# Date 2008-01-16 Time 00:51:32 PST -0800 (1200473492.31 s)
#phil __OFF__

Command line arguments: "../177.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 21548
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 177

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (68.845, 46.93, 84.6622, 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: 3.29, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 46.93, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6941 1.96048
Completeness in resolution range: 0.966976
Completeness with d_max=infinity: 0.963931

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.6941
                             d_min =   1.9605

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (68.845, 46.93, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6941 1.96048
Completeness in resolution range: 0.966976
Completeness with d_max=infinity: 0.963931

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.6945 -  4.1941 [2123/2151]  1912   211   9.9%
  bin  2:  4.1941 -  3.3418 [2037/2056]  1831   206  10.1%
  bin  3:  3.3418 -  2.9232 [2026/2047]  1824   202  10.0%
  bin  4:  2.9232 -  2.6576 [1990/2014]  1794   196   9.8%
  bin  5:  2.6576 -  2.4681 [1987/2008]  1786   201  10.1%
  bin  6:  2.4681 -  2.3232 [1967/2012]  1774   193   9.8%
  bin  7:  2.3232 -  2.2072 [1963/1996]  1765   198  10.1%
  bin  8:  2.2072 -  2.1114 [1961/1996]  1760   201  10.2%
  bin  9:  2.1114 -  2.0304 [1942/1972]  1752   190   9.8%
  bin 10:  2.0304 -  1.9605 [1593/2006]  1432   161  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_177/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: 0.13 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:
        1.14 -     1.89: 12
        1.89 -     2.64: 112
        2.64 -     3.40: 4431
        3.40 -     4.15: 9585
        4.15 -     4.90: 14791
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.141 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.393 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.487 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.508 3.040 -x+1,y+1/2,-z+1/2
  " OD2 ASP A 107 " - " OG ASER A 216 "  1.678 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28926 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_177/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_177/model_refine_001.geo

CPU time processing inputs: 9.25


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 68.845 46.93 84.6622 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4778   r_free= 0.4731   ksol= 0.00   Bsol= 0.00   scale= 0.808    |
|                                                                             |
| 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:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.275673                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6945 -  4.6774 0.99   1381  154 0.3928 0.3857      6.5804      6.6023|
|  2:  4.6774 -  3.7326 0.99   1328  146 0.4019 0.3901      6.7652      6.7814|
|  3:  3.7326 -  3.2667 0.99   1305  148 0.4272 0.4139      6.6661      6.7407|
|  4:  3.2667 -  2.9707 0.99   1296  137 0.4496 0.4671      6.5148      6.4873|
|  5:  2.9707 -  2.7593 0.99   1280  146 0.4933 0.5131      6.3823      6.3825|
|  6:  2.7593 -  2.5976 0.98   1284  142 0.5057 0.5219      6.2842      6.2285|
|  7:  2.5976 -  2.4681 0.99   1273  143 0.5218 0.5046      6.2563      6.1565|
|  8:  2.4681 -  2.3611 0.98   1268  140 0.5133 0.4946      6.1853      6.1824|
|  9:  2.3611 -  2.2706 0.98   1275  146 0.5288 0.5123      6.1288      6.1479|
| 10:  2.2706 -  2.1925 0.97   1235  132 0.5325 0.5364      6.1154      6.0904|
| 11:  2.1925 -  2.1241 0.99   1272  144 0.5378 0.5473      6.0435      6.0968|
| 12:  2.1241 -  2.0636 0.98   1271  135 0.5182 0.4983       5.987      5.9951|
| 13:  2.0636 -  2.0094 0.97   1229  137 0.5504 0.5583      5.8999      5.9018|
| 14:  2.0094 -  1.9605 0.73    933  109 0.5307 0.4901      5.8586      5.7335|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6945 -  4.6774  1381   154  0.67  37.06   0.81     0.69      79388.16|
|  2:  4.6774 -  3.7326  1328   146  0.68  37.26   0.89     0.75     113635.32|
|  3:  3.7326 -  3.2667  1305   148  0.59  44.94   0.87     0.71     120453.33|
|  4:  3.2667 -  2.9707  1296   137  0.51  50.78   0.83     0.62     103324.65|
|  5:  2.9707 -  2.7593  1280   146  0.44  56.63   0.75     0.54      83726.31|
|  6:  2.7593 -  2.5976  1284   142  0.42  58.52   0.73     0.49      68953.56|
|  7:  2.5976 -  2.4681  1273   143  0.41  59.39   0.73     0.47      63034.52|
|  8:  2.4681 -  2.3611  1268   140  0.41  59.42   0.75     0.47      55152.83|
|  9:  2.3611 -  2.2706  1275   146  0.38  61.77   0.74     0.46      52674.18|
| 10:  2.2706 -  2.1925  1235   132  0.38  61.47   0.77     0.46      48020.70|
| 11:  2.1925 -  2.1241  1272   144  0.34  64.77   0.76     0.42      46949.19|
| 12:  2.1241 -  2.0636  1271   135  0.32  65.78   0.76     0.41      44625.07|
| 13:  2.0636 -  2.0094  1229   137  0.28  68.82   0.74     0.37      38810.63|
| 14:  2.0094 -  1.9605   933   109  0.31  66.88   0.74     0.34      29470.43|
|alpha:            min =        0.34 max =            0.75 mean =         0.52|
|beta:             min =    29470.43 max =       120453.33 mean =     68951.96|
|figures of merit: min =        0.00 max =            1.00 mean =         0.44|
|phase err.(work): min =        0.00 max =           89.99 mean =        56.23|
|phase err.(test): min =        0.00 max =           89.76 mean =        56.74|
|-----------------------------------------------------------------------------|

============================== 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 = 14.311964             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.092   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.150899              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 82.815   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  0.733 -  1.149:        1 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.149 -  1.566:        5 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.566 -  1.983:       45 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  1.983 -  2.400:      296 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.400 -  2.816:     1077 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.816 -  3.233:     2270 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.233 -  3.650:     3891 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.650 -  4.066:     5440 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.066 -  4.483:     7193 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.483 -  4.900:     8719 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       52.880 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.086    4.900  0.733 |       2.749 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.395)------------------------------------------|
|    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 = 11.395)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4835   r_free= 0.4786   ksol= 0.00   Bsol= 0.00   scale= 0.776    |
|                                                                             |
| 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: 6.277966                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4683   r_free= 0.4617   ksol= 0.37   Bsol= 7.35   scale= 1.008    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.96,7.67,9.29,0.00,0.00,0.00); trace/3= 8.30                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.269359                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.349924             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.425   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.133998              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.544   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4683      final r-factor (work) = 0.3859          |
| start r-factor (free) = 0.4617      final r-factor (free) = 0.4070          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 91.6423 = 12.35 * 0.50 * 6.2774 + 1.00 * 52.8798                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.3163 = 12.35 * 0.50 * 6.1805 + 1.00 * 0.1521                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3859      final r-factor (work) = 0.3356          |
| start r-factor (free) = 0.4070      final r-factor (free) = 0.3852          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.0230 = 1.13 * 1.00 * 6.1805 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.9193 = 1.13 * 1.00 * 6.0873 + 1.00 * 0.0163                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.395)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.08   12.84    None  None   None       |
|    all(noH): 2823   0      0.00    80.08   12.84    None  None   None       |
|    Sol.    : 438    0      0.00    80.08   26.63    None  None   None       |
|    Mac.    : 2385   0      0.00    73.38   10.31    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 -   8.008: 1258   |   5:    40.039 -  48.047:   70        |
|      1:     8.008 -  16.016:  735   |   6:    48.047 -  56.055:   30        |
|      2:    16.016 -  24.024:  385   |   7:    56.055 -  64.063:   13        |
|      3:    24.024 -  32.032:  209   |   8:    64.063 -  72.071:    2        |
|      4:    32.032 -  40.039:  116   |   9:    72.071 -  80.079:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3356 r_free = 0.3852             target_work(ml) = 6.061         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3353 r_free = 0.3850             target_work(ml) = 6.060         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3353   r_free= 0.3850   ksol= 0.37   Bsol= 7.35   scale= 1.107    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.96,7.67,9.29,0.00,0.00,0.00); trace/3= 8.30                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.060240                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3317   r_free= 0.3798   ksol= 0.34   Bsol= 26.91   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.36,4.03,6.08,0.00,0.00,0.00); trace/3= 4.82                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.058469                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.419392              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.966   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.505461              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.572  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3317      final r-factor (work) = 0.2412          |
| start r-factor (free) = 0.3798      final r-factor (free) = 0.2925          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.6751 = 6.42 * 0.50 * 6.0825 + 1.00 * 0.1521                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.1151 = 6.42 * 0.50 * 5.9311 + 1.00 * 0.0781                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2412      final r-factor (work) = 0.2177          |
| start r-factor (free) = 0.2925      final r-factor (free) = 0.2659          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0204 = 0.51 * 1.00 * 5.9311 + 1.00 * 0.0225                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9163 = 0.51 * 1.00 * 5.7450 + 1.00 * 0.0124                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.395)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    112.88  12.98    None  None   None       |
|    all(noH): 2823   0      0.00    112.88  12.98    None  None   None       |
|    Sol.    : 438    0      0.00    87.94   32.77    None  None   None       |
|    Mac.    : 2385   0      0.00    112.88  9.34     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 -  11.288: 1796   |   5:    56.439 -  67.727:   22        |
|      1:    11.288 -  22.576:  524   |   6:    67.727 -  79.015:    6        |
|      2:    22.576 -  33.863:  231   |   7:    79.015 -  90.302:    1        |
|      3:    33.863 -  45.151:  153   |   8:    90.302 - 101.590:    0        |
|      4:    45.151 -  56.439:   88   |   9:   101.590 - 112.878:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2177 r_free = 0.2659             target_work(ml) = 5.705         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2174 r_free = 0.2656             target_work(ml) = 5.705         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2174   r_free= 0.2656   ksol= 0.34   Bsol= 26.91   scale= 1.064   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.36,4.03,6.08,0.00,0.00,0.00); trace/3= 4.82                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.704555                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2152   r_free= 0.2643   ksol= 0.32   Bsol= 32.28   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.29,2.75,3.79,0.00,0.00,0.00); trace/3= 2.95                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.700951                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.456420              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.247  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.445849              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.581   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2152      final r-factor (work) = 0.1547          |
| start r-factor (free) = 0.2643      final r-factor (free) = 0.2005          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0166 = 3.46 * 0.50 * 5.7509 + 1.00 * 0.0778                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6855 = 3.46 * 0.50 * 5.5667 + 1.00 * 0.0650                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1547      final r-factor (work) = 0.1412          |
| start r-factor (free) = 0.2005      final r-factor (free) = 0.1863          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4942 = 0.45 * 1.00 * 5.5667 + 1.00 * 0.0123                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4078 = 0.45 * 1.00 * 5.3701 + 1.00 * 0.0136                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.395)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.10   13.19    None  None   None       |
|    all(noH): 2823   0      0.00    91.10   13.19    None  None   None       |
|    Sol.    : 438    0      2.16    83.86   36.63    None  None   None       |
|    Mac.    : 2385   0      0.00    91.10   8.89     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.110: 1673   |   5:    45.552 -  54.662:   87        |
|      1:     9.110 -  18.221:  568   |   6:    54.662 -  63.772:   49        |
|      2:    18.221 -  27.331:  168   |   7:    63.772 -  72.882:   20        |
|      3:    27.331 -  36.441:  128   |   8:    72.882 -  81.993:    6        |
|      4:    36.441 -  45.552:  121   |   9:    81.993 -  91.103:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1412 r_free = 0.1863             target_work(ml) = 5.327         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1410 r_free = 0.1862             target_work(ml) = 5.327         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1410   r_free= 0.1862   ksol= 0.32   Bsol= 32.28   scale= 1.033   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.29,2.75,3.79,0.00,0.00,0.00); trace/3= 2.95                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.326725                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1407   r_free= 0.1849   ksol= 0.32   Bsol= 29.05   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.56,2.30,2.88,0.00,0.00,0.00); trace/3= 2.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.325117                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.772871              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 111.513  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.152494              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.765   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1407      final r-factor (work) = 0.1250          |
| start r-factor (free) = 0.1849      final r-factor (free) = 0.1680          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8282 = 1.77 * 0.50 * 5.3734 + 1.00 * 0.0650                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7333 = 1.77 * 0.50 * 5.2757 + 1.00 * 0.0567                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1250      final r-factor (work) = 0.1236          |
| start r-factor (free) = 0.1680      final r-factor (free) = 0.1639          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8165 = 0.15 * 1.00 * 5.2757 + 1.00 * 0.0120                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8079 = 0.15 * 1.00 * 5.2210 + 1.00 * 0.0117                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.395)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.02   13.08    None  None   None       |
|    all(noH): 2823   0      0.00    91.02   13.08    None  None   None       |
|    Sol.    : 438    0      1.99    82.98   35.90    None  None   None       |
|    Mac.    : 2385   0      0.00    91.02   8.89     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.102: 1698   |   5:    45.508 -  54.610:   81        |
|      1:     9.102 -  18.203:  573   |   6:    54.610 -  63.712:   47        |
|      2:    18.203 -  27.305:  150   |   7:    63.712 -  72.814:   19        |
|      3:    27.305 -  36.407:  133   |   8:    72.814 -  81.915:    4        |
|      4:    36.407 -  45.508:  115   |   9:    81.915 -  91.017:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1236 r_free = 0.1639             target_work(ml) = 5.208         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1234 r_free = 0.1637             target_work(ml) = 5.207         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1234   r_free= 0.1637   ksol= 0.32   Bsol= 29.05   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.56,2.30,2.88,0.00,0.00,0.00); trace/3= 2.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.206915                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1234   r_free= 0.1637   ksol= 0.32   Bsol= 30.33   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.33,2.15,2.60,0.00,0.00,0.00); trace/3= 2.03                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.206621                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.680616              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 130.682  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.688601              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 103.943  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1234      final r-factor (work) = 0.1168          |
| start r-factor (free) = 0.1637      final r-factor (free) = 0.1576          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4427 = 1.68 * 0.50 * 5.2199 + 1.00 * 0.0564                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4121 = 1.68 * 0.50 * 5.1813 + 1.00 * 0.0582                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1168      final r-factor (work) = 0.1140          |
| start r-factor (free) = 0.1576      final r-factor (free) = 0.1589          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.7652 = 1.69 * 1.00 * 5.1813 + 1.00 * 0.0160                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.7056 = 1.69 * 1.00 * 5.1482 + 1.00 * 0.0124                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.395)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.52   13.26    None  None   None       |
|    all(noH): 2823   0      0.00    97.52   13.26    None  None   None       |
|    Sol.    : 438    0      1.50    83.60   37.27    None  None   None       |
|    Mac.    : 2385   0      0.00    97.52   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 -   9.752: 1772   |   5:    48.759 -  58.511:   67        |
|      1:     9.752 -  19.504:  531   |   6:    58.511 -  68.263:   48        |
|      2:    19.504 -  29.256:  142   |   7:    68.263 -  78.015:   19        |
|      3:    29.256 -  39.007:  123   |   8:    78.015 -  87.767:    2        |
|      4:    39.007 -  48.759:  116   |   9:    87.767 -  97.519:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1140 r_free = 0.1589             target_work(ml) = 5.154         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1139 r_free = 0.1588             target_work(ml) = 5.154         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1139   r_free= 0.1588   ksol= 0.32   Bsol= 30.33   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.33,2.15,2.60,0.00,0.00,0.00); trace/3= 2.03                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.153724                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6945 -  4.6774 0.99   1381  154 0.1041 0.1316      5.4311      5.5666|
|  2:  4.6774 -  3.7326 0.99   1328  146 0.0886 0.1113       5.456      5.6256|
|  3:  3.7326 -  3.2667 0.99   1305  148 0.1070 0.1470      5.4664      5.8112|
|  4:  3.2667 -  2.9707 0.99   1296  137 0.1251 0.1576      5.4629      5.6211|
|  5:  2.9707 -  2.7593 0.99   1280  146 0.1279 0.1608      5.3089      5.4565|
|  6:  2.7593 -  2.5976 0.98   1284  142 0.1270 0.1920      5.2248      5.4613|
|  7:  2.5976 -  2.4681 0.99   1273  143 0.1197 0.1684      5.1475      5.3653|
|  8:  2.4681 -  2.3611 0.98   1268  140 0.1179 0.1782      5.0972      5.3906|
|  9:  2.3611 -  2.2706 0.98   1275  146 0.1189 0.1805       5.038      5.3104|
| 10:  2.2706 -  2.1925 0.97   1235  132 0.1150 0.1706      4.9806      5.1645|
| 11:  2.1925 -  2.1241 0.99   1272  144 0.1134 0.1735      4.9271      5.2909|
| 12:  2.1241 -  2.0636 0.98   1271  135 0.1118 0.1817      4.8766      5.1803|
| 13:  2.0636 -  2.0094 0.97   1229  137 0.1182 0.1688      4.8228       5.031|
| 14:  2.0094 -  1.9605 0.73    933  109 0.1105 0.1835      4.7306      4.9825|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6945 -  4.6774  1381   154  0.94   9.47   0.99     0.97       7830.91|
|  2:  4.6774 -  3.7326  1328   146  0.95   7.83   1.03     1.02       9073.10|
|  3:  3.7326 -  3.2667  1305   148  0.93  11.09   1.04     1.03       9952.99|
|  4:  3.2667 -  2.9707  1296   137  0.92  13.03   1.02     1.02       9924.14|
|  5:  2.9707 -  2.7593  1280   146  0.91  15.11   1.00     0.97       7805.59|
|  6:  2.7593 -  2.5976  1284   142  0.90  15.85   0.99     0.96       7016.35|
|  7:  2.5976 -  2.4681  1273   143  0.91  15.36   0.99     0.96       6059.69|
|  8:  2.4681 -  2.3611  1268   140  0.91  15.48   1.00     0.98       5682.28|
|  9:  2.3611 -  2.2706  1275   146  0.90  15.84   1.02     1.00       5090.96|
| 10:  2.2706 -  2.1925  1235   132  0.90  15.54   1.01     0.98       4521.18|
| 11:  2.1925 -  2.1241  1272   144  0.90  15.68   1.01     0.97       4228.08|
| 12:  2.1241 -  2.0636  1271   135  0.91  14.91   1.02     1.00       3882.54|
| 13:  2.0636 -  2.0094  1229   137  0.90  16.15   1.01     1.01       3532.57|
| 14:  2.0094 -  1.9605   933   109  0.90  16.00   1.00     0.96       2932.15|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2932.15 max =         9952.99 mean =      6358.36|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.00|
|phase err.(test): min =        0.00 max =           87.33 mean =        13.61|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1142   r_free= 0.1590   ksol= 0.32   Bsol= 35.02   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.69,0.13,0.56,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.154908                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.69 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1142   r_free= 0.1590   ksol= 0.32   Bsol= 35.02   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.69,0.13,0.56,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.154908                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6945 -  4.6774 0.99   1381  154 0.1030 0.1320      5.4253      5.5659|
|  2:  4.6774 -  3.7326 0.99   1328  146 0.0904 0.1120      5.4726      5.6406|
|  3:  3.7326 -  3.2667 0.99   1305  148 0.1083 0.1484       5.476       5.812|
|  4:  3.2667 -  2.9707 0.99   1296  137 0.1257 0.1563      5.4652      5.6158|
|  5:  2.9707 -  2.7593 0.99   1280  146 0.1283 0.1612      5.3089      5.4616|
|  6:  2.7593 -  2.5976 0.98   1284  142 0.1267 0.1907      5.2231       5.457|
|  7:  2.5976 -  2.4681 0.99   1273  143 0.1198 0.1701      5.1471       5.371|
|  8:  2.4681 -  2.3611 0.98   1268  140 0.1178 0.1775      5.0966      5.3871|
|  9:  2.3611 -  2.2706 0.98   1275  146 0.1190 0.1812       5.038      5.3121|
| 10:  2.2706 -  2.1925 0.97   1235  132 0.1145 0.1719      4.9805      5.1677|
| 11:  2.1925 -  2.1241 0.99   1272  144 0.1129 0.1728      4.9273      5.2902|
| 12:  2.1241 -  2.0636 0.98   1271  135 0.1113 0.1826      4.8755      5.1831|
| 13:  2.0636 -  2.0094 0.97   1229  137 0.1181 0.1683      4.8216      5.0272|
| 14:  2.0094 -  1.9605 0.73    933  109 0.1107 0.1824      4.7277      4.9787|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6945 -  4.6774  1381   154  0.94   9.56   0.99     0.97       7844.99|
|  2:  4.6774 -  3.7326  1328   146  0.95   8.00   1.03     1.02       9280.03|
|  3:  3.7326 -  3.2667  1305   148  0.93  11.20   1.04     1.03      10119.42|
|  4:  3.2667 -  2.9707  1296   137  0.92  13.04   1.03     1.02       9912.51|
|  5:  2.9707 -  2.7593  1280   146  0.91  15.06   1.00     0.97       7756.85|
|  6:  2.7593 -  2.5976  1284   142  0.90  15.90   0.99     0.96       7031.92|
|  7:  2.5976 -  2.4681  1273   143  0.91  15.34   0.99     0.96       6043.02|
|  8:  2.4681 -  2.3611  1268   140  0.91  15.50   1.01     0.98       5686.92|
|  9:  2.3611 -  2.2706  1275   146  0.90  15.87   1.02     1.00       5102.28|
| 10:  2.2706 -  2.1925  1235   132  0.90  15.60   1.02     0.98       4544.59|
| 11:  2.1925 -  2.1241  1272   144  0.90  15.73   1.01     0.97       4245.45|
| 12:  2.1241 -  2.0636  1271   135  0.91  14.90   1.02     1.00       3880.51|
| 13:  2.0636 -  2.0094  1229   137  0.90  16.12   1.02     1.01       3518.95|
| 14:  2.0094 -  1.9605   933   109  0.90  15.94   1.00     0.97       2903.59|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2903.59 max =        10119.42 mean =      6384.34|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.77 mean =        14.03|
|phase err.(test): min =        0.00 max =           87.32 mean =        13.65|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.395)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.07    99.59   15.33    None  None   None       |
|    all(noH): 2823   0      2.07    99.59   15.33    None  None   None       |
|    Sol.    : 438    0      3.57    85.67   39.34    None  None   None       |
|    Mac.    : 2385   0      2.07    99.59   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:     2.068 -  11.820: 1772   |   5:    50.827 -  60.579:   67        |
|      1:    11.820 -  21.572:  531   |   6:    60.579 -  70.331:   48        |
|      2:    21.572 -  31.323:  142   |   7:    70.331 -  80.083:   19        |
|      3:    31.323 -  41.075:  123   |   8:    80.083 -  89.835:    2        |
|      4:    41.075 -  50.827:  116   |   9:    89.835 -  99.586:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 338         
Filter by distance & map next to the model:
   mapped sites are within: 0.262 - 5.811
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 335 from: 338
   mapped sites are within: 0.714 - 5.811

peak=   11.168 closest distance to " CB  VAL A 230 " =    1.426
peak=    9.465 closest distance to " CG2 VAL A 296 " =    1.376
peak=    5.783 closest distance to " O   HOH Z 278 " =    1.521
peak=    5.761 closest distance to " CD2 LEU A   5 " =    1.214
peak=    5.655 closest distance to " O   HOH Z 124 " =    1.562
peak=    5.642 closest distance to " CG  LEU A   5 " =    1.178
peak=    5.621 closest distance to " O   HOH Z 193 " =    1.810
peak=    5.469 closest distance to " NE2 GLN A  11 " =    1.080
peak=    5.376 closest distance to " O   HOH Z 209 " =    2.287
peak=    5.269 closest distance to " CB  ARG A 275 " =    0.996
peak=    5.243 closest distance to " O   HOH Z 126 " =    2.048
peak=    5.222 closest distance to " O   HOH Z 199 " =    1.099
peak=    5.119 closest distance to " O   HOH Z 142 " =    1.760
peak=    5.071 closest distance to " CD1AILE A 234 " =    0.944
peak=    4.976 closest distance to " O   HOH Z 236 " =    1.450
peak=    4.954 closest distance to " CB  GLN A 223 " =    1.498
peak=    4.882 closest distance to " O   HOH Z 403 " =    1.937
peak=    4.874 closest distance to " NH2 ARG A  56 " =    2.082
peak=    4.777 closest distance to " O   HOH Z  59 " =    1.974
peak=    4.763 closest distance to " O   HOH Z 427 " =    2.668
peak=    4.744 closest distance to " O   HOH Z  85 " =    1.486
peak=    4.741 closest distance to " CG  PRO A 213 " =    1.293
peak=    4.707 closest distance to " O   HOH Z 406 " =    1.188
peak=    4.697 closest distance to " CG  LEU A 228 " =    1.161
peak=    4.695 closest distance to " O   HOH Z 272 " =    1.905
peak=    4.679 closest distance to " CB  VAL A 230 " =    1.083
peak=    4.676 closest distance to " O   SER A  87 " =    2.335
peak=    4.596 closest distance to " O   HOH Z 232 " =    2.178
peak=    4.528 closest distance to " O   HOH Z 402 " =    1.461
peak=    4.527 closest distance to " O   HOH Z 278 " =    2.086
peak=    4.504 closest distance to " O   HOH Z 263 " =    1.516
peak=    4.454 closest distance to " CB  GLN A 183 " =    1.320
peak=    4.438 closest distance to " CB  VAL A 296 " =    0.942
peak=    4.434 closest distance to " O   HOH Z  78 " =    1.714
peak=    4.416 closest distance to " O   HOH Z  97 " =    1.893
peak=    4.405 closest distance to " O   HOH Z 368 " =    2.196
peak=    4.384 closest distance to " O   HOH Z 188 " =    1.026
peak=    4.383 closest distance to " CA  VAL A  41 " =    0.848
peak=    4.369 closest distance to " O   HOH Z 411 " =    3.665
peak=    4.350 closest distance to " CG  PRO A 198 " =    1.162
peak=    4.333 closest distance to " CG AARG A 275 " =    1.121
peak=    4.324 closest distance to " O   HOH Z 279 " =    1.109
peak=    4.293 closest distance to " O   HOH Z 346 " =    1.563
peak=    4.281 closest distance to " O   HOH Z 249 " =    1.091
peak=    4.280 closest distance to " O   HOH Z 132 " =    1.035
peak=    4.269 closest distance to " C   PRO A 198 " =    1.505
peak=    4.255 closest distance to " CB  SER A   3 " =    1.303
peak=    4.253 closest distance to " O   HOH Z 192 " =    1.363
peak=    4.162 closest distance to " O   HOH Z 423 " =    1.854
peak=    4.138 closest distance to " NZ  LYS A 117 " =    3.163
peak=    4.093 closest distance to " O   HOH Z 213 " =    1.781
peak=    4.079 closest distance to " O   HOH Z 303 " =    2.031
peak=    4.075 closest distance to " CB  GLU A 152 " =    1.135
peak=    4.072 closest distance to " O   HOH Z 234 " =    3.670
peak=    4.065 closest distance to " O   HOH Z 203 " =    1.545
peak=    4.063 closest distance to " O   HOH Z 118 " =    1.684
peak=    4.063 closest distance to " CB  VAL A 265 " =    1.175
peak=    4.060 closest distance to " O   HOH Z 250 " =    1.357
peak=    4.049 closest distance to " O   HOH Z 322 " =    1.957
peak=    4.045 closest distance to " O   HOH Z  43 " =    2.155
peak=    4.045 closest distance to " CB  SER A  63 " =    1.131
peak=    4.038 closest distance to " CD2 LEU A 228 " =    1.241
peak=    4.037 closest distance to " O   HOH Z 345 " =    2.828
peak=    4.029 closest distance to " O   HOH Z 134 " =    1.489
peak=    4.017 closest distance to " O   HOH Z 316 " =    2.754
peak=    4.014 closest distance to " O   HOH Z  54 " =    1.523
peak=    4.009 closest distance to " O   HOH Z  97 " =    2.281
peak=    4.006 closest distance to " O   HOH Z  50 " =    1.625
peak=    4.006 closest distance to " O   HOH Z  61 " =    1.602
peak=    4.004 closest distance to " CA  TYR A  30 " =    1.013
peak=    3.999 closest distance to " CB  ARG A 275 " =    1.028
peak=    3.998 closest distance to " O   HOH Z 369 " =    2.291
peak=    3.997 closest distance to " CD  ARG A 269 " =    1.083
peak=    3.984 closest distance to " OE1 GLU A   2 " =    2.183
peak=    3.958 closest distance to " CB  SER A  26 " =    1.609
peak=    3.945 closest distance to " CA  ALA A  21 " =    1.132
peak=    3.930 closest distance to " O   HOH Z 191 " =    1.454
peak=    3.923 closest distance to " O   HOH Z 298 " =    1.848
peak=    3.917 closest distance to " CG1BVAL A  72 " =    1.507
peak=    3.909 closest distance to " O   HOH Z 366 " =    2.938
peak=    3.901 closest distance to " CB  ALA A   9 " =    1.576
peak=    3.898 closest distance to " O   HOH Z 128 " =    1.972
peak=    3.889 closest distance to " O   HOH Z 392 " =    2.896
peak=    3.876 closest distance to " O   HOH Z 156 " =    3.226
peak=    3.873 closest distance to " CB  ASN A 148 " =    1.455
peak=    3.865 closest distance to " CB  VAL A 202 " =    1.620
peak=    3.858 closest distance to " O   HOH Z 247 " =    1.250
peak=    3.856 closest distance to " O   HOH Z 261 " =    1.794
peak=    3.847 closest distance to " CD2 TRP A 179 " =    1.417
peak=    3.835 closest distance to " O   HOH Z  15 " =    2.241
peak=    3.824 closest distance to " O   HOH Z  80 " =    1.628
peak=    3.819 closest distance to " O   HOH Z 130 " =    2.981
peak=    3.816 closest distance to " O   HOH Z 344 " =    1.452
peak=    3.807 closest distance to " CB  THR A  31 " =    1.630
peak=    3.805 closest distance to " O   HOH Z 260 " =    1.279
peak=    3.792 closest distance to " O   HOH Z 108 " =    2.083
peak=    3.791 closest distance to " O   HOH Z 427 " =    3.338
peak=    3.782 closest distance to " CB  TYR A 169 " =    0.831
peak=    3.776 closest distance to " O   HOH Z   3 " =    1.782
peak=    3.758 closest distance to " O   HOH Z 189 " =    2.328
peak=    3.757 closest distance to " O   HOH Z 214 " =    2.388
peak=    3.753 closest distance to " O   HOH Z 425 " =    1.339
peak=    3.746 closest distance to " CG  ARG A  66 " =    1.026
peak=    3.743 closest distance to " O   HOH Z 327 " =    1.746
peak=    3.741 closest distance to " CB  TRP A 179 " =    1.197
peak=    3.741 closest distance to " O   LYS A 290 " =    2.346
peak=    3.734 closest distance to " O   HOH Z  66 " =    2.126
peak=    3.733 closest distance to " O   HOH Z 118 " =    1.567
peak=    3.725 closest distance to " O   HOH Z 299 " =    4.214
peak=    3.723 closest distance to " O   HOH Z 227 " =    1.669
peak=    3.718 closest distance to " N   ASN A  39 " =    1.163
peak=    3.713 closest distance to " CG2 VAL A 257 " =    0.828
peak=    3.710 closest distance to " O   HOH Z 202 " =    1.001
peak=    3.683 closest distance to " O   HOH Z 344 " =    2.615
peak=    3.680 closest distance to " NE BARG A 275 " =    1.249
peak=    3.676 closest distance to " O   HOH Z  40 " =    1.446
peak=    3.663 closest distance to " NE2 GLN A  58 " =    5.811
peak=    3.649 closest distance to " ND2 ASN A 187 " =    1.461
peak=    3.646 closest distance to " O   HOH Z 148 " =    3.149
peak=    3.644 closest distance to " OD1 ASN A  69 " =    2.659
peak=    3.640 closest distance to " O   HOH Z 374 " =    2.441
peak=    3.637 closest distance to " O   HOH Z 407 " =    2.508
peak=    3.632 closest distance to " O   HOH Z 326 " =    1.391
peak=    3.628 closest distance to " O   HOH Z 245 " =    1.375
peak=    3.627 closest distance to " CB  ARG A  79 " =    1.355
peak=    3.623 closest distance to " O   HOH Z 276 " =    1.271
peak=    3.621 closest distance to " O   HOH Z  63 " =    2.240
peak=    3.621 closest distance to " CG2AVAL A 121 " =    2.282
peak=    3.609 closest distance to " O   HOH Z 128 " =    1.864
peak=    3.608 closest distance to " O   HOH Z 180 " =    2.211
peak=    3.607 closest distance to " O   HOH Z  48 " =    1.688
peak=    3.606 closest distance to " O   HOH Z 248 " =    1.753
peak=    3.605 closest distance to " O   HOH Z 334 " =    1.332
peak=    3.595 closest distance to " CB  GLN A  88 " =    1.215
peak=    3.595 closest distance to " O   HOH Z 357 " =    1.869
peak=    3.594 closest distance to " O   HOH Z 102 " =    1.156
peak=    3.592 closest distance to " CB  GLU A 128 " =    1.158
peak=    3.588 closest distance to " CG2 ILE A  20 " =    1.465
peak=    3.587 closest distance to " CG1 ILE A  33 " =    1.373
peak=    3.579 closest distance to " CB  ARG A 138 " =    0.950
peak=    3.579 closest distance to " CB  ASN A 110 " =    1.172
peak=    3.565 closest distance to " CA  ALA A  51 " =    1.058
peak=    3.565 closest distance to " CG2 ILE A 120 " =    1.238
peak=    3.564 closest distance to " CG  PRO A 243 " =    1.232
peak=    3.557 closest distance to " O   HOH Z 315 " =    1.902
peak=    3.555 closest distance to " CB  ALA A 248 " =    1.296
peak=    3.553 closest distance to " O   TRP A 274 " =    2.002
peak=    3.543 closest distance to " O   HOH Z 383 " =    1.744
peak=    3.540 closest distance to " O   HOH Z 172 " =    3.891
peak=    3.539 closest distance to " OG BSER A 164 " =    2.267
peak=    3.539 closest distance to " C   ALA A   1 " =    1.672
peak=    3.537 closest distance to " O   HOH Z 421 " =    1.383
peak=    3.537 closest distance to " CD BLYS A 290 " =    1.122
peak=    3.533 closest distance to " O   HOH Z  88 " =    2.963
peak=    3.531 closest distance to " CA  ARG A  36 " =    0.980
peak=    3.531 closest distance to " O   HOH Z  61 " =    1.542
peak=    3.519 closest distance to " CE  LYS A 119 " =    1.007
peak=    3.519 closest distance to " O   HOH Z  59 " =    2.152
peak=    3.517 closest distance to " O   HOH Z 215 " =    1.453
peak=    3.514 closest distance to " O   HOH Z 422 " =    2.506
peak=    3.514 closest distance to " O   HOH Z 222 " =    2.286
peak=    3.513 closest distance to " NZ  LYS A 119 " =    1.412
peak=    3.508 closest distance to " O   HOH Z 214 " =    1.182
peak=    3.508 closest distance to " O   HOH Z  43 " =    2.715
peak=    3.507 closest distance to " O   HOH Z 284 " =    2.918
peak=    3.502 closest distance to " O   HOH Z 137 " =    1.608
peak=    3.501 closest distance to " O   HOH Z 287 " =    1.633
peak=    3.499 closest distance to " CB  LEU A 255 " =    0.747
peak=    3.497 closest distance to " CA  ASN A 176 " =    1.052
peak=    3.491 closest distance to " CB BVAL A  41 " =    1.243
peak=    3.491 closest distance to " NH2BARG A 145 " =    1.246
peak=    3.489 closest distance to " O   HOH Z 193 " =    2.043
peak=    3.481 closest distance to " CG  MET A 188 " =    1.326
peak=    3.480 closest distance to " CB  GLU A 277 " =    3.495
peak=    3.476 closest distance to " CD  GLN A 194 " =    1.460
peak=    3.473 closest distance to " CZ AARG A 102 " =    1.640
peak=    3.471 closest distance to " NH1 ARG A  14 " =    1.010
peak=    3.469 closest distance to " OG  SER A  62 " =    2.810
peak=    3.469 closest distance to " O   HOH Z 273 " =    2.820
peak=    3.468 closest distance to " O   HOH Z 261 " =    1.939
peak=    3.467 closest distance to " O   HOH Z   4 " =    1.422
peak=    3.465 closest distance to " O   HOH Z 303 " =    1.620
peak=    3.462 closest distance to " NH2 ARG A 156 " =    1.084
peak=    3.460 closest distance to " O   HOH Z 352 " =    1.324
peak=    3.454 closest distance to " N   ARG A 156 " =    1.320
peak=    3.453 closest distance to " CE AMET A  47 " =    1.554
peak=    3.453 closest distance to " CA  LYS A 290 " =    1.245
peak=    3.446 closest distance to " CB  TRP A 266 " =    1.111
peak=    3.444 closest distance to " O   HOH Z 227 " =    1.455
peak=    3.442 closest distance to " ND1 HIS A  81 " =    1.390
peak=    3.441 closest distance to " O   HOH Z 361 " =    3.106
peak=    3.437 closest distance to " CA  LYS A 117 " =    1.275
peak=    3.430 closest distance to " CB  SER A 216 " =    0.875
peak=    3.427 closest distance to " NE2 GLN A  55 " =    1.324
peak=    3.426 closest distance to " O   HOH Z 417 " =    3.155
peak=    3.419 closest distance to " O   HOH Z 143 " =    0.938
peak=    3.415 closest distance to " O   HOH Z 173 " =    2.282
peak=    3.410 closest distance to " CA  VAL A 126 " =    0.955
peak=    3.410 closest distance to " O   HOH Z 425 " =    2.054
peak=    3.404 closest distance to " O   HOH Z 345 " =    1.587
peak=    3.401 closest distance to " O   HOH Z 108 " =    1.025
peak=    3.396 closest distance to " O   HOH Z 426 " =    1.462
peak=    3.395 closest distance to " O   HOH Z  10 " =    1.639
peak=    3.393 closest distance to " O   HOH Z 367 " =    3.510
peak=    3.391 closest distance to " CB  SER A 273 " =    0.885
peak=    3.389 closest distance to " CG  GLN A  58 " =    2.665
peak=    3.386 closest distance to " CB  MET A  47 " =    1.517
peak=    3.383 closest distance to " CA  ALA A 158 " =    1.233
peak=    3.383 closest distance to " NH2BARG A 145 " =    2.243
peak=    3.378 closest distance to " CG2 THR A 294 " =    1.579
peak=    3.377 closest distance to " OD2 ASP A 286 " =    2.527
peak=    3.376 closest distance to " O   HOH Z 292 " =    1.713
peak=    3.376 closest distance to " CG2 VAL A  67 " =    1.088
peak=    3.369 closest distance to " CB  SER A  62 " =    1.176
peak=    3.368 closest distance to " OG  SER A  97 " =    2.567
peak=    3.365 closest distance to " CD2 TYR A  30 " =    0.936
peak=    3.363 closest distance to " O   HOH Z 414 " =    1.439
peak=    3.359 closest distance to " CG  GLN A  77 " =    2.230
peak=    3.351 closest distance to " O   HOH Z 209 " =    2.296
peak=    3.350 closest distance to " O   HOH Z 244 " =    1.580
peak=    3.349 closest distance to " CA  PHE A 283 " =    1.178
peak=    3.348 closest distance to " CG  LEU A 167 " =    1.143
peak=    3.347 closest distance to " CG2 THR A 221 " =    1.162
peak=    3.347 closest distance to " OH  TYR A 116 " =    1.056
peak=    3.344 closest distance to " CB  SER A 141 " =    1.069
peak=    3.338 closest distance to " CE1 TYR A 186 " =    1.319
peak=    3.333 closest distance to " CA  GLN A 194 " =    1.113
peak=    3.332 closest distance to " O   HOH Z 329 " =    3.496
peak=    3.327 closest distance to " O   GLY A  91 " =    1.684
peak=    3.324 closest distance to " CA  LEU A 101 " =    1.457
peak=    3.321 closest distance to " CB  ALA A 100 " =    1.122
peak=    3.321 closest distance to " CG  PRO A  54 " =    1.513
peak=    3.320 closest distance to " CG  ARG A  66 " =    2.497
peak=    3.316 closest distance to " O   HOH Z 435 " =    2.013
peak=    3.310 closest distance to " OG BSER A 210 " =    1.432
peak=    3.308 closest distance to " CD1 ILE A 106 " =    1.266
peak=    3.306 closest distance to " O   HOH Z 389 " =    1.563
peak=    3.302 closest distance to " O   HOH Z 227 " =    2.173
peak=    3.301 closest distance to " CA  GLY A  80 " =    0.845
peak=    3.299 closest distance to " O   HOH Z  55 " =    2.340
peak=    3.297 closest distance to " O   HOH Z  47 " =    1.707
peak=    3.294 closest distance to " O   HOH Z 408 " =    1.596
peak=    3.294 closest distance to " O   HOH Z  30 " =    2.411
peak=    3.293 closest distance to " O   HOH Z 291 " =    1.618
peak=    3.289 closest distance to " CB  GLN A 278 " =    0.875
peak=    3.288 closest distance to " O   HOH Z  19 " =    1.908
peak=    3.283 closest distance to " O   HOH Z 380 " =    2.010
peak=    3.283 closest distance to " O   HOH Z  89 " =    1.655
peak=    3.283 closest distance to " O   HOH Z   9 " =    1.980
peak=    3.280 closest distance to " O   ASP A 124 " =    1.110
peak=    3.274 closest distance to " OE1 GLN A  11 " =    1.687
peak=    3.273 closest distance to " OD1 ASN A 148 " =    1.687
peak=    3.269 closest distance to " CB  TYR A  30 " =    1.667
peak=    3.264 closest distance to " CA  ARG A  66 " =    0.808
peak=    3.261 closest distance to " O   HOH Z 411 " =    1.806
peak=    3.258 closest distance to " N   SER A 135 " =    1.239
peak=    3.258 closest distance to " CA  ASN A 215 " =    1.131
peak=    3.254 closest distance to " O   HOH Z 151 " =    1.810
peak=    3.251 closest distance to " CB  LEU A 228 " =    1.421
peak=    3.251 closest distance to " CZ  PHE A 218 " =    1.197
peak=    3.251 closest distance to " CB  ALA A 295 " =    1.306
peak=    3.248 closest distance to " N   TYR A  15 " =    1.068
peak=    3.247 closest distance to " OD1 ASP A 286 " =    1.578
peak=    3.243 closest distance to " CB  VAL A 268 " =    0.827
peak=    3.239 closest distance to " CA  ASP A 140 " =    1.094
peak=    3.236 closest distance to " CZ2 TRP A 274 " =    1.629
peak=    3.235 closest distance to " NZ  LYS A  76 " =    1.524
peak=    3.233 closest distance to " C   ILE A 106 " =    1.821
peak=    3.226 closest distance to " O   HOH Z  28 " =    2.145
peak=    3.225 closest distance to " O   HOH Z 392 " =    1.770
peak=    3.224 closest distance to " CG AARG A 190 " =    1.278
peak=    3.223 closest distance to " O   SER A 164 " =    1.239
peak=    3.222 closest distance to " O   HOH Z 313 " =    1.877
peak=    3.219 closest distance to " O   HOH Z  13 " =    1.634
peak=    3.218 closest distance to " O   HOH Z 185 " =    1.509
peak=    3.216 closest distance to " O   HOH Z 112 " =    1.619
peak=    3.214 closest distance to " N   GLN A 278 " =    1.078
peak=    3.211 closest distance to " NH2BARG A 190 " =    1.991
peak=    3.206 closest distance to " CB  ARG A 139 " =    0.868
peak=    3.205 closest distance to " CB  ALA A 291 " =    1.267
peak=    3.196 closest distance to " O   HOH Z 257 " =    2.237
peak=    3.189 closest distance to " CA  ILE A 234 " =    0.881
peak=    3.182 closest distance to " N   GLU A 236 " =    0.904
peak=    3.182 closest distance to " O   HOH Z 278 " =    1.410
peak=    3.177 closest distance to " CD  LYS A 166 " =    1.350
peak=    3.174 closest distance to " CB  THR A 279 " =    1.644
peak=    3.174 closest distance to " CB  HIS A 108 " =    0.897
peak=    3.171 closest distance to " NH1AARG A 275 " =    0.968
peak=    3.171 closest distance to " CG  MET A 185 " =    1.199
peak=    3.171 closest distance to " O   HOH Z 274 " =    1.744
peak=    3.165 closest distance to " O   HOH Z 253 " =    1.461
peak=    3.162 closest distance to " CG2 THR A  82 " =    0.910
peak=    3.162 closest distance to " OE2 GLU A  53 " =    2.027
peak=    3.161 closest distance to " CB  PRO A 198 " =    1.048
peak=    3.157 closest distance to " CB  ARG A 190 " =    1.852
peak=    3.148 closest distance to " CB  ASN A  39 " =    0.771
peak=    3.144 closest distance to " O   HOH Z 394 " =    1.506
peak=    3.139 closest distance to " O   HOH Z 417 " =    2.380
peak=    3.136 closest distance to " O   HOH Z 135 " =    1.855
peak=    3.131 closest distance to " O   HOH Z 194 " =    2.120
peak=    3.129 closest distance to " CG  LYS A 119 " =    1.216
peak=    3.128 closest distance to " CD2 TYR A 186 " =    1.051
peak=    3.124 closest distance to " CB  ARG A 102 " =    0.734
peak=    3.124 closest distance to " O   HOH Z 433 " =    1.818
peak=    3.119 closest distance to " O   HOH Z 136 " =    1.143
peak=    3.118 closest distance to " CD1 LEU A  96 " =    0.714
peak=    3.116 closest distance to " O   HOH Z 283 " =    1.404
peak=    3.113 closest distance to " O   HOH Z 380 " =    2.026
peak=    3.111 closest distance to " CD  LYS A 119 " =    1.946
peak=    3.111 closest distance to " CG  ARG A 138 " =    1.075
peak=    3.105 closest distance to " O   HOH Z 155 " =    1.581
peak=    3.104 closest distance to " O   HOH Z 172 " =    3.534
peak=    3.103 closest distance to " CE  LYS A  48 " =    1.491
peak=    3.101 closest distance to " O   HOH Z 271 " =    1.704
peak=    3.092 closest distance to " CH2 TRP A 274 " =    2.221
peak=    3.090 closest distance to " OG BSER A 258 " =    2.772
peak=    3.089 closest distance to " CA  ALA A 295 " =    1.069
peak=    3.089 closest distance to " O   HOH Z 189 " =    2.488
peak=    3.088 closest distance to " O   HOH Z 148 " =    1.517
peak=    3.084 closest distance to " CG  LEU A 281 " =    0.933
peak=    3.083 closest distance to " CB  ASN A 215 " =    1.014
peak=    3.081 closest distance to " O   HOH Z  68 " =    1.518
peak=    3.080 closest distance to " O   HOH Z 389 " =    1.215
peak=    3.066 closest distance to " CE  LYS A 119 " =    1.151
peak=    3.061 closest distance to " O   HOH Z 260 " =    1.075
peak=    3.057 closest distance to " CB  ASN A 142 " =    1.123
peak=    3.054 closest distance to " O   HOH Z 233 " =    1.531
peak=    3.051 closest distance to " CD2 HIS A  81 " =    1.226
peak=    3.051 closest distance to " O   HOH Z 189 " =    2.386
peak=    3.042 closest distance to " CG1 ILE A 120 " =    1.225
peak=    3.034 closest distance to " O   HOH Z 342 " =    0.767
peak=    3.028 closest distance to " O   HOH Z 255 " =    1.598
peak=    3.020 closest distance to " N   ASP A 162 " =    1.322
peak=    3.015 closest distance to " CE  MET A  40 " =    1.150
peak=    3.007 closest distance to " CG  LEU A   5 " =    0.721

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 185         
Filter by distance & map next to the model:
   mapped sites are within: 0.803 - 5.665
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 185 from: 185
   mapped sites are within: 0.803 - 5.665

peak=   -4.632 closest distance to " CD  ARG A 156 " =    2.075
peak=   -4.615 closest distance to " CG2BVAL A  41 " =    2.702
peak=   -4.477 closest distance to " CG2 VAL A 230 " =    0.812
peak=   -4.473 closest distance to " SG  CYS A 254 " =    3.197
peak=   -4.469 closest distance to " CA  SER A 164 " =    2.007
peak=   -4.408 closest distance to " OXT GLY A 302 " =    2.769
peak=   -4.262 closest distance to " C   HIS A 108 " =    1.132
peak=   -4.205 closest distance to " CD1 LEU A 255 " =    2.669
peak=   -4.183 closest distance to " CB  ALA A 161 " =    2.517
peak=   -4.161 closest distance to " O   HOH Z 266 " =    4.472
peak=   -4.081 closest distance to " O   HOH Z  11 " =    1.751
peak=   -4.050 closest distance to " O   HOH Z  56 " =    2.118
peak=   -4.015 closest distance to " O   HOH Z 423 " =    2.194
peak=   -4.001 closest distance to " ND2 ASN A  45 " =    1.074
peak=   -3.997 closest distance to " N   ALA A 248 " =    1.666
peak=   -3.995 closest distance to " O   ALA A   8 " =    1.849
peak=   -3.983 closest distance to " CD1 LEU A 101 " =    2.386
peak=   -3.976 closest distance to " O   VAL A  67 " =    2.690
peak=   -3.915 closest distance to " CE2 TYR A  30 " =    2.843
peak=   -3.911 closest distance to " CD  GLN A  88 " =    1.190
peak=   -3.903 closest distance to " OD2 ASP A  50 " =    1.323
peak=   -3.851 closest distance to " O   HOH Z   3 " =    2.000
peak=   -3.847 closest distance to " ND2 ASN A 187 " =    1.639
peak=   -3.829 closest distance to " N   HIS A 115 " =    1.953
peak=   -3.826 closest distance to " O   ALA A 161 " =    1.544
peak=   -3.822 closest distance to " OG BSER A 134 " =    1.254
peak=   -3.815 closest distance to " O   HOH Z 191 " =    4.933
peak=   -3.809 closest distance to " O   HOH Z  98 " =    1.628
peak=   -3.808 closest distance to " O   HOH Z 166 " =    2.065
peak=   -3.806 closest distance to " O   HOH Z 362 " =    5.665
peak=   -3.787 closest distance to " CB  ALA A 248 " =    1.995
peak=   -3.786 closest distance to " OG  SER A   3 " =    1.361
peak=   -3.784 closest distance to " CB  ALA A  51 " =    1.870
peak=   -3.755 closest distance to " O   HOH Z 407 " =    2.803
peak=   -3.747 closest distance to " O   HOH Z  97 " =    1.311
peak=   -3.739 closest distance to " O   HOH Z 165 " =    2.026
peak=   -3.737 closest distance to " O   HOH Z 290 " =    1.052
peak=   -3.720 closest distance to " CD  ARG A 139 " =    1.569
peak=   -3.719 closest distance to " OD1 ASN A 249 " =    1.268
peak=   -3.714 closest distance to " OD1 ASN A  39 " =    2.125
peak=   -3.710 closest distance to " OG ASER A 134 " =    1.215
peak=   -3.702 closest distance to " CG  GLN A 223 " =    2.325
peak=   -3.696 closest distance to " N   SER A 276 " =    1.199
peak=   -3.687 closest distance to " O   THR A 182 " =    1.173
peak=   -3.685 closest distance to " CG  LYS A 193 " =    2.138
peak=   -3.681 closest distance to " N   ALA A 226 " =    1.883
peak=   -3.666 closest distance to " O   ALA A  51 " =    1.260
peak=   -3.660 closest distance to " O   PRO A 198 " =    1.241
peak=   -3.649 closest distance to " O   HOH Z 102 " =    1.775
peak=   -3.625 closest distance to " O   HOH Z 193 " =    1.636
peak=   -3.624 closest distance to " CG  ASP A  50 " =    2.438
peak=   -3.623 closest distance to " CD  GLN A  58 " =    1.355
peak=   -3.614 closest distance to " CG2 VAL A 296 " =    1.749
peak=   -3.613 closest distance to " O   MET A  40 " =    2.618
peak=   -3.606 closest distance to " N   GLN A  58 " =    1.757
peak=   -3.606 closest distance to " CZ  TYR A 169 " =    1.831
peak=   -3.602 closest distance to " OD1 ASP A 200 " =    1.234
peak=   -3.596 closest distance to " O   HOH Z 188 " =    4.612
peak=   -3.593 closest distance to " O   SER A 146 " =    0.877
peak=   -3.592 closest distance to " O   HOH Z 134 " =    2.600
peak=   -3.582 closest distance to " O   ASN A 187 " =    1.426
peak=   -3.581 closest distance to " NH2 ARG A  79 " =    1.984
peak=   -3.579 closest distance to " O   HOH Z 427 " =    1.486
peak=   -3.568 closest distance to " O   HOH Z 250 " =    1.419
peak=   -3.557 closest distance to " O   HOH Z 126 " =    1.931
peak=   -3.556 closest distance to " CB  ASN A  39 " =    2.122
peak=   -3.548 closest distance to " OD2 ASP A 191 " =    1.432
peak=   -3.548 closest distance to " CA  GLY A  23 " =    1.948
peak=   -3.547 closest distance to " O   HOH Z  13 " =    1.633
peak=   -3.541 closest distance to " CG  PHE A 283 " =    2.720
peak=   -3.526 closest distance to " CG  ASP A 231 " =    0.803
peak=   -3.522 closest distance to " CG  LEU A 228 " =    1.139
peak=   -3.518 closest distance to " CD  LYS A 289 " =    2.513
peak=   -3.510 closest distance to " CB  ALA A 100 " =    2.527
peak=   -3.509 closest distance to " O   HOH Z  37 " =    1.741
peak=   -3.503 closest distance to " O   HOH Z  11 " =    1.803
peak=   -3.486 closest distance to " CD2 LEU A 300 " =    2.819
peak=   -3.478 closest distance to " OG  SER A 206 " =    1.444
peak=   -3.474 closest distance to " O   TRP A  92 " =    1.809
peak=   -3.468 closest distance to " O   HOH Z 175 " =    4.349
peak=   -3.465 closest distance to " O   HOH Z 346 " =    1.811
peak=   -3.456 closest distance to " CE2 PHE A 218 " =    2.634
peak=   -3.441 closest distance to " O   HOH Z 397 " =    1.242
peak=   -3.434 closest distance to " C   MET A 188 " =    1.518
peak=   -3.432 closest distance to " CB  ASP A 132 " =    2.137
peak=   -3.430 closest distance to " C   THR A 279 " =    1.202
peak=   -3.427 closest distance to " O   HOH Z 114 " =    2.919
peak=   -3.424 closest distance to " O   SER A 135 " =    1.567
peak=   -3.422 closest distance to " CG  ASN A  45 " =    1.799
peak=   -3.416 closest distance to " C   GLN A 205 " =    1.845
peak=   -3.414 closest distance to " O   HOH Z 113 " =    2.081
peak=   -3.413 closest distance to " N   VAL A 230 " =    1.214
peak=   -3.412 closest distance to " O   HOH Z 234 " =    4.092
peak=   -3.410 closest distance to " C   ASN A 285 " =    2.246
peak=   -3.400 closest distance to " CD1 TYR A 247 " =    2.448
peak=   -3.399 closest distance to " O   HOH Z 197 " =    4.947
peak=   -3.394 closest distance to " O   HOH Z 313 " =    1.802
peak=   -3.393 closest distance to " CA  GLY A 203 " =    2.334
peak=   -3.390 closest distance to " O   HOH Z 431 " =    1.701
peak=   -3.385 closest distance to " O   HOH Z 426 " =    2.345
peak=   -3.381 closest distance to " CA  GLY A 133 " =    1.842
peak=   -3.379 closest distance to " CG2 VAL A 189 " =    1.988
peak=   -3.377 closest distance to " CB  ASP A 132 " =    2.232
peak=   -3.374 closest distance to " O   HOH Z 231 " =    1.983
peak=   -3.368 closest distance to " OG  SER A  97 " =    2.159
peak=   -3.353 closest distance to " O   HOH Z  93 " =    1.596
peak=   -3.350 closest distance to " O   HOH Z 166 " =    1.564
peak=   -3.349 closest distance to " O   HOH Z  60 " =    2.122
peak=   -3.348 closest distance to " O   HOH Z 193 " =    2.225
peak=   -3.343 closest distance to " O   HOH Z 310 " =    1.553
peak=   -3.341 closest distance to " CD1 LEU A 228 " =    2.056
peak=   -3.336 closest distance to " NH2AARG A 275 " =    4.769
peak=   -3.330 closest distance to " O   HOH Z  63 " =    1.093
peak=   -3.330 closest distance to " CD  GLN A  88 " =    2.116
peak=   -3.328 closest distance to " O   HOH Z 198 " =    1.841
peak=   -3.324 closest distance to " O   ALA A 184 " =    1.628
peak=   -3.322 closest distance to " O   HOH Z 388 " =    1.993
peak=   -3.321 closest distance to " C   ALA A 158 " =    1.132
peak=   -3.317 closest distance to " C   ASP A 231 " =    2.518
peak=   -3.303 closest distance to " CD1 PHE A  59 " =    2.235
peak=   -3.300 closest distance to " O   SER A 273 " =    1.407
peak=   -3.288 closest distance to " O   HOH Z 281 " =    3.226
peak=   -3.288 closest distance to " OG1 THR A  82 " =    1.352
peak=   -3.285 closest distance to " ND2 ASN A  45 " =    1.099
peak=   -3.278 closest distance to " ND2 ASN A  39 " =    1.183
peak=   -3.269 closest distance to " O   ALA A 160 " =    1.484
peak=   -3.265 closest distance to " N   THR A 220 " =    2.134
peak=   -3.256 closest distance to " O   SER A 210 " =    1.760
peak=   -3.250 closest distance to " CA  ASP A 298 " =    1.025
peak=   -3.236 closest distance to " OXT GLY A 302 " =    3.463
peak=   -3.234 closest distance to " O   HOH Z 423 " =    1.208
peak=   -3.229 closest distance to " CB  PRO A 243 " =    2.633
peak=   -3.228 closest distance to " CD2 TYR A 293 " =    2.129
peak=   -3.221 closest distance to " CG1 VAL A 112 " =    2.938
peak=   -3.213 closest distance to " ND2 ASN A 142 " =    1.964
peak=   -3.213 closest distance to " O   GLU A  44 " =    1.813
peak=   -3.212 closest distance to " ND2 ASN A 173 " =    1.679
peak=   -3.211 closest distance to " O   ILE A 120 " =    1.269
peak=   -3.207 closest distance to " O   HOH Z  17 " =    1.465
peak=   -3.206 closest distance to " OD1 ASN A 301 " =    1.986
peak=   -3.206 closest distance to " CD1 PHE A  59 " =    2.008
peak=   -3.205 closest distance to " O   GLY A  80 " =    2.566
peak=   -3.190 closest distance to " OG1 THR A 251 " =    2.751
peak=   -3.190 closest distance to " N   THR A 157 " =    1.353
peak=   -3.189 closest distance to " OG BSER A  99 " =    0.883
peak=   -3.189 closest distance to " CG2 ILE A 263 " =    2.197
peak=   -3.189 closest distance to " C   LEU A 143 " =    1.061
peak=   -3.184 closest distance to " O   HOH Z 406 " =    0.903
peak=   -3.183 closest distance to " O   HOH Z 131 " =    3.966
peak=   -3.180 closest distance to " O   HOH Z 139 " =    5.064
peak=   -3.180 closest distance to " O   HOH Z 377 " =    1.998
peak=   -3.179 closest distance to " O   ALA A   1 " =    1.783
peak=   -3.178 closest distance to " NH2 ARG A  66 " =    4.451
peak=   -3.176 closest distance to " O   HOH Z 407 " =    3.301
peak=   -3.175 closest distance to " N   THR A  52 " =    1.737
peak=   -3.171 closest distance to " O   HOH Z 202 " =    2.365
peak=   -3.170 closest distance to " O   HOH Z 222 " =    3.030
peak=   -3.165 closest distance to " O   HOH Z  44 " =    2.059
peak=   -3.164 closest distance to " CZ  PHE A 130 " =    0.972
peak=   -3.162 closest distance to " O   HOH Z 421 " =    3.244
peak=   -3.153 closest distance to " OD1 ASP A 191 " =    1.472
peak=   -3.150 closest distance to " O   HOH Z 150 " =    1.672
peak=   -3.150 closest distance to " C   ARG A 269 " =    1.451
peak=   -3.149 closest distance to " CZ  PHE A  38 " =    2.129
peak=   -3.149 closest distance to " N   GLY A  17 " =    1.441
peak=   -3.149 closest distance to " O   HOH Z 392 " =    1.751
peak=   -3.132 closest distance to " OH  TYR A 214 " =    1.311
peak=   -3.130 closest distance to " O   HOH Z 414 " =    2.490
peak=   -3.129 closest distance to " CG  GLU A 152 " =    1.209
peak=   -3.127 closest distance to " NE2 GLN A 194 " =    1.699
peak=   -3.127 closest distance to " O   HOH Z 137 " =    1.672
peak=   -3.126 closest distance to " OG BSER A  99 " =    1.245
peak=   -3.124 closest distance to " OG  SER A  63 " =    1.209
peak=   -3.120 closest distance to " OG1 THR A 246 " =    1.136
peak=   -3.119 closest distance to " O   HOH Z 185 " =    2.294
peak=   -3.115 closest distance to " CE1 HIS A  81 " =    1.426
peak=   -3.101 closest distance to " CD2 LEU A   5 " =    1.219
peak=   -3.101 closest distance to " OD1 ASP A 191 " =    1.327
peak=   -3.075 closest distance to " O   HOH Z 385 " =    1.757
peak=   -3.067 closest distance to " CE  MET A 105 " =    1.831
peak=   -3.057 closest distance to " CD2 TRP A 274 " =    1.042
peak=   -3.038 closest distance to " CB  ALA A  64 " =    2.535
peak=   -3.038 closest distance to " CD2 TYR A  30 " =    2.879
peak=   -3.023 closest distance to " SD  MET A 188 " =    2.305
peak=   -3.017 closest distance to " O   ASN A 252 " =    1.358

================= 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    :  0.4778 0.4731   6.275673e+00   6.267335e+00
   1_bss:  0.4683 0.4617   6.269359e+00   6.254982e+00
   1_xyz:  0.3859 0.4070   6.152075e+00   6.185528e+00
   1_adp:  0.3356 0.3852   6.061192e+00   6.148652e+00
   1_occ:  0.3353 0.3850   6.060240e+00   6.148526e+00
   2_bss:  0.3317 0.3798   6.058469e+00   6.145697e+00
   2_xyz:  0.2412 0.2925   5.794910e+00   5.942331e+00
   2_adp:  0.2177 0.2659   5.705076e+00   5.869007e+00
   2_occ:  0.2174 0.2656   5.704555e+00   5.868652e+00
   3_bss:  0.2152 0.2643   5.700951e+00   5.864719e+00
   3_xyz:  0.1547 0.2005   5.413088e+00   5.623536e+00
   3_adp:  0.1412 0.1863   5.327477e+00   5.542826e+00
   3_occ:  0.1410 0.1862   5.326725e+00   5.542077e+00
   4_bss:  0.1407 0.1849   5.325117e+00   5.538933e+00
   4_xyz:  0.1250 0.1680   5.224824e+00   5.443036e+00
   4_adp:  0.1236 0.1639   5.208243e+00   5.418319e+00
   4_occ:  0.1234 0.1637   5.206915e+00   5.416999e+00
   5_bss:  0.1234 0.1637   5.206621e+00   5.416730e+00
   5_xyz:  0.1168 0.1576   5.160658e+00   5.379780e+00
   5_adp:  0.1140 0.1589   5.153917e+00   5.387295e+00
   5_occ:  0.1139 0.1588   5.153724e+00   5.387150e+00
   5_bss:  0.1142 0.1590   5.154908e+00   5.388138e+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:  0.366   7.352   7.956   7.672   9.286   0.000   0.000   0.000
   1_xyz:  0.366   7.352   7.956   7.672   9.286   0.000   0.000   0.000
   1_adp:  0.366   7.352   7.956   7.672   9.286   0.000   0.000   0.000
   1_occ:  0.366   7.352   7.956   7.672   9.286   0.000   0.000   0.000
   2_bss:  0.345  26.911   4.358   4.027   6.076   0.000   0.000   0.000
   2_xyz:  0.345  26.911   4.358   4.027   6.076   0.000   0.000   0.000
   2_adp:  0.345  26.911   4.358   4.027   6.076   0.000   0.000   0.000
   2_occ:  0.345  26.911   4.358   4.027   6.076   0.000   0.000   0.000
   3_bss:  0.319  32.285   2.289   2.755   3.793   0.000   0.000   0.000
   3_xyz:  0.319  32.285   2.289   2.755   3.793   0.000   0.000   0.000
   3_adp:  0.319  32.285   2.289   2.755   3.793   0.000   0.000   0.000
   3_occ:  0.319  32.285   2.289   2.755   3.793   0.000   0.000   0.000
   4_bss:  0.317  29.048   1.559   2.295   2.879   0.000   0.000   0.000
   4_xyz:  0.317  29.048   1.559   2.295   2.879   0.000   0.000   0.000
   4_adp:  0.317  29.048   1.559   2.295   2.879   0.000   0.000   0.000
   4_occ:  0.317  29.048   1.559   2.295   2.879   0.000   0.000   0.000
   5_bss:  0.318  30.333   1.335   2.146   2.604   0.000   0.000   0.000
   5_xyz:  0.318  30.333   1.335   2.146   2.604   0.000   0.000   0.000
   5_adp:  0.318  30.333   1.335   2.146   2.604   0.000   0.000   0.000
   5_occ:  0.318  30.333   1.335   2.146   2.604   0.000   0.000   0.000
   5_bss:  0.317  35.015  -0.688   0.132   0.556   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  56.281 0.4425  0.5211    68942.596
   1_bss:  56.248 0.4405  0.6569    65158.534
   1_xyz:  47.372 0.5517  0.8123    48741.012
   1_adp:  42.556 0.6119  0.9305    42462.005
   1_occ:  42.503 0.6125  0.9307    42344.089
   2_bss:  42.059 0.6177  0.8296    41621.909
   2_xyz:  30.393 0.7527  0.9831    22618.245
   2_adp:  26.693 0.7939  1.0256    18512.222
   2_occ:  26.669 0.7941  1.0258    18493.849
   3_bss:  26.462 0.7961  0.9576    18214.559
   3_xyz:  19.237 0.8690  1.0045    10308.825
   3_adp:  17.295 0.8873  1.0118     8888.293
   3_occ:  17.280 0.8875  1.0116     8876.653
   4_bss:  17.212 0.8880  0.9857     8798.108
   4_xyz:  15.171 0.9054  0.9934     7138.718
   4_adp:  14.603 0.9104  0.9991     6843.621
   4_occ:  14.571 0.9107  0.9990     6822.485
   5_bss:  14.566 0.9108  0.9910     6821.016
   5_xyz:  13.811 0.9168  0.9929     6297.768
   5_adp:  13.963 0.9157  0.9883     6360.052
   5_occ:  13.959 0.9158  0.9882     6357.432
   5_bss:  13.992 0.9155  0.9892     6383.410
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.086   5.2880e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.086   5.2880e+01
   1_xyz:   1.748  0.014  0.111 18.359  0.007  4.106   1.5212e-01
   1_adp:   1.748  0.014  0.111 18.359  0.007  4.106   1.5212e-01
   1_occ:   1.748  0.014  0.111 18.359  0.007  4.106   1.5212e-01
   2_bss:   1.748  0.014  0.111 18.359  0.007  4.106   1.5212e-01
   2_xyz:   1.112  0.008  0.081 16.518  0.005  4.118   7.8125e-02
   2_adp:   1.112  0.008  0.081 16.518  0.005  4.118   7.8125e-02
   2_occ:   1.112  0.008  0.081 16.518  0.005  4.118   7.8125e-02
   3_bss:   1.112  0.008  0.081 16.518  0.005  4.118   7.8125e-02
   3_xyz:   1.047  0.006  0.075 15.883  0.004  4.113   6.5039e-02
   3_adp:   1.047  0.006  0.075 15.883  0.004  4.113   6.5039e-02
   3_occ:   1.047  0.006  0.075 15.883  0.004  4.113   6.5039e-02
   4_bss:   1.047  0.006  0.075 15.883  0.004  4.113   6.5039e-02
   4_xyz:   0.943  0.005  0.070 15.832  0.004  4.113   5.6694e-02
   4_adp:   0.943  0.005  0.070 15.832  0.004  4.113   5.6694e-02
   4_occ:   0.943  0.005  0.070 15.832  0.004  4.113   5.6694e-02
   5_bss:   0.943  0.005  0.070 15.832  0.004  4.113   5.6694e-02
   5_xyz:   0.978  0.005  0.072 15.637  0.004  4.108   5.8210e-02
   5_adp:   0.978  0.005  0.072 15.637  0.004  4.108   5.8210e-02
   5_occ:   0.978  0.005  0.072 15.637  0.004  4.108   5.8210e-02
   5_bss:   0.978  0.005  0.072 15.637  0.004  4.108   5.8210e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.733   6.8482e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.733   6.8482e+00
   1_xyz:  15.666  0.180  0.537 89.252  0.042  2.216   1.0583e-01
   1_adp:  15.666  0.180  0.537 89.252  0.042  2.216   1.0583e-01
   1_occ:  15.666  0.180  0.537 89.252  0.042  2.216   1.0583e-01
   2_bss:  15.666  0.180  0.537 89.252  0.042  2.216   1.0583e-01
   2_xyz:   7.295  0.095  0.406 88.920  0.045  2.296   6.6808e-02
   2_adp:   7.295  0.095  0.406 88.920  0.045  2.296   6.6808e-02
   2_occ:   7.295  0.095  0.406 88.920  0.045  2.296   6.6808e-02
   3_bss:   7.295  0.095  0.406 88.920  0.045  2.296   6.6808e-02
   3_xyz:   7.204  0.041  0.427 82.461  0.028  2.254   4.8772e-02
   3_adp:   7.204  0.041  0.427 82.461  0.028  2.254   4.8772e-02
   3_occ:   7.204  0.041  0.427 82.461  0.028  2.254   4.8772e-02
   4_bss:   7.204  0.041  0.427 82.461  0.028  2.254   4.8772e-02
   4_xyz:   6.434  0.035  0.388 82.069  0.027  2.365   3.5495e-02
   4_adp:   6.434  0.035  0.388 82.069  0.027  2.365   3.5495e-02
   4_occ:   6.434  0.035  0.388 82.069  0.027  2.365   3.5495e-02
   5_bss:   6.434  0.035  0.388 82.069  0.027  2.365   3.5495e-02
   5_xyz:   6.534  0.037  0.412 83.327  0.028  2.346   3.4150e-02
   5_adp:   6.534  0.037  0.412 83.327  0.028  2.346   3.4150e-02
   5_occ:   6.534  0.037  0.412 83.327  0.028  2.346   3.4150e-02
   5_bss:   6.534  0.037  0.412 83.327  0.028  2.346   3.4150e-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:  80.08   0.00  12.84  73.38   0.00  10.31  80.08   0.00  26.63
   1_occ:  80.08   0.00  12.84  73.38   0.00  10.31  80.08   0.00  26.63
   2_bss:  80.08   0.00  12.84  73.38   0.00  10.31  80.08   0.00  26.63
   2_xyz:  80.08   0.00  12.84  73.38   0.00  10.31  80.08   0.00  26.63
   2_adp: 112.88   0.00  12.98 112.88   0.00   9.34  87.94   0.00  32.77
   2_occ: 112.88   0.00  12.98 112.88   0.00   9.34  87.94   0.00  32.77
   3_bss: 112.88   0.00  12.98 112.88   0.00   9.34  87.94   0.00  32.77
   3_xyz: 112.88   0.00  12.98 112.88   0.00   9.34  87.94   0.00  32.77
   3_adp:  91.10   0.00  13.19  91.10   0.00   8.89  83.86   2.16  36.63
   3_occ:  91.10   0.00  13.19  91.10   0.00   8.89  83.86   2.16  36.63
   4_bss:  91.10   0.00  13.19  91.10   0.00   8.89  83.86   2.16  36.63
   4_xyz:  91.10   0.00  13.19  91.10   0.00   8.89  83.86   2.16  36.63
   4_adp:  91.02   0.00  13.08  91.02   0.00   8.89  82.98   1.99  35.90
   4_occ:  91.02   0.00  13.08  91.02   0.00   8.89  82.98   1.99  35.90
   5_bss:  91.02   0.00  13.08  91.02   0.00   8.89  82.98   1.99  35.90
   5_xyz:  91.02   0.00  13.08  91.02   0.00   8.89  82.98   1.99  35.90
   5_adp:  97.52   0.00  13.26  97.52   0.00   8.86  83.60   1.50  37.27
   5_occ:  97.52   0.00  13.26  97.52   0.00   8.86  83.60   1.50  37.27
   5_bss:  99.59   2.07  15.33  99.59   2.07  10.92  85.67   3.57  39.34
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.255    0.024    0.420
   1_adp:    1.255    0.024    0.420
   1_occ:    1.255    0.024    0.420
   2_bss:    1.255    0.024    0.420
   2_xyz:    1.578    0.036    0.578
   2_adp:    1.578    0.036    0.578
   2_occ:    1.578    0.036    0.578
   3_bss:    1.578    0.036    0.578
   3_xyz:    1.689    0.034    0.657
   3_adp:    1.689    0.034    0.657
   3_occ:    1.689    0.034    0.657
   4_bss:    1.689    0.034    0.657
   4_xyz:    1.653    0.046    0.689
   4_adp:    1.653    0.046    0.689
   4_occ:    1.653    0.046    0.689
   5_bss:    1.653    0.046    0.689
   5_xyz:    1.657    0.054    0.701
   5_adp:    1.657    0.054    0.701
   5_occ:    1.657    0.054    0.701
   5_bss:    1.657    0.054    0.701
------------------------------------------------------------------------

CPU time actual refinement: 324.15


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_177/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_177/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_177/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_177/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_177/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 323.98 
  Macro-tasks:
    bulk solvent and scale       = 42.67  
    individual site refinement   = 128.01 
    weights calculation          = 32.69  
    collect and process          = 6.55   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 210.04 
  Micro-tasks:
    mask                            = 2.29   
    f_calc                          = 97.60  
    alpha_beta                      = 8.02   
    target                          = 1.16   
    gradients_wrt_atomic_parameters = 107.26 
    fmodel                         = 7.07   
    r_factors                      = 0.21   
    phase_errors                   = 10.59  
    foms                           = 0.32   
    TOTAL for micro-tasks          = 234.52 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.633 micro seconds
Total CPU time: 5.63 minutes
from_scatterers_fft:    627 calls, 97.31 s
gradients_fft:          572 calls, 94.65 s

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

# Date 2008-01-16 Time 00:57:08 PST -0800 (1200473828.85 s)
Start R-work = 0.4778, R-free = 0.4731 (no bulk solvent and anisotropic scale)
Final R-work = 0.1313, R-free = 0.1756 (no bulk solvent and anisotropic scale)

Start R-work = 0.4683, R-free = 0.4617
Final R-work = 0.1142, R-free = 0.1590