# Date 2008-01-16 Time 03:36:35 PST -0800 (1200483395.33 s)
#phil __OFF__

Command line arguments: "../1303.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = idle.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 25534
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1303

-------------------------------------------------------------------------------
  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: (72.0062, 47.6339, 86.39, 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: 3.34, per 1000 atoms: 1.18


================================== 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: (72.0062, 47.6339, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2644 2.00119
Completeness in resolution range: 0.94977
Completeness with d_max=infinity: 0.946923

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2644
                             d_min =   2.0012

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: (72.0062, 47.6339, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2644 2.00119
Completeness in resolution range: 0.94977
Completeness with d_max=infinity: 0.946923

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2649 -  4.2827 [2165/2194]  1951   214   9.9%
  bin  2:  4.2827 -  3.4118 [2073/2089]  1864   209  10.1%
  bin  3:  3.4118 -  2.9842 [2048/2067]  1841   207  10.1%
  bin  4:  2.9842 -  2.7130 [2046/2076]  1848   198   9.7%
  bin  5:  2.7130 -  2.5194 [2036/2055]  1832   204  10.0%
  bin  6:  2.5194 -  2.3715 [2007/2043]  1799   208  10.4%
  bin  7:  2.3715 -  2.2531 [1984/2017]  1785   199  10.0%
  bin  8:  2.2531 -  2.1553 [2001/2034]  1807   194   9.7%
  bin  9:  2.1553 -  2.0725 [1987/2016]  1784   203  10.2%
  bin 10:  2.0725 -  2.0012 [1242/2034]  1119   123   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1303/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.22 -     1.96: 2
        1.96 -     2.69: 104
        2.69 -     3.43: 4404
        3.43 -     4.16: 9205
        4.16 -     4.90: 14101
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.219 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 206 " - " O   HOH Z 342 "  2.007 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 277 " - " O   HOH Z 343 "  2.140 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 343 " - " O   HOH Z 277 "  2.140 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 27811 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_1303/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1303/model_refine_001.geo

CPU time processing inputs: 8.93


============================ 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 = 72.00625 47.63395 86.39 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4866   r_free= 0.4700   ksol= 0.00   Bsol= 0.00   scale= 0.776    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.287486                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2649 -  4.7770 0.99   1400  157 0.3984 0.3816      6.5977      6.5633|
|  2:  4.7770 -  3.8110 0.99   1361  145 0.4053 0.4382      6.8136      6.8361|
|  3:  3.8110 -  3.3350 0.99   1321  151 0.4508 0.4013      6.6813      6.6672|
|  4:  3.3350 -  3.0327 0.99   1328  150 0.4775 0.4273       6.542      6.4737|
|  5:  3.0327 -  2.8168 0.99   1314  143 0.5121 0.5285      6.3788      6.3916|
|  6:  2.8168 -  2.6516 0.99   1294  145 0.5292 0.4970      6.2865      6.2555|
|  7:  2.6516 -  2.5194 0.99   1318  141 0.5186 0.5116      6.2537      6.2286|
|  8:  2.5194 -  2.4102 0.98   1273  150 0.5172 0.5042      6.1656      6.1873|
|  9:  2.4102 -  2.3178 0.98   1293  145 0.5373 0.5487      6.1298      6.1445|
| 10:  2.3178 -  2.2380 0.98   1277  135 0.5250 0.4926      6.1065      6.1154|
| 11:  2.2380 -  2.1683 1.00   1289  144 0.5326 0.4847      6.0485      6.0378|
| 12:  2.1683 -  2.1064 0.97   1262  139 0.5462 0.5206      5.9765      6.0099|
| 13:  2.1064 -  2.0511 0.98   1280  142 0.5286 0.5180       5.883      5.8095|
| 14:  2.0511 -  2.0012 0.47    620   72 0.5516 0.5243       5.845      5.7953|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2649 -  4.7770  1400   157  0.70  34.48   0.79     0.73      72134.87|
|  2:  4.7770 -  3.8110  1361   145  0.70  35.18   0.87     0.75     105144.67|
|  3:  3.8110 -  3.3350  1321   151  0.59  44.53   0.80     0.69     115325.69|
|  4:  3.3350 -  3.0327  1328   150  0.49  52.30   0.78     0.58     105044.97|
|  5:  3.0327 -  2.8168  1314   143  0.40  59.76   0.72     0.48      86101.25|
|  6:  2.8168 -  2.6516  1294   145  0.37  62.45   0.72     0.43      73421.74|
|  7:  2.6516 -  2.5194  1318   141  0.35  63.35   0.73     0.39      66561.90|
|  8:  2.5194 -  2.4102  1273   150  0.31  66.98   0.70     0.36      63780.82|
|  9:  2.4102 -  2.3178  1293   145  0.29  68.04   0.70     0.35      58799.14|
| 10:  2.3178 -  2.2380  1277   135  0.30  67.54   0.73     0.35      53871.01|
| 11:  2.2380 -  2.1683  1289   144  0.32  65.86   0.74     0.38      46819.78|
| 12:  2.1683 -  2.1064  1262   139  0.32  66.17   0.72     0.40      43071.74|
| 13:  2.1064 -  2.0511  1280   142  0.32  65.94   0.70     0.39      36379.11|
| 14:  2.0511 -  2.0012   620    72  0.32  66.29   0.70     0.37      30445.98|
|alpha:            min =        0.35 max =            0.75 mean =         0.48|
|beta:             min =    30445.98 max =       115325.69 mean =     70219.60|
|figures of merit: min =        0.00 max =            1.00 mean =         0.42|
|phase err.(work): min =        0.00 max =           89.99 mean =        57.89|
|phase err.(test): min =        0.00 max =           89.91 mean =        57.70|
|-----------------------------------------------------------------------------|

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

basic_wilson_outliers    = 0
extreme_wilson_outliers  = 0
beamstop_shadow_outliers = 1
total                    = 1

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 16.344213             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.908   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.427548              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.548   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       26 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      160 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      675 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1480 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2583 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3845 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4972 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6486 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7579 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.503 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.700 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.371)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.371)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4906   r_free= 0.4762   ksol= 0.00   Bsol= 0.00   scale= 0.749    |
|                                                                             |
| 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:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.288271                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4793   r_free= 0.4623   ksol= 0.30   Bsol= 28.25   scale= 0.959   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.75,9.20,6.42,0.00,0.00,0.00); trace/3= 8.12                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.283875                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.151747             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.372   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.238047              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.491   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4793      final r-factor (work) = 0.3962          |
| start r-factor (free) = 0.4623      final r-factor (free) = 0.4212          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 98.9754 = 14.15 * 0.50 * 6.2851 + 1.00 * 54.5031                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 44.0164 = 14.15 * 0.50 * 6.1988 + 1.00 * 0.1546                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3962      final r-factor (work) = 0.3537          |
| start r-factor (free) = 0.4212      final r-factor (free) = 0.3989          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6888 = 1.24 * 1.00 * 6.1988 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6032 = 1.24 * 1.00 * 6.1273 + 1.00 * 0.0173                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.371)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    117.32  13.06    None  None   None       |
|    all(noH): 2823   0      0.00    117.32  13.06    None  None   None       |
|    Sol.    : 438    0      0.00    117.32  26.92    None  None   None       |
|    Mac.    : 2385   0      0.00    82.13   10.51    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.732: 1685   |   5:    58.662 -  70.394:   24        |
|      1:    11.732 -  23.465:  700   |   6:    70.394 -  82.127:    6        |
|      2:    23.465 -  35.197:  243   |   7:    82.127 -  93.859:    4        |
|      3:    35.197 -  46.930:  101   |   8:    93.859 - 105.591:    1        |
|      4:    46.930 -  58.662:   57   |   9:   105.591 - 117.324:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3537 r_free = 0.3989             target_work(ml) = 6.108         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3531 r_free = 0.3991             target_work(ml) = 6.107         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3531   r_free= 0.3991   ksol= 0.30   Bsol= 28.25   scale= 1.052   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.75,9.20,6.42,0.00,0.00,0.00); trace/3= 8.12                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.106999                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3529   r_free= 0.3964   ksol= 0.30   Bsol= 28.25   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.38,6.58,4.95,0.00,0.00,0.00); trace/3= 5.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.109076                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.408537             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.202  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.604274              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 128.896  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3529      final r-factor (work) = 0.2645          |
| start r-factor (free) = 0.3964      final r-factor (free) = 0.3277          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 32.0263 = 10.41 * 0.50 * 6.1241 + 1.00 * 0.1546                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.3013 = 10.41 * 0.50 * 5.9958 + 1.00 * 0.0973                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2645      final r-factor (work) = 0.2429          |
| start r-factor (free) = 0.3277      final r-factor (free) = 0.3032          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6448 = 0.60 * 1.00 * 5.9958 + 1.00 * 0.0217                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5630 = 0.60 * 1.00 * 5.8416 + 1.00 * 0.0331                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.371)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.64  12.81    None  None   None       |
|    all(noH): 2823   0      0.00    110.64  12.81    None  None   None       |
|    Sol.    : 438    0      0.00    110.64  32.16    None  None   None       |
|    Mac.    : 2385   0      0.00    79.65   9.26     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.064: 1744   |   5:    55.319 -  66.382:   36        |
|      1:    11.064 -  22.128:  605   |   6:    66.382 -  77.446:   11        |
|      2:    22.128 -  33.191:  226   |   7:    77.446 -  88.510:    2        |
|      3:    33.191 -  44.255:  126   |   8:    88.510 -  99.574:    1        |
|      4:    44.255 -  55.319:   70   |   9:    99.574 - 110.637:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2429 r_free = 0.3032             target_work(ml) = 5.810         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2425 r_free = 0.3034             target_work(ml) = 5.809         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2425   r_free= 0.3034   ksol= 0.30   Bsol= 28.25   scale= 1.047   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.38,6.58,4.95,0.00,0.00,0.00); trace/3= 5.97                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.809340                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2406   r_free= 0.2996   ksol= 0.30   Bsol= 28.25   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.03,4.25,3.91,0.00,0.00,0.00); trace/3= 4.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.809333                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.438883              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.482  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.083844              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.048   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2406      final r-factor (work) = 0.1754          |
| start r-factor (free) = 0.2996      final r-factor (free) = 0.2232          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.9106 = 6.44 * 0.50 * 5.8436 + 1.00 * 0.0973                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.4031 = 6.44 * 0.50 * 5.6893 + 1.00 * 0.0866                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1754      final r-factor (work) = 0.1548          |
| start r-factor (free) = 0.2232      final r-factor (free) = 0.2051          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1845 = 1.08 * 1.00 * 5.6893 + 1.00 * 0.0181                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.9321 = 1.08 * 1.00 * 5.4587 + 1.00 * 0.0157                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.371)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.76   13.64    None  None   None       |
|    all(noH): 2823   0      0.00    93.76   13.64    None  None   None       |
|    Sol.    : 438    0      0.00    93.72   39.07    None  None   None       |
|    Mac.    : 2385   0      0.00    93.76   8.97     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.376: 1655   |   5:    46.881 -  56.257:   80        |
|      1:     9.376 -  18.752:  583   |   6:    56.257 -  65.633:   58        |
|      2:    18.752 -  28.128:  182   |   7:    65.633 -  75.009:   24        |
|      3:    28.128 -  37.505:  124   |   8:    75.009 -  84.385:   13        |
|      4:    37.505 -  46.881:   94   |   9:    84.385 -  93.761:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1548 r_free = 0.2051             target_work(ml) = 5.420         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1547 r_free = 0.2048             target_work(ml) = 5.419         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1547   r_free= 0.2048   ksol= 0.30   Bsol= 28.25   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.03,4.25,3.91,0.00,0.00,0.00); trace/3= 4.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.419420                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1535   r_free= 0.2048   ksol= 0.32   Bsol= 57.35   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.74,2.95,3.11,0.00,0.00,0.00); trace/3= 2.93                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.416087                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.556462              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 119.159  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.317272              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 141.975  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1535      final r-factor (work) = 0.1325          |
| start r-factor (free) = 0.2048      final r-factor (free) = 0.1852          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8019 = 3.56 * 0.50 * 5.4635 + 1.00 * 0.0866                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.6120 = 3.56 * 0.50 * 5.3595 + 1.00 * 0.0815                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1325      final r-factor (work) = 0.1292          |
| start r-factor (free) = 0.1852      final r-factor (free) = 0.1795          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7160 = 0.32 * 1.00 * 5.3595 + 1.00 * 0.0156                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6920 = 0.32 * 1.00 * 5.2932 + 1.00 * 0.0127                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.371)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.22   13.23    None  None   None       |
|    all(noH): 2823   0      0.00    92.22   13.23    None  None   None       |
|    Sol.    : 438    0      0.81    89.88   38.22    None  None   None       |
|    Mac.    : 2385   0      0.00    92.22   8.64     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.222: 1716   |   5:    46.109 -  55.331:   78        |
|      1:     9.222 -  18.444:  556   |   6:    55.331 -  64.553:   63        |
|      2:    18.444 -  27.666:  161   |   7:    64.553 -  73.775:   19        |
|      3:    27.666 -  36.888:  114   |   8:    73.775 -  82.997:   11        |
|      4:    36.888 -  46.109:   94   |   9:    82.997 -  92.219:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1292 r_free = 0.1795             target_work(ml) = 5.275         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1291 r_free = 0.1790             target_work(ml) = 5.274         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1291   r_free= 0.1790   ksol= 0.32   Bsol= 57.35   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.74,2.95,3.11,0.00,0.00,0.00); trace/3= 2.93                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.274204                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1295   r_free= 0.1783   ksol= 0.32   Bsol= 57.35   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.46,2.65,3.11,0.00,0.00,0.00); trace/3= 2.74                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.273178                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.137476              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 141.884  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.248303              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 145.413  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1295      final r-factor (work) = 0.1218          |
| start r-factor (free) = 0.1783      final r-factor (free) = 0.1701          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3850 = 3.14 * 0.50 * 5.2931 + 1.00 * 0.0815                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3173 = 3.14 * 0.50 * 5.2492 + 1.00 * 0.0826                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1218      final r-factor (work) = 0.1213          |
| start r-factor (free) = 0.1701      final r-factor (free) = 0.1693          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3159 = 0.25 * 1.00 * 5.2492 + 1.00 * 0.0125                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3086 = 0.25 * 1.00 * 5.2232 + 1.00 * 0.0116                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 31     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.371)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.49   13.03    None  None   None       |
|    all(noH): 2823   0      0.00    91.49   13.03    None  None   None       |
|    Sol.    : 438    0      1.34    88.54   37.54    None  None   None       |
|    Mac.    : 2385   0      0.00    91.49   8.53     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:     0.000 -   9.149: 1718   |   5:    45.746 -  54.896:   80        |
|      1:     9.149 -  18.299:  558   |   6:    54.896 -  64.045:   58        |
|      2:    18.299 -  27.448:  160   |   7:    64.045 -  73.194:   21        |
|      3:    27.448 -  36.597:  117   |   8:    73.194 -  82.343:    9        |
|      4:    36.597 -  45.746:   91   |   9:    82.343 -  91.493:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1213 r_free = 0.1693             target_work(ml) = 5.221         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1212 r_free = 0.1691             target_work(ml) = 5.220         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1212   r_free= 0.1691   ksol= 0.32   Bsol= 57.35   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.46,2.65,3.11,0.00,0.00,0.00); trace/3= 2.74                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.219941                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2649 -  4.7770 0.99   1400  157 0.1025 0.1352      5.4032      5.5561|
|  2:  4.7770 -  3.8110 0.99   1361  145 0.0871 0.1136      5.4561      5.6706|
|  3:  3.8110 -  3.3350 0.99   1321  151 0.1136 0.1569      5.5222      5.8648|
|  4:  3.3350 -  3.0327 0.99   1328  150 0.1309 0.1667      5.5184      5.6743|
|  5:  3.0327 -  2.8168 0.99   1314  143 0.1499 0.1965       5.437      5.6233|
|  6:  2.8168 -  2.6516 0.99   1294  145 0.1371 0.2054      5.3138      5.5794|
|  7:  2.6516 -  2.5194 0.99   1318  141 0.1371 0.1843      5.2522      5.4466|
|  8:  2.5194 -  2.4102 0.98   1273  150 0.1298 0.1847      5.1472      5.3908|
|  9:  2.4102 -  2.3178 0.98   1293  145 0.1285 0.1910      5.1101      5.3505|
| 10:  2.3178 -  2.2380 0.98   1277  135 0.1275 0.1877      5.0627      5.3015|
| 11:  2.2380 -  2.1683 1.00   1289  144 0.1286 0.1920      5.0366      5.3497|
| 12:  2.1683 -  2.1064 0.97   1262  139 0.1207 0.1809      4.9546      5.1793|
| 13:  2.1064 -  2.0511 0.98   1280  142 0.1304 0.1841      4.8446      5.0647|
| 14:  2.0511 -  2.0012 0.47    620   72 0.1073 0.1828      4.6783      4.9996|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2649 -  4.7770  1400   157  0.94   9.27   0.96     0.94       7598.35|
|  2:  4.7770 -  3.8110  1361   145  0.95   8.41   1.00     0.98       9463.06|
|  3:  3.8110 -  3.3350  1321   151  0.93  12.26   1.01     1.00      11415.93|
|  4:  3.3350 -  3.0327  1328   150  0.91  14.89   1.00     0.98      11754.41|
|  5:  3.0327 -  2.8168  1314   143  0.88  18.32   0.99     0.97      10448.57|
|  6:  2.8168 -  2.6516  1294   145  0.89  17.68   0.98     0.95       8653.87|
|  7:  2.6516 -  2.5194  1318   141  0.89  17.10   0.99     0.96       7356.67|
|  8:  2.5194 -  2.4102  1273   150  0.89  17.10   0.99     0.95       6223.11|
|  9:  2.4102 -  2.3178  1293   145  0.89  17.15   1.00     0.95       5841.31|
| 10:  2.3178 -  2.2380  1277   135  0.89  17.38   0.99     0.94       5281.48|
| 11:  2.2380 -  2.1683  1289   144  0.89  17.71   0.99     0.93       5067.95|
| 12:  2.1683 -  2.1064  1262   139  0.90  16.39   0.99     0.99       4641.83|
| 13:  2.1064 -  2.0511  1280   142  0.89  17.63   0.99     0.97       3633.75|
| 14:  2.0511 -  2.0012   620    72  0.91  15.10   0.97     0.94       2593.09|
|alpha:            min =        0.93 max =            1.00 mean =         0.96|
|beta:             min =     2593.09 max =        11754.41 mean =      7356.76|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.87 mean =        15.40|
|phase err.(test): min =        0.00 max =           89.87 mean =        14.78|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1212   r_free= 0.1692   ksol= 0.32   Bsol= 62.55   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.28,-0.15,0.43,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.219812                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.26 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1212   r_free= 0.1692   ksol= 0.32   Bsol= 62.55   scale= 0.986   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.28,-0.15,0.43,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.219812                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2649 -  4.7770 0.99   1400  157 0.1025 0.1353      5.4033      5.5574|
|  2:  4.7770 -  3.8110 0.99   1361  145 0.0874 0.1141      5.4578      5.6735|
|  3:  3.8110 -  3.3350 0.99   1321  151 0.1137 0.1569      5.5231      5.8648|
|  4:  3.3350 -  3.0327 0.99   1328  150 0.1308 0.1666      5.5179      5.6741|
|  5:  3.0327 -  2.8168 0.99   1314  143 0.1497 0.1965      5.4361      5.6229|
|  6:  2.8168 -  2.6516 0.99   1294  145 0.1370 0.2048       5.313      5.5775|
|  7:  2.6516 -  2.5194 0.99   1318  141 0.1370 0.1845      5.2514      5.4465|
|  8:  2.5194 -  2.4102 0.98   1273  150 0.1297 0.1845      5.1465      5.3899|
|  9:  2.4102 -  2.3178 0.98   1293  145 0.1284 0.1911      5.1097      5.3502|
| 10:  2.3178 -  2.2380 0.98   1277  135 0.1275 0.1878      5.0624      5.3019|
| 11:  2.2380 -  2.1683 1.00   1289  144 0.1286 0.1918      5.0364      5.3496|
| 12:  2.1683 -  2.1064 0.97   1262  139 0.1207 0.1811      4.9551      5.1799|
| 13:  2.1064 -  2.0511 0.98   1280  142 0.1304 0.1842      4.8444      5.0651|
| 14:  2.0511 -  2.0012 0.47    620   72 0.1073 0.1823      4.6776      4.9981|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2649 -  4.7770  1400   157  0.94   9.28   0.96     0.94       7613.23|
|  2:  4.7770 -  3.8110  1361   145  0.95   8.44   1.00     0.98       9497.93|
|  3:  3.8110 -  3.3350  1321   151  0.93  12.29   1.01     1.00      11452.44|
|  4:  3.3350 -  3.0327  1328   150  0.91  14.89   0.99     0.97      11751.69|
|  5:  3.0327 -  2.8168  1314   143  0.88  18.30   0.99     0.96      10428.99|
|  6:  2.8168 -  2.6516  1294   145  0.89  17.66   0.98     0.95       8636.60|
|  7:  2.6516 -  2.5194  1318   141  0.89  17.07   0.98     0.96       7346.08|
|  8:  2.5194 -  2.4102  1273   150  0.89  17.09   0.98     0.95       6215.86|
|  9:  2.4102 -  2.3178  1293   145  0.89  17.14   0.99     0.95       5837.15|
| 10:  2.3178 -  2.2380  1277   135  0.89  17.37   0.98     0.94       5279.81|
| 11:  2.2380 -  2.1683  1289   144  0.89  17.71   0.98     0.93       5069.95|
| 12:  2.1683 -  2.1064  1262   139  0.90  16.40   0.99     0.98       4648.10|
| 13:  2.1064 -  2.0511  1280   142  0.89  17.63   0.98     0.96       3632.63|
| 14:  2.0511 -  2.0012   620    72  0.91  15.08   0.96     0.93       2588.31|
|alpha:            min =        0.93 max =            1.00 mean =         0.96|
|beta:             min =     2588.31 max =        11751.69 mean =      7359.04|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.83 mean =        15.40|
|phase err.(test): min =        0.00 max =           89.73 mean =        14.78|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.371)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.64    94.13   15.67    None  None   None       |
|    all(noH): 2823   0      2.64    94.13   15.67    None  None   None       |
|    Sol.    : 438    0      3.97    91.18   40.18    None  None   None       |
|    Mac.    : 2385   0      2.64    94.13   11.16    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.638 -  11.787: 1718   |   5:    48.384 -  57.533:   80        |
|      1:    11.787 -  20.936:  558   |   6:    57.533 -  66.683:   58        |
|      2:    20.936 -  30.086:  160   |   7:    66.683 -  75.832:   21        |
|      3:    30.086 -  39.235:  117   |   8:    75.832 -  84.981:    9        |
|      4:    39.235 -  48.384:   91   |   9:    84.981 -  94.131:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 343         
Filter by distance & map next to the model:
   mapped sites are within: 0.393 - 4.543
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 331 from: 343
   mapped sites are within: 0.720 - 4.543

peak=    8.897 closest distance to " CG2 VAL A 230 " =    1.324
peak=    6.642 closest distance to " CG2 VAL A 296 " =    1.093
peak=    6.078 closest distance to " CG  LEU A   5 " =    1.252
peak=    5.677 closest distance to " O   HOH Z 111 " =    1.900
peak=    5.545 closest distance to " CB  SER A  63 " =    1.317
peak=    5.365 closest distance to " CB  VAL A 230 " =    1.310
peak=    5.348 closest distance to " O   HOH Z 102 " =    1.229
peak=    5.219 closest distance to " CB  GLN A 223 " =    1.393
peak=    5.081 closest distance to " O   HOH Z 210 " =    1.043
peak=    5.043 closest distance to " CG  LEU A 228 " =    1.255
peak=    5.006 closest distance to " CG  PRO A  54 " =    1.309
peak=    4.845 closest distance to " O   HOH Z 232 " =    2.166
peak=    4.774 closest distance to " CB  PRO A  54 " =    0.887
peak=    4.597 closest distance to " CZ  PHE A 192 " =    1.079
peak=    4.570 closest distance to " CB  VAL A 296 " =    1.163
peak=    4.533 closest distance to " CD1AILE A 234 " =    1.053
peak=    4.527 closest distance to " O   HOH Z  67 " =    1.963
peak=    4.514 closest distance to " O   HOH Z 433 " =    1.710
peak=    4.491 closest distance to " O   PRO A 198 " =    1.577
peak=    4.478 closest distance to " CG2 THR A 221 " =    1.018
peak=    4.436 closest distance to " CG  PRO A 213 " =    1.271
peak=    4.401 closest distance to " CD2 LEU A   5 " =    1.143
peak=    4.369 closest distance to " CG1 ILE A  33 " =    1.314
peak=    4.369 closest distance to " CB  GLU A 152 " =    1.177
peak=    4.328 closest distance to " O   HOH Z 303 " =    2.209
peak=    4.310 closest distance to " O   HOH Z 247 " =    1.523
peak=    4.298 closest distance to " CG  PRO A 243 " =    1.108
peak=    4.285 closest distance to " O   HOH Z 410 " =    1.081
peak=    4.283 closest distance to " CG  PRO A 280 " =    0.861
peak=    4.258 closest distance to " CG  PRO A 198 " =    1.376
peak=    4.197 closest distance to " O   HOH Z 236 " =    1.897
peak=    4.169 closest distance to " CB  TRP A 266 " =    0.933
peak=    4.160 closest distance to " O   HOH Z 369 " =    2.002
peak=    4.160 closest distance to " O   HOH Z 368 " =    2.321
peak=    4.150 closest distance to " O   HOH Z 126 " =    1.671
peak=    4.128 closest distance to " O   HOH Z  48 " =    1.831
peak=    4.128 closest distance to " O   HOH Z  63 " =    2.039
peak=    4.118 closest distance to " CG  ARG A 138 " =    1.251
peak=    4.108 closest distance to " CA  TYR A  30 " =    0.972
peak=    4.108 closest distance to " O   HOH Z 265 " =    2.168
peak=    4.091 closest distance to " NH1AARG A 145 " =    1.191
peak=    4.085 closest distance to " CB  GLU A 128 " =    1.169
peak=    4.084 closest distance to " CD  ARG A  66 " =    2.481
peak=    4.057 closest distance to " CB  GLN A 183 " =    1.226
peak=    4.047 closest distance to " O   HOH Z 134 " =    1.700
peak=    4.046 closest distance to " NE2 GLN A  11 " =    1.122
peak=    4.025 closest distance to " O   HOH Z 163 " =    1.722
peak=    4.025 closest distance to " O   HOH Z 425 " =    1.522
peak=    4.018 closest distance to " CB  ARG A 190 " =    1.707
peak=    4.014 closest distance to " CD2 LEU A 228 " =    1.211
peak=    4.004 closest distance to " CD1 LEU A 300 " =    1.177
peak=    3.986 closest distance to " O   HOH Z 234 " =    3.705
peak=    3.978 closest distance to " O   SER A  87 " =    2.321
peak=    3.978 closest distance to " CZ  PHE A 218 " =    1.148
peak=    3.963 closest distance to " O   HOH Z 411 " =    3.470
peak=    3.959 closest distance to " O   ASP A 124 " =    1.153
peak=    3.959 closest distance to " O   HOH Z 184 " =    1.631
peak=    3.957 closest distance to " CG BARG A 275 " =    1.438
peak=    3.956 closest distance to " O   HOH Z 272 " =    1.978
peak=    3.955 closest distance to " O   HOH Z  47 " =    1.634
peak=    3.951 closest distance to " O   HOH Z  49 " =    0.980
peak=    3.940 closest distance to " CA  MET A  40 " =    1.217
peak=    3.936 closest distance to " CB  ALA A 291 " =    1.317
peak=    3.925 closest distance to " O   HOH Z 298 " =    1.910
peak=    3.924 closest distance to " CD  ARG A 159 " =    0.787
peak=    3.913 closest distance to " CD ALYS A 290 " =    1.092
peak=    3.909 closest distance to " OE1 GLN A  11 " =    1.924
peak=    3.908 closest distance to " CB  ARG A 275 " =    0.869
peak=    3.905 closest distance to " OD1 ASN A 217 " =    1.594
peak=    3.892 closest distance to " O   HOH Z 112 " =    1.538
peak=    3.888 closest distance to " CG2 VAL A 296 " =    1.607
peak=    3.884 closest distance to " O   HOH Z 316 " =    3.122
peak=    3.881 closest distance to " CD  LYS A 166 " =    1.299
peak=    3.872 closest distance to " CB  ASN A 148 " =    1.282
peak=    3.851 closest distance to " CB  VAL A 202 " =    1.465
peak=    3.840 closest distance to " NH1 ARG A  56 " =    1.049
peak=    3.837 closest distance to " CA  ALA A 295 " =    1.036
peak=    3.827 closest distance to " CB  GLU A 277 " =    3.794
peak=    3.827 closest distance to " O   HOH Z  44 " =    2.144
peak=    3.823 closest distance to " O   HOH Z 183 " =    1.300
peak=    3.817 closest distance to " O   HOH Z 261 " =    1.771
peak=    3.814 closest distance to " CD1 LEU A   5 " =    1.341
peak=    3.811 closest distance to " O   HOH Z  88 " =    3.253
peak=    3.810 closest distance to " CB  ASP A 140 " =    0.784
peak=    3.804 closest distance to " O   HOH Z 427 " =    3.145
peak=    3.804 closest distance to " O   HOH Z  80 " =    1.928
peak=    3.803 closest distance to " CB  LEU A 143 " =    1.189
peak=    3.796 closest distance to " O   HOH Z 227 " =    1.694
peak=    3.785 closest distance to " CB  SER A 216 " =    0.869
peak=    3.780 closest distance to " O   HOH Z 389 " =    2.022
peak=    3.769 closest distance to " CG1 VAL A 153 " =    1.018
peak=    3.763 closest distance to " O   HOH Z  15 " =    2.024
peak=    3.756 closest distance to " O   HOH Z  21 " =    1.715
peak=    3.753 closest distance to " OG BSER A 164 " =    2.093
peak=    3.748 closest distance to " CB  ALA A 248 " =    1.138
peak=    3.745 closest distance to " O   HOH Z  78 " =    2.297
peak=    3.744 closest distance to " O   HOH Z 386 " =    2.278
peak=    3.744 closest distance to " O   HOH Z  61 " =    1.578
peak=    3.737 closest distance to " CG AARG A 275 " =    1.191
peak=    3.729 closest distance to " CB  TRP A 179 " =    1.452
peak=    3.722 closest distance to " O   HOH Z 359 " =    1.615
peak=    3.719 closest distance to " CG  MET A 185 " =    1.325
peak=    3.718 closest distance to " CB  SER A   3 " =    1.481
peak=    3.718 closest distance to " O   HOH Z  43 " =    1.971
peak=    3.715 closest distance to " OD1 ASN A  69 " =    2.453
peak=    3.714 closest distance to " CA  ASP A 191 " =    0.789
peak=    3.708 closest distance to " O   GLN A 278 " =    1.189
peak=    3.703 closest distance to " CA  LEU A 282 " =    1.083
peak=    3.701 closest distance to " CA  PRO A  54 " =    1.387
peak=    3.695 closest distance to " O   HOH Z 120 " =    0.811
peak=    3.695 closest distance to " O   HOH Z 403 " =    1.763
peak=    3.694 closest distance to " NH2 ARG A 156 " =    1.147
peak=    3.689 closest distance to " O   HOH Z 271 " =    2.709
peak=    3.687 closest distance to " O   ALA A 165 " =    1.318
peak=    3.683 closest distance to " O   HOH Z 214 " =    2.237
peak=    3.678 closest distance to " O   HOH Z 423 " =    1.690
peak=    3.678 closest distance to " CB  ALA A   9 " =    1.616
peak=    3.668 closest distance to " CB  LEU A 228 " =    1.213
peak=    3.666 closest distance to " O   HOH Z 383 " =    2.160
peak=    3.653 closest distance to " CA  ARG A 195 " =    1.249
peak=    3.642 closest distance to " O   HOH Z   4 " =    1.850
peak=    3.640 closest distance to " CB  ASN A 142 " =    1.009
peak=    3.635 closest distance to " CB  SER A 141 " =    1.056
peak=    3.633 closest distance to " O   HOH Z 437 " =    2.240
peak=    3.633 closest distance to " O   HOH Z 128 " =    2.217
peak=    3.630 closest distance to " CB  ASN A 187 " =    1.013
peak=    3.628 closest distance to " O  BHOH Z 338 " =    0.964
peak=    3.628 closest distance to " CB  ALA A 242 " =    0.855
peak=    3.622 closest distance to " ND2 ASN A 187 " =    1.472
peak=    3.614 closest distance to " CB  ASN A  39 " =    0.866
peak=    3.612 closest distance to " N   TYR A  15 " =    0.763
peak=    3.607 closest distance to " O   HOH Z 171 " =    3.953
peak=    3.602 closest distance to " CA  GLY A 267 " =    0.840
peak=    3.600 closest distance to " CD  ARG A 269 " =    0.905
peak=    3.600 closest distance to " CG  LEU A 167 " =    1.185
peak=    3.596 closest distance to " CA  GLU A 152 " =    0.903
peak=    3.586 closest distance to " CG2BVAL A  41 " =    1.183
peak=    3.586 closest distance to " O   HOH Z 133 " =    2.187
peak=    3.580 closest distance to " ND1 HIS A  81 " =    1.670
peak=    3.580 closest distance to " CG2 THR A  42 " =    0.841
peak=    3.578 closest distance to " O   HOH Z 346 " =    1.524
peak=    3.575 closest distance to " CA  ILE A 106 " =    0.793
peak=    3.571 closest distance to " CA  ALA A  21 " =    1.273
peak=    3.570 closest distance to " O   HOH Z 244 " =    1.749
peak=    3.568 closest distance to " O   HOH Z 245 " =    1.471
peak=    3.556 closest distance to " CA  ALA A  51 " =    0.994
peak=    3.555 closest distance to " CB  ARG A  79 " =    1.497
peak=    3.554 closest distance to " O   HOH Z 394 " =    1.625
peak=    3.549 closest distance to " O   HOH Z 174 " =    1.201
peak=    3.548 closest distance to " CB  ALA A 100 " =    1.383
peak=    3.538 closest distance to " CD1 TRP A 266 " =    1.067
peak=    3.538 closest distance to " O   MET A 105 " =    1.866
peak=    3.536 closest distance to " CB  TYR A 169 " =    0.909
peak=    3.534 closest distance to " CB  TYR A  30 " =    1.043
peak=    3.530 closest distance to " N   ASN A 127 " =    1.195
peak=    3.526 closest distance to " OD2 ASP A 286 " =    2.904
peak=    3.524 closest distance to " O   HOH Z 295 " =    1.542
peak=    3.520 closest distance to " OG  SER A  22 " =    2.909
peak=    3.516 closest distance to " CD2 LEU A 255 " =    1.398
peak=    3.515 closest distance to " O   HOH Z 355 " =    1.829
peak=    3.513 closest distance to " O   HOH Z  63 " =    1.208
peak=    3.513 closest distance to " O   HOH Z  57 " =    1.573
peak=    3.513 closest distance to " O   HOH Z  98 " =    2.065
peak=    3.509 closest distance to " O   HOH Z 117 " =    2.084
peak=    3.504 closest distance to " CB  VAL A 265 " =    1.329
peak=    3.496 closest distance to " O   HOH Z 193 " =    1.987
peak=    3.492 closest distance to " O   HOH Z 128 " =    2.150
peak=    3.482 closest distance to " O   HOH Z 326 " =    2.228
peak=    3.476 closest distance to " O   HOH Z 141 " =    1.729
peak=    3.475 closest distance to " O   HOH Z 158 " =    3.117
peak=    3.469 closest distance to " O   HOH Z 281 " =    4.343
peak=    3.462 closest distance to " O   HOH Z 280 " =    2.821
peak=    3.461 closest distance to " CB  PHE A 204 " =    0.994
peak=    3.449 closest distance to " CB  ALA A 137 " =    1.141
peak=    3.448 closest distance to " O   HOH Z 128 " =    1.859
peak=    3.447 closest distance to " O   HOH Z 132 " =    2.536
peak=    3.443 closest distance to " O   HOH Z  19 " =    2.333
peak=    3.441 closest distance to " O   HOH Z  32 " =    2.036
peak=    3.435 closest distance to " O   HOH Z 387 " =    3.113
peak=    3.434 closest distance to " CA  LYS A 117 " =    1.218
peak=    3.431 closest distance to " CA  ALA A 160 " =    1.013
peak=    3.428 closest distance to " O   HOH Z 420 " =    2.273
peak=    3.422 closest distance to " O   HOH Z 199 " =    1.712
peak=    3.414 closest distance to " O   HOH Z  54 " =    1.336
peak=    3.412 closest distance to " O   HOH Z 196 " =    1.207
peak=    3.408 closest distance to " CB  TRP A 150 " =    1.423
peak=    3.407 closest distance to " CE2 TYR A 186 " =    0.947
peak=    3.406 closest distance to " O   HOH Z 172 " =    3.765
peak=    3.401 closest distance to " CG1 ILE A  49 " =    1.623
peak=    3.399 closest distance to " O   TRP A 274 " =    1.888
peak=    3.389 closest distance to " CA  ILE A  33 " =    1.649
peak=    3.387 closest distance to " O   HOH Z 133 " =    1.763
peak=    3.386 closest distance to " CA  ASP A 162 " =    1.101
peak=    3.383 closest distance to " CB  ALA A  71 " =    1.217
peak=    3.381 closest distance to " CB  GLU A  46 " =    1.041
peak=    3.380 closest distance to " OG  SER A 276 " =    1.476
peak=    3.377 closest distance to " N   ARG A 190 " =    1.069
peak=    3.377 closest distance to " CB  ILE A 120 " =    1.397
peak=    3.376 closest distance to " CD1 LEU A  96 " =    0.775
peak=    3.374 closest distance to " O   HOH Z 213 " =    1.729
peak=    3.371 closest distance to " O   HOH Z 104 " =    2.712
peak=    3.367 closest distance to " O   PRO A 213 " =    1.551
peak=    3.366 closest distance to " O   HOH Z 327 " =    2.237
peak=    3.365 closest distance to " O   HOH Z 345 " =    3.662
peak=    3.360 closest distance to " O   HOH Z 180 " =    2.028
peak=    3.357 closest distance to " O   HOH Z 352 " =    1.873
peak=    3.355 closest distance to " O   HOH Z  89 " =    1.752
peak=    3.353 closest distance to " C   SER A  32 " =    1.008
peak=    3.351 closest distance to " O   ALA A 158 " =    1.396
peak=    3.351 closest distance to " CB  ALA A 256 " =    1.483
peak=    3.345 closest distance to " O   HOH Z 362 " =    3.531
peak=    3.344 closest distance to " O   HOH Z 298 " =    2.332
peak=    3.344 closest distance to " O   HOH Z 419 " =    2.873
peak=    3.343 closest distance to " CB  SER A 212 " =    1.200
peak=    3.342 closest distance to " CG2 ILE A 106 " =    0.908
peak=    3.338 closest distance to " O   HOH Z 344 " =    3.059
peak=    3.338 closest distance to " CA  TYR A 116 " =    1.420
peak=    3.332 closest distance to " O   HOH Z 125 " =    3.846
peak=    3.332 closest distance to " CA  ASP A 124 " =    0.720
peak=    3.332 closest distance to " NH2 ARG A  79 " =    1.452
peak=    3.332 closest distance to " CB  GLN A  88 " =    1.231
peak=    3.328 closest distance to " NH1 ARG A  14 " =    1.121
peak=    3.328 closest distance to " CB  ALA A  43 " =    0.981
peak=    3.320 closest distance to " N   PHE A 130 " =    1.199
peak=    3.316 closest distance to " CA  LYS A 181 " =    1.032
peak=    3.315 closest distance to " O   HOH Z 135 " =    2.055
peak=    3.310 closest distance to " N   ASN A  39 " =    1.236
peak=    3.309 closest distance to " CA  TRP A 274 " =    0.940
peak=    3.309 closest distance to " NZ  LYS A 166 " =    3.177
peak=    3.308 closest distance to " NH2BARG A 190 " =    1.781
peak=    3.304 closest distance to " O   HOH Z 134 " =    2.292
peak=    3.300 closest distance to " CA  SER A  87 " =    0.814
peak=    3.299 closest distance to " CG  MET A 188 " =    0.769
peak=    3.299 closest distance to " O   ASN A 209 " =    1.280
peak=    3.298 closest distance to " N   SER A 135 " =    1.416
peak=    3.297 closest distance to " N   VAL A 126 " =    1.439
peak=    3.297 closest distance to " O   HOH Z  30 " =    1.287
peak=    3.294 closest distance to " O   HOH Z 126 " =    2.048
peak=    3.294 closest distance to " NZ  LYS A 117 " =    3.252
peak=    3.288 closest distance to " O   HOH Z  56 " =    1.741
peak=    3.288 closest distance to " OE1 GLU A   2 " =    2.003
peak=    3.286 closest distance to " O   HOH Z 371 " =    3.115
peak=    3.286 closest distance to " O   HOH Z 368 " =    4.201
peak=    3.280 closest distance to " CD  PRO A  54 " =    1.042
peak=    3.278 closest distance to " CA  LYS A 290 " =    1.348
peak=    3.278 closest distance to " O   HOH Z  22 " =    2.590
peak=    3.277 closest distance to " O   HOH Z 271 " =    1.983
peak=    3.275 closest distance to " CZ3 TRP A  92 " =    1.422
peak=    3.275 closest distance to " CB  ALA A 104 " =    0.859
peak=    3.271 closest distance to " CG2 THR A 220 " =    0.836
peak=    3.267 closest distance to " CD1 LEU A 101 " =    1.039
peak=    3.266 closest distance to " O   HOH Z 256 " =    1.553
peak=    3.264 closest distance to " O   HOH Z 391 " =    3.020
peak=    3.264 closest distance to " CG1 VAL A 296 " =    1.200
peak=    3.262 closest distance to " O   HOH Z 131 " =    2.320
peak=    3.260 closest distance to " O   HOH Z 197 " =    2.376
peak=    3.256 closest distance to " CB  ILE A 199 " =    0.830
peak=    3.255 closest distance to " O   HOH Z 188 " =    2.986
peak=    3.254 closest distance to " CB  TYR A 116 " =    1.140
peak=    3.254 closest distance to " CZ3 TRP A  85 " =    0.956
peak=    3.253 closest distance to " CB  GLN A  89 " =    1.034
peak=    3.253 closest distance to " O   THR A  31 " =    1.533
peak=    3.250 closest distance to " CA  ALA A 291 " =    0.926
peak=    3.243 closest distance to " O   HOH Z 109 " =    2.258
peak=    3.242 closest distance to " CD  ARG A 219 " =    1.109
peak=    3.241 closest distance to " O   HOH Z 197 " =    1.953
peak=    3.238 closest distance to " O   HOH Z 392 " =    1.447
peak=    3.238 closest distance to " OE1 GLN A  55 " =    1.245
peak=    3.237 closest distance to " OG BSER A 134 " =    2.895
peak=    3.234 closest distance to " CE2 TYR A  30 " =    0.851
peak=    3.230 closest distance to " CA  GLY A 196 " =    0.812
peak=    3.225 closest distance to " O   HOH Z 114 " =    1.373
peak=    3.223 closest distance to " CA  ASP A 140 " =    1.235
peak=    3.220 closest distance to " O   HOH Z 116 " =    1.836
peak=    3.219 closest distance to " CB  MET A  40 " =    0.787
peak=    3.219 closest distance to " O   HOH Z 299 " =    4.543
peak=    3.217 closest distance to " CG2 THR A  29 " =    1.459
peak=    3.213 closest distance to " O   ASP A 200 " =    1.509
peak=    3.213 closest distance to " OE1 GLN A 278 " =    0.890
peak=    3.212 closest distance to " O   HOH Z 422 " =    2.657
peak=    3.208 closest distance to " O   HOH Z 327 " =    1.811
peak=    3.208 closest distance to " O   HOH Z 157 " =    1.351
peak=    3.207 closest distance to " O   HOH Z  99 " =    2.443
peak=    3.203 closest distance to " NZ  LYS A  48 " =    1.368
peak=    3.198 closest distance to " O   HOH Z 123 " =    2.281
peak=    3.196 closest distance to " O   HOH Z  58 " =    1.546
peak=    3.195 closest distance to " CD  ARG A  14 " =    1.266
peak=    3.193 closest distance to " O   HOH Z 148 " =    1.931
peak=    3.191 closest distance to " NZ  LYS A 181 " =    1.172
peak=    3.191 closest distance to " O   HOH Z 175 " =    3.730
peak=    3.183 closest distance to " C   VAL A 265 " =    1.242
peak=    3.183 closest distance to " CA  VAL A  41 " =    0.846
peak=    3.182 closest distance to " CB  ALA A  84 " =    0.906
peak=    3.182 closest distance to " CG  ARG A 219 " =    1.109
peak=    3.180 closest distance to " CA  ALA A 158 " =    1.187
peak=    3.178 closest distance to " NH2 ARG A 219 " =    1.767
peak=    3.178 closest distance to " O   HOH Z  78 " =    1.870
peak=    3.176 closest distance to " O   HOH Z 139 " =    3.240
peak=    3.176 closest distance to " CB  MET A  47 " =    1.052
peak=    3.175 closest distance to " O   HOH Z 423 " =    2.915
peak=    3.168 closest distance to " O   HOH Z 313 " =    1.867
peak=    3.168 closest distance to " CG  GLU A  37 " =    0.922
peak=    3.165 closest distance to " O   HOH Z 417 " =    3.203
peak=    3.159 closest distance to " CD1 ILE A  33 " =    1.529
peak=    3.154 closest distance to " O   HOH Z 438 " =    3.014
peak=    3.154 closest distance to " O   HOH Z 240 " =    2.196
peak=    3.142 closest distance to " CB  PRO A 198 " =    0.986
peak=    3.132 closest distance to " CA  ARG A  36 " =    1.200
peak=    3.131 closest distance to " O   HOH Z 350 " =    1.738
peak=    3.128 closest distance to " O   HOH Z 374 " =    2.957
peak=    3.127 closest distance to " NE2 HIS A 115 " =    0.995
peak=    3.125 closest distance to " O   HOH Z 185 " =    1.982
peak=    3.123 closest distance to " OD1 ASN A 301 " =    1.567
peak=    3.118 closest distance to " CE1 PHE A 208 " =    1.088
peak=    3.116 closest distance to " O   HOH Z 187 " =    2.332
peak=    3.114 closest distance to " O   HOH Z  40 " =    1.806
peak=    3.110 closest distance to " O   HOH Z  99 " =    2.132
peak=    3.107 closest distance to " CA  ALA A 100 " =    1.096
peak=    3.104 closest distance to " OG  SER A  62 " =    3.006
peak=    3.104 closest distance to " O   HOH Z 258 " =    2.363
peak=    3.102 closest distance to " CA  VAL A 112 " =    1.158
peak=    3.102 closest distance to " O   HOH Z 301 " =    1.915
peak=    3.096 closest distance to " O   HOH Z 435 " =    1.827
peak=    3.094 closest distance to " CA  GLU A  46 " =    0.759
peak=    3.090 closest distance to " OD2 ASP A 200 " =    1.304
peak=    3.080 closest distance to " O   TYR A 116 " =    1.228
peak=    3.079 closest distance to " C   ALA A 299 " =    0.970
peak=    3.069 closest distance to " O   HOH Z 353 " =    2.812
peak=    3.069 closest distance to " O   HOH Z 155 " =    3.300
peak=    3.056 closest distance to " O   HOH Z 420 " =    1.815
peak=    3.048 closest distance to " CA  CYS A 254 " =    1.348

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 214         
Filter by distance & map next to the model:
   mapped sites are within: 0.745 - 5.310
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 214 from: 214
   mapped sites are within: 0.745 - 5.310

peak=   -4.981 closest distance to " CG2 VAL A 230 " =    0.894
peak=   -4.278 closest distance to " O   HOH Z 231 " =    1.226
peak=   -4.245 closest distance to " O   HOH Z  52 " =    1.707
peak=   -4.100 closest distance to " CB  ALA A 161 " =    2.641
peak=   -4.084 closest distance to " CD2 LEU A 167 " =    1.786
peak=   -4.081 closest distance to " CD1 PHE A  59 " =    1.928
peak=   -4.057 closest distance to " O   PRO A 163 " =    2.202
peak=   -4.032 closest distance to " O   HOH Z 231 " =    1.807
peak=   -4.021 closest distance to " OG  SER A  26 " =    1.259
peak=   -3.990 closest distance to " O   HOH Z  19 " =    2.197
peak=   -3.985 closest distance to " O   HOH Z 411 " =    4.984
peak=   -3.947 closest distance to " O   HOH Z 166 " =    1.802
peak=   -3.942 closest distance to " CG  ASP A 231 " =    0.807
peak=   -3.927 closest distance to " CG2BVAL A  41 " =    2.687
peak=   -3.916 closest distance to " CZ3 TRP A 179 " =    1.099
peak=   -3.904 closest distance to " O   HOH Z 184 " =    1.266
peak=   -3.895 closest distance to " CD2 LEU A 237 " =    2.722
peak=   -3.889 closest distance to " O   HOH Z 177 " =    1.682
peak=   -3.877 closest distance to " O   HOH Z  13 " =    1.730
peak=   -3.870 closest distance to " CG  MET A 105 " =    0.899
peak=   -3.866 closest distance to " OG  SER A  97 " =    2.289
peak=   -3.865 closest distance to " NH2 ARG A  66 " =    1.547
peak=   -3.858 closest distance to " CD  ARG A 156 " =    1.991
peak=   -3.835 closest distance to " O   HOH Z 103 " =    2.291
peak=   -3.831 closest distance to " C   ALA A 158 " =    1.289
peak=   -3.827 closest distance to " CG  ARG A 269 " =    2.383
peak=   -3.810 closest distance to " O   HOH Z 426 " =    1.816
peak=   -3.808 closest distance to " O   HOH Z 407 " =    3.623
peak=   -3.791 closest distance to " O   HOH Z 290 " =    1.329
peak=   -3.786 closest distance to " CD1 LEU A   5 " =    2.579
peak=   -3.776 closest distance to " O   HOH Z 111 " =    2.053
peak=   -3.775 closest distance to " CG1 VAL A 296 " =    1.366
peak=   -3.774 closest distance to " CB  PRO A 243 " =    2.711
peak=   -3.756 closest distance to " OG1 THR A  82 " =    1.858
peak=   -3.754 closest distance to " CD2 PHE A  59 " =    2.571
peak=   -3.752 closest distance to " CA  GLY A 241 " =    3.107
peak=   -3.740 closest distance to " CB  ALA A 291 " =    2.554
peak=   -3.739 closest distance to " O   HOH Z  10 " =    1.649
peak=   -3.736 closest distance to " O   PRO A 198 " =    1.287
peak=   -3.736 closest distance to " CG  ARG A  66 " =    2.449
peak=   -3.733 closest distance to " N   ALA A 226 " =    2.250
peak=   -3.729 closest distance to " O   HOH Z 351 " =    1.561
peak=   -3.727 closest distance to " O   HOH Z  73 " =    2.164
peak=   -3.698 closest distance to " CD  GLN A 223 " =    1.261
peak=   -3.697 closest distance to " CZ2 TRP A  92 " =    2.866
peak=   -3.676 closest distance to " CE2 TYR A  30 " =    2.724
peak=   -3.670 closest distance to " O   HOH Z 241 " =    1.109
peak=   -3.668 closest distance to " O   HOH Z 113 " =    1.819
peak=   -3.666 closest distance to " O   HOH Z 234 " =    4.492
peak=   -3.659 closest distance to " OG  SER A  87 " =    1.680
peak=   -3.654 closest distance to " CG  TRP A 266 " =    1.858
peak=   -3.653 closest distance to " OXT GLY A 302 " =    2.905
peak=   -3.647 closest distance to " O   HOH Z  11 " =    1.859
peak=   -3.644 closest distance to " CA  ASP A 298 " =    1.078
peak=   -3.642 closest distance to " O   VAL A  67 " =    2.525
peak=   -3.625 closest distance to " O   SER A 271 " =    2.282
peak=   -3.623 closest distance to " CG  LEU A 101 " =    2.562
peak=   -3.598 closest distance to " CA  GLY A 133 " =    2.311
peak=   -3.594 closest distance to " CD  GLN A  88 " =    0.883
peak=   -3.582 closest distance to " O   HOH Z 308 " =    1.755
peak=   -3.572 closest distance to " CA  GLY A 203 " =    2.323
peak=   -3.571 closest distance to " CD1 ILE A 151 " =    2.379
peak=   -3.568 closest distance to " O   HOH Z 396 " =    1.819
peak=   -3.559 closest distance to " OE1 GLN A 223 " =    2.117
peak=   -3.546 closest distance to " CG1 VAL A  78 " =    2.630
peak=   -3.529 closest distance to " CD2 TYR A 293 " =    1.929
peak=   -3.528 closest distance to " N   TYR A  68 " =    2.847
peak=   -3.513 closest distance to " CA  GLU A   2 " =    2.322
peak=   -3.505 closest distance to " C   ASN A 285 " =    2.535
peak=   -3.504 closest distance to " CD  GLN A 223 " =    0.877
peak=   -3.491 closest distance to " CD2 LEU A 300 " =    2.857
peak=   -3.490 closest distance to " CD1 TYR A 247 " =    2.343
peak=   -3.482 closest distance to " O   HOH Z  38 " =    1.047
peak=   -3.476 closest distance to " CB  CYS A 254 " =    2.294
peak=   -3.468 closest distance to " O   TYR A 186 " =    2.578
peak=   -3.462 closest distance to " O   HOH Z 222 " =    1.538
peak=   -3.458 closest distance to " OG ASER A 134 " =    1.303
peak=   -3.455 closest distance to " O   HOH Z 136 " =    2.546
peak=   -3.453 closest distance to " OD2 ASP A  50 " =    2.322
peak=   -3.452 closest distance to " NH2AARG A 275 " =    5.310
peak=   -3.452 closest distance to " CB  TRP A  85 " =    2.583
peak=   -3.450 closest distance to " O   HOH Z 113 " =    1.969
peak=   -3.449 closest distance to " OE1 GLN A  88 " =    1.111
peak=   -3.448 closest distance to " SD  MET A  93 " =    2.643
peak=   -3.446 closest distance to " CG  ARG A 219 " =    2.798
peak=   -3.445 closest distance to " OD1 ASN A 148 " =    1.507
peak=   -3.445 closest distance to " CD  GLN A  58 " =    1.042
peak=   -3.438 closest distance to " O   HOH Z 210 " =    1.134
peak=   -3.433 closest distance to " O   HOH Z 128 " =    4.235
peak=   -3.430 closest distance to " O   HOH Z 275 " =    1.512
peak=   -3.428 closest distance to " NH2 ARG A  66 " =    1.140
peak=   -3.427 closest distance to " CA  GLY A 241 " =    2.274
peak=   -3.412 closest distance to " CB  ARG A  79 " =    2.643
peak=   -3.408 closest distance to " CD  ARG A  14 " =    3.223
peak=   -3.405 closest distance to " CB  PRO A 163 " =    2.655
peak=   -3.404 closest distance to " O   GLY A  80 " =    2.540
peak=   -3.402 closest distance to " SG ACYS A 201 " =    1.128
peak=   -3.402 closest distance to " O   HOH Z  49 " =    1.090
peak=   -3.399 closest distance to " O   HOH Z 377 " =    1.655
peak=   -3.397 closest distance to " CG  GLU A   2 " =    1.810
peak=   -3.394 closest distance to " OG BSER A 134 " =    1.924
peak=   -3.393 closest distance to " O   HOH Z 185 " =    2.538
peak=   -3.392 closest distance to " CD1 LEU A 101 " =    2.937
peak=   -3.392 closest distance to " O   HOH Z 394 " =    1.622
peak=   -3.388 closest distance to " CD  LYS A 289 " =    2.428
peak=   -3.388 closest distance to " CG2 THR A 221 " =    2.332
peak=   -3.388 closest distance to " CH2 TRP A 177 " =    2.222
peak=   -3.385 closest distance to " O   GLY A 262 " =    2.529
peak=   -3.381 closest distance to " O   HOH Z  17 " =    1.381
peak=   -3.380 closest distance to " O   HOH Z 183 " =    1.379
peak=   -3.372 closest distance to " O   ALA A   7 " =    1.433
peak=   -3.372 closest distance to " CA  GLY A  98 " =    2.275
peak=   -3.368 closest distance to " O   HOH Z 353 " =    2.349
peak=   -3.355 closest distance to " CD2 PHE A  61 " =    1.910
peak=   -3.352 closest distance to " CD  PRO A 213 " =    2.205
peak=   -3.349 closest distance to " O   HOH Z  60 " =    1.823
peak=   -3.349 closest distance to " O   HOH Z 348 " =    2.327
peak=   -3.349 closest distance to " O   VAL A 125 " =    2.271
peak=   -3.349 closest distance to " CB  ALA A 291 " =    2.336
peak=   -3.345 closest distance to " CB  SER A  63 " =    3.365
peak=   -3.345 closest distance to " O   HOH Z 166 " =    1.840
peak=   -3.344 closest distance to " O   HOH Z 174 " =    2.168
peak=   -3.344 closest distance to " CD1 TRP A 179 " =    1.046
peak=   -3.335 closest distance to " CG1 VAL A 112 " =    2.634
peak=   -3.335 closest distance to " O   HOH Z 151 " =    1.722
peak=   -3.334 closest distance to " NE2 GLN A 194 " =    1.928
peak=   -3.333 closest distance to " C   GLU A 236 " =    0.745
peak=   -3.331 closest distance to " N   THR A 235 " =    1.243
peak=   -3.324 closest distance to " C   THR A 279 " =    1.140
peak=   -3.324 closest distance to " C   GLN A 240 " =    2.346
peak=   -3.323 closest distance to " O   VAL A 189 " =    2.661
peak=   -3.322 closest distance to " ND2 ASN A  60 " =    1.634
peak=   -3.321 closest distance to " OG  SER A  62 " =    4.706
peak=   -3.321 closest distance to " C   SER A 206 " =    1.447
peak=   -3.316 closest distance to " N   ALA A  43 " =    2.669
peak=   -3.315 closest distance to " O   HOH Z 166 " =    1.690
peak=   -3.313 closest distance to " CA  ASN A 127 " =    1.074
peak=   -3.307 closest distance to " CA  GLU A 277 " =    1.395
peak=   -3.307 closest distance to " C   GLY A 133 " =    1.249
peak=   -3.306 closest distance to " O   HOH Z  94 " =    2.173
peak=   -3.299 closest distance to " N   GLY A  23 " =    2.313
peak=   -3.292 closest distance to " O   HOH Z  24 " =    2.044
peak=   -3.290 closest distance to " O   HOH Z 252 " =    3.818
peak=   -3.286 closest distance to " NE2 GLN A  88 " =    0.936
peak=   -3.285 closest distance to " ND2 ASN A  60 " =    1.958
peak=   -3.283 closest distance to " CD  ARG A 139 " =    1.681
peak=   -3.278 closest distance to " OG BSER A 212 " =    1.754
peak=   -3.276 closest distance to " CG  GLU A  53 " =    1.656
peak=   -3.273 closest distance to " CB  PRO A 163 " =    2.557
peak=   -3.272 closest distance to " O   HOH Z  60 " =    2.070
peak=   -3.271 closest distance to " O   HOH Z 389 " =    1.878
peak=   -3.269 closest distance to " CZ2 TRP A 274 " =    1.149
peak=   -3.265 closest distance to " O   GLY A 211 " =    1.668
peak=   -3.263 closest distance to " O   ALA A  10 " =    1.929
peak=   -3.258 closest distance to " C   LEU A 143 " =    1.168
peak=   -3.256 closest distance to " N   THR A 157 " =    1.614
peak=   -3.255 closest distance to " O   ASP A  27 " =    1.920
peak=   -3.255 closest distance to " CB  ALA A  10 " =    2.170
peak=   -3.251 closest distance to " O   HOH Z 198 " =    1.611
peak=   -3.247 closest distance to " ND2 ASN A  45 " =    2.138
peak=   -3.241 closest distance to " O   HOH Z 246 " =    1.599
peak=   -3.241 closest distance to " CB  VAL A 230 " =    0.997
peak=   -3.239 closest distance to " O   HOH Z 264 " =    1.812
peak=   -3.238 closest distance to " OD2 ASP A 171 " =    1.961
peak=   -3.234 closest distance to " OE2 GLU A 152 " =    2.233
peak=   -3.229 closest distance to " NH2 ARG A  79 " =    1.962
peak=   -3.227 closest distance to " O   HOH Z 417 " =    2.920
peak=   -3.221 closest distance to " O   HOH Z 106 " =    2.103
peak=   -3.219 closest distance to " SG  CYS A 254 " =    3.034
peak=   -3.216 closest distance to " O   HOH Z 292 " =    4.581
peak=   -3.214 closest distance to " NH1 ARG A 195 " =    2.647
peak=   -3.211 closest distance to " ND2 ASN A 249 " =    2.251
peak=   -3.209 closest distance to " CB  ASP A 286 " =    2.291
peak=   -3.204 closest distance to " N   SER A 212 " =    1.988
peak=   -3.191 closest distance to " O   HOH Z  43 " =    1.625
peak=   -3.184 closest distance to " CG  LYS A 166 " =    2.109
peak=   -3.183 closest distance to " N   GLN A  58 " =    1.584
peak=   -3.180 closest distance to " OD1 ASN A 249 " =    2.185
peak=   -3.180 closest distance to " O   HOH Z 156 " =    3.491
peak=   -3.179 closest distance to " O   HOH Z 236 " =    1.403
peak=   -3.176 closest distance to " O   HOH Z 136 " =    0.916
peak=   -3.174 closest distance to " CG2 VAL A 189 " =    2.036
peak=   -3.174 closest distance to " OE1 GLN A 278 " =    1.275
peak=   -3.173 closest distance to " O   HOH Z 111 " =    1.267
peak=   -3.173 closest distance to " ND2 ASN A  45 " =    1.106
peak=   -3.169 closest distance to " O   HOH Z 390 " =    2.336
peak=   -3.168 closest distance to " OD1 ASN A 173 " =    1.280
peak=   -3.153 closest distance to " CE3 TRP A 150 " =    2.215
peak=   -3.148 closest distance to " CB  ALA A 248 " =    2.003
peak=   -3.147 closest distance to " CB  SER A 146 " =    2.245
peak=   -3.146 closest distance to " OD1 ASN A 301 " =    1.836
peak=   -3.146 closest distance to " O   HOH Z 377 " =    1.242
peak=   -3.144 closest distance to " CB  ALA A 291 " =    2.143
peak=   -3.137 closest distance to " CD  ARG A 259 " =    2.615
peak=   -3.128 closest distance to " O   HOH Z 190 " =    2.235
peak=   -3.122 closest distance to " C   ALA A 165 " =    1.962
peak=   -3.115 closest distance to " OG BSER A 134 " =    1.455
peak=   -3.114 closest distance to " C   ASN A 187 " =    1.783
peak=   -3.112 closest distance to " CD1 LEU A 167 " =    2.174
peak=   -3.110 closest distance to " CB  ALA A 114 " =    2.375
peak=   -3.106 closest distance to " ND2 ASN A  45 " =    1.531
peak=   -3.104 closest distance to " O   GLY A 211 " =    1.837
peak=   -3.093 closest distance to " CD  ARG A 195 " =    5.036
peak=   -3.091 closest distance to " CG2BVAL A  41 " =    1.446
peak=   -3.089 closest distance to " CZ  PHE A  38 " =    2.029
peak=   -3.084 closest distance to " OG1 THR A 279 " =    1.428
peak=   -3.075 closest distance to " N   THR A  18 " =    1.289
peak=   -3.066 closest distance to " CE  MET A 105 " =    2.077
peak=   -3.058 closest distance to " O   HOH Z 423 " =    1.995
peak=   -3.054 closest distance to " OD2 ASP A 171 " =    2.348
peak=   -3.049 closest distance to " O   HOH Z 357 " =    2.133
peak=   -3.046 closest distance to " CB  ALA A   9 " =    2.636
peak=   -3.038 closest distance to " C   SER A 271 " =    1.350
peak=   -3.037 closest distance to " CB  ASN A  39 " =    2.031

================= 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    :  0.4866 0.4700   6.287486e+00   6.273805e+00
   1_bss:  0.4793 0.4623   6.283875e+00   6.268276e+00
   1_xyz:  0.3962 0.4212   6.176931e+00   6.215751e+00
   1_adp:  0.3537 0.3989   6.107918e+00   6.189208e+00
   1_occ:  0.3531 0.3991   6.106999e+00   6.189854e+00
   2_bss:  0.3529 0.3964   6.109076e+00   6.189349e+00
   2_xyz:  0.2645 0.3277   5.880160e+00   6.036767e+00
   2_adp:  0.2429 0.3032   5.809966e+00   5.977592e+00
   2_occ:  0.2425 0.3034   5.809340e+00   5.976969e+00
   3_bss:  0.2406 0.2996   5.809333e+00   5.974194e+00
   3_xyz:  0.1754 0.2232   5.514904e+00   5.713845e+00
   3_adp:  0.1548 0.2051   5.420084e+00   5.637259e+00
   3_occ:  0.1547 0.2048   5.419420e+00   5.636636e+00
   4_bss:  0.1535 0.2048   5.416087e+00   5.635648e+00
   4_xyz:  0.1325 0.1852   5.301257e+00   5.535198e+00
   4_adp:  0.1292 0.1795   5.275193e+00   5.504739e+00
   4_occ:  0.1291 0.1790   5.274204e+00   5.503439e+00
   5_bss:  0.1295 0.1783   5.273178e+00   5.501682e+00
   5_xyz:  0.1218 0.1701   5.224404e+00   5.457498e+00
   5_adp:  0.1213 0.1693   5.220534e+00   5.453414e+00
   5_occ:  0.1212 0.1691   5.219941e+00   5.452766e+00
   5_bss:  0.1212 0.1692   5.219812e+00   5.452853e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  28.246   8.749   9.200   6.416   0.000   0.000   0.000
   1_xyz:  0.300  28.246   8.749   9.200   6.416   0.000   0.000   0.000
   1_adp:  0.300  28.246   8.749   9.200   6.416   0.000   0.000   0.000
   1_occ:  0.300  28.246   8.749   9.200   6.416   0.000   0.000   0.000
   2_bss:  0.300  28.246   6.377   6.580   4.948   0.000   0.000   0.000
   2_xyz:  0.300  28.246   6.377   6.580   4.948   0.000   0.000   0.000
   2_adp:  0.300  28.246   6.377   6.580   4.948   0.000   0.000   0.000
   2_occ:  0.300  28.246   6.377   6.580   4.948   0.000   0.000   0.000
   3_bss:  0.300  28.246   4.029   4.251   3.908   0.000   0.000   0.000
   3_xyz:  0.300  28.246   4.029   4.251   3.908   0.000   0.000   0.000
   3_adp:  0.300  28.246   4.029   4.251   3.908   0.000   0.000   0.000
   3_occ:  0.300  28.246   4.029   4.251   3.908   0.000   0.000   0.000
   4_bss:  0.322  57.350   2.741   2.952   3.110   0.000   0.000   0.000
   4_xyz:  0.322  57.350   2.741   2.952   3.110   0.000   0.000   0.000
   4_adp:  0.322  57.350   2.741   2.952   3.110   0.000   0.000   0.000
   4_occ:  0.322  57.350   2.741   2.952   3.110   0.000   0.000   0.000
   5_bss:  0.317  57.350   2.462   2.651   3.111   0.000   0.000   0.000
   5_xyz:  0.317  57.350   2.462   2.651   3.111   0.000   0.000   0.000
   5_adp:  0.317  57.350   2.462   2.651   3.111   0.000   0.000   0.000
   5_occ:  0.317  57.350   2.462   2.651   3.111   0.000   0.000   0.000
   5_bss:  0.316  62.554  -0.281  -0.149   0.430   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  57.874 0.4212  0.4809    70218.494
   1_bss:  58.066 0.4170  0.5996    68401.610
   1_xyz:  50.652 0.5101  0.7152    53753.080
   1_adp:  46.818 0.5584  0.8090    48140.161
   1_occ:  46.835 0.5581  0.8079    48208.269
   2_bss:  46.731 0.5594  0.7535    48078.061
   2_xyz:  35.241 0.6971  0.9277    29432.886
   2_adp:  31.607 0.7396  0.9703    24963.036
   2_occ:  31.583 0.7398  0.9698    24924.828
   3_bss:  31.407 0.7418  0.9090    24672.145
   3_xyz:  21.934 0.8418  0.9853    12773.381
   3_adp:  19.897 0.8620  0.9892    10795.165
   3_occ:  19.880 0.8621  0.9891    10777.713
   4_bss:  19.814 0.8629  0.9514    10748.926
   4_xyz:  17.326 0.8863  0.9661     8649.909
   4_adp:  16.524 0.8939  0.9673     8197.873
   4_occ:  16.496 0.8942  0.9671     8181.293
   5_bss:  16.453 0.8944  0.9607     8123.698
   5_xyz:  15.484 0.9029  0.9641     7401.909
   5_adp:  15.345 0.9042  0.9624     7365.368
   5_occ:  15.336 0.9043  0.9624     7356.633
   5_bss:  15.334 0.9043  0.9589     7358.912
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4503e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4503e+01
   1_xyz:   1.775  0.014  0.113 18.121  0.007  4.111   1.5463e-01
   1_adp:   1.775  0.014  0.113 18.121  0.007  4.111   1.5463e-01
   1_occ:   1.775  0.014  0.113 18.121  0.007  4.111   1.5463e-01
   2_bss:   1.775  0.014  0.113 18.121  0.007  4.111   1.5463e-01
   2_xyz:   1.299  0.010  0.088 16.514  0.005  4.109   9.7343e-02
   2_adp:   1.299  0.010  0.088 16.514  0.005  4.109   9.7343e-02
   2_occ:   1.299  0.010  0.088 16.514  0.005  4.109   9.7343e-02
   3_bss:   1.299  0.010  0.088 16.514  0.005  4.109   9.7343e-02
   3_xyz:   1.216  0.010  0.089 16.180  0.004  4.139   8.6568e-02
   3_adp:   1.216  0.010  0.089 16.180  0.004  4.139   8.6568e-02
   3_occ:   1.216  0.010  0.089 16.180  0.004  4.139   8.6568e-02
   4_bss:   1.216  0.010  0.089 16.180  0.004  4.139   8.6568e-02
   4_xyz:   1.163  0.010  0.088 15.735  0.004  4.116   8.1501e-02
   4_adp:   1.163  0.010  0.088 15.735  0.004  4.116   8.1501e-02
   4_occ:   1.163  0.010  0.088 15.735  0.004  4.116   8.1501e-02
   5_bss:   1.163  0.010  0.088 15.735  0.004  4.116   8.1501e-02
   5_xyz:   1.175  0.011  0.091 15.696  0.004  4.123   8.2596e-02
   5_adp:   1.175  0.011  0.091 15.696  0.004  4.123   8.2596e-02
   5_occ:   1.175  0.011  0.091 15.696  0.004  4.123   8.2596e-02
   5_bss:   1.175  0.011  0.091 15.696  0.004  4.123   8.2596e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0666e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0666e+00
   1_xyz:  15.299  0.180  0.493 86.496  0.042  2.162   1.1171e-01
   1_adp:  15.299  0.180  0.493 86.496  0.042  2.162   1.1171e-01
   1_occ:  15.299  0.180  0.493 86.496  0.042  2.162   1.1171e-01
   2_bss:  15.299  0.180  0.493 86.496  0.042  2.162   1.1171e-01
   2_xyz:   7.404  0.088  0.315 84.228  0.035  2.140   6.4782e-02
   2_adp:   7.404  0.088  0.315 84.228  0.035  2.140   6.4782e-02
   2_occ:   7.404  0.088  0.315 84.228  0.035  2.140   6.4782e-02
   3_bss:   7.404  0.088  0.315 84.228  0.035  2.140   6.4782e-02
   3_xyz:   9.691  0.069  0.405 85.918  0.036  2.219   5.5098e-02
   3_adp:   9.691  0.069  0.405 85.918  0.036  2.219   5.5098e-02
   3_occ:   9.691  0.069  0.405 85.918  0.036  2.219   5.5098e-02
   4_bss:   9.691  0.069  0.405 85.918  0.036  2.219   5.5098e-02
   4_xyz:   8.740  0.057  0.551 81.803  0.038  2.312   5.2735e-02
   4_adp:   8.740  0.057  0.551 81.803  0.038  2.312   5.2735e-02
   4_occ:   8.740  0.057  0.551 81.803  0.038  2.312   5.2735e-02
   5_bss:   8.740  0.057  0.551 81.803  0.038  2.312   5.2735e-02
   5_xyz:   8.387  0.046  0.591 83.331  0.036  2.322   5.7464e-02
   5_adp:   8.387  0.046  0.591 83.331  0.036  2.322   5.7464e-02
   5_occ:   8.387  0.046  0.591 83.331  0.036  2.322   5.7464e-02
   5_bss:   8.387  0.046  0.591 83.331  0.036  2.322   5.7464e-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: 117.32   0.00  13.06  82.13   0.00  10.51 117.32   0.00  26.92
   1_occ: 117.32   0.00  13.06  82.13   0.00  10.51 117.32   0.00  26.92
   2_bss: 117.32   0.00  13.06  82.13   0.00  10.51 117.32   0.00  26.92
   2_xyz: 117.32   0.00  13.06  82.13   0.00  10.51 117.32   0.00  26.92
   2_adp: 110.64   0.00  12.81  79.65   0.00   9.26 110.64   0.00  32.16
   2_occ: 110.64   0.00  12.81  79.65   0.00   9.26 110.64   0.00  32.16
   3_bss: 110.64   0.00  12.81  79.65   0.00   9.26 110.64   0.00  32.16
   3_xyz: 110.64   0.00  12.81  79.65   0.00   9.26 110.64   0.00  32.16
   3_adp:  93.76   0.00  13.64  93.76   0.00   8.97  93.72   0.00  39.07
   3_occ:  93.76   0.00  13.64  93.76   0.00   8.97  93.72   0.00  39.07
   4_bss:  93.76   0.00  13.64  93.76   0.00   8.97  93.72   0.00  39.07
   4_xyz:  93.76   0.00  13.64  93.76   0.00   8.97  93.72   0.00  39.07
   4_adp:  92.22   0.00  13.23  92.22   0.00   8.64  89.88   0.81  38.22
   4_occ:  92.22   0.00  13.23  92.22   0.00   8.64  89.88   0.81  38.22
   5_bss:  92.22   0.00  13.23  92.22   0.00   8.64  89.88   0.81  38.22
   5_xyz:  92.22   0.00  13.23  92.22   0.00   8.64  89.88   0.81  38.22
   5_adp:  91.49   0.00  13.03  91.49   0.00   8.53  88.54   1.34  37.54
   5_occ:  91.49   0.00  13.03  91.49   0.00   8.53  88.54   1.34  37.54
   5_bss:  94.13   2.64  15.67  94.13   2.64  11.16  91.18   3.97  40.18
------------------------------------------------------------------------
 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:    1.199    0.026    0.418
   1_adp:    1.199    0.026    0.418
   1_occ:    1.199    0.026    0.418
   2_bss:    1.199    0.026    0.418
   2_xyz:    1.615    0.030    0.614
   2_adp:    1.615    0.030    0.614
   2_occ:    1.615    0.030    0.614
   3_bss:    1.615    0.030    0.614
   3_xyz:    1.592    0.036    0.733
   3_adp:    1.592    0.036    0.733
   3_occ:    1.592    0.036    0.733
   4_bss:    1.592    0.036    0.733
   4_xyz:    1.634    0.047    0.766
   4_adp:    1.634    0.047    0.766
   4_occ:    1.634    0.047    0.766
   5_bss:    1.634    0.047    0.766
   5_xyz:    1.654    0.048    0.787
   5_adp:    1.654    0.048    0.787
   5_occ:    1.654    0.048    0.787
   5_bss:    1.654    0.048    0.787
------------------------------------------------------------------------

CPU time actual refinement: 320.13


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1303/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_1303/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1303/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1303/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1303/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 319.98 
  Macro-tasks:
    bulk solvent and scale       = 38.81  
    individual site refinement   = 128.16 
    weights calculation          = 31.46  
    collect and process          = 6.51   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 205.05 
  Micro-tasks:
    mask                            = 2.18   
    f_calc                          = 100.00 
    alpha_beta                      = 8.37   
    target                          = 1.20   
    gradients_wrt_atomic_parameters = 104.33 
    fmodel                         = 6.92   
    r_factors                      = 0.14   
    phase_errors                   = 11.22  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 234.59 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.576 micro seconds
Total CPU time: 5.55 minutes
from_scatterers_fft:    634 calls, 99.64 s
gradients_fft:          578 calls, 93.52 s

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

# Date 2008-01-16 Time 03:42:08 PST -0800 (1200483728.67 s)
Start R-work = 0.4866, R-free = 0.4700 (no bulk solvent and anisotropic scale)
Final R-work = 0.1368, R-free = 0.1840 (no bulk solvent and anisotropic scale)

Start R-work = 0.4793, R-free = 0.4623
Final R-work = 0.1212, R-free = 0.1692