# Date 2008-01-16 Time 03:00:51 PST -0800 (1200481251.23 s)
#phil __OFF__

Command line arguments: "../1062.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 10502
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1062

-------------------------------------------------------------------------------
  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: (71.3037, 47.6339, 86.822, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.6339, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1778 2.0111
Completeness in resolution range: 0.968027
Completeness with d_max=infinity: 0.964975

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1778
                             d_min =   2.0111

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: (71.3037, 47.6339, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1778 2.0111
Completeness in resolution range: 0.968027
Completeness with d_max=infinity: 0.964975

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1782 -  4.3030 [2117/2144]  1906   211  10.0%
  bin  2:  4.3030 -  3.4283 [2041/2057]  1836   205  10.0%
  bin  3:  3.4283 -  2.9988 [2018/2037]  1814   204  10.1%
  bin  4:  2.9988 -  2.7263 [1999/2029]  1804   195   9.8%
  bin  5:  2.7263 -  2.5319 [1979/1998]  1779   200  10.1%
  bin  6:  2.5319 -  2.3832 [1960/1985]  1768   192   9.8%
  bin  7:  2.3832 -  2.2642 [1970/2002]  1769   201  10.2%
  bin  8:  2.2642 -  2.1660 [1955/1987]  1760   195  10.0%
  bin  9:  2.1660 -  2.0828 [1961/2003]  1766   195   9.9%
  bin 10:  2.0828 -  2.0111 [1589/1994]  1428   161  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1062/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.52 -     2.20: 5
        2.20 -     2.87: 1199
        2.87 -     3.55: 4354
        3.55 -     4.22: 9046
        4.22 -     4.90: 13219
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.525 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 206 " - " O   HOH Z 342 "  2.128 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 277 " - " O   HOH Z 343 "  2.151 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 343 " - " O   HOH Z 277 "  2.151 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 27818 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_1062/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1062/model_refine_001.geo

CPU time processing inputs: 9.09


============================ 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 = 71.30375 47.63395 86.82195 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4706   r_free= 0.4518   ksol= 0.00   Bsol= 0.00   scale= 0.788    |
|                                                                             |
| 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:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.271130                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1782 -  4.7991 0.99   1378  154 0.3834 0.3641      6.5702      6.4824|
|  2:  4.7991 -  3.8294 0.99   1334  145 0.3792 0.4116      6.7603      6.8439|
|  3:  3.8294 -  3.3512 0.99   1300  146 0.4282 0.3862      6.6681      6.6297|
|  4:  3.3512 -  3.0475 0.99   1291  145 0.4560 0.3984      6.5298      6.4232|
|  5:  3.0475 -  2.8306 0.99   1280  141 0.4979 0.4685       6.366      6.3843|
|  6:  2.8306 -  2.6647 0.99   1285  143 0.5051 0.5335      6.2898      6.2394|
|  7:  2.6647 -  2.5319 0.99   1271  141 0.5012 0.4698      6.2362      6.1883|
|  8:  2.5319 -  2.4221 0.98   1272  142 0.5174 0.4447      6.1843       6.132|
|  9:  2.4221 -  2.3292 0.98   1269  139 0.5117 0.5452       6.119      6.1578|
| 10:  2.3292 -  2.2491 0.99   1247  144 0.5225 0.5107      6.1127      6.1447|
| 11:  2.2491 -  2.1790 0.99   1275  139 0.5152 0.4730      6.0378      6.0639|
| 12:  2.1790 -  2.1169 0.97   1241  137 0.5376 0.4873      5.9985      6.0008|
| 13:  2.1169 -  2.0613 0.99   1249  142 0.5255 0.5235      5.8864      5.8552|
| 14:  2.0613 -  2.0111 0.73    938  101 0.5390 0.5239      5.8468      5.7596|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1782 -  4.7991  1378   154  0.71  33.04   0.80     0.74      65819.95|
|  2:  4.7991 -  3.8294  1334   145  0.73  32.57   0.88     0.77      93222.90|
|  3:  3.8294 -  3.3512  1300   146  0.65  39.94   0.82     0.73      99223.63|
|  4:  3.3512 -  3.0475  1291   145  0.57  46.34   0.80     0.64      87606.45|
|  5:  3.0475 -  2.8306  1280   141  0.48  53.23   0.73     0.56      72300.34|
|  6:  2.8306 -  2.6647  1285   143  0.46  54.95   0.72     0.52      63702.04|
|  7:  2.6647 -  2.5319  1271   141  0.43  57.29   0.74     0.48      59367.76|
|  8:  2.5319 -  2.4221  1272   142  0.39  60.74   0.72     0.45      57646.63|
|  9:  2.4221 -  2.3292  1269   139  0.36  62.77   0.71     0.41      53843.00|
| 10:  2.3292 -  2.2491  1247   144  0.36  62.72   0.73     0.41      49919.23|
| 11:  2.2491 -  2.1790  1275   139  0.37  62.49   0.75     0.43      43916.06|
| 12:  2.1790 -  2.1169  1241   137  0.36  62.82   0.74     0.44      41152.48|
| 13:  2.1169 -  2.0613  1249   142  0.33  65.29   0.71     0.39      36218.88|
| 14:  2.0613 -  2.0111   938   101  0.30  67.51   0.70     0.33      31267.26|
|alpha:            min =        0.33 max =            0.77 mean =         0.53|
|beta:             min =    31267.26 max =        99223.63 mean =     61970.49|
|figures of merit: min =        0.00 max =            1.00 mean =         0.47|
|phase err.(work): min =        0.00 max =           90.00 mean =        53.88|
|phase err.(test): min =        0.00 max =           89.88 mean =        53.79|
|-----------------------------------------------------------------------------|

============================== 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 = 12.127384             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.465   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.116689              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.870   (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:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       25 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      159 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      680 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1471 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2584 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3832 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4972 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6499 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7621 |
|-----------------------------------------------------------------------------|
|-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 |       54.443 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.093    4.900  1.196 |       1.662 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.324)------------------------------------------|
|    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 = 12.324)------------------------------------------|
|    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: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4758   r_free= 0.4576   ksol= 0.00   Bsol= 0.00   scale= 0.760    |
|                                                                             |
| 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:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.272869                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4638   r_free= 0.4422   ksol= 0.30   Bsol= 20.00   scale= 0.973   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.20,9.77,7.36,0.00,0.00,0.00); trace/3= 8.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.266178                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.905622             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.789   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.995183              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.835   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4638      final r-factor (work) = 0.3705          |
| start r-factor (free) = 0.4422      final r-factor (free) = 0.3923          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 88.6502 = 10.91 * 0.50 * 6.2733 + 1.00 * 54.4433                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.7335 = 10.91 * 0.50 * 6.1607 + 1.00 * 0.1402                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3705      final r-factor (work) = 0.3231          |
| start r-factor (free) = 0.3923      final r-factor (free) = 0.3626          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1454 = 1.00 * 1.00 * 6.1607 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.0476 = 1.00 * 1.00 * 6.0611 + 1.00 * 0.0157                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.324)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.90  12.17    None  None   None       |
|    all(noH): 2823   0      0.00    105.90  12.17    None  None   None       |
|    Sol.    : 438    0      0.00    105.90  26.97    None  None   None       |
|    Mac.    : 2385   0      0.00    75.06   9.45     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.590: 1686   |   5:    52.951 -  63.541:   29        |
|      1:    10.590 -  21.180:  659   |   6:    63.541 -  74.131:    7        |
|      2:    21.180 -  31.770:  265   |   7:    74.131 -  84.721:    3        |
|      3:    31.770 -  42.361:   99   |   8:    84.721 -  95.311:    1        |
|      4:    42.361 -  52.951:   72   |   9:    95.311 - 105.901:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3231 r_free = 0.3626             target_work(ml) = 6.035         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3227 r_free = 0.3626             target_work(ml) = 6.034         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3227   r_free= 0.3626   ksol= 0.30   Bsol= 20.00   scale= 1.059   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.20,9.77,7.36,0.00,0.00,0.00); trace/3= 8.11                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.033807                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3209   r_free= 0.3607   ksol= 0.32   Bsol= 53.96   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.64,6.78,4.95,0.00,0.00,0.00); trace/3= 5.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.50 A                  |
| x-ray target function (ml) for work reflections: 6.034703                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.265106              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.879   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.465373              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.283  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3209      final r-factor (work) = 0.2266          |
| start r-factor (free) = 0.3607      final r-factor (free) = 0.2765          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.1393 = 7.27 * 0.50 * 6.0561 + 1.00 * 0.1402                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.4772 = 7.27 * 0.50 * 5.8873 + 1.00 * 0.0912                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2266      final r-factor (work) = 0.2046          |
| start r-factor (free) = 0.2765      final r-factor (free) = 0.2531          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7566 = 0.47 * 1.00 * 5.8873 + 1.00 * 0.0168                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6658 = 0.47 * 1.00 * 5.6885 + 1.00 * 0.0185                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.324)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.79   12.37    None  None   None       |
|    all(noH): 2823   0      0.00    99.79   12.37    None  None   None       |
|    Sol.    : 438    0      0.00    99.79   32.90    None  None   None       |
|    Mac.    : 2385   0      0.00    74.73   8.60     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:     0.000 -   9.979: 1751   |   5:    49.894 -  59.873:   55        |
|      1:     9.979 -  19.958:  561   |   6:    59.873 -  69.852:   16        |
|      2:    19.958 -  29.937:  193   |   7:    69.852 -  79.831:    5        |
|      3:    29.937 -  39.915:  134   |   8:    79.831 -  89.809:    0        |
|      4:    39.915 -  49.894:  106   |   9:    89.809 -  99.788:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2046 r_free = 0.2531             target_work(ml) = 5.653         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2043 r_free = 0.2532             target_work(ml) = 5.652         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2043   r_free= 0.2532   ksol= 0.32   Bsol= 53.96   scale= 1.038   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.64,6.78,4.95,0.00,0.00,0.00); trace/3= 5.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.651903                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2020   r_free= 0.2522   ksol= 0.32   Bsol= 68.53   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.85,3.93,3.68,0.00,0.00,0.00); trace/3= 3.49                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.652095                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.723099              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.017   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.307501              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 100.605  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2020      final r-factor (work) = 0.1491          |
| start r-factor (free) = 0.2522      final r-factor (free) = 0.1910          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.5415 = 4.72 * 0.50 * 5.6955 + 1.00 * 0.0912                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.1348 = 4.72 * 0.50 * 5.5278 + 1.00 * 0.0807                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1491      final r-factor (work) = 0.1376          |
| start r-factor (free) = 0.1910      final r-factor (free) = 0.1808          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7146 = 0.31 * 1.00 * 5.5278 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6512 = 0.31 * 1.00 * 5.3332 + 1.00 * 0.0113                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.324)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.53   12.55    None  None   None       |
|    all(noH): 2823   0      0.00    90.53   12.55    None  None   None       |
|    Sol.    : 438    0      0.47    90.53   35.66    None  None   None       |
|    Mac.    : 2385   0      0.00    77.97   8.30     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.053: 1704   |   5:    45.263 -  54.316:   92        |
|      1:     9.053 -  18.105:  568   |   6:    54.316 -  63.369:   45        |
|      2:    18.105 -  27.158:  161   |   7:    63.369 -  72.421:   17        |
|      3:    27.158 -  36.211:  133   |   8:    72.421 -  81.474:    4        |
|      4:    36.211 -  45.263:   97   |   9:    81.474 -  90.527:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1376 r_free = 0.1808             target_work(ml) = 5.307         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1375 r_free = 0.1807             target_work(ml) = 5.306         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1375   r_free= 0.1807   ksol= 0.32   Bsol= 68.53   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.85,3.93,3.68,0.00,0.00,0.00); trace/3= 3.49                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.306434                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1375   r_free= 0.1808   ksol= 0.33   Bsol= 65.02   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.34,3.02,3.41,0.00,0.00,0.00); trace/3= 2.92                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.306179                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.975347              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 115.133  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.214176              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 155.409  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1375      final r-factor (work) = 0.1227          |
| start r-factor (free) = 0.1808      final r-factor (free) = 0.1684          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0171 = 2.98 * 0.50 * 5.3348 + 1.00 * 0.0807                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9029 = 2.98 * 0.50 * 5.2592 + 1.00 * 0.0790                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1227      final r-factor (work) = 0.1213          |
| start r-factor (free) = 0.1684      final r-factor (free) = 0.1673          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1375 = 0.21 * 1.00 * 5.2592 + 1.00 * 0.0111                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1278 = 0.21 * 1.00 * 5.2167 + 1.00 * 0.0105                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.324)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.26   12.34    None  None   None       |
|    all(noH): 2823   0      0.00    88.26   12.34    None  None   None       |
|    Sol.    : 438    0      1.27    88.26   35.21    None  None   None       |
|    Mac.    : 2385   0      0.00    77.79   8.14     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 -   8.826: 1715   |   5:    44.128 -  52.954:   95        |
|      1:     8.826 -  17.651:  560   |   6:    52.954 -  61.780:   49        |
|      2:    17.651 -  26.477:  155   |   7:    61.780 -  70.605:   16        |
|      3:    26.477 -  35.303:  126   |   8:    70.605 -  79.431:    6        |
|      4:    35.303 -  44.128:   99   |   9:    79.431 -  88.257:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1213 r_free = 0.1673             target_work(ml) = 5.211         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1212 r_free = 0.1672             target_work(ml) = 5.211         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1212   r_free= 0.1672   ksol= 0.33   Bsol= 65.02   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.34,3.02,3.41,0.00,0.00,0.00); trace/3= 2.92                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.211179                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1212   r_free= 0.1672   ksol= 0.33   Bsol= 65.02   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.32,2.81,3.48,0.00,0.00,0.00); trace/3= 2.87                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.210965                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.707654              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 148.826  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.620457              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 153.810  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1212      final r-factor (work) = 0.1227          |
| start r-factor (free) = 0.1672      final r-factor (free) = 0.1669          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5327 = 1.71 * 0.50 * 5.2162 + 1.00 * 0.0790                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5168 = 1.71 * 0.50 * 5.2181 + 1.00 * 0.0615                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1227      final r-factor (work) = 0.1207          |
| start r-factor (free) = 0.1669      final r-factor (free) = 0.1686          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.4661 = 1.62 * 1.00 * 5.2181 + 1.00 * 0.0105                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.4626 = 1.62 * 1.00 * 5.2078 + 1.00 * 0.0235                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.324)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.45   12.77    None  None   None       |
|    all(noH): 2823   0      0.00    91.45   12.77    None  None   None       |
|    Sol.    : 438    0      1.49    87.92   37.42    None  None   None       |
|    Mac.    : 2385   0      0.00    91.45   8.24     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.145: 1733   |   5:    45.723 -  54.867:   91        |
|      1:     9.145 -  18.289:  541   |   6:    54.867 -  64.012:   55        |
|      2:    18.289 -  27.434:  158   |   7:    64.012 -  73.157:   28        |
|      3:    27.434 -  36.578:  111   |   8:    73.157 -  82.301:   10        |
|      4:    36.578 -  45.723:   90   |   9:    82.301 -  91.446:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1207 r_free = 0.1686             target_work(ml) = 5.216         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1206 r_free = 0.1686             target_work(ml) = 5.216         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1206   r_free= 0.1686   ksol= 0.33   Bsol= 65.02   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.32,2.81,3.48,0.00,0.00,0.00); trace/3= 2.87                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.215902                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1782 -  4.7991 0.99   1378  154 0.1048 0.1360       5.421      5.5524|
|  2:  4.7991 -  3.8294 0.99   1334  145 0.0885 0.1082      5.4622      5.6227|
|  3:  3.8294 -  3.3512 0.99   1300  146 0.1103 0.1555       5.513      5.8915|
|  4:  3.3512 -  3.0475 0.99   1291  145 0.1282 0.1642      5.5119      5.6589|
|  5:  3.0475 -  2.8306 0.99   1280  141 0.1481 0.1953      5.4245      5.6087|
|  6:  2.8306 -  2.6647 0.99   1285  143 0.1338 0.2013      5.3102       5.536|
|  7:  2.6647 -  2.5319 0.99   1271  141 0.1378 0.1838      5.2459      5.4761|
|  8:  2.5319 -  2.4221 0.98   1272  142 0.1302 0.1804      5.1591      5.4021|
|  9:  2.4221 -  2.3292 0.98   1269  139 0.1268 0.1985      5.1134      5.3699|
| 10:  2.3292 -  2.2491 0.99   1247  144 0.1247 0.1808      5.0624      5.2924|
| 11:  2.2491 -  2.1790 0.99   1275  139 0.1266 0.1977      5.0279      5.3548|
| 12:  2.1790 -  2.1169 0.97   1241  137 0.1208 0.1791      4.9608      5.2298|
| 13:  2.1169 -  2.0613 0.99   1249  142 0.1251 0.1877      4.8742      5.1586|
| 14:  2.0613 -  2.0111 0.73    938  101 0.1148 0.1964      4.7585      5.0305|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1782 -  4.7991  1378   154  0.94   9.27   0.96     0.94       7561.98|
|  2:  4.7991 -  3.8294  1334   145  0.95   8.12   1.00     0.98       9215.62|
|  3:  3.8294 -  3.3512  1300   146  0.93  11.74   1.01     1.01      11098.62|
|  4:  3.3512 -  3.0475  1291   145  0.92  14.29   1.00     0.97      11381.69|
|  5:  3.0475 -  2.8306  1280   141  0.88  17.75   0.99     0.96      10003.18|
|  6:  2.8306 -  2.6647  1285   143  0.89  17.38   0.97     0.94       8573.99|
|  7:  2.6647 -  2.5319  1271   141  0.89  17.14   0.98     0.95       7210.88|
|  8:  2.5319 -  2.4221  1272   142  0.90  16.64   0.98     0.94       6252.37|
|  9:  2.4221 -  2.3292  1269   139  0.90  16.85   0.99     0.95       5891.61|
| 10:  2.3292 -  2.2491  1247   144  0.89  17.16   0.98     0.93       5314.30|
| 11:  2.2491 -  2.1790  1275   139  0.88  17.88   0.97     0.92       5049.64|
| 12:  2.1790 -  2.1169  1241   137  0.90  16.22   0.98     0.96       4595.09|
| 13:  2.1169 -  2.0613  1249   142  0.89  17.80   0.98     0.96       4033.88|
| 14:  2.0613 -  2.0111   938   101  0.90  16.58   0.95     0.90       3075.01|
|alpha:            min =        0.90 max =            1.01 mean =         0.95|
|beta:             min =     3075.01 max =        11381.69 mean =      7200.37|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        15.25|
|phase err.(test): min =        0.00 max =           89.03 mean =        14.69|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1206   r_free= 0.1685   ksol= 0.32   Bsol= 65.13   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.52,-0.10,0.62,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.215852                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.01 - 15.18 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1206   r_free= 0.1685   ksol= 0.32   Bsol= 65.13   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.52,-0.10,0.62,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.215852                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1782 -  4.7991 0.99   1378  154 0.1045 0.1359      5.4187      5.5526|
|  2:  4.7991 -  3.8294 0.99   1334  145 0.0885 0.1082      5.4623      5.6221|
|  3:  3.8294 -  3.3512 0.99   1300  146 0.1103 0.1555      5.5129      5.8917|
|  4:  3.3512 -  3.0475 0.99   1291  145 0.1282 0.1642      5.5122      5.6591|
|  5:  3.0475 -  2.8306 0.99   1280  141 0.1481 0.1953       5.425      5.6088|
|  6:  2.8306 -  2.6647 0.99   1285  143 0.1339 0.2014      5.3105      5.5361|
|  7:  2.6647 -  2.5319 0.99   1271  141 0.1378 0.1839      5.2462      5.4769|
|  8:  2.5319 -  2.4221 0.98   1272  142 0.1303 0.1804      5.1593       5.402|
|  9:  2.4221 -  2.3292 0.98   1269  139 0.1267 0.1985      5.1134      5.3698|
| 10:  2.3292 -  2.2491 0.99   1247  144 0.1247 0.1809      5.0627      5.2927|
| 11:  2.2491 -  2.1790 0.99   1275  139 0.1267 0.1976       5.028      5.3548|
| 12:  2.1790 -  2.1169 0.97   1241  137 0.1208 0.1791      4.9608      5.2302|
| 13:  2.1169 -  2.0613 0.99   1249  142 0.1251 0.1877      4.8741      5.1584|
| 14:  2.0613 -  2.0111 0.73    938  101 0.1148 0.1962      4.7582      5.0299|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1782 -  4.7991  1378   154  0.94   9.28   0.96     0.94       7571.32|
|  2:  4.7991 -  3.8294  1334   145  0.95   8.12   1.00     0.98       9221.48|
|  3:  3.8294 -  3.3512  1300   146  0.93  11.74   1.01     1.01      11097.23|
|  4:  3.3512 -  3.0475  1291   145  0.92  14.29   1.00     0.98      11385.15|
|  5:  3.0475 -  2.8306  1280   141  0.88  17.75   0.99     0.97      10009.23|
|  6:  2.8306 -  2.6647  1285   143  0.89  17.38   0.98     0.94       8578.76|
|  7:  2.6647 -  2.5319  1271   141  0.89  17.14   0.98     0.96       7213.69|
|  8:  2.5319 -  2.4221  1272   142  0.90  16.64   0.98     0.95       6252.29|
|  9:  2.4221 -  2.3292  1269   139  0.90  16.85   1.00     0.96       5894.00|
| 10:  2.3292 -  2.2491  1247   144  0.89  17.16   0.99     0.94       5314.99|
| 11:  2.2491 -  2.1790  1275   139  0.88  17.89   0.98     0.93       5051.66|
| 12:  2.1790 -  2.1169  1241   137  0.90  16.22   0.99     0.97       4596.32|
| 13:  2.1169 -  2.0613  1249   142  0.89  17.80   0.99     0.96       4032.27|
| 14:  2.0613 -  2.0111   938   101  0.90  16.57   0.96     0.91       3071.10|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     3071.10 max =        11385.15 mean =      7202.81|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        15.25|
|phase err.(test): min =        0.00 max =           89.02 mean =        14.70|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.324)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.04    94.49   15.82    None  None   None       |
|    all(noH): 2823   0      3.04    94.49   15.82    None  None   None       |
|    Sol.    : 438    0      4.54    90.96   40.47    None  None   None       |
|    Mac.    : 2385   0      3.04    94.49   11.29    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:     3.043 -  12.188: 1733   |   5:    48.766 -  57.911:   91        |
|      1:    12.188 -  21.332:  541   |   6:    57.911 -  67.055:   55        |
|      2:    21.332 -  30.477:  158   |   7:    67.055 -  76.200:   28        |
|      3:    30.477 -  39.622:  111   |   8:    76.200 -  85.344:   10        |
|      4:    39.622 -  48.766:   90   |   9:    85.344 -  94.489:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 337         
Filter by distance & map next to the model:
   mapped sites are within: 0.324 - 5.877
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 329 from: 337
   mapped sites are within: 0.726 - 5.877

peak=    9.301 closest distance to " CG2 VAL A 230 " =    1.308
peak=    7.134 closest distance to " CG2 VAL A 296 " =    1.119
peak=    6.050 closest distance to " CG  LEU A   5 " =    1.173
peak=    5.987 closest distance to " O   HOH Z 111 " =    2.262
peak=    5.751 closest distance to " CB  GLN A 223 " =    1.354
peak=    5.409 closest distance to " CG  PRO A 280 " =    0.955
peak=    5.352 closest distance to " CG  PRO A 198 " =    1.265
peak=    5.323 closest distance to " CG  LEU A 228 " =    1.179
peak=    5.193 closest distance to " CG  PRO A  54 " =    1.359
peak=    5.089 closest distance to " CB  VAL A 230 " =    1.249
peak=    4.979 closest distance to " CB  PRO A  54 " =    0.953
peak=    4.885 closest distance to " CB  SER A  63 " =    1.326
peak=    4.882 closest distance to " CD1AILE A 234 " =    1.024
peak=    4.729 closest distance to " CB  VAL A 296 " =    1.065
peak=    4.703 closest distance to " O   HOH Z 232 " =    2.274
peak=    4.686 closest distance to " CD2 LEU A   5 " =    1.091
peak=    4.639 closest distance to " CG  PRO A 213 " =    1.268
peak=    4.464 closest distance to " CB  GLN A 183 " =    1.282
peak=    4.454 closest distance to " CB  GLU A 128 " =    1.137
peak=    4.433 closest distance to " CZ  PHE A 218 " =    1.075
peak=    4.377 closest distance to " CA  TYR A  30 " =    0.955
peak=    4.364 closest distance to " CZ  PHE A 192 " =    1.010
peak=    4.361 closest distance to " CB  ASN A 148 " =    1.315
peak=    4.361 closest distance to " CB  ARG A 275 " =    0.915
peak=    4.293 closest distance to " CB  ARG A 190 " =    1.694
peak=    4.291 closest distance to " CG  PRO A 243 " =    1.172
peak=    4.269 closest distance to " O   HOH Z 298 " =    1.939
peak=    4.255 closest distance to " CB  TRP A 266 " =    0.978
peak=    4.252 closest distance to " O   HOH Z 265 " =    2.187
peak=    4.251 closest distance to " O   HOH Z 433 " =    1.693
peak=    4.238 closest distance to " O   HOH Z 247 " =    1.523
peak=    4.194 closest distance to " NE2 GLN A  11 " =    1.071
peak=    4.173 closest distance to " O   PRO A 198 " =    1.556
peak=    4.165 closest distance to " O   HOH Z 411 " =    3.757
peak=    4.148 closest distance to " O   HOH Z 184 " =    1.533
peak=    4.118 closest distance to " O   HOH Z 234 " =    3.704
peak=    4.100 closest distance to " CD  ARG A 269 " =    0.911
peak=    4.094 closest distance to " O   HOH Z  48 " =    1.760
peak=    4.088 closest distance to " O   HOH Z 369 " =    2.197
peak=    4.083 closest distance to " O   HOH Z 287 " =    1.954
peak=    4.080 closest distance to " CB  GLU A 277 " =    3.774
peak=    4.075 closest distance to " O   SER A  87 " =    2.330
peak=    4.055 closest distance to " O   HOH Z 423 " =    1.772
peak=    4.052 closest distance to " CB AVAL A  41 " =    1.039
peak=    4.040 closest distance to " O   HOH Z 427 " =    3.130
peak=    4.017 closest distance to " CB  ASP A 124 " =    0.733
peak=    4.015 closest distance to " CA  ALA A  51 " =    1.021
peak=    4.014 closest distance to " O   HOH Z  80 " =    1.879
peak=    4.005 closest distance to " CG2 THR A 221 " =    1.052
peak=    4.000 closest distance to " CD2 LEU A 228 " =    1.358
peak=    3.991 closest distance to " O   HOH Z  48 " =    1.914
peak=    3.976 closest distance to " CD  LYS A 166 " =    1.383
peak=    3.963 closest distance to " CB  TYR A 169 " =    0.770
peak=    3.954 closest distance to " CB  VAL A 202 " =    1.567
peak=    3.953 closest distance to " OD1 ASN A  69 " =    2.607
peak=    3.941 closest distance to " O   HOH Z  63 " =    1.386
peak=    3.910 closest distance to " O   HOH Z 316 " =    3.103
peak=    3.902 closest distance to " CD  ARG A  66 " =    2.725
peak=    3.900 closest distance to " O   HOH Z 403 " =    1.811
peak=    3.898 closest distance to " CB  ARG A  79 " =    1.422
peak=    3.895 closest distance to " O   HOH Z 102 " =    1.383
peak=    3.892 closest distance to " CG1 VAL A 153 " =    1.060
peak=    3.885 closest distance to " ND2 ASN A 249 " =    1.914
peak=    3.872 closest distance to " C   ILE A 106 " =    1.854
peak=    3.857 closest distance to " O   HOH Z 303 " =    2.194
peak=    3.854 closest distance to " O   HOH Z 189 " =    3.069
peak=    3.850 closest distance to " O   ASP A 124 " =    1.143
peak=    3.846 closest distance to " O   HOH Z 163 " =    1.640
peak=    3.844 closest distance to " O   HOH Z 280 " =    2.906
peak=    3.837 closest distance to " O   HOH Z 425 " =    1.455
peak=    3.834 closest distance to " O   HOH Z 134 " =    1.648
peak=    3.827 closest distance to " CG1 ILE A  33 " =    1.285
peak=    3.818 closest distance to " OG BSER A 164 " =    2.053
peak=    3.795 closest distance to " CB  ASP A 140 " =    0.934
peak=    3.793 closest distance to " CA  ASP A 191 " =    0.857
peak=    3.792 closest distance to " CB  GLU A 152 " =    1.150
peak=    3.789 closest distance to " O   HOH Z  44 " =    2.071
peak=    3.786 closest distance to " O   HOH Z 437 " =    2.014
peak=    3.784 closest distance to " O   HOH Z  15 " =    2.245
peak=    3.776 closest distance to " CB  LEU A 228 " =    1.251
peak=    3.772 closest distance to " O   HOH Z  43 " =    2.103
peak=    3.768 closest distance to " O   HOH Z 171 " =    3.879
peak=    3.768 closest distance to " O   HOH Z 261 " =    1.721
peak=    3.768 closest distance to " O   HOH Z 126 " =    1.639
peak=    3.767 closest distance to " O   HOH Z 368 " =    2.310
peak=    3.764 closest distance to " CB  VAL A 265 " =    1.239
peak=    3.760 closest distance to " CB  SER A   3 " =    1.333
peak=    3.754 closest distance to " CA  SER A  87 " =    1.024
peak=    3.752 closest distance to " CD ALYS A 290 " =    1.080
peak=    3.749 closest distance to " O   HOH Z 285 " =    3.049
peak=    3.743 closest distance to " CB  TRP A 179 " =    1.445
peak=    3.742 closest distance to " CB  MET A  40 " =    0.763
peak=    3.730 closest distance to " O   HOH Z 126 " =    2.179
peak=    3.724 closest distance to " CA  THR A 264 " =    0.757
peak=    3.719 closest distance to " CA  ARG A 195 " =    1.179
peak=    3.718 closest distance to " CD  ARG A 159 " =    0.789
peak=    3.715 closest distance to " O   HOH Z 383 " =    2.183
peak=    3.715 closest distance to " NH2 ARG A 156 " =    1.112
peak=    3.711 closest distance to " NH1AARG A 145 " =    1.214
peak=    3.695 closest distance to " CD1 LEU A   5 " =    1.391
peak=    3.693 closest distance to " CA  ALA A 295 " =    1.087
peak=    3.689 closest distance to " O   HOH Z 359 " =    1.510
peak=    3.684 closest distance to " O   HOH Z 271 " =    2.630
peak=    3.679 closest distance to " O   HOH Z  78 " =    1.766
peak=    3.677 closest distance to " CG  MET A 185 " =    1.260
peak=    3.672 closest distance to " CB  ASN A  39 " =    0.847
peak=    3.670 closest distance to " O   HOH Z 158 " =    3.085
peak=    3.668 closest distance to " CD1 LEU A  96 " =    0.741
peak=    3.665 closest distance to " CG  LEU A 167 " =    1.114
peak=    3.661 closest distance to " O   HOH Z 172 " =    3.876
peak=    3.660 closest distance to " O   HOH Z 402 " =    1.529
peak=    3.659 closest distance to " CG2 VAL A 257 " =    0.866
peak=    3.651 closest distance to " CD1 LEU A 300 " =    1.195
peak=    3.636 closest distance to " O   HOH Z 214 " =    2.339
peak=    3.635 closest distance to " CB  GLU A  46 " =    0.991
peak=    3.634 closest distance to " CB  ALA A 291 " =    1.357
peak=    3.624 closest distance to " CA  ALA A 160 " =    0.908
peak=    3.608 closest distance to " O   HOH Z 422 " =    2.706
peak=    3.607 closest distance to " O   HOH Z  68 " =    1.809
peak=    3.597 closest distance to " CB  ALA A   9 " =    1.625
peak=    3.595 closest distance to " CG  GLU A  37 " =    0.875
peak=    3.594 closest distance to " O   HOH Z  61 " =    1.534
peak=    3.587 closest distance to " CE1 TYR A 186 " =    1.269
peak=    3.583 closest distance to " O   TRP A 274 " =    1.852
peak=    3.583 closest distance to " O   GLN A 278 " =    1.336
peak=    3.580 closest distance to " CA  VAL A  41 " =    0.821
peak=    3.572 closest distance to " O   HOH Z 245 " =    1.366
peak=    3.565 closest distance to " O   ALA A 165 " =    1.406
peak=    3.563 closest distance to " CA  ASP A 140 " =    1.289
peak=    3.563 closest distance to " CB  LEU A 143 " =    1.236
peak=    3.559 closest distance to " O   HOH Z  19 " =    1.905
peak=    3.559 closest distance to " O   HOH Z 368 " =    3.530
peak=    3.558 closest distance to " CB  ASN A 142 " =    1.095
peak=    3.557 closest distance to " O   HOH Z  20 " =    1.795
peak=    3.552 closest distance to " O   HOH Z 346 " =    1.625
peak=    3.550 closest distance to " CG1 VAL A 296 " =    1.193
peak=    3.549 closest distance to " ND2 ASN A 187 " =    1.456
peak=    3.548 closest distance to " OG BSER A 134 " =    2.799
peak=    3.543 closest distance to " O   HOH Z  57 " =    1.453
peak=    3.536 closest distance to " CG2 THR A 220 " =    0.888
peak=    3.534 closest distance to " O   THR A 220 " =    1.139
peak=    3.534 closest distance to " O   HOH Z 117 " =    2.159
peak=    3.527 closest distance to " O   HOH Z 133 " =    2.284
peak=    3.527 closest distance to " O   HOH Z 128 " =    1.938
peak=    3.523 closest distance to " CB  SER A 216 " =    0.870
peak=    3.516 closest distance to " OD1 ASN A 217 " =    1.617
peak=    3.513 closest distance to " O   HOH Z 227 " =    1.681
peak=    3.510 closest distance to " CE  LYS A  76 " =    0.803
peak=    3.509 closest distance to " O   HOH Z 104 " =    2.727
peak=    3.505 closest distance to " CB  PRO A 198 " =    1.067
peak=    3.502 closest distance to " CA  LYS A 117 " =    1.248
peak=    3.498 closest distance to " O   HOH Z  21 " =    1.761
peak=    3.497 closest distance to " CA  ALA A  21 " =    1.309
peak=    3.492 closest distance to " CA  ARG A  36 " =    1.142
peak=    3.491 closest distance to " CD1 LEU A 222 " =    0.736
peak=    3.485 closest distance to " N   ASN A  39 " =    1.235
peak=    3.467 closest distance to " CZ3 TRP A 266 " =    1.114
peak=    3.466 closest distance to " CB  TYR A 247 " =    0.992
peak=    3.463 closest distance to " O   HOH Z 131 " =    2.485
peak=    3.461 closest distance to " CA  VAL A 125 " =    1.391
peak=    3.453 closest distance to " NH1 ARG A  14 " =    1.066
peak=    3.452 closest distance to " O   HOH Z  88 " =    3.221
peak=    3.445 closest distance to " O   HOH Z 248 " =    1.821
peak=    3.442 closest distance to " CB  ARG A  79 " =    0.919
peak=    3.441 closest distance to " CB  PRO A 243 " =    1.210
peak=    3.440 closest distance to " O   HOH Z 193 " =    2.279
peak=    3.434 closest distance to " CB  GLN A  89 " =    1.101
peak=    3.431 closest distance to " O   HOH Z 391 " =    3.026
peak=    3.429 closest distance to " OG  SER A  22 " =    2.861
peak=    3.428 closest distance to " CB  ASN A 187 " =    1.098
peak=    3.428 closest distance to " O   HOH Z 109 " =    2.360
peak=    3.425 closest distance to " O   HOH Z 327 " =    2.289
peak=    3.422 closest distance to " CA  ILE A 106 " =    0.781
peak=    3.422 closest distance to " N   SER A 135 " =    1.458
peak=    3.416 closest distance to " O   ALA A 158 " =    1.323
peak=    3.416 closest distance to " O   HOH Z 132 " =    2.698
peak=    3.411 closest distance to " CB  ALA A 137 " =    1.119
peak=    3.406 closest distance to " CA  GLU A 152 " =    0.847
peak=    3.403 closest distance to " O   HOH Z 139 " =    4.801
peak=    3.403 closest distance to " O   HOH Z 272 " =    1.948
peak=    3.403 closest distance to " CB  SER A 273 " =    0.875
peak=    3.402 closest distance to " CA  GLN A  88 " =    1.222
peak=    3.402 closest distance to " O   HOH Z  40 " =    1.733
peak=    3.397 closest distance to " O   ASN A  74 " =    1.587
peak=    3.394 closest distance to " O   HOH Z 353 " =    2.757
peak=    3.391 closest distance to " O   HOH Z 426 " =    1.465
peak=    3.391 closest distance to " NZ  LYS A 117 " =    3.197
peak=    3.391 closest distance to " CB  ALA A 248 " =    1.136
peak=    3.390 closest distance to " O   HOH Z 155 " =    3.253
peak=    3.388 closest distance to " N   ILE A  33 " =    0.986
peak=    3.388 closest distance to " CA  MET A  40 " =    1.180
peak=    3.385 closest distance to " CB  ALA A 248 " =    1.358
peak=    3.384 closest distance to " O   HOH Z  49 " =    1.018
peak=    3.383 closest distance to " C   ALA A 299 " =    0.988
peak=    3.379 closest distance to " O   PHE A  61 " =    1.242
peak=    3.371 closest distance to " O   HOH Z 295 " =    1.498
peak=    3.363 closest distance to " O   HOH Z 435 " =    1.958
peak=    3.360 closest distance to " OE1 GLN A  11 " =    1.852
peak=    3.359 closest distance to " C   TYR A 214 " =    1.581
peak=    3.359 closest distance to " CB  SER A  28 " =    1.174
peak=    3.357 closest distance to " O   HOH Z 210 " =    1.018
peak=    3.355 closest distance to " CB  TRP A 150 " =    1.442
peak=    3.351 closest distance to " O   HOH Z 387 " =    3.039
peak=    3.350 closest distance to " CD2 LEU A 297 " =    0.802
peak=    3.344 closest distance to " CG1BVAL A  72 " =    1.809
peak=    3.342 closest distance to " CB  MET A  47 " =    1.001
peak=    3.342 closest distance to " CA  MET A 105 " =    1.044
peak=    3.341 closest distance to " O   HOH Z 326 " =    2.290
peak=    3.340 closest distance to " CG1 ILE A  49 " =    1.587
peak=    3.340 closest distance to " O   HOH Z 141 " =    1.699
peak=    3.339 closest distance to " NZ  LYS A  48 " =    1.338
peak=    3.339 closest distance to " O   HOH Z 313 " =    1.745
peak=    3.338 closest distance to " CG2 ILE A 106 " =    0.905
peak=    3.335 closest distance to " CZ  PHE A  38 " =    1.274
peak=    3.329 closest distance to " O   HOH Z 352 " =    1.822
peak=    3.326 closest distance to " CE2 TYR A  30 " =    0.759
peak=    3.325 closest distance to " CA  ASN A 217 " =    1.327
peak=    3.324 closest distance to " O  BHOH Z 338 " =    2.458
peak=    3.319 closest distance to " CD  ARG A  66 " =    2.527
peak=    3.318 closest distance to " O   HOH Z 180 " =    2.131
peak=    3.317 closest distance to " O   HOH Z 199 " =    1.580
peak=    3.315 closest distance to " O   HOH Z 371 " =    3.068
peak=    3.314 closest distance to " CE1 HIS A 108 " =    1.141
peak=    3.313 closest distance to " CB  GLN A 103 " =    1.055
peak=    3.313 closest distance to " OE1 GLN A  55 " =    1.386
peak=    3.312 closest distance to " OH  TYR A 214 " =    1.207
peak=    3.311 closest distance to " OE1 GLU A   2 " =    1.776
peak=    3.310 closest distance to " O   THR A  31 " =    1.613
peak=    3.304 closest distance to " NH1 ARG A 269 " =    0.741
peak=    3.303 closest distance to " O   HOH Z 193 " =    1.707
peak=    3.303 closest distance to " O   HOH Z   4 " =    1.826
peak=    3.297 closest distance to " CB  SER A 212 " =    1.212
peak=    3.295 closest distance to " O   HOH Z 394 " =    1.437
peak=    3.295 closest distance to " CB  ALA A 256 " =    1.282
peak=    3.292 closest distance to " O   HOH Z 332 " =    1.567
peak=    3.291 closest distance to " CA  THR A 246 " =    1.109
peak=    3.291 closest distance to " CZ3 TRP A  85 " =    0.922
peak=    3.291 closest distance to " O   HOH Z 357 " =    2.080
peak=    3.290 closest distance to " O   HOH Z 197 " =    1.902
peak=    3.284 closest distance to " O   HOH Z 344 " =    3.054
peak=    3.281 closest distance to " CB  ALA A 104 " =    0.794
peak=    3.280 closest distance to " CA  THR A 221 " =    0.867
peak=    3.277 closest distance to " N   ASN A 127 " =    1.237
peak=    3.274 closest distance to " CB  LYS A 117 " =    1.151
peak=    3.272 closest distance to " O   ASP A 200 " =    1.615
peak=    3.270 closest distance to " N   GLY A  98 " =    1.066
peak=    3.270 closest distance to " O   HOH Z 133 " =    1.765
peak=    3.266 closest distance to " CG  GLN A  88 " =    1.056
peak=    3.266 closest distance to " O   HOH Z 125 " =    3.995
peak=    3.265 closest distance to " N   TYR A  15 " =    0.860
peak=    3.257 closest distance to " CB  THR A  31 " =    1.580
peak=    3.256 closest distance to " O   HOH Z 420 " =    5.877
peak=    3.255 closest distance to " O   HOH Z 329 " =    3.923
peak=    3.252 closest distance to " CB  SER A 210 " =    0.889
peak=    3.251 closest distance to " CG2 VAL A  78 " =    1.042
peak=    3.250 closest distance to " ND1 HIS A  81 " =    1.703
peak=    3.249 closest distance to " CA  ALA A 291 " =    0.888
peak=    3.247 closest distance to " CB  GLN A  88 " =    1.264
peak=    3.247 closest distance to " O   HOH Z 273 " =    2.977
peak=    3.244 closest distance to " CG  LEU A 281 " =    1.142
peak=    3.241 closest distance to " CA  ALA A 100 " =    1.100
peak=    3.238 closest distance to " O   HOH Z 193 " =    1.981
peak=    3.237 closest distance to " CB  ALA A  43 " =    0.878
peak=    3.236 closest distance to " CB  THR A  82 " =    1.440
peak=    3.234 closest distance to " O   HOH Z 112 " =    1.633
peak=    3.234 closest distance to " CA  GLU A  46 " =    0.751
peak=    3.231 closest distance to " O   GLY A 203 " =    1.454
peak=    3.231 closest distance to " CG  MET A 188 " =    0.918
peak=    3.226 closest distance to " N   PHE A 130 " =    1.237
peak=    3.226 closest distance to " N   VAL A 126 " =    1.519
peak=    3.226 closest distance to " OG1 THR A 157 " =    1.133
peak=    3.223 closest distance to " NH2BARG A 145 " =    2.155
peak=    3.217 closest distance to " CB  ASN A 285 " =    0.894
peak=    3.209 closest distance to " N   ARG A 190 " =    1.113
peak=    3.208 closest distance to " O   HOH Z 130 " =    2.219
peak=    3.207 closest distance to " CG2 VAL A 197 " =    1.117
peak=    3.202 closest distance to " O   HOH Z  10 " =    1.789
peak=    3.200 closest distance to " CB  ASN A 110 " =    1.307
peak=    3.199 closest distance to " O   HOH Z 420 " =    2.139
peak=    3.199 closest distance to " O   HOH Z 355 " =    1.886
peak=    3.198 closest distance to " O   HOH Z 258 " =    2.129
peak=    3.197 closest distance to " N   SER A 164 " =    1.021
peak=    3.194 closest distance to " CD1 ILE A 106 " =    0.911
peak=    3.192 closest distance to " O   HOH Z 291 " =    1.516
peak=    3.192 closest distance to " CA  LYS A 290 " =    1.239
peak=    3.191 closest distance to " CG ALYS A 290 " =    1.104
peak=    3.188 closest distance to " CA  ILE A  33 " =    1.680
peak=    3.188 closest distance to " CZ3 TRP A  92 " =    1.364
peak=    3.185 closest distance to " CG2 THR A  42 " =    0.839
peak=    3.182 closest distance to " O   HOH Z 421 " =    2.466
peak=    3.179 closest distance to " O   HOH Z 365 " =    2.957
peak=    3.179 closest distance to " OD1 ASP A 231 " =    1.904
peak=    3.176 closest distance to " O   HOH Z 271 " =    2.204
peak=    3.175 closest distance to " CE3 TRP A 150 " =    1.064
peak=    3.170 closest distance to " CB  ALA A 242 " =    0.815
peak=    3.169 closest distance to " O   HOH Z 294 " =    1.610
peak=    3.169 closest distance to " CB  THR A  52 " =    0.909
peak=    3.167 closest distance to " O   HOH Z 281 " =    4.696
peak=    3.166 closest distance to " CA  ALA A 158 " =    1.228
peak=    3.163 closest distance to " O   HOH Z 261 " =    1.698
peak=    3.163 closest distance to " O   HOH Z 417 " =    3.105
peak=    3.160 closest distance to " ND1 HIS A  86 " =    1.657
peak=    3.159 closest distance to " CB  ILE A 120 " =    1.384
peak=    3.159 closest distance to " CB  HIS A 108 " =    0.830
peak=    3.156 closest distance to " O   HOH Z 423 " =    3.175
peak=    3.152 closest distance to " CE2 TYR A 186 " =    0.883
peak=    3.148 closest distance to " CB  PHE A  61 " =    1.438
peak=    3.142 closest distance to " O   HOH Z 327 " =    1.732
peak=    3.138 closest distance to " CG  MET A 185 " =    1.050
peak=    3.133 closest distance to " NE2 HIS A 115 " =    0.972
peak=    3.123 closest distance to " CB  PHE A 204 " =    0.905
peak=    3.120 closest distance to " O   HOH Z 172 " =    3.330
peak=    3.117 closest distance to " CZ3 TRP A 274 " =    4.563
peak=    3.117 closest distance to " O   HOH Z 145 " =    3.338
peak=    3.116 closest distance to " CB  ALA A 100 " =    1.369
peak=    3.114 closest distance to " O   HOH Z 188 " =    1.982
peak=    3.114 closest distance to " O   HOH Z 116 " =    1.838
peak=    3.113 closest distance to " O   HOH Z 298 " =    2.444
peak=    3.101 closest distance to " O   HOH Z 196 " =    1.014
peak=    3.098 closest distance to " CB  ASN A 215 " =    1.248
peak=    3.092 closest distance to " NE2 HIS A 207 " =    1.210
peak=    3.090 closest distance to " O   HOH Z 171 " =    4.219
peak=    3.086 closest distance to " O   HOH Z 430 " =    4.010
peak=    3.080 closest distance to " O   HOH Z 301 " =    1.935
peak=    3.078 closest distance to " O   HOH Z 345 " =    3.466
peak=    3.035 closest distance to " OG  SER A 206 " =    1.203
peak=    3.010 closest distance to " O   HOH Z 256 " =    2.142
peak=    3.010 closest distance to " CB  ASP A 140 " =    0.726
peak=    3.003 closest distance to " CA  ALA A 248 " =    1.257

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 209         
Filter by distance & map next to the model:
   mapped sites are within: 0.807 - 5.613
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 208 from: 209
   mapped sites are within: 0.807 - 5.613

peak=   -5.141 closest distance to " CG2 VAL A 230 " =    0.874
peak=   -4.358 closest distance to " O   HOH Z 210 " =    0.840
peak=   -4.286 closest distance to " CB  ALA A 291 " =    2.575
peak=   -4.241 closest distance to " O   HOH Z 166 " =    1.718
peak=   -4.236 closest distance to " O   HOH Z 266 " =    5.172
peak=   -4.101 closest distance to " O   HOH Z  52 " =    1.738
peak=   -4.083 closest distance to " CD  GLN A  58 " =    1.030
peak=   -4.040 closest distance to " O   HOH Z 351 " =    1.498
peak=   -4.035 closest distance to " O   HOH Z  37 " =    1.992
peak=   -3.995 closest distance to " CG  ASP A 231 " =    0.807
peak=   -3.992 closest distance to " CD  ARG A 156 " =    2.082
peak=   -3.973 closest distance to " NH2 ARG A  66 " =    1.644
peak=   -3.964 closest distance to " C   HIS A 108 " =    1.114
peak=   -3.956 closest distance to " CG1 VAL A 250 " =    2.714
peak=   -3.947 closest distance to " O   HOH Z 177 " =    1.759
peak=   -3.939 closest distance to " CG1 VAL A 112 " =    2.635
peak=   -3.935 closest distance to " O   SER A 271 " =    2.173
peak=   -3.904 closest distance to " CG  ARG A 269 " =    2.463
peak=   -3.888 closest distance to " CE2 TYR A  30 " =    2.771
peak=   -3.882 closest distance to " CD1 PHE A  59 " =    1.887
peak=   -3.874 closest distance to " CA  ASP A 298 " =    1.046
peak=   -3.874 closest distance to " CG1 VAL A 296 " =    1.281
peak=   -3.851 closest distance to " O   HOH Z  10 " =    1.611
peak=   -3.839 closest distance to " O   HOH Z  73 " =    2.177
peak=   -3.830 closest distance to " CD2 LEU A 167 " =    1.796
peak=   -3.829 closest distance to " C   ASN A 285 " =    2.446
peak=   -3.827 closest distance to " CD  ARG A  14 " =    3.110
peak=   -3.820 closest distance to " O   HOH Z 394 " =    1.594
peak=   -3.808 closest distance to " OG  SER A  97 " =    2.331
peak=   -3.807 closest distance to " O   HOH Z 350 " =    1.838
peak=   -3.807 closest distance to " O   HOH Z  11 " =    1.879
peak=   -3.770 closest distance to " O   HOH Z 231 " =    2.157
peak=   -3.732 closest distance to " O   VAL A  67 " =    2.756
peak=   -3.731 closest distance to " OXT GLY A 302 " =    2.962
peak=   -3.718 closest distance to " O   HOH Z  13 " =    1.555
peak=   -3.717 closest distance to " CB  ALA A 161 " =    2.695
peak=   -3.716 closest distance to " CE3 TRP A 150 " =    2.226
peak=   -3.703 closest distance to " CZ3 TRP A 179 " =    1.182
peak=   -3.678 closest distance to " CG2 VAL A 112 " =    2.583
peak=   -3.675 closest distance to " CD2 TYR A 293 " =    1.889
peak=   -3.667 closest distance to " NH2AARG A 275 " =    5.255
peak=   -3.661 closest distance to " CB  PRO A 243 " =    2.729
peak=   -3.652 closest distance to " CD  GLN A 223 " =    1.450
peak=   -3.640 closest distance to " CA  GLY A 203 " =    2.419
peak=   -3.634 closest distance to " O   HOH Z 231 " =    1.827
peak=   -3.628 closest distance to " O   HOH Z  17 " =    1.475
peak=   -3.627 closest distance to " O   HOH Z 185 " =    2.357
peak=   -3.615 closest distance to " CB  ALA A  10 " =    2.218
peak=   -3.612 closest distance to " CA  GLY A 241 " =    3.137
peak=   -3.607 closest distance to " C   ALA A 158 " =    1.258
peak=   -3.603 closest distance to " O   HOH Z 407 " =    3.324
peak=   -3.603 closest distance to " O   HOH Z 290 " =    1.298
peak=   -3.589 closest distance to " O   HOH Z  19 " =    2.234
peak=   -3.584 closest distance to " O   HOH Z 292 " =    4.535
peak=   -3.581 closest distance to " CG  GLU A  53 " =    1.484
peak=   -3.579 closest distance to " N   ALA A 226 " =    2.199
peak=   -3.579 closest distance to " O   HOH Z 165 " =    1.812
peak=   -3.578 closest distance to " CD1 LEU A   5 " =    2.574
peak=   -3.577 closest distance to " O   HOH Z 184 " =    1.428
peak=   -3.576 closest distance to " CG  GLU A 277 " =    1.120
peak=   -3.560 closest distance to " O   PRO A 163 " =    2.169
peak=   -3.554 closest distance to " CD1 LEU A 101 " =    2.533
peak=   -3.546 closest distance to " OE1 GLN A 223 " =    2.127
peak=   -3.545 closest distance to " CG1 VAL A 112 " =    2.926
peak=   -3.539 closest distance to " O   HOH Z 285 " =    1.521
peak=   -3.535 closest distance to " CD1 LEU A  25 " =    2.474
peak=   -3.520 closest distance to " O   HOH Z 128 " =    2.589
peak=   -3.516 closest distance to " O   HOH Z 222 " =    1.540
peak=   -3.512 closest distance to " CG  TRP A 266 " =    1.917
peak=   -3.510 closest distance to " OD1 ASN A 148 " =    1.410
peak=   -3.509 closest distance to " O   HOH Z 252 " =    3.972
peak=   -3.489 closest distance to " CG  MET A 105 " =    0.889
peak=   -3.482 closest distance to " O   HOH Z 426 " =    1.820
peak=   -3.480 closest distance to " N   ALA A  43 " =    2.478
peak=   -3.478 closest distance to " O   HOH Z 234 " =    4.415
peak=   -3.462 closest distance to " OG BSER A 134 " =    1.233
peak=   -3.462 closest distance to " CD  ARG A 139 " =    1.529
peak=   -3.457 closest distance to " O   HOH Z  38 " =    1.344
peak=   -3.455 closest distance to " NE2 GLN A 103 " =    1.828
peak=   -3.451 closest distance to " CA  GLY A 241 " =    2.268
peak=   -3.446 closest distance to " O   HOH Z 241 " =    1.206
peak=   -3.446 closest distance to " O   HOH Z 111 " =    2.107
peak=   -3.442 closest distance to " O   VAL A 189 " =    2.564
peak=   -3.441 closest distance to " O   HOH Z 150 " =    1.795
peak=   -3.438 closest distance to " O   ASP A  27 " =    2.096
peak=   -3.436 closest distance to " C   LEU A 143 " =    1.106
peak=   -3.435 closest distance to " CB  ALA A 248 " =    2.102
peak=   -3.434 closest distance to " O   PRO A 198 " =    1.261
peak=   -3.432 closest distance to " O   HOH Z 114 " =    3.554
peak=   -3.428 closest distance to " CA  GLY A 133 " =    2.356
peak=   -3.426 closest distance to " O   GLY A  17 " =    1.361
peak=   -3.424 closest distance to " C   SER A 206 " =    1.467
peak=   -3.420 closest distance to " O   HOH Z  15 " =    1.584
peak=   -3.419 closest distance to " O   GLY A  80 " =    2.637
peak=   -3.418 closest distance to " ND2 ASN A  45 " =    1.068
peak=   -3.412 closest distance to " ND2BASN A 224 " =    1.816
peak=   -3.407 closest distance to " ND2 ASN A  45 " =    1.920
peak=   -3.406 closest distance to " N   THR A 235 " =    1.252
peak=   -3.395 closest distance to " O   HOH Z 193 " =    2.317
peak=   -3.385 closest distance to " O   HOH Z 308 " =    1.719
peak=   -3.383 closest distance to " N   SER A   3 " =    2.138
peak=   -3.368 closest distance to " CD2 LEU A 300 " =    2.616
peak=   -3.366 closest distance to " CB  ALA A 291 " =    2.359
peak=   -3.366 closest distance to " O   HOH Z 174 " =    2.265
peak=   -3.365 closest distance to " O   HOH Z 264 " =    1.841
peak=   -3.364 closest distance to " ND2 ASN A  45 " =    1.354
peak=   -3.362 closest distance to " CA  ASN A 127 " =    0.960
peak=   -3.360 closest distance to " O   HOH Z 423 " =    1.206
peak=   -3.360 closest distance to " NE2 GLN A  88 " =    1.052
peak=   -3.359 closest distance to " CB  PHE A 192 " =    1.871
peak=   -3.359 closest distance to " O   HOH Z  43 " =    1.612
peak=   -3.356 closest distance to " CA  VAL A 296 " =    1.043
peak=   -3.353 closest distance to " NE2 GLN A 194 " =    1.942
peak=   -3.351 closest distance to " OG  SER A  87 " =    1.643
peak=   -3.347 closest distance to " NH2 ARG A 159 " =    2.323
peak=   -3.345 closest distance to " O   HOH Z 292 " =    1.853
peak=   -3.345 closest distance to " O   HOH Z  60 " =    2.214
peak=   -3.337 closest distance to " O   HOH Z 166 " =    1.961
peak=   -3.329 closest distance to " O   HOH Z 396 " =    1.727
peak=   -3.327 closest distance to " OD2 ASP A 171 " =    1.847
peak=   -3.324 closest distance to " NH2 ARG A  79 " =    1.542
peak=   -3.322 closest distance to " O   HOH Z 236 " =    1.503
peak=   -3.317 closest distance to " CD2 PHE A  61 " =    2.026
peak=   -3.317 closest distance to " CB  PRO A 163 " =    2.660
peak=   -3.311 closest distance to " O   HOH Z 353 " =    2.274
peak=   -3.311 closest distance to " CB  VAL A 230 " =    1.076
peak=   -3.300 closest distance to " SG ACYS A 201 " =    1.075
peak=   -3.296 closest distance to " O   GLY A 203 " =    2.282
peak=   -3.296 closest distance to " O   HOH Z 275 " =    1.569
peak=   -3.296 closest distance to " CG  ASP A  50 " =    2.355
peak=   -3.292 closest distance to " CD  LYS A 289 " =    2.469
peak=   -3.292 closest distance to " ND2 ASN A  60 " =    1.864
peak=   -3.290 closest distance to " OG ASER A 134 " =    1.333
peak=   -3.288 closest distance to " CG  PRO A 243 " =    1.708
peak=   -3.288 closest distance to " N   TYR A  68 " =    2.828
peak=   -3.282 closest distance to " CG  GLN A  88 " =    0.931
peak=   -3.278 closest distance to " CA  ALA A   8 " =    1.558
peak=   -3.277 closest distance to " OD1 ASN A 187 " =    1.486
peak=   -3.276 closest distance to " NE2 GLN A  58 " =    2.744
peak=   -3.275 closest distance to " O   HOH Z 114 " =    1.582
peak=   -3.274 closest distance to " OG1 THR A  82 " =    1.480
peak=   -3.274 closest distance to " CB  ALA A 256 " =    2.801
peak=   -3.274 closest distance to " O   HOH Z  44 " =    2.154
peak=   -3.265 closest distance to " N   SER A 212 " =    1.877
peak=   -3.262 closest distance to " O   HOH Z 423 " =    2.216
peak=   -3.262 closest distance to " OE1 GLN A  88 " =    0.982
peak=   -3.262 closest distance to " CD  PRO A 213 " =    2.222
peak=   -3.256 closest distance to " O   HOH Z 106 " =    1.987
peak=   -3.256 closest distance to " O   HOH Z 431 " =    2.107
peak=   -3.248 closest distance to " O   HOH Z  94 " =    2.043
peak=   -3.246 closest distance to " OG  SER A  63 " =    1.158
peak=   -3.242 closest distance to " N   SER A 134 " =    1.176
peak=   -3.236 closest distance to " O   HOH Z 136 " =    2.339
peak=   -3.233 closest distance to " CB  ALA A 114 " =    2.561
peak=   -3.230 closest distance to " CB  ASP A 132 " =    2.336
peak=   -3.230 closest distance to " CB  GLN A  11 " =    1.567
peak=   -3.226 closest distance to " NH1 ARG A 195 " =    2.311
peak=   -3.225 closest distance to " CB  LEU A  83 " =    2.343
peak=   -3.223 closest distance to " CZ  TYR A 169 " =    1.702
peak=   -3.220 closest distance to " CG  ASN A 252 " =    1.375
peak=   -3.220 closest distance to " SG  CYS A 260 " =    2.457
peak=   -3.218 closest distance to " O   HOH Z 189 " =    1.972
peak=   -3.217 closest distance to " CA  VAL A 197 " =    1.101
peak=   -3.216 closest distance to " CE BMET A  47 " =    2.010
peak=   -3.210 closest distance to " O   HOH Z 191 " =    5.613
peak=   -3.210 closest distance to " O   VAL A  67 " =    2.713
peak=   -3.206 closest distance to " CD  GLU A 236 " =    1.056
peak=   -3.201 closest distance to " CD1 LEU A   5 " =    1.800
peak=   -3.200 closest distance to " CB  ALA A  43 " =    2.643
peak=   -3.196 closest distance to " O   HOH Z 102 " =    1.600
peak=   -3.194 closest distance to " OG1 THR A  82 " =    1.555
peak=   -3.186 closest distance to " N   VAL A 230 " =    1.058
peak=   -3.185 closest distance to " C   THR A 279 " =    1.221
peak=   -3.182 closest distance to " O   HOH Z 105 " =    2.073
peak=   -3.179 closest distance to " OE2 GLU A  53 " =    1.280
peak=   -3.179 closest distance to " O   ASP A 270 " =    1.593
peak=   -3.177 closest distance to " O   HOH Z 166 " =    1.583
peak=   -3.176 closest distance to " CG  ARG A 259 " =    2.558
peak=   -3.174 closest distance to " O   HOH Z 348 " =    2.295
peak=   -3.173 closest distance to " CD2 PHE A  61 " =    2.508
peak=   -3.172 closest distance to " C   GLY A  13 " =    0.966
peak=   -3.172 closest distance to " O   ALA A  10 " =    1.735
peak=   -3.168 closest distance to " CZ2 TRP A 274 " =    1.119
peak=   -3.164 closest distance to " O   GLY A 211 " =    1.491
peak=   -3.155 closest distance to " O   HOH Z   6 " =    1.768
peak=   -3.154 closest distance to " O   GLY A  80 " =    2.319
peak=   -3.148 closest distance to " O   HOH Z 149 " =    2.144
peak=   -3.147 closest distance to " O   HOH Z 313 " =    1.310
peak=   -3.146 closest distance to " O   HOH Z 251 " =    4.923
peak=   -3.144 closest distance to " O   HOH Z 133 " =    1.366
peak=   -3.141 closest distance to " CH2 TRP A 177 " =    2.154
peak=   -3.137 closest distance to " CG2 VAL A 189 " =    2.150
peak=   -3.132 closest distance to " C   ASP A 270 " =    1.236
peak=   -3.128 closest distance to " OG  SER A  26 " =    1.462
peak=   -3.118 closest distance to " O   HOH Z 389 " =    1.899
peak=   -3.114 closest distance to " N   ILE A 120 " =    1.086
peak=   -3.110 closest distance to " O   ALA A 100 " =    2.365
peak=   -3.108 closest distance to " CD1 LEU A 101 " =    2.656
peak=   -3.105 closest distance to " OG BSER A 134 " =    1.996
peak=   -3.102 closest distance to " O   HOH Z 397 " =    1.141
peak=   -3.089 closest distance to " NE  ARG A 138 " =    2.083
peak=   -3.087 closest distance to " O   HOH Z 392 " =    1.892
peak=   -3.071 closest distance to " CG1 VAL A  78 " =    2.660
peak=   -3.069 closest distance to " CA  SER A  62 " =    2.485
peak=   -3.061 closest distance to " O   ALA A  34 " =    2.624
peak=   -3.053 closest distance to " O   HOH Z 150 " =    2.134
peak=   -3.050 closest distance to " CG2 VAL A 296 " =    1.583
peak=   -3.019 closest distance to " O   HOH Z 110 " =    1.526

================= 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    :  0.4706 0.4518   6.271130e+00   6.250434e+00
   1_bss:  0.4638 0.4422   6.266178e+00   6.241837e+00
   1_xyz:  0.3705 0.3923   6.130488e+00   6.164032e+00
   1_adp:  0.3231 0.3626   6.034765e+00   6.119893e+00
   1_occ:  0.3227 0.3626   6.033807e+00   6.120637e+00
   2_bss:  0.3209 0.3607   6.034703e+00   6.119388e+00
   2_xyz:  0.2266 0.2765   5.741894e+00   5.897927e+00
   2_adp:  0.2046 0.2531   5.652562e+00   5.824015e+00
   2_occ:  0.2043 0.2532   5.651903e+00   5.823847e+00
   3_bss:  0.2020 0.2522   5.652095e+00   5.822468e+00
   3_xyz:  0.1491 0.1910   5.370658e+00   5.576900e+00
   3_adp:  0.1376 0.1808   5.306987e+00   5.525270e+00
   3_occ:  0.1375 0.1807   5.306434e+00   5.524878e+00
   4_bss:  0.1375 0.1808   5.306179e+00   5.523682e+00
   4_xyz:  0.1227 0.1684   5.221941e+00   5.454053e+00
   4_adp:  0.1213 0.1673   5.211408e+00   5.444442e+00
   4_occ:  0.1212 0.1672   5.211179e+00   5.444378e+00
   5_bss:  0.1212 0.1672   5.210965e+00   5.444206e+00
   5_xyz:  0.1227 0.1669   5.218692e+00   5.443779e+00
   5_adp:  0.1207 0.1686   5.216167e+00   5.453370e+00
   5_occ:  0.1206 0.1686   5.215902e+00   5.453136e+00
   5_bss:  0.1206 0.1685   5.215852e+00   5.453196e+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:  0.300  20.000   7.200   9.771   7.362   0.000   0.000   0.000
   1_xyz:  0.300  20.000   7.200   9.771   7.362   0.000   0.000   0.000
   1_adp:  0.300  20.000   7.200   9.771   7.362   0.000   0.000   0.000
   1_occ:  0.300  20.000   7.200   9.771   7.362   0.000   0.000   0.000
   2_bss:  0.322  53.959   4.641   6.782   4.953   0.000   0.000   0.000
   2_xyz:  0.322  53.959   4.641   6.782   4.953   0.000   0.000   0.000
   2_adp:  0.322  53.959   4.641   6.782   4.953   0.000   0.000   0.000
   2_occ:  0.322  53.959   4.641   6.782   4.953   0.000   0.000   0.000
   3_bss:  0.318  68.533   2.853   3.928   3.677   0.000   0.000   0.000
   3_xyz:  0.318  68.533   2.853   3.928   3.677   0.000   0.000   0.000
   3_adp:  0.318  68.533   2.853   3.928   3.677   0.000   0.000   0.000
   3_occ:  0.318  68.533   2.853   3.928   3.677   0.000   0.000   0.000
   4_bss:  0.329  65.025   2.342   3.016   3.409   0.000   0.000   0.000
   4_xyz:  0.329  65.025   2.342   3.016   3.409   0.000   0.000   0.000
   4_adp:  0.329  65.025   2.342   3.016   3.409   0.000   0.000   0.000
   4_occ:  0.329  65.025   2.342   3.016   3.409   0.000   0.000   0.000
   5_bss:  0.329  65.025   2.325   2.814   3.483   0.000   0.000   0.000
   5_xyz:  0.329  65.025   2.325   2.814   3.483   0.000   0.000   0.000
   5_adp:  0.329  65.025   2.325   2.814   3.483   0.000   0.000   0.000
   5_occ:  0.329  65.025   2.325   2.814   3.483   0.000   0.000   0.000
   5_bss:  0.319  65.126  -0.519  -0.101   0.619   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.872 0.4724  0.5279    61971.469
   1_bss:  53.603 0.4745  0.6710    60405.663
   1_xyz:  44.896 0.5821  0.8014    44058.016
   1_adp:  40.150 0.6404  0.8966    37517.995
   1_occ:  40.179 0.6400  0.8956    37584.501
   2_bss:  39.994 0.6422  0.8210    37381.816
   2_xyz:  28.432 0.7739  0.9675    20032.021
   2_adp:  25.311 0.8083  0.9962    16704.480
   2_occ:  25.323 0.8082  0.9953    16706.576
   3_bss:  25.231 0.8093  0.9290    16664.825
   3_xyz:  18.088 0.8796  0.9749     9326.702
   3_adp:  16.776 0.8917  0.9773     8367.344
   3_occ:  16.761 0.8918  0.9772     8365.058
   4_bss:  16.738 0.8920  0.9579     8340.581
   4_xyz:  15.233 0.9051  0.9640     7217.694
   4_adp:  14.971 0.9075  0.9618     7129.941
   4_occ:  14.970 0.9076  0.9616     7129.258
   5_bss:  14.964 0.9076  0.9602     7126.880
   5_xyz:  14.927 0.9081  0.9593     7087.175
   5_adp:  15.196 0.9057  0.9516     7203.453
   5_occ:  15.191 0.9058  0.9516     7200.686
   5_bss:  15.194 0.9058  0.9572     7203.125
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.093   5.4443e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.093   5.4443e+01
   1_xyz:   1.684  0.013  0.108 17.965  0.006  4.112   1.4018e-01
   1_adp:   1.684  0.013  0.108 17.965  0.006  4.112   1.4018e-01
   1_occ:   1.684  0.013  0.108 17.965  0.006  4.112   1.4018e-01
   2_bss:   1.684  0.013  0.108 17.965  0.006  4.112   1.4018e-01
   2_xyz:   1.235  0.010  0.079 16.264  0.005  4.112   9.1237e-02
   2_adp:   1.235  0.010  0.079 16.264  0.005  4.112   9.1237e-02
   2_occ:   1.235  0.010  0.079 16.264  0.005  4.112   9.1237e-02
   3_bss:   1.235  0.010  0.079 16.264  0.005  4.112   9.1237e-02
   3_xyz:   1.175  0.010  0.089 15.818  0.004  4.134   8.0668e-02
   3_adp:   1.175  0.010  0.089 15.818  0.004  4.134   8.0668e-02
   3_occ:   1.175  0.010  0.089 15.818  0.004  4.134   8.0668e-02
   4_bss:   1.175  0.010  0.089 15.818  0.004  4.134   8.0668e-02
   4_xyz:   1.134  0.010  0.091 15.762  0.004  4.116   7.8971e-02
   4_adp:   1.134  0.010  0.091 15.762  0.004  4.116   7.8971e-02
   4_occ:   1.134  0.010  0.091 15.762  0.004  4.116   7.8971e-02
   5_bss:   1.134  0.010  0.091 15.762  0.004  4.116   7.8971e-02
   5_xyz:   0.991  0.008  0.079 15.199  0.003  4.117   6.1464e-02
   5_adp:   0.991  0.008  0.079 15.199  0.003  4.117   6.1464e-02
   5_occ:   0.991  0.008  0.079 15.199  0.003  4.117   6.1464e-02
   5_bss:   0.991  0.008  0.079 15.199  0.003  4.117   6.1464e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0592e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0592e+00
   1_xyz:  14.281  0.169  0.459 86.622  0.039  2.260   1.0458e-01
   1_adp:  14.281  0.169  0.459 86.622  0.039  2.260   1.0458e-01
   1_occ:  14.281  0.169  0.459 86.622  0.039  2.260   1.0458e-01
   2_bss:  14.281  0.169  0.459 86.622  0.039  2.260   1.0458e-01
   2_xyz:   9.209  0.109  0.271 87.834  0.040  2.148   1.4567e-01
   2_adp:   9.209  0.109  0.271 87.834  0.040  2.148   1.4567e-01
   2_occ:   9.209  0.109  0.271 87.834  0.040  2.148   1.4567e-01
   3_bss:   9.209  0.109  0.271 87.834  0.040  2.148   1.4567e-01
   3_xyz:   7.597  0.070  0.511 83.155  0.042  2.303   7.0524e-02
   3_adp:   7.597  0.070  0.511 83.155  0.042  2.303   7.0524e-02
   3_occ:   7.597  0.070  0.511 83.155  0.042  2.303   7.0524e-02
   4_bss:   7.597  0.070  0.511 83.155  0.042  2.303   7.0524e-02
   4_xyz:   7.553  0.049  0.642 83.185  0.033  2.358   5.2714e-02
   4_adp:   7.553  0.049  0.642 83.185  0.033  2.358   5.2714e-02
   4_occ:   7.553  0.049  0.642 83.185  0.033  2.358   5.2714e-02
   5_bss:   7.553  0.049  0.642 83.185  0.033  2.358   5.2714e-02
   5_xyz:   7.655  0.043  0.472 81.144  0.035  2.412   3.8435e-02
   5_adp:   7.655  0.043  0.472 81.144  0.035  2.412   3.8435e-02
   5_occ:   7.655  0.043  0.472 81.144  0.035  2.412   3.8435e-02
   5_bss:   7.655  0.043  0.472 81.144  0.035  2.412   3.8435e-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: 105.90   0.00  12.17  75.06   0.00   9.45 105.90   0.00  26.97
   1_occ: 105.90   0.00  12.17  75.06   0.00   9.45 105.90   0.00  26.97
   2_bss: 105.90   0.00  12.17  75.06   0.00   9.45 105.90   0.00  26.97
   2_xyz: 105.90   0.00  12.17  75.06   0.00   9.45 105.90   0.00  26.97
   2_adp:  99.79   0.00  12.37  74.73   0.00   8.60  99.79   0.00  32.90
   2_occ:  99.79   0.00  12.37  74.73   0.00   8.60  99.79   0.00  32.90
   3_bss:  99.79   0.00  12.37  74.73   0.00   8.60  99.79   0.00  32.90
   3_xyz:  99.79   0.00  12.37  74.73   0.00   8.60  99.79   0.00  32.90
   3_adp:  90.53   0.00  12.55  77.97   0.00   8.30  90.53   0.47  35.66
   3_occ:  90.53   0.00  12.55  77.97   0.00   8.30  90.53   0.47  35.66
   4_bss:  90.53   0.00  12.55  77.97   0.00   8.30  90.53   0.47  35.66
   4_xyz:  90.53   0.00  12.55  77.97   0.00   8.30  90.53   0.47  35.66
   4_adp:  88.26   0.00  12.34  77.79   0.00   8.14  88.26   1.27  35.21
   4_occ:  88.26   0.00  12.34  77.79   0.00   8.14  88.26   1.27  35.21
   5_bss:  88.26   0.00  12.34  77.79   0.00   8.14  88.26   1.27  35.21
   5_xyz:  88.26   0.00  12.34  77.79   0.00   8.14  88.26   1.27  35.21
   5_adp:  91.45   0.00  12.77  91.45   0.00   8.24  87.92   1.49  37.42
   5_occ:  91.45   0.00  12.77  91.45   0.00   8.24  87.92   1.49  37.42
   5_bss:  94.49   3.04  15.82  94.49   3.04  11.29  90.96   4.54  40.47
------------------------------------------------------------------------
 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:    1.214    0.020    0.412
   1_adp:    1.214    0.020    0.412
   1_occ:    1.214    0.020    0.412
   2_bss:    1.214    0.020    0.412
   2_xyz:    1.608    0.022    0.595
   2_adp:    1.608    0.022    0.595
   2_occ:    1.608    0.022    0.595
   3_bss:    1.608    0.022    0.595
   3_xyz:    1.512    0.020    0.665
   3_adp:    1.512    0.020    0.665
   3_occ:    1.512    0.020    0.665
   4_bss:    1.512    0.020    0.665
   4_xyz:    1.523    0.061    0.699
   4_adp:    1.523    0.061    0.699
   4_occ:    1.523    0.061    0.699
   5_bss:    1.523    0.061    0.699
   5_xyz:    1.671    0.070    0.708
   5_adp:    1.671    0.070    0.708
   5_occ:    1.671    0.070    0.708
   5_bss:    1.671    0.070    0.708
------------------------------------------------------------------------

CPU time actual refinement: 323.41


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1062/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_1062/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1062/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1062/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1062/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 323.26 
  Macro-tasks:
    bulk solvent and scale       = 41.53  
    individual site refinement   = 127.67 
    weights calculation          = 30.61  
    collect and process          = 6.36   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 206.28 
  Micro-tasks:
    mask                            = 1.74   
    f_calc                          = 98.77  
    alpha_beta                      = 8.15   
    target                          = 1.12   
    gradients_wrt_atomic_parameters = 108.73 
    fmodel                         = 7.42   
    r_factors                      = 0.26   
    phase_errors                   = 10.72  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 237.14 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.604 micro seconds
Total CPU time: 5.61 minutes
from_scatterers_fft:    652 calls, 98.53 s
gradients_fft:          596 calls, 96.14 s

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

# Date 2008-01-16 Time 03:06:26 PST -0800 (1200481586.50 s)
Start R-work = 0.4706, R-free = 0.4518 (no bulk solvent and anisotropic scale)
Final R-work = 0.1362, R-free = 0.1833 (no bulk solvent and anisotropic scale)

Start R-work = 0.4638, R-free = 0.4422
Final R-work = 0.1206, R-free = 0.1685