# Date 2008-01-16 Time 01:14:57 PST -0800 (1200474897.23 s)
#phil __OFF__

Command line arguments: "../332.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 = 21017
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 332

-------------------------------------------------------------------------------
  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: (69.1963, 47.6339, 85.0941, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.25, 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: (69.1963, 47.6339, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8759 1.97052
Completeness in resolution range: 0.958038
Completeness with d_max=infinity: 0.955095

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8759
                             d_min =   1.9705

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.6339, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8759 1.97052
Completeness in resolution range: 0.958038
Completeness with d_max=infinity: 0.955095

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8763 -  4.2162 [2151/2180]  1935   216  10.0%
  bin  2:  4.2162 -  3.3592 [2051/2074]  1846   205  10.0%
  bin  3:  3.3592 -  2.9383 [2037/2062]  1832   205  10.1%
  bin  4:  2.9383 -  2.6713 [2012/2028]  1812   200   9.9%
  bin  5:  2.6713 -  2.4808 [1997/2035]  1795   202  10.1%
  bin  6:  2.4808 -  2.3351 [1996/2029]  1802   194   9.7%
  bin  7:  2.3351 -  2.2186 [1967/2004]  1770   197  10.0%
  bin  8:  2.2186 -  2.1223 [1993/2035]  1791   202  10.1%
  bin  9:  2.1223 -  2.0408 [1956/1994]  1763   193   9.9%
  bin 10:  2.0408 -  1.9705 [1429/2006]  1284   145  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_332/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:
        1.58 -     2.24: 26
        2.24 -     2.91: 1428
        2.91 -     3.57: 4538
        3.57 -     4.24: 9245
        4.24 -     4.90: 13308
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.576 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.676 3.040 -x+1,y+1/2,-z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.695 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.728 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28540 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_332/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_332/model_refine_001.geo

CPU time processing inputs: 9.09


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 47.63395 85.09415 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4878   r_free= 0.4779   ksol= 0.00   Bsol= 0.00   scale= 0.794    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.77 A                  |
| x-ray target function (ml) for work reflections: 6.286192                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8763 -  4.7023 0.99   1391  158 0.4000 0.3933      6.5906      6.6284|
|  2:  4.7023 -  3.7521 0.99   1343  144 0.4131 0.4063      6.7936       6.808|
|  3:  3.7521 -  3.2836 0.99   1316  152 0.4435 0.4121      6.6825      6.7087|
|  4:  3.2836 -  2.9861 0.99   1313  136 0.4628 0.4422      6.5173       6.484|
|  5:  2.9861 -  2.7735 0.98   1286  147 0.5198 0.5324       6.394      6.4067|
|  6:  2.7735 -  2.6109 0.99   1291  142 0.5109 0.5278      6.2808      6.2165|
|  7:  2.6109 -  2.4808 0.99   1280  149 0.5209 0.4722      6.2653      6.1686|
|  8:  2.4808 -  2.3732 0.99   1301  135 0.5305 0.5107      6.1845      6.1699|
|  9:  2.3732 -  2.2822 0.99   1272  148 0.5424 0.5655      6.1244      6.1789|
| 10:  2.2822 -  2.2037 0.98   1267  141 0.5297 0.5433      6.1234      6.1005|
| 11:  2.2037 -  2.1350 0.98   1251  141 0.5386 0.5439       6.044      6.0785|
| 12:  2.1350 -  2.0741 1.00   1284  140 0.5412 0.5412      5.9813      6.0012|
| 13:  2.0741 -  2.0197 0.96   1257  131 0.5500 0.5479      5.8907      5.9069|
| 14:  2.0197 -  1.9705 0.61    778   95 0.5548 0.4461      5.9024      5.7061|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8763 -  4.7023  1391   158  0.66  37.67   0.80     0.68      81703.71|
|  2:  4.7023 -  3.7521  1343   144  0.68  37.20   0.88     0.74     112751.92|
|  3:  3.7521 -  3.2836  1316   152  0.59  44.87   0.85     0.70     118635.80|
|  4:  3.2836 -  2.9861  1313   136  0.51  51.47   0.81     0.60     101837.74|
|  5:  2.9861 -  2.7735  1286   147  0.40  59.92   0.73     0.48      87220.49|
|  6:  2.7735 -  2.6109  1291   142  0.37  62.34   0.73     0.42      73352.29|
|  7:  2.6109 -  2.4808  1280   149  0.36  62.82   0.73     0.41      67042.67|
|  8:  2.4808 -  2.3732  1301   135  0.36  62.69   0.72     0.42      58768.34|
|  9:  2.3732 -  2.2822  1272   148  0.33  65.60   0.72     0.40      56073.64|
| 10:  2.2822 -  2.2037  1267   141  0.30  67.35   0.76     0.35      52529.19|
| 11:  2.2037 -  2.1350  1251   141  0.24  72.02   0.74     0.30      51576.71|
| 12:  2.1350 -  2.0741  1284   140  0.24  72.12   0.74     0.31      48399.98|
| 13:  2.0741 -  2.0197  1257   131  0.28  68.85   0.73     0.36      38575.79|
| 14:  2.0197 -  1.9705   778    95  0.44  57.21   0.73     0.48      25287.35|
|alpha:            min =        0.30 max =            0.74 mean =         0.48|
|beta:             min =    25287.35 max =       118635.80 mean =     71285.33|
|figures of merit: min =        0.00 max =            1.00 mean =         0.41|
|phase err.(work): min =        0.00 max =           90.00 mean =        58.48|
|phase err.(test): min =        0.00 max =           89.98 mean =        58.48|
|-----------------------------------------------------------------------------|

============================== 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 = 15.702132             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.030   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.327669              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 83.349   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.106 -  1.485:        5 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.485 -  1.865:       12 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.865 -  2.244:      137 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.244 -  2.624:      624 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.624 -  3.003:     1433 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.003 -  3.382:     2557 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.382 -  3.762:     3972 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.762 -  4.141:     5190 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.141 -  4.521:     6710 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.521 -  4.900:     7969 |
|-----------------------------------------------------------------------------|
|-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 |       53.328 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.106 |       2.255 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.679)------------------------------------------|
|    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 = 11.679)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4928   r_free= 0.4851   ksol= 0.00   Bsol= 0.00   scale= 0.764    |
|                                                                             |
| 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:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.286821                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4802   r_free= 0.4693   ksol= 0.36   Bsol= 20.00   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.06,10.16,7.82,0.00,0.00,0.00); trace/3= 8.35                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.281541                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.236025             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.616   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.329820              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.814   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4802      final r-factor (work) = 0.3997          |
| start r-factor (free) = 0.4693      final r-factor (free) = 0.4182          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 98.0790 = 14.24 * 0.50 * 6.2870 + 1.00 * 53.3281                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 44.2948 = 14.24 * 0.50 * 6.2008 + 1.00 * 0.1575                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3997      final r-factor (work) = 0.3560          |
| start r-factor (free) = 0.4182      final r-factor (free) = 0.3968          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.2602 = 1.33 * 1.00 * 6.2008 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.1595 = 1.33 * 1.00 * 6.1222 + 1.00 * 0.0181                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 14     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.679)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    67.15   12.87    None  None   None       |
|    all(noH): 2823   0      0.00    67.15   12.87    None  None   None       |
|    Sol.    : 438    0      0.00    67.15   24.08    None  None   None       |
|    Mac.    : 2385   0      0.00    54.01   10.81    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.715:  962   |   5:    33.573 -  40.287:   88        |
|      1:     6.715 -  13.429:  780   |   6:    40.287 -  47.002:   44        |
|      2:    13.429 -  20.144:  474   |   7:    47.002 -  53.717:   20        |
|      3:    20.144 -  26.858:  278   |   8:    53.717 -  60.431:    5        |
|      4:    26.858 -  33.573:  171   |   9:    60.431 -  67.146:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3560 r_free = 0.3968             target_work(ml) = 6.104         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3552 r_free = 0.3965             target_work(ml) = 6.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3552   r_free= 0.3965   ksol= 0.36   Bsol= 20.00   scale= 1.097   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.06,10.16,7.82,0.00,0.00,0.00); trace/3= 8.35                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.102484                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3532   r_free= 0.3925   ksol= 0.32   Bsol= 31.65   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.67,6.33,5.11,0.00,0.00,0.00); trace/3= 5.04                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.103656                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.868698              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.778   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.577696              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.518  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3532      final r-factor (work) = 0.2551          |
| start r-factor (free) = 0.3925      final r-factor (free) = 0.3064          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.2872 = 8.87 * 0.50 * 6.1181 + 1.00 * 0.1575                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.5901 = 8.87 * 0.50 * 5.9754 + 1.00 * 0.0932                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2551      final r-factor (work) = 0.2248          |
| start r-factor (free) = 0.3064      final r-factor (free) = 0.2801          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4704 = 0.58 * 1.00 * 5.9754 + 1.00 * 0.0184                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3549 = 0.58 * 1.00 * 5.7841 + 1.00 * 0.0134                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.679)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    73.90   13.13    None  None   None       |
|    all(noH): 2823   0      0.00    73.90   13.13    None  None   None       |
|    Sol.    : 438    0      1.27    73.90   32.10    None  None   None       |
|    Mac.    : 2385   0      0.00    72.39   9.65     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 -   7.390: 1233   |   5:    36.949 -  44.338:   88        |
|      1:     7.390 -  14.779:  780   |   6:    44.338 -  51.728:   63        |
|      2:    14.779 -  22.169:  309   |   7:    51.728 -  59.118:   38        |
|      3:    22.169 -  29.559:  167   |   8:    59.118 -  66.507:   15        |
|      4:    29.559 -  36.949:  123   |   9:    66.507 -  73.897:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2248 r_free = 0.2801             target_work(ml) = 5.740         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2245 r_free = 0.2798             target_work(ml) = 5.739         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2245   r_free= 0.2798   ksol= 0.32   Bsol= 31.65   scale= 1.062   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.67,6.33,5.11,0.00,0.00,0.00); trace/3= 5.04                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.739268                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2214   r_free= 0.2778   ksol= 0.33   Bsol= 43.78   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.83,3.79,3.23,0.00,0.00,0.00); trace/3= 2.95                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.736739                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.589436              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.755   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.192653              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 102.315  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2214      final r-factor (work) = 0.1626          |
| start r-factor (free) = 0.2778      final r-factor (free) = 0.2081          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.4835 = 3.59 * 0.50 * 5.7894 + 1.00 * 0.0932                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1482 = 3.59 * 0.50 * 5.6196 + 1.00 * 0.0626                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1626      final r-factor (work) = 0.1518          |
| start r-factor (free) = 0.2081      final r-factor (free) = 0.1924          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0953 = 0.19 * 1.00 * 5.6196 + 1.00 * 0.0127                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0555 = 0.19 * 1.00 * 5.4235 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 34     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.679)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.15   12.98    None  None   None       |
|    all(noH): 2823   0      0.00    72.15   12.98    None  None   None       |
|    Sol.    : 438    0      2.46    69.03   33.74    None  None   None       |
|    Mac.    : 2385   0      0.00    72.15   9.16     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 -   7.215: 1237   |   5:    36.073 -  43.287:  102        |
|      1:     7.215 -  14.429:  852   |   6:    43.287 -  50.502:   75        |
|      2:    14.429 -  21.644:  259   |   7:    50.502 -  57.716:   43        |
|      3:    21.644 -  28.858:  111   |   8:    57.716 -  64.931:   15        |
|      4:    28.858 -  36.073:  121   |   9:    64.931 -  72.145:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1518 r_free = 0.1924             target_work(ml) = 5.384         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1514 r_free = 0.1925             target_work(ml) = 5.383         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1514   r_free= 0.1925   ksol= 0.33   Bsol= 43.78   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.83,3.79,3.23,0.00,0.00,0.00); trace/3= 2.95                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.382536                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1513   r_free= 0.1922   ksol= 0.33   Bsol= 39.93   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.93,2.51,2.32,0.00,0.00,0.00); trace/3= 1.92                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.383355                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.693729              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.677  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.301499              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.541   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1513      final r-factor (work) = 0.1233          |
| start r-factor (free) = 0.1922      final r-factor (free) = 0.1652          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0927 = 3.69 * 0.50 * 5.4309 + 1.00 * 0.0626                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8499 = 3.69 * 0.50 * 5.2935 + 1.00 * 0.0735                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1233      final r-factor (work) = 0.1200          |
| start r-factor (free) = 0.1652      final r-factor (free) = 0.1638          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6056 = 0.30 * 1.00 * 5.2935 + 1.00 * 0.0097                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6257 = 0.30 * 1.00 * 5.1983 + 1.00 * 0.0584                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.679)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.37   13.02    None  None   None       |
|    all(noH): 2823   0      0.00    72.37   13.02    None  None   None       |
|    Sol.    : 438    0      2.44    69.03   34.07    None  None   None       |
|    Mac.    : 2385   0      0.00    72.37   9.15     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.237: 1238   |   5:    36.186 -  43.423:  104        |
|      1:     7.237 -  14.474:  857   |   6:    43.423 -  50.660:   75        |
|      2:    14.474 -  21.712:  249   |   7:    50.660 -  57.898:   46        |
|      3:    21.712 -  28.949:  113   |   8:    57.898 -  65.135:   16        |
|      4:    28.949 -  36.186:  117   |   9:    65.135 -  72.372:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1200 r_free = 0.1638             target_work(ml) = 5.194         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1198 r_free = 0.1637             target_work(ml) = 5.193         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1198   r_free= 0.1637   ksol= 0.33   Bsol= 39.93   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.93,2.51,2.32,0.00,0.00,0.00); trace/3= 1.92                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.192891                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1201   r_free= 0.1636   ksol= 0.32   Bsol= 39.93   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.81,2.12,2.19,0.00,0.00,0.00); trace/3= 1.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.194119                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.424861              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 142.638  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.777950              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.128   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1201      final r-factor (work) = 0.1163          |
| start r-factor (free) = 0.1636      final r-factor (free) = 0.1607          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3762 = 2.42 * 0.50 * 5.1984 + 1.00 * 0.0735                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.3480 = 2.42 * 0.50 * 5.1828 + 1.00 * 0.0642                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1163      final r-factor (work) = 0.1137          |
| start r-factor (free) = 0.1607      final r-factor (free) = 0.1611          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0463 = 0.78 * 1.00 * 5.1828 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0278 = 0.78 * 1.00 * 5.1633 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.679)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.67   13.15    None  None   None       |
|    all(noH): 2823   0      0.00    76.67   13.15    None  None   None       |
|    Sol.    : 438    0      1.72    69.34   35.45    None  None   None       |
|    Mac.    : 2385   0      0.00    76.67   9.06     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.667: 1373   |   5:    38.337 -  46.004:   97        |
|      1:     7.667 -  15.335:  781   |   6:    46.004 -  53.672:   87        |
|      2:    15.335 -  23.002:  204   |   7:    53.672 -  61.339:   43        |
|      3:    23.002 -  30.669:  119   |   8:    61.339 -  69.006:   10        |
|      4:    30.669 -  38.337:  102   |   9:    69.006 -  76.674:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1137 r_free = 0.1611             target_work(ml) = 5.165         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1136 r_free = 0.1612             target_work(ml) = 5.165         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1136   r_free= 0.1612   ksol= 0.32   Bsol= 39.93   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.81,2.12,2.19,0.00,0.00,0.00); trace/3= 1.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.164723                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8763 -  4.7023 0.99   1391  158 0.0993 0.1274      5.3714      5.5251|
|  2:  4.7023 -  3.7521 0.99   1343  144 0.0872 0.1090      5.4474      5.6604|
|  3:  3.7521 -  3.2836 0.99   1316  152 0.1060 0.1550      5.4874      5.8679|
|  4:  3.2836 -  2.9861 0.99   1313  136 0.1248 0.1565      5.4729       5.661|
|  5:  2.9861 -  2.7735 0.98   1286  147 0.1356 0.1637       5.353      5.4862|
|  6:  2.7735 -  2.6109 0.99   1291  142 0.1314 0.2067      5.2578      5.5344|
|  7:  2.6109 -  2.4808 0.99   1280  149 0.1213 0.1634      5.1734       5.396|
|  8:  2.4808 -  2.3732 0.99   1301  135 0.1193 0.1830      5.1115       5.369|
|  9:  2.3732 -  2.2822 0.99   1272  148 0.1218 0.1886      5.0588      5.3747|
| 10:  2.2822 -  2.2037 0.98   1267  141 0.1148 0.1851      5.0072      5.2199|
| 11:  2.2037 -  2.1350 0.98   1251  141 0.1178 0.1802       4.948      5.2804|
| 12:  2.1350 -  2.0741 1.00   1284  140 0.1101 0.1796      4.8655      5.1703|
| 13:  2.0741 -  2.0197 0.96   1257  131 0.1130 0.1749      4.7941      5.0817|
| 14:  2.0197 -  1.9705 0.61    778   95 0.1065 0.1709      4.7211      4.9239|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8763 -  4.7023  1391   158  0.94   8.72   0.98     0.96       6908.21|
|  2:  4.7023 -  3.7521  1343   144  0.95   8.18   1.02     1.00       9101.60|
|  3:  3.7521 -  3.2836  1316   152  0.93  11.54   1.03     1.02      11041.51|
|  4:  3.2836 -  2.9861  1313   136  0.92  14.10   1.01     0.99      10716.67|
|  5:  2.9861 -  2.7735  1286   147  0.90  16.34   0.99     0.96       8687.20|
|  6:  2.7735 -  2.6109  1291   142  0.89  16.88   0.98     0.95       7655.06|
|  7:  2.6109 -  2.4808  1280   149  0.90  15.89   0.98     0.95       6461.01|
|  8:  2.4808 -  2.3732  1301   135  0.90  15.92   1.00     0.97       5957.12|
|  9:  2.3732 -  2.2822  1272   148  0.90  16.70   1.00     0.98       5428.76|
| 10:  2.2822 -  2.2037  1267   141  0.90  16.42   1.00     0.96       4955.69|
| 11:  2.2037 -  2.1350  1251   141  0.90  16.03   1.00     0.96       4392.12|
| 12:  2.1350 -  2.0741  1284   140  0.91  15.12   1.00     0.98       3862.98|
| 13:  2.0741 -  2.0197  1257   131  0.90  16.67   1.00     1.00       3485.47|
| 14:  2.0197 -  1.9705   778    95  0.90  15.74   0.98     0.94       2904.28|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2904.28 max =        11041.51 mean =      6681.15|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.91 mean =        14.48|
|phase err.(test): min =        0.00 max =           87.71 mean =        13.83|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1136   r_free= 0.1612   ksol= 0.32   Bsol= 44.03   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.86,0.37,0.48,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.164685                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1136   r_free= 0.1612   ksol= 0.32   Bsol= 44.03   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.86,0.37,0.48,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.164685                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8763 -  4.7023 0.99   1391  158 0.0995 0.1278      5.3722      5.5274|
|  2:  4.7023 -  3.7521 0.99   1343  144 0.0875 0.1093      5.4498      5.6636|
|  3:  3.7521 -  3.2836 0.99   1316  152 0.1060 0.1552       5.489      5.8691|
|  4:  3.2836 -  2.9861 0.99   1313  136 0.1247 0.1566      5.4727      5.6612|
|  5:  2.9861 -  2.7735 0.98   1286  147 0.1354 0.1637      5.3521      5.4854|
|  6:  2.7735 -  2.6109 0.99   1291  142 0.1313 0.2063      5.2568       5.533|
|  7:  2.6109 -  2.4808 0.99   1280  149 0.1213 0.1635      5.1728      5.3961|
|  8:  2.4808 -  2.3732 0.99   1301  135 0.1192 0.1828       5.111       5.368|
|  9:  2.3732 -  2.2822 0.99   1272  148 0.1218 0.1886      5.0585      5.3749|
| 10:  2.2822 -  2.2037 0.98   1267  141 0.1148 0.1850      5.0067      5.2194|
| 11:  2.2037 -  2.1350 0.98   1251  141 0.1177 0.1800      4.9477      5.2802|
| 12:  2.1350 -  2.0741 1.00   1284  140 0.1101 0.1796      4.8651        5.17|
| 13:  2.0741 -  2.0197 0.96   1257  131 0.1131 0.1746      4.7938      5.0808|
| 14:  2.0197 -  1.9705 0.61    778   95 0.1064 0.1708      4.7203      4.9228|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8763 -  4.7023  1391   158  0.94   8.74   0.98     0.97       6931.25|
|  2:  4.7023 -  3.7521  1343   144  0.95   8.21   1.02     1.00       9146.78|
|  3:  3.7521 -  3.2836  1316   152  0.93  11.59   1.03     1.02      11095.62|
|  4:  3.2836 -  2.9861  1313   136  0.92  14.10   1.01     1.00      10717.81|
|  5:  2.9861 -  2.7735  1286   147  0.90  16.33   0.99     0.96       8674.08|
|  6:  2.7735 -  2.6109  1291   142  0.89  16.86   0.98     0.95       7638.94|
|  7:  2.6109 -  2.4808  1280   149  0.90  15.88   0.99     0.96       6453.08|
|  8:  2.4808 -  2.3732  1301   135  0.90  15.91   1.00     0.97       5950.66|
|  9:  2.3732 -  2.2822  1272   148  0.90  16.69   1.01     0.98       5425.82|
| 10:  2.2822 -  2.2037  1267   141  0.90  16.41   1.00     0.96       4949.52|
| 11:  2.2037 -  2.1350  1251   141  0.90  16.02   1.00     0.97       4388.47|
| 12:  2.1350 -  2.0741  1284   140  0.91  15.10   1.01     0.99       3858.77|
| 13:  2.0741 -  2.0197  1257   131  0.90  16.65   1.01     1.00       3480.07|
| 14:  2.0197 -  1.9705   778    95  0.90  15.72   0.99     0.94       2896.58|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2896.58 max =        11095.62 mean =      6685.40|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.48|
|phase err.(test): min =        0.00 max =           87.64 mean =        13.84|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.679)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.80    78.48   14.95    None  None   None       |
|    all(noH): 2823   0      1.80    78.48   14.95    None  None   None       |
|    Sol.    : 438    0      3.52    71.15   37.25    None  None   None       |
|    Mac.    : 2385   0      1.80    78.48   10.86    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:     1.804 -   9.472: 1373   |   5:    40.141 -  47.809:   97        |
|      1:     9.472 -  17.139:  781   |   6:    47.809 -  55.476:   87        |
|      2:    17.139 -  24.807:  204   |   7:    55.476 -  63.143:   43        |
|      3:    24.807 -  32.474:  119   |   8:    63.143 -  70.811:   10        |
|      4:    32.474 -  40.141:  102   |   9:    70.811 -  78.478:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 325         
Filter by distance & map next to the model:
   mapped sites are within: 0.461 - 4.407
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 320 from: 325
   mapped sites are within: 0.721 - 4.407

peak=   10.691 closest distance to " CB  VAL A 230 " =    1.411
peak=    6.553 closest distance to " CG2 VAL A 296 " =    1.083
peak=    6.143 closest distance to " CG  LEU A   5 " =    1.230
peak=    5.807 closest distance to " CB  VAL A 296 " =    1.043
peak=    5.393 closest distance to " O   HOH Z 402 " =    1.589
peak=    5.392 closest distance to " NH2 ARG A  56 " =    2.225
peak=    5.252 closest distance to " CB  ARG A 275 " =    0.974
peak=    5.140 closest distance to " O   HOH Z 193 " =    1.806
peak=    5.093 closest distance to " O   HOH Z 124 " =    1.590
peak=    5.001 closest distance to " CB  GLN A 223 " =    1.385
peak=    4.955 closest distance to " CG  LEU A 228 " =    1.155
peak=    4.937 closest distance to " O   HOH Z 209 " =    2.285
peak=    4.929 closest distance to " O   HOH Z 403 " =    1.860
peak=    4.927 closest distance to " CG  PRO A  54 " =    1.255
peak=    4.924 closest distance to " CD1AILE A 234 " =    1.043
peak=    4.855 closest distance to " O   HOH Z 120 " =    1.022
peak=    4.836 closest distance to " CB  SER A  63 " =    1.141
peak=    4.830 closest distance to " O   HOH Z 272 " =    1.889
peak=    4.771 closest distance to " O   SER A  87 " =    2.260
peak=    4.733 closest distance to " O   HOH Z  80 " =    1.939
peak=    4.638 closest distance to " CG  PRO A 213 " =    1.212
peak=    4.616 closest distance to " O   HOH Z  85 " =    1.704
peak=    4.614 closest distance to " CB  GLN A 183 " =    1.296
peak=    4.596 closest distance to " CA  TYR A  30 " =    0.949
peak=    4.558 closest distance to " O   HOH Z 142 " =    1.618
peak=    4.550 closest distance to " O   HOH Z 414 " =    1.964
peak=    4.549 closest distance to " CD2 LEU A   5 " =    1.147
peak=    4.543 closest distance to " CB  PRO A  54 " =    0.896
peak=    4.499 closest distance to " O   HOH Z  54 " =    1.648
peak=    4.493 closest distance to " CB  VAL A 230 " =    1.196
peak=    4.487 closest distance to " O   HOH Z  48 " =    1.793
peak=    4.431 closest distance to " O   HOH Z 126 " =    1.888
peak=    4.424 closest distance to " CB  SER A   3 " =    1.261
peak=    4.394 closest distance to " NE2 GLN A  11 " =    1.020
peak=    4.391 closest distance to " O   HOH Z 232 " =    2.379
peak=    4.372 closest distance to " O   HOH Z 247 " =    1.360
peak=    4.357 closest distance to " C   PRO A 198 " =    1.480
peak=    4.338 closest distance to " O   HOH Z  59 " =    2.319
peak=    4.307 closest distance to " O   HOH Z 128 " =    2.235
peak=    4.301 closest distance to " O   HOH Z 234 " =    3.597
peak=    4.299 closest distance to " O   HOH Z 357 " =    1.978
peak=    4.298 closest distance to " O   HOH Z 316 " =    2.793
peak=    4.265 closest distance to " CB  TRP A 179 " =    1.176
peak=    4.246 closest distance to " CG  ARG A  66 " =    1.066
peak=    4.228 closest distance to " O   HOH Z 426 " =    1.466
peak=    4.225 closest distance to " O   HOH Z 423 " =    1.779
peak=    4.223 closest distance to " O   HOH Z 327 " =    1.735
peak=    4.165 closest distance to " O   HOH Z 278 " =    1.127
peak=    4.146 closest distance to " CB  GLU A 152 " =    1.089
peak=    4.140 closest distance to " O   HOH Z 154 " =    1.492
peak=    4.137 closest distance to " CD  ARG A 269 " =    1.113
peak=    4.128 closest distance to " CG  PRO A 198 " =    1.191
peak=    4.101 closest distance to " O   HOH Z 389 " =    1.880
peak=    4.084 closest distance to " CD2 LEU A 228 " =    1.244
peak=    4.082 closest distance to " O   HOH Z 368 " =    2.199
peak=    4.071 closest distance to " NZ  LYS A 117 " =    3.051
peak=    4.067 closest distance to " O   HOH Z 303 " =    2.140
peak=    4.061 closest distance to " CA  ALA A  21 " =    1.307
peak=    4.047 closest distance to " CB  SER A  26 " =    1.700
peak=    4.033 closest distance to " O   HOH Z 128 " =    1.832
peak=    4.029 closest distance to " O   HOH Z 227 " =    1.589
peak=    4.011 closest distance to " O   HOH Z 102 " =    1.330
peak=    4.011 closest distance to " O   HOH Z 420 " =    2.077
peak=    4.010 closest distance to " O   HOH Z 345 " =    2.681
peak=    4.006 closest distance to " O   HOH Z 189 " =    2.421
peak=    4.002 closest distance to " O   HOH Z 369 " =    2.200
peak=    3.996 closest distance to " CA  ARG A 275 " =    1.902
peak=    3.994 closest distance to " O   HOH Z 346 " =    1.479
peak=    3.992 closest distance to " CG1 ILE A  33 " =    1.254
peak=    3.992 closest distance to " O   HOH Z 134 " =    1.717
peak=    3.982 closest distance to " O   HOH Z 406 " =    1.620
peak=    3.977 closest distance to " O   HOH Z 130 " =    2.811
peak=    3.975 closest distance to " O   HOH Z  97 " =    1.893
peak=    3.974 closest distance to " CG1BVAL A  72 " =    1.656
peak=    3.970 closest distance to " CB  GLU A 277 " =    3.542
peak=    3.953 closest distance to " O   HOH Z 203 " =    1.741
peak=    3.952 closest distance to " OD1 ASN A  69 " =    2.583
peak=    3.952 closest distance to " O   HOH Z  47 " =    1.654
peak=    3.943 closest distance to " OE1 GLU A   2 " =    2.124
peak=    3.939 closest distance to " O   HOH Z 411 " =    3.424
peak=    3.912 closest distance to " CB  GLU A 128 " =    1.192
peak=    3.909 closest distance to " O   HOH Z 245 " =    1.417
peak=    3.908 closest distance to " CE  LYS A 119 " =    0.989
peak=    3.907 closest distance to " CG  PRO A 243 " =    1.177
peak=    3.887 closest distance to " O   HOH Z 156 " =    3.222
peak=    3.875 closest distance to " N   ASN A  39 " =    1.213
peak=    3.849 closest distance to " O   HOH Z  61 " =    1.547
peak=    3.848 closest distance to " O   HOH Z  68 " =    1.973
peak=    3.841 closest distance to " CA  LYS A 117 " =    1.352
peak=    3.838 closest distance to " O   HOH Z  48 " =    1.734
peak=    3.830 closest distance to " O   HOH Z  63 " =    2.286
peak=    3.821 closest distance to " O   ASP A 124 " =    1.278
peak=    3.821 closest distance to " O   HOH Z 193 " =    2.111
peak=    3.813 closest distance to " O   HOH Z 236 " =    1.879
peak=    3.807 closest distance to " CG2 ILE A  20 " =    1.371
peak=    3.802 closest distance to " O   HOH Z 417 " =    3.189
peak=    3.792 closest distance to " O   HOH Z  15 " =    2.238
peak=    3.784 closest distance to " O   HOH Z  44 " =    1.942
peak=    3.783 closest distance to " CB  PRO A 198 " =    1.107
peak=    3.780 closest distance to " O   HOH Z  97 " =    2.437
peak=    3.771 closest distance to " O   HOH Z 273 " =    2.840
peak=    3.761 closest distance to " CG2 THR A 221 " =    1.220
peak=    3.755 closest distance to " CA  ASN A 176 " =    1.043
peak=    3.744 closest distance to " O   HOH Z 298 " =    1.838
peak=    3.742 closest distance to " NH2 ARG A 156 " =    1.061
peak=    3.729 closest distance to " OD2 ASP A 286 " =    2.745
peak=    3.727 closest distance to " O   HOH Z  66 " =    2.093
peak=    3.710 closest distance to " O   HOH Z 345 " =    1.715
peak=    3.710 closest distance to " O   HOH Z 280 " =    2.642
peak=    3.703 closest distance to " O   HOH Z 271 " =    2.436
peak=    3.703 closest distance to " CB  ALA A 248 " =    1.356
peak=    3.702 closest distance to " O   HOH Z 419 " =    1.617
peak=    3.700 closest distance to " CB  ARG A  79 " =    1.432
peak=    3.697 closest distance to " O   HOH Z 421 " =    1.887
peak=    3.696 closest distance to " O   HOH Z 248 " =    1.699
peak=    3.696 closest distance to " CG  PRO A  90 " =    1.152
peak=    3.691 closest distance to " CB  ALA A   9 " =    1.630
peak=    3.690 closest distance to " O   HOH Z 344 " =    1.888
peak=    3.689 closest distance to " O   HOH Z 214 " =    2.590
peak=    3.684 closest distance to " CE1 HIS A 108 " =    1.169
peak=    3.682 closest distance to " CB  VAL A 265 " =    1.239
peak=    3.674 closest distance to " CB  TYR A 169 " =    0.742
peak=    3.672 closest distance to " CB  ASN A 148 " =    1.365
peak=    3.665 closest distance to " O   HOH Z 126 " =    2.134
peak=    3.664 closest distance to " CD2 TRP A 179 " =    1.375
peak=    3.664 closest distance to " O   HOH Z 147 " =    1.833
peak=    3.663 closest distance to " O   HOH Z 367 " =    3.414
peak=    3.661 closest distance to " CG  GLN A  58 " =    2.592
peak=    3.647 closest distance to " CB  ASN A  39 " =    0.812
peak=    3.639 closest distance to " OG BSER A 164 " =    2.173
peak=    3.637 closest distance to " O   HOH Z  48 " =    1.686
peak=    3.633 closest distance to " CD  ARG A 159 " =    0.751
peak=    3.619 closest distance to " CB  VAL A 202 " =    1.456
peak=    3.619 closest distance to " O   HOH Z  48 " =    2.374
peak=    3.619 closest distance to " OG1 THR A 294 " =    2.278
peak=    3.612 closest distance to " O   HOH Z  40 " =    1.736
peak=    3.609 closest distance to " O   HOH Z 416 " =    2.799
peak=    3.607 closest distance to " CD  LYS A 166 " =    1.355
peak=    3.606 closest distance to " O   HOH Z  21 " =    1.832
peak=    3.602 closest distance to " CA  VAL A  41 " =    0.862
peak=    3.600 closest distance to " O   HOH Z 166 " =    1.462
peak=    3.597 closest distance to " O   HOH Z 197 " =    2.394
peak=    3.594 closest distance to " CG  GLN A  77 " =    2.297
peak=    3.591 closest distance to " CB  ARG A 139 " =    0.873
peak=    3.591 closest distance to " O   HOH Z  78 " =    1.681
peak=    3.590 closest distance to " CG2 ILE A 120 " =    1.275
peak=    3.586 closest distance to " NH2BARG A 145 " =    2.204
peak=    3.585 closest distance to " CZ AARG A 102 " =    1.728
peak=    3.583 closest distance to " CG2AVAL A 121 " =    2.042
peak=    3.578 closest distance to " OG  SER A 276 " =    1.415
peak=    3.576 closest distance to " O   HOH Z 253 " =    1.547
peak=    3.575 closest distance to " O   HOH Z 425 " =    2.162
peak=    3.572 closest distance to " CB  TRP A 266 " =    1.087
peak=    3.561 closest distance to " OE1 GLN A  11 " =    1.792
peak=    3.560 closest distance to " O   HOH Z 366 " =    2.912
peak=    3.557 closest distance to " O   HOH Z 334 " =    1.409
peak=    3.554 closest distance to " O   HOH Z 250 " =    1.397
peak=    3.553 closest distance to " CA  ARG A  36 " =    1.093
peak=    3.547 closest distance to " ND2 ASN A 187 " =    1.580
peak=    3.544 closest distance to " O   GLY A  23 " =    2.285
peak=    3.543 closest distance to " CG2 ILE A 106 " =    0.796
peak=    3.530 closest distance to " O   HOH Z 261 " =    2.035
peak=    3.529 closest distance to " CA  ALA A  51 " =    1.041
peak=    3.527 closest distance to " CB  ALA A 100 " =    1.180
peak=    3.522 closest distance to " O   HOH Z 250 " =    1.576
peak=    3.521 closest distance to " O   HOH Z  43 " =    1.329
peak=    3.518 closest distance to " O   HOH Z 344 " =    2.794
peak=    3.518 closest distance to " O   HOH Z 284 " =    2.907
peak=    3.507 closest distance to " CB  ARG A 190 " =    1.692
peak=    3.500 closest distance to " O   HOH Z 194 " =    2.133
peak=    3.500 closest distance to " CA  ARG A 195 " =    1.308
peak=    3.496 closest distance to " CA  ASP A 191 " =    1.121
peak=    3.494 closest distance to " O   HOH Z 394 " =    1.492
peak=    3.488 closest distance to " O   HOH Z 295 " =    1.508
peak=    3.486 closest distance to " O   HOH Z 261 " =    2.043
peak=    3.478 closest distance to " CG1 VAL A 296 " =    1.150
peak=    3.475 closest distance to " CE1 TYR A 186 " =    1.268
peak=    3.472 closest distance to " CD1 LEU A  96 " =    0.721
peak=    3.470 closest distance to " O   HOH Z 408 " =    1.633
peak=    3.466 closest distance to " CB  THR A  31 " =    1.633
peak=    3.465 closest distance to " O   HOH Z 109 " =    2.329
peak=    3.462 closest distance to " CD2 HIS A  81 " =    1.165
peak=    3.458 closest distance to " O   HOH Z 185 " =    1.622
peak=    3.451 closest distance to " CA  ASP A 140 " =    1.160
peak=    3.443 closest distance to " O   HOH Z 383 " =    1.900
peak=    3.441 closest distance to " O   HOH Z 132 " =    2.691
peak=    3.439 closest distance to " CD2 TYR A  30 " =    0.836
peak=    3.423 closest distance to " OD2 ASP A 298 " =    3.967
peak=    3.419 closest distance to " O   HOH Z 412 " =    3.895
peak=    3.416 closest distance to " O   HOH Z  39 " =    2.699
peak=    3.415 closest distance to " O   HOH Z 155 " =    1.554
peak=    3.406 closest distance to " O   HOH Z  88 " =    3.187
peak=    3.403 closest distance to " CB  THR A  52 " =    0.985
peak=    3.402 closest distance to " O   HOH Z 155 " =    2.926
peak=    3.401 closest distance to " O   HOH Z 260 " =    1.469
peak=    3.401 closest distance to " O   HOH Z 374 " =    2.525
peak=    3.400 closest distance to " CB  TYR A 247 " =    0.952
peak=    3.397 closest distance to " CB  SER A 141 " =    1.050
peak=    3.394 closest distance to " O   HOH Z 163 " =    1.327
peak=    3.394 closest distance to " O   HOH Z 148 " =    3.137
peak=    3.391 closest distance to " CD BLYS A 290 " =    1.075
peak=    3.390 closest distance to " CA  ARG A  66 " =    0.991
peak=    3.389 closest distance to " O   HOH Z  19 " =    1.991
peak=    3.388 closest distance to " OD1 ASP A 286 " =    1.805
peak=    3.388 closest distance to " O   HOH Z 422 " =    2.578
peak=    3.383 closest distance to " O   HOH Z 322 " =    2.172
peak=    3.381 closest distance to " O   HOH Z 145 " =    2.519
peak=    3.379 closest distance to " O   HOH Z 251 " =    1.694
peak=    3.379 closest distance to " CZ  PHE A  38 " =    1.349
peak=    3.374 closest distance to " CA  ALA A 295 " =    1.092
peak=    3.374 closest distance to " CA  GLY A  80 " =    0.997
peak=    3.369 closest distance to " OH  TYR A 116 " =    1.168
peak=    3.369 closest distance to " NH2AARG A 145 " =    2.257
peak=    3.366 closest distance to " O   HOH Z 197 " =    1.936
peak=    3.361 closest distance to " OD1 ASN A  60 " =    1.724
peak=    3.358 closest distance to " O   HOH Z  71 " =    2.050
peak=    3.357 closest distance to " CD  LYS A 119 " =    1.879
peak=    3.355 closest distance to " O   HOH Z 263 " =    1.480
peak=    3.353 closest distance to " CG  MET A 185 " =    1.156
peak=    3.353 closest distance to " NH2 ARG A  79 " =    1.326
peak=    3.351 closest distance to " CB  ALA A   1 " =    1.249
peak=    3.349 closest distance to " O   HOH Z 281 " =    4.407
peak=    3.343 closest distance to " O   ALA A 165 " =    1.318
peak=    3.339 closest distance to " CA  ALA A 158 " =    1.252
peak=    3.338 closest distance to " O   HOH Z 214 " =    2.339
peak=    3.337 closest distance to " O   HOH Z 427 " =    2.612
peak=    3.333 closest distance to " C   ILE A 106 " =    1.811
peak=    3.330 closest distance to " O   HOH Z 136 " =    1.272
peak=    3.328 closest distance to " O   HOH Z 112 " =    1.693
peak=    3.326 closest distance to " O   HOH Z 227 " =    1.559
peak=    3.322 closest distance to " O   HOH Z 261 " =    1.878
peak=    3.316 closest distance to " O   HOH Z 438 " =    2.389
peak=    3.308 closest distance to " O   HOH Z 227 " =    2.173
peak=    3.307 closest distance to " O   HOH Z 435 " =    1.788
peak=    3.304 closest distance to " CG AARG A 275 " =    1.105
peak=    3.302 closest distance to " CB  ALA A 295 " =    1.121
peak=    3.302 closest distance to " O   HOH Z 162 " =    1.591
peak=    3.299 closest distance to " O   HOH Z 279 " =    1.172
peak=    3.299 closest distance to " O   HOH Z 404 " =    2.103
peak=    3.298 closest distance to " CB  SER A 273 " =    0.819
peak=    3.295 closest distance to " O   HOH Z  66 " =    1.716
peak=    3.291 closest distance to " CB  GLN A 278 " =    0.870
peak=    3.288 closest distance to " CB  ASN A 215 " =    1.080
peak=    3.282 closest distance to " C   ALA A   1 " =    1.727
peak=    3.270 closest distance to " O   ALA A 158 " =    1.286
peak=    3.267 closest distance to " CH2 TRP A 274 " =    2.093
peak=    3.265 closest distance to " CB  MET A  47 " =    1.178
peak=    3.265 closest distance to " NZ  LYS A  76 " =    1.818
peak=    3.262 closest distance to " O   HOH Z 299 " =    4.251
peak=    3.262 closest distance to " CG2 VAL A 197 " =    1.076
peak=    3.260 closest distance to " O   HOH Z 215 " =    1.504
peak=    3.257 closest distance to " O   HOH Z 158 " =    2.967
peak=    3.256 closest distance to " CG1 VAL A 153 " =    1.044
peak=    3.252 closest distance to " O   HOH Z 380 " =    2.085
peak=    3.245 closest distance to " O   HOH Z 162 " =    1.980
peak=    3.245 closest distance to " O   HOH Z 130 " =    1.097
peak=    3.243 closest distance to " O   HOH Z 329 " =    3.831
peak=    3.241 closest distance to " O   HOH Z 411 " =    1.773
peak=    3.241 closest distance to " CG2 ILE A 234 " =    2.055
peak=    3.240 closest distance to " O   HOH Z 337 " =    3.666
peak=    3.225 closest distance to " CB  ARG A 259 " =    1.880
peak=    3.224 closest distance to " N   SER A 135 " =    1.233
peak=    3.220 closest distance to " NH1AARG A 145 " =    1.103
peak=    3.218 closest distance to " CA  GLN A 194 " =    1.103
peak=    3.215 closest distance to " CA  CYS A 260 " =    1.764
peak=    3.215 closest distance to " CE  MET A 105 " =    2.368
peak=    3.213 closest distance to " CB  SER A  62 " =    0.826
peak=    3.200 closest distance to " O   HOH Z 299 " =    2.196
peak=    3.200 closest distance to " N   GLU A 236 " =    1.027
peak=    3.199 closest distance to " CB  GLN A 205 " =    1.200
peak=    3.198 closest distance to " O   ILE A  33 " =    1.268
peak=    3.195 closest distance to " O   HOH Z 131 " =    2.466
peak=    3.193 closest distance to " O   HOH Z  88 " =    2.607
peak=    3.191 closest distance to " CG2 THR A 294 " =    1.503
peak=    3.189 closest distance to " O   HOH Z 353 " =    2.766
peak=    3.187 closest distance to " O   HOH Z 359 " =    1.627
peak=    3.182 closest distance to " NH1 ARG A 269 " =    0.866
peak=    3.180 closest distance to " O   HOH Z   1 " =    2.011
peak=    3.179 closest distance to " O   HOH Z 271 " =    1.421
peak=    3.178 closest distance to " CA  VAL A 126 " =    0.943
peak=    3.178 closest distance to " NZ  LYS A 166 " =    2.872
peak=    3.174 closest distance to " CG1 ILE A  49 " =    1.531
peak=    3.173 closest distance to " CB  ALA A 137 " =    1.235
peak=    3.172 closest distance to " CD  GLN A 194 " =    1.504
peak=    3.170 closest distance to " O   HOH Z 222 " =    2.478
peak=    3.168 closest distance to " O   HOH Z 236 " =    1.547
peak=    3.165 closest distance to " O   HOH Z 189 " =    2.802
peak=    3.158 closest distance to " O   HOH Z 361 " =    3.346
peak=    3.158 closest distance to " CA  ALA A 291 " =    0.882
peak=    3.154 closest distance to " O   HOH Z 279 " =    2.031
peak=    3.152 closest distance to " OG BSER A 210 " =    1.299
peak=    3.147 closest distance to " O   HOH Z 387 " =    1.960
peak=    3.145 closest distance to " O   HOH Z 364 " =    2.255
peak=    3.138 closest distance to " O   HOH Z 192 " =    1.840
peak=    3.130 closest distance to " O   HOH Z  90 " =    3.443
peak=    3.129 closest distance to " CA  LYS A 290 " =    1.083
peak=    3.127 closest distance to " CA  ASN A 215 " =    1.156
peak=    3.126 closest distance to " OG  SER A 245 " =    1.479
peak=    3.126 closest distance to " NH1 ARG A  14 " =    1.153
peak=    3.122 closest distance to " CD1 LEU A 101 " =    1.224
peak=    3.121 closest distance to " O   THR A  31 " =    1.508
peak=    3.120 closest distance to " OG  SER A  22 " =    2.701
peak=    3.119 closest distance to " OG BSER A 258 " =    3.165
peak=    3.119 closest distance to " O  BHOH Z  74 " =    1.493
peak=    3.112 closest distance to " OG  SER A  62 " =    2.866
peak=    3.109 closest distance to " O   HOH Z  46 " =    1.430
peak=    3.106 closest distance to " O   HOH Z 380 " =    1.917
peak=    3.100 closest distance to " O   HOH Z 387 " =    2.429
peak=    3.094 closest distance to " CA  ASN A 176 " =    1.241
peak=    3.088 closest distance to " OG BSER A 164 " =    1.934
peak=    3.086 closest distance to " CB  ALA A 291 " =    1.273
peak=    3.081 closest distance to " CB  ALA A 242 " =    1.014
peak=    3.078 closest distance to " CB  ASN A 148 " =    1.957
peak=    3.077 closest distance to " CB  ILE A 120 " =    1.701
peak=    3.069 closest distance to " NE1 TRP A 274 " =    0.898
peak=    3.065 closest distance to " CB  ALA A  71 " =    1.247
peak=    3.060 closest distance to " OD1 ASN A  45 " =    1.394
peak=    3.046 closest distance to " CA  ALA A 248 " =    1.041
peak=    3.043 closest distance to " O   HOH Z 110 " =    1.292
peak=    3.028 closest distance to " C   SER A  32 " =    1.093

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 212         
Filter by distance & map next to the model:
   mapped sites are within: 0.544 - 5.497
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 209 from: 212
   mapped sites are within: 0.791 - 5.497

peak=   -4.778 closest distance to " CG2 VAL A 230 " =    0.791
peak=   -4.629 closest distance to " CD  ARG A 156 " =    2.069
peak=   -4.426 closest distance to " O   PRO A 163 " =    2.076
peak=   -4.426 closest distance to " O   HOH Z 266 " =    4.393
peak=   -4.422 closest distance to " O   HOH Z  13 " =    1.729
peak=   -4.417 closest distance to " C   HIS A 108 " =    1.161
peak=   -4.349 closest distance to " O   HOH Z 166 " =    1.797
peak=   -4.202 closest distance to " CD1 LEU A 101 " =    2.501
peak=   -4.081 closest distance to " SG  CYS A 254 " =    3.178
peak=   -4.068 closest distance to " O   VAL A  67 " =    2.645
peak=   -4.051 closest distance to " N   ALA A 248 " =    1.750
peak=   -4.047 closest distance to " O   HOH Z 426 " =    1.759
peak=   -4.044 closest distance to " O   VAL A  67 " =    2.650
peak=   -4.017 closest distance to " OXT GLY A 302 " =    2.749
peak=   -4.004 closest distance to " CG  ASP A 231 " =    0.856
peak=   -3.997 closest distance to " C   THR A 279 " =    1.170
peak=   -3.988 closest distance to " O   HOH Z 196 " =    2.219
peak=   -3.970 closest distance to " O   HOH Z 231 " =    2.160
peak=   -3.929 closest distance to " O   HOH Z 377 " =    1.635
peak=   -3.925 closest distance to " OG BSER A 134 " =    1.362
peak=   -3.908 closest distance to " O   HOH Z  11 " =    1.847
peak=   -3.895 closest distance to " CD2 TYR A  30 " =    2.738
peak=   -3.893 closest distance to " CD1 PHE A  59 " =    1.936
peak=   -3.892 closest distance to " O   HOH Z 210 " =    0.878
peak=   -3.868 closest distance to " O   HOH Z 165 " =    1.898
peak=   -3.852 closest distance to " O   ASN A  45 " =    1.812
peak=   -3.840 closest distance to " CD  GLN A  58 " =    1.293
peak=   -3.832 closest distance to " OG ASER A 134 " =    1.153
peak=   -3.810 closest distance to " O   HOH Z 290 " =    0.968
peak=   -3.788 closest distance to " O   HOH Z 351 " =    1.434
peak=   -3.778 closest distance to " O   HOH Z  71 " =    1.473
peak=   -3.765 closest distance to " N   GLN A  58 " =    1.833
peak=   -3.761 closest distance to " CD2 LEU A 300 " =    2.668
peak=   -3.759 closest distance to " ND2 ASN A 187 " =    1.623
peak=   -3.758 closest distance to " O   HOH Z 407 " =    2.902
peak=   -3.753 closest distance to " CZ  TYR A 169 " =    1.816
peak=   -3.751 closest distance to " O   PRO A 198 " =    1.296
peak=   -3.744 closest distance to " CB  ALA A 161 " =    2.498
peak=   -3.742 closest distance to " CD1 LEU A 255 " =    2.676
peak=   -3.740 closest distance to " CB  ALA A 248 " =    1.879
peak=   -3.737 closest distance to " NE2 GLN A  88 " =    1.108
peak=   -3.731 closest distance to " CH2 TRP A 179 " =    1.253
peak=   -3.717 closest distance to " O   PHE A 218 " =    1.561
peak=   -3.696 closest distance to " ND2 ASN A  69 " =    1.434
peak=   -3.660 closest distance to " C   ALA A 158 " =    1.194
peak=   -3.655 closest distance to " O   HOH Z 118 " =    3.373
peak=   -3.646 closest distance to " O   HOH Z 166 " =    1.441
peak=   -3.624 closest distance to " CB  ALA A 291 " =    2.332
peak=   -3.614 closest distance to " O   HOH Z  37 " =    1.893
peak=   -3.614 closest distance to " CD  LYS A 289 " =    2.454
peak=   -3.613 closest distance to " O   ALA A 256 " =    1.416
peak=   -3.604 closest distance to " N   ALA A 226 " =    1.931
peak=   -3.567 closest distance to " O   ALA A   1 " =    1.883
peak=   -3.566 closest distance to " N   VAL A 189 " =    1.604
peak=   -3.564 closest distance to " CA  ASP A 298 " =    1.055
peak=   -3.561 closest distance to " CB  PHE A 192 " =    2.008
peak=   -3.558 closest distance to " O   HOH Z 191 " =    5.497
peak=   -3.553 closest distance to " C   VAL A 265 " =    0.845
peak=   -3.548 closest distance to " O   HOH Z  92 " =    1.629
peak=   -3.539 closest distance to " ND2 ASN A  39 " =    1.149
peak=   -3.535 closest distance to " CG  GLN A 223 " =    2.429
peak=   -3.523 closest distance to " O   HOH Z 283 " =    1.806
peak=   -3.515 closest distance to " O   HOH Z 166 " =    2.288
peak=   -3.513 closest distance to " CE  MET A 105 " =    1.929
peak=   -3.511 closest distance to " O   MET A  40 " =    2.766
peak=   -3.510 closest distance to " OG BSER A 134 " =    1.635
peak=   -3.506 closest distance to " ND2 ASN A  45 " =    0.992
peak=   -3.498 closest distance to " N   SER A 276 " =    1.415
peak=   -3.498 closest distance to " C   LEU A 143 " =    1.057
peak=   -3.496 closest distance to " CG  GLU A  53 " =    1.423
peak=   -3.496 closest distance to " OG  SER A  97 " =    2.240
peak=   -3.493 closest distance to " O   HOH Z 311 " =    3.455
peak=   -3.491 closest distance to " C   GLY A  91 " =    1.307
peak=   -3.490 closest distance to " O   HOH Z  17 " =    1.171
peak=   -3.483 closest distance to " O   HOH Z 353 " =    2.124
peak=   -3.482 closest distance to " CG  GLN A  11 " =    1.891
peak=   -3.477 closest distance to " CE3 TRP A 150 " =    2.225
peak=   -3.471 closest distance to " CB  PHE A 208 " =    2.227
peak=   -3.469 closest distance to " O   SER A  95 " =    1.654
peak=   -3.469 closest distance to " C   GLY A  80 " =    2.422
peak=   -3.468 closest distance to " CB  ALA A 248 " =    2.162
peak=   -3.466 closest distance to " CD  ARG A 195 " =    5.091
peak=   -3.463 closest distance to " N   THR A 235 " =    1.298
peak=   -3.453 closest distance to " CD1 LEU A 228 " =    2.191
peak=   -3.450 closest distance to " O   HOH Z  44 " =    2.084
peak=   -3.447 closest distance to " NE2 GLN A 103 " =    1.692
peak=   -3.444 closest distance to " O   HOH Z 250 " =    1.347
peak=   -3.444 closest distance to " O   SER A 146 " =    0.944
peak=   -3.444 closest distance to " CD1 TYR A 247 " =    2.384
peak=   -3.436 closest distance to " O   HOH Z 193 " =    1.515
peak=   -3.426 closest distance to " NH2 ARG A  66 " =    1.456
peak=   -3.425 closest distance to " CD  ARG A 139 " =    1.584
peak=   -3.423 closest distance to " O   ALA A 160 " =    1.395
peak=   -3.422 closest distance to " CD1 PHE A  59 " =    2.162
peak=   -3.422 closest distance to " O   ARG A 219 " =    1.835
peak=   -3.405 closest distance to " O   GLY A 196 " =    1.089
peak=   -3.404 closest distance to " NE2 GLN A 194 " =    1.713
peak=   -3.403 closest distance to " CG2 THR A 182 " =    2.212
peak=   -3.401 closest distance to " O   HOH Z 126 " =    1.869
peak=   -3.400 closest distance to " O   ASN A 187 " =    1.481
peak=   -3.399 closest distance to " O   HOH Z  43 " =    1.957
peak=   -3.396 closest distance to " CD1 LEU A  25 " =    2.436
peak=   -3.395 closest distance to " CG  ASP A  50 " =    2.446
peak=   -3.390 closest distance to " OXT GLY A 302 " =    3.566
peak=   -3.386 closest distance to " O   SER A 210 " =    1.819
peak=   -3.386 closest distance to " O   HOH Z  56 " =    2.242
peak=   -3.382 closest distance to " N   GLY A 133 " =    1.903
peak=   -3.382 closest distance to " CD  GLN A 223 " =    0.800
peak=   -3.381 closest distance to " CB  LEU A  83 " =    2.363
peak=   -3.378 closest distance to " N   SER A 206 " =    1.827
peak=   -3.377 closest distance to " CB  ASN A  39 " =    2.204
peak=   -3.376 closest distance to " OD2 ASP A 191 " =    1.515
peak=   -3.373 closest distance to " CD2 LEU A 237 " =    2.636
peak=   -3.373 closest distance to " N   THR A 157 " =    1.502
peak=   -3.372 closest distance to " NH2AARG A 275 " =    4.863
peak=   -3.372 closest distance to " O   HOH Z 234 " =    4.132
peak=   -3.369 closest distance to " NE2 GLN A  88 " =    2.008
peak=   -3.365 closest distance to " CG  GLU A   2 " =    1.746
peak=   -3.361 closest distance to " O   HOH Z 171 " =    2.005
peak=   -3.358 closest distance to " CA  GLY A 203 " =    2.246
peak=   -3.354 closest distance to " CG1 VAL A 112 " =    2.642
peak=   -3.351 closest distance to " O   HOH Z  60 " =    2.448
peak=   -3.349 closest distance to " CB  ALA A  43 " =    2.382
peak=   -3.348 closest distance to " NH2 ARG A  79 " =    1.949
peak=   -3.343 closest distance to " O   HOH Z 313 " =    1.307
peak=   -3.339 closest distance to " CG2 ILE A 263 " =    2.267
peak=   -3.338 closest distance to " O   HOH Z 193 " =    1.780
peak=   -3.333 closest distance to " CE  LYS A 166 " =    2.942
peak=   -3.333 closest distance to " O   TRP A  92 " =    1.898
peak=   -3.331 closest distance to " O   HOH Z 120 " =    1.090
peak=   -3.314 closest distance to " CG  GLU A 277 " =    1.133
peak=   -3.310 closest distance to " CG  LYS A 193 " =    2.238
peak=   -3.310 closest distance to " N   ARG A  66 " =    1.735
peak=   -3.310 closest distance to " O   HOH Z 136 " =    2.149
peak=   -3.307 closest distance to " O   HOH Z 172 " =    4.970
peak=   -3.307 closest distance to " C   SER A 206 " =    1.674
peak=   -3.304 closest distance to " CG2 VAL A 197 " =    2.219
peak=   -3.298 closest distance to " O   HOH Z 388 " =    1.991
peak=   -3.292 closest distance to " O   ALA A 161 " =    1.651
peak=   -3.287 closest distance to " CA  VAL A 296 " =    1.012
peak=   -3.286 closest distance to " O   HOH Z   6 " =    1.801
peak=   -3.285 closest distance to " O   HOH Z 265 " =    2.103
peak=   -3.284 closest distance to " O   HOH Z 414 " =    2.476
peak=   -3.283 closest distance to " OG  SER A  26 " =    1.298
peak=   -3.282 closest distance to " O   HOH Z 150 " =    1.785
peak=   -3.277 closest distance to " O   HOH Z 397 " =    1.200
peak=   -3.274 closest distance to " O   ASN A  69 " =    1.275
peak=   -3.274 closest distance to " O   HOH Z  48 " =    1.348
peak=   -3.272 closest distance to " CD2 TYR A 293 " =    1.942
peak=   -3.271 closest distance to " O   ALA A  10 " =    1.826
peak=   -3.270 closest distance to " OD1 ASN A 148 " =    1.528
peak=   -3.265 closest distance to " O   HOH Z 377 " =    1.719
peak=   -3.262 closest distance to " O   GLY A  80 " =    2.592
peak=   -3.259 closest distance to " O   LEU A 228 " =    2.410
peak=   -3.244 closest distance to " OG1 THR A  82 " =    1.288
peak=   -3.239 closest distance to " O   HOH Z  61 " =    1.524
peak=   -3.238 closest distance to " O   HOH Z 131 " =    4.069
peak=   -3.237 closest distance to " OD2 ASP A  50 " =    1.325
peak=   -3.237 closest distance to " O   HOH Z 422 " =    1.475
peak=   -3.236 closest distance to " CG2 VAL A 296 " =    1.490
peak=   -3.234 closest distance to " O   HOH Z 301 " =    2.255
peak=   -3.230 closest distance to " O   HOH Z  15 " =    1.533
peak=   -3.229 closest distance to " N   VAL A 230 " =    1.034
peak=   -3.226 closest distance to " OD1 ASN A  39 " =    2.128
peak=   -3.224 closest distance to " O   HOH Z 423 " =    2.276
peak=   -3.221 closest distance to " CB  ASN A  69 " =    0.954
peak=   -3.220 closest distance to " O   HOH Z 174 " =    4.287
peak=   -3.218 closest distance to " O   HOH Z  10 " =    1.598
peak=   -3.216 closest distance to " CG1 VAL A 296 " =    1.158
peak=   -3.216 closest distance to " O   HOH Z 389 " =    1.628
peak=   -3.202 closest distance to " CD  GLN A  88 " =    0.895
peak=   -3.198 closest distance to " O   HOH Z  11 " =    1.767
peak=   -3.198 closest distance to " O   HOH Z 211 " =    1.573
peak=   -3.189 closest distance to " CD  GLN A 103 " =    1.349
peak=   -3.184 closest distance to " O   VAL A 197 " =    1.379
peak=   -3.183 closest distance to " O  BHOH Z 338 " =    1.353
peak=   -3.179 closest distance to " NH1 ARG A  66 " =    5.039
peak=   -3.175 closest distance to " O   HOH Z 174 " =    2.151
peak=   -3.168 closest distance to " OD1 ASN A 249 " =    1.985
peak=   -3.167 closest distance to " O   HOH Z 310 " =    1.560
peak=   -3.166 closest distance to " NH2 ARG A  66 " =    4.793
peak=   -3.165 closest distance to " O   VAL A 174 " =    1.923
peak=   -3.164 closest distance to " O   HOH Z  78 " =    1.591
peak=   -3.161 closest distance to " N   ASP A 270 " =    1.550
peak=   -3.154 closest distance to " O   ALA A  51 " =    1.440
peak=   -3.147 closest distance to " OD2 ASP A 171 " =    2.386
peak=   -3.146 closest distance to " O   HOH Z 411 " =    1.575
peak=   -3.140 closest distance to " CD2 LEU A 167 " =    1.717
peak=   -3.138 closest distance to " O   HOH Z 313 " =    2.085
peak=   -3.130 closest distance to " O   SER A   3 " =    1.104
peak=   -3.129 closest distance to " O   HOH Z 137 " =    1.857
peak=   -3.126 closest distance to " O   HOH Z 154 " =    1.482
peak=   -3.125 closest distance to " O   ALA A  34 " =    2.466
peak=   -3.118 closest distance to " O   HOH Z 139 " =    3.299
peak=   -3.105 closest distance to " CD  GLN A  73 " =    2.203
peak=   -3.102 closest distance to " OD1 ASN A 301 " =    1.959
peak=   -3.099 closest distance to " CA  TYR A  68 " =    2.989
peak=   -3.089 closest distance to " C   ASN A 148 " =    0.947
peak=   -3.087 closest distance to " OG  SER A   3 " =    1.459
peak=   -3.080 closest distance to " OD1 ASP A 191 " =    1.434
peak=   -3.077 closest distance to " CB  PRO A 243 " =    2.657
peak=   -3.075 closest distance to " CG  GLN A  11 " =    1.232
peak=   -3.073 closest distance to " CD  ARG A 259 " =    2.455
peak=   -3.057 closest distance to " O   HOH Z 310 " =    3.469
peak=   -3.055 closest distance to " O   HOH Z 297 " =    2.738
peak=   -3.053 closest distance to " O   HOH Z 185 " =    2.330
peak=   -3.037 closest distance to " O   PRO A 198 " =    1.244
peak=   -3.020 closest distance to " CG  ARG A 269 " =    2.185
peak=   -3.000 closest distance to " SG  CYS A 254 " =    2.466

================= 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    :  0.4878 0.4779   6.286192e+00   6.275410e+00
   1_bss:  0.4802 0.4693   6.281541e+00   6.268288e+00
   1_xyz:  0.3997 0.4182   6.175405e+00   6.207001e+00
   1_adp:  0.3560 0.3968   6.103561e+00   6.181338e+00
   1_occ:  0.3552 0.3965   6.102484e+00   6.181094e+00
   2_bss:  0.3532 0.3925   6.103656e+00   6.180756e+00
   2_xyz:  0.2551 0.3064   5.840854e+00   5.990515e+00
   2_adp:  0.2248 0.2801   5.740027e+00   5.910610e+00
   2_occ:  0.2245 0.2798   5.739268e+00   5.910189e+00
   3_bss:  0.2214 0.2778   5.736739e+00   5.906601e+00
   3_xyz:  0.1626 0.2081   5.457201e+00   5.658118e+00
   3_adp:  0.1518 0.1924   5.383505e+00   5.576439e+00
   3_occ:  0.1514 0.1925   5.382536e+00   5.576137e+00
   4_bss:  0.1513 0.1922   5.383355e+00   5.575039e+00
   4_xyz:  0.1233 0.1652   5.212551e+00   5.433428e+00
   4_adp:  0.1200 0.1638   5.193967e+00   5.423864e+00
   4_occ:  0.1198 0.1637   5.192891e+00   5.423230e+00
   5_bss:  0.1201 0.1636   5.194119e+00   5.423806e+00
   5_xyz:  0.1163 0.1607   5.174713e+00   5.411310e+00
   5_adp:  0.1137 0.1611   5.164778e+00   5.412973e+00
   5_occ:  0.1136 0.1612   5.164723e+00   5.413156e+00
   5_bss:  0.1136 0.1612   5.164685e+00   5.413282e+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:  0.359  20.000   7.058  10.158   7.821   0.000   0.000   0.000
   1_xyz:  0.359  20.000   7.058  10.158   7.821   0.000   0.000   0.000
   1_adp:  0.359  20.000   7.058  10.158   7.821   0.000   0.000   0.000
   1_occ:  0.359  20.000   7.058  10.158   7.821   0.000   0.000   0.000
   2_bss:  0.318  31.650   3.675   6.333   5.106   0.000   0.000   0.000
   2_xyz:  0.318  31.650   3.675   6.333   5.106   0.000   0.000   0.000
   2_adp:  0.318  31.650   3.675   6.333   5.106   0.000   0.000   0.000
   2_occ:  0.318  31.650   3.675   6.333   5.106   0.000   0.000   0.000
   3_bss:  0.327  43.781   1.834   3.786   3.229   0.000   0.000   0.000
   3_xyz:  0.327  43.781   1.834   3.786   3.229   0.000   0.000   0.000
   3_adp:  0.327  43.781   1.834   3.786   3.229   0.000   0.000   0.000
   3_occ:  0.327  43.781   1.834   3.786   3.229   0.000   0.000   0.000
   4_bss:  0.326  39.926   0.930   2.512   2.318   0.000   0.000   0.000
   4_xyz:  0.326  39.926   0.930   2.512   2.318   0.000   0.000   0.000
   4_adp:  0.326  39.926   0.930   2.512   2.318   0.000   0.000   0.000
   4_occ:  0.326  39.926   0.930   2.512   2.318   0.000   0.000   0.000
   5_bss:  0.322  39.926   0.813   2.123   2.191   0.000   0.000   0.000
   5_xyz:  0.322  39.926   0.813   2.123   2.191   0.000   0.000   0.000
   5_adp:  0.322  39.926   0.813   2.123   2.191   0.000   0.000   0.000
   5_occ:  0.322  39.926   0.813   2.123   2.191   0.000   0.000   0.000
   5_bss:  0.324  44.028  -0.856   0.374   0.482   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  58.482 0.4137  0.4800    71272.579
   1_bss:  58.771 0.4078  0.6003    68900.676
   1_xyz:  50.032 0.5177  0.7511    52172.529
   1_adp:  45.730 0.5720  0.8748    46405.579
   1_occ:  45.643 0.5731  0.8749    46255.049
   2_bss:  45.394 0.5761  0.7843    45855.559
   2_xyz:  32.886 0.7242  0.9673    25683.774
   2_adp:  28.868 0.7699  1.0068    20940.310
   2_occ:  28.834 0.7703  1.0070    20905.470
   3_bss:  28.669 0.7719  0.9357    20678.687
   3_xyz:  20.288 0.8585  0.9998    11215.126
   3_adp:  18.080 0.8802  1.0141     9513.603
   3_occ:  18.069 0.8803  1.0143     9509.818
   4_bss:  18.033 0.8806  0.9768     9473.209
   4_xyz:  15.039 0.9063  0.9882     7047.059
   4_adp:  14.808 0.9084  0.9882     6956.590
   4_occ:  14.792 0.9086  0.9881     6950.371
   5_bss:  14.817 0.9084  0.9800     6975.882
   5_xyz:  14.420 0.9119  0.9802     6710.649
   5_adp:  14.419 0.9120  0.9745     6674.742
   5_occ:  14.419 0.9120  0.9744     6679.891
   5_bss:  14.419 0.9120  0.9780     6684.144
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3328e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3328e+01
   1_xyz:   1.801  0.014  0.113 18.289  0.007  4.109   1.5754e-01
   1_adp:   1.801  0.014  0.113 18.289  0.007  4.109   1.5754e-01
   1_occ:   1.801  0.014  0.113 18.289  0.007  4.109   1.5754e-01
   2_bss:   1.801  0.014  0.113 18.289  0.007  4.109   1.5754e-01
   2_xyz:   1.256  0.010  0.088 16.419  0.006  4.108   9.3188e-02
   2_adp:   1.256  0.010  0.088 16.419  0.006  4.108   9.3188e-02
   2_occ:   1.256  0.010  0.088 16.419  0.006  4.108   9.3188e-02
   3_bss:   1.256  0.010  0.088 16.419  0.006  4.108   9.3188e-02
   3_xyz:   1.017  0.007  0.072 15.471  0.004  4.123   6.2589e-02
   3_adp:   1.017  0.007  0.072 15.471  0.004  4.123   6.2589e-02
   3_occ:   1.017  0.007  0.072 15.471  0.004  4.123   6.2589e-02
   4_bss:   1.017  0.007  0.072 15.471  0.004  4.123   6.2589e-02
   4_xyz:   1.130  0.008  0.089 15.546  0.005  4.109   7.3529e-02
   4_adp:   1.130  0.008  0.089 15.546  0.005  4.109   7.3529e-02
   4_occ:   1.130  0.008  0.089 15.546  0.005  4.109   7.3529e-02
   5_bss:   1.130  0.008  0.089 15.546  0.005  4.109   7.3529e-02
   5_xyz:   1.046  0.007  0.081 15.265  0.004  4.111   6.4165e-02
   5_adp:   1.046  0.007  0.081 15.265  0.004  4.111   6.4165e-02
   5_occ:   1.046  0.007  0.081 15.265  0.004  4.111   6.4165e-02
   5_bss:   1.046  0.007  0.081 15.265  0.004  4.111   6.4165e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.106   6.9102e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.106   6.9102e+00
   1_xyz:  16.516  0.178  0.571 86.100  0.052  2.165   1.1056e-01
   1_adp:  16.516  0.178  0.571 86.100  0.052  2.165   1.1056e-01
   1_occ:  16.516  0.178  0.571 86.100  0.052  2.165   1.1056e-01
   2_bss:  16.516  0.178  0.571 86.100  0.052  2.165   1.1056e-01
   2_xyz:   9.546  0.121  0.363 83.341  0.047  2.229   1.1721e-01
   2_adp:   9.546  0.121  0.363 83.341  0.047  2.229   1.1721e-01
   2_occ:   9.546  0.121  0.363 83.341  0.047  2.229   1.1721e-01
   3_bss:   9.546  0.121  0.363 83.341  0.047  2.229   1.1721e-01
   3_xyz:   6.966  0.046  0.392 80.927  0.042  2.293   5.1429e-02
   3_adp:   6.966  0.046  0.392 80.927  0.042  2.293   5.1429e-02
   3_occ:   6.966  0.046  0.392 80.927  0.042  2.293   5.1429e-02
   4_bss:   6.966  0.046  0.392 80.927  0.042  2.293   5.1429e-02
   4_xyz:   7.655  0.046  0.671 83.631  0.042  2.204   5.4987e-02
   4_adp:   7.655  0.046  0.671 83.631  0.042  2.204   5.4987e-02
   4_occ:   7.655  0.046  0.671 83.631  0.042  2.204   5.4987e-02
   5_bss:   7.655  0.046  0.671 83.631  0.042  2.204   5.4987e-02
   5_xyz:   7.235  0.049  0.579 81.199  0.039  2.332   4.9894e-02
   5_adp:   7.235  0.049  0.579 81.199  0.039  2.332   4.9894e-02
   5_occ:   7.235  0.049  0.579 81.199  0.039  2.332   4.9894e-02
   5_bss:   7.235  0.049  0.579 81.199  0.039  2.332   4.9894e-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:  67.15   0.00  12.87  54.01   0.00  10.81  67.15   0.00  24.08
   1_occ:  67.15   0.00  12.87  54.01   0.00  10.81  67.15   0.00  24.08
   2_bss:  67.15   0.00  12.87  54.01   0.00  10.81  67.15   0.00  24.08
   2_xyz:  67.15   0.00  12.87  54.01   0.00  10.81  67.15   0.00  24.08
   2_adp:  73.90   0.00  13.13  72.39   0.00   9.65  73.90   1.27  32.10
   2_occ:  73.90   0.00  13.13  72.39   0.00   9.65  73.90   1.27  32.10
   3_bss:  73.90   0.00  13.13  72.39   0.00   9.65  73.90   1.27  32.10
   3_xyz:  73.90   0.00  13.13  72.39   0.00   9.65  73.90   1.27  32.10
   3_adp:  72.15   0.00  12.98  72.15   0.00   9.16  69.03   2.46  33.74
   3_occ:  72.15   0.00  12.98  72.15   0.00   9.16  69.03   2.46  33.74
   4_bss:  72.15   0.00  12.98  72.15   0.00   9.16  69.03   2.46  33.74
   4_xyz:  72.15   0.00  12.98  72.15   0.00   9.16  69.03   2.46  33.74
   4_adp:  72.37   0.00  13.02  72.37   0.00   9.15  69.03   2.44  34.07
   4_occ:  72.37   0.00  13.02  72.37   0.00   9.15  69.03   2.44  34.07
   5_bss:  72.37   0.00  13.02  72.37   0.00   9.15  69.03   2.44  34.07
   5_xyz:  72.37   0.00  13.02  72.37   0.00   9.15  69.03   2.44  34.07
   5_adp:  76.67   0.00  13.15  76.67   0.00   9.06  69.34   1.72  35.45
   5_occ:  76.67   0.00  13.15  76.67   0.00   9.06  69.34   1.72  35.45
   5_bss:  78.48   1.80  14.95  78.48   1.80  10.86  71.15   3.52  37.25
------------------------------------------------------------------------
 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:    1.177    0.023    0.422
   1_adp:    1.177    0.023    0.422
   1_occ:    1.177    0.023    0.422
   2_bss:    1.177    0.023    0.422
   2_xyz:    1.647    0.023    0.634
   2_adp:    1.647    0.023    0.634
   2_occ:    1.647    0.023    0.634
   3_bss:    1.647    0.023    0.634
   3_xyz:    1.658    0.010    0.698
   3_adp:    1.658    0.010    0.698
   3_occ:    1.658    0.010    0.698
   4_bss:    1.658    0.010    0.698
   4_xyz:    1.749    0.060    0.759
   4_adp:    1.749    0.060    0.759
   4_occ:    1.749    0.060    0.759
   5_bss:    1.749    0.060    0.759
   5_xyz:    1.816    0.052    0.766
   5_adp:    1.816    0.052    0.766
   5_occ:    1.816    0.052    0.766
   5_bss:    1.816    0.052    0.766
------------------------------------------------------------------------

CPU time actual refinement: 339.10


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_332/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_332/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_332/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_332/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_332/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 338.94 
  Macro-tasks:
    bulk solvent and scale       = 40.54  
    individual site refinement   = 140.20 
    weights calculation          = 32.06  
    collect and process          = 6.53   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 219.47 
  Micro-tasks:
    mask                            = 2.41   
    f_calc                          = 105.23 
    alpha_beta                      = 8.07   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 115.59 
    fmodel                         = 7.24   
    r_factors                      = 0.24   
    phase_errors                   = 10.51  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 250.71 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.763 micro seconds
Total CPU time: 5.87 minutes
from_scatterers_fft:    654 calls, 104.95 s
gradients_fft:          599 calls, 102.46 s

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

# Date 2008-01-16 Time 01:20:49 PST -0800 (1200475249.20 s)
Start R-work = 0.4878, R-free = 0.4779 (no bulk solvent and anisotropic scale)
Final R-work = 0.1313, R-free = 0.1774 (no bulk solvent and anisotropic scale)

Start R-work = 0.4802, R-free = 0.4693
Final R-work = 0.1136, R-free = 0.1612