# Date 2008-01-16 Time 01:40:05 PST -0800 (1200476405.13 s)
#phil __OFF__

Command line arguments: "../513.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 4979
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 513

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.8988, 46.2261, 87.2539, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

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


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.2261, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.979 1.97246
Completeness in resolution range: 0.954537
Completeness with d_max=infinity: 0.951615

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9790
                             d_min =   1.9725

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.8988, 46.2261, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.979 1.97246
Completeness in resolution range: 0.954537
Completeness with d_max=infinity: 0.951615

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9794 -  4.2208 [2156/2180]  1937   219  10.2%
  bin  2:  4.2208 -  3.3626 [2061/2081]  1856   205   9.9%
  bin  3:  3.3626 -  2.9412 [2049/2068]  1846   203   9.9%
  bin  4:  2.9412 -  2.6740 [2021/2051]  1819   202  10.0%
  bin  5:  2.6740 -  2.4832 [2008/2027]  1807   201  10.0%
  bin  6:  2.4832 -  2.3374 [2003/2028]  1799   204  10.2%
  bin  7:  2.3374 -  2.2207 [2005/2033]  1805   200  10.0%
  bin  8:  2.2207 -  2.1244 [1969/2005]  1773   196  10.0%
  bin  9:  2.1244 -  2.0428 [1963/2005]  1771   192   9.8%
  bin 10:  2.0428 -  1.9725 [1354/2044]  1217   137  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_513/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.79 -     2.41: 33
        2.41 -     3.03: 2114
        3.03 -     3.65: 4700
        3.65 -     4.28: 9142
        4.28 -     4.90: 12452
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.785 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.962 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.091 3.040 x,y+1,z
  " O   HOH Z  42 " - " O   HOH Z 183 "  2.095 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28436 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_513/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_513/model_refine_001.geo

CPU time processing inputs: 9.09


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.89875 46.22605 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4661   r_free= 0.4559   ksol= 0.00   Bsol= 0.00   scale= 0.805    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.267822                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9794 -  4.7078 0.99   1396  154 0.3896 0.3748      6.5778      6.5525|
|  2:  4.7078 -  3.7561 0.99   1348  153 0.3721 0.3566      6.7322      6.7083|
|  3:  3.7561 -  3.2870 0.99   1318  141 0.4088 0.3652       6.634      6.5948|
|  4:  3.2870 -  2.9891 0.99   1311  151 0.4509 0.4415        6.52      6.4832|
|  5:  2.9891 -  2.7763 0.99   1305  145 0.4946 0.4746      6.3553      6.3639|
|  6:  2.7763 -  2.6135 0.99   1302  143 0.4916 0.5363      6.2693      6.2114|
|  7:  2.6135 -  2.4832 0.99   1285  143 0.5059 0.5038      6.2248      6.1931|
|  8:  2.4832 -  2.3756 0.98   1279  142 0.5220 0.4658      6.1962      6.1811|
|  9:  2.3756 -  2.2845 0.98   1283  146 0.5011 0.5340      6.0963      6.1782|
| 10:  2.2845 -  2.2059 1.00   1290  139 0.5406 0.5176      6.1219      6.0666|
| 11:  2.2059 -  2.1371 0.98   1282  139 0.5164 0.4849      6.0338      6.0395|
| 12:  2.1371 -  2.0762 0.98   1256  144 0.5176 0.5104      5.9751      5.9798|
| 13:  2.0762 -  2.0217 0.99   1286  141 0.5155 0.5178      5.8699      5.8274|
| 14:  2.0217 -  1.9725 0.53    689   78 0.5492 0.5679      5.8999      5.7925|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9794 -  4.7078  1396   154  0.71  33.65   0.80     0.75      69177.61|
|  2:  4.7078 -  3.7561  1348   153  0.74  31.76   0.88     0.81      89283.44|
|  3:  3.7561 -  3.2870  1318   141  0.66  39.06   0.87     0.77      94956.37|
|  4:  3.2870 -  2.9891  1311   151  0.57  46.43   0.81     0.65      88072.45|
|  5:  2.9891 -  2.7763  1305   145  0.45  55.50   0.76     0.54      76525.55|
|  6:  2.7763 -  2.6135  1302   143  0.42  58.47   0.73     0.47      69375.46|
|  7:  2.6135 -  2.4832  1285   143  0.36  62.82   0.74     0.42      66270.81|
|  8:  2.4832 -  2.3756  1279   142  0.35  63.61   0.73     0.41      60269.11|
|  9:  2.3756 -  2.2845  1283   146  0.37  61.88   0.74     0.44      53369.07|
| 10:  2.2845 -  2.2059  1290   139  0.40  59.94   0.75     0.48      45578.13|
| 11:  2.2059 -  2.1371  1282   139  0.39  60.38   0.77     0.50      43883.48|
| 12:  2.1371 -  2.0762  1256   144  0.37  62.67   0.78     0.46      40962.03|
| 13:  2.0762 -  2.0217  1286   141  0.34  64.82   0.72     0.42      36308.40|
| 14:  2.0217 -  1.9725   689    78  0.36  62.89   0.73     0.41      30163.30|
|alpha:            min =        0.41 max =            0.81 mean =         0.55|
|beta:             min =    30163.30 max =        94956.37 mean =     63098.51|
|figures of merit: min =        0.00 max =            1.00 mean =         0.47|
|phase err.(work): min =        0.00 max =           90.00 mean =        54.02|
|phase err.(test): min =        0.00 max =           90.00 mean =        54.29|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.645443             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.357   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.071699              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.595   (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:       33 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      172 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      688 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1522 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2633 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3974 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5081 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6622 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7730 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.530 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.898 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.747)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.747)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4742   r_free= 0.4569   ksol= 0.00   Bsol= 0.00   scale= 0.774    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.271328                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4584   r_free= 0.4408   ksol= 0.37   Bsol= 20.00   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.72,9.71,9.13,0.00,0.00,0.00); trace/3= 8.52                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.262608                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.381681              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.963   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.941325              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.438   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4584      final r-factor (work) = 0.3680          |
| start r-factor (free) = 0.4408      final r-factor (free) = 0.3868          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 82.9274 = 9.38 * 0.50 * 6.2670 + 1.00 * 53.5299                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.0264 = 9.38 * 0.50 * 6.1600 + 1.00 * 0.1309                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3680      final r-factor (work) = 0.3171          |
| start r-factor (free) = 0.3868      final r-factor (free) = 0.3697          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8130 = 0.94 * 1.00 * 6.1600 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7100 = 0.94 * 1.00 * 6.0501 + 1.00 * 0.0149                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 41     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.747)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.27   12.77    None  None   None       |
|    all(noH): 2823   0      0.00    77.27   12.77    None  None   None       |
|    Sol.    : 438    0      0.00    77.27   26.46    None  None   None       |
|    Mac.    : 2385   0      0.00    65.50   10.25    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.727: 1186   |   5:    38.633 -  46.360:   60        |
|      1:     7.727 -  15.453:  791   |   6:    46.360 -  54.087:   33        |
|      2:    15.453 -  23.180:  424   |   7:    54.087 -  61.813:   12        |
|      3:    23.180 -  30.907:  178   |   8:    61.813 -  69.540:    7        |
|      4:    30.907 -  38.633:  131   |   9:    69.540 -  77.267:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3171 r_free = 0.3697             target_work(ml) = 6.027         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3166 r_free = 0.3698             target_work(ml) = 6.027         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3166   r_free= 0.3698   ksol= 0.37   Bsol= 20.00   scale= 1.115   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.72,9.71,9.13,0.00,0.00,0.00); trace/3= 8.52                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 6.026677                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3125   r_free= 0.3643   ksol= 0.34   Bsol= 37.65   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.32,5.24,5.39,0.00,0.00,0.00); trace/3= 4.65                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.027166                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.240627              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.358   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.460701              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 140.930  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3125      final r-factor (work) = 0.2223          |
| start r-factor (free) = 0.3643      final r-factor (free) = 0.2772          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.0065 = 6.24 * 0.50 * 6.0493 + 1.00 * 0.1309                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.4366 = 6.24 * 0.50 * 5.8805 + 1.00 * 0.0876                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2223      final r-factor (work) = 0.1954          |
| start r-factor (free) = 0.2772      final r-factor (free) = 0.2507          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7241 = 0.46 * 1.00 * 5.8805 + 1.00 * 0.0149                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6211 = 0.46 * 1.00 * 5.6646 + 1.00 * 0.0115                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.747)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.33   12.63    None  None   None       |
|    all(noH): 2823   0      0.00    85.33   12.63    None  None   None       |
|    Sol.    : 438    0      0.00    85.33   33.07    None  None   None       |
|    Mac.    : 2385   0      0.00    67.80   8.88     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.533: 1480   |   5:    42.665 -  51.198:   89        |
|      1:     8.533 -  17.066:  718   |   6:    51.198 -  59.731:   32        |
|      2:    17.066 -  25.599:  208   |   7:    59.731 -  68.265:   11        |
|      3:    25.599 -  34.132:  163   |   8:    68.265 -  76.798:    1        |
|      4:    34.132 -  42.665:  120   |   9:    76.798 -  85.331:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1954 r_free = 0.2507             target_work(ml) = 5.620         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1953 r_free = 0.2504             target_work(ml) = 5.620         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1953   r_free= 0.2504   ksol= 0.34   Bsol= 37.65   scale= 1.053   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.32,5.24,5.39,0.00,0.00,0.00); trace/3= 4.65                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.619502                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1937   r_free= 0.2483   ksol= 0.33   Bsol= 46.81   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.14,2.89,3.94,0.00,0.00,0.00); trace/3= 2.99                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.618094                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.757175              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.490   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.682951              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.573  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1937      final r-factor (work) = 0.1484          |
| start r-factor (free) = 0.2483      final r-factor (free) = 0.1964          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9066 = 2.76 * 0.50 * 5.6718 + 1.00 * 0.0876                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6477 = 2.76 * 0.50 * 5.5040 + 1.00 * 0.0599                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1484      final r-factor (work) = 0.1377          |
| start r-factor (free) = 0.1964      final r-factor (free) = 0.1875          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7704 = 0.68 * 1.00 * 5.5040 + 1.00 * 0.0115                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6642 = 0.68 * 1.00 * 5.3468 + 1.00 * 0.0126                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.747)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.95   13.02    None  None   None       |
|    all(noH): 2823   0      0.00    85.95   13.02    None  None   None       |
|    Sol.    : 438    0      1.64    85.95   36.76    None  None   None       |
|    Mac.    : 2385   0      0.00    75.34   8.66     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.595: 1576   |   5:    42.976 -  51.571:  104        |
|      1:     8.595 -  17.190:  638   |   6:    51.571 -  60.166:   64        |
|      2:    17.190 -  25.785:  183   |   7:    60.166 -  68.761:   21        |
|      3:    25.785 -  34.380:  107   |   8:    68.761 -  77.356:    6        |
|      4:    34.380 -  42.976:  123   |   9:    77.356 -  85.951:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1377 r_free = 0.1875             target_work(ml) = 5.324         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1376 r_free = 0.1875             target_work(ml) = 5.324         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1376   r_free= 0.1875   ksol= 0.33   Bsol= 46.81   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.14,2.89,3.94,0.00,0.00,0.00); trace/3= 2.99                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.323766                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1375   r_free= 0.1873   ksol= 0.33   Bsol= 46.81   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.82,2.13,3.67,0.00,0.00,0.00); trace/3= 2.54                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.322142                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.220860              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.508  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.929983              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.709  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1375      final r-factor (work) = 0.1228          |
| start r-factor (free) = 0.1873      final r-factor (free) = 0.1713          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9979 = 2.22 * 0.50 * 5.3475 + 1.00 * 0.0599                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9165 = 2.22 * 0.50 * 5.2756 + 1.00 * 0.0583                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1228      final r-factor (work) = 0.1197          |
| start r-factor (free) = 0.1713      final r-factor (free) = 0.1677          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9188 = 0.93 * 1.00 * 5.2756 + 1.00 * 0.0125                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8664 = 0.93 * 1.00 * 5.2154 + 1.00 * 0.0162                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.747)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.39   13.05    None  None   None       |
|    all(noH): 2823   0      0.00    87.39   13.05    None  None   None       |
|    Sol.    : 438    0      1.61    87.39   37.66    None  None   None       |
|    Mac.    : 2385   0      0.00    85.27   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 -   8.739: 1640   |   5:    43.694 -  52.432:   93        |
|      1:     8.739 -  17.477:  604   |   6:    52.432 -  61.171:   61        |
|      2:    17.477 -  26.216:  164   |   7:    61.171 -  69.910:   34        |
|      3:    26.216 -  34.955:  110   |   8:    69.910 -  78.648:   14        |
|      4:    34.955 -  43.694:  100   |   9:    78.648 -  87.387:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1197 r_free = 0.1677             target_work(ml) = 5.205         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1196 r_free = 0.1675             target_work(ml) = 5.204         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1196   r_free= 0.1675   ksol= 0.33   Bsol= 46.81   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.82,2.13,3.67,0.00,0.00,0.00); trace/3= 2.54                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.204464                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1195   r_free= 0.1674   ksol= 0.32   Bsol= 48.39   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.94,2.12,3.77,0.00,0.00,0.00); trace/3= 2.61                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.204203                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.815362              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 142.986  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.796740              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 94.101   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1195      final r-factor (work) = 0.1157          |
| start r-factor (free) = 0.1674      final r-factor (free) = 0.1626          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7921 = 1.82 * 0.50 * 5.2153 + 1.00 * 0.0583                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7663 = 1.82 * 0.50 * 5.1912 + 1.00 * 0.0543                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1157      final r-factor (work) = 0.1152          |
| start r-factor (free) = 0.1626      final r-factor (free) = 0.1619          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1506 = 0.80 * 1.00 * 5.1912 + 1.00 * 0.0146                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1531 = 0.80 * 1.00 * 5.1771 + 1.00 * 0.0284                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.747)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.46   12.88    None  None   None       |
|    all(noH): 2823   0      0.00    88.46   12.88    None  None   None       |
|    Sol.    : 438    0      1.42    86.63   37.18    None  None   None       |
|    Mac.    : 2385   0      0.00    88.46   8.42     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.846: 1662   |   5:    44.228 -  53.074:   88        |
|      1:     8.846 -  17.691:  592   |   6:    53.074 -  61.919:   55        |
|      2:    17.691 -  26.537:  161   |   7:    61.919 -  70.765:   31        |
|      3:    26.537 -  35.382:  116   |   8:    70.765 -  79.610:   14        |
|      4:    35.382 -  44.228:  101   |   9:    79.610 -  88.456:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1152 r_free = 0.1619             target_work(ml) = 5.175         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1149 r_free = 0.1619             target_work(ml) = 5.174         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1149   r_free= 0.1619   ksol= 0.32   Bsol= 48.39   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.94,2.12,3.77,0.00,0.00,0.00); trace/3= 2.61                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.174179                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9794 -  4.7078 0.99   1396  154 0.1000 0.1260       5.387      5.5354|
|  2:  4.7078 -  3.7561 0.99   1348  153 0.0868 0.1156      5.4472       5.644|
|  3:  3.7561 -  3.2870 0.99   1318  141 0.1081 0.1487      5.4959      5.8528|
|  4:  3.2870 -  2.9891 0.99   1311  151 0.1246 0.1765      5.4724      5.6294|
|  5:  2.9891 -  2.7763 0.99   1305  145 0.1350 0.1734      5.3513       5.583|
|  6:  2.7763 -  2.6135 0.99   1302  143 0.1225 0.2035      5.2198      5.5138|
|  7:  2.6135 -  2.4832 0.99   1285  143 0.1317 0.1650       5.202      5.3571|
|  8:  2.4832 -  2.3756 0.98   1279  142 0.1197 0.1681      5.1068      5.3512|
|  9:  2.3756 -  2.2845 0.98   1283  146 0.1241 0.1892      5.0835      5.3589|
| 10:  2.2845 -  2.2059 1.00   1290  139 0.1181 0.1666      5.0058      5.2061|
| 11:  2.2059 -  2.1371 0.98   1282  139 0.1189 0.1903       4.989      5.3346|
| 12:  2.1371 -  2.0762 0.98   1256  144 0.1183 0.1772       4.923      5.2335|
| 13:  2.0762 -  2.0217 0.99   1286  141 0.1153 0.1722      4.8005      5.0435|
| 14:  2.0217 -  1.9725 0.53    689   78 0.0994 0.1615      4.6615      4.8682|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9794 -  4.7078  1396   154  0.94   9.24   0.98     0.95       7243.15|
|  2:  4.7078 -  3.7561  1348   153  0.95   7.96   1.02     1.00       9172.71|
|  3:  3.7561 -  3.2870  1318   141  0.93  11.47   1.04     1.03      10699.59|
|  4:  3.2870 -  2.9891  1311   151  0.92  13.87   1.01     0.99      10603.93|
|  5:  2.9891 -  2.7763  1305   145  0.90  16.10   1.01     0.98       8700.12|
|  6:  2.7763 -  2.6135  1302   143  0.90  16.39   0.98     0.96       7276.65|
|  7:  2.6135 -  2.4832  1285   143  0.90  16.04   0.99     0.96       6477.26|
|  8:  2.4832 -  2.3756  1279   142  0.90  15.87   0.99     0.97       5738.61|
|  9:  2.3756 -  2.2845  1283   146  0.90  16.06   1.00     0.97       5602.32|
| 10:  2.2845 -  2.2059  1290   139  0.89  17.11   1.00     0.96       4959.38|
| 11:  2.2059 -  2.1371  1282   139  0.89  17.24   0.99     0.95       4816.92|
| 12:  2.1371 -  2.0762  1256   144  0.90  16.43   1.01     1.00       4350.99|
| 13:  2.0762 -  2.0217  1286   141  0.90  16.48   1.00     0.98       3430.54|
| 14:  2.0217 -  1.9725   689    78  0.92  13.51   0.99     0.96       2521.89|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2521.89 max =        10699.59 mean =      6712.74|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.87 mean =        14.53|
|phase err.(test): min =        0.00 max =           89.42 mean =        13.99|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1148   r_free= 0.1618   ksol= 0.32   Bsol= 51.09   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.64,-0.53,1.18,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.174180                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.98 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1148   r_free= 0.1618   ksol= 0.32   Bsol= 51.09   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.64,-0.53,1.18,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.174180                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9794 -  4.7078 0.99   1396  154 0.1000 0.1261      5.3875      5.5362|
|  2:  4.7078 -  3.7561 0.99   1348  153 0.0868 0.1156      5.4475      5.6441|
|  3:  3.7561 -  3.2870 0.99   1318  141 0.1081 0.1487       5.496       5.853|
|  4:  3.2870 -  2.9891 0.99   1311  151 0.1246 0.1765      5.4723      5.6293|
|  5:  2.9891 -  2.7763 0.99   1305  145 0.1350 0.1733      5.3511      5.5827|
|  6:  2.7763 -  2.6135 0.99   1302  143 0.1225 0.2035      5.2195      5.5135|
|  7:  2.6135 -  2.4832 0.99   1285  143 0.1318 0.1652       5.202      5.3575|
|  8:  2.4832 -  2.3756 0.98   1279  142 0.1197 0.1680      5.1069      5.3509|
|  9:  2.3756 -  2.2845 0.98   1283  146 0.1242 0.1890      5.0835      5.3585|
| 10:  2.2845 -  2.2059 1.00   1290  139 0.1181 0.1666      5.0057      5.2068|
| 11:  2.2059 -  2.1371 0.98   1282  139 0.1189 0.1903      4.9892      5.3347|
| 12:  2.1371 -  2.0762 0.98   1256  144 0.1183 0.1773       4.923      5.2335|
| 13:  2.0762 -  2.0217 0.99   1286  141 0.1153 0.1719      4.8002      5.0426|
| 14:  2.0217 -  1.9725 0.53    689   78 0.0994 0.1613      4.6609      4.8677|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9794 -  4.7078  1396   154  0.94   9.25   0.98     0.95       7252.83|
|  2:  4.7078 -  3.7561  1348   153  0.95   7.97   1.02     1.01       9180.28|
|  3:  3.7561 -  3.2870  1318   141  0.93  11.47   1.04     1.03      10702.23|
|  4:  3.2870 -  2.9891  1311   151  0.92  13.87   1.02     1.00      10601.90|
|  5:  2.9891 -  2.7763  1305   145  0.90  16.09   1.01     0.99       8694.30|
|  6:  2.7763 -  2.6135  1302   143  0.90  16.38   0.99     0.96       7274.40|
|  7:  2.6135 -  2.4832  1285   143  0.90  16.04   0.99     0.96       6476.68|
|  8:  2.4832 -  2.3756  1279   142  0.90  15.87   1.00     0.97       5737.93|
|  9:  2.3756 -  2.2845  1283   146  0.90  16.06   1.01     0.97       5602.01|
| 10:  2.2845 -  2.2059  1290   139  0.89  17.11   1.01     0.96       4959.88|
| 11:  2.2059 -  2.1371  1282   139  0.89  17.24   1.00     0.95       4818.94|
| 12:  2.1371 -  2.0762  1256   144  0.90  16.43   1.01     1.01       4352.48|
| 13:  2.0762 -  2.0217  1286   141  0.90  16.48   1.01     0.98       3427.48|
| 14:  2.0217 -  1.9725   689    78  0.92  13.48   0.99     0.97       2516.19|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2516.19 max =        10702.23 mean =      6713.27|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.87 mean =        14.52|
|phase err.(test): min =        0.00 max =           89.42 mean =        14.00|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.747)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.70    91.16   15.58    None  None   None       |
|    all(noH): 2823   0      2.70    91.16   15.58    None  None   None       |
|    Sol.    : 438    0      4.12    89.34   39.89    None  None   None       |
|    Mac.    : 2385   0      2.70    91.16   11.12    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:     2.704 -  11.550: 1662   |   5:    46.932 -  55.778:   88        |
|      1:    11.550 -  20.396:  592   |   6:    55.778 -  64.624:   55        |
|      2:    20.396 -  29.241:  161   |   7:    64.624 -  73.469:   31        |
|      3:    29.241 -  38.087:  116   |   8:    73.469 -  82.315:   14        |
|      4:    38.087 -  46.932:  101   |   9:    82.315 -  91.160:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 315         
Filter by distance & map next to the model:
   mapped sites are within: 0.263 - 4.728
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 313 from: 315
   mapped sites are within: 0.701 - 4.728

peak=   11.075 closest distance to " CB  VAL A 230 " =    1.441
peak=   10.081 closest distance to " CB  VAL A 296 " =    1.553
peak=    7.337 closest distance to " O   HOH Z 130 " =    1.336
peak=    6.317 closest distance to " CD2 LEU A   5 " =    1.257
peak=    6.120 closest distance to " NE2 GLN A  11 " =    1.180
peak=    5.705 closest distance to " CG  PRO A  54 " =    1.416
peak=    5.680 closest distance to " CG  LEU A   5 " =    1.177
peak=    5.638 closest distance to " NH2 ARG A  56 " =    2.060
peak=    5.473 closest distance to " O   HOH Z   9 " =    2.053
peak=    5.405 closest distance to " CG  LEU A 228 " =    1.131
peak=    5.340 closest distance to " CD1AILE A 234 " =    1.035
peak=    5.257 closest distance to " O   HOH Z 142 " =    2.015
peak=    5.230 closest distance to " O   HOH Z 232 " =    2.304
peak=    5.125 closest distance to " O   HOH Z 427 " =    2.479
peak=    5.061 closest distance to " CB  PRO A  54 " =    1.025
peak=    5.001 closest distance to " O   HOH Z  65 " =    1.052
peak=    4.779 closest distance to " CG  PRO A 198 " =    1.210
peak=    4.742 closest distance to " CB  GLN A 223 " =    1.456
peak=    4.635 closest distance to " O   HOH Z 126 " =    2.155
peak=    4.592 closest distance to " CB  ARG A 275 " =    0.965
peak=    4.572 closest distance to " O   HOH Z 209 " =    2.330
peak=    4.531 closest distance to " CB  VAL A 230 " =    1.168
peak=    4.527 closest distance to " CB  ASN A 148 " =    1.394
peak=    4.496 closest distance to " CB  GLN A 183 " =    1.248
peak=    4.491 closest distance to " O   HOH Z 425 " =    1.490
peak=    4.468 closest distance to " O   HOH Z 287 " =    1.850
peak=    4.353 closest distance to " O   HOH Z 423 " =    1.559
peak=    4.350 closest distance to " ND2 ASN A 187 " =    1.671
peak=    4.317 closest distance to " O   HOH Z  78 " =    1.639
peak=    4.312 closest distance to " O   HOH Z 380 " =    1.875
peak=    4.308 closest distance to " CB  VAL A 265 " =    1.358
peak=    4.281 closest distance to " CB  VAL A 202 " =    1.729
peak=    4.280 closest distance to " CB BVAL A  41 " =    1.321
peak=    4.280 closest distance to " O   HOH Z  55 " =    2.150
peak=    4.245 closest distance to " O   HOH Z 112 " =    1.096
peak=    4.220 closest distance to " CB  SER A   3 " =    1.370
peak=    4.214 closest distance to " O   HOH Z 346 " =    1.567
peak=    4.204 closest distance to " CG  PRO A 213 " =    1.217
peak=    4.197 closest distance to " O   HOH Z 272 " =    1.766
peak=    4.190 closest distance to " O   HOH Z 422 " =    2.587
peak=    4.185 closest distance to " CB  ASN A 142 " =    1.054
peak=    4.177 closest distance to " O   HOH Z   2 " =    1.648
peak=    4.175 closest distance to " CB  TRP A 266 " =    1.063
peak=    4.173 closest distance to " O   HOH Z 298 " =    1.663
peak=    4.171 closest distance to " CG  LEU A 167 " =    1.238
peak=    4.143 closest distance to " O   HOH Z 369 " =    2.239
peak=    4.132 closest distance to " NH1 ARG A 138 " =    1.046
peak=    4.122 closest distance to " CB  SER A  63 " =    1.281
peak=    4.074 closest distance to " O   HOH Z 130 " =    2.422
peak=    4.053 closest distance to " O   SER A  87 " =    2.357
peak=    4.051 closest distance to " NH2AARG A 190 " =    1.861
peak=    4.050 closest distance to " CG  PRO A 243 " =    1.176
peak=    4.043 closest distance to " CG2 VAL A 257 " =    0.863
peak=    4.031 closest distance to " O   HOH Z 359 " =    1.404
peak=    4.012 closest distance to " O   HOH Z 362 " =    2.471
peak=    4.007 closest distance to " CB  ASN A  39 " =    0.991
peak=    4.003 closest distance to " O   HOH Z 417 " =    1.293
peak=    4.002 closest distance to " CB  ARG A  79 " =    1.372
peak=    3.998 closest distance to " O   HOH Z 234 " =    3.618
peak=    3.992 closest distance to " CB  SER A 216 " =    0.859
peak=    3.981 closest distance to " OG ASER A 258 " =    3.044
peak=    3.963 closest distance to " O   PRO A 198 " =    1.561
peak=    3.941 closest distance to " CB  GLU A 277 " =    3.508
peak=    3.922 closest distance to " O   HOH Z  30 " =    1.643
peak=    3.896 closest distance to " O   HOH Z   1 " =    1.759
peak=    3.895 closest distance to " O   HOH Z 222 " =    2.383
peak=    3.891 closest distance to " O   HOH Z 214 " =    2.350
peak=    3.880 closest distance to " CB  ARG A 190 " =    1.668
peak=    3.874 closest distance to " O   PRO A 198 " =    1.299
peak=    3.866 closest distance to " CB  SER A  26 " =    1.660
peak=    3.857 closest distance to " O   HOH Z  61 " =    1.582
peak=    3.842 closest distance to " CA  SER A  87 " =    0.992
peak=    3.831 closest distance to " CB  TRP A 179 " =    1.383
peak=    3.828 closest distance to " CA  TYR A  30 " =    0.951
peak=    3.828 closest distance to " CD2 LEU A 228 " =    1.154
peak=    3.828 closest distance to " O   HOH Z 303 " =    2.193
peak=    3.825 closest distance to " CB  GLU A 128 " =    1.105
peak=    3.824 closest distance to " O   HOH Z 411 " =    3.656
peak=    3.822 closest distance to " O   HOH Z  59 " =    1.667
peak=    3.811 closest distance to " O   HOH Z 124 " =    1.269
peak=    3.807 closest distance to " O   HOH Z 203 " =    1.755
peak=    3.784 closest distance to " CA  PHE A 283 " =    1.278
peak=    3.783 closest distance to " O   HOH Z 117 " =    2.090
peak=    3.776 closest distance to " CD  ARG A 269 " =    1.033
peak=    3.773 closest distance to " CB  LYS A 117 " =    1.229
peak=    3.772 closest distance to " O   HOH Z 261 " =    2.081
peak=    3.770 closest distance to " O   HOH Z 419 " =    2.065
peak=    3.760 closest distance to " CG BARG A 102 " =    1.888
peak=    3.759 closest distance to " CD  ARG A 159 " =    0.723
peak=    3.757 closest distance to " O   HOH Z 188 " =    3.015
peak=    3.742 closest distance to " O   HOH Z  63 " =    1.304
peak=    3.726 closest distance to " O   HOH Z 425 " =    2.054
peak=    3.720 closest distance to " CA  LYS A 117 " =    1.222
peak=    3.720 closest distance to " O   HOH Z  68 " =    2.136
peak=    3.717 closest distance to " CB  GLN A  88 " =    1.263
peak=    3.706 closest distance to " O   HOH Z 193 " =    1.716
peak=    3.700 closest distance to " O   HOH Z 368 " =    3.517
peak=    3.697 closest distance to " O   HOH Z 405 " =    1.372
peak=    3.694 closest distance to " O   HOH Z 403 " =    1.556
peak=    3.694 closest distance to " O   HOH Z   7 " =    1.343
peak=    3.691 closest distance to " O   HOH Z 193 " =    1.910
peak=    3.685 closest distance to " N   PHE A 130 " =    1.300
peak=    3.679 closest distance to " CE  LYS A  76 " =    0.863
peak=    3.677 closest distance to " OG BSER A 212 " =    2.864
peak=    3.676 closest distance to " OE2 GLU A   2 " =    1.938
peak=    3.675 closest distance to " O   HOH Z   3 " =    1.992
peak=    3.660 closest distance to " O   HOH Z 146 " =    1.550
peak=    3.657 closest distance to " O   HOH Z 193 " =    1.601
peak=    3.652 closest distance to " CH2 TRP A 266 " =    1.080
peak=    3.651 closest distance to " OG  SER A  62 " =    2.700
peak=    3.638 closest distance to " CB  ASN A 187 " =    1.108
peak=    3.635 closest distance to " OG BSER A 164 " =    2.116
peak=    3.631 closest distance to " O   HOH Z 368 " =    1.987
peak=    3.615 closest distance to " CZ  PHE A 218 " =    1.137
peak=    3.614 closest distance to " CA  ASN A 215 " =    1.100
peak=    3.612 closest distance to " NZ  LYS A 117 " =    2.953
peak=    3.610 closest distance to " CD  LYS A  76 " =    1.855
peak=    3.596 closest distance to " ND2 ASN A 249 " =    0.834
peak=    3.584 closest distance to " O   HOH Z  43 " =    1.917
peak=    3.584 closest distance to " O   HOH Z  44 " =    1.763
peak=    3.584 closest distance to " CG1 ILE A  33 " =    1.340
peak=    3.583 closest distance to " OD1 ASN A  69 " =    2.416
peak=    3.580 closest distance to " CG2 THR A 221 " =    1.122
peak=    3.580 closest distance to " O   HOH Z 424 " =    2.387
peak=    3.576 closest distance to " O   HOH Z 133 " =    2.619
peak=    3.565 closest distance to " O   HOH Z 371 " =    2.781
peak=    3.565 closest distance to " CB  GLN A  89 " =    1.214
peak=    3.563 closest distance to " CB  ASP A 124 " =    0.814
peak=    3.557 closest distance to " CB  TYR A 169 " =    0.702
peak=    3.553 closest distance to " CD2 TRP A 179 " =    1.295
peak=    3.544 closest distance to " CB  HIS A 108 " =    0.846
peak=    3.542 closest distance to " CB  ASN A 110 " =    1.067
peak=    3.539 closest distance to " O   HOH Z 175 " =    2.190
peak=    3.534 closest distance to " CG  GLN A  88 " =    1.102
peak=    3.532 closest distance to " NZ  LYS A  48 " =    1.208
peak=    3.529 closest distance to " O   HOH Z 158 " =    3.141
peak=    3.529 closest distance to " O   HOH Z 236 " =    1.588
peak=    3.525 closest distance to " O   HOH Z  10 " =    1.767
peak=    3.516 closest distance to " C   ALA A 299 " =    0.982
peak=    3.510 closest distance to " CA  LYS A 290 " =    1.268
peak=    3.509 closest distance to " CA  ASN A 127 " =    1.059
peak=    3.505 closest distance to " CB  ASN A 215 " =    1.232
peak=    3.504 closest distance to " O   HOH Z 128 " =    1.866
peak=    3.492 closest distance to " O   HOH Z 128 " =    2.123
peak=    3.487 closest distance to " NH1AARG A 145 " =    1.164
peak=    3.486 closest distance to " CB  THR A 157 " =    1.151
peak=    3.485 closest distance to " O   HOH Z 366 " =    2.923
peak=    3.483 closest distance to " CG  MET A 113 " =    1.067
peak=    3.483 closest distance to " ND1 HIS A  86 " =    1.767
peak=    3.483 closest distance to " O   HOH Z 290 " =    1.004
peak=    3.482 closest distance to " O   HOH Z  22 " =    2.025
peak=    3.478 closest distance to " N   SER A 135 " =    1.306
peak=    3.470 closest distance to " CD  LYS A 166 " =    1.363
peak=    3.470 closest distance to " O   HOH Z 427 " =    1.227
peak=    3.468 closest distance to " CB  VAL A 250 " =    1.060
peak=    3.468 closest distance to " CG1BVAL A  72 " =    1.513
peak=    3.465 closest distance to " CB  ALA A 114 " =    1.399
peak=    3.465 closest distance to " O   HOH Z 143 " =    1.383
peak=    3.457 closest distance to " CE3 TRP A 150 " =    1.021
peak=    3.451 closest distance to " N   ASN A 127 " =    1.383
peak=    3.451 closest distance to " CA  ALA A  51 " =    1.062
peak=    3.447 closest distance to " CG2 ILE A  20 " =    1.568
peak=    3.442 closest distance to " O   HOH Z 130 " =    2.511
peak=    3.442 closest distance to " CG1 ILE A 151 " =    1.178
peak=    3.437 closest distance to " CG AARG A 275 " =    1.130
peak=    3.436 closest distance to " O   HOH Z 145 " =    1.939
peak=    3.435 closest distance to " O   HOH Z  88 " =    3.062
peak=    3.430 closest distance to " CB  GLU A 152 " =    1.119
peak=    3.426 closest distance to " O   HOH Z  40 " =    1.997
peak=    3.424 closest distance to " CA  ALA A 158 " =    1.280
peak=    3.419 closest distance to " O   HOH Z 126 " =    1.478
peak=    3.416 closest distance to " O   HOH Z 180 " =    2.086
peak=    3.414 closest distance to " CD1 ILE A  33 " =    1.746
peak=    3.413 closest distance to " O   HOH Z 343 " =    3.194
peak=    3.411 closest distance to " CA  ILE A 234 " =    0.995
peak=    3.411 closest distance to " O   HOH Z 248 " =    1.621
peak=    3.406 closest distance to " O   HOH Z 213 " =    2.231
peak=    3.401 closest distance to " CB  SER A  62 " =    1.127
peak=    3.381 closest distance to " O  BHOH Z 338 " =    2.449
peak=    3.377 closest distance to " O   HOH Z  40 " =    2.156
peak=    3.375 closest distance to " CB  GLN A 278 " =    0.918
peak=    3.374 closest distance to " O   HOH Z 250 " =    1.380
peak=    3.371 closest distance to " CB  THR A  52 " =    1.024
peak=    3.367 closest distance to " O   HOH Z 437 " =    1.964
peak=    3.367 closest distance to " CD1 LEU A 281 " =    1.059
peak=    3.360 closest distance to " O   HOH Z 389 " =    1.240
peak=    3.360 closest distance to " CA  ASN A 217 " =    1.235
peak=    3.358 closest distance to " CB  SER A 210 " =    0.781
peak=    3.354 closest distance to " CB  SER A 276 " =    1.156
peak=    3.350 closest distance to " O   HOH Z 273 " =    2.966
peak=    3.347 closest distance to " O   HOH Z 329 " =    3.984
peak=    3.346 closest distance to " O   HOH Z  61 " =    1.551
peak=    3.342 closest distance to " O   HOH Z 392 " =    1.233
peak=    3.341 closest distance to " CB  LEU A 143 " =    1.118
peak=    3.341 closest distance to " CG2 VAL A 197 " =    1.106
peak=    3.339 closest distance to " NE2 HIS A 207 " =    1.226
peak=    3.337 closest distance to " O   HOH Z 305 " =    3.416
peak=    3.335 closest distance to " CE1 TYR A 186 " =    1.278
peak=    3.331 closest distance to " CG2 ILE A 234 " =    0.766
peak=    3.330 closest distance to " O   HOH Z 258 " =    2.169
peak=    3.329 closest distance to " O   HOH Z 303 " =    2.831
peak=    3.328 closest distance to " O   HOH Z 423 " =    1.660
peak=    3.327 closest distance to " O   HOH Z 327 " =    1.515
peak=    3.324 closest distance to " CB  SER A 212 " =    1.280
peak=    3.319 closest distance to " CB  PHE A 204 " =    1.021
peak=    3.318 closest distance to " O   HOH Z 357 " =    2.059
peak=    3.314 closest distance to " OG  SER A  62 " =    2.947
peak=    3.314 closest distance to " CD2 LEU A 297 " =    0.909
peak=    3.313 closest distance to " O   HOH Z 424 " =    2.467
peak=    3.309 closest distance to " O   HOH Z 116 " =    2.884
peak=    3.308 closest distance to " CB  ALA A 248 " =    1.287
peak=    3.308 closest distance to " CG1 VAL A 153 " =    0.919
peak=    3.307 closest distance to " O   HOH Z 373 " =    1.481
peak=    3.306 closest distance to " O   HOH Z 145 " =    3.820
peak=    3.304 closest distance to " NE  ARG A  56 " =    3.483
peak=    3.301 closest distance to " N   ALA A 256 " =    0.977
peak=    3.300 closest distance to " O   HOH Z 260 " =    1.495
peak=    3.299 closest distance to " CA  ALA A 291 " =    0.875
peak=    3.293 closest distance to " CA  ARG A  36 " =    1.023
peak=    3.289 closest distance to " CA  MET A 105 " =    0.956
peak=    3.286 closest distance to " CG  LYS A 119 " =    1.102
peak=    3.281 closest distance to " CG2 ILE A 120 " =    1.258
peak=    3.280 closest distance to " CB  THR A  31 " =    1.662
peak=    3.276 closest distance to " O   HOH Z   1 " =    1.733
peak=    3.269 closest distance to " CB  LEU A 228 " =    1.309
peak=    3.267 closest distance to " O   PHE A 192 " =    1.393
peak=    3.266 closest distance to " O   HOH Z 336 " =    1.902
peak=    3.264 closest distance to " N   GLN A 278 " =    1.330
peak=    3.263 closest distance to " O   HOH Z  88 " =    2.908
peak=    3.261 closest distance to " O   HOH Z 153 " =    3.699
peak=    3.259 closest distance to " CA  GLY A 267 " =    0.951
peak=    3.258 closest distance to " CG  GLN A  89 " =    1.438
peak=    3.258 closest distance to " O   TYR A 116 " =    1.251
peak=    3.257 closest distance to " O   HOH Z 389 " =    1.672
peak=    3.255 closest distance to " CG  MET A 185 " =    1.199
peak=    3.255 closest distance to " N   SER A 146 " =    1.733
peak=    3.253 closest distance to " O   HOH Z 119 " =    1.635
peak=    3.251 closest distance to " O   HOH Z  97 " =    2.510
peak=    3.249 closest distance to " NH2AARG A 145 " =    1.055
peak=    3.246 closest distance to " CB  MET A  40 " =    0.831
peak=    3.245 closest distance to " O   HOH Z 389 " =    3.144
peak=    3.243 closest distance to " O   HOH Z 423 " =    2.147
peak=    3.241 closest distance to " O   HOH Z 325 " =    2.058
peak=    3.241 closest distance to " O   HOH Z 406 " =    1.597
peak=    3.238 closest distance to " O   ASP A 124 " =    1.143
peak=    3.234 closest distance to " CA  ALA A 160 " =    0.935
peak=    3.234 closest distance to " O   HOH Z 371 " =    1.711
peak=    3.231 closest distance to " NH2BARG A 145 " =    2.045
peak=    3.229 closest distance to " O   CYS A 168 " =    1.174
peak=    3.224 closest distance to " CB  ARG A 139 " =    0.997
peak=    3.215 closest distance to " N   ASP A 162 " =    1.073
peak=    3.213 closest distance to " O   HOH Z 421 " =    1.987
peak=    3.211 closest distance to " N   SER A 271 " =    1.000
peak=    3.211 closest distance to " O   HOH Z 272 " =    2.226
peak=    3.210 closest distance to " N   ASN A  39 " =    1.197
peak=    3.209 closest distance to " O   HOH Z 148 " =    2.315
peak=    3.206 closest distance to " O   HOH Z 263 " =    1.603
peak=    3.204 closest distance to " CB  THR A 235 " =    1.071
peak=    3.202 closest distance to " CB  PRO A  90 " =    1.168
peak=    3.201 closest distance to " CD2 TYR A 186 " =    1.065
peak=    3.200 closest distance to " O   HOH Z  21 " =    1.747
peak=    3.198 closest distance to " CB  GLU A  46 " =    0.990
peak=    3.198 closest distance to " CA  ALA A 248 " =    1.223
peak=    3.194 closest distance to " CG2 ILE A 239 " =    0.701
peak=    3.189 closest distance to " O   HOH Z 352 " =    1.286
peak=    3.188 closest distance to " CB  LEU A 300 " =    0.864
peak=    3.187 closest distance to " OH  TYR A 116 " =    1.047
peak=    3.186 closest distance to " NH1 ARG A  14 " =    1.102
peak=    3.183 closest distance to " O   HOH Z 109 " =    2.521
peak=    3.182 closest distance to " CA  ILE A 106 " =    0.739
peak=    3.182 closest distance to " O   HOH Z 323 " =    1.570
peak=    3.179 closest distance to " O   HOH Z 145 " =    1.475
peak=    3.179 closest distance to " CD1 LEU A   5 " =    1.578
peak=    3.178 closest distance to " CA  ARG A 195 " =    1.176
peak=    3.176 closest distance to " O   HOH Z 124 " =    1.986
peak=    3.175 closest distance to " CG1 ILE A  49 " =    1.499
peak=    3.173 closest distance to " CD  ARG A  24 " =    1.037
peak=    3.172 closest distance to " CA  THR A 264 " =    0.765
peak=    3.171 closest distance to " O   HOH Z  85 " =    1.400
peak=    3.169 closest distance to " ND2 ASN A 110 " =    1.617
peak=    3.169 closest distance to " CB  ASP A 140 " =    0.960
peak=    3.165 closest distance to " CA  ARG A 102 " =    1.131
peak=    3.161 closest distance to " CB  TRP A 150 " =    1.364
peak=    3.159 closest distance to " O   HOH Z  59 " =    2.119
peak=    3.156 closest distance to " CD1 LEU A  96 " =    0.767
peak=    3.155 closest distance to " CA  ASP A 162 " =    0.935
peak=    3.154 closest distance to " O   ASN A  74 " =    1.522
peak=    3.149 closest distance to " O   HOH Z 172 " =    3.108
peak=    3.146 closest distance to " O   HOH Z 251 " =    1.528
peak=    3.146 closest distance to " O   HOH Z 132 " =    2.380
peak=    3.145 closest distance to " N   SER A  97 " =    0.814
peak=    3.137 closest distance to " CB  ALA A 180 " =    1.288
peak=    3.135 closest distance to " CB  TYR A  30 " =    1.609
peak=    3.127 closest distance to " CA  ALA A 154 " =    0.998
peak=    3.114 closest distance to " CA  ARG A 156 " =    0.952
peak=    3.108 closest distance to " O   HOH Z  85 " =    2.062
peak=    3.105 closest distance to " CA  LEU A 101 " =    1.625
peak=    3.103 closest distance to " CB  ALA A   1 " =    4.728
peak=    3.101 closest distance to " O   HOH Z 344 " =    2.912
peak=    3.101 closest distance to " CZ3 TRP A  92 " =    1.203
peak=    3.101 closest distance to " O   HOH Z 128 " =    2.055
peak=    3.097 closest distance to " O   PRO A  90 " =    1.714
peak=    3.088 closest distance to " O   THR A 182 " =    1.447
peak=    3.082 closest distance to " O   HOH Z 130 " =    1.827
peak=    3.071 closest distance to " O   HOH Z 371 " =    3.285
peak=    3.069 closest distance to " O   HOH Z   4 " =    1.503
peak=    3.065 closest distance to " NZ  LYS A  48 " =    1.553
peak=    3.050 closest distance to " O   HOH Z  89 " =    2.062
peak=    3.044 closest distance to " CG  GLN A 278 " =    1.283
peak=    3.035 closest distance to " CA  GLY A 136 " =    1.131
peak=    3.029 closest distance to " CG  ARG A 138 " =    1.267
peak=    3.028 closest distance to " N   ALA A 233 " =    0.736
peak=    3.022 closest distance to " O   HOH Z 426 " =    2.077

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 204         
Filter by distance & map next to the model:
   mapped sites are within: 0.744 - 5.435
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 203 from: 204
   mapped sites are within: 0.744 - 5.435

peak=   -4.731 closest distance to " CG2 VAL A 230 " =    0.744
peak=   -4.513 closest distance to " CD  ARG A 156 " =    2.023
peak=   -4.237 closest distance to " O   HOH Z 266 " =    5.277
peak=   -4.224 closest distance to " OG BSER A 134 " =    1.284
peak=   -4.137 closest distance to " CD1 LEU A 255 " =    2.759
peak=   -4.111 closest distance to " CD  ARG A  14 " =    3.185
peak=   -4.054 closest distance to " CB  PRO A 243 " =    2.694
peak=   -4.003 closest distance to " C   HIS A 108 " =    1.260
peak=   -3.977 closest distance to " CG  GLN A  58 " =    1.001
peak=   -3.976 closest distance to " O   HOH Z 185 " =    2.114
peak=   -3.949 closest distance to " O   HOH Z 231 " =    1.889
peak=   -3.915 closest distance to " O   VAL A  67 " =    2.476
peak=   -3.881 closest distance to " O   HOH Z 351 " =    1.513
peak=   -3.878 closest distance to " CB  ALA A  43 " =    2.523
peak=   -3.837 closest distance to " CZ2 TRP A 274 " =    0.896
peak=   -3.826 closest distance to " N   ALA A  43 " =    2.587
peak=   -3.815 closest distance to " O   HOH Z  43 " =    1.825
peak=   -3.786 closest distance to " NH2 ARG A  79 " =    2.062
peak=   -3.780 closest distance to " O   HOH Z 290 " =    1.133
peak=   -3.779 closest distance to " O   HOH Z 359 " =    1.611
peak=   -3.771 closest distance to " O   HOH Z 394 " =    1.504
peak=   -3.771 closest distance to " O   PRO A 163 " =    2.009
peak=   -3.763 closest distance to " N   THR A 157 " =    1.405
peak=   -3.756 closest distance to " CE2 PHE A 218 " =    2.484
peak=   -3.731 closest distance to " CG2 VAL A 296 " =    2.036
peak=   -3.729 closest distance to " O   HOH Z 191 " =    5.435
peak=   -3.726 closest distance to " CE2 TYR A  30 " =    2.703
peak=   -3.723 closest distance to " O   PRO A 198 " =    1.147
peak=   -3.720 closest distance to " O   HOH Z  52 " =    1.275
peak=   -3.716 closest distance to " CD  GLN A 223 " =    2.261
peak=   -3.689 closest distance to " O   HOH Z 359 " =    3.241
peak=   -3.683 closest distance to " CB  PHE A 192 " =    1.802
peak=   -3.677 closest distance to " O   HOH Z 131 " =    4.049
peak=   -3.668 closest distance to " ND2 ASN A 249 " =    2.468
peak=   -3.664 closest distance to " O   HOH Z 231 " =    1.187
peak=   -3.656 closest distance to " O   SER A 135 " =    1.421
peak=   -3.645 closest distance to " CE BMET A  47 " =    1.104
peak=   -3.640 closest distance to " CG2 VAL A 202 " =    2.691
peak=   -3.624 closest distance to " O   HOH Z 389 " =    2.108
peak=   -3.621 closest distance to " CB  ALA A 161 " =    2.493
peak=   -3.621 closest distance to " CA  GLY A 241 " =    2.265
peak=   -3.620 closest distance to " O   SER A  22 " =    2.356
peak=   -3.616 closest distance to " CB  VAL A 230 " =    1.128
peak=   -3.612 closest distance to " O   HOH Z  65 " =    1.185
peak=   -3.611 closest distance to " O   HOH Z 211 " =    1.317
peak=   -3.607 closest distance to " O   HOH Z 389 " =    1.464
peak=   -3.598 closest distance to " CB  ALA A 248 " =    2.062
peak=   -3.587 closest distance to " ND2 ASN A 187 " =    1.529
peak=   -3.586 closest distance to " O   ILE A  49 " =    1.690
peak=   -3.581 closest distance to " OG  SER A  87 " =    1.496
peak=   -3.573 closest distance to " OG  SER A  63 " =    1.233
peak=   -3.568 closest distance to " CA  GLY A 203 " =    2.390
peak=   -3.566 closest distance to " OG  SER A  97 " =    2.208
peak=   -3.565 closest distance to " O   HOH Z  11 " =    1.787
peak=   -3.559 closest distance to " OG  SER A  62 " =    4.370
peak=   -3.555 closest distance to " O   HOH Z 350 " =    1.788
peak=   -3.551 closest distance to " O   HOH Z 102 " =    1.582
peak=   -3.545 closest distance to " CD2 TYR A 293 " =    1.842
peak=   -3.543 closest distance to " O   HOH Z  51 " =    0.870
peak=   -3.540 closest distance to " CB  TYR A  15 " =    2.156
peak=   -3.538 closest distance to " CB  ALA A 114 " =    2.409
peak=   -3.531 closest distance to " ND2 ASN A  45 " =    1.193
peak=   -3.527 closest distance to " OE1 GLN A  88 " =    1.107
peak=   -3.509 closest distance to " CB  ALA A 244 " =    2.100
peak=   -3.508 closest distance to " O   HOH Z 377 " =    1.034
peak=   -3.507 closest distance to " CD2 LEU A 237 " =    2.793
peak=   -3.506 closest distance to " C   MET A 188 " =    1.452
peak=   -3.505 closest distance to " O   PRO A 243 " =    2.541
peak=   -3.505 closest distance to " N   ALA A 226 " =    2.043
peak=   -3.493 closest distance to " O   ARG A 145 " =    1.470
peak=   -3.492 closest distance to " CG  LEU A   5 " =    0.947
peak=   -3.488 closest distance to " O   VAL A  67 " =    2.879
peak=   -3.487 closest distance to " O   HOH Z 427 " =    1.673
peak=   -3.485 closest distance to " CA  ASN A 127 " =    1.202
peak=   -3.480 closest distance to " CD  PRO A 213 " =    2.046
peak=   -3.473 closest distance to " CG1 VAL A 112 " =    2.946
peak=   -3.467 closest distance to " O   HOH Z 292 " =    1.607
peak=   -3.452 closest distance to " CE  MET A 105 " =    2.461
peak=   -3.447 closest distance to " CG  TRP A 266 " =    1.944
peak=   -3.441 closest distance to " CA  GLY A  35 " =    2.089
peak=   -3.438 closest distance to " O   HOH Z 134 " =    3.969
peak=   -3.438 closest distance to " CB  PRO A 280 " =    2.157
peak=   -3.438 closest distance to " CE  LYS A  76 " =    2.682
peak=   -3.437 closest distance to " O   HOH Z 166 " =    1.911
peak=   -3.436 closest distance to " CA  GLY A 133 " =    1.984
peak=   -3.435 closest distance to " CD2 LEU A   5 " =    1.032
peak=   -3.433 closest distance to " CB  ASP A 132 " =    2.373
peak=   -3.432 closest distance to " CD  LYS A 289 " =    2.403
peak=   -3.423 closest distance to " O   HOH Z 114 " =    2.979
peak=   -3.420 closest distance to " CA  GLY A  98 " =    1.854
peak=   -3.417 closest distance to " O   GLU A 152 " =    1.428
peak=   -3.410 closest distance to " CD1 LEU A 101 " =    2.223
peak=   -3.410 closest distance to " OE2 GLU A 152 " =    1.188
peak=   -3.410 closest distance to " CG2 ILE A 151 " =    2.579
peak=   -3.402 closest distance to " O   HOH Z 140 " =    1.476
peak=   -3.399 closest distance to " CD2 HIS A 207 " =    2.281
peak=   -3.391 closest distance to " OG  SER A   3 " =    1.665
peak=   -3.390 closest distance to " CG1 VAL A 230 " =    1.887
peak=   -3.376 closest distance to " O   HOH Z  73 " =    2.361
peak=   -3.371 closest distance to " CG1 VAL A 112 " =    2.635
peak=   -3.366 closest distance to " CD1 ILE A 199 " =    2.496
peak=   -3.363 closest distance to " O   HOH Z 423 " =    2.428
peak=   -3.360 closest distance to " O   HOH Z  39 " =    1.151
peak=   -3.360 closest distance to " OD1 ASN A 148 " =    1.372
peak=   -3.359 closest distance to " O   HOH Z 165 " =    2.148
peak=   -3.357 closest distance to " CB  ALA A   7 " =    2.130
peak=   -3.354 closest distance to " OG ASER A 134 " =    1.210
peak=   -3.349 closest distance to " CA  ASP A  27 " =    2.395
peak=   -3.345 closest distance to " O   VAL A 189 " =    2.489
peak=   -3.339 closest distance to " CB  SER A 210 " =    1.114
peak=   -3.339 closest distance to " O   HOH Z 407 " =    3.023
peak=   -3.335 closest distance to " CB  PRO A 163 " =    2.386
peak=   -3.327 closest distance to " O   HOH Z 111 " =    4.301
peak=   -3.321 closest distance to " CB  ASN A  39 " =    2.265
peak=   -3.319 closest distance to " O   HOH Z 198 " =    2.020
peak=   -3.319 closest distance to " CB  GLN A  55 " =    1.246
peak=   -3.316 closest distance to " NE2 GLN A 278 " =    1.873
peak=   -3.316 closest distance to " OD2 ASP A 191 " =    1.279
peak=   -3.315 closest distance to " CE2 TRP A  70 " =    2.227
peak=   -3.314 closest distance to " O   GLY A  80 " =    2.464
peak=   -3.313 closest distance to " O   HOH Z 313 " =    1.606
peak=   -3.311 closest distance to " CB  CYS A 254 " =    2.087
peak=   -3.303 closest distance to " CA  ASP A 298 " =    1.052
peak=   -3.303 closest distance to " O   PRO A 198 " =    1.338
peak=   -3.291 closest distance to " O   HOH Z 103 " =    1.850
peak=   -3.290 closest distance to " CZ  TYR A 169 " =    1.702
peak=   -3.283 closest distance to " O   HOH Z 208 " =    2.166
peak=   -3.278 closest distance to " OE1 GLN A 183 " =    1.565
peak=   -3.276 closest distance to " N   ALA A 248 " =    1.529
peak=   -3.274 closest distance to " O   ALA A  10 " =    1.753
peak=   -3.273 closest distance to " ND2 ASN A  45 " =    2.065
peak=   -3.270 closest distance to " CB  ALA A  10 " =    2.330
peak=   -3.268 closest distance to " O   HOH Z 100 " =    1.129
peak=   -3.264 closest distance to " C   LEU A 222 " =    0.925
peak=   -3.260 closest distance to " ND2 ASN A 252 " =    1.909
peak=   -3.260 closest distance to " O   HOH Z 281 " =    2.619
peak=   -3.257 closest distance to " O   PHE A 218 " =    1.503
peak=   -3.254 closest distance to " CE1 PHE A  59 " =    1.927
peak=   -3.254 closest distance to " N   MET A 188 " =    1.829
peak=   -3.251 closest distance to " O   HOH Z  44 " =    2.299
peak=   -3.249 closest distance to " O   GLY A 229 " =    1.925
peak=   -3.248 closest distance to " CB  PRO A  90 " =    1.648
peak=   -3.246 closest distance to " O   HOH Z 286 " =    1.699
peak=   -3.243 closest distance to " O   HOH Z 348 " =    1.819
peak=   -3.242 closest distance to " OH  TYR A 172 " =    1.848
peak=   -3.242 closest distance to " O   HOH Z 414 " =    2.571
peak=   -3.239 closest distance to " O   SER A 271 " =    2.121
peak=   -3.237 closest distance to " N   VAL A  72 " =    1.599
peak=   -3.236 closest distance to " O   HOH Z 243 " =    2.025
peak=   -3.235 closest distance to " CG  PHE A 283 " =    2.644
peak=   -3.222 closest distance to " N   GLN A  58 " =    1.839
peak=   -3.221 closest distance to " O   HOH Z 149 " =    2.238
peak=   -3.219 closest distance to " ND2BASN A 224 " =    1.624
peak=   -3.216 closest distance to " O   HOH Z 134 " =    3.452
peak=   -3.212 closest distance to " O   HOH Z 111 " =    1.982
peak=   -3.210 closest distance to " CZ3 TRP A 179 " =    1.266
peak=   -3.210 closest distance to " O   HOH Z 108 " =    1.573
peak=   -3.207 closest distance to " O   ALA A   1 " =    1.628
peak=   -3.205 closest distance to " O   ASN A 301 " =    1.559
peak=   -3.204 closest distance to " O   HOH Z 138 " =    1.276
peak=   -3.203 closest distance to " CB  TRP A  85 " =    2.588
peak=   -3.197 closest distance to " N   ASP A 270 " =    1.396
peak=   -3.195 closest distance to " CB  CYS A 201 " =    2.512
peak=   -3.195 closest distance to " CG  ASP A 231 " =    0.766
peak=   -3.194 closest distance to " OXT GLY A 302 " =    3.019
peak=   -3.191 closest distance to " O   GLN A 240 " =    2.013
peak=   -3.189 closest distance to " O   HOH Z  63 " =    1.900
peak=   -3.186 closest distance to " O   HOH Z 371 " =    2.297
peak=   -3.177 closest distance to " C   ASN A 285 " =    2.212
peak=   -3.176 closest distance to " O   HOH Z 357 " =    2.054
peak=   -3.173 closest distance to " NH2AARG A 275 " =    5.186
peak=   -3.166 closest distance to " CZ  ARG A 259 " =    0.948
peak=   -3.162 closest distance to " O   HOH Z 353 " =    1.908
peak=   -3.162 closest distance to " C   LYS A  76 " =    1.457
peak=   -3.153 closest distance to " O   SER A 210 " =    1.899
peak=   -3.151 closest distance to " CB  PHE A 130 " =    1.188
peak=   -3.150 closest distance to " N   SER A 276 " =    1.338
peak=   -3.148 closest distance to " CB  ALA A 248 " =    2.349
peak=   -3.143 closest distance to " O   HOH Z 318 " =    2.045
peak=   -3.141 closest distance to " CG1 VAL A 197 " =    2.348
peak=   -3.135 closest distance to " O   HOH Z   1 " =    1.538
peak=   -3.132 closest distance to " O   HOH Z 216 " =    1.463
peak=   -3.129 closest distance to " CG2 THR A  42 " =    1.677
peak=   -3.128 closest distance to " CB  ALA A 291 " =    2.160
peak=   -3.127 closest distance to " NH1 ARG A  66 " =    3.630
peak=   -3.126 closest distance to " O   HOH Z 412 " =    4.031
peak=   -3.125 closest distance to " CD1 PHE A  61 " =    2.950
peak=   -3.124 closest distance to " O   HOH Z 384 " =    2.125
peak=   -3.118 closest distance to " OD1 ASN A 301 " =    2.032
peak=   -3.114 closest distance to " ND2 ASN A  45 " =    1.467
peak=   -3.112 closest distance to " CA  GLY A  57 " =    2.133
peak=   -3.110 closest distance to " O   TRP A  70 " =    1.403
peak=   -3.106 closest distance to " O   HOH Z 235 " =    1.210
peak=   -3.101 closest distance to " OD1 ASP A 200 " =    1.613
peak=   -3.097 closest distance to " O   HOH Z 166 " =    1.488
peak=   -3.095 closest distance to " O   LEU A 101 " =    2.780
peak=   -3.095 closest distance to " O   ALA A 292 " =    2.009
peak=   -3.072 closest distance to " CD1 TYR A 247 " =    2.801
peak=   -3.071 closest distance to " NH2 ARG A 219 " =    1.708
peak=   -3.071 closest distance to " CE  LYS A 166 " =    1.248
peak=   -3.063 closest distance to " OG  SER A 206 " =    1.649
peak=   -3.056 closest distance to " CD1 LEU A 228 " =    2.256
peak=   -3.029 closest distance to " OE1 GLU A 277 " =    2.194

================= 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    :  0.4661 0.4559   6.267822e+00   6.247028e+00
   1_bss:  0.4584 0.4408   6.262608e+00   6.233862e+00
   1_xyz:  0.3680 0.3868   6.127362e+00   6.149823e+00
   1_adp:  0.3171 0.3697   6.027309e+00   6.121130e+00
   1_occ:  0.3166 0.3698   6.026677e+00   6.122231e+00
   2_bss:  0.3125 0.3643   6.027166e+00   6.119107e+00
   2_xyz:  0.2223 0.2772   5.728257e+00   5.885772e+00
   2_adp:  0.1954 0.2507   5.620245e+00   5.803189e+00
   2_occ:  0.1953 0.2504   5.619502e+00   5.802964e+00
   3_bss:  0.1937 0.2483   5.618094e+00   5.800239e+00
   3_xyz:  0.1484 0.1964   5.381362e+00   5.593996e+00
   3_adp:  0.1377 0.1875   5.323877e+00   5.548345e+00
   3_occ:  0.1376 0.1875   5.323766e+00   5.548583e+00
   4_bss:  0.1375 0.1873   5.322142e+00   5.546574e+00
   4_xyz:  0.1228 0.1713   5.225723e+00   5.460812e+00
   4_adp:  0.1197 0.1677   5.204660e+00   5.439242e+00
   4_occ:  0.1196 0.1675   5.204464e+00   5.438951e+00
   5_bss:  0.1195 0.1674   5.204203e+00   5.438787e+00
   5_xyz:  0.1157 0.1626   5.178924e+00   5.418163e+00
   5_adp:  0.1152 0.1619   5.175388e+00   5.415484e+00
   5_occ:  0.1149 0.1619   5.174179e+00   5.414630e+00
   5_bss:  0.1148 0.1618   5.174180e+00   5.414611e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.366  20.000   6.721   9.709   9.128   0.000   0.000   0.000
   1_xyz:  0.366  20.000   6.721   9.709   9.128   0.000   0.000   0.000
   1_adp:  0.366  20.000   6.721   9.709   9.128   0.000   0.000   0.000
   1_occ:  0.366  20.000   6.721   9.709   9.128   0.000   0.000   0.000
   2_bss:  0.345  37.649   3.316   5.244   5.391   0.000   0.000   0.000
   2_xyz:  0.345  37.649   3.316   5.244   5.391   0.000   0.000   0.000
   2_adp:  0.345  37.649   3.316   5.244   5.391   0.000   0.000   0.000
   2_occ:  0.345  37.649   3.316   5.244   5.391   0.000   0.000   0.000
   3_bss:  0.329  46.811   2.135   2.892   3.945   0.000   0.000   0.000
   3_xyz:  0.329  46.811   2.135   2.892   3.945   0.000   0.000   0.000
   3_adp:  0.329  46.811   2.135   2.892   3.945   0.000   0.000   0.000
   3_occ:  0.329  46.811   2.135   2.892   3.945   0.000   0.000   0.000
   4_bss:  0.325  46.811   1.823   2.130   3.670   0.000   0.000   0.000
   4_xyz:  0.325  46.811   1.823   2.130   3.670   0.000   0.000   0.000
   4_adp:  0.325  46.811   1.823   2.130   3.670   0.000   0.000   0.000
   4_occ:  0.325  46.811   1.823   2.130   3.670   0.000   0.000   0.000
   5_bss:  0.323  48.389   1.944   2.116   3.771   0.000   0.000   0.000
   5_xyz:  0.323  48.389   1.944   2.116   3.771   0.000   0.000   0.000
   5_adp:  0.323  48.389   1.944   2.116   3.771   0.000   0.000   0.000
   5_occ:  0.323  48.389   1.944   2.116   3.771   0.000   0.000   0.000
   5_bss:  0.323  51.093  -0.645  -0.535   1.180  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  54.043 0.4700  0.5455    63100.611
   1_bss:  53.556 0.4744  0.7067    59989.316
   1_xyz:  43.646 0.5972  0.8647    42557.760
   1_adp:  40.004 0.6419  0.9667    37954.696
   1_occ:  40.125 0.6403  0.9631    38042.580
   2_bss:  39.733 0.6450  0.8460    37499.941
   2_xyz:  27.863 0.7803  0.9878    19519.783
   2_adp:  24.388 0.8181  1.0114    15868.475
   2_occ:  24.372 0.8182  1.0116    15854.447
   3_bss:  24.238 0.8195  0.9537    15732.074
   3_xyz:  18.683 0.8741  0.9890     9865.467
   3_adp:  17.513 0.8851  0.9883     9019.251
   3_occ:  17.516 0.8851  0.9881     9020.896
   4_bss:  17.471 0.8854  0.9719     8964.095
   4_xyz:  15.620 0.9014  0.9804     7407.502
   4_adp:  15.099 0.9061  0.9772     7102.893
   4_occ:  15.095 0.9061  0.9770     7093.654
   5_bss:  15.090 0.9061  0.9796     7091.170
   5_xyz:  14.606 0.9103  0.9808     6769.707
   5_adp:  14.491 0.9114  0.9768     6726.127
   5_occ:  14.472 0.9116  0.9766     6713.021
   5_bss:  14.472 0.9116  0.9800     6713.544
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3530e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3530e+01
   1_xyz:   1.627  0.012  0.104 18.116  0.006  4.108   1.3085e-01
   1_adp:   1.627  0.012  0.104 18.116  0.006  4.108   1.3085e-01
   1_occ:   1.627  0.012  0.104 18.116  0.006  4.108   1.3085e-01
   2_bss:   1.627  0.012  0.104 18.116  0.006  4.108   1.3085e-01
   2_xyz:   1.173  0.009  0.083 16.037  0.005  4.108   8.7594e-02
   2_adp:   1.173  0.009  0.083 16.037  0.005  4.108   8.7594e-02
   2_occ:   1.173  0.009  0.083 16.037  0.005  4.108   8.7594e-02
   3_bss:   1.173  0.009  0.083 16.037  0.005  4.108   8.7594e-02
   3_xyz:   0.989  0.006  0.075 15.809  0.003  4.118   5.9909e-02
   3_adp:   0.989  0.006  0.075 15.809  0.003  4.118   5.9909e-02
   3_occ:   0.989  0.006  0.075 15.809  0.003  4.118   5.9909e-02
   4_bss:   0.989  0.006  0.075 15.809  0.003  4.118   5.9909e-02
   4_xyz:   0.965  0.006  0.074 15.747  0.003  4.122   5.8301e-02
   4_adp:   0.965  0.006  0.074 15.747  0.003  4.122   5.8301e-02
   4_occ:   0.965  0.006  0.074 15.747  0.003  4.122   5.8301e-02
   5_bss:   0.965  0.006  0.074 15.747  0.003  4.122   5.8301e-02
   5_xyz:   0.924  0.006  0.072 15.353  0.003  4.110   5.4304e-02
   5_adp:   0.924  0.006  0.072 15.353  0.003  4.110   5.4304e-02
   5_occ:   0.924  0.006  0.072 15.353  0.003  4.110   5.4304e-02
   5_bss:   0.924  0.006  0.072 15.353  0.003  4.110   5.4304e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9390e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9390e+00
   1_xyz:  12.897  0.161  0.396 85.724  0.032  2.174   9.2809e-02
   1_adp:  12.897  0.161  0.396 85.724  0.032  2.174   9.2809e-02
   1_occ:  12.897  0.161  0.396 85.724  0.032  2.174   9.2809e-02
   2_bss:  12.897  0.161  0.396 85.724  0.032  2.174   9.2809e-02
   2_xyz:   7.509  0.094  0.264 84.589  0.030  2.289   1.6358e-01
   2_adp:   7.509  0.094  0.264 84.589  0.030  2.289   1.6358e-01
   2_occ:   7.509  0.094  0.264 84.589  0.030  2.289   1.6358e-01
   3_bss:   7.509  0.094  0.264 84.589  0.030  2.289   1.6358e-01
   3_xyz:   7.186  0.048  0.325 85.046  0.031  2.313   4.3926e-02
   3_adp:   7.186  0.048  0.325 85.046  0.031  2.313   4.3926e-02
   3_occ:   7.186  0.048  0.325 85.046  0.031  2.313   4.3926e-02
   4_bss:   7.186  0.048  0.325 85.046  0.031  2.313   4.3926e-02
   4_xyz:   8.121  0.050  0.288 82.365  0.035  2.353   3.6904e-02
   4_adp:   8.121  0.050  0.288 82.365  0.035  2.353   3.6904e-02
   4_occ:   8.121  0.050  0.288 82.365  0.035  2.353   3.6904e-02
   5_bss:   8.121  0.050  0.288 82.365  0.035  2.353   3.6904e-02
   5_xyz:   6.423  0.042  0.278 84.393  0.038  2.340   3.4920e-02
   5_adp:   6.423  0.042  0.278 84.393  0.038  2.340   3.4920e-02
   5_occ:   6.423  0.042  0.278 84.393  0.038  2.340   3.4920e-02
   5_bss:   6.423  0.042  0.278 84.393  0.038  2.340   3.4920e-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:  77.27   0.00  12.77  65.50   0.00  10.25  77.27   0.00  26.46
   1_occ:  77.27   0.00  12.77  65.50   0.00  10.25  77.27   0.00  26.46
   2_bss:  77.27   0.00  12.77  65.50   0.00  10.25  77.27   0.00  26.46
   2_xyz:  77.27   0.00  12.77  65.50   0.00  10.25  77.27   0.00  26.46
   2_adp:  85.33   0.00  12.63  67.80   0.00   8.88  85.33   0.00  33.07
   2_occ:  85.33   0.00  12.63  67.80   0.00   8.88  85.33   0.00  33.07
   3_bss:  85.33   0.00  12.63  67.80   0.00   8.88  85.33   0.00  33.07
   3_xyz:  85.33   0.00  12.63  67.80   0.00   8.88  85.33   0.00  33.07
   3_adp:  85.95   0.00  13.02  75.34   0.00   8.66  85.95   1.64  36.76
   3_occ:  85.95   0.00  13.02  75.34   0.00   8.66  85.95   1.64  36.76
   4_bss:  85.95   0.00  13.02  75.34   0.00   8.66  85.95   1.64  36.76
   4_xyz:  85.95   0.00  13.02  75.34   0.00   8.66  85.95   1.64  36.76
   4_adp:  87.39   0.00  13.05  85.27   0.00   8.53  87.39   1.61  37.66
   4_occ:  87.39   0.00  13.05  85.27   0.00   8.53  87.39   1.61  37.66
   5_bss:  87.39   0.00  13.05  85.27   0.00   8.53  87.39   1.61  37.66
   5_xyz:  87.39   0.00  13.05  85.27   0.00   8.53  87.39   1.61  37.66
   5_adp:  88.46   0.00  12.88  88.46   0.00   8.42  86.63   1.42  37.18
   5_occ:  88.46   0.00  12.88  88.46   0.00   8.42  86.63   1.42  37.18
   5_bss:  91.16   2.70  15.58  91.16   2.70  11.12  89.34   4.12  39.89
------------------------------------------------------------------------
 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:    1.250    0.013    0.405
   1_adp:    1.250    0.013    0.405
   1_occ:    1.250    0.013    0.405
   2_bss:    1.250    0.013    0.405
   2_xyz:    1.494    0.041    0.578
   2_adp:    1.494    0.041    0.578
   2_occ:    1.494    0.041    0.578
   3_bss:    1.494    0.041    0.578
   3_xyz:    1.517    0.034    0.626
   3_adp:    1.517    0.034    0.626
   3_occ:    1.517    0.034    0.626
   4_bss:    1.517    0.034    0.626
   4_xyz:    1.644    0.039    0.660
   4_adp:    1.644    0.039    0.660
   4_occ:    1.644    0.039    0.660
   5_bss:    1.644    0.039    0.660
   5_xyz:    1.641    0.038    0.670
   5_adp:    1.641    0.038    0.670
   5_occ:    1.641    0.038    0.670
   5_bss:    1.641    0.038    0.670
------------------------------------------------------------------------

CPU time actual refinement: 336.65


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_513/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_513/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_513/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_513/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_513/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 336.49 
  Macro-tasks:
    bulk solvent and scale       = 41.29  
    individual site refinement   = 139.37 
    weights calculation          = 31.67  
    collect and process          = 6.57   
    model show statistics        = 0.15   
    TOTAL for macro-tasks        = 219.05 
  Micro-tasks:
    mask                            = 1.78   
    f_calc                          = 103.25 
    alpha_beta                      = 8.30   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 114.66 
    fmodel                         = 7.28   
    r_factors                      = 0.27   
    phase_errors                   = 10.69  
    foms                           = 0.22   
    TOTAL for micro-tasks          = 247.62 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.711 micro seconds
Total CPU time: 5.83 minutes
from_scatterers_fft:    664 calls, 102.96 s
gradients_fft:          609 calls, 101.14 s

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

# Date 2008-01-16 Time 01:45:54 PST -0800 (1200476754.25 s)
Start R-work = 0.4661, R-free = 0.4559 (no bulk solvent and anisotropic scale)
Final R-work = 0.1322, R-free = 0.1782 (no bulk solvent and anisotropic scale)

Start R-work = 0.4584, R-free = 0.4408
Final R-work = 0.1148, R-free = 0.1618