# Date 2008-01-16 Time 00:33:09 PST -0800 (1200472389.28 s)
#phil __OFF__

Command line arguments: "../46.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 31604
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 46

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

Command line parameter definitions:
  refinement.modify_start_model.adp.set_b_iso = 10

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.4938, 46.6953, 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: (68.4938, 46.6953, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6593 1.95062
Completeness in resolution range: 0.958366
Completeness with d_max=infinity: 0.955375

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.6593
                             d_min =   1.9506

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.4938, 46.6953, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6593 1.95062
Completeness in resolution range: 0.958366
Completeness with d_max=infinity: 0.955375

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.6597 -  4.1732 [2158/2186]  1942   216  10.0%
  bin  2:  4.1732 -  3.3251 [2045/2065]  1841   204  10.0%
  bin  3:  3.3251 -  2.9085 [2048/2068]  1843   205  10.0%
  bin  4:  2.9085 -  2.6443 [2009/2033]  1809   200  10.0%
  bin  5:  2.6443 -  2.4557 [2011/2032]  1805   206  10.2%
  bin  6:  2.4557 -  2.3115 [1979/2025]  1790   189   9.6%
  bin  7:  2.3115 -  2.1961 [1992/2024]  1789   203  10.2%
  bin  8:  2.1961 -  2.1008 [1974/2009]  1773   201  10.2%
  bin  9:  2.1008 -  2.0202 [1953/1984]  1760   193   9.9%
  bin 10:  2.0202 -  1.9506 [1420/2014]  1278   142  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_46/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:
        1.07 -     1.83: 14
        1.83 -     2.60: 107
        2.60 -     3.37: 4235
        3.37 -     4.13: 9669
        4.13 -     4.90: 15020
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.066 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.069 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.297 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 107 " - " O   HOH Z 349 "  1.640 3.040 -x+1/2,-y+1,z+1/2
  " OD2 ASP A 107 " - " OG ASER A 216 "  1.658 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 29040 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_46/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_46/model_refine_001.geo

CPU time processing inputs: 9.18


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.49375 46.69535 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: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4832   r_free= 0.4726   ksol= 0.00   Bsol= 0.00   scale= 0.807    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.281248                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6597 -  4.6542 0.99   1396  156 0.3971 0.3941       6.589      6.6174|
|  2:  4.6542 -  3.7140 0.99   1335  149 0.4063 0.4025      6.7747      6.7992|
|  3:  3.7140 -  3.2503 0.99   1324  150 0.4441 0.4192      6.6746      6.7313|
|  4:  3.2503 -  2.9558 0.99   1308  135 0.4591 0.4599      6.5195       6.481|
|  5:  2.9558 -  2.7454 0.99   1295  146 0.5026 0.5156      6.3814      6.3894|
|  6:  2.7454 -  2.5845 0.98   1290  143 0.5194 0.5469      6.2841      6.2169|
|  7:  2.5845 -  2.4557 0.99   1292  152 0.5139 0.4709      6.2594      6.1581|
|  8:  2.4557 -  2.3493 0.98   1296  135 0.5277 0.5001      6.1815      6.1866|
|  9:  2.3493 -  2.2591 0.98   1269  145 0.5187 0.5336      6.1158      6.1646|
| 10:  2.2591 -  2.1814 0.97   1251  137 0.5330 0.5037      6.1199       6.066|
| 11:  2.1814 -  2.1134 0.99   1285  149 0.5440 0.5321      6.0396      6.0865|
| 12:  2.1134 -  2.0532 0.98   1277  139 0.5240 0.5087      5.9836       6.004|
| 13:  2.0532 -  1.9993 0.97   1259  133 0.5587 0.5187       5.903      5.8486|
| 14:  1.9993 -  1.9506 0.60    753   90 0.5281 0.5177      5.8588      5.7728|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6597 -  4.6542  1396   156  0.66  37.67   0.80     0.69      81066.63|
|  2:  4.6542 -  3.7140  1335   149  0.67  37.50   0.89     0.74     115593.33|
|  3:  3.7140 -  3.2503  1324   150  0.58  45.79   0.87     0.71     121416.40|
|  4:  3.2503 -  2.9558  1308   135  0.50  51.47   0.82     0.62     104908.54|
|  5:  2.9558 -  2.7454  1295   146  0.42  58.13   0.74     0.52      84570.12|
|  6:  2.7454 -  2.5845  1290   143  0.39  60.64   0.72     0.47      71666.21|
|  7:  2.5845 -  2.4557  1292   152  0.39  60.60   0.75     0.45      64459.84|
|  8:  2.4557 -  2.3493  1296   135  0.39  60.51   0.74     0.47      56707.35|
|  9:  2.3493 -  2.2591  1269   145  0.39  60.87   0.74     0.48      52283.32|
| 10:  2.2591 -  2.1814  1251   137  0.40  60.25   0.78     0.48      46328.82|
| 11:  2.1814 -  2.1134  1285   149  0.35  63.46   0.75     0.45      45655.43|
| 12:  2.1134 -  2.0532  1277   139  0.32  65.77   0.77     0.42      44493.68|
| 13:  2.0532 -  1.9993  1259   133  0.23  72.67   0.74     0.31      40327.90|
| 14:  1.9993 -  1.9506   753    90  0.16  77.98   0.75     0.17      31695.54|
|alpha:            min =        0.17 max =            0.74 mean =         0.51|
|beta:             min =    31695.54 max =       121416.40 mean =     70257.20|
|figures of merit: min =        0.00 max =            1.00 mean =         0.43|
|phase err.(work): min =        0.00 max =           89.97 mean =        57.24|
|phase err.(test): min =        0.00 max =           89.99 mean =        57.61|
|-----------------------------------------------------------------------------|

============================== 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 = 10.748697             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.529   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.210530              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.020   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  0.971 -  1.364:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.364 -  1.757:       18 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.757 -  2.149:       99 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.149 -  2.542:      502 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.542 -  2.935:     1312 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.935 -  3.328:     2493 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.328 -  3.721:     4038 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.721 -  4.114:     5339 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.114 -  4.507:     6932 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.507 -  4.900:     8304 |
|-----------------------------------------------------------------------------|
|-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 |       52.768 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.085    4.900  0.971 |       3.316 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.322)------------------------------------------|
|    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 = 11.322)------------------------------------------|
|    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: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4877   r_free= 0.4800   ksol= 0.00   Bsol= 0.00   scale= 0.775    |
|                                                                             |
| 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: 6.282804                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4734   r_free= 0.4631   ksol= 0.35   Bsol= 0.00   scale= 1.011    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.59,8.12,8.77,0.00,0.00,0.00); trace/3= 8.49                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.273924                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.001462              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.875   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.173418              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.638   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4734      final r-factor (work) = 0.4086          |
| start r-factor (free) = 0.4631      final r-factor (free) = 0.4220          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 81.0403 = 9.00 * 0.50 * 6.2817 + 1.00 * 52.7682                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.0596 = 9.00 * 0.50 * 6.2051 + 1.00 * 0.1323                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4086      final r-factor (work) = 0.3607          |
| start r-factor (free) = 0.4220      final r-factor (free) = 0.4077          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.2958 = 1.17 * 1.00 * 6.2051 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.2098 = 1.17 * 1.00 * 6.1294 + 1.00 * 0.0174                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.322)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    73.24   13.58    None  None   None       |
|    all(noH): 2823   0      0.00    73.24   13.58    None  None   None       |
|    Sol.    : 438    0      0.00    73.24   26.81    None  None   None       |
|    Mac.    : 2385   0      0.00    71.94   11.15    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 -   7.324: 1069   |   5:    36.619 -  43.942:   78        |
|      1:     7.324 -  14.648:  753   |   6:    43.942 -  51.266:   50        |
|      2:    14.648 -  21.971:  428   |   7:    51.266 -  58.590:   16        |
|      3:    21.971 -  29.295:  260   |   8:    58.590 -  65.914:    7        |
|      4:    29.295 -  36.619:  154   |   9:    65.914 -  73.237:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3607 r_free = 0.4077             target_work(ml) = 6.111         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3602 r_free = 0.4075             target_work(ml) = 6.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3602   r_free= 0.4075   ksol= 0.35   Bsol= 0.00   scale= 1.118    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.59,8.12,8.77,0.00,0.00,0.00); trace/3= 8.49                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.109970                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3561   r_free= 0.4044   ksol= 0.33   Bsol= 20.00   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.49,3.68,5.16,0.00,0.00,0.00); trace/3= 4.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.109209                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.069453              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.705   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.541960              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 126.771  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3561      final r-factor (work) = 0.2724          |
| start r-factor (free) = 0.4044      final r-factor (free) = 0.3215          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.6559 = 5.07 * 0.50 * 6.1246 + 1.00 * 0.1317                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.2789 = 5.07 * 0.50 * 5.9974 + 1.00 * 0.0770                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2724      final r-factor (work) = 0.2498          |
| start r-factor (free) = 0.3215      final r-factor (free) = 0.3000          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2780 = 0.54 * 1.00 * 5.9974 + 1.00 * 0.0276                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1899 = 0.54 * 1.00 * 5.8475 + 1.00 * 0.0208                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.322)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.83   14.02    None  None   None       |
|    all(noH): 2823   0      0.00    83.83   14.02    None  None   None       |
|    Sol.    : 438    0      0.00    81.57   33.46    None  None   None       |
|    Mac.    : 2385   0      0.00    83.83   10.45    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.383: 1303   |   5:    41.914 -  50.297:   87        |
|      1:     8.383 -  16.766:  756   |   6:    50.297 -  58.679:   51        |
|      2:    16.766 -  25.148:  281   |   7:    58.679 -  67.062:   23        |
|      3:    25.148 -  33.531:  189   |   8:    67.062 -  75.445:   11        |
|      4:    33.531 -  41.914:  119   |   9:    75.445 -  83.828:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2498 r_free = 0.3000             target_work(ml) = 5.824         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2495 r_free = 0.2996             target_work(ml) = 5.823         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2495   r_free= 0.2996   ksol= 0.33   Bsol= 20.00   scale= 1.068   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.49,3.68,5.16,0.00,0.00,0.00); trace/3= 4.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.823158                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2474   r_free= 0.2988   ksol= 0.33   Bsol= 31.54   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.23,2.15,3.29,0.00,0.00,0.00); trace/3= 2.56                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.820982                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.447414              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.119  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.893254              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.588   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2474      final r-factor (work) = 0.1704          |
| start r-factor (free) = 0.2988      final r-factor (free) = 0.2178          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 16.0119 = 5.45 * 0.50 * 5.8504 + 1.00 * 0.0770                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.5222 = 5.45 * 0.50 * 5.6719 + 1.00 * 0.0737                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1704      final r-factor (work) = 0.1575          |
| start r-factor (free) = 0.2178      final r-factor (free) = 0.2076          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0842 = 0.89 * 1.00 * 5.6719 + 1.00 * 0.0178                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9094 = 0.89 * 1.00 * 5.4538 + 1.00 * 0.0377                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 9      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.322)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.40   14.06    None  None   None       |
|    all(noH): 2823   0      0.00    84.40   14.06    None  None   None       |
|    Sol.    : 438    0      1.38    81.76   34.42    None  None   None       |
|    Mac.    : 2385   0      0.00    84.40   10.32    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.440: 1348   |   5:    42.202 -  50.642:   88        |
|      1:     8.440 -  16.881:  741   |   6:    50.642 -  59.082:   49        |
|      2:    16.881 -  25.321:  251   |   7:    59.082 -  67.523:   24        |
|      3:    25.321 -  33.761:  189   |   8:    67.523 -  75.963:   11        |
|      4:    33.761 -  42.202:  118   |   9:    75.963 -  84.403:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1575 r_free = 0.2076             target_work(ml) = 5.431         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1570 r_free = 0.2072             target_work(ml) = 5.429         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1570   r_free= 0.2072   ksol= 0.33   Bsol= 31.54   scale= 1.048   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.23,2.15,3.29,0.00,0.00,0.00); trace/3= 2.56                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.428973                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1566   r_free= 0.2062   ksol= 0.32   Bsol= 31.54   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.96,1.54,2.35,0.00,0.00,0.00); trace/3= 1.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.426091                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.830196              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.179  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.419006              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 90.049   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1566      final r-factor (work) = 0.1381          |
| start r-factor (free) = 0.2062      final r-factor (free) = 0.1883          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.7991 = 2.83 * 0.50 * 5.4592 + 1.00 * 0.0737                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6683 = 2.83 * 0.50 * 5.3754 + 1.00 * 0.0616                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1381      final r-factor (work) = 0.1255          |
| start r-factor (free) = 0.1883      final r-factor (free) = 0.1718          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3084 = 0.42 * 1.00 * 5.3754 + 1.00 * 0.0561                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2274 = 0.42 * 1.00 * 5.2922 + 1.00 * 0.0100                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.322)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.60   13.88    None  None   None       |
|    all(noH): 2823   0      0.00    87.60   13.88    None  None   None       |
|    Sol.    : 438    0      2.24    80.40   36.89    None  None   None       |
|    Mac.    : 2385   0      0.00    87.60   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 -   8.760: 1481   |   5:    43.798 -  52.557:   95        |
|      1:     8.760 -  17.519:  732   |   6:    52.557 -  61.317:   54        |
|      2:    17.519 -  26.279:  176   |   7:    61.317 -  70.076:   25        |
|      3:    26.279 -  35.038:  134   |   8:    70.076 -  78.836:    5        |
|      4:    35.038 -  43.798:  115   |   9:    78.836 -  87.595:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1255 r_free = 0.1718             target_work(ml) = 5.237         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1254 r_free = 0.1718             target_work(ml) = 5.236         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1254   r_free= 0.1718   ksol= 0.32   Bsol= 31.54   scale= 1.026   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.96,1.54,2.35,0.00,0.00,0.00); trace/3= 1.62                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.236022                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1253   r_free= 0.1717   ksol= 0.32   Bsol= 31.81   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.52,1.26,2.02,0.00,0.00,0.00); trace/3= 1.27                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.235470                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.674972              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 126.975  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.625022              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.381  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1253      final r-factor (work) = 0.1154          |
| start r-factor (free) = 0.1717      final r-factor (free) = 0.1615          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1404 = 2.67 * 0.50 * 5.2928 + 1.00 * 0.0614                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0195 = 2.67 * 0.50 * 5.1990 + 1.00 * 0.0659                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1154      final r-factor (work) = 0.1129          |
| start r-factor (free) = 0.1615      final r-factor (free) = 0.1596          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2594 = 0.63 * 1.00 * 5.1990 + 1.00 * 0.0100                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2350 = 0.63 * 1.00 * 5.1590 + 1.00 * 0.0105                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.322)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.21   13.86    None  None   None       |
|    all(noH): 2823   0      0.00    91.21   13.86    None  None   None       |
|    Sol.    : 438    0      3.16    84.79   37.41    None  None   None       |
|    Mac.    : 2385   0      0.00    91.21   9.53     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.121: 1576   |   5:    45.605 -  54.726:  101        |
|      1:     9.121 -  18.242:  677   |   6:    54.726 -  63.847:   45        |
|      2:    18.242 -  27.363:  163   |   7:    63.847 -  72.968:   22        |
|      3:    27.363 -  36.484:  121   |   8:    72.968 -  82.089:    6        |
|      4:    36.484 -  45.605:  108   |   9:    82.089 -  91.210:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1129 r_free = 0.1596             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1128 r_free = 0.1596             target_work(ml) = 5.153         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1128   r_free= 0.1596   ksol= 0.32   Bsol= 31.81   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.52,1.26,2.02,0.00,0.00,0.00); trace/3= 1.27                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.152797                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6597 -  4.6542 0.99   1396  156 0.1042 0.1309      5.4358      5.5739|
|  2:  4.6542 -  3.7140 0.99   1335  149 0.0863 0.1100      5.4429      5.6478|
|  3:  3.7140 -  3.2503 0.99   1324  150 0.1051 0.1447      5.4622      5.7851|
|  4:  3.2503 -  2.9558 0.99   1308  135 0.1196 0.1697      5.4409      5.6454|
|  5:  2.9558 -  2.7454 0.99   1295  146 0.1276 0.1610      5.3027      5.4774|
|  6:  2.7454 -  2.5845 0.98   1290  143 0.1224 0.1954      5.2001      5.4571|
|  7:  2.5845 -  2.4557 0.99   1292  152 0.1183 0.1597       5.134        5.35|
|  8:  2.4557 -  2.3493 0.98   1296  135 0.1180 0.1678      5.0971      5.3389|
|  9:  2.3493 -  2.2591 0.98   1269  145 0.1208 0.1838      5.0321      5.3365|
| 10:  2.2591 -  2.1814 0.97   1251  137 0.1159 0.1691      4.9775      5.1528|
| 11:  2.1814 -  2.1134 0.99   1285  149 0.1136 0.1765      4.9331      5.2914|
| 12:  2.1134 -  2.0532 0.98   1277  139 0.1142 0.1822      4.8926      5.1994|
| 13:  2.0532 -  1.9993 0.97   1259  133 0.1153 0.1772      4.8165      5.0445|
| 14:  1.9993 -  1.9506 0.60    753   90 0.1102 0.1773      4.7317      4.9834|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6597 -  4.6542  1396   156  0.94   9.70   0.99     0.97       7987.62|
|  2:  4.6542 -  3.7140  1335   149  0.95   7.90   1.03     1.02       9022.17|
|  3:  3.7140 -  3.2503  1324   150  0.93  11.16   1.05     1.04      10184.00|
|  4:  3.2503 -  2.9558  1308   135  0.92  13.30   1.03     1.03       9983.63|
|  5:  2.9558 -  2.7454  1295   146  0.90  15.44   1.01     0.97       7922.02|
|  6:  2.7454 -  2.5845  1290   143  0.90  16.03   0.99     0.95       6813.47|
|  7:  2.5845 -  2.4557  1292   152  0.91  15.28   0.99     0.96       5927.75|
|  8:  2.4557 -  2.3493  1296   135  0.91  15.38   1.01     0.99       5643.84|
|  9:  2.3493 -  2.2591  1269   145  0.91  15.74   1.02     0.99       5018.97|
| 10:  2.2591 -  2.1814  1251   137  0.90  16.24   1.01     0.98       4597.14|
| 11:  2.1814 -  2.1134  1285   149  0.90  16.06   1.01     0.98       4367.62|
| 12:  2.1134 -  2.0532  1277   139  0.91  15.74   1.03     1.01       4077.19|
| 13:  2.0532 -  1.9993  1259   133  0.90  16.76   1.02     1.02       3587.16|
| 14:  1.9993 -  1.9506   753    90  0.91  15.55   1.00     0.97       2915.24|
|alpha:            min =        0.95 max =            1.04 mean =         0.99|
|beta:             min =     2915.24 max =        10184.00 mean =      6432.75|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.21|
|phase err.(test): min =        0.00 max =           88.80 mean =        13.73|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1128   r_free= 0.1596   ksol= 0.32   Bsol= 34.50   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.75,-0.00,0.75,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.151944                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.66 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1128   r_free= 0.1596   ksol= 0.32   Bsol= 34.50   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.75,-0.00,0.75,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.151944                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6597 -  4.6542 0.99   1396  156 0.1016 0.1308      5.4174      5.5708|
|  2:  4.6542 -  3.7140 0.99   1335  149 0.0877 0.1092      5.4521      5.6364|
|  3:  3.7140 -  3.2503 0.99   1324  150 0.1060 0.1459      5.4659      5.7877|
|  4:  3.2503 -  2.9558 0.99   1308  135 0.1203 0.1663      5.4403      5.6331|
|  5:  2.9558 -  2.7454 0.99   1295  146 0.1277 0.1632      5.3021      5.4836|
|  6:  2.7454 -  2.5845 0.98   1290  143 0.1225 0.1940       5.201       5.454|
|  7:  2.5845 -  2.4557 0.99   1292  152 0.1181 0.1612      5.1353      5.3569|
|  8:  2.4557 -  2.3493 0.98   1296  135 0.1179 0.1684      5.0962      5.3393|
|  9:  2.3493 -  2.2591 0.98   1269  145 0.1206 0.1839      5.0318      5.3377|
| 10:  2.2591 -  2.1814 0.97   1251  137 0.1150 0.1688      4.9751      5.1525|
| 11:  2.1814 -  2.1134 0.99   1285  149 0.1134 0.1757      4.9337       5.288|
| 12:  2.1134 -  2.0532 0.98   1277  139 0.1138 0.1824      4.8909      5.2025|
| 13:  2.0532 -  1.9993 0.97   1259  133 0.1151 0.1765      4.8154      5.0403|
| 14:  1.9993 -  1.9506 0.60    753   90 0.1103 0.1773       4.731      4.9846|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6597 -  4.6542  1396   156  0.94   9.60   0.99     0.96       7912.07|
|  2:  4.6542 -  3.7140  1335   149  0.95   7.98   1.03     1.02       9033.45|
|  3:  3.7140 -  3.2503  1324   150  0.93  11.14   1.05     1.04      10094.32|
|  4:  3.2503 -  2.9558  1308   135  0.92  13.25   1.03     1.03       9904.38|
|  5:  2.9558 -  2.7454  1295   146  0.90  15.40   1.01     0.97       7886.18|
|  6:  2.7454 -  2.5845  1290   143  0.90  16.10   0.99     0.95       6852.83|
|  7:  2.5845 -  2.4557  1292   152  0.91  15.33   0.99     0.96       5969.31|
|  8:  2.4557 -  2.3493  1296   135  0.91  15.38   1.01     0.99       5646.64|
|  9:  2.3493 -  2.2591  1269   145  0.91  15.76   1.02     0.99       5029.30|
| 10:  2.2591 -  2.1814  1251   137  0.90  16.25   1.01     0.98       4594.57|
| 11:  2.1814 -  2.1134  1285   149  0.90  16.10   1.01     0.98       4376.93|
| 12:  2.1134 -  2.0532  1277   139  0.91  15.73   1.03     1.01       4069.46|
| 13:  2.0532 -  1.9993  1259   133  0.90  16.74   1.02     1.02       3580.77|
| 14:  1.9993 -  1.9506   753    90  0.91  15.54   1.00     0.97       2909.74|
|alpha:            min =        0.95 max =            1.04 mean =         0.99|
|beta:             min =     2909.74 max =        10094.32 mean =      6418.50|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.21|
|phase err.(test): min =        0.00 max =           89.16 mean =        13.72|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.322)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.27    92.48   15.12    None  None   None       |
|    all(noH): 2823   0      1.27    92.48   15.12    None  None   None       |
|    Sol.    : 438    0      4.42    86.06   38.68    None  None   None       |
|    Mac.    : 2385   0      1.27    92.48   10.80    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.266 -  10.387: 1576   |   5:    46.871 -  55.992:  101        |
|      1:    10.387 -  19.508:  677   |   6:    55.992 -  65.113:   45        |
|      2:    19.508 -  28.629:  163   |   7:    65.113 -  74.234:   22        |
|      3:    28.629 -  37.750:  121   |   8:    74.234 -  83.355:    6        |
|      4:    37.750 -  46.871:  108   |   9:    83.355 -  92.476:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 315         
Filter by distance & map next to the model:
   mapped sites are within: 0.733 - 5.746
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 314 from: 315
   mapped sites are within: 0.733 - 5.746

peak=   11.002 closest distance to " CB  VAL A 296 " =    1.562
peak=   10.868 closest distance to " CB  VAL A 230 " =    1.401
peak=    6.065 closest distance to " CG  LEU A   5 " =    1.169
peak=    5.928 closest distance to " O   HOH Z 193 " =    1.832
peak=    5.746 closest distance to " O   HOH Z 142 " =    1.860
peak=    5.680 closest distance to " CD2 LEU A   5 " =    1.183
peak=    5.649 closest distance to " NE2 GLN A  11 " =    1.109
peak=    5.517 closest distance to " O   HOH Z 124 " =    1.492
peak=    5.425 closest distance to " O   HOH Z 236 " =    1.486
peak=    5.398 closest distance to " O   HOH Z 278 " =    1.282
peak=    5.373 closest distance to " CD1AILE A 234 " =    0.944
peak=    5.359 closest distance to " O   HOH Z 126 " =    1.998
peak=    5.265 closest distance to " O   HOH Z  85 " =    1.621
peak=    5.138 closest distance to " CB  ARG A 275 " =    0.985
peak=    5.131 closest distance to " O   HOH Z 406 " =    1.293
peak=    4.932 closest distance to " NH2 ARG A  56 " =    2.035
peak=    4.890 closest distance to " O   HOH Z 209 " =    2.195
peak=    4.843 closest distance to " CB  GLN A 183 " =    1.340
peak=    4.798 closest distance to " CG  LEU A 228 " =    1.135
peak=    4.797 closest distance to " O   SER A  87 " =    2.259
peak=    4.749 closest distance to " O   HOH Z 403 " =    1.879
peak=    4.734 closest distance to " O   HOH Z 272 " =    1.856
peak=    4.672 closest distance to " CB  VAL A 230 " =    1.116
peak=    4.602 closest distance to " CB  GLN A 223 " =    1.549
peak=    4.591 closest distance to " CG  PRO A 213 " =    1.239
peak=    4.582 closest distance to " O   HOH Z 232 " =    2.149
peak=    4.532 closest distance to " O   HOH Z  59 " =    1.880
peak=    4.509 closest distance to " O   HOH Z 263 " =    1.548
peak=    4.471 closest distance to " O   HOH Z  78 " =    1.669
peak=    4.463 closest distance to " O   HOH Z   3 " =    2.063
peak=    4.452 closest distance to " O   HOH Z 249 " =    1.109
peak=    4.444 closest distance to " O   HOH Z 411 " =    3.792
peak=    4.439 closest distance to " O   HOH Z 427 " =    2.589
peak=    4.310 closest distance to " OE1 GLU A   2 " =    2.178
peak=    4.309 closest distance to " O   HOH Z  97 " =    1.692
peak=    4.307 closest distance to " O   HOH Z 346 " =    1.629
peak=    4.275 closest distance to " NZ  LYS A 117 " =    3.107
peak=    4.228 closest distance to " O   HOH Z  69 " =    1.085
peak=    4.225 closest distance to " O   HOH Z 188 " =    0.991
peak=    4.223 closest distance to " O   HOH Z 130 " =    1.118
peak=    4.207 closest distance to " O   HOH Z  95 " =    1.490
peak=    4.179 closest distance to " CG AARG A 275 " =    1.139
peak=    4.167 closest distance to " CB  SER A   3 " =    1.274
peak=    4.159 closest distance to " CD2 LEU A 228 " =    1.325
peak=    4.149 closest distance to " O   HOH Z 303 " =    2.111
peak=    4.128 closest distance to " O   HOH Z 250 " =    1.401
peak=    4.126 closest distance to " O   HOH Z 369 " =    2.042
peak=    4.094 closest distance to " O   HOH Z 368 " =    2.166
peak=    4.079 closest distance to " O   HOH Z 192 " =    1.351
peak=    4.077 closest distance to " CB  VAL A 265 " =    1.200
peak=    4.068 closest distance to " CB  SER A  26 " =    1.670
peak=    4.067 closest distance to " O   HOH Z 234 " =    3.430
peak=    4.064 closest distance to " C   PRO A 198 " =    1.508
peak=    4.043 closest distance to " CD2 TRP A 179 " =    1.390
peak=    4.040 closest distance to " O   HOH Z 298 " =    1.834
peak=    4.038 closest distance to " O   HOH Z 261 " =    1.822
peak=    4.034 closest distance to " CA  TYR A  30 " =    1.021
peak=    4.025 closest distance to " O   HOH Z 322 " =    2.210
peak=    4.020 closest distance to " O   HOH Z  61 " =    1.584
peak=    4.018 closest distance to " O   HOH Z 238 " =    1.018
peak=    3.999 closest distance to " CB  ASN A 148 " =    1.426
peak=    3.998 closest distance to " CB  SER A  63 " =    1.167
peak=    3.983 closest distance to " O   HOH Z 345 " =    2.940
peak=    3.971 closest distance to " O   HOH Z  54 " =    1.592
peak=    3.967 closest distance to " CB  VAL A 202 " =    1.681
peak=    3.959 closest distance to " O   HOH Z 118 " =    1.902
peak=    3.958 closest distance to " O   HOH Z 134 " =    1.334
peak=    3.957 closest distance to " CB  GLN A  88 " =    1.320
peak=    3.944 closest distance to " O   HOH Z  43 " =    2.137
peak=    3.939 closest distance to " O   HOH Z 316 " =    2.869
peak=    3.929 closest distance to " O   HOH Z 414 " =    1.278
peak=    3.928 closest distance to " O   HOH Z 402 " =    1.411
peak=    3.923 closest distance to " CB  ARG A  79 " =    1.420
peak=    3.919 closest distance to " O   HOH Z 423 " =    1.858
peak=    3.915 closest distance to " O   HOH Z 327 " =    1.656
peak=    3.909 closest distance to " O   HOH Z 132 " =    0.953
peak=    3.906 closest distance to " O   HOH Z 130 " =    2.605
peak=    3.892 closest distance to " O   HOH Z  44 " =    1.892
peak=    3.888 closest distance to " O   HOH Z  66 " =    2.158
peak=    3.867 closest distance to " O   HOH Z  10 " =    1.719
peak=    3.863 closest distance to " O   HOH Z 189 " =    2.376
peak=    3.862 closest distance to " O   HOH Z 227 " =    1.741
peak=    3.862 closest distance to " O   HOH Z   9 " =    2.192
peak=    3.859 closest distance to " O   HOH Z 392 " =    2.660
peak=    3.859 closest distance to " O   HOH Z 425 " =    1.383
peak=    3.852 closest distance to " CG  PRO A 198 " =    1.179
peak=    3.844 closest distance to " O   HOH Z 261 " =    2.034
peak=    3.826 closest distance to " O   HOH Z 357 " =    1.833
peak=    3.825 closest distance to " O   HOH Z 156 " =    3.046
peak=    3.799 closest distance to " CG  ARG A  66 " =    1.016
peak=    3.798 closest distance to " NH2AARG A 145 " =    2.242
peak=    3.794 closest distance to " CA  ARG A 275 " =    1.983
peak=    3.782 closest distance to " O   HOH Z  59 " =    2.055
peak=    3.775 closest distance to " CB  GLU A 152 " =    1.099
peak=    3.762 closest distance to " O   HOH Z 191 " =    1.400
peak=    3.762 closest distance to " CA  ALA A  21 " =    1.113
peak=    3.762 closest distance to " O   HOH Z 118 " =    1.657
peak=    3.757 closest distance to " CB  ALA A   9 " =    1.583
peak=    3.750 closest distance to " O   HOH Z  43 " =    1.151
peak=    3.741 closest distance to " CD  ARG A 269 " =    1.077
peak=    3.738 closest distance to " OG BSER A 164 " =    2.118
peak=    3.728 closest distance to " O   HOH Z 143 " =    1.250
peak=    3.725 closest distance to " O   HOH Z  80 " =    1.545
peak=    3.719 closest distance to " O   HOH Z  78 " =    1.982
peak=    3.708 closest distance to " O   HOH Z 148 " =    3.302
peak=    3.707 closest distance to " O   HOH Z 222 " =    2.255
peak=    3.703 closest distance to " CB  GLU A 128 " =    1.121
peak=    3.702 closest distance to " O   HOH Z 203 " =    1.457
peak=    3.700 closest distance to " O   HOH Z 248 " =    1.696
peak=    3.699 closest distance to " CA  VAL A  41 " =    0.863
peak=    3.691 closest distance to " CB  TRP A 266 " =    1.194
peak=    3.688 closest distance to " O   HOH Z 344 " =    2.703
peak=    3.687 closest distance to " O   HOH Z  97 " =    2.057
peak=    3.685 closest distance to " NH2BARG A 145 " =    2.207
peak=    3.682 closest distance to " O   HOH Z 366 " =    2.649
peak=    3.679 closest distance to " CB  TRP A 179 " =    1.159
peak=    3.670 closest distance to " O   HOH Z 137 " =    1.544
peak=    3.669 closest distance to " CB  THR A  52 " =    1.174
peak=    3.664 closest distance to " O   HOH Z  61 " =    1.462
peak=    3.659 closest distance to " ND1 HIS A  81 " =    1.423
peak=    3.659 closest distance to " O   HOH Z 352 " =    1.337
peak=    3.655 closest distance to " CE AMET A  47 " =    1.468
peak=    3.650 closest distance to " CB  THR A  31 " =    1.721
peak=    3.648 closest distance to " CB  TYR A 169 " =    1.116
peak=    3.648 closest distance to " O   HOH Z 227 " =    2.152
peak=    3.645 closest distance to " CA  ALA A  51 " =    1.024
peak=    3.641 closest distance to " CG1BVAL A  72 " =    1.423
peak=    3.631 closest distance to " CG1 ILE A  33 " =    1.376
peak=    3.629 closest distance to " O   HOH Z 435 " =    1.984
peak=    3.628 closest distance to " O   HOH Z 422 " =    2.364
peak=    3.626 closest distance to " O   HOH Z 303 " =    1.676
peak=    3.626 closest distance to " O   HOH Z 337 " =    1.596
peak=    3.625 closest distance to " O   HOH Z 151 " =    1.679
peak=    3.621 closest distance to " CB  ALA A 248 " =    1.374
peak=    3.617 closest distance to " CE  LYS A 119 " =    1.047
peak=    3.615 closest distance to " CB  VAL A 268 " =    0.840
peak=    3.607 closest distance to " O   HOH Z 407 " =    2.325
peak=    3.606 closest distance to " O   HOH Z 170 " =    1.902
peak=    3.604 closest distance to " O   HOH Z 245 " =    1.400
peak=    3.603 closest distance to " O   HOH Z 261 " =    2.082
peak=    3.596 closest distance to " CG2 ILE A  20 " =    1.623
peak=    3.592 closest distance to " CB BVAL A  41 " =    1.135
peak=    3.590 closest distance to " CG2 VAL A 257 " =    0.855
peak=    3.584 closest distance to " CD  GLN A 194 " =    1.476
peak=    3.579 closest distance to " O   HOH Z 389 " =    1.299
peak=    3.577 closest distance to " O   HOH Z  40 " =    1.466
peak=    3.564 closest distance to " O   HOH Z 344 " =    1.343
peak=    3.563 closest distance to " O   HOH Z  47 " =    1.709
peak=    3.563 closest distance to " O   HOH Z 214 " =    2.272
peak=    3.556 closest distance to " O   HOH Z 334 " =    1.232
peak=    3.541 closest distance to " N   PHE A 130 " =    1.364
peak=    3.534 closest distance to " O   HOH Z 255 " =    1.705
peak=    3.532 closest distance to " O   LYS A 290 " =    2.289
peak=    3.523 closest distance to " CG2 THR A 221 " =    1.187
peak=    3.516 closest distance to " O   HOH Z 128 " =    1.988
peak=    3.515 closest distance to " CG2 ILE A 120 " =    1.296
peak=    3.503 closest distance to " CB  TYR A  30 " =    1.726
peak=    3.502 closest distance to " NH1AARG A 275 " =    1.004
peak=    3.496 closest distance to " O   HOH Z 417 " =    3.245
peak=    3.495 closest distance to " O   HOH Z 426 " =    1.487
peak=    3.494 closest distance to " O   HOH Z 299 " =    4.174
peak=    3.493 closest distance to " OG BSER A 210 " =    1.477
peak=    3.487 closest distance to " O   HOH Z 365 " =    1.834
peak=    3.484 closest distance to " OH  TYR A 116 " =    1.093
peak=    3.481 closest distance to " N   TYR A  15 " =    1.137
peak=    3.479 closest distance to " CE1 HIS A 108 " =    1.126
peak=    3.468 closest distance to " O   HOH Z 108 " =    2.121
peak=    3.466 closest distance to " CB  ASN A 110 " =    1.160
peak=    3.463 closest distance to " O   HOH Z  39 " =    1.236
peak=    3.463 closest distance to " CA  ASN A 215 " =    1.014
peak=    3.459 closest distance to " O   HOH Z 173 " =    2.069
peak=    3.458 closest distance to " CD2 TYR A  30 " =    0.865
peak=    3.453 closest distance to " OD1 ASN A  69 " =    2.645
peak=    3.453 closest distance to " O   HOH Z 244 " =    1.628
peak=    3.448 closest distance to " CB  PRO A  90 " =    1.272
peak=    3.443 closest distance to " CZ AARG A 102 " =    1.630
peak=    3.443 closest distance to " N   ARG A 156 " =    1.298
peak=    3.438 closest distance to " CG AARG A 190 " =    1.247
peak=    3.433 closest distance to " CD1 ILE A 106 " =    1.197
peak=    3.432 closest distance to " OG  SER A  62 " =    2.769
peak=    3.429 closest distance to " CG  LEU A 167 " =    1.213
peak=    3.426 closest distance to " CB  GLU A 277 " =    3.467
peak=    3.424 closest distance to " NH1 ARG A  14 " =    1.088
peak=    3.422 closest distance to " NH2 ARG A 156 " =    1.088
peak=    3.418 closest distance to " CE1 TYR A 186 " =    1.287
peak=    3.412 closest distance to " N   ASN A  39 " =    1.167
peak=    3.411 closest distance to " O   HOH Z 273 " =    2.856
peak=    3.408 closest distance to " O   HOH Z  89 " =    1.729
peak=    3.406 closest distance to " NE BARG A 275 " =    1.138
peak=    3.399 closest distance to " O   HOH Z 380 " =    1.731
peak=    3.396 closest distance to " O   HOH Z  68 " =    2.547
peak=    3.392 closest distance to " O   HOH Z  47 " =    1.604
peak=    3.385 closest distance to " O   HOH Z 213 " =    1.760
peak=    3.382 closest distance to " O   HOH Z 193 " =    1.878
peak=    3.377 closest distance to " O   HOH Z  88 " =    2.360
peak=    3.376 closest distance to " O   HOH Z 287 " =    1.604
peak=    3.375 closest distance to " CA  VAL A 126 " =    1.057
peak=    3.375 closest distance to " ND2 ASN A 187 " =    1.522
peak=    3.374 closest distance to " O   HOH Z 417 " =    2.390
peak=    3.374 closest distance to " O   HOH Z 313 " =    1.935
peak=    3.369 closest distance to " O   ARG A  56 " =    2.717
peak=    3.365 closest distance to " O   HOH Z 109 " =    1.992
peak=    3.362 closest distance to " O   HOH Z 374 " =    2.447
peak=    3.361 closest distance to " CG  PRO A 243 " =    1.173
peak=    3.355 closest distance to " SD BMET A  47 " =    1.303
peak=    3.354 closest distance to " CB  LEU A 255 " =    0.763
peak=    3.354 closest distance to " CG  MET A 185 " =    1.224
peak=    3.352 closest distance to " O   HOH Z 345 " =    1.535
peak=    3.350 closest distance to " ND2 ASN A 110 " =    1.632
peak=    3.348 closest distance to " O   HOH Z  88 " =    2.893
peak=    3.346 closest distance to " O   GLY A  91 " =    1.567
peak=    3.343 closest distance to " O   HOH Z 254 " =    1.520
peak=    3.342 closest distance to " CB  ALA A  10 " =    1.357
peak=    3.339 closest distance to " O   HOH Z 223 " =    1.684
peak=    3.338 closest distance to " O   HOH Z 433 " =    1.889
peak=    3.336 closest distance to " CA  ASN A 176 " =    1.033
peak=    3.325 closest distance to " O   HOH Z 421 " =    1.296
peak=    3.323 closest distance to " O   HOH Z 284 " =    2.763
peak=    3.320 closest distance to " O   HOH Z  59 " =    2.148
peak=    3.313 closest distance to " CG  LYS A 119 " =    1.156
peak=    3.310 closest distance to " O   HOH Z 409 " =    1.515
peak=    3.307 closest distance to " CG  GLN A  77 " =    2.237
peak=    3.306 closest distance to " CB  GLN A 278 " =    0.816
peak=    3.303 closest distance to " OD2 ASP A 286 " =    2.497
peak=    3.303 closest distance to " O   HOH Z  11 " =    1.393
peak=    3.301 closest distance to " CB  ARG A 139 " =    0.988
peak=    3.300 closest distance to " O   HOH Z 257 " =    2.245
peak=    3.297 closest distance to " O   HOH Z 389 " =    1.515
peak=    3.296 closest distance to " CG  LYS A  76 " =    1.502
peak=    3.293 closest distance to " O   HOH Z 371 " =    1.511
peak=    3.293 closest distance to " O   HOH Z 172 " =    3.837
peak=    3.287 closest distance to " O   HOH Z 361 " =    3.126
peak=    3.286 closest distance to " NE2 GLN A  58 " =    5.746
peak=    3.285 closest distance to " CE ALYS A 290 " =    1.168
peak=    3.285 closest distance to " O   HOH Z 233 " =    1.484
peak=    3.278 closest distance to " CG  GLN A  88 " =    1.052
peak=    3.278 closest distance to " O   HOH Z 260 " =    1.496
peak=    3.276 closest distance to " CG2 THR A 294 " =    1.531
peak=    3.267 closest distance to " CB  ASN A 142 " =    1.119
peak=    3.258 closest distance to " O   HOH Z  80 " =    2.168
peak=    3.257 closest distance to " O   HOH Z 267 " =    1.987
peak=    3.253 closest distance to " ND1 HIS A  81 " =    1.225
peak=    3.249 closest distance to " CD1 LEU A 228 " =    1.620
peak=    3.248 closest distance to " NE2 GLN A  55 " =    1.336
peak=    3.240 closest distance to " CB  HIS A 108 " =    0.878
peak=    3.239 closest distance to " O   HOH Z 392 " =    1.823
peak=    3.239 closest distance to " O   HOH Z 281 " =    1.540
peak=    3.239 closest distance to " CA  LEU A  83 " =    1.351
peak=    3.238 closest distance to " CE3 TRP A 274 " =    2.451
peak=    3.233 closest distance to " O   HOH Z 411 " =    1.762
peak=    3.232 closest distance to " N   SER A 146 " =    1.962
peak=    3.227 closest distance to " O   GLN A  58 " =    1.371
peak=    3.225 closest distance to " O   HOH Z 251 " =    1.586
peak=    3.225 closest distance to " CG  LYS A  76 " =    1.073
peak=    3.225 closest distance to " O   HOH Z  96 " =    1.521
peak=    3.221 closest distance to " O   ASP A 124 " =    1.199
peak=    3.219 closest distance to " O   HOH Z 222 " =    2.117
peak=    3.217 closest distance to " CG  MET A 188 " =    1.402
peak=    3.214 closest distance to " CZ2 TRP A 150 " =    1.163
peak=    3.213 closest distance to " CA  GLN A 194 " =    1.151
peak=    3.210 closest distance to " O   HOH Z  71 " =    1.316
peak=    3.209 closest distance to " O   HOH Z 253 " =    1.502
peak=    3.209 closest distance to " OD1BASN A 224 " =    2.174
peak=    3.202 closest distance to " O   HOH Z 128 " =    2.093
peak=    3.200 closest distance to " O   HOH Z 438 " =    2.295
peak=    3.200 closest distance to " O   HOH Z 329 " =    3.564
peak=    3.197 closest distance to " O   HOH Z 145 " =    3.453
peak=    3.194 closest distance to " O   HOH Z 109 " =    1.177
peak=    3.192 closest distance to " O   HOH Z 189 " =    2.443
peak=    3.190 closest distance to " O   HOH Z  33 " =    1.669
peak=    3.186 closest distance to " O   HOH Z 234 " =    2.014
peak=    3.184 closest distance to " CE BMET A  47 " =    1.356
peak=    3.182 closest distance to " CA  LYS A 117 " =    1.243
peak=    3.182 closest distance to " CE2 TRP A 179 " =    1.427
peak=    3.179 closest distance to " CB  ALA A 295 " =    1.322
peak=    3.178 closest distance to " O   HOH Z 215 " =    1.451
peak=    3.166 closest distance to " CE BLYS A 290 " =    0.808
peak=    3.158 closest distance to " CB  ILE A 120 " =    1.474
peak=    3.154 closest distance to " CD2 LEU A 297 " =    1.010
peak=    3.154 closest distance to " O   HOH Z 130 " =    2.344
peak=    3.152 closest distance to " O   HOH Z 430 " =    5.657
peak=    3.147 closest distance to " CB  ASN A 215 " =    1.044
peak=    3.147 closest distance to " OG BSER A 258 " =    2.784
peak=    3.145 closest distance to " CA  LYS A 290 " =    1.189
peak=    3.144 closest distance to " NH1 ARG A 138 " =    1.554
peak=    3.143 closest distance to " O   HOH Z 148 " =    1.549
peak=    3.141 closest distance to " O   HOH Z 113 " =    1.736
peak=    3.139 closest distance to " O   HOH Z 194 " =    2.028
peak=    3.138 closest distance to " O   HOH Z 368 " =    2.399
peak=    3.137 closest distance to " CA  ALA A 158 " =    1.291
peak=    3.126 closest distance to " CB  ALA A 114 " =    1.491
peak=    3.125 closest distance to " O  BHOH Z 338 " =    2.414
peak=    3.124 closest distance to " O   HOH Z 295 " =    1.485
peak=    3.123 closest distance to " CA  LEU A 101 " =    1.440
peak=    3.119 closest distance to " CA  ARG A  36 " =    1.068
peak=    3.116 closest distance to " O   HOH Z 380 " =    1.905
peak=    3.116 closest distance to " N   GLU A 236 " =    0.910
peak=    3.112 closest distance to " CA  GLY A  80 " =    0.733
peak=    3.111 closest distance to " O   HOH Z 281 " =    4.669
peak=    3.104 closest distance to " CB  ALA A  10 " =    0.764
peak=    3.103 closest distance to " OD1 ASN A 148 " =    1.655
peak=    3.098 closest distance to " N   SER A 135 " =    1.198
peak=    3.097 closest distance to " CB  ARG A 138 " =    1.005
peak=    3.096 closest distance to " O   HOH Z 148 " =    2.258
peak=    3.093 closest distance to " O   HOH Z   4 " =    1.422
peak=    3.086 closest distance to " CB  PHE A 204 " =    1.015
peak=    3.082 closest distance to " O   HOH Z 102 " =    1.114
peak=    3.073 closest distance to " OE2 GLU A  53 " =    2.114
peak=    3.069 closest distance to " O   ILE A  33 " =    1.243
peak=    3.065 closest distance to " N   ASP A 162 " =    1.303
peak=    3.061 closest distance to " CB  ASN A  39 " =    0.811
peak=    3.059 closest distance to " CB  ARG A 190 " =    1.843
peak=    3.051 closest distance to " N   TYR A 116 " =    1.805
peak=    3.003 closest distance to " O   HOH Z 189 " =    2.554

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 209         
Filter by distance & map next to the model:
   mapped sites are within: 0.623 - 5.727
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 207 from: 209
   mapped sites are within: 0.750 - 5.727

peak=   -4.587 closest distance to " CD  ARG A 156 " =    2.125
peak=   -4.555 closest distance to " C   HIS A 108 " =    1.203
peak=   -4.490 closest distance to " CG2 VAL A 230 " =    0.750
peak=   -4.400 closest distance to " O   VAL A  67 " =    2.606
peak=   -4.371 closest distance to " O   PRO A 163 " =    1.965
peak=   -4.368 closest distance to " SG  CYS A 254 " =    3.150
peak=   -4.192 closest distance to " O   HOH Z  56 " =    2.072
peak=   -4.190 closest distance to " OXT GLY A 302 " =    2.792
peak=   -4.142 closest distance to " O   HOH Z 290 " =    1.094
peak=   -4.129 closest distance to " N   ALA A 248 " =    1.676
peak=   -4.117 closest distance to " O   HOH Z 266 " =    4.553
peak=   -4.094 closest distance to " OG BSER A 134 " =    1.311
peak=   -4.082 closest distance to " CG2 ILE A  20 " =    2.846
peak=   -3.981 closest distance to " O   HOH Z  11 " =    1.824
peak=   -3.977 closest distance to " CE2 TYR A  30 " =    2.772
peak=   -3.960 closest distance to " CD1 LEU A 255 " =    2.647
peak=   -3.957 closest distance to " O   HOH Z 429 " =    1.935
peak=   -3.955 closest distance to " O   HOH Z 423 " =    2.200
peak=   -3.922 closest distance to " O   ALA A   8 " =    1.828
peak=   -3.917 closest distance to " N   HIS A 115 " =    2.047
peak=   -3.910 closest distance to " CD  GLN A  88 " =    1.182
peak=   -3.883 closest distance to " O   HOH Z  97 " =    1.245
peak=   -3.867 closest distance to " O   ALA A 161 " =    1.579
peak=   -3.853 closest distance to " O   ASN A 187 " =    1.468
peak=   -3.845 closest distance to " C   GLN A 205 " =    1.866
peak=   -3.844 closest distance to " O   PRO A 198 " =    1.226
peak=   -3.838 closest distance to " OG  SER A   3 " =    1.246
peak=   -3.830 closest distance to " ND2 ASN A  45 " =    1.087
peak=   -3.802 closest distance to " CA  GLY A  23 " =    1.804
peak=   -3.797 closest distance to " CB  ALA A 291 " =    2.416
peak=   -3.783 closest distance to " CB  ALA A  51 " =    1.845
peak=   -3.782 closest distance to " O   HOH Z 191 " =    4.980
peak=   -3.781 closest distance to " NH2 ARG A  79 " =    1.973
peak=   -3.711 closest distance to " CG  PHE A 283 " =    2.578
peak=   -3.703 closest distance to " OD1 ASN A 301 " =    1.893
peak=   -3.696 closest distance to " O   HOH Z  69 " =    1.578
peak=   -3.690 closest distance to " CB  ALA A 161 " =    2.504
peak=   -3.679 closest distance to " O   HOH Z 114 " =    2.872
peak=   -3.658 closest distance to " O   HOH Z 134 " =    2.741
peak=   -3.658 closest distance to " OD2 ASP A 191 " =    1.402
peak=   -3.652 closest distance to " O   HOH Z 165 " =    2.224
peak=   -3.651 closest distance to " O   HOH Z 407 " =    2.580
peak=   -3.649 closest distance to " O   ALA A  51 " =    1.161
peak=   -3.648 closest distance to " O   HOH Z 111 " =    4.159
peak=   -3.647 closest distance to " O   HOH Z  11 " =    2.008
peak=   -3.644 closest distance to " CG  ARG A 219 " =    2.307
peak=   -3.644 closest distance to " O   HOH Z 100 " =    1.140
peak=   -3.634 closest distance to " O   HOH Z 126 " =    1.852
peak=   -3.632 closest distance to " ND2 ASN A 187 " =    1.592
peak=   -3.629 closest distance to " O   SER A 146 " =    0.837
peak=   -3.627 closest distance to " N   PHE A  59 " =    2.218
peak=   -3.621 closest distance to " CG2 VAL A 230 " =    1.092
peak=   -3.613 closest distance to " CB  ASP A 132 " =    2.272
peak=   -3.608 closest distance to " OD1 ASN A  39 " =    2.107
peak=   -3.584 closest distance to " CD1 LEU A 101 " =    2.258
peak=   -3.576 closest distance to " O   HOH Z 193 " =    1.708
peak=   -3.573 closest distance to " N   SER A 276 " =    1.165
peak=   -3.564 closest distance to " CB  ALA A 244 " =    2.052
peak=   -3.554 closest distance to " O   HOH Z 362 " =    5.727
peak=   -3.532 closest distance to " O   HOH Z 250 " =    1.367
peak=   -3.532 closest distance to " CG2 THR A  52 " =    2.935
peak=   -3.525 closest distance to " CA  GLY A 133 " =    1.853
peak=   -3.517 closest distance to " CD1 LEU A 228 " =    1.997
peak=   -3.512 closest distance to " O   HOH Z  37 " =    1.697
peak=   -3.509 closest distance to " O   HOH Z 231 " =    2.282
peak=   -3.508 closest distance to " ND2 ASN A 173 " =    1.393
peak=   -3.504 closest distance to " O   HOH Z 313 " =    1.625
peak=   -3.499 closest distance to " O   HOH Z 166 " =    1.637
peak=   -3.497 closest distance to " C   ASN A 285 " =    2.213
peak=   -3.487 closest distance to " O   HOH Z 427 " =    1.519
peak=   -3.486 closest distance to " O   MET A  40 " =    2.652
peak=   -3.482 closest distance to " O   HOH Z 102 " =    1.742
peak=   -3.480 closest distance to " O   HOH Z 281 " =    3.146
peak=   -3.480 closest distance to " CE3 TRP A 274 " =    2.120
peak=   -3.476 closest distance to " OG  SER A  97 " =    2.151
peak=   -3.456 closest distance to " CZ  TYR A 169 " =    1.818
peak=   -3.455 closest distance to " CG  GLN A  58 " =    1.256
peak=   -3.455 closest distance to " C   LEU A 143 " =    0.998
peak=   -3.446 closest distance to " O   HOH Z 211 " =    1.481
peak=   -3.438 closest distance to " CB  ALA A 131 " =    1.955
peak=   -3.436 closest distance to " O   TRP A  92 " =    1.813
peak=   -3.434 closest distance to " O   HOH Z 175 " =    4.159
peak=   -3.434 closest distance to " CG  ASP A 231 " =    0.856
peak=   -3.431 closest distance to " OG  SER A 206 " =    1.383
peak=   -3.428 closest distance to " O   HOH Z 197 " =    4.852
peak=   -3.426 closest distance to " N   SER A 210 " =    1.389
peak=   -3.424 closest distance to " CA  GLY A 203 " =    2.390
peak=   -3.424 closest distance to " O   HOH Z 139 " =    5.052
peak=   -3.415 closest distance to " O   HOH Z  88 " =    2.006
peak=   -3.412 closest distance to " O   ALA A 292 " =    2.240
peak=   -3.405 closest distance to " O   THR A 182 " =    1.212
peak=   -3.403 closest distance to " OD2 ASP A  50 " =    1.397
peak=   -3.397 closest distance to " CG  GLU A   2 " =    2.101
peak=   -3.390 closest distance to " CB  TRP A 274 " =    2.833
peak=   -3.389 closest distance to " OE1 GLN A 183 " =    1.321
peak=   -3.382 closest distance to " CB  ALA A 291 " =    2.140
peak=   -3.382 closest distance to " OD1 ASP A 191 " =    1.397
peak=   -3.381 closest distance to " N   THR A  52 " =    1.661
peak=   -3.379 closest distance to " CG  LEU A 228 " =    1.062
peak=   -3.377 closest distance to " CD1 LEU A 255 " =    2.553
peak=   -3.373 closest distance to " O   ALA A 256 " =    1.526
peak=   -3.370 closest distance to " O   HOH Z 193 " =    1.602
peak=   -3.368 closest distance to " O   SER A 273 " =    1.378
peak=   -3.363 closest distance to " O   TYR A 247 " =    2.825
peak=   -3.356 closest distance to " O   HOH Z 431 " =    1.589
peak=   -3.354 closest distance to " CG  ARG A 219 " =    2.421
peak=   -3.353 closest distance to " OD1 ASN A 249 " =    1.385
peak=   -3.351 closest distance to " O   HOH Z 388 " =    2.002
peak=   -3.351 closest distance to " C   ARG A 269 " =    1.288
peak=   -3.347 closest distance to " O   HOH Z 421 " =    3.127
peak=   -3.345 closest distance to " CD2 TYR A 293 " =    2.022
peak=   -3.344 closest distance to " O   HOH Z  60 " =    2.136
peak=   -3.342 closest distance to " NE1 TRP A 274 " =    1.197
peak=   -3.342 closest distance to " CB  ALA A  64 " =    2.628
peak=   -3.340 closest distance to " N   ALA A 226 " =    1.921
peak=   -3.337 closest distance to " N   GLN A  58 " =    1.852
peak=   -3.335 closest distance to " CB  ASN A  39 " =    2.217
peak=   -3.334 closest distance to " O   HOH Z 385 " =    1.813
peak=   -3.331 closest distance to " N   GLN A  77 " =    1.598
peak=   -3.325 closest distance to " ND2 ASN A  45 " =    1.152
peak=   -3.325 closest distance to " CD1 TYR A 247 " =    2.524
peak=   -3.320 closest distance to " O   HOH Z 234 " =    3.902
peak=   -3.317 closest distance to " O   HOH Z  98 " =    1.938
peak=   -3.316 closest distance to " ND2 ASN A  39 " =    1.158
peak=   -3.316 closest distance to " O   HOH Z 351 " =    1.538
peak=   -3.312 closest distance to " O   PHE A 218 " =    1.514
peak=   -3.310 closest distance to " CB  ASP A 132 " =    2.181
peak=   -3.310 closest distance to " C   MET A 188 " =    1.529
peak=   -3.310 closest distance to " O   ILE A 120 " =    1.258
peak=   -3.309 closest distance to " O   HOH Z 387 " =    2.549
peak=   -3.305 closest distance to " CZ  PHE A 130 " =    0.944
peak=   -3.300 closest distance to " O   HOH Z 198 " =    2.017
peak=   -3.295 closest distance to " OG ASER A 134 " =    1.248
peak=   -3.295 closest distance to " O   HOH Z 131 " =    4.039
peak=   -3.295 closest distance to " O   HOH Z 414 " =    2.469
peak=   -3.294 closest distance to " CD  ARG A 139 " =    1.526
peak=   -3.286 closest distance to " CG  LYS A 193 " =    2.096
peak=   -3.286 closest distance to " CD2 LEU A 300 " =    2.799
peak=   -3.280 closest distance to " CB  PRO A 163 " =    2.668
peak=   -3.275 closest distance to " OG BSER A 134 " =    1.580
peak=   -3.274 closest distance to " CG  ASP A  50 " =    2.328
peak=   -3.271 closest distance to " O   SER A 135 " =    1.596
peak=   -3.268 closest distance to " CD  GLN A  88 " =    2.063
peak=   -3.267 closest distance to " CE2 PHE A 218 " =    2.593
peak=   -3.262 closest distance to " CB  ALA A  43 " =    2.218
peak=   -3.262 closest distance to " O   HOH Z 339 " =    1.681
peak=   -3.262 closest distance to " C   GLY A  91 " =    1.406
peak=   -3.262 closest distance to " CG1 VAL A 296 " =    1.958
peak=   -3.261 closest distance to " OE1 GLN A  88 " =    1.058
peak=   -3.255 closest distance to " O   HOH Z 311 " =    3.570
peak=   -3.250 closest distance to " N   PRO A 163 " =    1.454
peak=   -3.250 closest distance to " CA  ASP A 298 " =    1.058
peak=   -3.246 closest distance to " O   HOH Z 137 " =    1.645
peak=   -3.239 closest distance to " OG1 THR A 178 " =    1.133
peak=   -3.238 closest distance to " CD1 PHE A  61 " =    2.888
peak=   -3.237 closest distance to " O   LYS A 289 " =    2.525
peak=   -3.236 closest distance to " OD1 ASP A 200 " =    1.319
peak=   -3.234 closest distance to " OE2 GLU A   2 " =    1.270
peak=   -3.226 closest distance to " ND2 ASN A 142 " =    2.012
peak=   -3.223 closest distance to " O   VAL A 197 " =    1.235
peak=   -3.220 closest distance to " CG  ASN A  45 " =    1.900
peak=   -3.213 closest distance to " NE  ARG A 259 " =    0.919
peak=   -3.208 closest distance to " OH  TYR A 172 " =    1.729
peak=   -3.208 closest distance to " O   HOH Z 397 " =    1.281
peak=   -3.208 closest distance to " N   ALA A  43 " =    2.376
peak=   -3.204 closest distance to " O   HOH Z 346 " =    1.809
peak=   -3.203 closest distance to " N   THR A 220 " =    2.035
peak=   -3.192 closest distance to " ND2 ASN A 209 " =    1.951
peak=   -3.187 closest distance to " OD1 ASN A 176 " =    1.172
peak=   -3.186 closest distance to " CG  GLU A 152 " =    1.311
peak=   -3.177 closest distance to " C   ALA A 158 " =    1.202
peak=   -3.177 closest distance to " O   HOH Z 249 " =    1.123
peak=   -3.176 closest distance to " O   HOH Z 423 " =    1.213
peak=   -3.176 closest distance to " O   HOH Z 192 " =    0.923
peak=   -3.175 closest distance to " OXT GLY A 302 " =    3.566
peak=   -3.171 closest distance to " CG2 THR A  31 " =    2.855
peak=   -3.170 closest distance to " O   HOH Z 344 " =    2.347
peak=   -3.170 closest distance to " O   HOH Z  16 " =    1.661
peak=   -3.170 closest distance to " CG2 VAL A 189 " =    1.987
peak=   -3.167 closest distance to " CG1 VAL A 112 " =    2.629
peak=   -3.163 closest distance to " O   SER A  22 " =    2.250
peak=   -3.161 closest distance to " O   HOH Z  47 " =    1.531
peak=   -3.161 closest distance to " OH  TYR A 169 " =    0.851
peak=   -3.161 closest distance to " O   HOH Z 185 " =    2.181
peak=   -3.161 closest distance to " CD2 HIS A 115 " =    0.914
peak=   -3.160 closest distance to " CE BMET A  47 " =    1.294
peak=   -3.157 closest distance to " OD1 ASP A 191 " =    1.569
peak=   -3.156 closest distance to " CG  PRO A 243 " =    1.426
peak=   -3.155 closest distance to " OD1 ASP A 171 " =    1.404
peak=   -3.154 closest distance to " CG2 THR A  42 " =    1.893
peak=   -3.151 closest distance to " O   LEU A 261 " =    1.713
peak=   -3.147 closest distance to " CG  GLN A 278 " =    1.989
peak=   -3.143 closest distance to " CG  LYS A  76 " =    2.952
peak=   -3.139 closest distance to " O   HOH Z 139 " =    3.192
peak=   -3.132 closest distance to " O   HOH Z 100 " =    1.457
peak=   -3.130 closest distance to " O   HOH Z 326 " =    1.530
peak=   -3.130 closest distance to " O   HOH Z 426 " =    1.616
peak=   -3.126 closest distance to " OG  SER A  22 " =    4.352
peak=   -3.123 closest distance to " CD2 LEU A 237 " =    2.585
peak=   -3.120 closest distance to " O   HOH Z 389 " =    1.491
peak=   -3.117 closest distance to " NH2AARG A 275 " =    4.740
peak=   -3.107 closest distance to " ND2 ASN A 127 " =    1.732
peak=   -3.098 closest distance to " C   THR A 279 " =    1.222
peak=   -3.082 closest distance to " O   GLY A  75 " =    1.658
peak=   -3.061 closest distance to " CD2 TRP A 274 " =    1.046
peak=   -3.055 closest distance to " O   HOH Z 218 " =    3.113
peak=   -3.018 closest distance to " O   HOH Z 407 " =    3.137

================= 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    :  0.4832 0.4726   6.281248e+00   6.272006e+00
   1_bss:  0.4734 0.4631   6.273924e+00   6.261665e+00
   1_xyz:  0.4086 0.4220   6.189303e+00   6.211520e+00
   1_adp:  0.3607 0.4077   6.110988e+00   6.184722e+00
   1_occ:  0.3602 0.4075   6.109970e+00   6.185218e+00
   2_bss:  0.3561 0.4044   6.109209e+00   6.184313e+00
   2_xyz:  0.2724 0.3215   5.891673e+00   6.021754e+00
   2_adp:  0.2498 0.3000   5.823790e+00   5.970793e+00
   2_occ:  0.2495 0.2996   5.823158e+00   5.970160e+00
   3_bss:  0.2474 0.2988   5.820982e+00   5.969179e+00
   3_xyz:  0.1704 0.2178   5.494826e+00   5.696319e+00
   3_adp:  0.1575 0.2076   5.431087e+00   5.651770e+00
   3_occ:  0.1570 0.2072   5.428973e+00   5.649217e+00
   4_bss:  0.1566 0.2062   5.426091e+00   5.643370e+00
   4_xyz:  0.1381 0.1883   5.333006e+00   5.560234e+00
   4_adp:  0.1255 0.1718   5.236626e+00   5.461667e+00
   4_occ:  0.1254 0.1718   5.236022e+00   5.460933e+00
   5_bss:  0.1253 0.1717   5.235470e+00   5.460513e+00
   5_xyz:  0.1154 0.1615   5.168015e+00   5.405588e+00
   5_adp:  0.1129 0.1596   5.152976e+00   5.393337e+00
   5_occ:  0.1128 0.1596   5.152797e+00   5.393181e+00
   5_bss:  0.1128 0.1596   5.151944e+00   5.392021e+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:  0.355   0.000   8.593   8.115   8.771   0.000   0.000   0.000
   1_xyz:  0.355   0.000   8.593   8.115   8.771   0.000   0.000   0.000
   1_adp:  0.355   0.000   8.593   8.115   8.771   0.000   0.000   0.000
   1_occ:  0.355   0.000   8.593   8.115   8.771   0.000   0.000   0.000
   2_bss:  0.328  20.001   4.488   3.683   5.158   0.000   0.000   0.000
   2_xyz:  0.328  20.001   4.488   3.683   5.158   0.000   0.000   0.000
   2_adp:  0.328  20.001   4.488   3.683   5.158   0.000   0.000   0.000
   2_occ:  0.328  20.001   4.488   3.683   5.158   0.000   0.000   0.000
   3_bss:  0.326  31.544   2.229   2.149   3.288   0.000   0.000   0.000
   3_xyz:  0.326  31.544   2.229   2.149   3.288   0.000   0.000   0.000
   3_adp:  0.326  31.544   2.229   2.149   3.288   0.000   0.000   0.000
   3_occ:  0.326  31.544   2.229   2.149   3.288   0.000   0.000   0.000
   4_bss:  0.323  31.544   0.964   1.541   2.354   0.000   0.000   0.000
   4_xyz:  0.323  31.544   0.964   1.541   2.354   0.000   0.000   0.000
   4_adp:  0.323  31.544   0.964   1.541   2.354   0.000   0.000   0.000
   4_occ:  0.323  31.544   0.964   1.541   2.354   0.000   0.000   0.000
   5_bss:  0.318  31.808   0.516   1.262   2.018   0.000   0.000   0.000
   5_xyz:  0.318  31.808   0.516   1.262   2.018   0.000   0.000   0.000
   5_adp:  0.318  31.808   0.516   1.262   2.018   0.000   0.000   0.000
   5_occ:  0.318  31.808   0.516   1.262   2.018   0.000   0.000   0.000
   5_bss:  0.316  34.496  -0.749  -0.003   0.753   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  57.280 0.4294  0.5096    70246.561
   1_bss:  57.379 0.4258  0.6416    66927.398
   1_xyz:  48.831 0.5342  0.7984    52877.229
   1_adp:  44.843 0.5843  0.9232    47914.167
   1_occ:  44.847 0.5843  0.9219    47885.561
   2_bss:  44.596 0.5873  0.8057    47568.730
   2_xyz:  33.369 0.7199  0.9634    27533.325
   2_adp:  30.479 0.7529  1.0055    23963.009
   2_occ:  30.457 0.7532  1.0057    23953.493
   3_bss:  30.329 0.7545  0.9403    23804.637
   3_xyz:  21.151 0.8501  1.0144    12067.225
   3_adp:  19.906 0.8625  1.0261    10992.593
   3_occ:  19.862 0.8629  1.0266    10936.316
   4_bss:  19.708 0.8642  0.9916    10742.679
   4_xyz:  17.648 0.8838  0.9999     8954.756
   4_adp:  15.551 0.9022  1.0053     7394.685
   4_occ:  15.540 0.9023  1.0054     7384.399
   5_bss:  15.531 0.9024  0.9921     7371.028
   5_xyz:  14.429 0.9114  0.9949     6572.475
   5_adp:  14.160 0.9139  0.9918     6433.096
   5_occ:  14.158 0.9139  0.9917     6431.345
   5_bss:  14.158 0.9138  0.9914     6417.135
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.085   5.2768e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.085   5.2768e+01
   1_xyz:   1.568  0.012  0.101 18.375  0.006  4.115   1.3227e-01
   1_adp:   1.568  0.012  0.101 18.375  0.006  4.115   1.3227e-01
   1_occ:   1.568  0.012  0.101 18.375  0.006  4.115   1.3227e-01
   2_bss:   1.568  0.012  0.101 18.375  0.006  4.115   1.3227e-01
   2_xyz:   1.123  0.007  0.078 16.340  0.005  4.116   7.7050e-02
   2_adp:   1.123  0.007  0.078 16.340  0.005  4.116   7.7050e-02
   2_occ:   1.123  0.007  0.078 16.340  0.005  4.116   7.7050e-02
   3_bss:   1.123  0.007  0.078 16.340  0.005  4.116   7.7050e-02
   3_xyz:   1.139  0.007  0.081 15.984  0.004  4.111   7.3706e-02
   3_adp:   1.139  0.007  0.081 15.984  0.004  4.111   7.3706e-02
   3_occ:   1.139  0.007  0.081 15.984  0.004  4.111   7.3706e-02
   4_bss:   1.139  0.007  0.081 15.984  0.004  4.111   7.3706e-02
   4_xyz:   0.996  0.006  0.071 15.889  0.004  4.113   6.1604e-02
   4_adp:   0.996  0.006  0.071 15.889  0.004  4.113   6.1604e-02
   4_occ:   0.996  0.006  0.071 15.889  0.004  4.113   6.1604e-02
   5_bss:   0.996  0.006  0.071 15.889  0.004  4.113   6.1604e-02
   5_xyz:   1.053  0.007  0.075 15.857  0.004  4.105   6.5918e-02
   5_adp:   1.053  0.007  0.075 15.857  0.004  4.105   6.5918e-02
   5_occ:   1.053  0.007  0.075 15.857  0.004  4.105   6.5918e-02
   5_bss:   1.053  0.007  0.075 15.857  0.004  4.105   6.5918e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.971   6.8291e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.971   6.8291e+00
   1_xyz:  13.237  0.152  0.405 89.349  0.036  2.162   8.5540e-02
   1_adp:  13.237  0.152  0.405 89.349  0.036  2.162   8.5540e-02
   1_occ:  13.237  0.152  0.405 89.349  0.036  2.162   8.5540e-02
   2_bss:  13.237  0.152  0.405 89.349  0.036  2.162   8.5540e-02
   2_xyz:   6.581  0.075  0.414 80.797  0.035  2.275   5.2701e-02
   2_adp:   6.581  0.075  0.414 80.797  0.035  2.275   5.2701e-02
   2_occ:   6.581  0.075  0.414 80.797  0.035  2.275   5.2701e-02
   3_bss:   6.581  0.075  0.414 80.797  0.035  2.275   5.2701e-02
   3_xyz:   7.280  0.045  0.383 84.304  0.027  2.281   6.0314e-02
   3_adp:   7.280  0.045  0.383 84.304  0.027  2.281   6.0314e-02
   3_occ:   7.280  0.045  0.383 84.304  0.027  2.281   6.0314e-02
   4_bss:   7.280  0.045  0.383 84.304  0.027  2.281   6.0314e-02
   4_xyz:   6.995  0.035  0.276 82.591  0.035  2.308   4.1903e-02
   4_adp:   6.995  0.035  0.276 82.591  0.035  2.308   4.1903e-02
   4_occ:   6.995  0.035  0.276 82.591  0.035  2.308   4.1903e-02
   5_bss:   6.995  0.035  0.276 82.591  0.035  2.308   4.1903e-02
   5_xyz:   7.289  0.043  0.281 83.352  0.034  2.310   4.9592e-02
   5_adp:   7.289  0.043  0.281 83.352  0.034  2.310   4.9592e-02
   5_occ:   7.289  0.043  0.281 83.352  0.034  2.310   4.9592e-02
   5_bss:   7.289  0.043  0.281 83.352  0.034  2.310   4.9592e-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:  73.24   0.00  13.58  71.94   0.00  11.15  73.24   0.00  26.81
   1_occ:  73.24   0.00  13.58  71.94   0.00  11.15  73.24   0.00  26.81
   2_bss:  73.24   0.00  13.58  71.94   0.00  11.15  73.24   0.00  26.81
   2_xyz:  73.24   0.00  13.58  71.94   0.00  11.15  73.24   0.00  26.81
   2_adp:  83.83   0.00  14.02  83.83   0.00  10.45  81.57   0.00  33.46
   2_occ:  83.83   0.00  14.02  83.83   0.00  10.45  81.57   0.00  33.46
   3_bss:  83.83   0.00  14.02  83.83   0.00  10.45  81.57   0.00  33.46
   3_xyz:  83.83   0.00  14.02  83.83   0.00  10.45  81.57   0.00  33.46
   3_adp:  84.40   0.00  14.06  84.40   0.00  10.32  81.76   1.38  34.42
   3_occ:  84.40   0.00  14.06  84.40   0.00  10.32  81.76   1.38  34.42
   4_bss:  84.40   0.00  14.06  84.40   0.00  10.32  81.76   1.38  34.42
   4_xyz:  84.40   0.00  14.06  84.40   0.00  10.32  81.76   1.38  34.42
   4_adp:  87.60   0.00  13.88  87.60   0.00   9.65  80.40   2.24  36.89
   4_occ:  87.60   0.00  13.88  87.60   0.00   9.65  80.40   2.24  36.89
   5_bss:  87.60   0.00  13.88  87.60   0.00   9.65  80.40   2.24  36.89
   5_xyz:  87.60   0.00  13.88  87.60   0.00   9.65  80.40   2.24  36.89
   5_adp:  91.21   0.00  13.86  91.21   0.00   9.53  84.79   3.16  37.41
   5_occ:  91.21   0.00  13.86  91.21   0.00   9.53  84.79   3.16  37.41
   5_bss:  92.48   1.27  15.12  92.48   1.27  10.80  86.06   4.42  38.68
------------------------------------------------------------------------
 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:    1.207    0.023    0.399
   1_adp:    1.207    0.023    0.399
   1_occ:    1.207    0.023    0.399
   2_bss:    1.207    0.023    0.399
   2_xyz:    1.656    0.013    0.553
   2_adp:    1.656    0.013    0.553
   2_occ:    1.656    0.013    0.553
   3_bss:    1.656    0.013    0.553
   3_xyz:    1.710    0.042    0.663
   3_adp:    1.710    0.042    0.663
   3_occ:    1.710    0.042    0.663
   4_bss:    1.710    0.042    0.663
   4_xyz:    1.660    0.027    0.693
   4_adp:    1.660    0.027    0.693
   4_occ:    1.660    0.027    0.693
   5_bss:    1.660    0.027    0.693
   5_xyz:    1.635    0.037    0.716
   5_adp:    1.635    0.037    0.716
   5_occ:    1.635    0.037    0.716
   5_bss:    1.635    0.037    0.716
------------------------------------------------------------------------

CPU time actual refinement: 337.08


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_46/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_46/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_46/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_46/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_46/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 336.93 
  Macro-tasks:
    bulk solvent and scale       = 47.54  
    individual site refinement   = 132.20 
    weights calculation          = 33.00  
    collect and process          = 6.51   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 219.37 
  Micro-tasks:
    mask                            = 2.37   
    f_calc                          = 101.40 
    alpha_beta                      = 8.17   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 110.73 
    fmodel                         = 7.85   
    r_factors                      = 0.38   
    phase_errors                   = 10.55  
    foms                           = 0.28   
    TOTAL for micro-tasks          = 242.90 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.750 micro seconds
Total CPU time: 5.84 minutes
from_scatterers_fft:    648 calls, 101.01 s
gradients_fft:          592 calls,  97.74 s

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

# Date 2008-01-16 Time 00:38:59 PST -0800 (1200472739.78 s)
Start R-work = 0.4832, R-free = 0.4726 (no bulk solvent and anisotropic scale)
Final R-work = 0.1302, R-free = 0.1757 (no bulk solvent and anisotropic scale)

Start R-work = 0.4734, R-free = 0.4631
Final R-work = 0.1128, R-free = 0.1596