# Date 2008-01-16 Time 01:15:04 PST -0800 (1200474904.25 s)
#phil __OFF__

Command line arguments: "../333.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 21380
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 333

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 47.6339, 85.5261, 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: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.6339, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.885 1.97061
Completeness in resolution range: 0.953839
Completeness with d_max=infinity: 0.950876

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8850
                             d_min =   1.9706

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.6339, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.885 1.97061
Completeness in resolution range: 0.953839
Completeness with d_max=infinity: 0.950876

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8855 -  4.2164 [2162/2190]  1946   216  10.0%
  bin  2:  4.2164 -  3.3593 [2065/2088]  1858   207  10.0%
  bin  3:  3.3593 -  2.9384 [2046/2071]  1841   205  10.0%
  bin  4:  2.9384 -  2.6714 [2024/2040]  1822   202  10.0%
  bin  5:  2.6714 -  2.4809 [2004/2042]  1798   206  10.3%
  bin  6:  2.4809 -  2.3352 [2003/2036]  1811   192   9.6%
  bin  7:  2.3352 -  2.2187 [1983/2020]  1784   199  10.0%
  bin  8:  2.2187 -  2.1224 [1986/2028]  1787   199  10.0%
  bin  9:  2.1224 -  2.0409 [1975/2014]  1779   196   9.9%
  bin 10:  2.0409 -  1.9706 [1341/2008]  1204   137  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_333/model_refine_data.mtz


========================== Anomalous scatterer groups =========================

All atoms refined with f_prime=0 and f_double_prime=0.

========================== Set up restraints manager ==========================

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.55 -     2.22: 17
        2.22 -     2.89: 1340
        2.89 -     3.56: 4520
        3.56 -     4.23: 9224
        4.23 -     4.90: 13367
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.551 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.785 3.040 -x+1,y+1/2,-z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.798 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.851 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28463 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_333/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_333/model_refine_001.geo

CPU time processing inputs: 9.14


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 47.63395 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4798   r_free= 0.4670   ksol= 0.00   Bsol= 0.00   scale= 0.798    |
|                                                                             |
| 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:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.279110                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8855 -  4.7026 0.99   1398  158 0.3927 0.3837      6.5772      6.6185|
|  2:  4.7026 -  3.7523 0.99   1350  148 0.3999 0.3929      6.7728      6.7898|
|  3:  3.7523 -  3.2838 0.99   1318  149 0.4378 0.4086      6.6689      6.6856|
|  4:  3.2838 -  2.9862 0.99   1321  136 0.4559 0.4194      6.5062       6.447|
|  5:  2.9862 -  2.7736 0.98   1296  147 0.5143 0.5165      6.3836      6.4052|
|  6:  2.7736 -  2.6110 0.99   1293  144 0.4991 0.5221      6.2694      6.2056|
|  7:  2.6110 -  2.4809 0.99   1289  154 0.5103 0.4696      6.2625      6.1674|
|  8:  2.4809 -  2.3733 0.99   1311  132 0.5224 0.5069      6.1741      6.1702|
|  9:  2.3733 -  2.2823 0.99   1273  149 0.5330 0.5496      6.1191       6.166|
| 10:  2.2823 -  2.2038 0.98   1270  139 0.5258 0.5399      6.1218      6.1002|
| 11:  2.2038 -  2.1351 0.98   1274  146 0.5310 0.5153      6.0359      6.0666|
| 12:  2.1351 -  2.0742 1.00   1286  142 0.5383 0.5401      5.9713       6.005|
| 13:  2.0742 -  2.0198 0.96   1272  130 0.5467 0.5156      5.9004      5.8705|
| 14:  2.0198 -  1.9706 0.54    679   85 0.5441 0.4718      5.8819      5.7274|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8855 -  4.7026  1398   158  0.67  36.59   0.80     0.69      77129.32|
|  2:  4.7026 -  3.7523  1350   148  0.69  36.05   0.89     0.75     106157.38|
|  3:  3.7523 -  3.2838  1318   149  0.61  43.18   0.85     0.72     110564.39|
|  4:  3.2838 -  2.9862  1321   136  0.54  48.83   0.81     0.63      93448.43|
|  5:  2.9862 -  2.7736  1296   147  0.43  57.22   0.73     0.52      80629.69|
|  6:  2.7736 -  2.6110  1293   144  0.41  59.21   0.74     0.47      69480.77|
|  7:  2.6110 -  2.4809  1289   154  0.39  60.61   0.75     0.44      64171.88|
|  8:  2.4809 -  2.3733  1311   132  0.39  60.97   0.73     0.45      56541.10|
|  9:  2.3733 -  2.2823  1273   149  0.36  63.27   0.72     0.43      53694.61|
| 10:  2.2823 -  2.2038  1270   139  0.35  63.96   0.76     0.41      49941.63|
| 11:  2.2038 -  2.1351  1274   146  0.30  67.66   0.74     0.37      48774.47|
| 12:  2.1351 -  2.0742  1286   142  0.30  67.84   0.75     0.39      45451.57|
| 13:  2.0742 -  2.0198  1272   130  0.33  65.43   0.73     0.41      36933.88|
| 14:  2.0198 -  1.9706   679    85  0.44  56.87   0.72     0.49      24647.72|
|alpha:            min =        0.37 max =            0.75 mean =         0.51|
|beta:             min =    24647.72 max =       110564.39 mean =     67360.77|
|figures of merit: min =        0.00 max =            1.00 mean =         0.45|
|phase err.(work): min =        0.00 max =           90.00 mean =        55.99|
|phase err.(test): min =        0.00 max =           89.61 mean =        55.88|
|-----------------------------------------------------------------------------|

============================== 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 = 13.443727             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.955   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.123121              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.338   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.034 -  1.420:        5 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.420 -  1.807:        7 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.807 -  2.194:       99 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.194 -  2.580:      548 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.580 -  2.967:     1349 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.967 -  3.353:     2475 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.353 -  3.740:     3969 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.740 -  4.127:     5214 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.127 -  4.513:     6780 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.513 -  4.900:     8078 |
|-----------------------------------------------------------------------------|
|-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 |       53.448 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.034 |       2.161 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.729)------------------------------------------|
|    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 = 11.729)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4853   r_free= 0.4744   ksol= 0.00   Bsol= 0.00   scale= 0.768    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.280432                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4713   r_free= 0.4591   ksol= 0.36   Bsol= 20.00   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.24,10.48,7.58,0.00,0.00,0.00); trace/3= 8.43                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.272457                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.655993             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.439   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.153168              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.655   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4713      final r-factor (work) = 0.3837          |
| start r-factor (free) = 0.4591      final r-factor (free) = 0.4056          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 93.1947 = 12.66 * 0.50 * 6.2811 + 1.00 * 53.4479                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 39.2606 = 12.66 * 0.50 * 6.1802 + 1.00 * 0.1522                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3837      final r-factor (work) = 0.3363          |
| start r-factor (free) = 0.4056      final r-factor (free) = 0.3784          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.1415 = 1.15 * 1.00 * 6.1802 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.0343 = 1.15 * 1.00 * 6.0849 + 1.00 * 0.0174                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.729)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.42   13.05    None  None   None       |
|    all(noH): 2823   0      0.00    87.42   13.05    None  None   None       |
|    Sol.    : 438    0      0.00    87.42   26.94    None  None   None       |
|    Mac.    : 2385   0      0.00    80.23   10.50    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 -   8.742: 1353   |   5:    43.709 -  52.451:   60        |
|      1:     8.742 -  17.484:  734   |   6:    52.451 -  61.193:   21        |
|      2:    17.484 -  26.226:  357   |   7:    61.193 -  69.935:   11        |
|      3:    26.226 -  34.968:  193   |   8:    69.935 -  78.677:    4        |
|      4:    34.968 -  43.709:   87   |   9:    78.677 -  87.419:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3363 r_free = 0.3784             target_work(ml) = 6.060         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3358 r_free = 0.3778             target_work(ml) = 6.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3358   r_free= 0.3778   ksol= 0.36   Bsol= 20.00   scale= 1.100   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.24,10.48,7.58,0.00,0.00,0.00); trace/3= 8.43                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.058666                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3337   r_free= 0.3729   ksol= 0.30   Bsol= 20.00   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.98,6.68,4.89,0.00,0.00,0.00); trace/3= 5.18                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.059880                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.844417              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.282   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.445498              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.198  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3337      final r-factor (work) = 0.2280          |
| start r-factor (free) = 0.3729      final r-factor (free) = 0.2740          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.0850 = 9.84 * 0.50 * 6.0814 + 1.00 * 0.1512                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.1681 = 9.84 * 0.50 * 5.9063 + 1.00 * 0.0960                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2280      final r-factor (work) = 0.1992          |
| start r-factor (free) = 0.2740      final r-factor (free) = 0.2504          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6493 = 0.45 * 1.00 * 5.9063 + 1.00 * 0.0180                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5452 = 0.45 * 1.00 * 5.6821 + 1.00 * 0.0138                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.729)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.22   12.84    None  None   None       |
|    all(noH): 2823   0      0.00    80.22   12.84    None  None   None       |
|    Sol.    : 438    0      2.01    75.80   32.35    None  None   None       |
|    Mac.    : 2385   0      0.00    80.22   9.26     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 -   8.023: 1405   |   5:    40.112 -  48.135:   89        |
|      1:     8.023 -  16.045:  723   |   6:    48.135 -  56.157:   58        |
|      2:    16.045 -  24.068:  256   |   7:    56.157 -  64.180:   14        |
|      3:    24.068 -  32.090:  156   |   8:    64.180 -  72.202:   14        |
|      4:    32.090 -  40.112:  103   |   9:    72.202 -  80.225:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1992 r_free = 0.2504             target_work(ml) = 5.631         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1990 r_free = 0.2501             target_work(ml) = 5.630         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1990   r_free= 0.2501   ksol= 0.30   Bsol= 20.00   scale= 1.063   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.98,6.68,4.89,0.00,0.00,0.00); trace/3= 5.18                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.629592                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1958   r_free= 0.2482   ksol= 0.32   Bsol= 41.28   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.86,3.79,3.31,0.00,0.00,0.00); trace/3= 2.99                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.625930                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.377838              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.185  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.192626              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 101.825  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1958      final r-factor (work) = 0.1474          |
| start r-factor (free) = 0.2482      final r-factor (free) = 0.1901          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.7123 = 3.38 * 0.50 * 5.6937 + 1.00 * 0.0960                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3763 = 3.38 * 0.50 * 5.5139 + 1.00 * 0.0637                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1474      final r-factor (work) = 0.1393          |
| start r-factor (free) = 0.1901      final r-factor (free) = 0.1776          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0781 = 0.19 * 1.00 * 5.5139 + 1.00 * 0.0160                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0505 = 0.19 * 1.00 * 5.3399 + 1.00 * 0.0219                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.729)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.78   12.74    None  None   None       |
|    all(noH): 2823   0      0.00    79.78   12.74    None  None   None       |
|    Sol.    : 438    0      1.57    71.03   33.88    None  None   None       |
|    Mac.    : 2385   0      0.00    79.78   8.86     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.978: 1463   |   5:    39.888 -  47.865:  101        |
|      1:     7.978 -  15.955:  744   |   6:    47.865 -  55.843:   59        |
|      2:    15.955 -  23.933:  185   |   7:    55.843 -  63.820:   24        |
|      3:    23.933 -  31.910:  115   |   8:    63.820 -  71.798:    9        |
|      4:    31.910 -  39.888:  120   |   9:    71.798 -  79.775:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1393 r_free = 0.1776             target_work(ml) = 5.307         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1390 r_free = 0.1774             target_work(ml) = 5.306         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1390   r_free= 0.1774   ksol= 0.32   Bsol= 41.28   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.86,3.79,3.31,0.00,0.00,0.00); trace/3= 2.99                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.306163                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1390   r_free= 0.1775   ksol= 0.33   Bsol= 41.28   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.14,2.68,2.67,0.00,0.00,0.00); trace/3= 2.16                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.308721                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.654849              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 114.897  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.282914              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.295   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1390      final r-factor (work) = 0.1251          |
| start r-factor (free) = 0.1775      final r-factor (free) = 0.1646          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4876 = 1.65 * 0.50 * 5.3465 + 1.00 * 0.0637                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4096 = 1.65 * 0.50 * 5.2617 + 1.00 * 0.0560                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1251      final r-factor (work) = 0.1222          |
| start r-factor (free) = 0.1646      final r-factor (free) = 0.1631          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4987 = 0.28 * 1.00 * 5.2617 + 1.00 * 0.0101                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4847 = 0.28 * 1.00 * 5.2104 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.729)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.41   12.86    None  None   None       |
|    all(noH): 2823   0      0.00    80.41   12.86    None  None   None       |
|    Sol.    : 438    0      2.06    71.15   34.81    None  None   None       |
|    Mac.    : 2385   0      0.00    80.41   8.82     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:     0.000 -   8.041: 1480   |   5:    40.205 -  48.246:  100        |
|      1:     8.041 -  16.082:  740   |   6:    48.246 -  56.287:   65        |
|      2:    16.082 -  24.123:  159   |   7:    56.287 -  64.328:   28        |
|      3:    24.123 -  32.164:  121   |   8:    64.328 -  72.369:    6        |
|      4:    32.164 -  40.205:  119   |   9:    72.369 -  80.410:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1222 r_free = 0.1631             target_work(ml) = 5.206         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1221 r_free = 0.1632             target_work(ml) = 5.206         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1221   r_free= 0.1632   ksol= 0.33   Bsol= 41.28   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.14,2.68,2.67,0.00,0.00,0.00); trace/3= 2.16                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.205540                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1221   r_free= 0.1631   ksol= 0.33   Bsol= 43.56   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.09,2.42,2.60,0.00,0.00,0.00); trace/3= 2.04                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.205293                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.070968              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 126.195  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.759544              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 102.344  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1221      final r-factor (work) = 0.1154          |
| start r-factor (free) = 0.1631      final r-factor (free) = 0.1581          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4509 = 2.07 * 0.50 * 5.2101 + 1.00 * 0.0560                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4271 = 2.07 * 0.50 * 5.1796 + 1.00 * 0.0637                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1154      final r-factor (work) = 0.1138          |
| start r-factor (free) = 0.1581      final r-factor (free) = 0.1593          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9467 = 0.76 * 1.00 * 5.1796 + 1.00 * 0.0125                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9284 = 0.76 * 1.00 * 5.1572 + 1.00 * 0.0113                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.729)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.39   12.95    None  None   None       |
|    all(noH): 2823   0      0.00    81.39   12.95    None  None   None       |
|    Sol.    : 438    0      1.65    70.90   35.57    None  None   None       |
|    Mac.    : 2385   0      0.00    81.39   8.79     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 -   8.139: 1521   |   5:    40.693 -  48.832:   98        |
|      1:     8.139 -  16.277:  690   |   6:    48.832 -  56.971:   71        |
|      2:    16.277 -  24.416:  175   |   7:    56.971 -  65.109:   34        |
|      3:    24.416 -  32.555:  117   |   8:    65.109 -  73.248:    6        |
|      4:    32.555 -  40.693:  106   |   9:    73.248 -  81.387:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1138 r_free = 0.1593             target_work(ml) = 5.161         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1138 r_free = 0.1594             target_work(ml) = 5.161         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1138   r_free= 0.1594   ksol= 0.33   Bsol= 43.56   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.09,2.42,2.60,0.00,0.00,0.00); trace/3= 2.04                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.161444                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8855 -  4.7026 0.99   1398  158 0.1007 0.1297      5.3874      5.5449|
|  2:  4.7026 -  3.7523 0.99   1350  148 0.0875 0.1080      5.4502      5.6453|
|  3:  3.7523 -  3.2838 0.99   1318  149 0.1058 0.1540      5.4849      5.8755|
|  4:  3.2838 -  2.9862 0.99   1321  136 0.1242 0.1561      5.4618      5.6386|
|  5:  2.9862 -  2.7736 0.98   1296  147 0.1372 0.1637      5.3527      5.4841|
|  6:  2.7736 -  2.6110 0.99   1293  144 0.1311 0.2084      5.2578      5.5435|
|  7:  2.6110 -  2.4809 0.99   1289  154 0.1222 0.1643      5.1681      5.3883|
|  8:  2.4809 -  2.3733 0.99   1311  132 0.1201 0.1771      5.0998      5.3473|
|  9:  2.3733 -  2.2823 0.99   1273  149 0.1202 0.1906      5.0415      5.3468|
| 10:  2.2823 -  2.2038 0.98   1270  139 0.1148 0.1734      4.9935      5.1885|
| 11:  2.2038 -  2.1351 0.98   1274  146 0.1147 0.1723      4.9324      5.2624|
| 12:  2.1351 -  2.0742 1.00   1286  142 0.1091 0.1726      4.8508      5.1549|
| 13:  2.0742 -  2.0198 0.96   1272  130 0.1138 0.1728      4.7975      5.0543|
| 14:  2.0198 -  1.9706 0.54    679   85 0.1096 0.1709      4.7064      4.9215|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8855 -  4.7026  1398   158  0.94   8.89   0.98     0.96       7086.01|
|  2:  4.7026 -  3.7523  1350   148  0.95   8.24   1.02     1.00       9252.00|
|  3:  3.7523 -  3.2838  1318   149  0.93  11.34   1.03     1.02      10783.40|
|  4:  3.2838 -  2.9862  1321   136  0.92  13.87   1.01     0.99      10424.66|
|  5:  2.9862 -  2.7736  1296   147  0.89  16.63   0.99     0.97       8690.02|
|  6:  2.7736 -  2.6110  1293   144  0.90  16.73   0.98     0.94       7596.05|
|  7:  2.6110 -  2.4809  1289   154  0.91  15.49   0.98     0.95       6253.13|
|  8:  2.4809 -  2.3733  1311   132  0.91  15.46   1.00     0.97       5680.40|
|  9:  2.3733 -  2.2823  1273   149  0.90  16.30   1.00     0.97       5177.06|
| 10:  2.2823 -  2.2038  1270   139  0.90  16.27   1.00     0.97       4816.24|
| 11:  2.2038 -  2.1351  1274   146  0.90  15.88   1.00     0.96       4311.50|
| 12:  2.1351 -  2.0742  1286   142  0.91  15.03   1.01     0.98       3757.79|
| 13:  2.0742 -  2.0198  1272   130  0.90  16.23   1.00     1.00       3408.92|
| 14:  2.0198 -  1.9706   679    85  0.91  15.69   0.98     0.94       2808.95|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2808.95 max =        10783.40 mean =      6593.70|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.87 mean =        14.32|
|phase err.(test): min =        0.00 max =           89.51 mean =        13.72|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1138   r_free= 0.1596   ksol= 0.32   Bsol= 45.63   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.90,0.33,0.57,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.162677                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1138   r_free= 0.1596   ksol= 0.32   Bsol= 45.63   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.90,0.33,0.57,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.162677                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8855 -  4.7026 0.99   1398  158 0.0997 0.1317      5.3946      5.5662|
|  2:  4.7026 -  3.7523 0.99   1350  148 0.0883 0.1084      5.4645       5.656|
|  3:  3.7523 -  3.2838 0.99   1318  149 0.1057 0.1531      5.4872      5.8667|
|  4:  3.2838 -  2.9862 0.99   1321  136 0.1247 0.1555      5.4631      5.6363|
|  5:  2.9862 -  2.7736 0.98   1296  147 0.1370 0.1639      5.3521      5.4837|
|  6:  2.7736 -  2.6110 0.99   1293  144 0.1308 0.2088      5.2568      5.5415|
|  7:  2.6110 -  2.4809 0.99   1289  154 0.1217 0.1645      5.1656      5.3908|
|  8:  2.4809 -  2.3733 0.99   1311  132 0.1198 0.1763       5.098       5.345|
|  9:  2.3733 -  2.2823 0.99   1273  149 0.1200 0.1904      5.0404       5.344|
| 10:  2.2823 -  2.2038 0.98   1270  139 0.1145 0.1738      4.9924      5.1892|
| 11:  2.2038 -  2.1351 0.98   1274  146 0.1145 0.1721      4.9319      5.2611|
| 12:  2.1351 -  2.0742 1.00   1286  142 0.1090 0.1730      4.8506       5.157|
| 13:  2.0742 -  2.0198 0.96   1272  130 0.1138 0.1725       4.797      5.0542|
| 14:  2.0198 -  1.9706 0.54    679   85 0.1097 0.1706      4.7058      4.9193|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8855 -  4.7026  1398   158  0.94   9.31   0.98     0.96       7439.25|
|  2:  4.7026 -  3.7523  1350   148  0.95   8.45   1.02     1.00       9567.86|
|  3:  3.7523 -  3.2838  1318   149  0.93  11.43   1.03     1.02      10902.05|
|  4:  3.2838 -  2.9862  1321   136  0.92  13.83   1.01     1.00      10366.09|
|  5:  2.9862 -  2.7736  1296   147  0.89  16.58   1.00     0.97       8658.57|
|  6:  2.7736 -  2.6110  1293   144  0.90  16.74   0.98     0.95       7602.66|
|  7:  2.6110 -  2.4809  1289   154  0.91  15.49   0.99     0.96       6245.83|
|  8:  2.4809 -  2.3733  1311   132  0.91  15.43   1.00     0.97       5660.72|
|  9:  2.3733 -  2.2823  1273   149  0.90  16.27   1.01     0.98       5165.43|
| 10:  2.2823 -  2.2038  1270   139  0.90  16.26   1.00     0.97       4808.60|
| 11:  2.2038 -  2.1351  1274   146  0.90  15.89   1.00     0.97       4311.44|
| 12:  2.1351 -  2.0742  1286   142  0.91  15.03   1.01     0.99       3759.04|
| 13:  2.0742 -  2.0198  1272   130  0.90  16.22   1.01     1.00       3406.04|
| 14:  2.0198 -  1.9706   679    85  0.91  15.69   0.98     0.94       2801.13|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2801.13 max =        10902.05 mean =      6644.75|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.37|
|phase err.(test): min =        0.00 max =           89.83 mean =        13.77|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.729)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.12    83.51   15.07    None  None   None       |
|    all(noH): 2823   0      2.12    83.51   15.07    None  None   None       |
|    Sol.    : 438    0      3.77    73.02   37.69    None  None   None       |
|    Mac.    : 2385   0      2.12    83.51   10.92    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:     2.124 -  10.262: 1521   |   5:    42.817 -  50.956:   98        |
|      1:    10.262 -  18.401:  690   |   6:    50.956 -  59.094:   71        |
|      2:    18.401 -  26.540:  175   |   7:    59.094 -  67.233:   34        |
|      3:    26.540 -  34.678:  117   |   8:    67.233 -  75.372:    6        |
|      4:    34.678 -  42.817:  106   |   9:    75.372 -  83.510:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 313         
Filter by distance & map next to the model:
   mapped sites are within: 0.379 - 4.857
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 308 from: 313
   mapped sites are within: 0.743 - 4.857

peak=   10.563 closest distance to " CB  VAL A 230 " =    1.419
peak=    7.289 closest distance to " CG2 VAL A 296 " =    1.153
peak=    6.095 closest distance to " CG  LEU A   5 " =    1.216
peak=    5.484 closest distance to " O   HOH Z 403 " =    1.912
peak=    5.430 closest distance to " O   HOH Z 402 " =    1.642
peak=    5.350 closest distance to " O   HOH Z 124 " =    1.564
peak=    5.342 closest distance to " NH2 ARG A  56 " =    2.238
peak=    5.289 closest distance to " CB  VAL A 296 " =    1.027
peak=    5.175 closest distance to " O   HOH Z 193 " =    1.824
peak=    5.128 closest distance to " CB  SER A  63 " =    1.170
peak=    5.067 closest distance to " CD1AILE A 234 " =    1.037
peak=    5.017 closest distance to " O   HOH Z 209 " =    2.343
peak=    4.970 closest distance to " CG  LEU A 228 " =    1.133
peak=    4.897 closest distance to " CB  ARG A 275 " =    0.957
peak=    4.845 closest distance to " CG  PRO A  54 " =    1.253
peak=    4.810 closest distance to " CB  GLN A 223 " =    1.381
peak=    4.769 closest distance to " O   HOH Z  85 " =    1.625
peak=    4.727 closest distance to " CG  PRO A 213 " =    1.243
peak=    4.727 closest distance to " CD2 LEU A   5 " =    1.085
peak=    4.717 closest distance to " O   HOH Z 272 " =    1.941
peak=    4.696 closest distance to " O   SER A  87 " =    2.247
peak=    4.646 closest distance to " CB  PRO A  54 " =    0.893
peak=    4.618 closest distance to " CB  GLN A 183 " =    1.301
peak=    4.565 closest distance to " O   HOH Z  80 " =    1.864
peak=    4.562 closest distance to " O   HOH Z 142 " =    1.665
peak=    4.505 closest distance to " O   HOH Z 232 " =    2.313
peak=    4.429 closest distance to " CA  TYR A  30 " =    0.938
peak=    4.414 closest distance to " CG  PRO A 198 " =    1.166
peak=    4.380 closest distance to " O   HOH Z  59 " =    2.251
peak=    4.373 closest distance to " O   HOH Z 126 " =    1.842
peak=    4.361 closest distance to " O   HOH Z 102 " =    1.367
peak=    4.358 closest distance to " CD2 LEU A 228 " =    1.238
peak=    4.350 closest distance to " NE2 GLN A  11 " =    1.046
peak=    4.343 closest distance to " O   HOH Z 423 " =    1.794
peak=    4.329 closest distance to " O   HOH Z  63 " =    2.302
peak=    4.324 closest distance to " O   HOH Z 414 " =    1.860
peak=    4.324 closest distance to " O   HOH Z 154 " =    1.596
peak=    4.309 closest distance to " O   HOH Z 327 " =    1.746
peak=    4.291 closest distance to " C   PRO A 198 " =    1.459
peak=    4.282 closest distance to " CB  SER A   3 " =    1.262
peak=    4.267 closest distance to " CB  GLU A 152 " =    1.117
peak=    4.263 closest distance to " O   HOH Z 247 " =    1.384
peak=    4.230 closest distance to " O   HOH Z 346 " =    1.490
peak=    4.228 closest distance to " CG1 ILE A  33 " =    1.256
peak=    4.219 closest distance to " O   HOH Z 369 " =    2.221
peak=    4.204 closest distance to " O   HOH Z  97 " =    1.980
peak=    4.203 closest distance to " O   HOH Z 130 " =    2.799
peak=    4.181 closest distance to " CB  TRP A 179 " =    1.201
peak=    4.170 closest distance to " O   HOH Z 368 " =    2.202
peak=    4.169 closest distance to " O   HOH Z 426 " =    1.445
peak=    4.149 closest distance to " O   HOH Z 298 " =    1.893
peak=    4.114 closest distance to " O   HOH Z  40 " =    1.771
peak=    4.111 closest distance to " O   HOH Z 234 " =    3.557
peak=    4.104 closest distance to " CD  ARG A 269 " =    1.097
peak=    4.094 closest distance to " CB  VAL A 230 " =    1.173
peak=    4.090 closest distance to " O   HOH Z  48 " =    1.762
peak=    4.061 closest distance to " O   HOH Z  54 " =    1.519
peak=    4.059 closest distance to " O   HOH Z 189 " =    2.439
peak=    4.034 closest distance to " CB  GLU A 277 " =    3.586
peak=    4.030 closest distance to " O   HOH Z 345 " =    2.746
peak=    4.029 closest distance to " O   HOH Z  48 " =    1.722
peak=    4.001 closest distance to " OE1 GLU A   2 " =    2.121
peak=    3.996 closest distance to " O   HOH Z 389 " =    1.940
peak=    3.983 closest distance to " CG1BVAL A  72 " =    1.685
peak=    3.983 closest distance to " CA  ARG A 275 " =    1.894
peak=    3.968 closest distance to " CA  ALA A  51 " =    1.050
peak=    3.967 closest distance to " CA  VAL A  41 " =    0.870
peak=    3.965 closest distance to " CG  ARG A  66 " =    1.016
peak=    3.956 closest distance to " CD2 TRP A 179 " =    1.383
peak=    3.930 closest distance to " O   HOH Z 214 " =    2.725
peak=    3.919 closest distance to " O   HOH Z  43 " =    1.367
peak=    3.917 closest distance to " CG  PRO A  90 " =    1.174
peak=    3.915 closest distance to " CB  ASN A 148 " =    1.411
peak=    3.909 closest distance to " N   ASN A  39 " =    1.288
peak=    3.897 closest distance to " CB  GLU A 128 " =    1.176
peak=    3.885 closest distance to " O   HOH Z 411 " =    3.473
peak=    3.881 closest distance to " O   HOH Z 227 " =    1.637
peak=    3.867 closest distance to " NZ  LYS A 117 " =    3.094
peak=    3.865 closest distance to " O   HOH Z 357 " =    2.017
peak=    3.856 closest distance to " O   HOH Z  15 " =    2.107
peak=    3.855 closest distance to " O   HOH Z 128 " =    2.306
peak=    3.839 closest distance to " CG  PRO A 243 " =    1.195
peak=    3.825 closest distance to " CB  TYR A 169 " =    0.792
peak=    3.822 closest distance to " O   HOH Z 303 " =    2.139
peak=    3.818 closest distance to " ND2 ASN A 187 " =    1.692
peak=    3.812 closest distance to " O   HOH Z 406 " =    1.484
peak=    3.799 closest distance to " O   HOH Z 316 " =    2.923
peak=    3.792 closest distance to " O   HOH Z 263 " =    1.486
peak=    3.780 closest distance to " O   HOH Z 156 " =    3.232
peak=    3.777 closest distance to " O   HOH Z 245 " =    1.433
peak=    3.775 closest distance to " CE  LYS A 119 " =    1.056
peak=    3.773 closest distance to " O   HOH Z 352 " =    1.759
peak=    3.773 closest distance to " O   ASP A 124 " =    1.302
peak=    3.761 closest distance to " O   HOH Z 394 " =    1.482
peak=    3.759 closest distance to " O   HOH Z  47 " =    1.610
peak=    3.757 closest distance to " O   HOH Z 134 " =    1.652
peak=    3.749 closest distance to " CA  LYS A 117 " =    1.312
peak=    3.748 closest distance to " O   HOH Z  68 " =    1.892
peak=    3.738 closest distance to " O   HOH Z 420 " =    1.999
peak=    3.737 closest distance to " O   HOH Z 128 " =    1.556
peak=    3.736 closest distance to " O   HOH Z 366 " =    2.893
peak=    3.735 closest distance to " O   HOH Z 248 " =    1.676
peak=    3.726 closest distance to " CA  ALA A  21 " =    1.282
peak=    3.725 closest distance to " O   HOH Z  43 " =    2.270
peak=    3.723 closest distance to " OD1 ASN A  69 " =    2.533
peak=    3.712 closest distance to " OG1 THR A 294 " =    2.272
peak=    3.711 closest distance to " O   HOH Z 261 " =    1.956
peak=    3.710 closest distance to " CB  VAL A 265 " =    1.267
peak=    3.708 closest distance to " CB  ARG A  79 " =    1.352
peak=    3.706 closest distance to " O   HOH Z 126 " =    1.894
peak=    3.705 closest distance to " CE1 HIS A 108 " =    1.125
peak=    3.703 closest distance to " O   HOH Z 422 " =    2.545
peak=    3.700 closest distance to " CG2 ILE A  20 " =    1.466
peak=    3.682 closest distance to " O   HOH Z 419 " =    1.736
peak=    3.675 closest distance to " CB  SER A  26 " =    1.693
peak=    3.662 closest distance to " CB  ARG A 139 " =    0.779
peak=    3.653 closest distance to " O   GLY A  91 " =    1.424
peak=    3.648 closest distance to " O   HOH Z  66 " =    2.160
peak=    3.644 closest distance to " O   HOH Z 412 " =    3.859
peak=    3.643 closest distance to " O   HOH Z  44 " =    1.885
peak=    3.638 closest distance to " O   HOH Z 253 " =    1.572
peak=    3.638 closest distance to " CB  ARG A 190 " =    1.760
peak=    3.636 closest distance to " CD  LYS A 166 " =    1.377
peak=    3.635 closest distance to " CB  ASN A  39 " =    0.777
peak=    3.634 closest distance to " CG2 THR A 221 " =    1.246
peak=    3.634 closest distance to " O   HOH Z 404 " =    1.560
peak=    3.626 closest distance to " CB  ALA A 100 " =    1.205
peak=    3.622 closest distance to " OD1 ASP A 286 " =    1.754
peak=    3.616 closest distance to " CB  ALA A 248 " =    1.391
peak=    3.615 closest distance to " O   HOH Z 284 " =    2.946
peak=    3.615 closest distance to " NH2 ARG A 156 " =    1.084
peak=    3.611 closest distance to " O   HOH Z 345 " =    1.677
peak=    3.611 closest distance to " CB  ALA A   9 " =    1.581
peak=    3.600 closest distance to " O   HOH Z 273 " =    2.800
peak=    3.600 closest distance to " OG BSER A 164 " =    2.160
peak=    3.592 closest distance to " O   HOH Z 287 " =    1.802
peak=    3.585 closest distance to " O   HOH Z 162 " =    1.698
peak=    3.583 closest distance to " O   HOH Z  78 " =    1.723
peak=    3.571 closest distance to " CB  THR A  31 " =    1.591
peak=    3.565 closest distance to " O   HOH Z 250 " =    1.550
peak=    3.558 closest distance to " N   SER A 135 " =    1.294
peak=    3.558 closest distance to " CB  ARG A  79 " =    0.887
peak=    3.556 closest distance to " NH2BARG A 145 " =    2.185
peak=    3.553 closest distance to " CG  GLN A  58 " =    2.646
peak=    3.551 closest distance to " O   HOH Z 197 " =    2.501
peak=    3.547 closest distance to " CB  VAL A 202 " =    1.472
peak=    3.544 closest distance to " CE1 TYR A 186 " =    1.283
peak=    3.538 closest distance to " CD  ARG A 159 " =    0.769
peak=    3.538 closest distance to " O   HOH Z  21 " =    1.789
peak=    3.536 closest distance to " O   HOH Z 128 " =    1.774
peak=    3.535 closest distance to " O   HOH Z 128 " =    1.831
peak=    3.535 closest distance to " CG  MET A 185 " =    1.068
peak=    3.534 closest distance to " CB  SER A 141 " =    1.050
peak=    3.532 closest distance to " O   HOH Z 193 " =    2.161
peak=    3.520 closest distance to " O   HOH Z 359 " =    1.519
peak=    3.509 closest distance to " O   HOH Z 162 " =    1.956
peak=    3.500 closest distance to " O   HOH Z   1 " =    1.975
peak=    3.499 closest distance to " O   HOH Z 261 " =    2.169
peak=    3.498 closest distance to " CA  ASN A 176 " =    1.082
peak=    3.494 closest distance to " O   HOH Z 166 " =    1.400
peak=    3.493 closest distance to " CA  ASP A 162 " =    1.125
peak=    3.485 closest distance to " O   HOH Z 132 " =    2.657
peak=    3.483 closest distance to " O   HOH Z 417 " =    3.273
peak=    3.477 closest distance to " OD1 ASN A  60 " =    1.770
peak=    3.476 closest distance to " CD1 LEU A  96 " =    0.743
peak=    3.473 closest distance to " CB  PRO A 198 " =    1.059
peak=    3.472 closest distance to " O   HOH Z 214 " =    1.415
peak=    3.467 closest distance to " O   HOH Z 126 " =    1.560
peak=    3.465 closest distance to " O   HOH Z 189 " =    2.731
peak=    3.464 closest distance to " CA  ASP A 191 " =    1.066
peak=    3.463 closest distance to " O   HOH Z 408 " =    1.602
peak=    3.463 closest distance to " CA  ARG A  36 " =    1.053
peak=    3.457 closest distance to " CD  LYS A 119 " =    2.017
peak=    3.457 closest distance to " O   HOH Z  97 " =    2.439
peak=    3.452 closest distance to " O   HOH Z 406 " =    1.217
peak=    3.451 closest distance to " CG2AVAL A 121 " =    2.082
peak=    3.449 closest distance to " CB  THR A  52 " =    1.051
peak=    3.441 closest distance to " CA  ARG A 195 " =    1.297
peak=    3.439 closest distance to " O   HOH Z 158 " =    2.956
peak=    3.438 closest distance to " CA  ASP A 140 " =    1.127
peak=    3.433 closest distance to " O   HOH Z 344 " =    1.889
peak=    3.432 closest distance to " O   HOH Z  88 " =    3.231
peak=    3.429 closest distance to " O   HOH Z 433 " =    1.382
peak=    3.426 closest distance to " NZ  LYS A  76 " =    1.877
peak=    3.422 closest distance to " CG AARG A 275 " =    1.179
peak=    3.421 closest distance to " O   HOH Z 250 " =    1.374
peak=    3.421 closest distance to " CG2 ILE A 234 " =    2.051
peak=    3.418 closest distance to " OD2 ASP A 286 " =    2.738
peak=    3.417 closest distance to " O   HOH Z 344 " =    2.949
peak=    3.416 closest distance to " O   HOH Z 265 " =    2.342
peak=    3.415 closest distance to " O   HOH Z 425 " =    1.337
peak=    3.411 closest distance to " O   HOH Z 136 " =    1.337
peak=    3.409 closest distance to " O   HOH Z  61 " =    1.487
peak=    3.403 closest distance to " CB  TYR A 247 " =    0.965
peak=    3.393 closest distance to " O   HOH Z 185 " =    1.623
peak=    3.392 closest distance to " CA  ALA A 295 " =    1.042
peak=    3.388 closest distance to " O   HOH Z 421 " =    1.850
peak=    3.387 closest distance to " O   HOH Z   4 " =    1.649
peak=    3.385 closest distance to " O   HOH Z 329 " =    3.849
peak=    3.384 closest distance to " O   HOH Z 163 " =    1.345
peak=    3.384 closest distance to " O   HOH Z 337 " =    3.708
peak=    3.379 closest distance to " O   HOH Z 280 " =    2.624
peak=    3.379 closest distance to " OD2 ASP A 298 " =    3.968
peak=    3.377 closest distance to " CB BVAL A  41 " =    1.083
peak=    3.375 closest distance to " O   HOH Z  78 " =    2.001
peak=    3.360 closest distance to " CZ  PHE A  38 " =    1.338
peak=    3.355 closest distance to " CA  VAL A 126 " =    1.014
peak=    3.354 closest distance to " CB  TRP A 266 " =    1.053
peak=    3.351 closest distance to " O   HOH Z 197 " =    1.957
peak=    3.336 closest distance to " CG2 ILE A 120 " =    1.263
peak=    3.335 closest distance to " O   HOH Z 109 " =    2.268
peak=    3.334 closest distance to " O   HOH Z 383 " =    1.981
peak=    3.334 closest distance to " O   HOH Z 387 " =    2.474
peak=    3.328 closest distance to " OE1 GLN A  11 " =    1.798
peak=    3.324 closest distance to " CG BARG A 102 " =    1.782
peak=    3.319 closest distance to " O   HOH Z 427 " =    2.610
peak=    3.318 closest distance to " CA  ALA A  84 " =    1.327
peak=    3.313 closest distance to " O   HOH Z 147 " =    1.833
peak=    3.311 closest distance to " O   HOH Z  88 " =    2.662
peak=    3.306 closest distance to " NH1AARG A 145 " =    1.077
peak=    3.301 closest distance to " CA  LYS A 290 " =    1.096
peak=    3.299 closest distance to " O   HOH Z 155 " =    3.044
peak=    3.296 closest distance to " CG2 ILE A 234 " =    1.023
peak=    3.294 closest distance to " O   HOH Z 301 " =    1.974
peak=    3.290 closest distance to " O   HOH Z 389 " =    1.776
peak=    3.285 closest distance to " O   HOH Z 257 " =    2.227
peak=    3.282 closest distance to " O   HOH Z 438 " =    2.309
peak=    3.280 closest distance to " O   HOH Z 271 " =    2.407
peak=    3.280 closest distance to " CA  GLY A 211 " =    1.311
peak=    3.278 closest distance to " CA  ARG A  66 " =    0.906
peak=    3.276 closest distance to " CG  GLN A  77 " =    2.328
peak=    3.269 closest distance to " CD  ARG A 195 " =    0.881
peak=    3.266 closest distance to " CG2 VAL A 197 " =    1.056
peak=    3.265 closest distance to " O   HOH Z 374 " =    2.507
peak=    3.257 closest distance to " OG  SER A 245 " =    1.517
peak=    3.255 closest distance to " CG2 THR A 294 " =    1.483
peak=    3.253 closest distance to " CB  ARG A 259 " =    1.900
peak=    3.249 closest distance to " O   HOH Z 435 " =    1.885
peak=    3.249 closest distance to " OH  TYR A 116 " =    1.161
peak=    3.248 closest distance to " O   HOH Z 362 " =    3.469
peak=    3.248 closest distance to " O   HOH Z 416 " =    2.761
peak=    3.246 closest distance to " O   HOH Z 112 " =    1.645
peak=    3.245 closest distance to " O   HOH Z 425 " =    2.061
peak=    3.244 closest distance to " O   HOH Z 313 " =    1.650
peak=    3.243 closest distance to " CB  SER A 273 " =    0.860
peak=    3.239 closest distance to " CB  ASN A 215 " =    1.113
peak=    3.238 closest distance to " O   HOH Z 261 " =    2.025
peak=    3.234 closest distance to " CD  GLN A 194 " =    1.522
peak=    3.232 closest distance to " CG1 VAL A 296 " =    1.174
peak=    3.230 closest distance to " O   HOH Z 427 " =    3.062
peak=    3.229 closest distance to " CG1 ILE A  49 " =    1.513
peak=    3.229 closest distance to " NH1BARG A 190 " =    2.088
peak=    3.224 closest distance to " OG  SER A  62 " =    2.835
peak=    3.220 closest distance to " O   HOH Z 298 " =    4.857
peak=    3.219 closest distance to " NH1 ARG A  14 " =    1.159
peak=    3.219 closest distance to " O   HOH Z 423 " =    3.245
peak=    3.219 closest distance to " O   HOH Z 130 " =    2.332
peak=    3.217 closest distance to " OG BSER A 210 " =    1.237
peak=    3.213 closest distance to " CD2 HIS A  81 " =    1.065
peak=    3.209 closest distance to " CB  MET A  47 " =    1.098
peak=    3.208 closest distance to " O   HOH Z  63 " =    2.090
peak=    3.201 closest distance to " O   HOH Z 395 " =    1.334
peak=    3.198 closest distance to " O   HOH Z 227 " =    2.215
peak=    3.195 closest distance to " O   ALA A   1 " =    1.702
peak=    3.189 closest distance to " O   HOH Z 417 " =    1.875
peak=    3.183 closest distance to " ND2 ASN A 110 " =    1.556
peak=    3.177 closest distance to " O   HOH Z 299 " =    4.258
peak=    3.177 closest distance to " CB  ALA A 295 " =    1.177
peak=    3.174 closest distance to " NH2AARG A 145 " =    2.223
peak=    3.169 closest distance to " CB  LEU A   5 " =    1.207
peak=    3.168 closest distance to " CA  GLY A  80 " =    1.028
peak=    3.167 closest distance to " O   HOH Z 367 " =    3.414
peak=    3.167 closest distance to " O   ILE A  33 " =    1.251
peak=    3.166 closest distance to " O   HOH Z 334 " =    1.429
peak=    3.159 closest distance to " CB  ALA A   1 " =    1.163
peak=    3.156 closest distance to " O   HOH Z 236 " =    1.543
peak=    3.156 closest distance to " CB  ALA A  71 " =    1.316
peak=    3.154 closest distance to " O   ALA A 165 " =    1.339
peak=    3.152 closest distance to " O   HOH Z 303 " =    1.589
peak=    3.151 closest distance to " O   HOH Z 173 " =    2.389
peak=    3.149 closest distance to " N   ASP A 162 " =    1.311
peak=    3.146 closest distance to " O   HOH Z 146 " =    1.325
peak=    3.145 closest distance to " O   HOH Z 227 " =    1.543
peak=    3.145 closest distance to " C   ALA A 299 " =    0.904
peak=    3.137 closest distance to " CD1 ILE A 199 " =    0.927
peak=    3.135 closest distance to " O   HOH Z 281 " =    4.466
peak=    3.135 closest distance to " O   HOH Z   9 " =    2.428
peak=    3.132 closest distance to " CA  THR A  82 " =    1.501
peak=    3.131 closest distance to " O   HOH Z 406 " =    1.577
peak=    3.122 closest distance to " O   HOH Z 130 " =    1.138
peak=    3.120 closest distance to " CA  LEU A  83 " =    1.367
peak=    3.117 closest distance to " O   HOH Z 148 " =    3.155
peak=    3.115 closest distance to " O   HOH Z  46 " =    1.379
peak=    3.114 closest distance to " O   HOH Z  90 " =    3.442
peak=    3.113 closest distance to " CG1 VAL A 153 " =    1.000
peak=    3.112 closest distance to " O   HOH Z  43 " =    2.816
peak=    3.110 closest distance to " O   HOH Z 244 " =    1.632
peak=    3.104 closest distance to " CD2 LEU A 297 " =    0.847
peak=    3.097 closest distance to " NZ  LYS A 166 " =    2.983
peak=    3.097 closest distance to " O   HOH Z 419 " =    2.309
peak=    3.087 closest distance to " CG  LYS A 119 " =    1.191
peak=    3.082 closest distance to " CB  ASN A 110 " =    1.100
peak=    3.079 closest distance to " OG1 THR A 157 " =    1.153
peak=    3.078 closest distance to " O   HOH Z 380 " =    2.007
peak=    3.071 closest distance to " O   HOH Z 145 " =    2.523
peak=    3.047 closest distance to " OG BSER A 258 " =    3.246
peak=    3.036 closest distance to " CB  GLN A 278 " =    0.889
peak=    3.001 closest distance to " O   HOH Z 286 " =    2.314

                           ----------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: 0.739 - 5.553
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 202 from: 203
   mapped sites are within: 0.739 - 5.553

peak=   -5.154 closest distance to " CG2 VAL A 230 " =    0.739
peak=   -4.639 closest distance to " O   PRO A 163 " =    2.084
peak=   -4.605 closest distance to " CD  ARG A 156 " =    2.055
peak=   -4.559 closest distance to " O   HOH Z 266 " =    4.622
peak=   -4.454 closest distance to " CG2BVAL A  41 " =    2.561
peak=   -4.274 closest distance to " C   HIS A 108 " =    1.191
peak=   -4.234 closest distance to " O   HOH Z  13 " =    1.677
peak=   -4.217 closest distance to " SG  CYS A 254 " =    3.151
peak=   -4.205 closest distance to " O   HOH Z 166 " =    1.714
peak=   -4.161 closest distance to " CD  GLN A  58 " =    1.233
peak=   -4.154 closest distance to " OXT GLY A 302 " =    2.794
peak=   -4.127 closest distance to " O   HOH Z 426 " =    1.815
peak=   -4.094 closest distance to " CD2 TYR A  30 " =    2.733
peak=   -4.082 closest distance to " CB  ALA A 161 " =    2.551
peak=   -4.081 closest distance to " O   HOH Z 290 " =    0.923
peak=   -4.060 closest distance to " CD1 LEU A 101 " =    2.469
peak=   -4.017 closest distance to " OG BSER A 134 " =    1.313
peak=   -4.001 closest distance to " O   HOH Z 351 " =    1.547
peak=   -3.938 closest distance to " O   HOH Z 165 " =    1.989
peak=   -3.933 closest distance to " O   HOH Z  37 " =    1.902
peak=   -3.932 closest distance to " O   ASN A  45 " =    1.815
peak=   -3.907 closest distance to " CD2 LEU A 300 " =    2.662
peak=   -3.899 closest distance to " O   VAL A  67 " =    2.701
peak=   -3.883 closest distance to " O   VAL A  67 " =    1.875
peak=   -3.867 closest distance to " CB  ALA A 248 " =    1.976
peak=   -3.850 closest distance to " O   HOH Z 196 " =    2.223
peak=   -3.822 closest distance to " CD1 PHE A  59 " =    1.978
peak=   -3.819 closest distance to " O   HOH Z 231 " =    2.215
peak=   -3.815 closest distance to " C   THR A 279 " =    1.179
peak=   -3.813 closest distance to " CG  ASP A 231 " =    0.884
peak=   -3.788 closest distance to " O   HOH Z  11 " =    1.829
peak=   -3.772 closest distance to " CB  PHE A 208 " =    2.314
peak=   -3.756 closest distance to " ND2 ASN A 187 " =    1.541
peak=   -3.750 closest distance to " CG  ARG A 219 " =    2.402
peak=   -3.712 closest distance to " O   HOH Z 407 " =    3.049
peak=   -3.692 closest distance to " OG ASER A 134 " =    1.227
peak=   -3.685 closest distance to " N   ALA A 226 " =    2.036
peak=   -3.678 closest distance to " O   HOH Z 283 " =    1.781
peak=   -3.649 closest distance to " CG2 VAL A 296 " =    1.223
peak=   -3.642 closest distance to " O   HOH Z 435 " =    2.564
peak=   -3.641 closest distance to " O   SER A 146 " =    1.029
peak=   -3.638 closest distance to " CD1 LEU A  25 " =    2.464
peak=   -3.630 closest distance to " N   ALA A 248 " =    1.744
peak=   -3.627 closest distance to " CB  ALA A 248 " =    2.199
peak=   -3.622 closest distance to " O   HOH Z 114 " =    3.323
peak=   -3.621 closest distance to " O   HOH Z 377 " =    1.762
peak=   -3.618 closest distance to " CD1 TYR A 247 " =    2.477
peak=   -3.609 closest distance to " ND2 ASN A  45 " =    1.058
peak=   -3.603 closest distance to " ND2 ASN A  39 " =    1.149
peak=   -3.597 closest distance to " CD  GLN A 223 " =    0.750
peak=   -3.589 closest distance to " NE2 GLN A  88 " =    1.040
peak=   -3.588 closest distance to " CZ  TYR A 169 " =    1.841
peak=   -3.585 closest distance to " NE2 GLN A 194 " =    1.719
peak=   -3.584 closest distance to " O   PHE A 218 " =    1.598
peak=   -3.584 closest distance to " O   PRO A 198 " =    1.284
peak=   -3.583 closest distance to " OG  SER A  97 " =    2.316
peak=   -3.582 closest distance to " O   HOH Z 353 " =    2.233
peak=   -3.565 closest distance to " CA  GLY A 203 " =    2.318
peak=   -3.563 closest distance to " CA  ASP A 298 " =    1.027
peak=   -3.550 closest distance to " O   HOH Z  60 " =    2.229
peak=   -3.547 closest distance to " CE  LYS A 166 " =    3.041
peak=   -3.545 closest distance to " CD2 LEU A 237 " =    2.726
peak=   -3.534 closest distance to " O   HOH Z 136 " =    2.269
peak=   -3.531 closest distance to " CG1 VAL A 112 " =    2.628
peak=   -3.528 closest distance to " C   GLY A  80 " =    2.460
peak=   -3.527 closest distance to " CD  ARG A 195 " =    5.081
peak=   -3.527 closest distance to " O   HOH Z 313 " =    1.235
peak=   -3.521 closest distance to " O   TRP A  92 " =    1.893
peak=   -3.521 closest distance to " N   THR A 235 " =    1.316
peak=   -3.520 closest distance to " NH2 ARG A  66 " =    1.453
peak=   -3.511 closest distance to " O   HOH Z  71 " =    1.592
peak=   -3.510 closest distance to " CH2 TRP A 179 " =    1.257
peak=   -3.505 closest distance to " O   ALA A 256 " =    1.538
peak=   -3.498 closest distance to " N   GLN A  58 " =    1.866
peak=   -3.496 closest distance to " O   HOH Z 423 " =    2.247
peak=   -3.495 closest distance to " ND2 ASN A  69 " =    1.610
peak=   -3.475 closest distance to " OD1 ASN A  39 " =    2.167
peak=   -3.471 closest distance to " CB  GLN A  11 " =    1.884
peak=   -3.457 closest distance to " O   HOH Z 265 " =    2.091
peak=   -3.453 closest distance to " OXT GLY A 302 " =    3.464
peak=   -3.446 closest distance to " CB  PHE A 192 " =    2.008
peak=   -3.442 closest distance to " CD1 LEU A 228 " =    2.181
peak=   -3.432 closest distance to " NE2 GLN A 103 " =    1.723
peak=   -3.426 closest distance to " CG  GLU A  53 " =    1.485
peak=   -3.421 closest distance to " CE3 TRP A 150 " =    2.289
peak=   -3.418 closest distance to " O   HOH Z  15 " =    1.489
peak=   -3.413 closest distance to " CD1 PHE A  59 " =    2.078
peak=   -3.410 closest distance to " O   GLY A 196 " =    1.031
peak=   -3.407 closest distance to " O   HOH Z 234 " =    4.024
peak=   -3.397 closest distance to " O   VAL A 125 " =    2.325
peak=   -3.397 closest distance to " CD2 LEU A 167 " =    1.633
peak=   -3.396 closest distance to " CD2 TYR A 293 " =    1.958
peak=   -3.386 closest distance to " O   HOH Z 422 " =    1.524
peak=   -3.385 closest distance to " OG BSER A 134 " =    1.706
peak=   -3.384 closest distance to " O   HOH Z 397 " =    1.224
peak=   -3.383 closest distance to " O   ALA A   1 " =    1.890
peak=   -3.381 closest distance to " NH2AARG A 275 " =    4.772
peak=   -3.381 closest distance to " O   HOH Z 388 " =    2.035
peak=   -3.381 closest distance to " O   HOH Z 210 " =    0.876
peak=   -3.378 closest distance to " O   HOH Z 193 " =    1.810
peak=   -3.375 closest distance to " O   HOH Z  48 " =    1.410
peak=   -3.374 closest distance to " O   SER A 210 " =    1.880
peak=   -3.373 closest distance to " NE2 GLN A  58 " =    2.579
peak=   -3.372 closest distance to " O   ALA A  10 " =    1.780
peak=   -3.371 closest distance to " CG2 THR A 221 " =    2.307
peak=   -3.370 closest distance to " O   HOH Z  56 " =    2.217
peak=   -3.370 closest distance to " O   HOH Z 250 " =    1.278
peak=   -3.363 closest distance to " O   HOH Z 126 " =    1.848
peak=   -3.359 closest distance to " O   HOH Z  44 " =    2.140
peak=   -3.356 closest distance to " CB  SER A 210 " =    1.288
peak=   -3.356 closest distance to " O   HOH Z   6 " =    1.882
peak=   -3.355 closest distance to " CG1 VAL A 296 " =    1.346
peak=   -3.354 closest distance to " CG  ASP A 132 " =    2.322
peak=   -3.352 closest distance to " CG  ASP A  50 " =    2.377
peak=   -3.352 closest distance to " O   ALA A 161 " =    1.639
peak=   -3.352 closest distance to " N   SER A 276 " =    1.391
peak=   -3.345 closest distance to " CD  ARG A 139 " =    1.657
peak=   -3.344 closest distance to " CD  LYS A 289 " =    2.482
peak=   -3.336 closest distance to " C   SER A 206 " =    1.571
peak=   -3.335 closest distance to " NH2 ARG A  79 " =    1.972
peak=   -3.334 closest distance to " CG  TRP A 266 " =    2.086
peak=   -3.332 closest distance to " C   ALA A 158 " =    1.246
peak=   -3.332 closest distance to " O   HOH Z  92 " =    1.679
peak=   -3.329 closest distance to " CG  ARG A 269 " =    2.183
peak=   -3.327 closest distance to " O   HOH Z 174 " =    2.126
peak=   -3.326 closest distance to " O   HOH Z  11 " =    1.842
peak=   -3.324 closest distance to " O   HOH Z 311 " =    3.600
peak=   -3.323 closest distance to " O   SER A 271 " =    2.000
peak=   -3.316 closest distance to " O   HOH Z 166 " =    1.611
peak=   -3.308 closest distance to " CD1 TRP A 179 " =    1.170
peak=   -3.304 closest distance to " O   HOH Z 131 " =    4.089
peak=   -3.302 closest distance to " O   HOH Z 193 " =    1.554
peak=   -3.301 closest distance to " O   HOH Z 191 " =    5.553
peak=   -3.289 closest distance to " N   THR A  52 " =    1.640
peak=   -3.286 closest distance to " CB  PRO A 163 " =    2.649
peak=   -3.285 closest distance to " O   HOH Z 369 " =    2.192
peak=   -3.280 closest distance to " O   HOH Z 252 " =    4.061
peak=   -3.280 closest distance to " O   HOH Z 172 " =    5.142
peak=   -3.275 closest distance to " O   HOH Z  88 " =    4.259
peak=   -3.265 closest distance to " O   HOH Z 150 " =    1.760
peak=   -3.265 closest distance to " O   MET A  40 " =    2.760
peak=   -3.260 closest distance to " N   VAL A 189 " =    1.615
peak=   -3.260 closest distance to " N   LEU A 281 " =    1.880
peak=   -3.253 closest distance to " CA  GLY A  23 " =    1.883
peak=   -3.251 closest distance to " OD2 ASP A  50 " =    1.373
peak=   -3.246 closest distance to " O   ASN A 187 " =    1.466
peak=   -3.244 closest distance to " O   HOH Z 151 " =    1.304
peak=   -3.240 closest distance to " O   HOH Z 150 " =    2.238
peak=   -3.237 closest distance to " OG  SER A   3 " =    1.571
peak=   -3.237 closest distance to " C   GLY A  91 " =    1.356
peak=   -3.234 closest distance to " OD1 ASN A 301 " =    1.979
peak=   -3.234 closest distance to " O   HOH Z  10 " =    1.595
peak=   -3.233 closest distance to " NH1 ARG A  66 " =    0.819
peak=   -3.231 closest distance to " N   ALA A  43 " =    2.607
peak=   -3.230 closest distance to " O   HOH Z 377 " =    1.523
peak=   -3.226 closest distance to " CG1 VAL A 197 " =    2.183
peak=   -3.218 closest distance to " OD2 ASP A 191 " =    1.528
peak=   -3.218 closest distance to " CB  ALA A 291 " =    2.311
peak=   -3.216 closest distance to " O   MET A 188 " =    1.874
peak=   -3.216 closest distance to " O   ALA A 160 " =    1.417
peak=   -3.213 closest distance to " O   HOH Z 339 " =    1.742
peak=   -3.209 closest distance to " NE2 GLN A  88 " =    1.941
peak=   -3.209 closest distance to " O   HOH Z  52 " =    1.805
peak=   -3.200 closest distance to " CE BMET A  47 " =    1.402
peak=   -3.199 closest distance to " CG2 ILE A 263 " =    2.259
peak=   -3.198 closest distance to " O   HOH Z 174 " =    4.209
peak=   -3.192 closest distance to " CE  MET A 105 " =    1.957
peak=   -3.190 closest distance to " OD1 ASN A 249 " =    2.126
peak=   -3.188 closest distance to " O   HOH Z 171 " =    2.098
peak=   -3.187 closest distance to " O   HOH Z 119 " =    2.080
peak=   -3.186 closest distance to " O   VAL A 174 " =    2.009
peak=   -3.182 closest distance to " O   HOH Z  97 " =    1.424
peak=   -3.181 closest distance to " CD2 LEU A 237 " =    2.703
peak=   -3.178 closest distance to " CB  PRO A 243 " =    2.642
peak=   -3.174 closest distance to " O   HOH Z 310 " =    3.504
peak=   -3.167 closest distance to " O   ASP A 171 " =    1.943
peak=   -3.165 closest distance to " OD1 ASN A 148 " =    1.530
peak=   -3.161 closest distance to " CE3 TRP A 274 " =    2.383
peak=   -3.155 closest distance to " CB  ALA A 291 " =    2.118
peak=   -3.151 closest distance to " O   HOH Z 154 " =    1.437
peak=   -3.149 closest distance to " CA  GLY A 241 " =    2.369
peak=   -3.140 closest distance to " ND2 ASN A  45 " =    1.725
peak=   -3.136 closest distance to " CG  GLU A 277 " =    1.119
peak=   -3.132 closest distance to " CD  GLN A  88 " =    0.907
peak=   -3.127 closest distance to " CG  LYS A 193 " =    2.328
peak=   -3.125 closest distance to " O   GLU A 152 " =    1.656
peak=   -3.118 closest distance to " O   HOH Z 301 " =    2.315
peak=   -3.110 closest distance to " O   LYS A 117 " =    1.612
peak=   -3.108 closest distance to " O   HOH Z 285 " =    3.753
peak=   -3.090 closest distance to " CG2 VAL A 189 " =    2.107
peak=   -3.087 closest distance to " O   HOH Z 139 " =    3.237
peak=   -3.085 closest distance to " OD1 ASP A 200 " =    1.319
peak=   -3.081 closest distance to " O   GLY A  80 " =    2.681
peak=   -3.077 closest distance to " OG  SER A  26 " =    1.284
peak=   -3.074 closest distance to " NH1 ARG A 195 " =    2.542
peak=   -3.072 closest distance to " O   HOH Z 429 " =    2.130
peak=   -3.071 closest distance to " CD  ARG A 259 " =    2.498
peak=   -3.051 closest distance to " O   HOH Z 414 " =    2.408
peak=   -3.048 closest distance to " O   HOH Z 185 " =    2.395
peak=   -3.047 closest distance to " N   SER A 271 " =    1.335
peak=   -3.028 closest distance to " CA  ASP A  27 " =    2.292
peak=   -3.025 closest distance to " O   ALA A  51 " =    1.442

================= 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    :  0.4798 0.4670   6.279110e+00   6.267516e+00
   1_bss:  0.4713 0.4591   6.272457e+00   6.260060e+00
   1_xyz:  0.3837 0.4056   6.149227e+00   6.184570e+00
   1_adp:  0.3363 0.3784   6.059792e+00   6.146253e+00
   1_occ:  0.3358 0.3778   6.058666e+00   6.145625e+00
   2_bss:  0.3337 0.3729   6.059880e+00   6.144193e+00
   2_xyz:  0.2280 0.2740   5.743247e+00   5.908043e+00
   2_adp:  0.1992 0.2504   5.630535e+00   5.814474e+00
   2_occ:  0.1990 0.2501   5.629592e+00   5.814041e+00
   3_bss:  0.1958 0.2482   5.625930e+00   5.808618e+00
   3_xyz:  0.1474 0.1901   5.367677e+00   5.572910e+00
   3_adp:  0.1393 0.1776   5.306971e+00   5.504331e+00
   3_occ:  0.1390 0.1774   5.306163e+00   5.504407e+00
   4_bss:  0.1390 0.1775   5.308721e+00   5.505077e+00
   4_xyz:  0.1251 0.1646   5.222660e+00   5.432277e+00
   4_adp:  0.1222 0.1631   5.205804e+00   5.423848e+00
   4_occ:  0.1221 0.1632   5.205540e+00   5.423842e+00
   5_bss:  0.1221 0.1631   5.205293e+00   5.423800e+00
   5_xyz:  0.1154 0.1581   5.164436e+00   5.397425e+00
   5_adp:  0.1138 0.1593   5.161482e+00   5.404385e+00
   5_occ:  0.1138 0.1594   5.161444e+00   5.404574e+00
   5_bss:  0.1138 0.1596   5.162677e+00   5.405921e+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:  0.360  20.000   7.238  10.481   7.582   0.000   0.000   0.000
   1_xyz:  0.360  20.000   7.238  10.481   7.582   0.000   0.000   0.000
   1_adp:  0.360  20.000   7.238  10.481   7.582   0.000   0.000   0.000
   1_occ:  0.360  20.000   7.238  10.481   7.582   0.000   0.000   0.000
   2_bss:  0.303  20.000   3.981   6.678   4.890   0.000   0.000   0.000
   2_xyz:  0.303  20.000   3.981   6.678   4.890   0.000   0.000   0.000
   2_adp:  0.303  20.000   3.981   6.678   4.890   0.000   0.000   0.000
   2_occ:  0.303  20.000   3.981   6.678   4.890   0.000   0.000   0.000
   3_bss:  0.324  41.276   1.860   3.793   3.305   0.000   0.000   0.000
   3_xyz:  0.324  41.276   1.860   3.793   3.305   0.000   0.000   0.000
   3_adp:  0.324  41.276   1.860   3.793   3.305   0.000   0.000   0.000
   3_occ:  0.324  41.276   1.860   3.793   3.305   0.000   0.000   0.000
   4_bss:  0.326  41.276   1.137   2.683   2.666   0.000   0.000   0.000
   4_xyz:  0.326  41.276   1.137   2.683   2.666   0.000   0.000   0.000
   4_adp:  0.326  41.276   1.137   2.683   2.666   0.000   0.000   0.000
   4_occ:  0.326  41.276   1.137   2.683   2.666   0.000   0.000   0.000
   5_bss:  0.325  43.558   1.093   2.421   2.605   0.000   0.000   0.000
   5_xyz:  0.325  43.558   1.093   2.421   2.605   0.000   0.000   0.000
   5_adp:  0.325  43.558   1.093   2.421   2.605   0.000   0.000   0.000
   5_occ:  0.325  43.558   1.093   2.421   2.605   0.000   0.000   0.000
   5_bss:  0.322  45.634  -0.905   0.334   0.571   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  55.977 0.4462  0.5147    67347.433
   1_bss:  56.073 0.4430  0.6544    65250.757
   1_xyz:  46.980 0.5560  0.8051    47545.624
   1_adp:  41.843 0.6201  0.9351    40855.322
   1_occ:  41.745 0.6213  0.9352    40698.087
   2_bss:  41.496 0.6241  0.8372    40250.656
   2_xyz:  29.128 0.7659  0.9968    20576.520
   2_adp:  25.158 0.8096  1.0310    16355.687
   2_occ:  25.133 0.8098  1.0310    16318.698
   3_bss:  24.949 0.8117  0.9551    16091.931
   3_xyz:  18.199 0.8781  0.9987     9276.512
   3_adp:  16.538 0.8937  1.0088     8135.610
   3_occ:  16.537 0.8937  1.0088     8136.905
   4_bss:  16.534 0.8938  0.9788     8165.505
   4_xyz:  14.930 0.9077  0.9826     7001.105
   4_adp:  14.684 0.9099  0.9818     6902.785
   4_occ:  14.677 0.9100  0.9818     6907.080
   5_bss:  14.673 0.9100  0.9778     6908.453
   5_xyz:  14.149 0.9142  0.9795     6541.444
   5_adp:  14.263 0.9133  0.9751     6588.961
   5_occ:  14.263 0.9133  0.9750     6591.979
   5_bss:  14.308 0.9130  0.9776     6643.083
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3448e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3448e+01
   1_xyz:   1.765  0.014  0.112 18.165  0.007  4.119   1.5219e-01
   1_adp:   1.765  0.014  0.112 18.165  0.007  4.119   1.5219e-01
   1_occ:   1.765  0.014  0.112 18.165  0.007  4.119   1.5219e-01
   2_bss:   1.765  0.014  0.112 18.165  0.007  4.119   1.5219e-01
   2_xyz:   1.308  0.011  0.086 16.368  0.006  4.126   9.6050e-02
   2_adp:   1.308  0.011  0.086 16.368  0.006  4.126   9.6050e-02
   2_occ:   1.308  0.011  0.086 16.368  0.006  4.126   9.6050e-02
   3_bss:   1.308  0.011  0.086 16.368  0.006  4.126   9.6050e-02
   3_xyz:   1.033  0.007  0.075 15.529  0.004  4.109   6.3695e-02
   3_adp:   1.033  0.007  0.075 15.529  0.004  4.109   6.3695e-02
   3_occ:   1.033  0.007  0.075 15.529  0.004  4.109   6.3695e-02
   4_bss:   1.033  0.007  0.075 15.529  0.004  4.109   6.3695e-02
   4_xyz:   0.951  0.006  0.074 15.167  0.004  4.113   5.6006e-02
   4_adp:   0.951  0.006  0.074 15.167  0.004  4.113   5.6006e-02
   4_occ:   0.951  0.006  0.074 15.167  0.004  4.113   5.6006e-02
   5_bss:   0.951  0.006  0.074 15.167  0.004  4.113   5.6006e-02
   5_xyz:   1.046  0.007  0.083 15.268  0.004  4.116   6.3654e-02
   5_adp:   1.046  0.007  0.083 15.268  0.004  4.116   6.3654e-02
   5_occ:   1.046  0.007  0.083 15.268  0.004  4.116   6.3654e-02
   5_bss:   1.046  0.007  0.083 15.268  0.004  4.116   6.3654e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.034   6.9264e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.034   6.9264e+00
   1_xyz:  16.436  0.176  0.570 85.849  0.045  2.207   1.0945e-01
   1_adp:  16.436  0.176  0.570 85.849  0.045  2.207   1.0945e-01
   1_occ:  16.436  0.176  0.570 85.849  0.045  2.207   1.0945e-01
   2_bss:  16.436  0.176  0.570 85.849  0.045  2.207   1.0945e-01
   2_xyz:   8.487  0.145  0.296 82.818  0.053  2.155   9.0384e-02
   2_adp:   8.487  0.145  0.296 82.818  0.053  2.155   9.0384e-02
   2_occ:   8.487  0.145  0.296 82.818  0.053  2.155   9.0384e-02
   3_bss:   8.487  0.145  0.296 82.818  0.053  2.155   9.0384e-02
   3_xyz:   6.857  0.053  0.440 81.080  0.042  2.263   4.7967e-02
   3_adp:   6.857  0.053  0.440 81.080  0.042  2.263   4.7967e-02
   3_occ:   6.857  0.053  0.440 81.080  0.042  2.263   4.7967e-02
   4_bss:   6.857  0.053  0.440 81.080  0.042  2.263   4.7967e-02
   4_xyz:   6.567  0.040  0.452 83.875  0.037  2.281   4.3577e-02
   4_adp:   6.567  0.040  0.452 83.875  0.037  2.281   4.3577e-02
   4_occ:   6.567  0.040  0.452 83.875  0.037  2.281   4.3577e-02
   5_bss:   6.567  0.040  0.452 83.875  0.037  2.281   4.3577e-02
   5_xyz:   7.277  0.051  0.614 81.728  0.034  2.310   3.8447e-02
   5_adp:   7.277  0.051  0.614 81.728  0.034  2.310   3.8447e-02
   5_occ:   7.277  0.051  0.614 81.728  0.034  2.310   3.8447e-02
   5_bss:   7.277  0.051  0.614 81.728  0.034  2.310   3.8447e-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:  87.42   0.00  13.05  80.23   0.00  10.50  87.42   0.00  26.94
   1_occ:  87.42   0.00  13.05  80.23   0.00  10.50  87.42   0.00  26.94
   2_bss:  87.42   0.00  13.05  80.23   0.00  10.50  87.42   0.00  26.94
   2_xyz:  87.42   0.00  13.05  80.23   0.00  10.50  87.42   0.00  26.94
   2_adp:  80.22   0.00  12.84  80.22   0.00   9.26  75.80   2.01  32.35
   2_occ:  80.22   0.00  12.84  80.22   0.00   9.26  75.80   2.01  32.35
   3_bss:  80.22   0.00  12.84  80.22   0.00   9.26  75.80   2.01  32.35
   3_xyz:  80.22   0.00  12.84  80.22   0.00   9.26  75.80   2.01  32.35
   3_adp:  79.78   0.00  12.74  79.78   0.00   8.86  71.03   1.57  33.88
   3_occ:  79.78   0.00  12.74  79.78   0.00   8.86  71.03   1.57  33.88
   4_bss:  79.78   0.00  12.74  79.78   0.00   8.86  71.03   1.57  33.88
   4_xyz:  79.78   0.00  12.74  79.78   0.00   8.86  71.03   1.57  33.88
   4_adp:  80.41   0.00  12.86  80.41   0.00   8.82  71.15   2.06  34.81
   4_occ:  80.41   0.00  12.86  80.41   0.00   8.82  71.15   2.06  34.81
   5_bss:  80.41   0.00  12.86  80.41   0.00   8.82  71.15   2.06  34.81
   5_xyz:  80.41   0.00  12.86  80.41   0.00   8.82  71.15   2.06  34.81
   5_adp:  81.39   0.00  12.95  81.39   0.00   8.79  70.90   1.65  35.57
   5_occ:  81.39   0.00  12.95  81.39   0.00   8.79  70.90   1.65  35.57
   5_bss:  83.51   2.12  15.07  83.51   2.12  10.92  73.02   3.77  37.69
------------------------------------------------------------------------
 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:    1.169    0.024    0.420
   1_adp:    1.169    0.024    0.420
   1_occ:    1.169    0.024    0.420
   2_bss:    1.169    0.024    0.420
   2_xyz:    1.613    0.024    0.622
   2_adp:    1.613    0.024    0.622
   2_occ:    1.613    0.024    0.622
   3_bss:    1.613    0.024    0.622
   3_xyz:    1.677    0.025    0.677
   3_adp:    1.677    0.025    0.677
   3_occ:    1.677    0.025    0.677
   4_bss:    1.677    0.025    0.677
   4_xyz:    1.823    0.045    0.716
   4_adp:    1.823    0.045    0.716
   4_occ:    1.823    0.045    0.716
   5_bss:    1.823    0.045    0.716
   5_xyz:    1.904    0.036    0.730
   5_adp:    1.904    0.036    0.730
   5_occ:    1.904    0.036    0.730
   5_bss:    1.904    0.036    0.730
------------------------------------------------------------------------

CPU time actual refinement: 329.28


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_333/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_333/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_333/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_333/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_333/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 329.13 
  Macro-tasks:
    bulk solvent and scale       = 45.37  
    individual site refinement   = 130.28 
    weights calculation          = 31.76  
    collect and process          = 6.43   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 213.94 
  Micro-tasks:
    mask                            = 2.46   
    f_calc                          = 99.82  
    alpha_beta                      = 8.02   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 109.02 
    fmodel                         = 7.89   
    r_factors                      = 0.26   
    phase_errors                   = 10.63  
    foms                           = 0.22   
    TOTAL for micro-tasks          = 239.48 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.663 micro seconds
Total CPU time: 5.71 minutes
from_scatterers_fft:    633 calls, 99.49 s
gradients_fft:          577 calls, 96.41 s

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

# Date 2008-01-16 Time 01:20:45 PST -0800 (1200475245.66 s)
Start R-work = 0.4798, R-free = 0.4670 (no bulk solvent and anisotropic scale)
Final R-work = 0.1313, R-free = 0.1751 (no bulk solvent and anisotropic scale)

Start R-work = 0.4713, R-free = 0.4591
Final R-work = 0.1138, R-free = 0.1596