.325  44.884   0.075   2.344   1.736   0.000   0.000   0.000
   4_occ:  0.325  44.884   0.075   2.344   1.736   0.000   0.000   0.000
   5_bss:  0.320  44.884  -0.282   1.619   1.571   0.000   0.000   0.000
   5_xyz:  0.320  44.884  -0.282   1.619   1.571   0.000   0.000   0.000
   5_adp:  0.320  44.884  -0.282   1.619   1.571   0.000   0.000   0.000
   5_occ:  0.320  44.884  -0.282   1.619   1.571   0.000   0.000   0.000
   5_bss:  0.325  52.538  -1.155   0.523   0.632   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  60.540 0.3875  0.4571    75986.537
   1_bss:  60.907 0.3812  0.5752    74631.934
   1_xyz:  53.222 0.4780  0.7050    58830.962
   1_adp:  49.457 0.5261  0.8426    54360.229
   1_occ:  49.302 0.5280  0.8444    54114.902
   2_bss:  49.006 0.5318  0.7582    53719.918
   2_xyz:  37.633 0.6691  0.9357    32795.918
   2_adp:  34.469 0.7068  0.9764    28681.085
   2_occ:  34.446 0.7070  0.9766    28661.295
   3_bss:  34.089 0.7110  0.9001    28147.016
   3_xyz:  25.197 0.8091  0.9827    16373.997
   3_adp:  22.603 0.8367  1.0018    13929.379
   3_occ:  22.612 0.8366  1.0021    13953.885
   4_bss:  22.547 0.8372  0.9591    13894.252
   4_xyz:  18.063 0.8796  0.9835     9250.576
   4_adp:  17.158 0.8882  0.9867     8650.549
   4_occ:  17.156 0.8883  0.9866     8658.491
   5_bss:  17.213 0.8879  0.9719     8746.911
   5_xyz:  15.514 0.9025  0.9771     7413.126
   5_adp:  15.354 0.9041  0.9711     7334.033
   5_occ:  15.351 0.9041  0.9711     7334.852
   5_bss:  15.346 0.9042  0.9752     7341.030
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.3584e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.3584e+01
   1_xyz:   1.811  0.015  0.113 18.306  0.007  4.119   1.6221e-01
   1_adp:   1.811  0.015  0.113 18.306  0.007  4.119   1.6221e-01
   1_occ:   1.811  0.015  0.113 18.306  0.007  4.119   1.6221e-01
   2_bss:   1.811  0.015  0.113 18.306  0.007  4.119   1.6221e-01
   2_xyz:   1.472  0.012  0.092 16.977  0.006  4.105   1.2197e-01
   2_adp:   1.472  0.012  0.092 16.977  0.006  4.105   1.2197e-01
   2_occ:   1.472  0.012  0.092 16.977  0.006  4.105   1.2197e-01
   3_bss:   1.472  0.012  0.092 16.977  0.006  4.105   1.2197e-01
   3_xyz:   1.055  0.007  0.073 15.469  0.005  4.123   6.6331e-02
   3_adp:   1.055  0.007  0.073 15.469  0.005  4.123   6.6331e-02
   3_occ:   1.055  0.007  0.073 15.469  0.005  4.123   6.6331e-02
   4_bss:   1.055  0.007  0.073 15.469  0.005  4.123   6.6331e-02
   4_xyz:   0.998  0.006  0.071 15.015  0.004  4.118   5.8507e-02
   4_adp:   0.998  0.006  0.071 15.015  0.004  4.118   5.8507e-02
   4_occ:   0.998  0.006  0.071 15.015  0.004  4.118   5.8507e-02
   5_bss:   0.998  0.006  0.071 15.015  0.004  4.118   5.8507e-02
   5_xyz:   1.113  0.008  0.086 15.286  0.005  4.111   7.0768e-02
   5_adp:   1.113  0.008  0.086 15.286  0.005  4.111   7.0768e-02
   5_occ:   1.113  0.008  0.086 15.286  0.005  4.111   7.0768e-02
   5_bss:   1.113  0.008  0.086 15.286  0.005  4.111   7.0768e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.778   6.9407e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.778   6.9407e+00
   1_xyz:  17.005  0.176  0.593 85.741  0.041  2.174   1.1238e-01
   1_adp:  17.005  0.176  0.593 85.741  0.041  2.174   1.1238e-01
   1_occ:  17.005  0.176  0.593 85.741  0.041  2.174   1.1238e-01
   2_bss:  17.005  0.176  0.593 85.741  0.041  2.174   1.1238e-01
   2_xyz:   9.498  0.173  0.355 83.864  0.058  2.145   1.0608e-01
   2_adp:   9.498  0.173  0.355 83.864  0.058  2.145   1.0608e-01
   2_occ:   9.498  0.173  0.355 83.864  0.058  2.145   1.0608e-01
   3_bss:   9.498  0.173  0.355 83.864  0.058  2.145   1.0608e-01
   3_xyz:   6.854  0.058  0.247 84.034  0.044  2.249   5.3788e-02
   3_adp:   6.854  0.058  0.247 84.034  0.044  2.249   5.3788e-02
   3_occ:   6.854  0.058  0.247 84.034  0.044  2.249   5.3788e-02
   4_bss:   6.854  0.058  0.247 84.034  0.044  2.249   5.3788e-02
   4_xyz:   6.822  0.036  0.269 79.786  0.032  2.217   4.4213e-02
   4_adp:   6.822  0.036  0.269 79.786  0.032  2.217   4.4213e-02
   4_occ:   6.822  0.036  0.269 79.786  0.032  2.217   4.4213e-02
   5_bss:   6.822  0.036  0.269 79.786  0.032  2.217   4.4213e-02
   5_xyz:   7.676  0.050  0.519 83.870  0.041  2.248   5.1597e-02
   5_adp:   7.676  0.050  0.519 83.870  0.041  2.248   5.1597e-02
   5_occ:   7.676  0.050  0.519 83.870  0.041  2.248   5.1597e-02
   5_bss:   7.676  0.050  0.519 83.870  0.041  2.248   5.1597e-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: 102.54   0.00  15.10  72.90   0.00  12.99 102.54   0.00  26.60
   1_occ: 102.54   0.00  15.10  72.90   0.00  12.99 102.54   0.00  26.60
   2_bss: 102.54   0.00  15.10  72.90   0.00  12.99 102.54   0.00  26.60
   2_xyz: 102.54   0.00  15.10  72.90   0.00  12.99 102.54   0.00  26.60
   2_adp:  97.90   0.00  14.40  79.39   0.00  11.28  97.90   0.00  31.40
   2_occ:  97.90   0.00  14.40  79.39   0.00  11.28  97.90   0.00  31.40
   3_bss:  97.90   0.00  14.40  79.39   0.00  11.28  97.90   0.00  31.40
   3_xyz:  97.90   0.00  14.40  79.39   0.00  11.28  97.90   0.00  31.40
   3_adp:  86.95   0.00  14.12  78.68   0.00  10.39  86.95   3.54  34.40
   3_occ:  86.95   0.00  14.12  78.68   0.00  10.39  86.95   3.54  34.40
   4_bss:  86.95   0.00  14.12  78.68   0.00  10.39  86.95   3.54  34.40
   4_xyz:  86.95   0.00  14.12  78.68   0.00  10.39  86.95   3.54  34.40
   4_adp:  81.52   0.00  14.29  80.95   0.00  10.17  81.52   2.70  36.74
   4_occ:  81.52   0.00  14.29  80.95   0.00  10.17  81.52   2.70  36.74
   5_bss:  81.52   0.00  14.29  80.95   0.00  10.17  81.52   2.70  36.74
   5_xyz:  81.52   0.00  14.29  80.95   0.00  10.17  81.52   2.70  36.74
   5_adp:  93.50   0.00  14.84  93.50   0.00  10.17  90.67   2.56  40.27
   5_occ:  93.50   0.00  14.84  93.50   0.00  10.17  90.67   2.56  40.27
   5_bss:  94.58   1.07  15.91  94.58   1.07  11.24  91.74   3.63  41.34
------------------------------------------------------------------------
 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:    1.158    0.013    0.421
   1_adp:    1.158    0.013    0.421
   1_occ:    1.158    0.013    0.421
   2_bss:    1.158    0.013    0.421
   2_xyz:    1.630    0.030    0.656
   2_adp:    1.630    0.030    0.656
   2_occ:    1.630    0.030    0.656
   3_bss:    1.630    0.030    0.656
   3_xyz:    1.860    0.080    0.719
   3_adp:    1.860    0.080    0.719
   3_occ:    1.860    0.080    0.719
   4_bss:    1.860    0.080    0.719
   4_xyz:    1.985    0.054    0.805
   4_adp:    1.985    0.054    0.805
   4_occ:    1.985    0.054    0.805
   5_bss:    1.985    0.054    0.805
   5_xyz:    2.023    0.037    0.836
   5_adp:    2.023    0.037    0.836
   5_occ:    2.023    0.037    0.836
   5_bss:    2.023    0.037    0.836
------------------------------------------------------------------------

CPU time actual refinement: 337.02


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_224/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_224/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_224/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_224/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_224/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 336.85 
  Macro-tasks:
    bulk solvent and scale       = 45.55  
    individual site refinement   = 133.77 
    weights calculation          = 32.04  
    collect and process          = 6.35   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 217.81 
  Micro-tasks:
    mask                            = 2.36   
    f_calc                          = 103.64 
    alpha_beta                      = 7.97   
    target                          = 1.09   
    gradients_wrt_atomic_parameters = 112.97 
    fmodel                         = 7.44   
    r_factors                      = 0.30   
    phase_errors                   = 10.34  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 246.34 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.782 micro seconds
Total CPU time: 5.84 minutes
from_scatterers_fft:    638 calls, 103.44 s
gradients_fft:          584 calls, 100.11 s

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

# Date 2008-01-16 Time 01:03:23 PST -0800 (1200474203.86 s)
Start R-work = 0.5004, R-free = 0.4839 (no bulk solvent and anisotropic scale)
Final R-work = 0.1365, R-free = 0.1820 (no bulk solvent and anisotropic scale)

Start R-work = 0.4928, R-free = 0.4791
Final R-work = 0.1190, R-free = 0.1672