# Date 2008-01-16 Time 01:34:34 PST -0800 (1200476074.38 s)
#phil __OFF__

Command line arguments: "../486.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 28067
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 486

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 45.7567, 85.0941, 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: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 45.7567, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8779 1.95275
Completeness in resolution range: 0.961235
Completeness with d_max=infinity: 0.958319

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8779
                             d_min =   1.9527

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 45.7567, 85.0941, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8779 1.95275
Completeness in resolution range: 0.961235
Completeness with d_max=infinity: 0.958319

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8783 -  4.1789 [2139/2164]  1926   213  10.0%
  bin  2:  4.1789 -  3.3291 [2049/2069]  1844   205  10.0%
  bin  3:  3.3291 -  2.9119 [2045/2064]  1840   205  10.0%
  bin  4:  2.9119 -  2.6473 [2007/2037]  1807   200  10.0%
  bin  5:  2.6473 -  2.4585 [2014/2033]  1818   196   9.7%
  bin  6:  2.4585 -  2.3141 [1978/2003]  1772   206  10.4%
  bin  7:  2.3141 -  2.1986 [1978/2006]  1780   198  10.0%
  bin  8:  2.1986 -  2.1031 [1970/2006]  1772   198  10.1%
  bin  9:  2.1031 -  2.0224 [1970/2012]  1777   193   9.8%
  bin 10:  2.0224 -  1.9527 [1439/1985]  1294   145  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_486/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:
        1.66 -     2.31: 39
        2.31 -     2.96: 1757
        2.96 -     3.60: 4676
        3.60 -     4.25: 9373
        4.25 -     4.90: 13121
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 271 " - " O   HOH Z 342 "  1.661 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.711 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.737 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  ... (remaining 28961 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_486/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_486/model_refine_001.geo

CPU time processing inputs: 9.59


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 45.75675 85.09415 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5025   r_free= 0.5044   ksol= 0.00   Bsol= 0.00   scale= 0.786    |
|                                                                             |
| 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:   0.89 A                  |
| x-ray target function (ml) for work reflections: 6.303427                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8783 -  4.6612 0.99   1390  155 0.4359 0.4489      6.6501      6.7231|
|  2:  4.6612 -  3.7187 0.99   1341  150 0.4530 0.4205      6.8633      6.8013|
|  3:  3.7187 -  3.2543 0.99   1313  141 0.4728 0.4621       6.728      6.7843|
|  4:  3.2543 -  2.9593 0.99   1304  152 0.4935 0.4560      6.5765      6.4945|
|  5:  2.9593 -  2.7486 0.99   1299  144 0.5253 0.5658      6.3881      6.4206|
|  6:  2.7486 -  2.5874 0.99   1295  137 0.5244 0.5752      6.3012       6.217|
|  7:  2.5874 -  2.4585 0.99   1293  140 0.5324 0.4884      6.2565      6.2453|
|  8:  2.4585 -  2.3519 0.98   1263  148 0.5510 0.5333       6.195      6.1683|
|  9:  2.3519 -  2.2617 0.98   1257  145 0.5278 0.5705      6.1304      6.1739|
| 10:  2.2617 -  2.1839 1.00   1295  138 0.5254 0.5501      6.1183      6.1279|
| 11:  2.1839 -  2.1158 0.98   1268  140 0.5232 0.5010      6.0431      6.0763|
| 12:  2.1158 -  2.0555 0.98   1255  141 0.5102 0.5687      5.9892      6.0186|
| 13:  2.0555 -  2.0015 0.99   1274  139 0.5493 0.5295       5.888      5.8342|
| 14:  2.0015 -  1.9527 0.61    783   89 0.5580 0.4779      5.8631      5.7999|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8783 -  4.6612  1390   155  0.56  45.77   0.78     0.63     114400.04|
|  2:  4.6612 -  3.7187  1341   150  0.62  42.13   0.85     0.72     143816.90|
|  3:  3.7187 -  3.2543  1313   141  0.52  50.28   0.84     0.67     144094.88|
|  4:  3.2543 -  2.9593  1304   152  0.43  57.37   0.80     0.54     123539.56|
|  5:  2.9593 -  2.7486  1299   144  0.32  66.26   0.74     0.40      97713.19|
|  6:  2.7486 -  2.5874  1295   137  0.29  68.38   0.72     0.33      82813.63|
|  7:  2.5874 -  2.4585  1293   140  0.23  72.86   0.73     0.27      75350.21|
|  8:  2.4585 -  2.3519  1263   148  0.21  74.12   0.73     0.26      69486.57|
|  9:  2.3519 -  2.2617  1257   145  0.21  74.02   0.72     0.26      63032.52|
| 10:  2.2617 -  2.1839  1295   138  0.25  71.41   0.77     0.30      54890.99|
| 11:  2.1839 -  2.1158  1268   140  0.23  72.91   0.77     0.29      53363.27|
| 12:  2.1158 -  2.0555  1255   141  0.21  74.22   0.81     0.28      50070.79|
| 13:  2.0555 -  2.0015  1274   139  0.19  76.05   0.73     0.26      42973.17|
| 14:  2.0015 -  1.9527   783    89  0.27  70.22   0.73     0.30      30966.25|
|alpha:            min =        0.26 max =            0.72 mean =         0.40|
|beta:             min =    30966.25 max =       144094.88 mean =     84023.98|
|figures of merit: min =        0.00 max =            1.00 mean =         0.33|
|phase err.(work): min =        0.00 max =           89.98 mean =        65.03|
|phase err.(test): min =        0.00 max =           90.00 mean =        65.25|
|-----------------------------------------------------------------------------|

============================== 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 = 24.940693             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.896   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.411821              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 82.648   (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:        7 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       35 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      183 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      733 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1554 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2703 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     4029 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5167 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6690 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7923 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       52.744 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.087    4.900  1.196 |       2.602 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.367)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

                ----------Modify initial isotropic ADP----------               

Randomizing
|-ADP statistics (Wilson B = 11.367)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5061   r_free= 0.5056   ksol= 0.00   Bsol= 0.00   scale= 0.756    |
|                                                                             |
| 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:   0.90 A                  |
| x-ray target function (ml) for work reflections: 6.303959                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4942   r_free= 0.4924   ksol= 0.39   Bsol= 2.24   scale= 0.966    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.13,9.30,7.81,0.00,0.00,0.00); trace/3= 7.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.90 A                  |
| x-ray target function (ml) for work reflections: 6.298952                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 19.645854             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.659   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.207806              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.844   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4942      final r-factor (work) = 0.4398          |
| start r-factor (free) = 0.4924      final r-factor (free) = 0.4686          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 114.6293 = 19.65 * 0.50 * 6.3001 + 1.00 * 52.7436                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 61.6226 = 19.65 * 0.50 * 6.2584 + 1.00 * 0.1471                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4398      final r-factor (work) = 0.4014          |
| start r-factor (free) = 0.4686      final r-factor (free) = 0.4643          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.8317 = 2.21 * 1.00 * 6.2584 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 13.7422 = 2.21 * 1.00 * 6.2133 + 1.00 * 0.0245                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.367)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.58  15.95    None  None   None       |
|    all(noH): 2823   0      0.00    100.58  15.95    None  None   None       |
|    Sol.    : 438    0      0.00    100.58  22.82    None  None   None       |
|    Mac.    : 2385   0      0.00    96.24   14.69    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 -  10.058: 1118   |   5:    50.291 -  60.349:   50        |
|      1:    10.058 -  20.116:  880   |   6:    60.349 -  70.407:   13        |
|      2:    20.116 -  30.174:  445   |   7:    70.407 -  80.465:    1        |
|      3:    30.174 -  40.233:  221   |   8:    80.465 -  90.523:    3        |
|      4:    40.233 -  50.291:   89   |   9:    90.523 - 100.581:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4014 r_free = 0.4643             target_work(ml) = 6.205         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4010 r_free = 0.4645             target_work(ml) = 6.205         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4010   r_free= 0.4645   ksol= 0.39   Bsol= 2.24   scale= 1.098    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.13,9.30,7.81,0.00,0.00,0.00); trace/3= 7.75                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.204665                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3995   r_free= 0.4614   ksol= 0.38   Bsol= 32.66   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.26,5.53,4.89,0.00,0.00,0.00); trace/3= 4.56                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.73 A                  |
| x-ray target function (ml) for work reflections: 6.204487                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.636728             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.489  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.897133              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.101  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3995      final r-factor (work) = 0.3575          |
| start r-factor (free) = 0.4614      final r-factor (free) = 0.4280          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 33.1686 = 10.64 * 0.50 * 6.2090 + 1.00 * 0.1471                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.8487 = 10.64 * 0.50 * 6.1600 + 1.00 * 0.0877                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3575      final r-factor (work) = 0.3449          |
| start r-factor (free) = 0.4280      final r-factor (free) = 0.4195          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5513 = 0.90 * 1.00 * 6.1600 + 1.00 * 0.0249                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5011 = 0.90 * 1.00 * 6.1153 + 1.00 * 0.0149                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.367)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.23  15.41    None  None   None       |
|    all(noH): 2823   0      0.00    105.23  15.41    None  None   None       |
|    Sol.    : 438    0      0.00    105.23  24.59    None  None   None       |
|    Mac.    : 2385   0      0.00    99.22   13.73    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 -  10.523: 1151   |   5:    52.616 -  63.140:   20        |
|      1:    10.523 -  21.047:  941   |   6:    63.140 -  73.663:    7        |
|      2:    21.047 -  31.570:  477   |   7:    73.663 -  84.186:    1        |
|      3:    31.570 -  42.093:  168   |   8:    84.186 -  94.709:    2        |
|      4:    42.093 -  52.616:   53   |   9:    94.709 - 105.233:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3449 r_free = 0.4195             target_work(ml) = 6.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3448 r_free = 0.4195             target_work(ml) = 6.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3448   r_free= 0.4195   ksol= 0.38   Bsol= 32.66   scale= 1.063   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.26,5.53,4.89,0.00,0.00,0.00); trace/3= 4.56                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.103640                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3447   r_free= 0.4188   ksol= 0.37   Bsol= 54.42   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.02,3.45,3.24,0.00,0.00,0.00); trace/3= 2.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.105027                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.455388              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.065  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.039336              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 152.518  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3447      final r-factor (work) = 0.3003          |
| start r-factor (free) = 0.4188      final r-factor (free) = 0.3773          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.8781 = 7.46 * 0.50 * 6.1139 + 1.00 * 0.0873                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.6509 = 7.46 * 0.50 * 6.0536 + 1.00 * 0.0849                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3003      final r-factor (work) = 0.2790          |
| start r-factor (free) = 0.3773      final r-factor (free) = 0.3726          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 18.4136 = 3.04 * 1.00 * 6.0536 + 1.00 * 0.0146                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 18.1786 = 3.04 * 1.00 * 5.9723 + 1.00 * 0.0268                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.367)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    127.46  17.50    None  None   None       |
|    all(noH): 2823   0      0.00    127.46  17.50    None  None   None       |
|    Sol.    : 438    0      0.00    127.46  33.83    None  None   None       |
|    Mac.    : 2385   0      0.00    118.65  14.50    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  12.746: 1388   |   5:    63.728 -  76.474:   35        |
|      1:    12.746 -  25.491:  757   |   6:    76.474 -  89.219:   10        |
|      2:    25.491 -  38.237:  366   |   7:    89.219 - 101.965:    5        |
|      3:    38.237 -  50.982:  175   |   8:   101.965 - 114.710:    1        |
|      4:    50.982 -  63.728:   83   |   9:   114.710 - 127.456:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2790 r_free = 0.3726             target_work(ml) = 5.964         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2788 r_free = 0.3724             target_work(ml) = 5.964         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2788   r_free= 0.3724   ksol= 0.37   Bsol= 54.42   scale= 1.053   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.02,3.45,3.24,0.00,0.00,0.00); trace/3= 2.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 5.963958                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2790   r_free= 0.3714   ksol= 0.36   Bsol= 62.19   scale= 1.035   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.67,2.27,2.77,0.00,0.00,0.00); trace/3= 2.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 5.962628                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.114067              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 108.844  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.362342              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.749  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2790      final r-factor (work) = 0.2404          |
| start r-factor (free) = 0.3714      final r-factor (free) = 0.3230          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.3382 = 6.11 * 0.50 * 5.9709 + 1.00 * 0.0849                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.1318 = 6.11 * 0.50 * 5.9077 + 1.00 * 0.0716                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2404      final r-factor (work) = 0.2261          |
| start r-factor (free) = 0.3230      final r-factor (free) = 0.2928          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1678 = 0.36 * 1.00 * 5.9077 + 1.00 * 0.0271                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1170 = 0.36 * 1.00 * 5.8130 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.367)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    123.40  15.15    None  None   None       |
|    all(noH): 2823   0      0.00    123.40  15.15    None  None   None       |
|    Sol.    : 438    0      0.00    123.40  34.49    None  None   None       |
|    Mac.    : 2385   0      0.00    112.41  11.60    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 -  12.340: 1629   |   5:    61.700 -  74.040:   18        |
|      1:    12.340 -  24.680:  682   |   6:    74.040 -  86.380:    8        |
|      2:    24.680 -  37.020:  273   |   7:    86.380 -  98.719:    2        |
|      3:    37.020 -  49.360:  146   |   8:    98.719 - 111.059:    1        |
|      4:    49.360 -  61.700:   61   |   9:   111.059 - 123.399:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2261 r_free = 0.2928             target_work(ml) = 5.771         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2257 r_free = 0.2918             target_work(ml) = 5.769         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2257   r_free= 0.2918   ksol= 0.36   Bsol= 62.19   scale= 1.043   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.67,2.27,2.77,0.00,0.00,0.00); trace/3= 2.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.768662                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2255   r_free= 0.2895   ksol= 0.34   Bsol= 47.15   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.00,1.28,2.06,0.00,0.00,0.00); trace/3= 1.45                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.766768                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.157976              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.181  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.246938              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.210  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2255      final r-factor (work) = 0.1752          |
| start r-factor (free) = 0.2895      final r-factor (free) = 0.2318          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.0599 = 5.16 * 0.50 * 5.8117 + 1.00 * 0.0716                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.6687 = 5.16 * 0.50 * 5.6599 + 1.00 * 0.0720                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1752      final r-factor (work) = 0.1552          |
| start r-factor (free) = 0.2318      final r-factor (free) = 0.2169          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.7280 = 2.25 * 1.00 * 5.6599 + 1.00 * 0.0106                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.3118 = 2.25 * 1.00 * 5.4730 + 1.00 * 0.0142                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.367)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    122.87  15.55    None  None   None       |
|    all(noH): 2823   0      0.00    122.87  15.55    None  None   None       |
|    Sol.    : 438    0      2.79    122.87  42.10    None  None   None       |
|    Mac.    : 2385   0      0.00    116.74  10.68    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 -  12.287: 1780   |   5:    61.433 -  73.719:   53        |
|      1:    12.287 -  24.573:  523   |   6:    73.719 -  86.006:   16        |
|      2:    24.573 -  36.860:  179   |   7:    86.006 -  98.292:    2        |
|      3:    36.860 -  49.146:  143   |   8:    98.292 - 110.579:    1        |
|      4:    49.146 -  61.433:  123   |   9:   110.579 - 122.865:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1552 r_free = 0.2169             target_work(ml) = 5.438         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1550 r_free = 0.2164             target_work(ml) = 5.437         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1550   r_free= 0.2164   ksol= 0.34   Bsol= 47.15   scale= 1.035   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.00,1.28,2.06,0.00,0.00,0.00); trace/3= 1.45                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.436640                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8783 -  4.6612 0.99   1390  155 0.1161 0.1533      5.5593      5.7381|
|  2:  4.6612 -  3.7187 0.99   1341  150 0.1124 0.1711      5.7032      6.0588|
|  3:  3.7187 -  3.2543 0.99   1313  141 0.1499 0.1930      5.7963      6.0644|
|  4:  3.2543 -  2.9593 0.99   1304  152 0.1674 0.2320      5.7517      5.9286|
|  5:  2.9593 -  2.7486 0.99   1299  144 0.1814 0.2457      5.6169      5.8497|
|  6:  2.7486 -  2.5874 0.99   1295  137 0.1667 0.2383      5.4962      5.6665|
|  7:  2.5874 -  2.4585 0.99   1293  140 0.1781 0.2147      5.4503      5.6227|
|  8:  2.4585 -  2.3519 0.98   1263  148 0.1721 0.2587       5.402      5.6809|
|  9:  2.3519 -  2.2617 0.98   1257  145 0.1707 0.2420      5.3338      5.5722|
| 10:  2.2617 -  2.1839 1.00   1295  138 0.1582 0.2468       5.285       5.503|
| 11:  2.1839 -  2.1158 0.98   1268  140 0.1632 0.2615      5.2528      5.6003|
| 12:  2.1158 -  2.0555 0.98   1255  141 0.1582 0.2291      5.1831      5.4828|
| 13:  2.0555 -  2.0015 0.99   1274  139 0.1645 0.2268      5.0761      5.2913|
| 14:  2.0015 -  1.9527 0.61    783   89 0.1566 0.2123       4.977      5.2164|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8783 -  4.6612  1390   155  0.91  12.44   0.98     0.96      11114.91|
|  2:  4.6612 -  3.7187  1341   150  0.92  12.55   1.05     1.04      16298.12|
|  3:  3.7187 -  3.2543  1313   141  0.88  18.02   1.08     1.06      21277.46|
|  4:  3.2543 -  2.9593  1304   152  0.86  20.66   1.05     0.99      19918.07|
|  5:  2.9593 -  2.7486  1299   144  0.84  22.75   1.03     0.98      15784.03|
|  6:  2.7486 -  2.5874  1295   137  0.84  23.04   1.01     0.96      13269.64|
|  7:  2.5874 -  2.4585  1293   140  0.83  23.38   1.03     1.00      11885.59|
|  8:  2.4585 -  2.3519  1263   148  0.83  23.51   1.03     0.99      11028.91|
|  9:  2.3519 -  2.2617  1257   145  0.84  22.43   1.03     0.98       9463.96|
| 10:  2.2617 -  2.1839  1295   138  0.83  23.41   1.03     0.96       9047.77|
| 11:  2.1839 -  2.1158  1268   140  0.83  24.03   1.06     0.98       8564.99|
| 12:  2.1158 -  2.0555  1255   141  0.84  23.21   1.07     1.03       7935.09|
| 13:  2.0555 -  2.0015  1274   139  0.84  23.05   1.06     1.02       5960.89|
| 14:  2.0015 -  1.9527   783    89  0.87  19.89   1.03     0.97       4383.97|
|alpha:            min =        0.96 max =            1.06 mean =         0.99|
|beta:             min =     4383.97 max =        21277.46 mean =     12119.12|
|figures of merit: min =        0.00 max =            1.00 mean =         0.85|
|phase err.(work): min =        0.00 max =           89.99 mean =        20.82|
|phase err.(test): min =        0.00 max =           89.80 mean =        19.58|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1552   r_free= 0.2161   ksol= 0.32   Bsol= 43.57   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.27,-0.44,0.71,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.433906                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.88 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1552   r_free= 0.2161   ksol= 0.32   Bsol= 43.57   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.27,-0.44,0.71,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.433906                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8783 -  4.6612 0.99   1390  155 0.1155 0.1511      5.5366      5.7084|
|  2:  4.6612 -  3.7187 0.99   1341  150 0.1139 0.1687      5.6984      6.0583|
|  3:  3.7187 -  3.2543 0.99   1313  141 0.1498 0.1928      5.7952      6.0632|
|  4:  3.2543 -  2.9593 0.99   1304  152 0.1672 0.2319      5.7501      5.9261|
|  5:  2.9593 -  2.7486 0.99   1299  144 0.1809 0.2454      5.6156      5.8492|
|  6:  2.7486 -  2.5874 0.99   1295  137 0.1668 0.2389      5.4951      5.6665|
|  7:  2.5874 -  2.4585 0.99   1293  140 0.1779 0.2159      5.4503      5.6233|
|  8:  2.4585 -  2.3519 0.98   1263  148 0.1721 0.2594      5.4027      5.6833|
|  9:  2.3519 -  2.2617 0.98   1257  145 0.1707 0.2421      5.3339        5.57|
| 10:  2.2617 -  2.1839 1.00   1295  138 0.1578 0.2476      5.2843       5.505|
| 11:  2.1839 -  2.1158 0.98   1268  140 0.1631 0.2619      5.2526      5.6026|
| 12:  2.1158 -  2.0555 0.98   1255  141 0.1581 0.2292      5.1835      5.4833|
| 13:  2.0555 -  2.0015 0.99   1274  139 0.1645 0.2260      5.0749      5.2879|
| 14:  2.0015 -  1.9527 0.61    783   89 0.1562 0.2110       4.974      5.2129|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8783 -  4.6612  1390   155  0.92  11.93   0.97     0.95      10277.80|
|  2:  4.6612 -  3.7187  1341   150  0.92  12.29   1.04     1.03      15678.37|
|  3:  3.7187 -  3.2543  1313   141  0.88  17.93   1.07     1.05      21203.44|
|  4:  3.2543 -  2.9593  1304   152  0.86  20.57   1.03     0.98      19757.20|
|  5:  2.9593 -  2.7486  1299   144  0.84  22.70   1.01     0.96      15726.25|
|  6:  2.7486 -  2.5874  1295   137  0.84  23.00   0.99     0.94      13240.48|
|  7:  2.5874 -  2.4585  1293   140  0.83  23.38   1.01     0.97      11895.44|
|  8:  2.4585 -  2.3519  1263   148  0.83  23.55   1.01     0.97      11073.87|
|  9:  2.3519 -  2.2617  1257   145  0.84  22.43   1.00     0.95       9471.17|
| 10:  2.2617 -  2.1839  1295   138  0.83  23.41   1.00     0.93       9053.88|
| 11:  2.1839 -  2.1158  1268   140  0.83  24.04   1.03     0.95       8573.85|
| 12:  2.1158 -  2.0555  1255   141  0.84  23.22   1.03     0.99       7940.34|
| 13:  2.0555 -  2.0015  1274   139  0.84  22.99   1.02     0.99       5934.95|
| 14:  2.0015 -  1.9527   783    89  0.87  19.74   0.99     0.94       4332.80|
|alpha:            min =        0.93 max =            1.05 mean =         0.97|
|beta:             min =     4332.80 max =        21203.44 mean =     11983.93|
|figures of merit: min =        0.00 max =            1.00 mean =         0.85|
|phase err.(work): min =        0.00 max =           89.85 mean =        20.73|
|phase err.(test): min =        0.00 max =           89.70 mean =        19.52|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.367)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.85    123.72  16.40    None  None   None       |
|    all(noH): 2823   0      0.85    123.72  16.40    None  None   None       |
|    Sol.    : 438    0      3.65    123.72  42.95    None  None   None       |
|    Mac.    : 2385   0      0.85    117.59  11.53    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:     0.851 -  13.137: 1780   |   5:    62.283 -  74.570:   53        |
|      1:    13.137 -  25.424:  523   |   6:    74.570 -  86.856:   16        |
|      2:    25.424 -  37.710:  179   |   7:    86.856 -  99.143:    2        |
|      3:    37.710 -  49.997:  143   |   8:    99.143 - 111.429:    1        |
|      4:    49.997 -  62.283:  123   |   9:   111.429 - 123.716:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 367         
Filter by distance & map next to the model:
   mapped sites are within: 0.403 - 5.761
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 360 from: 367
   mapped sites are within: 0.709 - 5.761

peak=    7.483 closest distance to " CG2 VAL A 296 " =    1.451
peak=    7.360 closest distance to " CB  VAL A 230 " =    1.435
peak=    7.330 closest distance to " O   HOH Z 390 " =    1.721
peak=    6.457 closest distance to " O   HOH Z  15 " =    1.394
peak=    6.451 closest distance to " O   HOH Z 381 " =    1.387
peak=    6.371 closest distance to " OD1 ASP A  27 " =    1.091
peak=    6.370 closest distance to " O   HOH Z 415 " =    1.671
peak=    6.222 closest distance to " O   HOH Z 291 " =    1.524
peak=    5.931 closest distance to " CD  ARG A 138 " =    1.228
peak=    5.866 closest distance to " O   HOH Z 289 " =    1.769
peak=    5.863 closest distance to " O   HOH Z 387 " =    1.756
peak=    5.828 closest distance to " O   HOH Z 375 " =    1.456
peak=    5.687 closest distance to " O   HOH Z 130 " =    1.740
peak=    5.648 closest distance to " NH2 ARG A  56 " =    2.236
peak=    5.519 closest distance to " O   HOH Z 350 " =    1.335
peak=    5.454 closest distance to " NZ BLYS A 290 " =    1.222
peak=    5.350 closest distance to " C   PRO A 198 " =    1.459
peak=    5.318 closest distance to " CD1AILE A 234 " =    0.993
peak=    5.311 closest distance to " O   HOH Z   9 " =    1.780
peak=    5.307 closest distance to " O   HOH Z 161 " =    1.012
peak=    5.219 closest distance to " CG  LEU A   5 " =    1.583
peak=    5.199 closest distance to " O   HOH Z  65 " =    2.155
peak=    5.092 closest distance to " O   HOH Z  46 " =    1.372
peak=    5.053 closest distance to " O   HOH Z 363 " =    1.273
peak=    5.044 closest distance to " CB  ARG A 275 " =    1.297
peak=    5.042 closest distance to " O   HOH Z 279 " =    1.194
peak=    5.002 closest distance to " O   HOH Z  54 " =    1.407
peak=    4.956 closest distance to " O   HOH Z 120 " =    1.054
peak=    4.939 closest distance to " N   TYR A  15 " =    1.058
peak=    4.930 closest distance to " O   HOH Z  24 " =    1.912
peak=    4.860 closest distance to " OD1 ASP A 286 " =    1.190
peak=    4.846 closest distance to " O   HOH Z  28 " =    2.056
peak=    4.840 closest distance to " O   HOH Z 400 " =    1.021
peak=    4.826 closest distance to " O   HOH Z 268 " =    1.098
peak=    4.780 closest distance to " O   HOH Z  61 " =    1.436
peak=    4.759 closest distance to " O   VAL A  72 " =    0.968
peak=    4.727 closest distance to " O   HOH Z  53 " =    2.230
peak=    4.718 closest distance to " O   HOH Z  59 " =    1.414
peak=    4.696 closest distance to " O   HOH Z 124 " =    1.758
peak=    4.639 closest distance to " O   HOH Z 142 " =    2.132
peak=    4.608 closest distance to " CD  ARG A 138 " =    0.981
peak=    4.596 closest distance to " O   ASN A 285 " =    0.938
peak=    4.593 closest distance to " O   HOH Z 214 " =    1.527
peak=    4.587 closest distance to " NE1 TRP A 266 " =    1.999
peak=    4.517 closest distance to " O   HOH Z 278 " =    1.533
peak=    4.494 closest distance to " O   HOH Z 179 " =    0.890
peak=    4.482 closest distance to " NH2BARG A 145 " =    1.574
peak=    4.479 closest distance to " O   HOH Z 139 " =    1.727
peak=    4.476 closest distance to " O   HOH Z 250 " =    2.007
peak=    4.473 closest distance to " CB  ALA A  10 " =    1.032
peak=    4.443 closest distance to " OG  SER A 276 " =    0.956
peak=    4.439 closest distance to " O   HOH Z 410 " =    1.463
peak=    4.414 closest distance to " O   HOH Z 428 " =    1.737
peak=    4.393 closest distance to " NH2 ARG A 138 " =    1.363
peak=    4.385 closest distance to " O   HOH Z 416 " =    1.466
peak=    4.384 closest distance to " NE2 GLN A  11 " =    1.250
peak=    4.352 closest distance to " CG1AVAL A 121 " =    1.033
peak=    4.351 closest distance to " CB  PRO A  54 " =    1.142
peak=    4.327 closest distance to " CG2 THR A 279 " =    1.117
peak=    4.308 closest distance to " O   HOH Z 403 " =    1.776
peak=    4.299 closest distance to " O   HOH Z  97 " =    1.330
peak=    4.285 closest distance to " OD1 ASN A  45 " =    1.109
peak=    4.278 closest distance to " O   HOH Z 215 " =    1.622
peak=    4.251 closest distance to " O   HOH Z 222 " =    1.375
peak=    4.250 closest distance to " O   HOH Z 359 " =    1.568
peak=    4.197 closest distance to " O   HOH Z   7 " =    2.045
peak=    4.190 closest distance to " O   HOH Z 245 " =    1.308
peak=    4.180 closest distance to " O   HOH Z 143 " =    1.593
peak=    4.161 closest distance to " O   HOH Z 126 " =    1.822
peak=    4.157 closest distance to " CE AMET A  47 " =    1.368
peak=    4.148 closest distance to " N   ARG A 275 " =    0.861
peak=    4.141 closest distance to " O   SER A  62 " =    0.940
peak=    4.140 closest distance to " O   HOH Z 358 " =    1.472
peak=    4.127 closest distance to " O   HOH Z 293 " =    1.431
peak=    4.126 closest distance to " OG ASER A 258 " =    3.048
peak=    4.113 closest distance to " NH1 ARG A 138 " =    0.921
peak=    4.104 closest distance to " O   HOH Z  51 " =    1.738
peak=    4.085 closest distance to " O   HOH Z 132 " =    1.295
peak=    4.077 closest distance to " CG2 THR A 294 " =    1.233
peak=    4.065 closest distance to " O   HOH Z  63 " =    1.869
peak=    4.051 closest distance to " OE1 GLU A   2 " =    1.909
peak=    4.040 closest distance to " NH2 ARG A 269 " =    0.794
peak=    4.035 closest distance to " CD1 LEU A   5 " =    1.510
peak=    4.027 closest distance to " N   SER A  63 " =    0.734
peak=    4.015 closest distance to " O   HOH Z 112 " =    1.536
peak=    4.012 closest distance to " O   HOH Z 127 " =    1.049
peak=    4.010 closest distance to " O   HOH Z 123 " =    1.637
peak=    4.007 closest distance to " CD2 LEU A 228 " =    1.237
peak=    4.006 closest distance to " O   HOH Z 389 " =    1.522
peak=    4.004 closest distance to " OG BSER A  12 " =    0.957
peak=    3.993 closest distance to " O   HOH Z 422 " =    0.974
peak=    3.992 closest distance to " O   HOH Z 417 " =    1.602
peak=    3.982 closest distance to " O   HOH Z 244 " =    1.354
peak=    3.978 closest distance to " O   HOH Z 374 " =    1.103
peak=    3.974 closest distance to " O   HOH Z 363 " =    2.457
peak=    3.970 closest distance to " O   HOH Z  92 " =    1.248
peak=    3.968 closest distance to " CG2 THR A 246 " =    0.961
peak=    3.966 closest distance to " CB  SER A   3 " =    1.291
peak=    3.950 closest distance to " O   HOH Z 108 " =    1.767
peak=    3.941 closest distance to " O   HOH Z 344 " =    1.257
peak=    3.931 closest distance to " CE  MET A  93 " =    1.494
peak=    3.922 closest distance to " CB  ALA A   1 " =    1.395
peak=    3.915 closest distance to " O   HOH Z 225 " =    1.425
peak=    3.910 closest distance to " CG  ARG A  66 " =    2.418
peak=    3.899 closest distance to " O   HOH Z 431 " =    0.945
peak=    3.890 closest distance to " O   HOH Z 427 " =    1.333
peak=    3.888 closest distance to " NE BARG A 275 " =    1.213
peak=    3.885 closest distance to " O   HOH Z 204 " =    1.524
peak=    3.875 closest distance to " NE2 GLN A  73 " =    1.721
peak=    3.865 closest distance to " O   HOH Z 427 " =    2.360
peak=    3.864 closest distance to " CB  TRP A 179 " =    1.477
peak=    3.847 closest distance to " CB  ASN A 187 " =    1.195
peak=    3.839 closest distance to " CG  LYS A 119 " =    1.101
peak=    3.830 closest distance to " O   HOH Z 247 " =    1.464
peak=    3.822 closest distance to " N   GLU A   2 " =    1.320
peak=    3.810 closest distance to " O   HOH Z  57 " =    1.293
peak=    3.807 closest distance to " NH2AARG A 145 " =    2.252
peak=    3.802 closest distance to " CG2 ILE A 234 " =    0.873
peak=    3.801 closest distance to " NE2 GLN A  58 " =    5.372
peak=    3.800 closest distance to " O   HOH Z 178 " =    1.174
peak=    3.800 closest distance to " OE1 GLN A  77 " =    0.884
peak=    3.798 closest distance to " O   HOH Z 334 " =    1.452
peak=    3.797 closest distance to " O   HOH Z 192 " =    1.488
peak=    3.785 closest distance to " OG ASER A 134 " =    1.365
peak=    3.780 closest distance to " O   HOH Z 236 " =    2.041
peak=    3.776 closest distance to " CB  ALA A 248 " =    1.357
peak=    3.776 closest distance to " CE AMET A  47 " =    1.509
peak=    3.776 closest distance to " CA  ASN A 127 " =    1.211
peak=    3.773 closest distance to " OD2 ASP A 270 " =    1.064
peak=    3.766 closest distance to " O   HOH Z 331 " =    1.359
peak=    3.763 closest distance to " O   HOH Z 347 " =    1.171
peak=    3.762 closest distance to " CA  LEU A 282 " =    1.013
peak=    3.758 closest distance to " O   HOH Z  27 " =    1.163
peak=    3.751 closest distance to " CB  SER A 216 " =    1.056
peak=    3.751 closest distance to " O   HOH Z 233 " =    1.528
peak=    3.743 closest distance to " O   HOH Z 366 " =    2.603
peak=    3.741 closest distance to " O   HOH Z 357 " =    1.989
peak=    3.717 closest distance to " O   HOH Z 361 " =    1.631
peak=    3.714 closest distance to " ND2 ASN A 284 " =    0.884
peak=    3.711 closest distance to " CB  VAL A 202 " =    1.702
peak=    3.704 closest distance to " CG1BVAL A 121 " =    1.995
peak=    3.703 closest distance to " O   HOH Z 223 " =    1.096
peak=    3.701 closest distance to " O   HOH Z  89 " =    1.552
peak=    3.697 closest distance to " O   HOH Z 263 " =    1.733
peak=    3.695 closest distance to " O   HOH Z 418 " =    1.357
peak=    3.690 closest distance to " N   GLY A 287 " =    0.821
peak=    3.686 closest distance to " CB  ARG A 138 " =    0.872
peak=    3.683 closest distance to " O   HOH Z 225 " =    1.791
peak=    3.679 closest distance to " O   HOH Z 402 " =    1.501
peak=    3.678 closest distance to " O   HOH Z 425 " =    1.483
peak=    3.665 closest distance to " CA  ILE A 234 " =    1.218
peak=    3.664 closest distance to " CB  LYS A 290 " =    1.508
peak=    3.663 closest distance to " CG2 ILE A 151 " =    1.051
peak=    3.660 closest distance to " C   GLN A  73 " =    1.021
peak=    3.651 closest distance to " N   ASN A 285 " =    0.795
peak=    3.647 closest distance to " O   HOH Z 405 " =    1.990
peak=    3.646 closest distance to " CE2 PHE A  16 " =    0.810
peak=    3.634 closest distance to " N   LYS A 119 " =    0.836
peak=    3.632 closest distance to " O   HOH Z 240 " =    1.906
peak=    3.629 closest distance to " CB  ASP A 132 " =    3.667
peak=    3.627 closest distance to " CB  LYS A 290 " =    1.232
peak=    3.626 closest distance to " CB  VAL A 230 " =    1.211
peak=    3.624 closest distance to " CB  GLN A 223 " =    1.761
peak=    3.623 closest distance to " O   HOH Z 143 " =    2.470
peak=    3.618 closest distance to " N   ARG A 156 " =    1.274
peak=    3.618 closest distance to " O   HOH Z 162 " =    1.539
peak=    3.616 closest distance to " CB  TRP A 266 " =    1.027
peak=    3.580 closest distance to " CG  ASP A 238 " =    0.754
peak=    3.577 closest distance to " CG  LEU A 228 " =    0.980
peak=    3.577 closest distance to " CG  GLN A  11 " =    1.957
peak=    3.570 closest distance to " OG  SER A  22 " =    2.611
peak=    3.561 closest distance to " NE1 TRP A 274 " =    1.114
peak=    3.546 closest distance to " O   HOH Z 191 " =    4.631
peak=    3.545 closest distance to " O   HOH Z 262 " =    2.257
peak=    3.540 closest distance to " CG  GLN A  88 " =    1.024
peak=    3.535 closest distance to " O   HOH Z 133 " =    1.794
peak=    3.519 closest distance to " O   HOH Z  91 " =    1.219
peak=    3.513 closest distance to " CB  ASN A  60 " =    0.916
peak=    3.511 closest distance to " O   HOH Z 369 " =    1.393
peak=    3.508 closest distance to " NZ  LYS A 117 " =    1.218
peak=    3.505 closest distance to " O   ALA A 165 " =    1.235
peak=    3.499 closest distance to " O   HOH Z 434 " =    5.761
peak=    3.496 closest distance to " O   HOH Z 108 " =    1.685
peak=    3.493 closest distance to " O   HOH Z  57 " =    2.156
peak=    3.488 closest distance to " CG  PRO A 213 " =    1.206
peak=    3.484 closest distance to " O   HOH Z 371 " =    1.821
peak=    3.483 closest distance to " O   HOH Z 262 " =    1.272
peak=    3.477 closest distance to " OG BSER A 258 " =    1.112
peak=    3.475 closest distance to " CB  ALA A 137 " =    0.928
peak=    3.472 closest distance to " O   HOH Z  22 " =    1.946
peak=    3.471 closest distance to " O   HOH Z 302 " =    1.716
peak=    3.468 closest distance to " ND1 HIS A  81 " =    1.187
peak=    3.466 closest distance to " ND2 ASN A 285 " =    0.716
peak=    3.464 closest distance to " CB  ASP A 200 " =    0.932
peak=    3.461 closest distance to " CE  LYS A  48 " =    1.013
peak=    3.461 closest distance to " O   HOH Z 130 " =    1.604
peak=    3.456 closest distance to " CA  TYR A  30 " =    0.940
peak=    3.455 closest distance to " O   HOH Z 422 " =    2.441
peak=    3.447 closest distance to " CG  PRO A 243 " =    1.134
peak=    3.446 closest distance to " O   HOH Z 414 " =    1.940
peak=    3.439 closest distance to " CD2 TRP A 179 " =    2.346
peak=    3.439 closest distance to " O   HOH Z 217 " =    1.569
peak=    3.438 closest distance to " O   HOH Z 119 " =    1.619
peak=    3.435 closest distance to " CZ  ARG A  14 " =    1.124
peak=    3.435 closest distance to " O   HOH Z 180 " =    2.168
peak=    3.432 closest distance to " O   HOH Z 172 " =    1.506
peak=    3.430 closest distance to " O   HOH Z 279 " =    2.922
peak=    3.430 closest distance to " OD2 ASP A 286 " =    2.218
peak=    3.429 closest distance to " CD1 LEU A 281 " =    1.038
peak=    3.425 closest distance to " O   HOH Z 384 " =    1.851
peak=    3.419 closest distance to " CB  ALA A 291 " =    1.376
peak=    3.415 closest distance to " O   HOH Z 294 " =    1.593
peak=    3.410 closest distance to " CA  THR A 246 " =    1.257
peak=    3.403 closest distance to " O   HOH Z 158 " =    2.295
peak=    3.403 closest distance to " O   HOH Z 167 " =    1.378
peak=    3.393 closest distance to " O   HOH Z 159 " =    1.106
peak=    3.391 closest distance to " O   HOH Z 193 " =    1.754
peak=    3.391 closest distance to " CB  SER A  62 " =    1.386
peak=    3.390 closest distance to " O   HOH Z 271 " =    2.313
peak=    3.390 closest distance to " SG ACYS A 201 " =    0.795
peak=    3.386 closest distance to " CB  SER A 210 " =    0.964
peak=    3.381 closest distance to " O   HOH Z   6 " =    2.089
peak=    3.376 closest distance to " NH2 ARG A  66 " =    1.814
peak=    3.375 closest distance to " O   ARG A  14 " =    1.019
peak=    3.374 closest distance to " CE1 PHE A  16 " =    0.981
peak=    3.372 closest distance to " O   HOH Z  45 " =    0.987
peak=    3.372 closest distance to " CG2AVAL A  72 " =    0.888
peak=    3.371 closest distance to " O   HOH Z  97 " =    1.768
peak=    3.368 closest distance to " O   HOH Z 371 " =    3.057
peak=    3.368 closest distance to " CZ3 TRP A  70 " =    0.946
peak=    3.367 closest distance to " CA  ALA A   1 " =    1.770
peak=    3.364 closest distance to " CB  ILE A 234 " =    0.944
peak=    3.362 closest distance to " O   HOH Z 369 " =    2.012
peak=    3.360 closest distance to " CB  ALA A 104 " =    1.197
peak=    3.358 closest distance to " CD1 PHE A 283 " =    0.975
peak=    3.355 closest distance to " O   HOH Z 426 " =    1.204
peak=    3.352 closest distance to " O   HOH Z 113 " =    1.590
peak=    3.349 closest distance to " O   GLY A 302 " =    1.547
peak=    3.347 closest distance to " O   HOH Z 410 " =    3.104
peak=    3.343 closest distance to " CG  LEU A 297 " =    0.957
peak=    3.342 closest distance to " O   HOH Z 222 " =    2.288
peak=    3.341 closest distance to " O   HOH Z   5 " =    1.420
peak=    3.340 closest distance to " O   SER A 164 " =    1.514
peak=    3.334 closest distance to " O   HOH Z 423 " =    1.800
peak=    3.334 closest distance to " O   HOH Z 425 " =    2.030
peak=    3.329 closest distance to " CB  ALA A 114 " =    1.340
peak=    3.327 closest distance to " O   HOH Z  80 " =    3.283
peak=    3.326 closest distance to " O   HOH Z 128 " =    1.865
peak=    3.325 closest distance to " CB  MET A  47 " =    1.449
peak=    3.322 closest distance to " NH2 ARG A  36 " =    1.060
peak=    3.321 closest distance to " O   HOH Z 368 " =    3.482
peak=    3.320 closest distance to " O   HOH Z 166 " =    1.387
peak=    3.315 closest distance to " O   HOH Z 133 " =    2.321
peak=    3.314 closest distance to " CB  ARG A  36 " =    1.008
peak=    3.314 closest distance to " CZ3 TRP A 274 " =    1.265
peak=    3.313 closest distance to " O   HOH Z 112 " =    2.202
peak=    3.312 closest distance to " CA  GLY A 267 " =    1.272
peak=    3.307 closest distance to " O   HOH Z 257 " =    2.117
peak=    3.304 closest distance to " O   HOH Z 326 " =    1.407
peak=    3.303 closest distance to " N   CYS A 260 " =    1.167
peak=    3.299 closest distance to " CD2 LEU A 101 " =    1.240
peak=    3.299 closest distance to " O   HOH Z  59 " =    2.154
peak=    3.296 closest distance to " O   HOH Z 423 " =    1.971
peak=    3.293 closest distance to " CE2 TRP A  70 " =    1.804
peak=    3.293 closest distance to " O   HOH Z 158 " =    1.330
peak=    3.293 closest distance to " NH1AARG A 145 " =    1.073
peak=    3.292 closest distance to " O   HOH Z 128 " =    2.294
peak=    3.289 closest distance to " N   GLN A 278 " =    1.132
peak=    3.286 closest distance to " CB  PHE A 204 " =    0.861
peak=    3.285 closest distance to " O   HOH Z 117 " =    1.017
peak=    3.283 closest distance to " CA  ASN A 284 " =    0.901
peak=    3.283 closest distance to " CG1 VAL A 153 " =    0.991
peak=    3.282 closest distance to " O   HOH Z 388 " =    1.009
peak=    3.282 closest distance to " CG2 THR A 246 " =    1.853
peak=    3.282 closest distance to " O   SER A 273 " =    0.849
peak=    3.281 closest distance to " O   HOH Z  32 " =    1.914
peak=    3.281 closest distance to " N   ASN A 142 " =    1.140
peak=    3.281 closest distance to " CB  ASP A 124 " =    1.028
peak=    3.278 closest distance to " C   GLY A 111 " =    1.627
peak=    3.276 closest distance to " O   HOH Z 364 " =    1.375
peak=    3.272 closest distance to " O   GLU A   2 " =    0.761
peak=    3.271 closest distance to " CD2 HIS A 115 " =    0.973
peak=    3.270 closest distance to " CA  ARG A  36 " =    1.496
peak=    3.269 closest distance to " O   HOH Z 353 " =    1.689
peak=    3.265 closest distance to " O   HOH Z 236 " =    1.360
peak=    3.265 closest distance to " O   HOH Z 153 " =    3.356
peak=    3.264 closest distance to " OG  SER A  62 " =    3.277
peak=    3.262 closest distance to " O   ALA A 242 " =    0.909
peak=    3.260 closest distance to " O   HOH Z 428 " =    1.299
peak=    3.260 closest distance to " O   HOH Z 172 " =    1.736
peak=    3.259 closest distance to " O   HOH Z 276 " =    1.627
peak=    3.258 closest distance to " O   HOH Z  88 " =    2.700
peak=    3.256 closest distance to " CE1 TYR A  68 " =    1.074
peak=    3.253 closest distance to " CG2 THR A 264 " =    1.286
peak=    3.250 closest distance to " CE1 PHE A  38 " =    0.813
peak=    3.249 closest distance to " CG2 VAL A 232 " =    1.170
peak=    3.245 closest distance to " CB  ASN A 142 " =    1.132
peak=    3.244 closest distance to " O   HOH Z 272 " =    1.855
peak=    3.244 closest distance to " CA  ARG A  56 " =    2.107
peak=    3.241 closest distance to " CB  GLN A  73 " =    1.111
peak=    3.241 closest distance to " O   HOH Z 151 " =    1.942
peak=    3.240 closest distance to " N   MET A  40 " =    1.745
peak=    3.236 closest distance to " O   HOH Z 298 " =    2.460
peak=    3.235 closest distance to " CB  ASP A 140 " =    1.081
peak=    3.235 closest distance to " O   HOH Z 176 " =    1.708
peak=    3.233 closest distance to " O   GLY A 147 " =    1.201
peak=    3.220 closest distance to " CG  MET A 188 " =    1.050
peak=    3.217 closest distance to " CG  ASN A  60 " =    1.351
peak=    3.216 closest distance to " CB  MET A  40 " =    0.868
peak=    3.212 closest distance to " O   HOH Z  69 " =    1.041
peak=    3.204 closest distance to " O   HOH Z 193 " =    1.420
peak=    3.204 closest distance to " O   HOH Z 380 " =    2.128
peak=    3.193 closest distance to " CG2 ILE A  20 " =    1.163
peak=    3.192 closest distance to " O   THR A 251 " =    0.967
peak=    3.188 closest distance to " CB  THR A 157 " =    1.080
peak=    3.187 closest distance to " OD1 ASN A 170 " =    1.275
peak=    3.187 closest distance to " CA  GLU A  46 " =    0.709
peak=    3.185 closest distance to " CA  GLY A 136 " =    0.979
peak=    3.181 closest distance to " CB  ASN A 148 " =    1.794
peak=    3.179 closest distance to " CB  ALA A 131 " =    1.506
peak=    3.177 closest distance to " O   HOH Z  24 " =    2.080
peak=    3.177 closest distance to " CB  GLN A  11 " =    1.410
peak=    3.166 closest distance to " CB  TRP A  85 " =    1.541
peak=    3.163 closest distance to " OD2 ASP A  65 " =    1.967
peak=    3.157 closest distance to " OG BSER A 212 " =    2.773
peak=    3.151 closest distance to " CA  ALA A  21 " =    1.155
peak=    3.150 closest distance to " CG2 THR A 221 " =    1.404
peak=    3.149 closest distance to " O   HOH Z 373 " =    1.394
peak=    3.148 closest distance to " O   HOH Z  64 " =    2.044
peak=    3.148 closest distance to " O   HOH Z 137 " =    1.668
peak=    3.147 closest distance to " CA  ASN A  74 " =    1.180
peak=    3.146 closest distance to " CB  ALA A   8 " =    0.974
peak=    3.141 closest distance to " CB  TYR A  30 " =    1.871
peak=    3.140 closest distance to " C   ASN A 215 " =    1.372
peak=    3.138 closest distance to " CG  LYS A 193 " =    1.563
peak=    3.136 closest distance to " N   PHE A 130 " =    1.245
peak=    3.134 closest distance to " O   HOH Z 281 " =    4.782
peak=    3.133 closest distance to " N   GLY A 111 " =    1.232
peak=    3.130 closest distance to " O   HOH Z 213 " =    1.479
peak=    3.128 closest distance to " CA  GLY A 203 " =    1.833
peak=    3.125 closest distance to " O   HOH Z 334 " =    2.075
peak=    3.123 closest distance to " NH2 ARG A  66 " =    5.118
peak=    3.115 closest distance to " O   HOH Z  77 " =    1.157
peak=    3.114 closest distance to " O   THR A  52 " =    1.968
peak=    3.111 closest distance to " O   HOH Z  88 " =    1.082
peak=    3.110 closest distance to " CZ AARG A 102 " =    1.820
peak=    3.106 closest distance to " OG1 THR A 246 " =    3.352
peak=    3.093 closest distance to " CB  LYS A 290 " =    0.790
peak=    3.087 closest distance to " CG2 THR A 279 " =    1.918
peak=    3.086 closest distance to " CG  LYS A 166 " =    1.462
peak=    3.085 closest distance to " NH1AARG A 275 " =    1.299
peak=    3.076 closest distance to " O   HOH Z 392 " =    1.582
peak=    3.074 closest distance to " CG  GLU A  37 " =    0.766
peak=    3.074 closest distance to " O   HOH Z 258 " =    2.271
peak=    3.065 closest distance to " N   LYS A  76 " =    1.320
peak=    3.055 closest distance to " O   HOH Z  69 " =    2.079
peak=    3.051 closest distance to " O   HOH Z  71 " =    1.547
peak=    3.028 closest distance to " O   HOH Z 186 " =    1.202
peak=    3.008 closest distance to " CG  GLN A  77 " =    1.525
peak=    3.006 closest distance to " N   ARG A 275 " =    0.794

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 190         
Filter by distance & map next to the model:
   mapped sites are within: 0.651 - 5.254
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 188 from: 190
   mapped sites are within: 0.705 - 5.254

peak=   -4.999 closest distance to " CD  ARG A 138 " =    1.117
peak=   -4.636 closest distance to " O   PRO A 198 " =    1.216
peak=   -4.355 closest distance to " OG  SER A  97 " =    2.288
peak=   -4.172 closest distance to " CE2 PHE A 218 " =    2.513
peak=   -4.137 closest distance to " O   SER A  62 " =    1.082
peak=   -4.137 closest distance to " OG ASER A 134 " =    0.970
peak=   -4.102 closest distance to " OE1 GLU A 277 " =    2.345
peak=   -4.099 closest distance to " O   SER A  22 " =    1.129
peak=   -3.988 closest distance to " CG1AVAL A  72 " =    1.992
peak=   -3.934 closest distance to " O   GLN A  11 " =    1.651
peak=   -3.928 closest distance to " CD  ARG A  14 " =    2.975
peak=   -3.900 closest distance to " OD1 ASN A 249 " =    1.354
peak=   -3.898 closest distance to " CB  ASN A 285 " =    2.097
peak=   -3.890 closest distance to " CD1 LEU A  96 " =    2.341
peak=   -3.871 closest distance to " O   ASN A 301 " =    1.104
peak=   -3.852 closest distance to " O   HOH Z 264 " =    1.072
peak=   -3.844 closest distance to " O   ILE A  49 " =    1.619
peak=   -3.831 closest distance to " O   HOH Z 404 " =    0.984
peak=   -3.818 closest distance to " O   SER A 135 " =    1.630
peak=   -3.810 closest distance to " CG2 VAL A 230 " =    0.958
peak=   -3.808 closest distance to " N   ALA A  64 " =    1.129
peak=   -3.803 closest distance to " O   GLY A 287 " =    2.044
peak=   -3.792 closest distance to " CE1 PHE A  16 " =    1.440
peak=   -3.790 closest distance to " O   GLY A 136 " =    1.475
peak=   -3.789 closest distance to " O   VAL A  72 " =    0.823
peak=   -3.773 closest distance to " O   HOH Z 336 " =    4.673
peak=   -3.772 closest distance to " CG2 VAL A  78 " =    2.650
peak=   -3.771 closest distance to " O   HOH Z 385 " =    0.967
peak=   -3.770 closest distance to " CD1 TRP A 179 " =    1.185
peak=   -3.750 closest distance to " O   HOH Z  52 " =    1.067
peak=   -3.748 closest distance to " CE BMET A  47 " =    1.450
peak=   -3.732 closest distance to " ND2 ASN A 173 " =    1.699
peak=   -3.680 closest distance to " NH2AARG A 275 " =    5.254
peak=   -3.661 closest distance to " NH2 ARG A 138 " =    0.817
peak=   -3.656 closest distance to " OG1 THR A 178 " =    0.975
peak=   -3.644 closest distance to " O   HOH Z 125 " =    3.182
peak=   -3.642 closest distance to " O   HOH Z  75 " =    1.755
peak=   -3.630 closest distance to " O   HOH Z 210 " =    1.932
peak=   -3.617 closest distance to " CG  ASN A 284 " =    1.243
peak=   -3.605 closest distance to " O   HOH Z  95 " =    1.151
peak=   -3.591 closest distance to " O   ALA A  10 " =    1.687
peak=   -3.591 closest distance to " O   ASP A 286 " =    1.246
peak=   -3.589 closest distance to " O   HOH Z  68 " =    1.187
peak=   -3.562 closest distance to " C   ASP A 124 " =    1.062
peak=   -3.562 closest distance to " CA  GLY A  98 " =    1.743
peak=   -3.557 closest distance to " CG  GLN A  11 " =    2.143
peak=   -3.553 closest distance to " CD2 TRP A 150 " =    1.390
peak=   -3.534 closest distance to " O   PRO A 198 " =    1.338
peak=   -3.530 closest distance to " O   ASN A 285 " =    1.030
peak=   -3.516 closest distance to " O   HOH Z 163 " =    1.714
peak=   -3.515 closest distance to " CA  GLY A  35 " =    1.811
peak=   -3.515 closest distance to " CG1 VAL A 112 " =    2.624
peak=   -3.510 closest distance to " O   HOH Z 354 " =    2.572
peak=   -3.509 closest distance to " N   GLY A  98 " =    2.142
peak=   -3.507 closest distance to " O   GLN A  73 " =    1.266
peak=   -3.501 closest distance to " CD2 LEU A 297 " =    1.079
peak=   -3.488 closest distance to " CA  GLY A 133 " =    1.934
peak=   -3.487 closest distance to " CG  TRP A 266 " =    1.437
peak=   -3.479 closest distance to " CD  GLN A  11 " =    0.995
peak=   -3.468 closest distance to " CB  ALA A   9 " =    2.576
peak=   -3.466 closest distance to " CG  PRO A 243 " =    2.003
peak=   -3.453 closest distance to " CG  PRO A 213 " =    2.214
peak=   -3.450 closest distance to " O   HOH Z 359 " =    2.374
peak=   -3.448 closest distance to " O   HOH Z 426 " =    1.500
peak=   -3.446 closest distance to " O   HOH Z 268 " =    1.258
peak=   -3.445 closest distance to " O   HOH Z  88 " =    1.292
peak=   -3.445 closest distance to " CA  TYR A  68 " =    1.260
peak=   -3.443 closest distance to " O   HOH Z 313 " =    1.149
peak=   -3.443 closest distance to " OD1 ASP A  27 " =    0.772
peak=   -3.439 closest distance to " CA  GLY A 203 " =    2.298
peak=   -3.437 closest distance to " CG2 THR A 178 " =    2.396
peak=   -3.436 closest distance to " OG  SER A   3 " =    0.916
peak=   -3.431 closest distance to " O   HOH Z 410 " =    1.989
peak=   -3.431 closest distance to " O   HOH Z 234 " =    4.459
peak=   -3.430 closest distance to " CG2 VAL A 296 " =    2.051
peak=   -3.428 closest distance to " SG  CYS A 168 " =    1.310
peak=   -3.427 closest distance to " O   VAL A  41 " =    1.790
peak=   -3.427 closest distance to " CB  TRP A 274 " =    2.690
peak=   -3.422 closest distance to " O   HOH Z 258 " =    4.729
peak=   -3.411 closest distance to " OG  SER A 276 " =    0.966
peak=   -3.409 closest distance to " O   HOH Z 376 " =    2.299
peak=   -3.404 closest distance to " N   GLN A  58 " =    1.149
peak=   -3.404 closest distance to " O   HOH Z 337 " =    2.065
peak=   -3.389 closest distance to " O   HOH Z 381 " =    0.793
peak=   -3.386 closest distance to " NH2 ARG A  79 " =    1.876
peak=   -3.380 closest distance to " CG  ARG A 259 " =    2.820
peak=   -3.376 closest distance to " CZ  ARG A  56 " =    0.801
peak=   -3.370 closest distance to " O   HOH Z 431 " =    0.975
peak=   -3.369 closest distance to " O   HOH Z 131 " =    4.032
peak=   -3.361 closest distance to " O   HOH Z 378 " =    2.193
peak=   -3.358 closest distance to " O   HOH Z 411 " =    4.658
peak=   -3.356 closest distance to " CG  GLN A  88 " =    0.885
peak=   -3.354 closest distance to " O   HOH Z  69 " =    1.898
peak=   -3.351 closest distance to " O   HOH Z 298 " =    0.768
peak=   -3.350 closest distance to " O   LYS A  76 " =    0.888
peak=   -3.345 closest distance to " O   ALA A  51 " =    1.357
peak=   -3.345 closest distance to " OD2 ASP A 171 " =    1.440
peak=   -3.343 closest distance to " CB  ALA A 100 " =    2.494
peak=   -3.341 closest distance to " N   ARG A 275 " =    0.752
peak=   -3.341 closest distance to " CA  VAL A  67 " =    2.854
peak=   -3.340 closest distance to " CG  MET A 105 " =    0.851
peak=   -3.339 closest distance to " CD2 LEU A   5 " =    0.977
peak=   -3.331 closest distance to " N   VAL A 189 " =    1.514
peak=   -3.322 closest distance to " O   LYS A 119 " =    0.781
peak=   -3.317 closest distance to " OE1 GLN A 223 " =    2.416
peak=   -3.314 closest distance to " O   HOH Z 359 " =    1.753
peak=   -3.314 closest distance to " CA  ILE A 106 " =    2.208
peak=   -3.313 closest distance to " SG  CYS A 260 " =    1.832
peak=   -3.311 closest distance to " O   HOH Z  56 " =    0.782
peak=   -3.308 closest distance to " O   HOH Z 135 " =    1.072
peak=   -3.307 closest distance to " O   HOH Z  30 " =    0.983
peak=   -3.301 closest distance to " O   ASP A 191 " =    1.889
peak=   -3.298 closest distance to " NE1 TRP A  70 " =    1.316
peak=   -3.298 closest distance to " O   HOH Z 414 " =    1.972
peak=   -3.296 closest distance to " O   HOH Z 263 " =    5.082
peak=   -3.294 closest distance to " CG  ASN A  60 " =    1.276
peak=   -3.292 closest distance to " CD  ARG A 139 " =    1.306
peak=   -3.290 closest distance to " CG  PRO A 163 " =    2.506
peak=   -3.280 closest distance to " N   HIS A 115 " =    1.789
peak=   -3.279 closest distance to " CZ  PHE A  16 " =    0.908
peak=   -3.278 closest distance to " CB  LEU A 297 " =    1.336
peak=   -3.276 closest distance to " O   HOH Z   1 " =    3.240
peak=   -3.275 closest distance to " O   ASP A 200 " =    0.860
peak=   -3.268 closest distance to " O   HOH Z 235 " =    0.834
peak=   -3.267 closest distance to " O   TRP A  92 " =    1.481
peak=   -3.266 closest distance to " O   TRP A 266 " =    1.596
peak=   -3.266 closest distance to " O   HOH Z 286 " =    1.378
peak=   -3.265 closest distance to " O   HOH Z 331 " =    1.571
peak=   -3.264 closest distance to " CG BLYS A 290 " =    0.881
peak=   -3.264 closest distance to " O   HOH Z 290 " =    0.996
peak=   -3.260 closest distance to " OD2 ASP A 191 " =    1.404
peak=   -3.259 closest distance to " O   HOH Z 389 " =    2.093
peak=   -3.256 closest distance to " O   HOH Z  77 " =    1.688
peak=   -3.254 closest distance to " CZ  ARG A  66 " =    1.141
peak=   -3.250 closest distance to " O   HOH Z 345 " =    2.266
peak=   -3.249 closest distance to " ND2 ASN A  60 " =    1.285
peak=   -3.241 closest distance to " O   HOH Z  71 " =    1.035
peak=   -3.235 closest distance to " CB  ALA A 248 " =    2.112
peak=   -3.235 closest distance to " CZ  ARG A  36 " =    1.434
peak=   -3.232 closest distance to " CE2 TYR A  30 " =    2.679
peak=   -3.232 closest distance to " O   HOH Z 350 " =    1.731
peak=   -3.231 closest distance to " O   GLU A 152 " =    1.757
peak=   -3.225 closest distance to " CG2 ILE A 120 " =    1.490
peak=   -3.224 closest distance to " O   HOH Z  16 " =    1.339
peak=   -3.224 closest distance to " O   HOH Z  24 " =    1.014
peak=   -3.223 closest distance to " O   HOH Z 156 " =    1.993
peak=   -3.222 closest distance to " O   SER A 273 " =    0.832
peak=   -3.219 closest distance to " O   HOH Z 102 " =    1.677
peak=   -3.215 closest distance to " O   HOH Z  60 " =    1.419
peak=   -3.214 closest distance to " O   SER A 271 " =    1.761
peak=   -3.212 closest distance to " CE  MET A 185 " =    2.596
peak=   -3.207 closest distance to " CB  SER A 276 " =    1.372
peak=   -3.204 closest distance to " N   LYS A 289 " =    0.892
peak=   -3.202 closest distance to " O   HOH Z 407 " =    3.210
peak=   -3.200 closest distance to " CG1BVAL A  72 " =    4.474
peak=   -3.200 closest distance to " O   VAL A 189 " =    2.476
peak=   -3.194 closest distance to " SG BCYS A 201 " =    0.921
peak=   -3.193 closest distance to " O   HOH Z  93 " =    1.699
peak=   -3.182 closest distance to " O   HOH Z 111 " =    1.035
peak=   -3.178 closest distance to " N   GLN A  55 " =    1.226
peak=   -3.173 closest distance to " OE1 GLN A 183 " =    1.498
peak=   -3.173 closest distance to " O   HOH Z 185 " =    1.963
peak=   -3.172 closest distance to " CA  SER A  63 " =    1.169
peak=   -3.160 closest distance to " OG  SER A  87 " =    1.490
peak=   -3.156 closest distance to " CG1 ILE A 234 " =    1.731
peak=   -3.146 closest distance to " CB  ALA A 248 " =    1.966
peak=   -3.145 closest distance to " CB  VAL A 125 " =    1.442
peak=   -3.142 closest distance to " O   HOH Z 202 " =    0.705
peak=   -3.140 closest distance to " O   HOH Z 435 " =    2.422
peak=   -3.138 closest distance to " O   HOH Z 368 " =    1.615
peak=   -3.137 closest distance to " O   HOH Z  95 " =    1.594
peak=   -3.134 closest distance to " C   PRO A 198 " =    2.352
peak=   -3.131 closest distance to " O   HOH Z 236 " =    2.164
peak=   -3.131 closest distance to " O   HOH Z 429 " =    1.887
peak=   -3.130 closest distance to " O   HOH Z  72 " =    0.952
peak=   -3.126 closest distance to " NH2 ARG A  24 " =    0.806
peak=   -3.120 closest distance to " O   TYR A  30 " =    1.624
peak=   -3.115 closest distance to " O   HOH Z 140 " =    1.853
peak=   -3.114 closest distance to " O   HOH Z 428 " =    1.592
peak=   -3.108 closest distance to " O   SER A  22 " =    2.508
peak=   -3.107 closest distance to " CB  GLN A  73 " =    1.292
peak=   -3.101 closest distance to " O   HOH Z 392 " =    3.229
peak=   -3.083 closest distance to " O   GLN A 205 " =    1.548
peak=   -3.078 closest distance to " C   ASP A 124 " =    2.096
peak=   -3.077 closest distance to " O   HOH Z 205 " =    1.256
peak=   -3.055 closest distance to " O   HOH Z 373 " =    1.023
peak=   -3.050 closest distance to " O   GLY A 118 " =    1.492
peak=   -3.007 closest distance to " N   HIS A 115 " =    1.034

================= 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    :  0.5025 0.5044   6.303427e+00   6.297551e+00
   1_bss:  0.4942 0.4924   6.298952e+00   6.290012e+00
   1_xyz:  0.4398 0.4686   6.245016e+00   6.268127e+00
   1_adp:  0.4014 0.4643   6.204998e+00   6.263536e+00
   1_occ:  0.4010 0.4645   6.204665e+00   6.263866e+00
   2_bss:  0.3995 0.4614   6.204487e+00   6.262242e+00
   2_xyz:  0.3575 0.4280   6.121240e+00   6.224614e+00
   2_adp:  0.3449 0.4195   6.104019e+00   6.212067e+00
   2_occ:  0.3448 0.4195   6.103640e+00   6.211938e+00
   3_bss:  0.3447 0.4188   6.105027e+00   6.211621e+00
   3_xyz:  0.3003 0.3773   6.002256e+00   6.139727e+00
   3_adp:  0.2790 0.3726   5.964038e+00   6.130967e+00
   3_occ:  0.2788 0.3724   5.963958e+00   6.131294e+00
   4_bss:  0.2790 0.3714   5.962628e+00   6.129916e+00
   4_xyz:  0.2404 0.3230   5.829328e+00   6.022817e+00
   4_adp:  0.2261 0.2928   5.770652e+00   5.949429e+00
   4_occ:  0.2257 0.2918   5.768662e+00   5.947121e+00
   5_bss:  0.2255 0.2895   5.766768e+00   5.943650e+00
   5_xyz:  0.1752 0.2318   5.529554e+00   5.741621e+00
   5_adp:  0.1552 0.2169   5.437794e+00   5.680588e+00
   5_occ:  0.1550 0.2164   5.436640e+00   5.679084e+00
   5_bss:  0.1552 0.2161   5.433906e+00   5.676378e+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:  0.386   2.244   6.131   9.304   7.810   0.000   0.000   0.000
   1_xyz:  0.386   2.244   6.131   9.304   7.810   0.000   0.000   0.000
   1_adp:  0.386   2.244   6.131   9.304   7.810   0.000   0.000   0.000
   1_occ:  0.386   2.244   6.131   9.304   7.810   0.000   0.000   0.000
   2_bss:  0.376  32.658   3.262   5.534   4.893   0.000   0.000   0.000
   2_xyz:  0.376  32.658   3.262   5.534   4.893   0.000   0.000   0.000
   2_adp:  0.376  32.658   3.262   5.534   4.893   0.000   0.000   0.000
   2_occ:  0.376  32.658   3.262   5.534   4.893   0.000   0.000   0.000
   3_bss:  0.372  54.420   2.022   3.451   3.242   0.000   0.000   0.000
   3_xyz:  0.372  54.420   2.022   3.451   3.242   0.000   0.000   0.000
   3_adp:  0.372  54.420   2.022   3.451   3.242   0.000   0.000   0.000
   3_occ:  0.372  54.420   2.022   3.451   3.242   0.000   0.000   0.000
   4_bss:  0.359  62.190   1.668   2.275   2.770   0.000   0.000   0.000
   4_xyz:  0.359  62.190   1.668   2.275   2.770   0.000   0.000   0.000
   4_adp:  0.359  62.190   1.668   2.275   2.770   0.000   0.000   0.000
   4_occ:  0.359  62.190   1.668   2.275   2.770   0.000   0.000   0.000
   5_bss:  0.340  47.152   1.003   1.280   2.059   0.000   0.000   0.000
   5_xyz:  0.340  47.152   1.003   1.280   2.059   0.000   0.000   0.000
   5_adp:  0.340  47.152   1.003   1.280   2.059   0.000   0.000   0.000
   5_occ:  0.340  47.152   1.003   1.280   2.059   0.000   0.000   0.000
   5_bss:  0.318  43.570  -0.266  -0.444   0.710   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  65.048 0.3288  0.3996    84025.046
   1_bss:  64.541 0.3343  0.5018    81275.480
   1_xyz:  57.918 0.4196  0.6219    70271.698
   1_adp:  56.774 0.4341  0.6985    68799.306
   1_occ:  56.781 0.4341  0.6971    69056.292
   2_bss:  56.244 0.4409  0.6415    68286.846
   2_xyz:  49.863 0.5211  0.7566    56108.654
   2_adp:  47.746 0.5481  0.8122    53388.169
   2_occ:  47.728 0.5483  0.8122    53346.043
   3_bss:  47.610 0.5497  0.7680    53186.340
   3_xyz:  41.324 0.6264  0.8661    41377.468
   3_adp:  40.051 0.6421  0.8795    40159.727
   3_occ:  40.085 0.6417  0.8785    40158.093
   4_bss:  39.966 0.6430  0.8593    39867.001
   4_xyz:  33.769 0.7150  0.9344    28347.938
   4_adp:  29.782 0.7609  0.9667    23260.822
   4_occ:  29.698 0.7618  0.9671    23102.594
   5_bss:  29.587 0.7627  0.9402    22826.535
   5_xyz:  22.537 0.8368  0.9971    13893.623
   5_adp:  20.740 0.8548  0.9949    12176.555
   5_occ:  20.698 0.8552  0.9950    12119.040
   5_bss:  20.612 0.8558  0.9731    11983.788
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.087   5.2744e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.087   5.2744e+01
   1_xyz:   1.708  0.013  0.106 18.375  0.007  4.105   1.4706e-01
   1_adp:   1.708  0.013  0.106 18.375  0.007  4.105   1.4706e-01
   1_occ:   1.708  0.013  0.106 18.375  0.007  4.105   1.4706e-01
   2_bss:   1.708  0.013  0.106 18.375  0.007  4.105   1.4706e-01
   2_xyz:   1.163  0.008  0.077 16.159  0.004  4.116   8.7684e-02
   2_adp:   1.163  0.008  0.077 16.159  0.004  4.116   8.7684e-02
   2_occ:   1.163  0.008  0.077 16.159  0.004  4.116   8.7684e-02
   3_bss:   1.163  0.008  0.077 16.159  0.004  4.116   8.7684e-02
   3_xyz:   1.213  0.008  0.083 16.089  0.004  4.102   8.4898e-02
   3_adp:   1.213  0.008  0.083 16.089  0.004  4.102   8.4898e-02
   3_occ:   1.213  0.008  0.083 16.089  0.004  4.102   8.4898e-02
   4_bss:   1.213  0.008  0.083 16.089  0.004  4.102   8.4898e-02
   4_xyz:   1.048  0.008  0.074 15.594  0.004  4.109   7.1617e-02
   4_adp:   1.048  0.008  0.074 15.594  0.004  4.109   7.1617e-02
   4_occ:   1.048  0.008  0.074 15.594  0.004  4.109   7.1617e-02
   5_bss:   1.048  0.008  0.074 15.594  0.004  4.109   7.1617e-02
   5_xyz:   1.082  0.008  0.077 15.888  0.004  4.106   7.1981e-02
   5_adp:   1.082  0.008  0.077 15.888  0.004  4.106   7.1981e-02
   5_occ:   1.082  0.008  0.077 15.888  0.004  4.106   7.1981e-02
   5_bss:   1.082  0.008  0.077 15.888  0.004  4.106   7.1981e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.8318e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.8318e+00
   1_xyz:  13.314  0.194  0.427 86.142  0.053  2.187   9.8147e-02
   1_adp:  13.314  0.194  0.427 86.142  0.053  2.187   9.8147e-02
   1_occ:  13.314  0.194  0.427 86.142  0.053  2.187   9.8147e-02
   2_bss:  13.314  0.194  0.427 86.142  0.053  2.187   9.8147e-02
   2_xyz:   7.197  0.085  0.277 82.366  0.038  2.102   6.6230e-02
   2_adp:   7.197  0.085  0.277 82.366  0.038  2.102   6.6230e-02
   2_occ:   7.197  0.085  0.277 82.366  0.038  2.102   6.6230e-02
   3_bss:   7.197  0.085  0.277 82.366  0.038  2.102   6.6230e-02
   3_xyz:   8.295  0.065  0.298 76.801  0.035  2.136   5.6536e-02
   3_adp:   8.295  0.065  0.298 76.801  0.035  2.136   5.6536e-02
   3_occ:   8.295  0.065  0.298 76.801  0.035  2.136   5.6536e-02
   4_bss:   8.295  0.065  0.298 76.801  0.035  2.136   5.6536e-02
   4_xyz:   7.454  0.072  0.239 83.953  0.031  2.231   7.0266e-02
   4_adp:   7.454  0.072  0.239 83.953  0.031  2.231   7.0266e-02
   4_occ:   7.454  0.072  0.239 83.953  0.031  2.231   7.0266e-02
   5_bss:   7.454  0.072  0.239 83.953  0.031  2.231   7.0266e-02
   5_xyz:   8.119  0.051  0.325 85.316  0.022  2.226   6.1958e-02
   5_adp:   8.119  0.051  0.325 85.316  0.022  2.226   6.1958e-02
   5_occ:   8.119  0.051  0.325 85.316  0.022  2.226   6.1958e-02
   5_bss:   8.119  0.051  0.325 85.316  0.022  2.226   6.1958e-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: 100.58   0.00  15.95  96.24   0.00  14.69 100.58   0.00  22.82
   1_occ: 100.58   0.00  15.95  96.24   0.00  14.69 100.58   0.00  22.82
   2_bss: 100.58   0.00  15.95  96.24   0.00  14.69 100.58   0.00  22.82
   2_xyz: 100.58   0.00  15.95  96.24   0.00  14.69 100.58   0.00  22.82
   2_adp: 105.23   0.00  15.41  99.22   0.00  13.73 105.23   0.00  24.59
   2_occ: 105.23   0.00  15.41  99.22   0.00  13.73 105.23   0.00  24.59
   3_bss: 105.23   0.00  15.41  99.22   0.00  13.73 105.23   0.00  24.59
   3_xyz: 105.23   0.00  15.41  99.22   0.00  13.73 105.23   0.00  24.59
   3_adp: 127.46   0.00  17.50 118.65   0.00  14.50 127.46   0.00  33.83
   3_occ: 127.46   0.00  17.50 118.65   0.00  14.50 127.46   0.00  33.83
   4_bss: 127.46   0.00  17.50 118.65   0.00  14.50 127.46   0.00  33.83
   4_xyz: 127.46   0.00  17.50 118.65   0.00  14.50 127.46   0.00  33.83
   4_adp: 123.40   0.00  15.15 112.41   0.00  11.60 123.40   0.00  34.49
   4_occ: 123.40   0.00  15.15 112.41   0.00  11.60 123.40   0.00  34.49
   5_bss: 123.40   0.00  15.15 112.41   0.00  11.60 123.40   0.00  34.49
   5_xyz: 123.40   0.00  15.15 112.41   0.00  11.60 123.40   0.00  34.49
   5_adp: 122.87   0.00  15.55 116.74   0.00  10.68 122.87   2.79  42.10
   5_occ: 122.87   0.00  15.55 116.74   0.00  10.68 122.87   2.79  42.10
   5_bss: 123.72   0.85  16.40 117.59   0.85  11.53 123.72   3.65  42.95
------------------------------------------------------------------------
 stage        Deviation of refined
              model from start model
               max      min     mean
   0    :    0.000    0.000    0.000
   1_bss:    0.000    0.000    0.000
   1_xyz:    1.266    0.018    0.411
   1_adp:    1.266    0.018    0.411
   1_occ:    1.266    0.018    0.411
   2_bss:    1.266    0.018    0.411
   2_xyz:    1.668    0.020    0.547
   2_adp:    1.668    0.020    0.547
   2_occ:    1.668    0.020    0.547
   3_bss:    1.668    0.020    0.547
   3_xyz:    1.601    0.041    0.654
   3_adp:    1.601    0.041    0.654
   3_occ:    1.601    0.041    0.654
   4_bss:    1.601    0.041    0.654
   4_xyz:    1.785    0.034    0.770
   4_adp:    1.785    0.034    0.770
   4_occ:    1.785    0.034    0.770
   5_bss:    1.785    0.034    0.770
   5_xyz:    1.971    0.050    0.877
   5_adp:    1.971    0.050    0.877
   5_occ:    1.971    0.050    0.877
   5_bss:    1.971    0.050    0.877
------------------------------------------------------------------------

CPU time actual refinement: 342.23


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_486/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_486/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_486/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_486/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_486/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 342.07 
  Macro-tasks:
    bulk solvent and scale       = 41.87  
    individual site refinement   = 141.79 
    weights calculation          = 32.68  
    collect and process          = 6.31   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 222.78 
  Micro-tasks:
    mask                            = 3.03   
    f_calc                          = 106.90 
    alpha_beta                      = 8.37   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 116.25 
    fmodel                         = 7.07   
    r_factors                      = 0.21   
    phase_errors                   = 9.57   
    foms                           = 0.27   
    TOTAL for micro-tasks          = 252.84 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.863 micro seconds
Total CPU time: 5.94 minutes
from_scatterers_fft:    633 calls, 106.52 s
gradients_fft:          578 calls, 103.46 s

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

# Date 2008-01-16 Time 01:40:30 PST -0800 (1200476430.65 s)
Start R-work = 0.5025, R-free = 0.5044 (no bulk solvent and anisotropic scale)
Final R-work = 0.1689, R-free = 0.2298 (no bulk solvent and anisotropic scale)

Start R-work = 0.4942, R-free = 0.4924
Final R-work = 0.1552, R-free = 0.2161