# Date 2008-01-16 Time 00:39:39 PST -0800 (1200472779.17 s)
#phil __OFF__

Command line arguments: "../105.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 31221
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 105

-------------------------------------------------------------------------------
  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, 47.8686, 86.822, 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: 3.30, per 1000 atoms: 1.17


================================== 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, 47.8686, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9766 1.95088
Completeness in resolution range: 0.916573
Completeness with d_max=infinity: 0.913879

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9766
                             d_min =   1.9509

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, 47.8686, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9766 1.95088
Completeness in resolution range: 0.916573
Completeness with d_max=infinity: 0.913879

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9770 -  4.1755 [2243/2272]  2014   229  10.2%
  bin  2:  4.1755 -  3.3262 [2151/2174]  1935   216  10.0%
  bin  3:  3.3262 -  2.9092 [2126/2151]  1922   204   9.6%
  bin  4:  2.9092 -  2.6448 [2101/2128]  1887   214  10.2%
  bin  5:  2.6448 -  2.4561 [2079/2112]  1867   212  10.2%
  bin  6:  2.4561 -  2.3119 [2084/2112]  1878   206   9.9%
  bin  7:  2.3119 -  2.1965 [2072/2108]  1872   200   9.7%
  bin  8:  2.1965 -  2.1011 [2076/2118]  1866   210  10.1%
  bin  9:  2.1011 -  2.0204 [1995/2096]  1797   198   9.9%
  bin 10:  2.0204 -  1.9509 [ 662/2101]   592    70  10.6%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_105/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:
        0.99 -     1.77: 8
        1.77 -     2.55: 59
        2.55 -     3.33: 3966
        3.33 -     4.12: 9429
        4.12 -     4.90: 14970
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 109 " - " O   HOH Z 417 "  0.985 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.036 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.204 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  70 " - " O   HOH Z 296 "  1.460 3.040 -x+1/2,-y+1,z+1/2
  " N   TRP A  92 " - " O   HOH Z 401 "  1.565 3.120 -x+1,y-1/2,-z+1/2
  ... (remaining 28427 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_105/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_105/model_refine_001.geo

CPU time processing inputs: 9.42


============================ 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 47.8686 86.82195 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 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5094   r_free= 0.5007   ksol= 0.00   Bsol= 0.00   scale= 0.772    |
|                                                                             |
| 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:   0.87 A                  |
| x-ray target function (ml) for work reflections: 6.306184                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9770 -  4.6577 0.99   1461  161 0.4192 0.4210      6.6458       6.702|
|  2:  4.6577 -  3.7156 0.99   1403  154 0.4400 0.4468      6.8437      6.8631|
|  3:  3.7156 -  3.2514 0.99   1363  153 0.4890 0.4689      6.7111       6.725|
|  4:  3.2514 -  2.9566 0.98   1375  148 0.5014 0.4720      6.5323      6.5114|
|  5:  2.9566 -  2.7461 0.99   1335  155 0.5500 0.5405      6.3787      6.3943|
|  6:  2.7461 -  2.5850 0.99   1377  150 0.5416 0.5441      6.2945      6.2125|
|  7:  2.5850 -  2.4561 0.98   1311  154 0.5250 0.5036      6.2385      6.1674|
|  8:  2.4561 -  2.3497 0.98   1344  143 0.5486 0.5112      6.1816      6.1845|
|  9:  2.3497 -  2.2595 0.99   1341  140 0.5503 0.5548        6.12      6.1656|
| 10:  2.2595 -  2.1818 0.99   1352  147 0.5526 0.5584      6.0969      6.1123|
| 11:  2.1818 -  2.1138 0.97   1308  156 0.5659 0.5451      6.0217       6.059|
| 12:  2.1138 -  2.0535 0.98   1316  151 0.5480 0.5471      5.9545       5.939|
| 13:  2.0535 -  1.9996 0.80   1084  114 0.5525 0.5741      5.8705      5.8055|
| 14:  1.9996 -  1.9509 0.19    260   33 0.5930 0.4581      5.9303      5.7222|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9770 -  4.6577  1461   161  0.62  40.88   0.79     0.64      93734.50|
|  2:  4.6577 -  3.7156  1403   154  0.63  41.51   0.86     0.68     135441.84|
|  3:  3.7156 -  3.2514  1363   153  0.51  50.99   0.81     0.64     139594.00|
|  4:  3.2514 -  2.9566  1375   148  0.43  57.42   0.77     0.54     115398.41|
|  5:  2.9566 -  2.7461  1335   155  0.33  64.80   0.70     0.43      93038.61|
|  6:  2.7461 -  2.5850  1377   150  0.30  67.22   0.70     0.36      80154.62|
|  7:  2.5850 -  2.4561  1311   154  0.27  69.82   0.73     0.32      73697.05|
|  8:  2.4561 -  2.3497  1344   143  0.28  69.25   0.71     0.34      63907.26|
|  9:  2.3497 -  2.2595  1341   140  0.28  68.99   0.70     0.35      60123.15|
| 10:  2.2595 -  2.1818  1352   147  0.28  68.84   0.73     0.35      53017.77|
| 11:  2.1818 -  2.1138  1308   156  0.25  71.36   0.72     0.33      51747.05|
| 12:  2.1138 -  2.0535  1316   151  0.22  73.35   0.74     0.31      48261.39|
| 13:  2.0535 -  1.9996  1084   114  0.19  75.56   0.72     0.27      42090.79|
| 14:  1.9996 -  1.9509   260    33  0.20  74.90   0.71     0.21      31960.82|
|alpha:            min =        0.21 max =            0.68 mean =         0.43|
|beta:             min =    31960.82 max =       139594.00 mean =     81136.51|
|figures of merit: min =        0.00 max =            1.00 mean =         0.36|
|phase err.(work): min =        0.00 max =           90.00 mean =        62.79|
|phase err.(test): min =        0.00 max =           89.98 mean =        62.93|
|-----------------------------------------------------------------------------|

============================== Outliers rejection =============================

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 0
total                    = 0

====================== Target weights (before refinement) =====================

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.432876             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.405   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.867390              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.653   (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 |  0.722 -  1.140:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.140 -  1.558:        7 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.558 -  1.975:       39 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  1.975 -  2.393:      283 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.393 -  2.811:     1024 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.811 -  3.229:     2245 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.229 -  3.647:     3817 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.647 -  4.064:     5334 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.064 -  4.482:     7093 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.482 -  4.900:     8601 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.644 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.087    4.900  0.722 |       3.315 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.737)------------------------------------------|
|    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 = 11.737)------------------------------------------|
|    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 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5139   r_free= 0.5036   ksol= 0.00   Bsol= 0.00   scale= 0.743    |
|                                                                             |
| 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:   0.91 A                  |
| x-ray target function (ml) for work reflections: 6.306428                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5030   r_free= 0.4961   ksol= 0.32   Bsol= 1.41   scale= 0.975    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.65,11.36,7.97,0.00,0.00,0.00); trace/3= 8.99                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.91 A                  |
| x-ray target function (ml) for work reflections: 6.299631                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.515336             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.952   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.877246              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.531   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5030      final r-factor (work) = 0.4501          |
| start r-factor (free) = 0.4961      final r-factor (free) = 0.4633          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 99.3962 = 14.52 * 0.50 * 6.3039 + 1.00 * 53.6443                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 45.5761 = 14.52 * 0.50 * 6.2614 + 1.00 * 0.1326                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4501      final r-factor (work) = 0.4071          |
| start r-factor (free) = 0.4633      final r-factor (free) = 0.4655          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.7690 = 1.88 * 1.00 * 6.2614 + 1.00 * 0.0147                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.6898 = 1.88 * 1.00 * 6.2146 + 1.00 * 0.0234                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.737)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    104.95  17.66    None  None   None       |
|    all(noH): 2823   0      0.00    104.95  17.66    None  None   None       |
|    Sol.    : 438    0      0.00    104.95  28.25    None  None   None       |
|    Mac.    : 2385   0      0.00    82.88   15.72    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.495: 1081   |   5:    52.476 -  62.972:   38        |
|      1:    10.495 -  20.991:  827   |   6:    62.972 -  73.467:   29        |
|      2:    20.991 -  31.486:  471   |   7:    73.467 -  83.962:   14        |
|      3:    31.486 -  41.981:  238   |   8:    83.962 -  94.458:    2        |
|      4:    41.981 -  52.476:  120   |   9:    94.458 - 104.953:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4071 r_free = 0.4655             target_work(ml) = 6.205         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4066 r_free = 0.4655             target_work(ml) = 6.204         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4066   r_free= 0.4655   ksol= 0.32   Bsol= 1.41   scale= 1.136    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.65,11.36,7.97,0.00,0.00,0.00); trace/3= 8.99                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.203814                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4041   r_free= 0.4571   ksol= 0.33   Bsol= 30.76   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.50,6.26,4.26,0.00,0.00,0.00); trace/3= 4.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.203134                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.137263             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.507  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.663604              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.133  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4041      final r-factor (work) = 0.3325          |
| start r-factor (free) = 0.4571      final r-factor (free) = 0.3934          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 40.9290 = 13.14 * 0.50 * 6.2108 + 1.00 * 0.1324                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 40.3340 = 13.14 * 0.50 * 6.1239 + 1.00 * 0.1086                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3325      final r-factor (work) = 0.3127          |
| start r-factor (free) = 0.3934      final r-factor (free) = 0.3763          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0874 = 0.66 * 1.00 * 6.1239 + 1.00 * 0.0235                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0150 = 0.66 * 1.00 * 6.0320 + 1.00 * 0.0121                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.737)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.92   16.53    None  None   None       |
|    all(noH): 2823   0      0.00    92.92   16.53    None  None   None       |
|    Sol.    : 438    0      0.00    92.92   31.08    None  None   None       |
|    Mac.    : 2385   0      0.00    78.66   13.85    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.292: 1008   |   5:    46.462 -  55.754:   42        |
|      1:     9.292 -  18.585:  892   |   6:    55.754 -  65.046:   32        |
|      2:    18.585 -  27.877:  434   |   7:    65.046 -  74.338:   16        |
|      3:    27.877 -  37.169:  264   |   8:    74.338 -  83.631:    6        |
|      4:    37.169 -  46.462:  127   |   9:    83.631 -  92.923:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3127 r_free = 0.3763             target_work(ml) = 6.012         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3124 r_free = 0.3757             target_work(ml) = 6.011         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3124   r_free= 0.3757   ksol= 0.33   Bsol= 30.76   scale= 1.083   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.50,6.26,4.26,0.00,0.00,0.00); trace/3= 4.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.011128                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3090   r_free= 0.3736   ksol= 0.30   Bsol= 30.76   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.77,3.25,2.24,0.00,0.00,0.00); trace/3= 2.09                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.010693                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.716072              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.534  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.278565              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.891  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3090      final r-factor (work) = 0.2262          |
| start r-factor (free) = 0.3736      final r-factor (free) = 0.2795          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.4041 = 8.72 * 0.50 * 6.0338 + 1.00 * 0.1086                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.8464 = 8.72 * 0.50 * 5.9069 + 1.00 * 0.1037                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2262      final r-factor (work) = 0.2032          |
| start r-factor (free) = 0.2795      final r-factor (free) = 0.2489          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6576 = 0.28 * 1.00 * 5.9069 + 1.00 * 0.0122                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5997 = 0.28 * 1.00 * 5.6956 + 1.00 * 0.0131                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.737)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.54   15.61    None  None   None       |
|    all(noH): 2823   0      0.00    84.54   15.61    None  None   None       |
|    Sol.    : 438    0      4.42    84.54   35.09    None  None   None       |
|    Mac.    : 2385   0      0.00    80.51   12.03    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 -   8.454: 1011   |   5:    42.269 -  50.722:  102        |
|      1:     8.454 -  16.908: 1006   |   6:    50.722 -  59.176:   53        |
|      2:    16.908 -  25.361:  304   |   7:    59.176 -  67.630:   15        |
|      3:    25.361 -  33.815:  185   |   8:    67.630 -  76.084:    8        |
|      4:    33.815 -  42.269:  134   |   9:    76.084 -  84.537:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2032 r_free = 0.2489             target_work(ml) = 5.647         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2028 r_free = 0.2482             target_work(ml) = 5.645         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2028   r_free= 0.2482   ksol= 0.30   Bsol= 30.76   scale= 1.049   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.77,3.25,2.24,0.00,0.00,0.00); trace/3= 2.09                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.645223                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2007   r_free= 0.2463   ksol= 0.32   Bsol= 46.73   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.06,1.17,0.81,0.00,0.00,0.00); trace/3= 0.31                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.642527                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.428101              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.132   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.423470              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.752   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2007      final r-factor (work) = 0.1520          |
| start r-factor (free) = 0.2463      final r-factor (free) = 0.1956          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.7333 = 4.43 * 0.50 * 5.7043 + 1.00 * 0.1037                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.3178 = 4.43 * 0.50 * 5.5297 + 1.00 * 0.0747                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1520      final r-factor (work) = 0.1449          |
| start r-factor (free) = 0.1956      final r-factor (free) = 0.1909          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3514 = 0.42 * 1.00 * 5.5297 + 1.00 * 0.0098                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2927 = 0.42 * 1.00 * 5.3759 + 1.00 * 0.0162                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 13     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.737)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.24   15.67    None  None   None       |
|    all(noH): 2823   0      0.00    84.24   15.67    None  None   None       |
|    Sol.    : 438    0      4.71    84.24   35.94    None  None   None       |
|    Mac.    : 2385   0      0.00    80.99   11.95    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 -   8.424:  983   |   5:    42.120 -  50.545:  101        |
|      1:     8.424 -  16.848: 1056   |   6:    50.545 -  58.969:   59        |
|      2:    16.848 -  25.272:  283   |   7:    58.969 -  67.393:   15        |
|      3:    25.272 -  33.696:  172   |   8:    67.393 -  75.817:   10        |
|      4:    33.696 -  42.120:  139   |   9:    75.817 -  84.241:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1449 r_free = 0.1909             target_work(ml) = 5.363         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1447 r_free = 0.1907             target_work(ml) = 5.362         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1447   r_free= 0.1907   ksol= 0.32   Bsol= 46.73   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.06,1.17,0.81,0.00,0.00,0.00); trace/3= 0.31                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.362022                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1450   r_free= 0.1914   ksol= 0.32   Bsol= 45.51   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.63,0.26,0.52,0.00,0.00,0.00); trace/3= -0.29                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.364062                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.660589              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 121.484  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.185906              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.820   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1450      final r-factor (work) = 0.1322          |
| start r-factor (free) = 0.1914      final r-factor (free) = 0.1810          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.2300 = 2.66 * 0.50 * 5.3787 + 1.00 * 0.0747                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1536 = 2.66 * 0.50 * 5.3273 + 1.00 * 0.0667                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1322      final r-factor (work) = 0.1269          |
| start r-factor (free) = 0.1810      final r-factor (free) = 0.1732          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9958 = 0.19 * 1.00 * 5.3273 + 1.00 * 1.0054                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9898 = 0.19 * 1.00 * 5.2814 + 1.00 * 0.0080                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.737)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.54    82.44   15.46    None  None   None       |
|    all(noH): 2823   0      1.54    82.44   15.46    None  None   None       |
|    Sol.    : 438    0      5.08    82.44   36.28    None  None   None       |
|    Mac.    : 2385   0      1.54    80.84   11.64    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:     1.544 -   9.634: 1251   |   5:    41.991 -  50.081:   96        |
|      1:     9.634 -  17.723:  891   |   6:    50.081 -  58.170:   65        |
|      2:    17.723 -  25.812:  213   |   7:    58.170 -  66.260:   17        |
|      3:    25.812 -  33.902:  141   |   8:    66.260 -  74.349:    9        |
|      4:    33.902 -  41.991:  134   |   9:    74.349 -  82.439:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1269 r_free = 0.1732             target_work(ml) = 5.257         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1268 r_free = 0.1733             target_work(ml) = 5.257         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1268   r_free= 0.1733   ksol= 0.32   Bsol= 45.51   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.63,0.26,0.52,0.00,0.00,0.00); trace/3= -0.29                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.256957                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9770 -  4.6577 0.99   1461  161 0.1018 0.1421      5.4371      5.6332|
|  2:  4.6577 -  3.7156 0.99   1403  154 0.0910 0.1108      5.4999      5.6721|
|  3:  3.7156 -  3.2514 0.99   1363  153 0.1198 0.1684      5.5589      5.9163|
|  4:  3.2514 -  2.9566 0.98   1375  148 0.1425 0.1775       5.549      5.7249|
|  5:  2.9566 -  2.7461 0.99   1335  155 0.1570 0.1840      5.4498      5.6114|
|  6:  2.7461 -  2.5850 0.99   1377  150 0.1402 0.2214      5.3185      5.5438|
|  7:  2.5850 -  2.4561 0.98   1311  154 0.1419 0.1802      5.2684      5.4236|
|  8:  2.4561 -  2.3497 0.98   1344  143 0.1363 0.1960      5.1888      5.4165|
|  9:  2.3497 -  2.2595 0.99   1341  140 0.1374 0.2073      5.1281      5.4074|
| 10:  2.2595 -  2.1818 0.99   1352  147 0.1330 0.1972       5.076      5.2788|
| 11:  2.1818 -  2.1138 0.97   1308  156 0.1324 0.1878      5.0097       5.293|
| 12:  2.1138 -  2.0535 0.98   1316  151 0.1340 0.1735      4.9634      5.1605|
| 13:  2.0535 -  1.9996 0.80   1084  114 0.1269 0.2001      4.8566       5.104|
| 14:  1.9996 -  1.9509 0.19    260   33 0.1153 0.1826      4.7882      4.9458|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9770 -  4.6577  1461   161  0.93  10.22   0.98     0.96       8629.56|
|  2:  4.6577 -  3.7156  1403   154  0.95   8.99   1.02     1.01      10430.84|
|  3:  3.7156 -  3.2514  1363   153  0.92  12.64   1.02     1.01      11995.80|
|  4:  3.2514 -  2.9566  1375   148  0.90  16.44   1.01     1.00      12477.45|
|  5:  2.9566 -  2.7461  1335   155  0.88  18.31   1.00     0.97      10554.05|
|  6:  2.7461 -  2.5850  1377   150  0.88  18.60   0.98     0.94       8709.67|
|  7:  2.5850 -  2.4561  1311   154  0.89  17.97   0.99     0.95       7620.57|
|  8:  2.4561 -  2.3497  1344   143  0.88  18.39   1.01     0.97       6993.46|
|  9:  2.3497 -  2.2595  1341   140  0.88  18.15   1.00     0.96       6113.07|
| 10:  2.2595 -  2.1818  1352   147  0.88  18.34   1.01     0.98       5644.30|
| 11:  2.1818 -  2.1138  1308   156  0.88  18.15   1.01     0.97       5039.42|
| 12:  2.1138 -  2.0535  1316   151  0.89  18.16   1.01     1.00       4634.03|
| 13:  2.0535 -  1.9996  1084   114  0.88  18.15   1.00     0.98       3854.71|
| 14:  1.9996 -  1.9509   260    33  0.91  15.36   0.99     0.94       3048.90|
|alpha:            min =        0.94 max =            1.01 mean =         0.98|
|beta:             min =     3048.90 max =        12477.45 mean =      7924.65|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.78 mean =        16.23|
|phase err.(test): min =        0.00 max =           89.83 mean =        15.71|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1267   r_free= 0.1733   ksol= 0.32   Bsol= 46.47   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.71,0.04,0.51,-0.00,0.00,0.00); trace/3= -0.38                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.256871                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1267   r_free= 0.1733   ksol= 0.32   Bsol= 46.47   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.71,0.04,0.51,-0.00,0.00,0.00); trace/3= -0.38                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.256871                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9770 -  4.6577 0.99   1461  161 0.1019 0.1421      5.4369      5.6327|
|  2:  4.6577 -  3.7156 0.99   1403  154 0.0911 0.1109      5.5007       5.673|
|  3:  3.7156 -  3.2514 0.99   1363  153 0.1199 0.1685      5.5596       5.917|
|  4:  3.2514 -  2.9566 0.98   1375  148 0.1424 0.1773      5.5491      5.7246|
|  5:  2.9566 -  2.7461 0.99   1335  155 0.1569 0.1836      5.4493      5.6104|
|  6:  2.7461 -  2.5850 0.99   1377  150 0.1400 0.2214      5.3178      5.5436|
|  7:  2.5850 -  2.4561 0.98   1311  154 0.1419 0.1803      5.2677      5.4236|
|  8:  2.4561 -  2.3497 0.98   1344  143 0.1361 0.1957      5.1885      5.4166|
|  9:  2.3497 -  2.2595 0.99   1341  140 0.1372 0.2074      5.1279      5.4067|
| 10:  2.2595 -  2.1818 0.99   1352  147 0.1329 0.1975      5.0758      5.2802|
| 11:  2.1818 -  2.1138 0.97   1308  156 0.1323 0.1879      5.0098      5.2934|
| 12:  2.1138 -  2.0535 0.98   1316  151 0.1340 0.1737      4.9639      5.1611|
| 13:  2.0535 -  1.9996 0.80   1084  114 0.1270 0.1996      4.8567      5.1025|
| 14:  1.9996 -  1.9509 0.19    260   33 0.1152 0.1824      4.7869      4.9453|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9770 -  4.6577  1461   161  0.93  10.21   0.98     0.96       8622.53|
|  2:  4.6577 -  3.7156  1403   154  0.95   8.99   1.02     1.01      10440.87|
|  3:  3.7156 -  3.2514  1363   153  0.92  12.65   1.02     1.01      12017.64|
|  4:  3.2514 -  2.9566  1375   148  0.90  16.44   1.01     0.99      12482.44|
|  5:  2.9566 -  2.7461  1335   155  0.88  18.29   1.00     0.97      10532.50|
|  6:  2.7461 -  2.5850  1377   150  0.88  18.58   0.97     0.93       8699.77|
|  7:  2.5850 -  2.4561  1311   154  0.89  17.96   0.99     0.94       7613.40|
|  8:  2.4561 -  2.3497  1344   143  0.88  18.39   1.00     0.97       6996.71|
|  9:  2.3497 -  2.2595  1341   140  0.88  18.15   0.99     0.96       6116.15|
| 10:  2.2595 -  2.1818  1352   147  0.88  18.34   1.01     0.97       5647.37|
| 11:  2.1818 -  2.1138  1308   156  0.88  18.15   1.00     0.96       5046.40|
| 12:  2.1138 -  2.0535  1316   151  0.89  18.16   1.00     0.99       4637.91|
| 13:  2.0535 -  1.9996  1084   114  0.88  18.13   0.99     0.97       3850.39|
| 14:  1.9996 -  1.9509   260    33  0.91  15.33   0.98     0.93       3038.39|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     3038.39 max =        12482.44 mean =      7925.11|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.82 mean =        16.22|
|phase err.(test): min =        0.00 max =           89.82 mean =        15.71|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.737)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.49    82.38   15.41    None  None   None       |
|    all(noH): 2823   0      1.49    82.38   15.41    None  None   None       |
|    Sol.    : 438    0      5.03    82.38   36.22    None  None   None       |
|    Mac.    : 2385   0      1.49    80.78   11.59    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:     1.489 -   9.579: 1251   |   5:    41.936 -  50.026:   96        |
|      1:     9.579 -  17.668:  891   |   6:    50.026 -  58.115:   65        |
|      2:    17.668 -  25.758:  213   |   7:    58.115 -  66.205:   17        |
|      3:    25.758 -  33.847:  141   |   8:    66.205 -  74.294:    9        |
|      4:    33.847 -  41.936:  134   |   9:    74.294 -  82.384:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 329         
Filter by distance & map next to the model:
   mapped sites are within: 0.203 - 4.606
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 322 from: 329
   mapped sites are within: 0.706 - 4.606

peak=   10.069 closest distance to " CB  VAL A 230 " =    1.437
peak=    7.131 closest distance to " CD1AILE A 234 " =    1.420
peak=    5.437 closest distance to " O   HOH Z 120 " =    0.962
peak=    5.346 closest distance to " CG  LEU A   5 " =    1.378
peak=    5.331 closest distance to " O   HOH Z 403 " =    2.007
peak=    5.316 closest distance to " CG1 VAL A 296 " =    1.197
peak=    5.222 closest distance to " O   HOH Z 404 " =    1.510
peak=    5.121 closest distance to " O   HOH Z 248 " =    1.554
peak=    5.013 closest distance to " O   HOH Z 124 " =    1.571
peak=    5.002 closest distance to " CB  VAL A 296 " =    1.170
peak=    4.957 closest distance to " CB  ARG A 275 " =    0.918
peak=    4.870 closest distance to " O   HOH Z 193 " =    1.950
peak=    4.803 closest distance to " O   HOH Z 210 " =    1.186
peak=    4.790 closest distance to " CD2 LEU A   5 " =    1.188
peak=    4.721 closest distance to " O   HOH Z 402 " =    1.673
peak=    4.685 closest distance to " O   HOH Z 154 " =    2.136
peak=    4.677 closest distance to " O   HOH Z 238 " =    1.523
peak=    4.638 closest distance to " O   HOH Z 102 " =    1.474
peak=    4.592 closest distance to " CA  TYR A  30 " =    1.062
peak=    4.583 closest distance to " O   HOH Z 130 " =    1.146
peak=    4.570 closest distance to " O   HOH Z  85 " =    2.050
peak=    4.562 closest distance to " O   HOH Z 130 " =    2.466
peak=    4.549 closest distance to " NH2 ARG A  56 " =    2.206
peak=    4.538 closest distance to " O   HOH Z  44 " =    1.650
peak=    4.529 closest distance to " O   HOH Z 128 " =    1.844
peak=    4.445 closest distance to " CB  GLN A 223 " =    1.429
peak=    4.439 closest distance to " CB  PRO A  54 " =    1.009
peak=    4.403 closest distance to " CG AARG A 275 " =    1.208
peak=    4.389 closest distance to " O   HOH Z  43 " =    2.141
peak=    4.388 closest distance to " O   HOH Z  80 " =    2.092
peak=    4.350 closest distance to " CB  VAL A 230 " =    1.232
peak=    4.346 closest distance to " CG  PRO A  54 " =    1.337
peak=    4.345 closest distance to " CB  SER A  63 " =    1.182
peak=    4.340 closest distance to " NH1AARG A 275 " =    1.098
peak=    4.314 closest distance to " CG2 VAL A 296 " =    1.007
peak=    4.305 closest distance to " CG  PRO A 198 " =    1.317
peak=    4.269 closest distance to " O   HOH Z 236 " =    1.344
peak=    4.269 closest distance to " O   HOH Z  49 " =    1.457
peak=    4.233 closest distance to " CZ  PHE A  38 " =    1.144
peak=    4.210 closest distance to " CB  GLN A 183 " =    1.238
peak=    4.207 closest distance to " O   HOH Z 144 " =    1.770
peak=    4.192 closest distance to " O   HOH Z  97 " =    1.371
peak=    4.190 closest distance to " NH2 ARG A 156 " =    1.153
peak=    4.145 closest distance to " O   HOH Z 247 " =    1.347
peak=    4.142 closest distance to " O   SER A  87 " =    2.293
peak=    4.140 closest distance to " O   HOH Z 126 " =    1.561
peak=    4.128 closest distance to " CD  LYS A 166 " =    1.568
peak=    4.085 closest distance to " O   HOH Z 272 " =    1.962
peak=    4.072 closest distance to " O   HOH Z  46 " =    1.008
peak=    4.070 closest distance to " O   HOH Z 346 " =    1.618
peak=    4.068 closest distance to " CA  ALA A  51 " =    1.109
peak=    4.065 closest distance to " O   HOH Z  68 " =    2.046
peak=    4.065 closest distance to " O   HOH Z 234 " =    3.510
peak=    4.064 closest distance to " O   HOH Z 142 " =    2.417
peak=    4.063 closest distance to " O   HOH Z 414 " =    2.536
peak=    4.059 closest distance to " CB BVAL A  41 " =    1.101
peak=    4.040 closest distance to " O   HOH Z 389 " =    1.925
peak=    4.032 closest distance to " CD2 TRP A 179 " =    1.375
peak=    4.013 closest distance to " O   HOH Z 359 " =    1.742
peak=    3.998 closest distance to " O   HOH Z 394 " =    1.775
peak=    3.991 closest distance to " CG  ARG A  66 " =    0.973
peak=    3.986 closest distance to " O   HOH Z  40 " =    2.058
peak=    3.970 closest distance to " CG  PRO A 243 " =    1.143
peak=    3.948 closest distance to " CB  SER A   3 " =    1.319
peak=    3.946 closest distance to " CB  GLU A 152 " =    1.111
peak=    3.942 closest distance to " O   HOH Z 203 " =    1.423
peak=    3.918 closest distance to " O   PRO A 198 " =    1.569
peak=    3.916 closest distance to " O   HOH Z 409 " =    3.283
peak=    3.916 closest distance to " CD2 LEU A 297 " =    0.953
peak=    3.913 closest distance to " O   HOH Z 403 " =    1.526
peak=    3.894 closest distance to " CB  SER A  26 " =    1.786
peak=    3.894 closest distance to " O   HOH Z 132 " =    2.681
peak=    3.889 closest distance to " O   HOH Z 380 " =    1.930
peak=    3.883 closest distance to " O   HOH Z 126 " =    2.373
peak=    3.883 closest distance to " O   HOH Z 209 " =    2.396
peak=    3.879 closest distance to " CZ  PHE A 218 " =    1.156
peak=    3.869 closest distance to " CG2 ILE A  20 " =    1.341
peak=    3.848 closest distance to " O   HOH Z 327 " =    1.715
peak=    3.847 closest distance to " O   GLY A  23 " =    2.361
peak=    3.830 closest distance to " CB  PRO A 198 " =    1.102
peak=    3.821 closest distance to " O   HOH Z  61 " =    1.563
peak=    3.819 closest distance to " O   HOH Z 433 " =    1.516
peak=    3.812 closest distance to " CG  LEU A 228 " =    1.187
peak=    3.810 closest distance to " O   HOH Z 364 " =    2.268
peak=    3.810 closest distance to " O   HOH Z  39 " =    1.289
peak=    3.799 closest distance to " O   ASP A 124 " =    1.536
peak=    3.797 closest distance to " O   GLY A  91 " =    1.354
peak=    3.794 closest distance to " NE2 GLN A  11 " =    1.019
peak=    3.790 closest distance to " NZ  LYS A 117 " =    2.782
peak=    3.789 closest distance to " O   HOH Z 109 " =    1.868
peak=    3.787 closest distance to " O   HOH Z 423 " =    2.134
peak=    3.783 closest distance to " O   HOH Z 383 " =    1.916
peak=    3.782 closest distance to " O   HOH Z 265 " =    2.129
peak=    3.779 closest distance to " O   HOH Z 126 " =    1.844
peak=    3.776 closest distance to " O   HOH Z   9 " =    2.318
peak=    3.776 closest distance to " CB  GLU A 175 " =    1.221
peak=    3.771 closest distance to " O   HOH Z  78 " =    1.474
peak=    3.771 closest distance to " OG BSER A 212 " =    2.719
peak=    3.763 closest distance to " O   HOH Z 142 " =    1.672
peak=    3.763 closest distance to " O   HOH Z 357 " =    2.029
peak=    3.754 closest distance to " CD2 LEU A 228 " =    1.258
peak=    3.753 closest distance to " O   HOH Z 322 " =    2.345
peak=    3.744 closest distance to " CA  TRP A  85 " =    1.074
peak=    3.725 closest distance to " CB  TRP A 179 " =    1.154
peak=    3.723 closest distance to " N   ASN A  39 " =    1.327
peak=    3.719 closest distance to " O   HOH Z 134 " =    1.912
peak=    3.715 closest distance to " CA  ARG A  36 " =    1.063
peak=    3.710 closest distance to " CB  SER A 141 " =    1.083
peak=    3.709 closest distance to " O   HOH Z 146 " =    1.473
peak=    3.708 closest distance to " O   HOH Z 422 " =    2.659
peak=    3.696 closest distance to " O   HOH Z 411 " =    3.607
peak=    3.683 closest distance to " O   HOH Z 232 " =    2.413
peak=    3.678 closest distance to " O   HOH Z 408 " =    1.959
peak=    3.673 closest distance to " O   HOH Z 369 " =    2.269
peak=    3.670 closest distance to " CG  PRO A 213 " =    1.276
peak=    3.667 closest distance to " CA  ALA A  21 " =    1.070
peak=    3.664 closest distance to " CB  GLU A 277 " =    0.807
peak=    3.662 closest distance to " O   HOH Z 257 " =    2.212
peak=    3.653 closest distance to " O   ALA A 165 " =    1.369
peak=    3.648 closest distance to " O   HOH Z 126 " =    1.859
peak=    3.621 closest distance to " O   HOH Z 406 " =    1.460
peak=    3.619 closest distance to " NZ  LYS A 117 " =    1.542
peak=    3.618 closest distance to " O   HOH Z  63 " =    2.044
peak=    3.611 closest distance to " O   HOH Z 371 " =    3.233
peak=    3.599 closest distance to " O   HOH Z 345 " =    1.876
peak=    3.598 closest distance to " CA  SER A  12 " =    1.588
peak=    3.597 closest distance to " O   HOH Z 146 " =    1.307
peak=    3.585 closest distance to " CG1 ILE A  33 " =    1.242
peak=    3.577 closest distance to " CD  ARG A 159 " =    0.837
peak=    3.576 closest distance to " CE1 HIS A 108 " =    1.166
peak=    3.564 closest distance to " O   HOH Z 345 " =    2.503
peak=    3.562 closest distance to " O   HOH Z 423 " =    1.759
peak=    3.561 closest distance to " O   HOH Z 368 " =    2.305
peak=    3.561 closest distance to " CB  THR A 235 " =    1.280
peak=    3.560 closest distance to " OG1 THR A 294 " =    2.342
peak=    3.554 closest distance to " O   HOH Z 236 " =    1.729
peak=    3.554 closest distance to " OG  SER A  97 " =    2.863
peak=    3.551 closest distance to " CD  PRO A  54 " =    0.952
peak=    3.540 closest distance to " O   HOH Z 193 " =    1.917
peak=    3.539 closest distance to " CB  ASN A 148 " =    1.177
peak=    3.531 closest distance to " CG2 THR A 220 " =    0.784
peak=    3.529 closest distance to " O   HOH Z 417 " =    3.262
peak=    3.529 closest distance to " O   HOH Z 183 " =    1.888
peak=    3.529 closest distance to " O   HOH Z 303 " =    2.439
peak=    3.525 closest distance to " O   HOH Z 344 " =    1.824
peak=    3.525 closest distance to " CD  ARG A 195 " =    0.991
peak=    3.524 closest distance to " CD  LYS A 119 " =    1.770
peak=    3.520 closest distance to " O   HOH Z 419 " =    1.824
peak=    3.511 closest distance to " CB  ASN A 285 " =    0.987
peak=    3.511 closest distance to " O   HOH Z 147 " =    1.683
peak=    3.508 closest distance to " O   HOH Z 427 " =    2.569
peak=    3.507 closest distance to " O   HOH Z 313 " =    1.794
peak=    3.505 closest distance to " O   HOH Z   4 " =    1.572
peak=    3.501 closest distance to " CA  ALA A 295 " =    0.909
peak=    3.494 closest distance to " O   HOH Z 245 " =    1.563
peak=    3.491 closest distance to " O   HOH Z 197 " =    2.023
peak=    3.490 closest distance to " O   HOH Z 156 " =    2.150
peak=    3.488 closest distance to " CD  ARG A 269 " =    1.106
peak=    3.486 closest distance to " O   HOH Z 387 " =    2.076
peak=    3.483 closest distance to " NE BARG A 190 " =    1.558
peak=    3.468 closest distance to " O   HOH Z 271 " =    2.414
peak=    3.467 closest distance to " O   HOH Z 337 " =    1.952
peak=    3.465 closest distance to " O   HOH Z  88 " =    3.336
peak=    3.464 closest distance to " CD1 LEU A   5 " =    1.564
peak=    3.464 closest distance to " CG2 ILE A 120 " =    1.435
peak=    3.463 closest distance to " O   GLU A   2 " =    1.716
peak=    3.462 closest distance to " O   HOH Z 361 " =    2.884
peak=    3.461 closest distance to " OE1 GLU A   2 " =    2.051
peak=    3.458 closest distance to " O  BHOH Z 338 " =    2.203
peak=    3.456 closest distance to " O   HOH Z 425 " =    1.406
peak=    3.452 closest distance to " CB  ARG A  79 " =    1.319
peak=    3.448 closest distance to " CE1 TYR A 186 " =    1.300
peak=    3.448 closest distance to " CZ3 TRP A  85 " =    0.982
peak=    3.442 closest distance to " NZ  LYS A  76 " =    0.882
peak=    3.440 closest distance to " CA  VAL A  41 " =    0.827
peak=    3.437 closest distance to " O   HOH Z  97 " =    1.826
peak=    3.435 closest distance to " O   HOH Z 425 " =    1.925
peak=    3.433 closest distance to " N   ALA A   1 " =    1.056
peak=    3.433 closest distance to " CD  LYS A  76 " =    1.826
peak=    3.432 closest distance to " OH  TYR A 116 " =    1.170
peak=    3.431 closest distance to " CB  THR A  31 " =    1.334
peak=    3.427 closest distance to " O   HOH Z 117 " =    1.970
peak=    3.423 closest distance to " OG  SER A  62 " =    2.714
peak=    3.422 closest distance to " ND2 ASN A 187 " =    1.707
peak=    3.420 closest distance to " N   THR A  42 " =    1.537
peak=    3.420 closest distance to " CB  VAL A 202 " =    1.413
peak=    3.417 closest distance to " CB  ARG A 259 " =    1.847
peak=    3.414 closest distance to " O   HOH Z 298 " =    4.200
peak=    3.412 closest distance to " CG2 VAL A 197 " =    1.128
peak=    3.403 closest distance to " CB  TRP A 266 " =    1.162
peak=    3.392 closest distance to " CA  THR A 246 " =    1.039
peak=    3.389 closest distance to " O   HOH Z 199 " =    1.573
peak=    3.387 closest distance to " O   HOH Z  11 " =    1.351
peak=    3.380 closest distance to " O   ASP A 200 " =    1.652
peak=    3.377 closest distance to " CG1 ILE A  49 " =    1.521
peak=    3.375 closest distance to " O   HOH Z 316 " =    2.910
peak=    3.374 closest distance to " O   HOH Z 214 " =    1.508
peak=    3.373 closest distance to " O   HOH Z 315 " =    1.766
peak=    3.367 closest distance to " O   HOH Z 268 " =    1.769
peak=    3.363 closest distance to " CA  ALA A 100 " =    1.217
peak=    3.355 closest distance to " O   HOH Z 388 " =    2.264
peak=    3.350 closest distance to " O   HOH Z 216 " =    2.652
peak=    3.350 closest distance to " CB  SER A  28 " =    0.916
peak=    3.344 closest distance to " NH1 ARG A  14 " =    1.057
peak=    3.343 closest distance to " O   HOH Z   1 " =    2.266
peak=    3.343 closest distance to " O   HOH Z 251 " =    1.806
peak=    3.339 closest distance to " CB  TYR A 169 " =    0.737
peak=    3.339 closest distance to " OE1 GLN A  11 " =    1.861
peak=    3.328 closest distance to " CB  TRP A 179 " =    1.421
peak=    3.326 closest distance to " O   HOH Z 412 " =    3.534
peak=    3.326 closest distance to " CG2AVAL A 121 " =    1.972
peak=    3.322 closest distance to " O   HOH Z 280 " =    2.500
peak=    3.321 closest distance to " O   HOH Z 227 " =    1.689
peak=    3.320 closest distance to " O   HOH Z  59 " =    1.946
peak=    3.319 closest distance to " O   PRO A 213 " =    1.240
peak=    3.317 closest distance to " CD  GLN A 194 " =    1.586
peak=    3.311 closest distance to " CB  ARG A  79 " =    0.862
peak=    3.301 closest distance to " O   HOH Z 423 " =    3.091
peak=    3.300 closest distance to " CB  PHE A 204 " =    0.746
peak=    3.297 closest distance to " O   PHE A  61 " =    1.395
peak=    3.297 closest distance to " CG1BVAL A  72 " =    1.781
peak=    3.295 closest distance to " O   HOH Z 415 " =    1.142
peak=    3.292 closest distance to " CG2 THR A 221 " =    1.276
peak=    3.289 closest distance to " N   GLN A 205 " =    1.080
peak=    3.287 closest distance to " O   HOH Z 366 " =    2.276
peak=    3.284 closest distance to " O   HOH Z 435 " =    1.678
peak=    3.282 closest distance to " CB  ALA A   1 " =    1.163
peak=    3.281 closest distance to " N   ASN A 252 " =    1.127
peak=    3.281 closest distance to " OG BSER A 164 " =    2.371
peak=    3.273 closest distance to " CA  ASP A 149 " =    1.162
peak=    3.265 closest distance to " O   HOH Z 298 " =    1.848
peak=    3.265 closest distance to " CB  ARG A 269 " =    1.657
peak=    3.264 closest distance to " O   HOH Z  28 " =    1.983
peak=    3.261 closest distance to " CA  ASN A 215 " =    1.050
peak=    3.256 closest distance to " CD1 ILE A 199 " =    1.152
peak=    3.252 closest distance to " NH2 ARG A  79 " =    1.299
peak=    3.247 closest distance to " O   ALA A 158 " =    1.080
peak=    3.244 closest distance to " O   HOH Z 173 " =    2.519
peak=    3.243 closest distance to " N   GLU A  44 " =    1.625
peak=    3.241 closest distance to " CA  ASP A 191 " =    0.989
peak=    3.241 closest distance to " NE2 GLN A  77 " =    3.162
peak=    3.239 closest distance to " CA  ASP A 162 " =    1.111
peak=    3.237 closest distance to " CB  MET A  47 " =    1.117
peak=    3.236 closest distance to " CB  ARG A 139 " =    1.022
peak=    3.231 closest distance to " CB  TRP A 150 " =    1.449
peak=    3.231 closest distance to " O   HOH Z 196 " =    1.167
peak=    3.229 closest distance to " CD2 TYR A 186 " =    1.048
peak=    3.227 closest distance to " O   HOH Z 250 " =    1.443
peak=    3.226 closest distance to " NH2BARG A 145 " =    2.208
peak=    3.222 closest distance to " CB  THR A  52 " =    0.970
peak=    3.221 closest distance to " O   HOH Z 337 " =    3.611
peak=    3.220 closest distance to " CE1 TYR A  30 " =    1.032
peak=    3.219 closest distance to " O   HOH Z 158 " =    3.054
peak=    3.219 closest distance to " CZ2 TRP A 274 " =    1.066
peak=    3.218 closest distance to " OD1 ASN A  60 " =    1.644
peak=    3.214 closest distance to " O   HOH Z  54 " =    1.646
peak=    3.211 closest distance to " CB  ALA A  71 " =    1.318
peak=    3.206 closest distance to " O   HOH Z 111 " =    1.621
peak=    3.206 closest distance to " CB  ARG A 219 " =    1.307
peak=    3.206 closest distance to " CA  SER A  32 " =    1.723
peak=    3.202 closest distance to " N   LYS A 166 " =    0.946
peak=    3.201 closest distance to " O   HOH Z  83 " =    1.544
peak=    3.200 closest distance to " CG2 VAL A 268 " =    1.057
peak=    3.196 closest distance to " O   HOH Z 426 " =    1.465
peak=    3.194 closest distance to " O   HOH Z  54 " =    0.994
peak=    3.193 closest distance to " O   HOH Z 281 " =    4.523
peak=    3.190 closest distance to " O   HOH Z  44 " =    2.487
peak=    3.189 closest distance to " CG2 THR A   4 " =    0.963
peak=    3.188 closest distance to " CG  LYS A 119 " =    1.120
peak=    3.186 closest distance to " O   HOH Z 214 " =    3.076
peak=    3.185 closest distance to " CB  ASP A 272 " =    1.041
peak=    3.184 closest distance to " O   HOH Z 249 " =    1.019
peak=    3.184 closest distance to " O   HOH Z 250 " =    1.678
peak=    3.183 closest distance to " CD1 LEU A  96 " =    0.706
peak=    3.173 closest distance to " CB  ALA A 100 " =    1.223
peak=    3.173 closest distance to " CG1 ILE A  20 " =    1.280
peak=    3.173 closest distance to " N   ASP A 162 " =    2.126
peak=    3.171 closest distance to " CB  TRP A 179 " =    1.725
peak=    3.167 closest distance to " CA  ALA A 129 " =    1.021
peak=    3.164 closest distance to " OE2 GLU A 277 " =    1.994
peak=    3.164 closest distance to " O   HOH Z 234 " =    2.011
peak=    3.161 closest distance to " CB  ASN A  39 " =    0.793
peak=    3.161 closest distance to " NH1 ARG A 269 " =    0.820
peak=    3.160 closest distance to " O   HOH Z 435 " =    2.002
peak=    3.154 closest distance to " CG1 VAL A 153 " =    1.080
peak=    3.147 closest distance to " O  BHOH Z  74 " =    1.395
peak=    3.145 closest distance to " O   HOH Z 132 " =    2.787
peak=    3.142 closest distance to " O   HOH Z 170 " =    1.804
peak=    3.141 closest distance to " CD1 LEU A 167 " =    0.883
peak=    3.134 closest distance to " CA  GLU A 152 " =    0.987
peak=    3.132 closest distance to " NZ  LYS A 166 " =    3.016
peak=    3.129 closest distance to " CG2 THR A  29 " =    1.221
peak=    3.124 closest distance to " CG2 THR A 246 " =    0.973
peak=    3.121 closest distance to " CD2 PHE A 225 " =    0.959
peak=    3.119 closest distance to " CG2 THR A 294 " =    1.327
peak=    3.119 closest distance to " CB  ALA A 248 " =    1.416
peak=    3.117 closest distance to " O   HOH Z  55 " =    2.380
peak=    3.117 closest distance to " CB  GLN A  73 " =    1.921
peak=    3.115 closest distance to " O   HOH Z 334 " =    1.389
peak=    3.114 closest distance to " CE  LYS A 119 " =    1.021
peak=    3.111 closest distance to " O   HOH Z 438 " =    1.926
peak=    3.110 closest distance to " CD1 ILE A  33 " =    1.614
peak=    3.107 closest distance to " CB  ALA A 137 " =    1.588
peak=    3.105 closest distance to " CG  LEU A 167 " =    1.130
peak=    3.105 closest distance to " OG  SER A 245 " =    1.422
peak=    3.104 closest distance to " O   HOH Z 109 " =    2.039
peak=    3.100 closest distance to " CB  ALA A 226 " =    1.074
peak=    3.099 closest distance to " O   HOH Z 152 " =    1.726
peak=    3.097 closest distance to " CG2 ILE A 234 " =    1.053
peak=    3.096 closest distance to " CB  PHE A  16 " =    1.193
peak=    3.094 closest distance to " O   HOH Z 361 " =    2.519
peak=    3.093 closest distance to " CA  ASN A 217 " =    1.313
peak=    3.091 closest distance to " CA  THR A  82 " =    1.494
peak=    3.089 closest distance to " ND1 HIS A 207 " =    0.729
peak=    3.088 closest distance to " O   HOH Z 420 " =    2.024
peak=    3.082 closest distance to " O   HOH Z 420 " =    4.606
peak=    3.072 closest distance to " CA  ASN A 176 " =    1.194
peak=    3.066 closest distance to " CZ AARG A 102 " =    1.791
peak=    3.050 closest distance to " O   HOH Z 392 " =    2.290
peak=    3.043 closest distance to " CB  TYR A 116 " =    1.181
peak=    3.035 closest distance to " CG  PHE A 204 " =    1.012
peak=    3.025 closest distance to " CB  ARG A 190 " =    1.832

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 203         
Filter by distance & map next to the model:
   mapped sites are within: 0.563 - 5.840
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 196 from: 203
   mapped sites are within: 0.733 - 5.840

peak=   -4.463 closest distance to " C   THR A 279 " =    1.162
peak=   -4.382 closest distance to " O   HOH Z 290 " =    0.733
peak=   -4.262 closest distance to " CB  ALA A 248 " =    2.115
peak=   -4.261 closest distance to " O   HOH Z 166 " =    1.182
peak=   -4.256 closest distance to " O   HOH Z 166 " =    1.567
peak=   -4.200 closest distance to " CD2 LEU A 237 " =    2.460
peak=   -4.177 closest distance to " O   HOH Z 266 " =    5.233
peak=   -4.162 closest distance to " O   VAL A  67 " =    2.572
peak=   -4.145 closest distance to " CD  ARG A  14 " =    3.206
peak=   -4.129 closest distance to " CE2 TYR A  30 " =    2.723
peak=   -4.111 closest distance to " O   GLY A 241 " =    2.219
peak=   -4.077 closest distance to " N   ALA A   1 " =    2.315
peak=   -4.034 closest distance to " CG  GLN A  58 " =    1.113
peak=   -3.984 closest distance to " CG  PRO A 243 " =    1.645
peak=   -3.951 closest distance to " CB  PHE A 208 " =    2.403
peak=   -3.944 closest distance to " CD1 PHE A  59 " =    1.899
peak=   -3.944 closest distance to " O   HOH Z 340 " =    0.832
peak=   -3.938 closest distance to " CA  VAL A  67 " =    2.929
peak=   -3.887 closest distance to " O   HOH Z 120 " =    1.199
peak=   -3.872 closest distance to " CH2 TRP A 179 " =    1.253
peak=   -3.848 closest distance to " O   HOH Z 174 " =    2.129
peak=   -3.843 closest distance to " CD  ARG A 156 " =    1.958
peak=   -3.841 closest distance to " O   HOH Z   6 " =    1.953
peak=   -3.825 closest distance to " CD1 LEU A 101 " =    2.379
peak=   -3.811 closest distance to " CG1 VAL A 296 " =    0.963
peak=   -3.810 closest distance to " O   HOH Z 109 " =    5.840
peak=   -3.809 closest distance to " CG1 VAL A 112 " =    2.545
peak=   -3.767 closest distance to " O   GLN A  11 " =    0.973
peak=   -3.767 closest distance to " CD  GLN A  58 " =    1.134
peak=   -3.761 closest distance to " O   HOH Z 351 " =    1.561
peak=   -3.759 closest distance to " OG  SER A  97 " =    2.381
peak=   -3.742 closest distance to " OXT GLY A 302 " =    2.892
peak=   -3.719 closest distance to " O   HOH Z 422 " =    1.400
peak=   -3.715 closest distance to " CB  ASP A 132 " =    2.371
peak=   -3.679 closest distance to " O   HOH Z 183 " =    1.447
peak=   -3.677 closest distance to " CG2 THR A 182 " =    2.351
peak=   -3.674 closest distance to " O   PRO A 163 " =    2.071
peak=   -3.671 closest distance to " CB  ALA A 161 " =    2.246
peak=   -3.668 closest distance to " O   HOH Z  78 " =    1.952
peak=   -3.665 closest distance to " CZ2 TRP A  92 " =    2.760
peak=   -3.663 closest distance to " O   HOH Z  13 " =    1.759
peak=   -3.660 closest distance to " O   SER A 273 " =    1.131
peak=   -3.658 closest distance to " O   HOH Z 210 " =    0.796
peak=   -3.656 closest distance to " O   PRO A 198 " =    1.235
peak=   -3.654 closest distance to " O   HOH Z  92 " =    1.499
peak=   -3.651 closest distance to " O   HOH Z 423 " =    2.292
peak=   -3.627 closest distance to " SG  CYS A 260 " =    2.059
peak=   -3.626 closest distance to " CA  ASP A 298 " =    1.083
peak=   -3.624 closest distance to " CG  ASP A 231 " =    0.825
peak=   -3.607 closest distance to " O   HOH Z  10 " =    1.492
peak=   -3.599 closest distance to " O   HOH Z 124 " =    1.382
peak=   -3.596 closest distance to " OH  TYR A 172 " =    1.837
peak=   -3.595 closest distance to " C   HIS A 108 " =    1.232
peak=   -3.594 closest distance to " SD  MET A 105 " =    0.902
peak=   -3.582 closest distance to " O  BHOH Z 338 " =    1.217
peak=   -3.576 closest distance to " O   MET A  40 " =    2.881
peak=   -3.557 closest distance to " O   HOH Z 109 " =    2.690
peak=   -3.555 closest distance to " CG  GLN A 103 " =    2.449
peak=   -3.542 closest distance to " CB  SER A 210 " =    1.297
peak=   -3.532 closest distance to " O   TYR A  15 " =    1.893
peak=   -3.525 closest distance to " CG  LEU A  83 " =    1.974
peak=   -3.523 closest distance to " ND2 ASN A 249 " =    1.210
peak=   -3.515 closest distance to " O   ALA A 227 " =    1.150
peak=   -3.513 closest distance to " O   HOH Z  52 " =    2.111
peak=   -3.513 closest distance to " O   HOH Z 165 " =    1.956
peak=   -3.513 closest distance to " O   HOH Z 110 " =    1.450
peak=   -3.510 closest distance to " CD2 PHE A 192 " =    2.114
peak=   -3.507 closest distance to " N   ARG A  66 " =    1.872
peak=   -3.500 closest distance to " OD1 ASN A 148 " =    1.417
peak=   -3.496 closest distance to " O   HOH Z  15 " =    1.413
peak=   -3.493 closest distance to " OG BSER A 134 " =    1.546
peak=   -3.493 closest distance to " O   SER A  95 " =    1.686
peak=   -3.488 closest distance to " CG2 VAL A 296 " =    1.167
peak=   -3.483 closest distance to " OD1 ASN A 173 " =    1.642
peak=   -3.476 closest distance to " O   HOH Z 388 " =    2.064
peak=   -3.476 closest distance to " O   HOH Z 411 " =    1.560
peak=   -3.459 closest distance to " O   HOH Z 394 " =    1.590
peak=   -3.456 closest distance to " O   HOH Z 174 " =    3.855
peak=   -3.444 closest distance to " CD1 TRP A 179 " =    1.146
peak=   -3.430 closest distance to " O   GLN A  94 " =    2.338
peak=   -3.418 closest distance to " C   SER A 206 " =    1.566
peak=   -3.418 closest distance to " CG  LEU A   5 " =    0.837
peak=   -3.418 closest distance to " CD  PRO A 243 " =    1.872
peak=   -3.417 closest distance to " NH2 ARG A  66 " =    5.693
peak=   -3.407 closest distance to " O   HOH Z 171 " =    2.252
peak=   -3.404 closest distance to " O   HOH Z 285 " =    1.297
peak=   -3.401 closest distance to " CG  ARG A 219 " =    2.584
peak=   -3.401 closest distance to " O   PHE A 218 " =    1.435
peak=   -3.397 closest distance to " OD1 ASP A 298 " =    2.024
peak=   -3.389 closest distance to " NH1 ARG A 195 " =    2.534
peak=   -3.374 closest distance to " CA  HIS A  86 " =    2.262
peak=   -3.370 closest distance to " O   HOH Z 426 " =    2.292
peak=   -3.366 closest distance to " O   HOH Z 193 " =    1.329
peak=   -3.365 closest distance to " O   HOH Z 126 " =    1.907
peak=   -3.364 closest distance to " O   HOH Z 377 " =    2.207
peak=   -3.357 closest distance to " ND2 ASN A  39 " =    1.122
peak=   -3.356 closest distance to " O   TRP A  92 " =    2.105
peak=   -3.354 closest distance to " CD2 LEU A 237 " =    2.867
peak=   -3.350 closest distance to " O   HOH Z  31 " =    2.190
peak=   -3.337 closest distance to " O   VAL A 174 " =    2.105
peak=   -3.335 closest distance to " CD  GLN A 223 " =    1.756
peak=   -3.329 closest distance to " CD1 PHE A 130 " =    2.253
peak=   -3.326 closest distance to " CD1 TRP A  70 " =    1.835
peak=   -3.325 closest distance to " N   GLN A  58 " =    1.721
peak=   -3.323 closest distance to " CZ  TYR A 169 " =    1.685
peak=   -3.317 closest distance to " CA  GLY A 133 " =    2.334
peak=   -3.316 closest distance to " C   LYS A  76 " =    1.697
peak=   -3.313 closest distance to " C   ALA A 158 " =    1.442
peak=   -3.312 closest distance to " CG2 VAL A 189 " =    2.098
peak=   -3.312 closest distance to " O   SER A 271 " =    1.521
peak=   -3.310 closest distance to " O   HOH Z 432 " =    1.104
peak=   -3.306 closest distance to " O   HOH Z 216 " =    0.887
peak=   -3.304 closest distance to " O   HOH Z 397 " =    1.139
peak=   -3.303 closest distance to " O   HOH Z 428 " =    2.494
peak=   -3.300 closest distance to " O   HOH Z 198 " =    0.802
peak=   -3.300 closest distance to " N   SER A 276 " =    1.465
peak=   -3.294 closest distance to " C   VAL A 265 " =    0.880
peak=   -3.292 closest distance to " O   GLY A  80 " =    2.618
peak=   -3.278 closest distance to " O   HOH Z 368 " =    1.832
peak=   -3.277 closest distance to " O   HOH Z 250 " =    1.653
peak=   -3.272 closest distance to " O   HOH Z 246 " =    0.970
peak=   -3.272 closest distance to " O   HOH Z 231 " =    2.189
peak=   -3.261 closest distance to " CG  GLU A  46 " =    2.735
peak=   -3.260 closest distance to " CE1 TYR A 247 " =    2.543
peak=   -3.256 closest distance to " NE2 GLN A  88 " =    1.039
peak=   -3.255 closest distance to " N   ALA A 226 " =    1.998
peak=   -3.245 closest distance to " CA  GLY A 133 " =    2.099
peak=   -3.245 closest distance to " O   HOH Z 233 " =    2.388
peak=   -3.244 closest distance to " CB  LEU A 167 " =    2.121
peak=   -3.244 closest distance to " CB  ALA A  43 " =    2.473
peak=   -3.241 closest distance to " O   HOH Z 353 " =    1.113
peak=   -3.240 closest distance to " OD1 ASN A 301 " =    0.962
peak=   -3.239 closest distance to " OG  SER A  32 " =    1.143
peak=   -3.227 closest distance to " O   HOH Z 140 " =    1.137
peak=   -3.225 closest distance to " CD2 TYR A 293 " =    1.789
peak=   -3.224 closest distance to " OD2 ASP A 272 " =    1.728
peak=   -3.223 closest distance to " O   LYS A 289 " =    1.046
peak=   -3.223 closest distance to " CG  ARG A 139 " =    0.878
peak=   -3.222 closest distance to " NE1 TRP A 266 " =    2.183
peak=   -3.219 closest distance to " CB  GLN A  55 " =    1.473
peak=   -3.213 closest distance to " CD2 LEU A 167 " =    1.799
peak=   -3.212 closest distance to " O   ALA A 161 " =    1.681
peak=   -3.208 closest distance to " O   ASN A  45 " =    1.852
peak=   -3.207 closest distance to " O   HOH Z 312 " =    1.490
peak=   -3.206 closest distance to " CB  PRO A 163 " =    2.692
peak=   -3.203 closest distance to " ND2 ASN A 301 " =    1.768
peak=   -3.202 closest distance to " N   VAL A 296 " =    2.634
peak=   -3.201 closest distance to " O   ASP A 200 " =    1.128
peak=   -3.197 closest distance to " O   HOH Z 193 " =    1.655
peak=   -3.194 closest distance to " N   PHE A  59 " =    2.089
peak=   -3.191 closest distance to " OG  SER A  26 " =    1.209
peak=   -3.187 closest distance to " O   SER A 276 " =    1.805
peak=   -3.187 closest distance to " CD2 PHE A  61 " =    2.548
peak=   -3.182 closest distance to " CD2 PHE A 225 " =    1.075
peak=   -3.180 closest distance to " O   HOH Z 109 " =    2.767
peak=   -3.178 closest distance to " CA  GLY A  75 " =    2.602
peak=   -3.178 closest distance to " O   HOH Z 366 " =    1.030
peak=   -3.172 closest distance to " CD2 LEU A 300 " =    2.967
peak=   -3.172 closest distance to " O   HOH Z 151 " =    1.146
peak=   -3.171 closest distance to " O   HOH Z 195 " =    3.645
peak=   -3.169 closest distance to " N   ALA A  43 " =    2.917
peak=   -3.168 closest distance to " OG  SER A  63 " =    1.221
peak=   -3.167 closest distance to " CD  ARG A 195 " =    5.106
peak=   -3.166 closest distance to " O   HOH Z 394 " =    5.447
peak=   -3.164 closest distance to " O   HOH Z 215 " =    3.800
peak=   -3.164 closest distance to " CG1 VAL A  78 " =    2.573
peak=   -3.159 closest distance to " O   HOH Z 198 " =    1.158
peak=   -3.159 closest distance to " CD1 TYR A 247 " =    2.462
peak=   -3.157 closest distance to " CG  ARG A 219 " =    2.360
peak=   -3.156 closest distance to " O   HOH Z 384 " =    0.879
peak=   -3.151 closest distance to " CG2 ILE A 263 " =    2.234
peak=   -3.150 closest distance to " ND2 ASN A  45 " =    1.163
peak=   -3.149 closest distance to " O   ILE A 234 " =    1.206
peak=   -3.145 closest distance to " CD2 TYR A 172 " =    1.935
peak=   -3.144 closest distance to " O   HOH Z 265 " =    1.160
peak=   -3.141 closest distance to " O   HOH Z  71 " =    1.968
peak=   -3.134 closest distance to " CD2 LEU A 143 " =    2.407
peak=   -3.130 closest distance to " CE  LYS A 119 " =    2.251
peak=   -3.128 closest distance to " CD2 LEU A 297 " =    1.133
peak=   -3.126 closest distance to " O   ILE A 106 " =    1.353
peak=   -3.123 closest distance to " O   ALA A  34 " =    2.583
peak=   -3.112 closest distance to " NH2 ARG A  79 " =    2.032
peak=   -3.109 closest distance to " N   THR A 235 " =    1.089
peak=   -3.107 closest distance to " CH2 TRP A 150 " =    1.015
peak=   -3.106 closest distance to " N   SER A   3 " =    2.234
peak=   -3.103 closest distance to " NE1 TRP A 150 " =    1.042
peak=   -3.091 closest distance to " O   HOH Z 384 " =    2.158
peak=   -3.085 closest distance to " O   HOH Z 191 " =    5.717
peak=   -3.075 closest distance to " O   HOH Z 340 " =    1.994
peak=   -3.072 closest distance to " O   HOH Z 388 " =    1.701
peak=   -3.071 closest distance to " O   HOH Z 164 " =    0.893
peak=   -3.063 closest distance to " OD2 ASP A 191 " =    1.760
peak=   -3.061 closest distance to " C   VAL A 174 " =    1.727
peak=   -3.055 closest distance to " CB  ALA A 248 " =    2.035
peak=   -3.053 closest distance to " CB  CYS A 254 " =    2.119
peak=   -3.010 closest distance to " O   HOH Z 140 " =    1.562

================= 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    :  0.5094 0.5007   6.306184e+00   6.299163e+00
   1_bss:  0.5030 0.4961   6.299631e+00   6.298030e+00
   1_xyz:  0.4501 0.4633   6.252925e+00   6.268664e+00
   1_adp:  0.4071 0.4655   6.204517e+00   6.263395e+00
   1_occ:  0.4066 0.4655   6.203814e+00   6.263766e+00
   2_bss:  0.4041 0.4571   6.203134e+00   6.262720e+00
   2_xyz:  0.3325 0.3934   6.056597e+00   6.175253e+00
   2_adp:  0.3127 0.3763   6.012000e+00   6.144941e+00
   2_occ:  0.3124 0.3757   6.011128e+00   6.144270e+00
   3_bss:  0.3090 0.3736   6.010693e+00   6.143615e+00
   3_xyz:  0.2262 0.2795   5.743496e+00   5.916859e+00
   3_adp:  0.2032 0.2489   5.646514e+00   5.820630e+00
   3_occ:  0.2028 0.2482   5.645223e+00   5.819913e+00
   4_bss:  0.2007 0.2463   5.642527e+00   5.815756e+00
   4_xyz:  0.1520 0.1956   5.399154e+00   5.604063e+00
   4_adp:  0.1449 0.1909   5.363088e+00   5.577107e+00
   4_occ:  0.1447 0.1907   5.362022e+00   5.575859e+00
   5_bss:  0.1450 0.1914   5.364062e+00   5.576625e+00
   5_xyz:  0.1322 0.1810   5.297403e+00   5.519406e+00
   5_adp:  0.1269 0.1732   5.257125e+00   5.475787e+00
   5_occ:  0.1268 0.1733   5.256957e+00   5.475802e+00
   5_bss:  0.1267 0.1733   5.256871e+00   5.475817e+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:  0.319   1.408   7.647  11.362   7.967   0.000   0.000   0.000
   1_xyz:  0.319   1.408   7.647  11.362   7.967   0.000   0.000   0.000
   1_adp:  0.319   1.408   7.647  11.362   7.967   0.000   0.000   0.000
   1_occ:  0.319   1.408   7.647  11.362   7.967   0.000   0.000   0.000
   2_bss:  0.328  30.758   3.503   6.258   4.256   0.000   0.000   0.000
   2_xyz:  0.328  30.758   3.503   6.258   4.256   0.000   0.000   0.000
   2_adp:  0.328  30.758   3.503   6.258   4.256   0.000   0.000   0.000
   2_occ:  0.328  30.758   3.503   6.258   4.256   0.000   0.000   0.000
   3_bss:  0.301  30.758   0.775   3.250   2.245   0.000   0.000   0.000
   3_xyz:  0.301  30.758   0.775   3.250   2.245   0.000   0.000   0.000
   3_adp:  0.301  30.758   0.775   3.250   2.245   0.000   0.000   0.000
   3_occ:  0.301  30.758   0.775   3.250   2.245   0.000   0.000   0.000
   4_bss:  0.324  46.727  -1.056   1.172   0.814   0.000   0.000   0.000
   4_xyz:  0.324  46.727  -1.056   1.172   0.814   0.000   0.000   0.000
   4_adp:  0.324  46.727  -1.056   1.172   0.814   0.000   0.000   0.000
   4_occ:  0.324  46.727  -1.056   1.172   0.814   0.000   0.000   0.000
   5_bss:  0.323  45.513  -1.629   0.256   0.517   0.000   0.000   0.000
   5_xyz:  0.323  45.513  -1.629   0.256   0.517   0.000   0.000   0.000
   5_adp:  0.323  45.513  -1.629   0.256   0.517   0.000   0.000   0.000
   5_occ:  0.323  45.513  -1.629   0.256   0.517   0.000   0.000   0.000
   5_bss:  0.324  46.465  -1.707   0.040   0.513  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  62.801 0.3581  0.4296    81126.088
   1_bss:  64.319 0.3368  0.5193    81617.504
   1_xyz:  58.067 0.4165  0.6292    68532.397
   1_adp:  55.350 0.4517  0.7728    65745.969
   1_occ:  55.333 0.4519  0.7719    65719.253
   2_bss:  54.496 0.4626  0.6898    64439.951
   2_xyz:  44.634 0.5858  0.8715    45983.055
   2_adp:  41.746 0.6214  0.9234    41417.826
   2_occ:  41.707 0.6218  0.9231    41254.919
   3_bss:  41.504 0.6242  0.8455    40947.297
   3_xyz:  29.498 0.7616  0.9831    21212.382
   3_adp:  25.506 0.8060  1.0094    16948.080
   3_occ:  25.447 0.8066  1.0099    16881.498
   4_bss:  25.242 0.8088  0.9500    16669.525
   4_xyz:  19.097 0.8697  0.9893    10062.521
   4_adp:  18.421 0.8764  0.9951     9628.926
   4_occ:  18.400 0.8766  0.9956     9617.562
   5_bss:  18.423 0.8765  0.9747     9669.487
   5_xyz:  17.144 0.8882  0.9766     8579.683
   5_adp:  16.180 0.8969  0.9766     7918.988
   5_occ:  16.177 0.8970  0.9766     7923.668
   5_bss:  16.173 0.8970  0.9715     7924.120
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.087   5.3644e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.087   5.3644e+01
   1_xyz:   1.578  0.012  0.102 18.425  0.006  4.118   1.3263e-01
   1_adp:   1.578  0.012  0.102 18.425  0.006  4.118   1.3263e-01
   1_occ:   1.578  0.012  0.102 18.425  0.006  4.118   1.3263e-01
   2_bss:   1.578  0.012  0.102 18.425  0.006  4.118   1.3263e-01
   2_xyz:   1.363  0.010  0.083 16.981  0.005  4.105   1.0860e-01
   2_adp:   1.363  0.010  0.083 16.981  0.005  4.105   1.0860e-01
   2_occ:   1.363  0.010  0.083 16.981  0.005  4.105   1.0860e-01
   3_bss:   1.363  0.010  0.083 16.981  0.005  4.105   1.0860e-01
   3_xyz:   1.322  0.010  0.087 16.167  0.005  4.107   1.0374e-01
   3_adp:   1.322  0.010  0.087 16.167  0.005  4.107   1.0374e-01
   3_occ:   1.322  0.010  0.087 16.167  0.005  4.107   1.0374e-01
   4_bss:   1.322  0.010  0.087 16.167  0.005  4.107   1.0374e-01
   4_xyz:   1.133  0.008  0.082 15.638  0.004  4.121   7.4692e-02
   4_adp:   1.133  0.008  0.082 15.638  0.004  4.121   7.4692e-02
   4_occ:   1.133  0.008  0.082 15.638  0.004  4.121   7.4692e-02
   5_bss:   1.133  0.008  0.082 15.638  0.004  4.121   7.4692e-02
   5_xyz:   1.073  0.007  0.082 15.418  0.004  4.113   6.6737e-02
   5_adp:   1.073  0.007  0.082 15.418  0.004  4.113   6.6737e-02
   5_occ:   1.073  0.007  0.082 15.418  0.004  4.113   6.6737e-02
   5_bss:   1.073  0.007  0.082 15.418  0.004  4.113   6.6737e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.722   6.9424e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.722   6.9424e+00
   1_xyz:  13.457  0.147  0.415 86.351  0.044  2.210   8.6739e-02
   1_adp:  13.457  0.147  0.415 86.351  0.044  2.210   8.6739e-02
   1_occ:  13.457  0.147  0.415 86.351  0.044  2.210   8.6739e-02
   2_bss:  13.457  0.147  0.415 86.351  0.044  2.210   8.6739e-02
   2_xyz:   7.991  0.153  0.279 83.939  0.050  2.099   8.5633e-02
   2_adp:   7.991  0.153  0.279 83.939  0.050  2.099   8.5633e-02
   2_occ:   7.991  0.153  0.279 83.939  0.050  2.099   8.5633e-02
   3_bss:   7.991  0.153  0.279 83.939  0.050  2.099   8.5633e-02
   3_xyz:   8.952  0.097  0.264 81.503  0.050  2.233   2.1104e-01
   3_adp:   8.952  0.097  0.264 81.503  0.050  2.233   2.1104e-01
   3_occ:   8.952  0.097  0.264 81.503  0.050  2.233   2.1104e-01
   4_bss:   8.952  0.097  0.264 81.503  0.050  2.233   2.1104e-01
   4_xyz:   7.663  0.048  0.402 80.674  0.046  2.078   5.6482e-02
   4_adp:   7.663  0.048  0.402 80.674  0.046  2.078   5.6482e-02
   4_occ:   7.663  0.048  0.402 80.674  0.046  2.078   5.6482e-02
   5_bss:   7.663  0.048  0.402 80.674  0.046  2.078   5.6482e-02
   5_xyz:   7.403  0.049  0.443 81.641  0.037  2.218   4.4656e-02
   5_adp:   7.403  0.049  0.443 81.641  0.037  2.218   4.4656e-02
   5_occ:   7.403  0.049  0.443 81.641  0.037  2.218   4.4656e-02
   5_bss:   7.403  0.049  0.443 81.641  0.037  2.218   4.4656e-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: 104.95   0.00  17.66  82.88   0.00  15.72 104.95   0.00  28.25
   1_occ: 104.95   0.00  17.66  82.88   0.00  15.72 104.95   0.00  28.25
   2_bss: 104.95   0.00  17.66  82.88   0.00  15.72 104.95   0.00  28.25
   2_xyz: 104.95   0.00  17.66  82.88   0.00  15.72 104.95   0.00  28.25
   2_adp:  92.92   0.00  16.53  78.66   0.00  13.85  92.92   0.00  31.08
   2_occ:  92.92   0.00  16.53  78.66   0.00  13.85  92.92   0.00  31.08
   3_bss:  92.92   0.00  16.53  78.66   0.00  13.85  92.92   0.00  31.08
   3_xyz:  92.92   0.00  16.53  78.66   0.00  13.85  92.92   0.00  31.08
   3_adp:  84.54   0.00  15.61  80.51   0.00  12.03  84.54   4.42  35.09
   3_occ:  84.54   0.00  15.61  80.51   0.00  12.03  84.54   4.42  35.09
   4_bss:  84.54   0.00  15.61  80.51   0.00  12.03  84.54   4.42  35.09
   4_xyz:  84.54   0.00  15.61  80.51   0.00  12.03  84.54   4.42  35.09
   4_adp:  84.24   0.00  15.67  80.99   0.00  11.95  84.24   4.71  35.94
   4_occ:  84.24   0.00  15.67  80.99   0.00  11.95  84.24   4.71  35.94
   5_bss:  84.24   0.00  15.67  80.99   0.00  11.95  84.24   4.71  35.94
   5_xyz:  84.24   0.00  15.67  80.99   0.00  11.95  84.24   4.71  35.94
   5_adp:  82.44   1.54  15.46  80.84   1.54  11.64  82.44   5.08  36.28
   5_occ:  82.44   1.54  15.46  80.84   1.54  11.64  82.44   5.08  36.28
   5_bss:  82.38   1.49  15.41  80.78   1.49  11.59  82.38   5.03  36.22
------------------------------------------------------------------------
 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:    1.190    0.009    0.396
   1_adp:    1.190    0.009    0.396
   1_occ:    1.190    0.009    0.396
   2_bss:    1.190    0.009    0.396
   2_xyz:    1.780    0.031    0.602
   2_adp:    1.780    0.031    0.602
   2_occ:    1.780    0.031    0.602
   3_bss:    1.780    0.031    0.602
   3_xyz:    2.042    0.043    0.762
   3_adp:    2.042    0.043    0.762
   3_occ:    2.042    0.043    0.762
   4_bss:    2.042    0.043    0.762
   4_xyz:    2.086    0.080    0.842
   4_adp:    2.086    0.080    0.842
   4_occ:    2.086    0.080    0.842
   5_bss:    2.086    0.080    0.842
   5_xyz:    2.139    0.063    0.876
   5_adp:    2.139    0.063    0.876
   5_occ:    2.139    0.063    0.876
   5_bss:    2.139    0.063    0.876
------------------------------------------------------------------------

CPU time actual refinement: 339.34


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_105/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_105/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_105/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_105/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_105/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 339.19 
  Macro-tasks:
    bulk solvent and scale       = 43.29  
    individual site refinement   = 135.44 
    weights calculation          = 32.48  
    collect and process          = 6.33   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 217.64 
  Micro-tasks:
    mask                            = 2.42   
    f_calc                          = 106.13 
    alpha_beta                      = 8.28   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 114.16 
    fmodel                         = 7.21   
    r_factors                      = 0.26   
    phase_errors                   = 9.83   
    foms                           = 0.25   
    TOTAL for micro-tasks          = 249.71 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.839 micro seconds
Total CPU time: 5.88 minutes
from_scatterers_fft:    636 calls, 105.81 s
gradients_fft:          580 calls, 101.75 s

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

# Date 2008-01-16 Time 00:45:31 PST -0800 (1200473131.72 s)
Start R-work = 0.5094, R-free = 0.5007 (no bulk solvent and anisotropic scale)
Final R-work = 0.1466, R-free = 0.1882 (no bulk solvent and anisotropic scale)

Start R-work = 0.5030, R-free = 0.4961
Final R-work = 0.1267, R-free = 0.1733