# Date 2008-01-16 Time 01:42:02 PST -0800 (1200476522.43 s)
#phil __OFF__

Command line arguments: "../529.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 10707
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 529

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 46.6953, 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: 2.81, per 1000 atoms: 1.00


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.6953, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.857 1.96115
Completeness in resolution range: 0.958085
Completeness with d_max=infinity: 0.955142

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8570
                             d_min =   1.9612

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.6953, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.857 1.96115
Completeness in resolution range: 0.958085
Completeness with d_max=infinity: 0.955142

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8574 -  4.1964 [2141/2169]  1929   212   9.9%
  bin  2:  4.1964 -  3.3433 [2058/2074]  1849   209  10.2%
  bin  3:  3.3433 -  2.9243 [2033/2052]  1830   203  10.0%
  bin  4:  2.9243 -  2.6586 [2025/2055]  1827   198   9.8%
  bin  5:  2.6586 -  2.4690 [2008/2027]  1807   201  10.0%
  bin  6:  2.4690 -  2.3240 [1984/2020]  1785   199  10.0%
  bin  7:  2.3240 -  2.2080 [1967/2000]  1768   199  10.1%
  bin  8:  2.2080 -  2.1122 [1995/2029]  1796   199  10.0%
  bin  9:  2.1122 -  2.0311 [1977/2005]  1779   198  10.0%
  bin 10:  2.0311 -  1.9612 [1401/2015]  1260   141  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_529/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:
        1.79 -     2.41: 35
        2.41 -     3.03: 2168
        3.03 -     3.65: 4745
        3.65 -     4.28: 9176
        4.28 -     4.90: 12616
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.786 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.842 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.878 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.879 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28735 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_529/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_529/model_refine_001.geo

CPU time processing inputs: 7.95


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 46.69535 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 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4567   r_free= 0.4522   ksol= 0.00   Bsol= 0.00   scale= 0.818    |
|                                                                             |
| 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:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.254651                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8574 -  4.6805 0.99   1386  154 0.3801 0.3723       6.553      6.5404|
|  2:  4.6805 -  3.7344 0.99   1355  147 0.3674 0.3605      6.7192      6.7287|
|  3:  3.7344 -  3.2681 0.99   1305  150 0.4086 0.3789      6.6245      6.6904|
|  4:  3.2681 -  2.9719 0.99   1310  145 0.4278 0.4374      6.4832      6.4475|
|  5:  2.9719 -  2.7604 0.99   1306  143 0.4715 0.4871      6.3485      6.3423|
|  6:  2.7604 -  2.5985 0.99   1285  145 0.4810 0.5319      6.2516      6.2585|
|  7:  2.5985 -  2.4690 0.99   1295  139 0.4972 0.4508      6.2365      6.1728|
|  8:  2.4690 -  2.3620 0.98   1274  149 0.5081 0.5116      6.1625      6.1536|
|  9:  2.3620 -  2.2714 0.98   1278  142 0.4988 0.4781      6.1042      6.0863|
| 10:  2.2714 -  2.1932 0.98   1272  134 0.5176 0.5178      6.1115      6.1046|
| 11:  2.1932 -  2.1249 1.00   1268  147 0.5262 0.4971      6.0477      6.0448|
| 12:  2.1249 -  2.0643 0.97   1262  134 0.4894 0.5051      5.9597       5.988|
| 13:  2.0643 -  2.0101 0.98   1269  145 0.5188 0.5186       5.881      5.8335|
| 14:  2.0101 -  1.9612 0.59    765   85 0.5422 0.5238      5.8368      5.7561|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8574 -  4.6805  1386   154  0.69  34.92   0.81     0.73      71366.83|
|  2:  4.6805 -  3.7344  1355   147  0.73  32.92   0.90     0.80      95003.86|
|  3:  3.7344 -  3.2681  1305   150  0.64  40.71   0.87     0.77     100532.89|
|  4:  3.2681 -  2.9719  1310   145  0.57  46.32   0.84     0.67      88981.91|
|  5:  2.9719 -  2.7604  1306   143  0.47  53.99   0.76     0.57      75970.58|
|  6:  2.7604 -  2.5985  1285   145  0.44  56.45   0.75     0.52      65906.85|
|  7:  2.5985 -  2.4690  1295   139  0.44  57.03   0.75     0.50      59672.10|
|  8:  2.4690 -  2.3620  1274   149  0.43  57.62   0.74     0.51      53654.44|
|  9:  2.3620 -  2.2714  1278   142  0.45  56.34   0.76     0.52      47000.20|
| 10:  2.2714 -  2.1932  1272   134  0.45  56.44   0.77     0.53      42737.10|
| 11:  2.1932 -  2.1249  1268   147  0.43  57.88   0.78     0.52      39845.18|
| 12:  2.1249 -  2.0643  1262   134  0.39  60.52   0.78     0.48      40271.12|
| 13:  2.0643 -  2.0101  1269   145  0.32  66.04   0.76     0.41      36517.01|
| 14:  2.0101 -  1.9612   765    85  0.28  69.18   0.73     0.32      31432.47|
|alpha:            min =        0.32 max =            0.80 mean =         0.57|
|beta:             min =    31432.47 max =       100532.89 mean =     61889.11|
|figures of merit: min =        0.00 max =            1.00 mean =         0.49|
|phase err.(work): min =        0.00 max =           89.99 mean =        52.60|
|phase err.(test): min =        0.00 max =           89.83 mean =        52.94|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.133850             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.942   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.925242              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.985   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       27 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      171 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      711 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1537 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2684 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3974 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5162 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6634 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7818 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.142 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.196 |       1.946 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.566)------------------------------------------|
|    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 = 11.566)------------------------------------------|
|    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 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4643   r_free= 0.4596   ksol= 0.00   Bsol= 0.00   scale= 0.785    |
|                                                                             |
| 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:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.258797                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4477   r_free= 0.4413   ksol= 0.38   Bsol= 20.00   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.77,7.95,9.44,0.00,0.00,0.00); trace/3= 8.05                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.250097                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.755185              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.488   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.855208              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.742   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4477      final r-factor (work) = 0.3592          |
| start r-factor (free) = 0.4413      final r-factor (free) = 0.3777          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 80.5362 = 8.76 * 0.50 * 6.2578 + 1.00 * 53.1418                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.0258 = 8.76 * 0.50 * 6.1446 + 1.00 * 0.1272                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3592      final r-factor (work) = 0.3061          |
| start r-factor (free) = 0.3777      final r-factor (free) = 0.3492          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2696 = 0.86 * 1.00 * 6.1446 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1637 = 0.86 * 1.00 * 6.0217 + 1.00 * 0.0139                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.566)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    60.70   11.59    None  None   None       |
|    all(noH): 2823   0      0.00    60.70   11.59    None  None   None       |
|    Sol.    : 438    0      0.00    60.70   25.88    None  None   None       |
|    Mac.    : 2385   0      0.00    58.95   8.96     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.070: 1055   |   5:    30.349 -  36.418:  101        |
|      1:     6.070 -  12.139:  774   |   6:    36.418 -  42.488:   65        |
|      2:    12.139 -  18.209:  403   |   7:    42.488 -  48.558:   24        |
|      3:    18.209 -  24.279:  233   |   8:    48.558 -  54.627:   13        |
|      4:    24.279 -  30.349:  152   |   9:    54.627 -  60.697:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3061 r_free = 0.3492             target_work(ml) = 5.994         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3056 r_free = 0.3497             target_work(ml) = 5.993         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3056   r_free= 0.3497   ksol= 0.38   Bsol= 20.00   scale= 1.101   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.77,7.95,9.44,0.00,0.00,0.00); trace/3= 8.05                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.993243                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3010   r_free= 0.3452   ksol= 0.34   Bsol= 28.99   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.32,3.93,6.17,0.00,0.00,0.00); trace/3= 4.47                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.992228                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.962215              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.174   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.422134              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.642  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3010      final r-factor (work) = 0.2122          |
| start r-factor (free) = 0.3452      final r-factor (free) = 0.2620          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.0699 = 4.96 * 0.50 * 6.0229 + 1.00 * 0.1264                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.5584 = 4.96 * 0.50 * 5.8404 + 1.00 * 0.0677                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2122      final r-factor (work) = 0.1899          |
| start r-factor (free) = 0.2620      final r-factor (free) = 0.2386          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4953 = 0.42 * 1.00 * 5.8404 + 1.00 * 0.0298                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3946 = 0.42 * 1.00 * 5.6396 + 1.00 * 0.0140                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.566)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    66.08   11.97    None  None   None       |
|    all(noH): 2823   0      0.00    66.08   11.97    None  None   None       |
|    Sol.    : 438    0      1.23    59.33   31.76    None  None   None       |
|    Mac.    : 2385   0      0.00    66.08   8.33     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.608: 1285   |   5:    33.039 -  39.647:  130        |
|      1:     6.608 -  13.216:  764   |   6:    39.647 -  46.254:   91        |
|      2:    13.216 -  19.823:  255   |   7:    46.254 -  52.862:   36        |
|      3:    19.823 -  26.431:  126   |   8:    52.862 -  59.470:   23        |
|      4:    26.431 -  33.039:  111   |   9:    59.470 -  66.077:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1899 r_free = 0.2386             target_work(ml) = 5.594         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1896 r_free = 0.2384             target_work(ml) = 5.594         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1896   r_free= 0.2384   ksol= 0.34   Bsol= 28.99   scale= 1.046   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.32,3.93,6.17,0.00,0.00,0.00); trace/3= 4.47                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.593503                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1886   r_free= 0.2373   ksol= 0.32   Bsol= 34.24   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.34,2.67,3.95,0.00,0.00,0.00); trace/3= 2.98                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.591172                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.633181              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.829  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.822562              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.015   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1886      final r-factor (work) = 0.1391          |
| start r-factor (free) = 0.2373      final r-factor (free) = 0.1835          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.3246 = 3.63 * 0.50 * 5.6462 + 1.00 * 0.0677                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.9907 = 3.63 * 0.50 * 5.4647 + 1.00 * 0.0636                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1391      final r-factor (work) = 0.1278          |
| start r-factor (free) = 0.1835      final r-factor (free) = 0.1732          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5060 = 0.82 * 1.00 * 5.4647 + 1.00 * 0.0109                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3536 = 0.82 * 1.00 * 5.2781 + 1.00 * 0.0121                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.566)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.87   12.57    None  None   None       |
|    all(noH): 2823   0      0.00    77.87   12.57    None  None   None       |
|    Sol.    : 438    0      1.95    71.90   36.27    None  None   None       |
|    Mac.    : 2385   0      0.00    77.87   8.22     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.787: 1578   |   5:    38.933 -  46.720:   92        |
|      1:     7.787 -  15.573:  612   |   6:    46.720 -  54.506:   78        |
|      2:    15.573 -  23.360:  180   |   7:    54.506 -  62.293:   44        |
|      3:    23.360 -  31.146:   94   |   8:    62.293 -  70.079:   22        |
|      4:    31.146 -  38.933:  118   |   9:    70.079 -  77.866:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1278 r_free = 0.1732             target_work(ml) = 5.246         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1276 r_free = 0.1732             target_work(ml) = 5.246         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1276   r_free= 0.1732   ksol= 0.32   Bsol= 34.24   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.34,2.67,3.95,0.00,0.00,0.00); trace/3= 2.98                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.245850                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1277   r_free= 0.1727   ksol= 0.32   Bsol= 35.77   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.24,2.51,3.31,0.00,0.00,0.00); trace/3= 2.69                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.244291                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.294288              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 129.766  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.307619              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.394  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1277      final r-factor (work) = 0.1160          |
| start r-factor (free) = 0.1727      final r-factor (free) = 0.1614          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.1186 = 2.29 * 0.50 * 5.2783 + 1.00 * 0.0636                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0310 = 2.29 * 0.50 * 5.2058 + 1.00 * 0.0592                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1160      final r-factor (work) = 0.1145          |
| start r-factor (free) = 0.1614      final r-factor (free) = 0.1597          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6134 = 0.31 * 1.00 * 5.2058 + 1.00 * 0.0120                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5999 = 0.31 * 1.00 * 5.1667 + 1.00 * 0.0105                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.566)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.43   12.24    None  None   None       |
|    all(noH): 2823   0      0.00    79.43   12.24    None  None   None       |
|    Sol.    : 438    0      1.77    73.18   34.86    None  None   None       |
|    Mac.    : 2385   0      0.00    79.43   8.09     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.943: 1611   |   5:    39.713 -  47.656:   87        |
|      1:     7.943 -  15.885:  623   |   6:    47.656 -  55.598:   63        |
|      2:    15.885 -  23.828:  161   |   7:    55.598 -  63.541:   39        |
|      3:    23.828 -  31.770:  109   |   8:    63.541 -  71.483:   10        |
|      4:    31.770 -  39.713:  115   |   9:    71.483 -  79.426:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1145 r_free = 0.1597             target_work(ml) = 5.159         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1144 r_free = 0.1597             target_work(ml) = 5.158         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1144   r_free= 0.1597   ksol= 0.32   Bsol= 35.77   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.24,2.51,3.31,0.00,0.00,0.00); trace/3= 2.69                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.157872                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1144   r_free= 0.1597   ksol= 0.32   Bsol= 35.77   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.24,2.51,3.31,0.00,0.00,0.00); trace/3= 2.69                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.157952                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.042033              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 142.260  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.230789              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 155.615  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1144      final r-factor (work) = 0.1085          |
| start r-factor (free) = 0.1597      final r-factor (free) = 0.1567          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9171 = 3.04 * 0.50 * 5.1664 + 1.00 * 0.0589                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8813 = 3.04 * 0.50 * 5.1352 + 1.00 * 0.0706                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1085      final r-factor (work) = 0.1086          |
| start r-factor (free) = 0.1567      final r-factor (free) = 0.1564          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1957 = 0.23 * 1.00 * 5.1352 + 1.00 * 0.0105                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1926 = 0.23 * 1.00 * 5.1264 + 1.00 * 0.0095                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.566)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.16   11.88    None  None   None       |
|    all(noH): 2823   0      0.00    81.16   11.88    None  None   None       |
|    Sol.    : 438    0      1.34    70.42   33.30    None  None   None       |
|    Mac.    : 2385   0      0.00    81.16   7.95     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.116: 1658   |   5:    40.581 -  48.698:   92        |
|      1:     8.116 -  16.233:  601   |   6:    48.698 -  56.814:   53        |
|      2:    16.233 -  24.349:  157   |   7:    56.814 -  64.930:   24        |
|      3:    24.349 -  32.465:  130   |   8:    64.930 -  73.046:    7        |
|      4:    32.465 -  40.581:   98   |   9:    73.046 -  81.162:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1086 r_free = 0.1564             target_work(ml) = 5.127         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1086 r_free = 0.1564             target_work(ml) = 5.126         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1086   r_free= 0.1564   ksol= 0.32   Bsol= 35.77   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.24,2.51,3.31,0.00,0.00,0.00); trace/3= 2.69                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.126062                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8574 -  4.6805 0.99   1386  154 0.0989 0.1300      5.3801      5.5351|
|  2:  4.6805 -  3.7344 0.99   1355  147 0.0847 0.1138      5.4234      5.6386|
|  3:  3.7344 -  3.2681 0.99   1305  150 0.1029 0.1509      5.4535      5.8329|
|  4:  3.2681 -  2.9719 0.99   1310  145 0.1177 0.1560      5.4349      5.5925|
|  5:  2.9719 -  2.7604 0.99   1306  143 0.1242 0.1639      5.2914      5.4869|
|  6:  2.7604 -  2.5985 0.99   1285  145 0.1163 0.1759      5.1774      5.4307|
|  7:  2.5985 -  2.4690 0.99   1295  139 0.1197 0.1615      5.1415      5.3638|
|  8:  2.4690 -  2.3620 0.98   1274  149 0.1128 0.1764      5.0484      5.3284|
|  9:  2.3620 -  2.2714 0.98   1278  142 0.1140 0.1792      5.0221       5.307|
| 10:  2.2714 -  2.1932 0.98   1272  134 0.1079 0.1775      4.9361      5.2003|
| 11:  2.1932 -  2.1249 1.00   1268  147 0.1110 0.1721      4.9232      5.2706|
| 12:  2.1249 -  2.0643 0.97   1262  134 0.1070 0.1631      4.8485      5.0905|
| 13:  2.0643 -  2.0101 0.98   1269  145 0.1120 0.1755      4.7774      5.0676|
| 14:  2.0101 -  1.9612 0.59    765   85 0.1032 0.1596      4.6484      4.8668|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8574 -  4.6805  1386   154  0.94   8.97   0.99     0.97       7133.16|
|  2:  4.6805 -  3.7344  1355   147  0.95   7.73   1.03     1.01       8776.40|
|  3:  3.7344 -  3.2681  1305   150  0.93  11.34   1.03     1.03      10162.54|
|  4:  3.2681 -  2.9719  1310   145  0.92  13.56   1.01     1.00      10144.03|
|  5:  2.9719 -  2.7604  1306   143  0.90  15.44   0.99     0.96       7792.03|
|  6:  2.7604 -  2.5985  1285   145  0.91  15.51   0.99     0.96       6740.05|
|  7:  2.5985 -  2.4690  1295   139  0.91  14.99   1.00     0.96       5938.02|
|  8:  2.4690 -  2.3620  1274   149  0.91  15.24   1.00     0.97       5233.07|
|  9:  2.3620 -  2.2714  1278   142  0.91  15.04   1.02     1.00       4974.99|
| 10:  2.2714 -  2.1932  1272   134  0.90  15.29   1.01     0.98       4261.93|
| 11:  2.1932 -  2.1249  1268   147  0.90  16.12   1.01     0.98       4265.36|
| 12:  2.1249 -  2.0643  1262   134  0.92  14.63   1.02     1.00       3766.74|
| 13:  2.0643 -  2.0101  1269   145  0.90  16.15   1.02     1.02       3282.95|
| 14:  2.0101 -  1.9612   765    85  0.91  14.39   1.00     0.98       2450.27|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2450.27 max =        10162.54 mean =      6211.30|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.88 mean =        13.81|
|phase err.(test): min =        0.00 max =           88.43 mean =        13.37|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1086   r_free= 0.1563   ksol= 0.32   Bsol= 38.42   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.42,-0.14,0.56,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.126014                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1086   r_free= 0.1563   ksol= 0.32   Bsol= 38.42   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.42,-0.14,0.56,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.126014                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8574 -  4.6805 0.99   1386  154 0.0989 0.1299      5.3807      5.5356|
|  2:  4.6805 -  3.7344 0.99   1355  147 0.0846 0.1138       5.423      5.6382|
|  3:  3.7344 -  3.2681 0.99   1305  150 0.1028 0.1510      5.4532      5.8331|
|  4:  3.2681 -  2.9719 0.99   1310  145 0.1177 0.1560      5.4349      5.5928|
|  5:  2.9719 -  2.7604 0.99   1306  143 0.1242 0.1638      5.2914      5.4868|
|  6:  2.7604 -  2.5985 0.99   1285  145 0.1163 0.1761      5.1776      5.4317|
|  7:  2.5985 -  2.4690 0.99   1295  139 0.1198 0.1615      5.1418      5.3638|
|  8:  2.4690 -  2.3620 0.98   1274  149 0.1129 0.1763      5.0486      5.3287|
|  9:  2.3620 -  2.2714 0.98   1278  142 0.1140 0.1792      5.0221      5.3071|
| 10:  2.2714 -  2.1932 0.98   1272  134 0.1079 0.1776      4.9359      5.1994|
| 11:  2.1932 -  2.1249 1.00   1268  147 0.1109 0.1720      4.9229      5.2701|
| 12:  2.1249 -  2.0643 0.97   1262  134 0.1070 0.1632       4.848        5.09|
| 13:  2.0643 -  2.0101 0.98   1269  145 0.1119 0.1752      4.7771      5.0663|
| 14:  2.0101 -  1.9612 0.59    765   85 0.1032 0.1598      4.6486      4.8681|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8574 -  4.6805  1386   154  0.94   8.98   0.99     0.97       7145.88|
|  2:  4.6805 -  3.7344  1355   147  0.95   7.73   1.03     1.01       8777.27|
|  3:  3.7344 -  3.2681  1305   150  0.93  11.34   1.03     1.03      10158.51|
|  4:  3.2681 -  2.9719  1310   145  0.92  13.56   1.01     0.99      10145.02|
|  5:  2.9719 -  2.7604  1306   143  0.90  15.45   0.99     0.96       7798.45|
|  6:  2.7604 -  2.5985  1285   145  0.90  15.51   0.99     0.96       6742.83|
|  7:  2.5985 -  2.4690  1295   139  0.91  15.00   0.99     0.96       5942.94|
|  8:  2.4690 -  2.3620  1274   149  0.91  15.24   1.00     0.97       5233.49|
|  9:  2.3620 -  2.2714  1278   142  0.91  15.04   1.02     1.00       4974.11|
| 10:  2.2714 -  2.1932  1272   134  0.90  15.28   1.01     0.98       4259.56|
| 11:  2.1932 -  2.1249  1268   147  0.90  16.12   1.01     0.98       4262.60|
| 12:  2.1249 -  2.0643  1262   134  0.92  14.62   1.02     0.99       3760.95|
| 13:  2.0643 -  2.0101  1269   145  0.90  16.14   1.02     1.02       3280.49|
| 14:  2.0101 -  1.9612   765    85  0.91  14.39   1.00     0.98       2451.69|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2451.69 max =        10158.51 mean =      6212.25|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.88 mean =        13.81|
|phase err.(test): min =        0.00 max =           88.43 mean =        13.37|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.566)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.65    83.82   14.54    None  None   None       |
|    all(noH): 2823   0      2.65    83.82   14.54    None  None   None       |
|    Sol.    : 438    0      3.99    73.07   35.95    None  None   None       |
|    Mac.    : 2385   0      2.65    83.82   10.60    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:     2.653 -  10.769: 1658   |   5:    43.234 -  51.350:   92        |
|      1:    10.769 -  18.885:  601   |   6:    51.350 -  59.467:   53        |
|      2:    18.885 -  27.002:  157   |   7:    59.467 -  67.583:   24        |
|      3:    27.002 -  35.118:  130   |   8:    67.583 -  75.699:    7        |
|      4:    35.118 -  43.234:   98   |   9:    75.699 -  83.815:    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)= 327         
Filter by distance & map next to the model:
   mapped sites are within: 0.404 - 5.610
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 323 from: 327
   mapped sites are within: 0.716 - 5.610

peak=   11.152 closest distance to " CB  VAL A 230 " =    1.438
peak=    7.802 closest distance to " CG2 VAL A 296 " =    1.180
peak=    6.361 closest distance to " CG  LEU A   5 " =    1.225
peak=    5.835 closest distance to " NE2 GLN A  11 " =    1.179
peak=    5.710 closest distance to " O   HOH Z 278 " =    1.220
peak=    5.381 closest distance to " O   HOH Z 126 " =    1.887
peak=    5.376 closest distance to " NH2 ARG A  56 " =    2.080
peak=    5.246 closest distance to " O   HOH Z 193 " =    1.682
peak=    5.234 closest distance to " CB  VAL A 296 " =    1.137
peak=    5.179 closest distance to " CG  LEU A 228 " =    1.205
peak=    5.126 closest distance to " CD2 LEU A   5 " =    1.213
peak=    5.109 closest distance to " CB  SER A  63 " =    1.214
peak=    5.042 closest distance to " O   HOH Z 142 " =    1.779
peak=    4.967 closest distance to " CG  PRO A  54 " =    1.181
peak=    4.963 closest distance to " O   HOH Z 124 " =    1.445
peak=    4.956 closest distance to " CB  GLN A 183 " =    1.250
peak=    4.735 closest distance to " O   HOH Z 232 " =    2.373
peak=    4.706 closest distance to " CB  GLN A 223 " =    1.494
peak=    4.703 closest distance to " C   PRO A 198 " =    1.513
peak=    4.670 closest distance to " OD1 ASN A  69 " =    2.592
peak=    4.574 closest distance to " CB  ARG A 275 " =    0.875
peak=    4.559 closest distance to " CB  GLU A 152 " =    1.176
peak=    4.492 closest distance to " CB  VAL A 230 " =    1.174
peak=    4.462 closest distance to " O   HOH Z 427 " =    2.835
peak=    4.420 closest distance to " O   HOH Z 272 " =    1.840
peak=    4.419 closest distance to " O   HOH Z 316 " =    2.915
peak=    4.401 closest distance to " O   HOH Z 368 " =    1.993
peak=    4.393 closest distance to " O   HOH Z 236 " =    1.843
peak=    4.379 closest distance to " CB  SER A   3 " =    1.326
peak=    4.364 closest distance to " O   SER A  87 " =    2.325
peak=    4.351 closest distance to " CB  ASN A 148 " =    1.425
peak=    4.345 closest distance to " O   HOH Z 203 " =    1.646
peak=    4.332 closest distance to " O   HOH Z  59 " =    1.961
peak=    4.318 closest distance to " O   HOH Z 234 " =    3.596
peak=    4.291 closest distance to " O   HOH Z 202 " =    1.250
peak=    4.276 closest distance to " CB  PRO A  54 " =    0.914
peak=    4.263 closest distance to " O   HOH Z 128 " =    1.981
peak=    4.258 closest distance to " CB  TYR A 169 " =    0.868
peak=    4.255 closest distance to " O   HOH Z  54 " =    1.616
peak=    4.251 closest distance to " O   HOH Z 298 " =    1.796
peak=    4.210 closest distance to " O   HOH Z 303 " =    1.997
peak=    4.193 closest distance to " OG BSER A 164 " =    2.142
peak=    4.181 closest distance to " O   HOH Z 263 " =    1.527
peak=    4.158 closest distance to " CD2 LEU A 228 " =    1.198
peak=    4.154 closest distance to " ND2 ASN A 187 " =    1.581
peak=    4.140 closest distance to " OD2 ASP A 286 " =    2.741
peak=    4.133 closest distance to " CG  PRO A 213 " =    1.169
peak=    4.120 closest distance to " O   HOH Z 322 " =    2.098
peak=    4.108 closest distance to " O   HOH Z 371 " =    3.094
peak=    4.108 closest distance to " O   HOH Z  93 " =    2.420
peak=    4.107 closest distance to " O   HOH Z 280 " =    2.980
peak=    4.103 closest distance to " CG1BVAL A  72 " =    1.500
peak=    4.102 closest distance to " O   HOH Z 369 " =    1.932
peak=    4.095 closest distance to " O   HOH Z  97 " =    1.966
peak=    4.093 closest distance to " O   HOH Z 411 " =    3.731
peak=    4.020 closest distance to " O   HOH Z   9 " =    2.230
peak=    4.016 closest distance to " CB  ARG A  79 " =    1.424
peak=    4.008 closest distance to " CA  ALA A  21 " =    1.100
peak=    4.005 closest distance to " CB  TRP A 179 " =    1.322
peak=    3.997 closest distance to " O   HOH Z 346 " =    1.573
peak=    3.995 closest distance to " O   HOH Z  48 " =    1.573
peak=    3.990 closest distance to " O   HOH Z  78 " =    1.854
peak=    3.973 closest distance to " O   HOH Z  44 " =    1.851
peak=    3.961 closest distance to " CB  GLN A  88 " =    1.251
peak=    3.951 closest distance to " O   HOH Z 158 " =    3.071
peak=    3.946 closest distance to " O   HOH Z 423 " =    1.906
peak=    3.942 closest distance to " O   HOH Z 403 " =    1.701
peak=    3.938 closest distance to " CB  VAL A 265 " =    1.274
peak=    3.937 closest distance to " O   HOH Z 260 " =    1.348
peak=    3.935 closest distance to " O   HOH Z  61 " =    1.573
peak=    3.930 closest distance to " CB  ARG A 139 " =    1.004
peak=    3.923 closest distance to " CB  GLU A 128 " =    1.015
peak=    3.896 closest distance to " O   HOH Z 344 " =    2.666
peak=    3.884 closest distance to " O   HOH Z 426 " =    1.460
peak=    3.866 closest distance to " O   HOH Z 193 " =    1.917
peak=    3.865 closest distance to " O   HOH Z 132 " =    0.850
peak=    3.858 closest distance to " O   HOH Z 248 " =    1.717
peak=    3.857 closest distance to " O   HOH Z 392 " =    3.059
peak=    3.855 closest distance to " CB  ASN A  39 " =    0.844
peak=    3.824 closest distance to " O   HOH Z 130 " =    2.337
peak=    3.819 closest distance to " CA  ASN A 215 " =    1.106
peak=    3.813 closest distance to " O   HOH Z   3 " =    1.856
peak=    3.807 closest distance to " O   HOH Z 427 " =    3.353
peak=    3.796 closest distance to " O   HOH Z 407 " =    2.427
peak=    3.769 closest distance to " O   HOH Z 250 " =    1.296
peak=    3.768 closest distance to " O   HOH Z 227 " =    2.180
peak=    3.762 closest distance to " O   HOH Z 329 " =    3.726
peak=    3.737 closest distance to " CA  TYR A  30 " =    0.968
peak=    3.719 closest distance to " O   HOH Z 273 " =    2.721
peak=    3.719 closest distance to " O   HOH Z 374 " =    2.460
peak=    3.719 closest distance to " O   TRP A 274 " =    1.905
peak=    3.710 closest distance to " O   HOH Z 189 " =    2.526
peak=    3.708 closest distance to " O   HOH Z 144 " =    2.278
peak=    3.688 closest distance to " O   HOH Z  61 " =    1.585
peak=    3.687 closest distance to " O   HOH Z  85 " =    1.364
peak=    3.676 closest distance to " O   HOH Z 147 " =    1.641
peak=    3.673 closest distance to " O   HOH Z  10 " =    1.832
peak=    3.672 closest distance to " O   HOH Z 425 " =    2.102
peak=    3.669 closest distance to " O   HOH Z 251 " =    1.595
peak=    3.669 closest distance to " CB  TRP A 266 " =    1.024
peak=    3.663 closest distance to " OE1 GLU A   2 " =    2.150
peak=    3.659 closest distance to " O   HOH Z 108 " =    1.125
peak=    3.655 closest distance to " O   HOH Z 145 " =    1.895
peak=    3.653 closest distance to " CA  VAL A  41 " =    0.829
peak=    3.645 closest distance to " O   HOH Z 265 " =    2.258
peak=    3.640 closest distance to " O   HOH Z 327 " =    1.591
peak=    3.635 closest distance to " O   HOH Z 112 " =    1.617
peak=    3.626 closest distance to " O   HOH Z 389 " =    1.769
peak=    3.624 closest distance to " N   PHE A 130 " =    1.376
peak=    3.614 closest distance to " CA  ALA A 248 " =    1.340
peak=    3.608 closest distance to " CD1 ILE A 106 " =    1.237
peak=    3.605 closest distance to " O   HOH Z 227 " =    1.752
peak=    3.602 closest distance to " O   HOH Z 299 " =    4.185
peak=    3.602 closest distance to " O   HOH Z 164 " =    2.066
peak=    3.599 closest distance to " OD1 ASN A 148 " =    1.700
peak=    3.598 closest distance to " O   HOH Z   9 " =    1.934
peak=    3.594 closest distance to " CG2 ILE A 120 " =    1.289
peak=    3.593 closest distance to " O   LYS A 290 " =    2.381
peak=    3.580 closest distance to " O   HOH Z 345 " =    3.193
peak=    3.579 closest distance to " CB  VAL A 202 " =    1.556
peak=    3.576 closest distance to " O   HOH Z 151 " =    1.707
peak=    3.575 closest distance to " CA  THR A 221 " =    0.930
peak=    3.574 closest distance to " O   HOH Z 133 " =    1.467
peak=    3.569 closest distance to " O   HOH Z  40 " =    1.930
peak=    3.556 closest distance to " O   HOH Z 128 " =    2.066
peak=    3.552 closest distance to " O   MET A 105 " =    1.795
peak=    3.549 closest distance to " O   HOH Z 344 " =    1.304
peak=    3.545 closest distance to " O   HOH Z  43 " =    2.038
peak=    3.542 closest distance to " O   HOH Z 406 " =    1.616
peak=    3.538 closest distance to " O   HOH Z  21 " =    1.797
peak=    3.538 closest distance to " N   ASN A  39 " =    1.160
peak=    3.535 closest distance to " O   HOH Z  59 " =    2.025
peak=    3.533 closest distance to " CE2 TRP A 179 " =    1.598
peak=    3.533 closest distance to " O   HOH Z 209 " =    2.250
peak=    3.531 closest distance to " CG1 ILE A  33 " =    1.321
peak=    3.529 closest distance to " O   HOH Z 366 " =    3.053
peak=    3.525 closest distance to " O   HOH Z 118 " =    1.280
peak=    3.521 closest distance to " CA  PHE A 283 " =    1.188
peak=    3.518 closest distance to " O   HOH Z 236 " =    1.475
peak=    3.517 closest distance to " CB BVAL A  41 " =    1.155
peak=    3.512 closest distance to " O   HOH Z  66 " =    2.111
peak=    3.508 closest distance to " O   HOH Z 209 " =    2.321
peak=    3.501 closest distance to " CB  GLU A 277 " =    3.439
peak=    3.500 closest distance to " CB  ILE A  20 " =    1.469
peak=    3.496 closest distance to " CB  SER A  26 " =    1.601
peak=    3.488 closest distance to " CG  ARG A  66 " =    2.706
peak=    3.485 closest distance to " O   HOH Z 419 " =    1.619
peak=    3.485 closest distance to " O   HOH Z 207 " =    1.715
peak=    3.484 closest distance to " CG2 ILE A  20 " =    1.546
peak=    3.484 closest distance to " CA  ALA A  51 " =    0.934
peak=    3.480 closest distance to " CD BLYS A 290 " =    1.207
peak=    3.478 closest distance to " O   HOH Z 108 " =    2.118
peak=    3.470 closest distance to " NH2 ARG A 156 " =    1.095
peak=    3.469 closest distance to " CE1 TYR A 186 " =    1.260
peak=    3.467 closest distance to " O   HOH Z 402 " =    1.378
peak=    3.466 closest distance to " CB  GLN A 278 " =    0.796
peak=    3.463 closest distance to " NZ  LYS A 117 " =    2.918
peak=    3.461 closest distance to " CA  VAL A 126 " =    0.947
peak=    3.455 closest distance to " CA  GLN A 194 " =    1.303
peak=    3.453 closest distance to " O  BHOH Z 338 " =    2.466
peak=    3.446 closest distance to " CA  THR A 264 " =    0.812
peak=    3.435 closest distance to " CA  ALA A 291 " =    0.968
peak=    3.434 closest distance to " O   HOH Z 425 " =    1.306
peak=    3.432 closest distance to " CD2 TRP A 179 " =    1.410
peak=    3.428 closest distance to " O   HOH Z 193 " =    1.796
peak=    3.427 closest distance to " CD1 LEU A 300 " =    1.262
peak=    3.426 closest distance to " CB  ASP A 140 " =    0.874
peak=    3.425 closest distance to " O   HOH Z  88 " =    3.060
peak=    3.423 closest distance to " O   HOH Z 180 " =    2.132
peak=    3.422 closest distance to " CG  MET A 185 " =    1.123
peak=    3.418 closest distance to " OG  SER A  22 " =    2.745
peak=    3.417 closest distance to " O   HOH Z 280 " =    1.673
peak=    3.415 closest distance to " O   HOH Z 303 " =    1.749
peak=    3.414 closest distance to " CG  LEU A 167 " =    1.164
peak=    3.409 closest distance to " O   HOH Z 175 " =    2.107
peak=    3.406 closest distance to " O   HOH Z 148 " =    3.270
peak=    3.401 closest distance to " CB  GLN A 205 " =    1.276
peak=    3.392 closest distance to " CB  ALA A  71 " =    1.393
peak=    3.391 closest distance to " CB  THR A  31 " =    1.693
peak=    3.389 closest distance to " O   HOH Z   1 " =    1.762
peak=    3.388 closest distance to " N   ARG A 156 " =    1.263
peak=    3.384 closest distance to " O   HOH Z 192 " =    1.696
peak=    3.375 closest distance to " O   HOH Z 411 " =    1.716
peak=    3.372 closest distance to " O   HOH Z 422 " =    2.662
peak=    3.370 closest distance to " O   HOH Z 214 " =    2.091
peak=    3.370 closest distance to " CB  LEU A 143 " =    1.158
peak=    3.369 closest distance to " CZ AARG A 102 " =    1.802
peak=    3.369 closest distance to " O   HOH Z 189 " =    2.640
peak=    3.368 closest distance to " CD1 ILE A  33 " =    1.618
peak=    3.362 closest distance to " CB  ALA A   9 " =    1.604
peak=    3.359 closest distance to " O   HOH Z 334 " =    1.426
peak=    3.358 closest distance to " CG2 THR A 221 " =    1.183
peak=    3.357 closest distance to " N   SER A 135 " =    1.299
peak=    3.354 closest distance to " O   HOH Z 279 " =    2.151
peak=    3.352 closest distance to " O   HOH Z 368 " =    3.630
peak=    3.352 closest distance to " O   HOH Z 291 " =    1.571
peak=    3.349 closest distance to " O   HOH Z 435 " =    1.985
peak=    3.339 closest distance to " O   HOH Z 245 " =    1.410
peak=    3.339 closest distance to " CA  ALA A 158 " =    1.189
peak=    3.336 closest distance to " O   HOH Z 151 " =    1.746
peak=    3.335 closest distance to " O   HOH Z 163 " =    1.965
peak=    3.330 closest distance to " O   HOH Z  50 " =    1.596
peak=    3.330 closest distance to " CB  LEU A 255 " =    0.838
peak=    3.329 closest distance to " O   HOH Z 271 " =    1.841
peak=    3.329 closest distance to " NZ  LYS A  76 " =    1.303
peak=    3.326 closest distance to " O   HOH Z  89 " =    2.332
peak=    3.319 closest distance to " CA  LYS A 290 " =    1.341
peak=    3.318 closest distance to " O   HOH Z 132 " =    2.543
peak=    3.316 closest distance to " CZ2 TRP A 274 " =    1.645
peak=    3.316 closest distance to " O   ALA A   1 " =    1.761
peak=    3.315 closest distance to " O   HOH Z 222 " =    2.380
peak=    3.313 closest distance to " CB  SER A 216 " =    0.716
peak=    3.313 closest distance to " O   HOH Z 116 " =    1.685
peak=    3.311 closest distance to " C   ALA A 299 " =    0.957
peak=    3.310 closest distance to " CG  PRO A 243 " =    1.186
peak=    3.308 closest distance to " O   HOH Z 134 " =    1.338
peak=    3.307 closest distance to " O   HOH Z 280 " =    2.448
peak=    3.303 closest distance to " CB  ARG A 190 " =    1.762
peak=    3.301 closest distance to " NH2 ARG A 219 " =    1.856
peak=    3.299 closest distance to " O   HOH Z 355 " =    1.758
peak=    3.294 closest distance to " NH2BARG A 145 " =    2.063
peak=    3.289 closest distance to " O   HOH Z 286 " =    2.348
peak=    3.287 closest distance to " CG2 VAL A 257 " =    0.822
peak=    3.282 closest distance to " CG  GLN A  89 " =    1.458
peak=    3.282 closest distance to " CA  ASP A 162 " =    1.005
peak=    3.279 closest distance to " CA  LYS A 117 " =    1.247
peak=    3.275 closest distance to " ND1 HIS A  81 " =    1.538
peak=    3.275 closest distance to " O   HOH Z 388 " =    1.858
peak=    3.271 closest distance to " O   HOH Z 171 " =    2.239
peak=    3.270 closest distance to " CD2 LEU A 255 " =    1.428
peak=    3.270 closest distance to " CA  ASN A 176 " =    1.031
peak=    3.266 closest distance to " NE2 GLN A  58 " =    5.610
peak=    3.260 closest distance to " O   HOH Z 337 " =    3.609
peak=    3.258 closest distance to " O   HOH Z 250 " =    1.422
peak=    3.257 closest distance to " N   VAL A 126 " =    1.239
peak=    3.249 closest distance to " CE  MET A  93 " =    1.507
peak=    3.245 closest distance to " O   HOH Z  43 " =    2.699
peak=    3.242 closest distance to " O   HOH Z  37 " =    2.056
peak=    3.239 closest distance to " CG  MET A 185 " =    1.233
peak=    3.239 closest distance to " CD2 HIS A  81 " =    1.148
peak=    3.239 closest distance to " O   HOH Z 172 " =    3.709
peak=    3.233 closest distance to " O   HOH Z 380 " =    1.774
peak=    3.231 closest distance to " O   HOH Z 281 " =    4.571
peak=    3.231 closest distance to " O   HOH Z 313 " =    1.607
peak=    3.229 closest distance to " CB  ALA A   1 " =    1.172
peak=    3.229 closest distance to " O   HOH Z 213 " =    2.125
peak=    3.229 closest distance to " O   HOH Z 128 " =    1.968
peak=    3.228 closest distance to " O   HOH Z 234 " =    1.714
peak=    3.222 closest distance to " O   HOH Z 188 " =    2.034
peak=    3.220 closest distance to " CB  ASN A 224 " =    1.043
peak=    3.218 closest distance to " CB  ALA A 248 " =    0.973
peak=    3.218 closest distance to " O   HOH Z 193 " =    2.210
peak=    3.218 closest distance to " O   HOH Z 173 " =    2.146
peak=    3.216 closest distance to " CG  GLU A 277 " =    2.158
peak=    3.215 closest distance to " CE BLYS A 290 " =    1.097
peak=    3.213 closest distance to " CD2 TYR A  30 " =    0.922
peak=    3.213 closest distance to " CB  TYR A  30 " =    1.083
peak=    3.212 closest distance to " O   HOH Z 258 " =    1.628
peak=    3.211 closest distance to " O   PHE A  38 " =    1.929
peak=    3.210 closest distance to " O   HOH Z 433 " =    1.787
peak=    3.209 closest distance to " O   HOH Z  59 " =    2.011
peak=    3.209 closest distance to " CB  TRP A 150 " =    1.458
peak=    3.208 closest distance to " O   HOH Z 409 " =    3.273
peak=    3.207 closest distance to " O   HOH Z 357 " =    1.784
peak=    3.206 closest distance to " O   HOH Z 336 " =    1.725
peak=    3.205 closest distance to " CD  ARG A 269 " =    1.035
peak=    3.202 closest distance to " O   HOH Z  71 " =    1.754
peak=    3.198 closest distance to " O   HOH Z 423 " =    2.933
peak=    3.196 closest distance to " O   HOH Z 332 " =    1.413
peak=    3.195 closest distance to " CG  GLN A  77 " =    2.332
peak=    3.194 closest distance to " CD2 LEU A 297 " =    1.015
peak=    3.191 closest distance to " O   HOH Z 276 " =    1.249
peak=    3.191 closest distance to " CB  THR A 157 " =    1.028
peak=    3.191 closest distance to " O   HOH Z 255 " =    1.556
peak=    3.188 closest distance to " CB  VAL A 268 " =    0.788
peak=    3.187 closest distance to " CD2 TYR A 186 " =    1.003
peak=    3.186 closest distance to " O   HOH Z  68 " =    1.540
peak=    3.183 closest distance to " CG  PRO A 198 " =    1.362
peak=    3.177 closest distance to " O   HOH Z 438 " =    2.037
peak=    3.173 closest distance to " CB  ASN A 142 " =    1.012
peak=    3.173 closest distance to " O   HOH Z  88 " =    2.403
peak=    3.172 closest distance to " O   HOH Z 420 " =    4.220
peak=    3.168 closest distance to " CB  LEU A 228 " =    1.295
peak=    3.166 closest distance to " O   HOH Z 163 " =    1.851
peak=    3.158 closest distance to " CA  ALA A 233 " =    1.145
peak=    3.154 closest distance to " CD2 LEU A 282 " =    1.799
peak=    3.152 closest distance to " O   THR A  31 " =    1.491
peak=    3.145 closest distance to " CG  LYS A 119 " =    1.081
peak=    3.145 closest distance to " OE2 GLU A  53 " =    2.050
peak=    3.144 closest distance to " OD1 ASP A 231 " =    1.888
peak=    3.143 closest distance to " NZ  LYS A  48 " =    2.186
peak=    3.143 closest distance to " O   HOH Z  85 " =    2.096
peak=    3.143 closest distance to " O   HOH Z  62 " =    2.230
peak=    3.138 closest distance to " O   HOH Z 313 " =    1.854
peak=    3.137 closest distance to " CB  ALA A 291 " =    1.395
peak=    3.136 closest distance to " O   HOH Z 187 " =    2.171
peak=    3.133 closest distance to " CD  LYS A 166 " =    1.302
peak=    3.127 closest distance to " O   HOH Z 195 " =    3.051
peak=    3.117 closest distance to " O   HOH Z  40 " =    2.293
peak=    3.117 closest distance to " CB  ASN A 215 " =    1.058
peak=    3.115 closest distance to " CA  ASP A 140 " =    1.172
peak=    3.111 closest distance to " O   HOH Z 367 " =    3.445
peak=    3.109 closest distance to " O   SER A 164 " =    1.251
peak=    3.108 closest distance to " CA  GLY A 267 " =    0.938
peak=    3.106 closest distance to " CB  ARG A 138 " =    0.912
peak=    3.106 closest distance to " CB  ALA A 295 " =    1.294
peak=    3.103 closest distance to " O   HOH Z 141 " =    1.500
peak=    3.102 closest distance to " OG BSER A 258 " =    3.358
peak=    3.097 closest distance to " O   HOH Z 302 " =    1.842
peak=    3.097 closest distance to " O   HOH Z 213 " =    1.883
peak=    3.092 closest distance to " O   HOH Z 140 " =    2.507
peak=    3.086 closest distance to " O   HOH Z 250 " =    1.787
peak=    3.081 closest distance to " CG  MET A 113 " =    1.140
peak=    3.073 closest distance to " CA  ALA A 154 " =    1.063
peak=    3.069 closest distance to " CA  ASP A 191 " =    0.786
peak=    3.064 closest distance to " O   HOH Z 437 " =    2.103
peak=    3.053 closest distance to " O   HOH Z  68 " =    2.635
peak=    3.053 closest distance to " O   HOH Z 353 " =    2.554
peak=    3.052 closest distance to " CB  SER A  62 " =    1.310
peak=    3.049 closest distance to " O   ALA A 158 " =    1.318
peak=    3.022 closest distance to " CB  ALA A 180 " =    1.182
peak=    3.012 closest distance to " CB  LYS A 290 " =    1.164
peak=    3.005 closest distance to " O   HOH Z 392 " =    1.882

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 197         
Filter by distance & map next to the model:
   mapped sites are within: 0.545 - 5.304
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 194 from: 197
   mapped sites are within: 0.744 - 5.304

peak=   -5.859 closest distance to " CG2 VAL A 230 " =    0.744
peak=   -4.593 closest distance to " CD  ARG A 156 " =    2.072
peak=   -4.453 closest distance to " O   VAL A  67 " =    2.612
peak=   -4.416 closest distance to " SG  CYS A 254 " =    3.176
peak=   -4.336 closest distance to " O   HOH Z 290 " =    1.043
peak=   -4.294 closest distance to " O   HOH Z 266 " =    4.481
peak=   -4.249 closest distance to " CG2 VAL A 296 " =    1.242
peak=   -4.175 closest distance to " N   GLN A  58 " =    1.717
peak=   -4.141 closest distance to " CB  ALA A 161 " =    2.530
peak=   -4.095 closest distance to " C   HIS A 108 " =    1.249
peak=   -4.037 closest distance to " O   HOH Z 435 " =    2.775
peak=   -4.027 closest distance to " N   HIS A 115 " =    1.975
peak=   -4.021 closest distance to " CB  PRO A 243 " =    2.532
peak=   -4.013 closest distance to " O   PRO A 163 " =    2.025
peak=   -3.996 closest distance to " CB  TYR A  15 " =    2.219
peak=   -3.987 closest distance to " CE2 TYR A  30 " =    2.845
peak=   -3.981 closest distance to " CA  GLY A  98 " =    1.900
peak=   -3.970 closest distance to " C   ASP A 231 " =    2.540
peak=   -3.966 closest distance to " CB  ASP A 132 " =    2.311
peak=   -3.946 closest distance to " CD2 LEU A 300 " =    2.821
peak=   -3.892 closest distance to " OG BSER A 134 " =    1.182
peak=   -3.891 closest distance to " CG  GLN A 223 " =    1.897
peak=   -3.884 closest distance to " CG  ASP A 231 " =    0.786
peak=   -3.881 closest distance to " O   HOH Z 231 " =    1.798
peak=   -3.881 closest distance to " O   PRO A 198 " =    1.267
peak=   -3.865 closest distance to " O   HOH Z 166 " =    1.466
peak=   -3.840 closest distance to " CG  LEU A 228 " =    0.976
peak=   -3.797 closest distance to " O   HOH Z  11 " =    1.838
peak=   -3.786 closest distance to " CB  PRO A 163 " =    2.632
peak=   -3.781 closest distance to " CB  ALA A 248 " =    1.936
peak=   -3.769 closest distance to " O   VAL A  67 " =    2.748
peak=   -3.768 closest distance to " CG  PHE A 283 " =    2.716
peak=   -3.756 closest distance to " OXT GLY A 302 " =    2.684
peak=   -3.734 closest distance to " CD1 LEU A 101 " =    2.429
peak=   -3.733 closest distance to " O   HOH Z 389 " =    1.792
peak=   -3.732 closest distance to " O   HOH Z  43 " =    1.867
peak=   -3.714 closest distance to " CD  ARG A 139 " =    1.641
peak=   -3.705 closest distance to " OG BSER A 134 " =    1.672
peak=   -3.673 closest distance to " NH2 ARG A  79 " =    1.813
peak=   -3.664 closest distance to " CB  ALA A 291 " =    2.374
peak=   -3.657 closest distance to " CZ  PHE A  59 " =    1.536
peak=   -3.621 closest distance to " O   HOH Z 407 " =    3.183
peak=   -3.620 closest distance to " O   HOH Z 429 " =    2.014
peak=   -3.605 closest distance to " N   THR A 157 " =    1.516
peak=   -3.599 closest distance to " O   ALA A   8 " =    1.860
peak=   -3.597 closest distance to " OXT GLY A 302 " =    3.632
peak=   -3.591 closest distance to " N   ALA A 248 " =    1.574
peak=   -3.589 closest distance to " O   HOH Z 148 " =    1.849
peak=   -3.588 closest distance to " O   ALA A 161 " =    1.677
peak=   -3.587 closest distance to " O   VAL A 153 " =    2.278
peak=   -3.583 closest distance to " O   HOH Z 198 " =    2.369
peak=   -3.576 closest distance to " CG1 VAL A 112 " =    2.742
peak=   -3.571 closest distance to " O   HOH Z 118 " =    2.790
peak=   -3.570 closest distance to " N   ALA A 226 " =    1.905
peak=   -3.563 closest distance to " N   SER A 276 " =    1.212
peak=   -3.557 closest distance to " CZ3 TRP A 179 " =    1.323
peak=   -3.554 closest distance to " O   HOH Z 385 " =    2.182
peak=   -3.549 closest distance to " C   GLN A 205 " =    1.975
peak=   -3.549 closest distance to " O   HOH Z  13 " =    1.470
peak=   -3.538 closest distance to " O   MET A  40 " =    2.623
peak=   -3.534 closest distance to " O   HOH Z  47 " =    1.499
peak=   -3.533 closest distance to " O   ALA A  51 " =    1.293
peak=   -3.529 closest distance to " CE2 PHE A 218 " =    2.648
peak=   -3.527 closest distance to " CZ  TYR A 169 " =    1.685
peak=   -3.524 closest distance to " NZ  LYS A 119 " =    3.376
peak=   -3.523 closest distance to " C   ALA A 158 " =    1.283
peak=   -3.523 closest distance to " O   HOH Z 211 " =    1.531
peak=   -3.515 closest distance to " C   ASN A 187 " =    1.875
peak=   -3.509 closest distance to " CG  TRP A 266 " =    1.745
peak=   -3.507 closest distance to " CB  ASN A  39 " =    2.164
peak=   -3.497 closest distance to " CG  ASP A  50 " =    2.316
peak=   -3.491 closest distance to " OG  SER A  97 " =    2.183
peak=   -3.481 closest distance to " CB  PRO A 280 " =    2.090
peak=   -3.480 closest distance to " CD1 LEU A 101 " =    2.605
peak=   -3.475 closest distance to " O   SER A  22 " =    2.331
peak=   -3.472 closest distance to " O   HOH Z 389 " =    4.626
peak=   -3.468 closest distance to " CE  MET A 105 " =    1.988
peak=   -3.462 closest distance to " CA  ASP A 298 " =    1.068
peak=   -3.461 closest distance to " CD1 PHE A  59 " =    1.903
peak=   -3.460 closest distance to " O   HOH Z 103 " =    1.804
peak=   -3.452 closest distance to " O   HOH Z 351 " =    1.521
peak=   -3.452 closest distance to " CB  PHE A 192 " =    1.787
peak=   -3.450 closest distance to " C   ASN A 285 " =    2.315
peak=   -3.447 closest distance to " O   HOH Z 191 " =    5.304
peak=   -3.447 closest distance to " O   HOH Z 175 " =    4.343
peak=   -3.446 closest distance to " NE2 GLN A  88 " =    2.113
peak=   -3.443 closest distance to " CD1 ILE A 263 " =    2.703
peak=   -3.441 closest distance to " NH2AARG A 275 " =    5.097
peak=   -3.437 closest distance to " N   THR A 235 " =    1.335
peak=   -3.433 closest distance to " ND2 ASN A  45 " =    1.005
peak=   -3.415 closest distance to " O   HOH Z 369 " =    2.147
peak=   -3.386 closest distance to " OG  SER A  26 " =    1.068
peak=   -3.380 closest distance to " O   HOH Z 166 " =    1.963
peak=   -3.373 closest distance to " O   HOH Z 102 " =    1.678
peak=   -3.372 closest distance to " O   HOH Z 423 " =    2.207
peak=   -3.369 closest distance to " CD  LYS A 289 " =    2.537
peak=   -3.369 closest distance to " O   HOH Z 165 " =    1.981
peak=   -3.363 closest distance to " CD  GLN A  88 " =    0.850
peak=   -3.360 closest distance to " O   GLY A 196 " =    1.115
peak=   -3.357 closest distance to " CD1 TYR A 247 " =    2.395
peak=   -3.356 closest distance to " CG  LYS A 193 " =    2.166
peak=   -3.350 closest distance to " O   HOH Z  90 " =    2.666
peak=   -3.345 closest distance to " O   HOH Z 353 " =    2.164
peak=   -3.339 closest distance to " N   PHE A  59 " =    2.110
peak=   -3.335 closest distance to " ND2 ASN A 187 " =    1.601
peak=   -3.332 closest distance to " CD1 LEU A 228 " =    2.138
peak=   -3.331 closest distance to " OG  SER A   3 " =    1.393
peak=   -3.330 closest distance to " OD1 ASP A 191 " =    1.462
peak=   -3.325 closest distance to " O   PHE A 218 " =    1.615
peak=   -3.325 closest distance to " CA  GLY A 133 " =    1.963
peak=   -3.322 closest distance to " NH1AARG A 275 " =    1.848
peak=   -3.315 closest distance to " O   PRO A 198 " =    1.262
peak=   -3.308 closest distance to " CG  MET A 105 " =    0.926
peak=   -3.297 closest distance to " O   HOH Z 281 " =    2.855
peak=   -3.296 closest distance to " O   VAL A 174 " =    1.979
peak=   -3.294 closest distance to " O   HOH Z 185 " =    2.247
peak=   -3.289 closest distance to " O   HOH Z 311 " =    3.587
peak=   -3.287 closest distance to " O   HOH Z  52 " =    1.491
peak=   -3.287 closest distance to " O   ASP A 231 " =    2.374
peak=   -3.286 closest distance to " O   HOH Z 426 " =    1.605
peak=   -3.284 closest distance to " O   HOH Z  71 " =    1.063
peak=   -3.284 closest distance to " O   LYS A 117 " =    1.559
peak=   -3.283 closest distance to " O   HOH Z 394 " =    1.493
peak=   -3.273 closest distance to " O   HOH Z 436 " =    1.404
peak=   -3.272 closest distance to " O   VAL A 197 " =    1.286
peak=   -3.272 closest distance to " CB  ALA A  51 " =    1.831
peak=   -3.269 closest distance to " O   HOH Z  15 " =    1.596
peak=   -3.269 closest distance to " CG  PRO A 163 " =    2.740
peak=   -3.268 closest distance to " O   HOH Z 344 " =    2.565
peak=   -3.266 closest distance to " O   SER A 210 " =    1.862
peak=   -3.265 closest distance to " ND2 ASN A  60 " =    1.458
peak=   -3.257 closest distance to " O   VAL A 125 " =    2.189
peak=   -3.256 closest distance to " O   HOH Z 196 " =    2.149
peak=   -3.254 closest distance to " O   HOH Z 385 " =    1.925
peak=   -3.252 closest distance to " CD  GLU A 152 " =    2.591
peak=   -3.252 closest distance to " SD BMET A  47 " =    2.806
peak=   -3.246 closest distance to " O   SER A  95 " =    1.491
peak=   -3.246 closest distance to " O   HOH Z 417 " =    2.753
peak=   -3.244 closest distance to " C   LEU A 143 " =    1.043
peak=   -3.244 closest distance to " C   MET A 188 " =    1.512
peak=   -3.241 closest distance to " O   HOH Z 174 " =    2.192
peak=   -3.240 closest distance to " CA  GLY A 241 " =    3.046
peak=   -3.238 closest distance to " CE3 TRP A 274 " =    2.407
peak=   -3.237 closest distance to " CG1 VAL A 112 " =    2.629
peak=   -3.235 closest distance to " CB  VAL A 296 " =    1.063
peak=   -3.230 closest distance to " O   ASN A 187 " =    1.531
peak=   -3.227 closest distance to " O   HOH Z  97 " =    1.636
peak=   -3.223 closest distance to " O   HOH Z 210 " =    1.041
peak=   -3.222 closest distance to " CB  ALA A  43 " =    2.318
peak=   -3.221 closest distance to " CE BMET A  47 " =    1.847
peak=   -3.220 closest distance to " O   HOH Z 222 " =    1.584
peak=   -3.220 closest distance to " O   HOH Z  11 " =    1.950
peak=   -3.219 closest distance to " CD2 TYR A 293 " =    2.154
peak=   -3.218 closest distance to " O   HOH Z 313 " =    1.829
peak=   -3.218 closest distance to " OG  SER A 206 " =    1.601
peak=   -3.214 closest distance to " O   HOH Z  93 " =    1.199
peak=   -3.214 closest distance to " O   SER A 146 " =    1.001
peak=   -3.210 closest distance to " N   ALA A  43 " =    2.430
peak=   -3.205 closest distance to " N   GLN A  77 " =    1.640
peak=   -3.195 closest distance to " CD1 ILE A 199 " =    2.408
peak=   -3.195 closest distance to " CB  ASP A 132 " =    2.157
peak=   -3.187 closest distance to " CG2 ILE A 263 " =    2.230
peak=   -3.185 closest distance to " CE  LYS A  76 " =    2.909
peak=   -3.177 closest distance to " O   HOH Z 359 " =    3.140
peak=   -3.176 closest distance to " O   HOH Z 100 " =    0.861
peak=   -3.172 closest distance to " SG ACYS A 201 " =    1.953
peak=   -3.170 closest distance to " NH1 ARG A  56 " =    2.482
peak=   -3.165 closest distance to " O   HOH Z 234 " =    4.114
peak=   -3.163 closest distance to " CA  TYR A  30 " =    2.845
peak=   -3.162 closest distance to " OG ASER A 134 " =    1.200
peak=   -3.153 closest distance to " O   HOH Z  63 " =    1.107
peak=   -3.148 closest distance to " O   HOH Z 292 " =    2.797
peak=   -3.135 closest distance to " CG  GLU A   2 " =    2.004
peak=   -3.131 closest distance to " CG1 VAL A 197 " =    2.198
peak=   -3.130 closest distance to " O   HOH Z 250 " =    1.454
peak=   -3.129 closest distance to " O   HOH Z 427 " =    1.457
peak=   -3.129 closest distance to " SG BCYS A 201 " =    1.977
peak=   -3.128 closest distance to " N   ASP A 171 " =    2.402
peak=   -3.127 closest distance to " O   GLN A 240 " =    2.265
peak=   -3.126 closest distance to " CA  ASP A  27 " =    2.331
peak=   -3.122 closest distance to " OG1 THR A 178 " =    1.183
peak=   -3.116 closest distance to " CZ  ARG A 259 " =    0.814
peak=   -3.115 closest distance to " OD1 ASP A 171 " =    1.617
peak=   -3.115 closest distance to " CD  GLN A  58 " =    1.181
peak=   -3.102 closest distance to " CG  GLU A 277 " =    1.177
peak=   -3.101 closest distance to " O   HOH Z 192 " =    2.454
peak=   -3.094 closest distance to " CE1 HIS A  81 " =    1.423
peak=   -3.081 closest distance to " O   HOH Z 193 " =    1.662
peak=   -3.075 closest distance to " CG1 VAL A 296 " =    1.508
peak=   -3.074 closest distance to " O   HOH Z  97 " =    2.442
peak=   -3.073 closest distance to " N   MET A 105 " =    2.627
peak=   -3.071 closest distance to " CA  GLY A 133 " =    2.175
peak=   -3.057 closest distance to " CG  ARG A 219 " =    2.752
peak=   -3.049 closest distance to " OD2 ASP A 270 " =    1.450

================= 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    :  0.4567 0.4522   6.254651e+00   6.244256e+00
   1_bss:  0.4477 0.4413   6.250097e+00   6.230441e+00
   1_xyz:  0.3592 0.3777   6.109435e+00   6.139567e+00
   1_adp:  0.3061 0.3492   5.993660e+00   6.088607e+00
   1_occ:  0.3056 0.3497   5.993243e+00   6.089699e+00
   2_bss:  0.3010 0.3452   5.992228e+00   6.086363e+00
   2_xyz:  0.2122 0.2620   5.691063e+00   5.858954e+00
   2_adp:  0.1899 0.2386   5.594346e+00   5.776276e+00
   2_occ:  0.1896 0.2384   5.593503e+00   5.775640e+00
   3_bss:  0.1886 0.2373   5.591172e+00   5.772929e+00
   3_xyz:  0.1391 0.1835   5.315991e+00   5.532929e+00
   3_adp:  0.1278 0.1732   5.246398e+00   5.473384e+00
   3_occ:  0.1276 0.1732   5.245850e+00   5.472984e+00
   4_bss:  0.1277 0.1727   5.244291e+00   5.470056e+00
   4_xyz:  0.1160 0.1614   5.170598e+00   5.409051e+00
   4_adp:  0.1145 0.1597   5.158506e+00   5.393850e+00
   4_occ:  0.1144 0.1597   5.157872e+00   5.393336e+00
   5_bss:  0.1144 0.1597   5.157952e+00   5.393405e+00
   5_xyz:  0.1085 0.1567   5.125481e+00   5.378309e+00
   5_adp:  0.1086 0.1564   5.126552e+00   5.378001e+00
   5_occ:  0.1086 0.1564   5.126062e+00   5.377515e+00
   5_bss:  0.1086 0.1563   5.126014e+00   5.377466e+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:  0.385  20.000   6.770   7.945   9.441   0.000   0.000   0.000
   1_xyz:  0.385  20.000   6.770   7.945   9.441   0.000   0.000   0.000
   1_adp:  0.385  20.000   6.770   7.945   9.441   0.000   0.000   0.000
   1_occ:  0.385  20.000   6.770   7.945   9.441   0.000   0.000   0.000
   2_bss:  0.342  28.993   3.321   3.928   6.169   0.000   0.000   0.000
   2_xyz:  0.342  28.993   3.321   3.928   6.169   0.000   0.000   0.000
   2_adp:  0.342  28.993   3.321   3.928   6.169   0.000   0.000   0.000
   2_occ:  0.342  28.993   3.321   3.928   6.169   0.000   0.000   0.000
   3_bss:  0.317  34.236   2.336   2.669   3.949   0.000   0.000   0.000
   3_xyz:  0.317  34.236   2.336   2.669   3.949   0.000   0.000   0.000
   3_adp:  0.317  34.236   2.336   2.669   3.949   0.000   0.000   0.000
   3_occ:  0.317  34.236   2.336   2.669   3.949   0.000   0.000   0.000
   4_bss:  0.319  35.766   2.244   2.509   3.309   0.000   0.000   0.000
   4_xyz:  0.319  35.766   2.244   2.509   3.309   0.000   0.000   0.000
   4_adp:  0.319  35.766   2.244   2.509   3.309   0.000   0.000   0.000
   4_occ:  0.319  35.766   2.244   2.509   3.309   0.000   0.000   0.000
   5_bss:  0.321  35.766   2.244   2.509   3.309   0.000   0.000   0.000
   5_xyz:  0.321  35.766   2.244   2.509   3.309   0.000   0.000   0.000
   5_adp:  0.321  35.766   2.244   2.509   3.309   0.000   0.000   0.000
   5_occ:  0.321  35.766   2.244   2.509   3.309   0.000   0.000   0.000
   5_bss:  0.324  38.419  -0.419  -0.138   0.557  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  52.639 0.4885  0.5698    61890.534
   1_bss:  52.780 0.4840  0.7110    58470.236
   1_xyz:  41.878 0.6195  0.8963    40539.177
   1_adp:  37.544 0.6718  0.9846    34403.785
   1_occ:  37.649 0.6705  0.9827    34502.644
   2_bss:  37.344 0.6739  0.8672    33977.607
   2_xyz:  26.785 0.7919  0.9876    18008.621
   2_adp:  23.505 0.8272  1.0162    14777.480
   2_occ:  23.475 0.8275  1.0160    14745.867
   3_bss:  23.289 0.8292  0.9635    14574.942
   3_xyz:  17.233 0.8871  0.9930     8534.096
   3_adp:  15.843 0.8996  0.9938     7612.316
   3_occ:  15.829 0.8997  0.9937     7594.451
   4_bss:  15.780 0.9000  0.9829     7537.193
   4_xyz:  14.465 0.9110  0.9891     6548.010
   4_adp:  14.111 0.9141  0.9900     6384.230
   4_occ:  14.099 0.9142  0.9899     6376.346
   5_bss:  14.100 0.9142  0.9899     6378.251
   5_xyz:  13.811 0.9165  0.9897     6213.875
   5_adp:  13.777 0.9169  0.9875     6218.714
   5_occ:  13.766 0.9170  0.9873     6211.620
   5_bss:  13.765 0.9170  0.9861     6212.567
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3142e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3142e+01
   1_xyz:   1.585  0.012  0.103 18.095  0.006  4.117   1.2717e-01
   1_adp:   1.585  0.012  0.103 18.095  0.006  4.117   1.2717e-01
   1_occ:   1.585  0.012  0.103 18.095  0.006  4.117   1.2717e-01
   2_bss:   1.585  0.012  0.103 18.095  0.006  4.117   1.2717e-01
   2_xyz:   1.019  0.007  0.075 15.964  0.004  4.117   6.7696e-02
   2_adp:   1.019  0.007  0.075 15.964  0.004  4.117   6.7696e-02
   2_occ:   1.019  0.007  0.075 15.964  0.004  4.117   6.7696e-02
   3_bss:   1.019  0.007  0.075 15.964  0.004  4.117   6.7696e-02
   3_xyz:   1.043  0.006  0.078 15.957  0.003  4.109   6.3560e-02
   3_adp:   1.043  0.006  0.078 15.957  0.003  4.109   6.3560e-02
   3_occ:   1.043  0.006  0.078 15.957  0.003  4.109   6.3560e-02
   4_bss:   1.043  0.006  0.078 15.957  0.003  4.109   6.3560e-02
   4_xyz:   0.976  0.006  0.077 15.674  0.004  4.110   5.9235e-02
   4_adp:   0.976  0.006  0.077 15.674  0.004  4.110   5.9235e-02
   4_occ:   0.976  0.006  0.077 15.674  0.004  4.110   5.9235e-02
   5_bss:   0.976  0.006  0.077 15.674  0.004  4.110   5.9235e-02
   5_xyz:   1.101  0.008  0.087 15.813  0.004  4.112   7.0577e-02
   5_adp:   1.101  0.008  0.087 15.813  0.004  4.112   7.0577e-02
   5_occ:   1.101  0.008  0.087 15.813  0.004  4.112   7.0577e-02
   5_bss:   1.101  0.008  0.087 15.813  0.004  4.112   7.0577e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.8883e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.8883e+00
   1_xyz:  13.439  0.153  0.450 85.202  0.047  2.271   9.0436e-02
   1_adp:  13.439  0.153  0.450 85.202  0.047  2.271   9.0436e-02
   1_occ:  13.439  0.153  0.450 85.202  0.047  2.271   9.0436e-02
   2_bss:  13.439  0.153  0.450 85.202  0.047  2.271   9.0436e-02
   2_xyz:   6.685  0.085  0.274 85.788  0.036  2.317   6.9471e-02
   2_adp:   6.685  0.085  0.274 85.788  0.036  2.317   6.9471e-02
   2_occ:   6.685  0.085  0.274 85.788  0.036  2.317   6.9471e-02
   3_bss:   6.685  0.085  0.274 85.788  0.036  2.317   6.9471e-02
   3_xyz:   7.545  0.043  0.484 85.342  0.030  2.298   3.9244e-02
   3_adp:   7.545  0.043  0.484 85.342  0.030  2.298   3.9244e-02
   3_occ:   7.545  0.043  0.484 85.342  0.030  2.298   3.9244e-02
   4_bss:   7.545  0.043  0.484 85.342  0.030  2.298   3.9244e-02
   4_xyz:   6.411  0.035  0.512 83.855  0.035  2.326   4.2230e-02
   4_adp:   6.411  0.035  0.512 83.855  0.035  2.326   4.2230e-02
   4_occ:   6.411  0.035  0.512 83.855  0.035  2.326   4.2230e-02
   5_bss:   6.411  0.035  0.512 83.855  0.035  2.326   4.2230e-02
   5_xyz:   6.782  0.046  0.645 82.960  0.037  2.230   5.5819e-02
   5_adp:   6.782  0.046  0.645 82.960  0.037  2.230   5.5819e-02
   5_occ:   6.782  0.046  0.645 82.960  0.037  2.230   5.5819e-02
   5_bss:   6.782  0.046  0.645 82.960  0.037  2.230   5.5819e-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:  60.70   0.00  11.59  58.95   0.00   8.96  60.70   0.00  25.88
   1_occ:  60.70   0.00  11.59  58.95   0.00   8.96  60.70   0.00  25.88
   2_bss:  60.70   0.00  11.59  58.95   0.00   8.96  60.70   0.00  25.88
   2_xyz:  60.70   0.00  11.59  58.95   0.00   8.96  60.70   0.00  25.88
   2_adp:  66.08   0.00  11.97  66.08   0.00   8.33  59.33   1.23  31.76
   2_occ:  66.08   0.00  11.97  66.08   0.00   8.33  59.33   1.23  31.76
   3_bss:  66.08   0.00  11.97  66.08   0.00   8.33  59.33   1.23  31.76
   3_xyz:  66.08   0.00  11.97  66.08   0.00   8.33  59.33   1.23  31.76
   3_adp:  77.87   0.00  12.57  77.87   0.00   8.22  71.90   1.95  36.27
   3_occ:  77.87   0.00  12.57  77.87   0.00   8.22  71.90   1.95  36.27
   4_bss:  77.87   0.00  12.57  77.87   0.00   8.22  71.90   1.95  36.27
   4_xyz:  77.87   0.00  12.57  77.87   0.00   8.22  71.90   1.95  36.27
   4_adp:  79.43   0.00  12.24  79.43   0.00   8.09  73.18   1.77  34.86
   4_occ:  79.43   0.00  12.24  79.43   0.00   8.09  73.18   1.77  34.86
   5_bss:  79.43   0.00  12.24  79.43   0.00   8.09  73.18   1.77  34.86
   5_xyz:  79.43   0.00  12.24  79.43   0.00   8.09  73.18   1.77  34.86
   5_adp:  81.16   0.00  11.88  81.16   0.00   7.95  70.42   1.34  33.30
   5_occ:  81.16   0.00  11.88  81.16   0.00   7.95  70.42   1.34  33.30
   5_bss:  83.82   2.65  14.54  83.82   2.65  10.60  73.07   3.99  35.95
------------------------------------------------------------------------
 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:    1.202    0.025    0.404
   1_adp:    1.202    0.025    0.404
   1_occ:    1.202    0.025    0.404
   2_bss:    1.202    0.025    0.404
   2_xyz:    1.430    0.039    0.545
   2_adp:    1.430    0.039    0.545
   2_occ:    1.430    0.039    0.545
   3_bss:    1.430    0.039    0.545
   3_xyz:    1.440    0.036    0.606
   3_adp:    1.440    0.036    0.606
   3_occ:    1.440    0.036    0.606
   4_bss:    1.440    0.036    0.606
   4_xyz:    1.567    0.062    0.630
   4_adp:    1.567    0.062    0.630
   4_occ:    1.567    0.062    0.630
   5_bss:    1.567    0.062    0.630
   5_xyz:    1.621    0.065    0.643
   5_adp:    1.621    0.065    0.643
   5_occ:    1.621    0.065    0.643
   5_bss:    1.621    0.065    0.643
------------------------------------------------------------------------

CPU time actual refinement: 287.33


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_529/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_529/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_529/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_529/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_529/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 287.19 
  Macro-tasks:
    bulk solvent and scale       = 35.10  
    individual site refinement   = 116.63 
    weights calculation          = 28.26  
    collect and process          = 5.65   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 185.76 
  Micro-tasks:
    mask                            = 1.51   
    f_calc                          = 88.92  
    alpha_beta                      = 7.43   
    target                          = 1.02   
    gradients_wrt_atomic_parameters = 97.18  
    fmodel                         = 6.29   
    r_factors                      = 0.28   
    phase_errors                   = 8.79   
    foms                           = 0.17   
    TOTAL for micro-tasks          = 211.59 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.051 micro seconds
Total CPU time: 4.98 minutes
from_scatterers_fft:    649 calls, 88.62 s
gradients_fft:          594 calls, 85.60 s

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

# Date 2008-01-16 Time 01:47:00 PST -0800 (1200476820.37 s)
Start R-work = 0.4567, R-free = 0.4522 (no bulk solvent and anisotropic scale)
Final R-work = 0.1262, R-free = 0.1730 (no bulk solvent and anisotropic scale)

Start R-work = 0.4477, R-free = 0.4413
Final R-work = 0.1086, R-free = 0.1563