# Date 2008-01-16 Time 02:14:14 PST -0800 (1200478454.83 s)
#phil __OFF__

Command line arguments: "../748.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 19780
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 748

-------------------------------------------------------------------------------
  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: (70.6012, 46.2261, 84.2302, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 46.2261, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9429 1.9511
Completeness in resolution range: 0.94839
Completeness with d_max=infinity: 0.945552

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9429
                             d_min =   1.9511

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: (70.6012, 46.2261, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9429 1.9511
Completeness in resolution range: 0.94839
Completeness with d_max=infinity: 0.945552

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9433 -  4.1758 [2161/2190]  1948   213   9.9%
  bin  2:  4.1758 -  3.3265 [2089/2105]  1880   209  10.0%
  bin  3:  3.3265 -  2.9095 [2042/2061]  1833   209  10.2%
  bin  4:  2.9095 -  2.6451 [2046/2076]  1849   197   9.6%
  bin  5:  2.6451 -  2.4564 [2041/2060]  1834   207  10.1%
  bin  6:  2.4564 -  2.3121 [2005/2030]  1799   206  10.3%
  bin  7:  2.3121 -  2.1967 [1991/2025]  1797   194   9.7%
  bin  8:  2.1967 -  2.1014 [2007/2037]  1804   203  10.1%
  bin  9:  2.1014 -  2.0207 [1990/2032]  1793   197   9.9%
  bin 10:  2.0207 -  1.9511 [1217/2039]  1093   124  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_748/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.71 -     2.35: 36
        2.35 -     2.98: 1890
        2.98 -     3.62: 4706
        3.62 -     4.26: 9292
        4.26 -     4.90: 12851
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.708 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.715 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.767 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 341 "  1.778 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.795 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28770 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_748/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_748/model_refine_001.geo

CPU time processing inputs: 9.22


============================ 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 = 70.60125 46.22605 84.23025 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4980   r_free= 0.4894   ksol= 0.00   Bsol= 0.00   scale= 0.790    |
|                                                                             |
| 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:   0.83 A                  |
| x-ray target function (ml) for work reflections: 6.295656                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9433 -  4.6579 0.99   1403  158 0.4177 0.4326      6.6179      6.6801|
|  2:  4.6579 -  3.7159 0.99   1358  143 0.4343 0.4088      6.8425      6.7965|
|  3:  3.7159 -  3.2517 0.99   1326  151 0.4644 0.4343      6.7059      6.7894|
|  4:  3.2517 -  2.9569 0.99   1333  154 0.4847 0.4436      6.5569      6.4989|
|  5:  2.9569 -  2.7463 0.99   1307  142 0.5272 0.5134      6.3829      6.3568|
|  6:  2.7463 -  2.5853 0.99   1303  148 0.5236 0.5643       6.289       6.298|
|  7:  2.5853 -  2.4564 0.99   1314  139 0.5229 0.4637      6.2671      6.1884|
|  8:  2.4564 -  2.3499 0.98   1274  147 0.5468 0.5287      6.1743      6.2007|
|  9:  2.3499 -  2.2598 0.98   1293  149 0.5237 0.5216      6.1233       6.106|
| 10:  2.2598 -  2.1820 0.99   1290  137 0.5500 0.5685      6.1061      6.1274|
| 11:  2.1820 -  2.1140 0.99   1283  137 0.5249 0.5245      6.0471       6.053|
| 12:  2.1140 -  2.0537 0.97   1262  146 0.5291 0.5571      5.9624      5.9962|
| 13:  2.0537 -  1.9998 0.97   1268  137 0.5538 0.5164      5.8884      5.8254|
| 14:  1.9998 -  1.9511 0.47    616   71 0.5705 0.5690      5.8458      5.8158|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9433 -  4.6579  1403   158  0.63  40.55   0.79     0.68      93042.90|
|  2:  4.6579 -  3.7159  1358   143  0.65  39.27   0.86     0.75     129139.57|
|  3:  3.7159 -  3.2517  1326   151  0.54  48.42   0.83     0.70     135375.90|
|  4:  3.2517 -  2.9569  1333   154  0.47  54.57   0.80     0.59     116576.52|
|  5:  2.9569 -  2.7463  1307   142  0.36  62.71   0.73     0.46      92196.97|
|  6:  2.7463 -  2.5853  1303   148  0.35  63.26   0.72     0.43      77632.09|
|  7:  2.5853 -  2.4564  1314   139  0.33  65.29   0.76     0.37      67827.06|
|  8:  2.4564 -  2.3499  1274   147  0.31  66.76   0.71     0.38      62949.07|
|  9:  2.3499 -  2.2598  1293   149  0.28  68.83   0.74     0.33      58250.91|
| 10:  2.2598 -  2.1820  1290   137  0.27  70.19   0.74     0.34      55530.23|
| 11:  2.1820 -  2.1140  1283   137  0.24  72.07   0.78     0.30      51859.98|
| 12:  2.1140 -  2.0537  1262   146  0.23  72.74   0.76     0.30      47589.86|
| 13:  2.0537 -  1.9998  1268   137  0.20  74.86   0.74     0.27      41297.66|
| 14:  1.9998 -  1.9511   616    71  0.20  75.36   0.70     0.24      34379.59|
|alpha:            min =        0.24 max =            0.75 mean =         0.45|
|beta:             min =    34379.59 max =       135375.90 mean =     78212.37|
|figures of merit: min =        0.00 max =            1.00 mean =         0.37|
|phase err.(work): min =        0.00 max =           90.00 mean =        61.69|
|phase err.(test): min =        0.00 max =           89.85 mean =        61.82|
|-----------------------------------------------------------------------------|

============================== 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 = 18.314629             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.030   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.926116              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 82.077   (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:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       31 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      188 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      717 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1548 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2684 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3995 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5157 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6655 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7826 |
|-----------------------------------------------------------------------------|
|-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 |       53.031 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.087    4.900  1.196 |       2.132 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.496)------------------------------------------|
|    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 = 11.496)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5023   r_free= 0.4934   ksol= 0.00   Bsol= 0.00   scale= 0.760    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.297196                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4894   r_free= 0.4780   ksol= 0.39   Bsol= 20.00   scale= 0.957   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.44,7.86,8.00,0.00,0.00,0.00); trace/3= 7.10                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.290983                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 14.055941             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.118   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.589760              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.305   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4894      final r-factor (work) = 0.4281          |
| start r-factor (free) = 0.4780      final r-factor (free) = 0.4472          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 97.2435 = 14.06 * 0.50 * 6.2909 + 1.00 * 53.0310                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 43.9646 = 14.06 * 0.50 * 6.2360 + 1.00 * 0.1384                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4281      final r-factor (work) = 0.3886          |
| start r-factor (free) = 0.4472      final r-factor (free) = 0.4443          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.9280 = 1.59 * 1.00 * 6.2360 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.8428 = 1.59 * 1.00 * 6.1783 + 1.00 * 0.0207                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.496)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    108.43  15.49    None  None   None       |
|    all(noH): 2823   0      0.00    108.43  15.49    None  None   None       |
|    Sol.    : 438    0      0.00    108.43  25.70    None  None   None       |
|    Mac.    : 2385   0      0.00    99.38   13.62    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.843: 1302   |   5:    54.215 -  65.058:   34        |
|      1:    10.843 -  21.686:  819   |   6:    65.058 -  75.901:   10        |
|      2:    21.686 -  32.529:  404   |   7:    75.901 -  86.744:    4        |
|      3:    32.529 -  43.372:  164   |   8:    86.744 -  97.587:    3        |
|      4:    43.372 -  54.215:   81   |   9:    97.587 - 108.431:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3886 r_free = 0.4443             target_work(ml) = 6.173         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3883 r_free = 0.4448             target_work(ml) = 6.173         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3883   r_free= 0.4448   ksol= 0.39   Bsol= 20.00   scale= 1.092   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.44,7.86,8.00,0.00,0.00,0.00); trace/3= 7.10                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.172617                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3870   r_free= 0.4415   ksol= 0.35   Bsol= 33.91   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.96,4.27,5.52,0.00,0.00,0.00); trace/3= 4.25                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.172970                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.289294              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.932   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.623584              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 127.353  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3870      final r-factor (work) = 0.3245          |
| start r-factor (free) = 0.4415      final r-factor (free) = 0.3854          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.6419 = 7.29 * 0.50 * 6.1744 + 1.00 * 0.1384                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.3361 = 7.29 * 0.50 * 6.1059 + 1.00 * 0.0823                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3245      final r-factor (work) = 0.3088          |
| start r-factor (free) = 0.3854      final r-factor (free) = 0.3690          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8281 = 0.62 * 1.00 * 6.1059 + 1.00 * 0.0206                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.7671 = 0.62 * 1.00 * 6.0219 + 1.00 * 0.0120                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.496)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.28  15.21    None  None   None       |
|    all(noH): 2823   0      0.00    105.28  15.21    None  None   None       |
|    Sol.    : 438    0      0.00    105.28  29.45    None  None   None       |
|    Mac.    : 2385   0      0.00    100.17  12.59    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.528: 1272   |   5:    52.641 -  63.169:   27        |
|      1:    10.528 -  21.056:  878   |   6:    63.169 -  73.697:    4        |
|      2:    21.056 -  31.584:  359   |   7:    73.697 -  84.225:    4        |
|      3:    31.584 -  42.113:  193   |   8:    84.225 -  94.753:    3        |
|      4:    42.113 -  52.641:   80   |   9:    94.753 - 105.281:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3088 r_free = 0.3690             target_work(ml) = 6.006         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3088 r_free = 0.3691             target_work(ml) = 6.006         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3088   r_free= 0.3691   ksol= 0.35   Bsol= 33.91   scale= 1.069   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.96,4.27,5.52,0.00,0.00,0.00); trace/3= 4.25                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.005721                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3079   r_free= 0.3685   ksol= 0.32   Bsol= 36.22   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.77,2.17,3.40,0.00,0.00,0.00); trace/3= 2.45                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.006809                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.545428              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.106  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.594335              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.316  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3079      final r-factor (work) = 0.2289          |
| start r-factor (free) = 0.3685      final r-factor (free) = 0.2887          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.7888 = 6.55 * 0.50 * 6.0215 + 1.00 * 0.0822                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.3687 = 6.55 * 0.50 * 5.8929 + 1.00 * 0.0828                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2289      final r-factor (work) = 0.1986          |
| start r-factor (free) = 0.2887      final r-factor (free) = 0.2709          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 27.0860 = 4.59 * 1.00 * 5.8929 + 1.00 * 0.0119                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 26.1967 = 4.59 * 1.00 * 5.6978 + 1.00 * 0.0191                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.496)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    112.48  16.37    None  None   None       |
|    all(noH): 2823   0      0.00    112.48  16.37    None  None   None       |
|    Sol.    : 438    0      1.07    109.20  42.26    None  None   None       |
|    Mac.    : 2385   0      0.00    112.48  11.61    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.248: 1545   |   5:    56.241 -  67.489:   78        |
|      1:    11.248 -  22.497:  644   |   6:    67.489 -  78.738:   35        |
|      2:    22.497 -  33.745:  226   |   7:    78.738 -  89.986:   13        |
|      3:    33.745 -  44.993:  164   |   8:    89.986 - 101.234:    4        |
|      4:    44.993 -  56.241:  110   |   9:   101.234 - 112.482:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1986 r_free = 0.2709             target_work(ml) = 5.662         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1985 r_free = 0.2708             target_work(ml) = 5.661         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1985   r_free= 0.2708   ksol= 0.32   Bsol= 36.22   scale= 1.053   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.77,2.17,3.40,0.00,0.00,0.00); trace/3= 2.45                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.661172                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1982   r_free= 0.2691   ksol= 0.33   Bsol= 45.04   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.09,0.95,2.02,0.00,0.00,0.00); trace/3= 1.35                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.657854                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.735611              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.063  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.459529              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.153  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1982      final r-factor (work) = 0.1648          |
| start r-factor (free) = 0.2691      final r-factor (free) = 0.2273          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8818 = 2.74 * 0.50 * 5.7019 + 1.00 * 0.0828                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6992 = 2.74 * 0.50 * 5.5899 + 1.00 * 0.0533                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1648      final r-factor (work) = 0.1547          |
| start r-factor (free) = 0.2273      final r-factor (free) = 0.2086          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5878 = 0.46 * 1.00 * 5.5899 + 1.00 * 0.0191                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5332 = 0.46 * 1.00 * 5.4767 + 1.00 * 0.0165                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.496)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    110.16  15.38    None  None   None       |
|    all(noH): 2823   0      0.00    110.16  15.38    None  None   None       |
|    Sol.    : 438    0      3.03    104.82  41.52    None  None   None       |
|    Mac.    : 2385   0      0.00    110.16  10.58    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.016: 1678   |   5:    55.079 -  66.095:   74        |
|      1:    11.016 -  22.032:  594   |   6:    66.095 -  77.111:   34        |
|      2:    22.032 -  33.048:  171   |   7:    77.111 -  88.127:    9        |
|      3:    33.048 -  44.064:  143   |   8:    88.127 -  99.143:    4        |
|      4:    44.064 -  55.079:  112   |   9:    99.143 - 110.159:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1547 r_free = 0.2086             target_work(ml) = 5.430         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1544 r_free = 0.2080             target_work(ml) = 5.429         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1544   r_free= 0.2080   ksol= 0.33   Bsol= 45.04   scale= 1.027   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.09,0.95,2.02,0.00,0.00,0.00); trace/3= 1.35                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.428685                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1545   r_free= 0.2083   ksol= 0.32   Bsol= 40.25   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.74,0.50,1.42,0.00,0.00,0.00); trace/3= 0.89                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.428225                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.007003              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.915   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.786724              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.748   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1545      final r-factor (work) = 0.1344          |
| start r-factor (free) = 0.2083      final r-factor (free) = 0.1811          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5493 = 2.01 * 0.50 * 5.4770 + 1.00 * 0.0532                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4431 = 2.01 * 0.50 * 5.3698 + 1.00 * 0.0545                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1344      final r-factor (work) = 0.1290          |
| start r-factor (free) = 0.1811      final r-factor (free) = 0.1758          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2395 = 0.79 * 1.00 * 5.3698 + 1.00 * 0.0149                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1632 = 0.79 * 1.00 * 5.2765 + 1.00 * 0.0120                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.496)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    112.15  15.25    None  None   None       |
|    all(noH): 2823   0      0.00    112.15  15.25    None  None   None       |
|    Sol.    : 438    0      3.50    104.95  41.98    None  None   None       |
|    Mac.    : 2385   0      0.00    112.15  10.35    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.216: 1748   |   5:    56.077 -  67.293:   77        |
|      1:    11.216 -  22.431:  567   |   6:    67.293 -  78.508:   29        |
|      2:    22.431 -  33.647:  144   |   7:    78.508 -  89.724:   13        |
|      3:    33.647 -  44.862:  126   |   8:    89.724 - 100.939:    4        |
|      4:    44.862 -  56.077:  111   |   9:   100.939 - 112.155:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1290 r_free = 0.1758             target_work(ml) = 5.261         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1289 r_free = 0.1755             target_work(ml) = 5.260         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1289   r_free= 0.1755   ksol= 0.32   Bsol= 40.25   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.74,0.50,1.42,0.00,0.00,0.00); trace/3= 0.89                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.260464                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9433 -  4.6579 0.99   1403  158 0.1072 0.1372      5.4601       5.632|
|  2:  4.6579 -  3.7159 0.99   1358  143 0.0969 0.1318      5.5546      5.8099|
|  3:  3.7159 -  3.2517 0.99   1326  151 0.1262 0.1613       5.621      5.8942|
|  4:  3.2517 -  2.9569 0.99   1333  154 0.1441 0.1825      5.5912      5.7422|
|  5:  2.9569 -  2.7463 0.99   1307  142 0.1498 0.1810      5.4149      5.5678|
|  6:  2.7463 -  2.5853 0.99   1303  148 0.1395 0.1981      5.3089      5.5465|
|  7:  2.5853 -  2.4564 0.99   1314  139 0.1419 0.1938      5.2779      5.5007|
|  8:  2.4564 -  2.3499 0.98   1274  147 0.1350 0.1828      5.1658      5.4078|
|  9:  2.3499 -  2.2598 0.98   1293  149 0.1343 0.2074      5.1353      5.3986|
| 10:  2.2598 -  2.1820 0.99   1290  137 0.1290 0.2008      5.0597      5.3119|
| 11:  2.1820 -  2.1140 0.99   1283  137 0.1328 0.1973      5.0557      5.3924|
| 12:  2.1140 -  2.0537 0.97   1262  146 0.1267 0.1802      4.9847      5.2038|
| 13:  2.0537 -  1.9998 0.97   1268  137 0.1356 0.2013      4.9156       5.142|
| 14:  1.9998 -  1.9511 0.47    616   71 0.1275 0.1820      4.7784      5.0482|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9433 -  4.6579  1403   158  0.93  10.19   0.98     0.96       8476.85|
|  2:  4.6579 -  3.7159  1358   143  0.94   9.50   1.03     1.01      11379.02|
|  3:  3.7159 -  3.2517  1326   151  0.91  13.89   1.05     1.04      13598.78|
|  4:  3.2517 -  2.9569  1333   154  0.90  15.78   1.03     1.01      12939.56|
|  5:  2.9569 -  2.7463  1307   142  0.88  17.70   1.01     0.97       9538.28|
|  6:  2.7463 -  2.5853  1303   148  0.89  17.87   1.00     0.97       8571.62|
|  7:  2.5853 -  2.4564  1314   139  0.89  17.52   1.01     0.98       7746.94|
|  8:  2.4564 -  2.3499  1274   147  0.89  17.73   1.00     0.95       6270.76|
|  9:  2.3499 -  2.2598  1293   149  0.89  17.07   1.02     1.01       6108.79|
| 10:  2.2598 -  2.1820  1290   137  0.89  17.26   1.02     0.98       5305.73|
| 11:  2.1820 -  2.1140  1283   137  0.88  18.81   1.02     0.97       5470.52|
| 12:  2.1140 -  2.0537  1262   146  0.89  17.59   1.03     1.01       5036.44|
| 13:  2.0537 -  1.9998  1268   137  0.88  18.83   1.02     1.01       4225.07|
| 14:  1.9998 -  1.9511   616    71  0.89  17.65   1.01     0.99       3234.26|
|alpha:            min =        0.95 max =            1.04 mean =         0.99|
|beta:             min =     3234.26 max =        13598.78 mean =      7935.19|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.92 mean =        16.11|
|phase err.(test): min =        0.00 max =           89.79 mean =        15.47|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1289   r_free= 0.1754   ksol= 0.32   Bsol= 40.95   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.10,-0.33,0.43,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.260284                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.94 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1289   r_free= 0.1754   ksol= 0.32   Bsol= 40.95   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.10,-0.33,0.43,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.260284                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9433 -  4.6579 0.99   1403  158 0.1071 0.1370       5.459      5.6308|
|  2:  4.6579 -  3.7159 0.99   1358  143 0.0968 0.1320      5.5542      5.8109|
|  3:  3.7159 -  3.2517 0.99   1326  151 0.1262 0.1613      5.6212      5.8942|
|  4:  3.2517 -  2.9569 0.99   1333  154 0.1441 0.1824      5.5911       5.742|
|  5:  2.9569 -  2.7463 0.99   1307  142 0.1498 0.1809      5.4148      5.5678|
|  6:  2.7463 -  2.5853 0.99   1303  148 0.1395 0.1984      5.3092       5.548|
|  7:  2.5853 -  2.4564 0.99   1314  139 0.1420 0.1936      5.2783      5.5009|
|  8:  2.4564 -  2.3499 0.98   1274  147 0.1350 0.1828      5.1656      5.4072|
|  9:  2.3499 -  2.2598 0.98   1293  149 0.1343 0.2074      5.1354      5.3991|
| 10:  2.2598 -  2.1820 0.99   1290  137 0.1290 0.2009      5.0593      5.3114|
| 11:  2.1820 -  2.1140 0.99   1283  137 0.1328 0.1971      5.0555      5.3917|
| 12:  2.1140 -  2.0537 0.97   1262  146 0.1267 0.1801      4.9838      5.2029|
| 13:  2.0537 -  1.9998 0.97   1268  137 0.1356 0.2009      4.9154      5.1411|
| 14:  1.9998 -  1.9511 0.47    616   71 0.1273 0.1824      4.7786      5.0501|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9433 -  4.6579  1403   158  0.93  10.18   0.98     0.96       8458.29|
|  2:  4.6579 -  3.7159  1358   143  0.94   9.50   1.03     1.01      11369.03|
|  3:  3.7159 -  3.2517  1326   151  0.91  13.89   1.05     1.04      13606.16|
|  4:  3.2517 -  2.9569  1333   154  0.90  15.77   1.02     1.00      12936.72|
|  5:  2.9569 -  2.7463  1307   142  0.88  17.70   1.00     0.96       9547.96|
|  6:  2.7463 -  2.5853  1303   148  0.88  17.87   0.99     0.97       8579.37|
|  7:  2.5853 -  2.4564  1314   139  0.89  17.53   1.00     0.97       7758.55|
|  8:  2.4564 -  2.3499  1274   147  0.89  17.72   0.99     0.95       6269.96|
|  9:  2.3499 -  2.2598  1293   149  0.89  17.06   1.01     1.00       6106.25|
| 10:  2.2598 -  2.1820  1290   137  0.89  17.25   1.01     0.97       5301.76|
| 11:  2.1820 -  2.1140  1283   137  0.88  18.80   1.01     0.96       5468.49|
| 12:  2.1140 -  2.0537  1262   146  0.89  17.57   1.02     1.00       5025.28|
| 13:  2.0537 -  1.9998  1268   137  0.88  18.81   1.01     1.00       4221.87|
| 14:  1.9998 -  1.9511   616    71  0.89  17.65   1.00     0.98       3237.58|
|alpha:            min =        0.95 max =            1.04 mean =         0.98|
|beta:             min =     3237.58 max =        13606.16 mean =      7933.84|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.92 mean =        16.11|
|phase err.(test): min =        0.00 max =           89.79 mean =        15.46|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.496)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.70    112.85  15.95    None  None   None       |
|    all(noH): 2823   0      0.70    112.85  15.95    None  None   None       |
|    Sol.    : 438    0      4.20    105.65  42.67    None  None   None       |
|    Mac.    : 2385   0      0.70    112.85  11.05    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:     0.699 -  11.914: 1748   |   5:    56.776 -  67.992:   77        |
|      1:    11.914 -  23.130:  567   |   6:    67.992 -  79.207:   29        |
|      2:    23.130 -  34.345:  144   |   7:    79.207 -  90.423:   13        |
|      3:    34.345 -  45.561:  126   |   8:    90.423 - 101.638:    4        |
|      4:    45.561 -  56.776:  111   |   9:   101.638 - 112.854:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 324         
Filter by distance & map next to the model:
   mapped sites are within: 0.636 - 5.549
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 322 from: 324
   mapped sites are within: 0.736 - 5.549

peak=    9.933 closest distance to " CB  VAL A 230 " =    1.416
peak=    8.646 closest distance to " CG2 VAL A 296 " =    1.422
peak=    7.228 closest distance to " CG  ARG A 138 " =    1.185
peak=    6.626 closest distance to " CD1AILE A 234 " =    1.191
peak=    6.610 closest distance to " O   HOH Z 130 " =    1.113
peak=    6.188 closest distance to " O   HOH Z 205 " =    1.334
peak=    5.879 closest distance to " O   HOH Z 278 " =    2.009
peak=    5.869 closest distance to " CD2 LEU A   5 " =    1.272
peak=    5.813 closest distance to " O   HOH Z 138 " =    1.046
peak=    5.792 closest distance to " O   HOH Z  37 " =    1.553
peak=    5.782 closest distance to " O   HOH Z  65 " =    1.109
peak=    5.681 closest distance to " O   HOH Z 385 " =    1.001
peak=    5.631 closest distance to " O   HOH Z   7 " =    1.720
peak=    5.627 closest distance to " O   HOH Z 214 " =    1.681
peak=    5.544 closest distance to " O   HOH Z 199 " =    1.260
peak=    5.410 closest distance to " O   HOH Z 120 " =    1.126
peak=    5.306 closest distance to " O   HOH Z  97 " =    1.463
peak=    5.237 closest distance to " O   HOH Z 124 " =    1.728
peak=    5.211 closest distance to " O   HOH Z 344 " =    1.477
peak=    5.204 closest distance to " O   HOH Z 132 " =    1.835
peak=    5.182 closest distance to " O   HOH Z 117 " =    1.486
peak=    5.154 closest distance to " CG  PRO A 213 " =    1.281
peak=    5.112 closest distance to " O   HOH Z 403 " =    1.459
peak=    5.103 closest distance to " CB  PRO A  54 " =    1.039
peak=    5.102 closest distance to " NH2 ARG A  56 " =    2.077
peak=    5.080 closest distance to " O   HOH Z 144 " =    2.048
peak=    4.991 closest distance to " NE2 GLN A  11 " =    1.276
peak=    4.908 closest distance to " O   HOH Z 427 " =    2.608
peak=    4.849 closest distance to " O   HOH Z 202 " =    1.507
peak=    4.836 closest distance to " O   HOH Z 134 " =    1.605
peak=    4.796 closest distance to " CG  PRO A 198 " =    1.357
peak=    4.795 closest distance to " CG  LEU A   5 " =    1.316
peak=    4.777 closest distance to " O   HOH Z 143 " =    1.679
peak=    4.772 closest distance to " CB  ASN A 148 " =    1.256
peak=    4.740 closest distance to " O   HOH Z  11 " =    1.426
peak=    4.734 closest distance to " CB  ARG A 275 " =    0.991
peak=    4.726 closest distance to " O   HOH Z 147 " =    1.435
peak=    4.712 closest distance to " CD2 LEU A 228 " =    1.223
peak=    4.699 closest distance to " CB  SER A   3 " =    1.382
peak=    4.685 closest distance to " CG  GLN A  11 " =    2.270
peak=    4.665 closest distance to " O   HOH Z 374 " =    1.133
peak=    4.613 closest distance to " CB  VAL A 230 " =    1.066
peak=    4.588 closest distance to " O   HOH Z 193 " =    1.782
peak=    4.565 closest distance to " O   PRO A 198 " =    1.288
peak=    4.562 closest distance to " CG  LEU A 167 " =    1.153
peak=    4.536 closest distance to " O   HOH Z 316 " =    2.618
peak=    4.527 closest distance to " O   HOH Z 247 " =    1.324
peak=    4.444 closest distance to " O   HOH Z 236 " =    1.656
peak=    4.423 closest distance to " O   HOH Z 411 " =    3.599
peak=    4.422 closest distance to " O   HOH Z  97 " =    1.882
peak=    4.411 closest distance to " O   HOH Z  61 " =    1.360
peak=    4.399 closest distance to " O   HOH Z 326 " =    1.587
peak=    4.348 closest distance to " NH1 ARG A 138 " =    1.062
peak=    4.345 closest distance to " O   HOH Z 116 " =    1.291
peak=    4.339 closest distance to " O   HOH Z 186 " =    1.330
peak=    4.326 closest distance to " CG  PRO A  54 " =    1.224
peak=    4.321 closest distance to " CG1AVAL A 121 " =    1.016
peak=    4.311 closest distance to " O   HOH Z 126 " =    1.967
peak=    4.271 closest distance to " O   HOH Z 108 " =    1.684
peak=    4.211 closest distance to " O   HOH Z 424 " =    1.119
peak=    4.199 closest distance to " CG2 THR A 221 " =    1.348
peak=    4.184 closest distance to " NH2BARG A 102 " =    0.987
peak=    4.163 closest distance to " O   HOH Z 260 " =    1.525
peak=    4.159 closest distance to " O   HOH Z 272 " =    1.909
peak=    4.158 closest distance to " O   HOH Z  63 " =    1.379
peak=    4.149 closest distance to " O   HOH Z 222 " =    1.068
peak=    4.134 closest distance to " O   HOH Z 284 " =    1.732
peak=    4.129 closest distance to " O   HOH Z 232 " =    2.215
peak=    4.118 closest distance to " CB  TRP A 179 " =    1.405
peak=    4.088 closest distance to " O   HOH Z 220 " =    1.380
peak=    4.085 closest distance to " O   HOH Z 284 " =    2.971
peak=    4.070 closest distance to " O   HOH Z  59 " =    1.624
peak=    4.048 closest distance to " NH2BARG A 190 " =    1.521
peak=    4.047 closest distance to " O   HOH Z 425 " =    1.449
peak=    4.038 closest distance to " O   HOH Z 126 " =    1.510
peak=    4.032 closest distance to " O   HOH Z 347 " =    1.032
peak=    4.027 closest distance to " NZ  LYS A 117 " =    1.009
peak=    4.020 closest distance to " O   HOH Z 287 " =    1.859
peak=    4.018 closest distance to " O   HOH Z 263 " =    1.333
peak=    3.986 closest distance to " CB  VAL A 265 " =    1.274
peak=    3.977 closest distance to " OG  SER A  62 " =    3.315
peak=    3.972 closest distance to " CA  LEU A 282 " =    1.277
peak=    3.945 closest distance to " O   HOH Z 390 " =    1.103
peak=    3.944 closest distance to " O   HOH Z 192 " =    1.312
peak=    3.933 closest distance to " O   HOH Z 280 " =    1.573
peak=    3.930 closest distance to " O   HOH Z 133 " =    1.563
peak=    3.929 closest distance to " O   HOH Z  78 " =    1.711
peak=    3.927 closest distance to " CB  VAL A 202 " =    1.596
peak=    3.926 closest distance to " O   HOH Z 227 " =    1.770
peak=    3.923 closest distance to " CG  PRO A 280 " =    0.891
peak=    3.910 closest distance to " CB  GLN A 183 " =    1.224
peak=    3.908 closest distance to " OD2 ASP A 286 " =    2.528
peak=    3.897 closest distance to " O   HOH Z 148 " =    2.015
peak=    3.894 closest distance to " O   HOH Z 123 " =    1.242
peak=    3.878 closest distance to " O   HOH Z 234 " =    3.500
peak=    3.855 closest distance to " CA  VAL A 126 " =    1.287
peak=    3.839 closest distance to " CG  GLN A  88 " =    1.008
peak=    3.831 closest distance to " CD  ARG A 138 " =    0.857
peak=    3.828 closest distance to " CG  ASN A  60 " =    1.065
peak=    3.823 closest distance to " CG  LEU A 228 " =    1.244
peak=    3.811 closest distance to " CB  GLU A 277 " =    3.535
peak=    3.811 closest distance to " CB  ALA A   1 " =    4.434
peak=    3.794 closest distance to " CB  LEU A 255 " =    0.925
peak=    3.782 closest distance to " O   HOH Z 423 " =    1.593
peak=    3.782 closest distance to " O   HOH Z 371 " =    2.948
peak=    3.782 closest distance to " CB  SER A  63 " =    1.350
peak=    3.781 closest distance to " CG  LYS A  76 " =    1.473
peak=    3.780 closest distance to " O   HOH Z 217 " =    1.469
peak=    3.773 closest distance to " O   HOH Z 369 " =    2.355
peak=    3.770 closest distance to " O   HOH Z 171 " =    2.847
peak=    3.768 closest distance to " O   HOH Z  89 " =    1.575
peak=    3.757 closest distance to " O   HOH Z 112 " =    1.090
peak=    3.746 closest distance to " CB  ASN A  60 " =    0.896
peak=    3.738 closest distance to " CE AMET A  47 " =    1.319
peak=    3.736 closest distance to " CB  TYR A 169 " =    0.916
peak=    3.735 closest distance to " O   HOH Z 222 " =    2.210
peak=    3.732 closest distance to " N   GLN A 278 " =    1.014
peak=    3.731 closest distance to " O   HOH Z 184 " =    1.314
peak=    3.725 closest distance to " NE2 GLN A  58 " =    5.549
peak=    3.725 closest distance to " O   HOH Z  39 " =    1.312
peak=    3.709 closest distance to " O   HOH Z 321 " =    0.779
peak=    3.706 closest distance to " CA  LEU A 101 " =    1.709
peak=    3.699 closest distance to " OG ASER A 134 " =    1.426
peak=    3.692 closest distance to " CA  ALA A  21 " =    1.124
peak=    3.688 closest distance to " O   HOH Z 427 " =    1.235
peak=    3.687 closest distance to " CG2 VAL A 257 " =    0.950
peak=    3.683 closest distance to " NH1 ARG A  14 " =    1.030
peak=    3.680 closest distance to " O   HOH Z   2 " =    1.844
peak=    3.678 closest distance to " O   HOH Z 193 " =    1.630
peak=    3.678 closest distance to " CA  ASN A 217 " =    1.179
peak=    3.675 closest distance to " CD2 TRP A 179 " =    2.197
peak=    3.674 closest distance to " CA  ALA A 295 " =    1.059
peak=    3.670 closest distance to " CG1 VAL A 153 " =    0.842
peak=    3.661 closest distance to " CB  GLN A 223 " =    1.418
peak=    3.656 closest distance to " O   ALA A 165 " =    1.177
peak=    3.635 closest distance to " OD1 ASN A  69 " =    2.737
peak=    3.629 closest distance to " N   TRP A 177 " =    1.711
peak=    3.622 closest distance to " CA  ILE A 234 " =    0.938
peak=    3.614 closest distance to " N   PHE A 130 " =    1.296
peak=    3.608 closest distance to " O   HOH Z 425 " =    2.109
peak=    3.596 closest distance to " O   HOH Z 259 " =    2.200
peak=    3.593 closest distance to " CD  ARG A 269 " =    1.036
peak=    3.592 closest distance to " CD BLYS A 290 " =    1.018
peak=    3.579 closest distance to " O   HOH Z 146 " =    1.726
peak=    3.574 closest distance to " O   HOH Z 180 " =    2.079
peak=    3.574 closest distance to " NH1 ARG A  56 " =    1.075
peak=    3.569 closest distance to " CB  MET A  47 " =    1.630
peak=    3.565 closest distance to " O   HOH Z 345 " =    3.184
peak=    3.546 closest distance to " NZ  LYS A 117 " =    3.456
peak=    3.544 closest distance to " CB  SER A 216 " =    0.989
peak=    3.542 closest distance to " NH2BARG A 145 " =    1.254
peak=    3.540 closest distance to " O   HOH Z 305 " =    3.257
peak=    3.537 closest distance to " O   SER A 164 " =    0.921
peak=    3.534 closest distance to " NH2 ARG A 219 " =    1.792
peak=    3.533 closest distance to " O   HOH Z 371 " =    1.731
peak=    3.532 closest distance to " O   HOH Z 392 " =    1.152
peak=    3.529 closest distance to " O   HOH Z  88 " =    2.995
peak=    3.526 closest distance to " NH1AARG A 145 " =    0.960
peak=    3.526 closest distance to " O   HOH Z 227 " =    2.102
peak=    3.525 closest distance to " O   HOH Z  48 " =    1.577
peak=    3.523 closest distance to " CB  ILE A 234 " =    0.988
peak=    3.521 closest distance to " O   HOH Z   1 " =    1.758
peak=    3.519 closest distance to " CD2 HIS A 115 " =    0.845
peak=    3.517 closest distance to " O   HOH Z   5 " =    1.298
peak=    3.517 closest distance to " O   HOH Z  78 " =    1.925
peak=    3.512 closest distance to " O   HOH Z 209 " =    1.078
peak=    3.509 closest distance to " NE AARG A 275 " =    1.317
peak=    3.509 closest distance to " O   HOH Z 282 " =    1.465
peak=    3.509 closest distance to " CB  PRO A 198 " =    1.021
peak=    3.506 closest distance to " O   HOH Z 302 " =    1.510
peak=    3.505 closest distance to " CB  ASN A 148 " =    1.852
peak=    3.503 closest distance to " O   HOH Z 204 " =    1.654
peak=    3.499 closest distance to " O   HOH Z 276 " =    1.523
peak=    3.495 closest distance to " O   HOH Z 128 " =    1.914
peak=    3.490 closest distance to " O   HOH Z  59 " =    2.242
peak=    3.490 closest distance to " O   SER A  26 " =    1.578
peak=    3.479 closest distance to " CB  ARG A 138 " =    1.765
peak=    3.479 closest distance to " O   HOH Z 249 " =    1.231
peak=    3.474 closest distance to " O   HOH Z 273 " =    1.014
peak=    3.470 closest distance to " CZ AARG A 102 " =    1.938
peak=    3.468 closest distance to " O   SER A  87 " =    2.396
peak=    3.448 closest distance to " O   HOH Z 126 " =    2.122
peak=    3.447 closest distance to " O   HOH Z 209 " =    2.107
peak=    3.447 closest distance to " CB  ALA A 291 " =    1.521
peak=    3.444 closest distance to " O   HOH Z 211 " =    1.149
peak=    3.440 closest distance to " CA  TYR A  30 " =    1.064
peak=    3.439 closest distance to " O   HOH Z 100 " =    1.275
peak=    3.438 closest distance to " OE1 GLU A   2 " =    1.948
peak=    3.436 closest distance to " NE1 TRP A 274 " =    1.001
peak=    3.430 closest distance to " O   HOH Z  68 " =    1.661
peak=    3.430 closest distance to " O   HOH Z 153 " =    3.377
peak=    3.426 closest distance to " C   ALA A 299 " =    0.907
peak=    3.424 closest distance to " O   HOH Z 355 " =    1.722
peak=    3.424 closest distance to " O   HOH Z 298 " =    1.826
peak=    3.422 closest distance to " O   HOH Z 158 " =    2.409
peak=    3.419 closest distance to " O   HOH Z 411 " =    2.157
peak=    3.415 closest distance to " O   HOH Z 214 " =    1.573
peak=    3.414 closest distance to " O   HOH Z 389 " =    1.289
peak=    3.413 closest distance to " O   HOH Z 207 " =    2.123
peak=    3.404 closest distance to " O   HOH Z 271 " =    1.804
peak=    3.397 closest distance to " CZ3 TRP A 123 " =    1.180
peak=    3.396 closest distance to " CB  ARG A 102 " =    0.860
peak=    3.380 closest distance to " O   HOH Z 289 " =    1.348
peak=    3.378 closest distance to " O   HOH Z 261 " =    1.678
peak=    3.374 closest distance to " NE2 HIS A 115 " =    1.125
peak=    3.371 closest distance to " O   HOH Z 412 " =    3.338
peak=    3.359 closest distance to " O   HOH Z 414 " =    1.282
peak=    3.359 closest distance to " CB  GLU A 128 " =    1.144
peak=    3.357 closest distance to " O   HOH Z  22 " =    2.009
peak=    3.355 closest distance to " CD1 ILE A  33 " =    1.592
peak=    3.353 closest distance to " CB  ARG A  56 " =    1.087
peak=    3.353 closest distance to " CA  ALA A 248 " =    1.236
peak=    3.352 closest distance to " O   HOH Z  43 " =    1.845
peak=    3.348 closest distance to " O   HOH Z 389 " =    1.585
peak=    3.347 closest distance to " O   HOH Z 129 " =    0.813
peak=    3.347 closest distance to " O   HOH Z 193 " =    1.893
peak=    3.341 closest distance to " O   HOH Z 426 " =    3.171
peak=    3.339 closest distance to " OD1 ASN A  45 " =    1.320
peak=    3.337 closest distance to " O   HOH Z 122 " =    1.537
peak=    3.334 closest distance to " O   HOH Z 423 " =    1.098
peak=    3.331 closest distance to " O   HOH Z 290 " =    1.096
peak=    3.331 closest distance to " CA  SER A  99 " =    0.742
peak=    3.329 closest distance to " O   HOH Z 183 " =    1.267
peak=    3.329 closest distance to " CD1 LEU A 300 " =    1.129
peak=    3.324 closest distance to " CB  LEU A 228 " =    1.389
peak=    3.319 closest distance to " O   HOH Z 293 " =    1.399
peak=    3.317 closest distance to " O   HOH Z 213 " =    2.258
peak=    3.317 closest distance to " O   HOH Z   9 " =    2.147
peak=    3.315 closest distance to " O   HOH Z 361 " =    1.560
peak=    3.313 closest distance to " CD1 LEU A 228 " =    1.457
peak=    3.313 closest distance to " O   HOH Z  64 " =    1.929
peak=    3.309 closest distance to " CB  PHE A  16 " =    0.920
peak=    3.308 closest distance to " ND1 HIS A  86 " =    1.876
peak=    3.308 closest distance to " CG1 ILE A 151 " =    1.078
peak=    3.304 closest distance to " O   HOH Z 426 " =    1.161
peak=    3.303 closest distance to " O   HOH Z  58 " =    1.641
peak=    3.302 closest distance to " CA  ASN A 284 " =    1.162
peak=    3.301 closest distance to " O   HOH Z 136 " =    1.081
peak=    3.301 closest distance to " O   HOH Z 134 " =    2.059
peak=    3.300 closest distance to " O   HOH Z 402 " =    1.712
peak=    3.298 closest distance to " CA  VAL A  41 " =    0.896
peak=    3.289 closest distance to " CA  THR A 264 " =    0.736
peak=    3.285 closest distance to " NH2AARG A 145 " =    0.980
peak=    3.276 closest distance to " O   HOH Z  96 " =    1.783
peak=    3.275 closest distance to " O   HOH Z 357 " =    1.428
peak=    3.273 closest distance to " O   HOH Z 269 " =    1.143
peak=    3.266 closest distance to " CB  ASP A 124 " =    0.994
peak=    3.266 closest distance to " O   HOH Z 130 " =    2.234
peak=    3.265 closest distance to " CA  ASP A  50 " =    0.958
peak=    3.264 closest distance to " O   HOH Z 158 " =    1.201
peak=    3.261 closest distance to " O   HOH Z 303 " =    1.679
peak=    3.260 closest distance to " O   HOH Z  92 " =    0.983
peak=    3.259 closest distance to " CB  LEU A 143 " =    1.041
peak=    3.255 closest distance to " O   HOH Z 116 " =    2.946
peak=    3.252 closest distance to " NE2 GLN A  73 " =    1.791
peak=    3.250 closest distance to " CG1BVAL A 121 " =    1.166
peak=    3.249 closest distance to " OE2 GLU A   2 " =    1.737
peak=    3.249 closest distance to " CG  ARG A  66 " =    2.841
peak=    3.247 closest distance to " O   HOH Z 133 " =    2.600
peak=    3.246 closest distance to " O   HOH Z 172 " =    3.375
peak=    3.245 closest distance to " CA  PHE A 283 " =    1.188
peak=    3.232 closest distance to " CG  LEU A 281 " =    1.181
peak=    3.227 closest distance to " O   HOH Z 285 " =    1.822
peak=    3.222 closest distance to " O   HOH Z 189 " =    2.118
peak=    3.222 closest distance to " CB  ALA A   1 " =    1.125
peak=    3.220 closest distance to " O   HOH Z  59 " =    2.341
peak=    3.220 closest distance to " O   HOH Z 258 " =    2.148
peak=    3.220 closest distance to " CB  PHE A 225 " =    1.351
peak=    3.218 closest distance to " CB  LYS A 117 " =    1.136
peak=    3.216 closest distance to " O   HOH Z 375 " =    2.323
peak=    3.215 closest distance to " O   HOH Z 423 " =    1.276
peak=    3.212 closest distance to " CG  MET A 188 " =    1.322
peak=    3.208 closest distance to " O   HOH Z   4 " =    1.218
peak=    3.206 closest distance to " C   THR A  18 " =    1.140
peak=    3.205 closest distance to " CB  ALA A  43 " =    1.131
peak=    3.205 closest distance to " O   ASN A 301 " =    2.475
peak=    3.202 closest distance to " CB  VAL A 296 " =    0.975
peak=    3.200 closest distance to " C   GLY A  80 " =    1.013
peak=    3.197 closest distance to " O   HOH Z 106 " =    2.186
peak=    3.195 closest distance to " CA  LYS A  48 " =    1.426
peak=    3.194 closest distance to " O   HOH Z 410 " =    1.496
peak=    3.191 closest distance to " O   HOH Z 419 " =    1.968
peak=    3.190 closest distance to " CB BVAL A  41 " =    1.226
peak=    3.186 closest distance to " O   HOH Z 350 " =    1.322
peak=    3.185 closest distance to " O   HOH Z 114 " =    1.580
peak=    3.183 closest distance to " CB  ALA A  10 " =    0.962
peak=    3.183 closest distance to " O   HOH Z 116 " =    5.539
peak=    3.183 closest distance to " O   HOH Z 393 " =    1.345
peak=    3.183 closest distance to " CB  GLN A  88 " =    1.377
peak=    3.182 closest distance to " O   HOH Z 380 " =    1.689
peak=    3.177 closest distance to " CB  GLU A 152 " =    1.353
peak=    3.176 closest distance to " NE2 GLN A 223 " =    1.740
peak=    3.167 closest distance to " O   HOH Z 433 " =    2.100
peak=    3.166 closest distance to " O   HOH Z 344 " =    2.782
peak=    3.164 closest distance to " N   ASN A 209 " =    1.582
peak=    3.163 closest distance to " NZ  LYS A  48 " =    1.963
peak=    3.159 closest distance to " O   HOH Z  30 " =    2.124
peak=    3.153 closest distance to " O   HOH Z 267 " =    2.219
peak=    3.153 closest distance to " CB  SER A  62 " =    1.312
peak=    3.152 closest distance to " O   HOH Z  30 " =    1.357
peak=    3.147 closest distance to " O   PRO A 198 " =    1.525
peak=    3.145 closest distance to " O   HOH Z 125 " =    2.248
peak=    3.145 closest distance to " NH2 ARG A 269 " =    0.917
peak=    3.136 closest distance to " O   HOH Z 279 " =    0.983
peak=    3.135 closest distance to " CB  MET A  40 " =    0.946
peak=    3.134 closest distance to " O   HOH Z 234 " =    2.092
peak=    3.132 closest distance to " O   HOH Z 251 " =    1.608
peak=    3.132 closest distance to " CA  SER A  62 " =    1.105
peak=    3.130 closest distance to " O   HOH Z 265 " =    2.046
peak=    3.129 closest distance to " O   HOH Z 328 " =    1.856
peak=    3.124 closest distance to " CD1 LEU A   5 " =    1.612
peak=    3.117 closest distance to " O   HOH Z  33 " =    1.414
peak=    3.110 closest distance to " CD2 LEU A  83 " =    1.841
peak=    3.100 closest distance to " OD1 ASP A 286 " =    1.296
peak=    3.093 closest distance to " OD1 ASP A 238 " =    0.937
peak=    3.093 closest distance to " O   MET A 105 " =    1.665
peak=    3.086 closest distance to " O   HOH Z 215 " =    1.667
peak=    3.083 closest distance to " CE  MET A  93 " =    1.483
peak=    3.035 closest distance to " O   HOH Z 127 " =    2.474
peak=    3.024 closest distance to " O   HOH Z 369 " =    1.405
peak=    3.022 closest distance to " CB  LEU A 237 " =    0.889
peak=    3.010 closest distance to " O   HOH Z 366 " =    3.095

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 181         
Filter by distance & map next to the model:
   mapped sites are within: 0.537 - 5.334
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 176 from: 181
   mapped sites are within: 0.772 - 5.334

peak=   -5.069 closest distance to " CD  ARG A 138 " =    1.181
peak=   -4.593 closest distance to " O   PRO A 198 " =    1.215
peak=   -4.519 closest distance to " CG2 VAL A 230 " =    0.849
peak=   -4.470 closest distance to " OG ASER A 134 " =    1.009
peak=   -4.456 closest distance to " O   HOH Z 198 " =    2.124
peak=   -4.326 closest distance to " O   HOH Z  43 " =    1.758
peak=   -4.302 closest distance to " O   HOH Z 266 " =    4.422
peak=   -4.240 closest distance to " O   HOH Z 231 " =    1.360
peak=   -4.214 closest distance to " CB  ASP A  27 " =    2.492
peak=   -4.210 closest distance to " CE2 TYR A  30 " =    2.928
peak=   -4.070 closest distance to " O   HOH Z 388 " =    1.615
peak=   -4.013 closest distance to " NH2 ARG A  79 " =    1.789
peak=   -4.000 closest distance to " O   HOH Z 410 " =    2.237
peak=   -3.995 closest distance to " O   SER A 135 " =    1.594
peak=   -3.984 closest distance to " CD  ARG A 156 " =    1.890
peak=   -3.978 closest distance to " O   HOH Z 377 " =    1.620
peak=   -3.966 closest distance to " CA  GLY A 133 " =    1.930
peak=   -3.951 closest distance to " CD  ARG A  14 " =    3.110
peak=   -3.948 closest distance to " NH2AARG A 275 " =    5.334
peak=   -3.933 closest distance to " O   GLY A  80 " =    2.471
peak=   -3.928 closest distance to " O   PRO A 163 " =    2.008
peak=   -3.899 closest distance to " CD  GLN A  88 " =    0.898
peak=   -3.895 closest distance to " CG  ARG A 138 " =    0.885
peak=   -3.889 closest distance to " O   HOH Z 407 " =    3.054
peak=   -3.886 closest distance to " OG BSER A 134 " =    1.157
peak=   -3.883 closest distance to " N   MET A 188 " =    1.863
peak=   -3.875 closest distance to " O   HOH Z 166 " =    1.464
peak=   -3.817 closest distance to " O   HOH Z 298 " =    1.214
peak=   -3.813 closest distance to " O   GLY A  98 " =    1.968
peak=   -3.812 closest distance to " CD1 LEU A 101 " =    2.273
peak=   -3.789 closest distance to " OD1 ASN A  39 " =    2.070
peak=   -3.782 closest distance to " CD  LYS A 289 " =    2.549
peak=   -3.778 closest distance to " O   ALA A   1 " =    1.126
peak=   -3.758 closest distance to " O   HOH Z  98 " =    1.741
peak=   -3.748 closest distance to " N   GLN A  58 " =    2.067
peak=   -3.743 closest distance to " O   HOH Z 207 " =    1.829
peak=   -3.743 closest distance to " OG  SER A   3 " =    1.363
peak=   -3.740 closest distance to " C   ASN A 285 " =    2.192
peak=   -3.739 closest distance to " O   HOH Z 387 " =    2.558
peak=   -3.711 closest distance to " O   ALA A  51 " =    1.435
peak=   -3.696 closest distance to " CE1 HIS A 115 " =    1.023
peak=   -3.695 closest distance to " CB  VAL A 230 " =    1.101
peak=   -3.685 closest distance to " O   HOH Z  61 " =    1.276
peak=   -3.685 closest distance to " O   HOH Z 359 " =    1.852
peak=   -3.669 closest distance to " O   ILE A  49 " =    1.809
peak=   -3.661 closest distance to " CD  LYS A 166 " =    2.681
peak=   -3.656 closest distance to " CB  ALA A 227 " =    2.366
peak=   -3.654 closest distance to " O   HOH Z  92 " =    1.298
peak=   -3.654 closest distance to " NE2 GLN A 194 " =    2.856
peak=   -3.648 closest distance to " CZ  PHE A  16 " =    1.269
peak=   -3.644 closest distance to " O   HOH Z 231 " =    1.064
peak=   -3.632 closest distance to " CD1 LEU A 255 " =    2.803
peak=   -3.595 closest distance to " OD2 ASP A  50 " =    1.497
peak=   -3.595 closest distance to " O   HOH Z 317 " =    3.022
peak=   -3.593 closest distance to " N   ALA A 248 " =    1.621
peak=   -3.590 closest distance to " CB  ALA A   7 " =    2.060
peak=   -3.588 closest distance to " O   HOH Z 427 " =    1.613
peak=   -3.577 closest distance to " CD  GLU A 152 " =    2.577
peak=   -3.574 closest distance to " CA  GLY A  35 " =    2.054
peak=   -3.571 closest distance to " CB  CYS A 201 " =    2.378
peak=   -3.565 closest distance to " CG  MET A 105 " =    0.901
peak=   -3.562 closest distance to " CE2 PHE A 218 " =    2.535
peak=   -3.560 closest distance to " N   GLN A  58 " =    1.181
peak=   -3.554 closest distance to " O   HOH Z 365 " =    1.095
peak=   -3.549 closest distance to " CG2 THR A   4 " =    1.882
peak=   -3.546 closest distance to " OG  SER A 206 " =    1.639
peak=   -3.545 closest distance to " CB  PRO A 163 " =    2.498
peak=   -3.544 closest distance to " O   ALA A 161 " =    1.713
peak=   -3.538 closest distance to " O   HOH Z 134 " =    2.124
peak=   -3.530 closest distance to " CZ  PHE A  59 " =    1.526
peak=   -3.530 closest distance to " O   HOH Z 111 " =    4.437
peak=   -3.526 closest distance to " O   VAL A 197 " =    1.536
peak=   -3.519 closest distance to " CG2BVAL A 121 " =    0.950
peak=   -3.517 closest distance to " O   HOH Z 350 " =    1.929
peak=   -3.503 closest distance to " O   HOH Z 137 " =    1.467
peak=   -3.500 closest distance to " O   HOH Z 117 " =    0.819
peak=   -3.498 closest distance to " OE1 GLN A  88 " =    1.026
peak=   -3.497 closest distance to " O   HOH Z 385 " =    1.263
peak=   -3.488 closest distance to " O   HOH Z  13 " =    1.326
peak=   -3.488 closest distance to " O   HOH Z 100 " =    1.309
peak=   -3.486 closest distance to " OG1 THR A 178 " =    1.063
peak=   -3.479 closest distance to " O   HOH Z 389 " =    1.888
peak=   -3.474 closest distance to " N   HIS A 115 " =    1.706
peak=   -3.473 closest distance to " O   HOH Z  93 " =    1.802
peak=   -3.469 closest distance to " NH1AARG A 102 " =    2.297
peak=   -3.462 closest distance to " CB  ALA A 248 " =    1.910
peak=   -3.456 closest distance to " NH2 ARG A  66 " =    2.936
peak=   -3.449 closest distance to " O   HOH Z 250 " =    1.438
peak=   -3.439 closest distance to " O   HOH Z  63 " =    1.013
peak=   -3.430 closest distance to " O   HOH Z 347 " =    0.926
peak=   -3.426 closest distance to " NH1 ARG A  56 " =    2.552
peak=   -3.425 closest distance to " O   HOH Z 139 " =    3.295
peak=   -3.419 closest distance to " OG  SER A 245 " =    1.339
peak=   -3.417 closest distance to " O   VAL A  67 " =    2.833
peak=   -3.412 closest distance to " CD2 LEU A   5 " =    1.086
peak=   -3.407 closest distance to " OD1 ASP A 200 " =    1.109
peak=   -3.394 closest distance to " O   HOH Z 430 " =    2.046
peak=   -3.392 closest distance to " O   HOH Z 435 " =    1.661
peak=   -3.389 closest distance to " O   HOH Z 292 " =    4.499
peak=   -3.386 closest distance to " OG ASER A 134 " =    1.704
peak=   -3.376 closest distance to " O   HOH Z 372 " =    2.470
peak=   -3.370 closest distance to " C   LEU A 143 " =    1.325
peak=   -3.369 closest distance to " CG2AVAL A  41 " =    2.665
peak=   -3.361 closest distance to " N   SER A 276 " =    1.097
peak=   -3.361 closest distance to " O   HOH Z 290 " =    1.066
peak=   -3.355 closest distance to " CG  ASN A 301 " =    2.086
peak=   -3.351 closest distance to " CG  GLU A 277 " =    1.153
peak=   -3.348 closest distance to " CB  ALA A  43 " =    2.368
peak=   -3.341 closest distance to " O   ALA A 165 " =    1.044
peak=   -3.330 closest distance to " O   SER A 146 " =    1.089
peak=   -3.324 closest distance to " CD  ARG A 219 " =    2.473
peak=   -3.312 closest distance to " O   TRP A  70 " =    1.443
peak=   -3.311 closest distance to " O   PRO A 163 " =    1.230
peak=   -3.305 closest distance to " O   HOH Z 165 " =    2.109
peak=   -3.305 closest distance to " NH1 ARG A 195 " =    2.340
peak=   -3.304 closest distance to " CA  TYR A  68 " =    2.671
peak=   -3.292 closest distance to " CB  ALA A 244 " =    2.082
peak=   -3.291 closest distance to " CB  ALA A  51 " =    1.797
peak=   -3.288 closest distance to " O   HOH Z  91 " =    1.373
peak=   -3.285 closest distance to " O   GLY A  57 " =    1.286
peak=   -3.282 closest distance to " CD1 ILE A 151 " =    2.253
peak=   -3.279 closest distance to " O   HOH Z 221 " =    1.164
peak=   -3.271 closest distance to " CG  ARG A 219 " =    2.282
peak=   -3.269 closest distance to " CG2 VAL A 296 " =    2.161
peak=   -3.263 closest distance to " O   HOH Z  40 " =    4.082
peak=   -3.259 closest distance to " CE3 TRP A 150 " =    1.986
peak=   -3.257 closest distance to " O   SER A  22 " =    2.560
peak=   -3.248 closest distance to " CB  PHE A 283 " =    2.479
peak=   -3.245 closest distance to " ND2 ASN A  45 " =    1.089
peak=   -3.245 closest distance to " O   GLN A  11 " =    1.594
peak=   -3.245 closest distance to " O   ALA A 256 " =    2.874
peak=   -3.245 closest distance to " O   PRO A 243 " =    2.442
peak=   -3.240 closest distance to " CA  GLN A  55 " =    1.244
peak=   -3.225 closest distance to " O   HOH Z 438 " =    0.823
peak=   -3.225 closest distance to " CG2BVAL A  72 " =    1.705
peak=   -3.224 closest distance to " CG  PRO A 163 " =    2.554
peak=   -3.222 closest distance to " O   HOH Z 417 " =    2.365
peak=   -3.221 closest distance to " OG  SER A  97 " =    2.115
peak=   -3.220 closest distance to " O   HOH Z 266 " =    4.852
peak=   -3.217 closest distance to " OH  TYR A 169 " =    0.954
peak=   -3.215 closest distance to " NZ  LYS A 119 " =    0.809
peak=   -3.213 closest distance to " CD  PRO A 198 " =    1.376
peak=   -3.213 closest distance to " O   HOH Z 189 " =    2.475
peak=   -3.204 closest distance to " O   HOH Z 111 " =    1.104
peak=   -3.203 closest distance to " CB  GLU A 277 " =    2.485
peak=   -3.197 closest distance to " CG1 VAL A 112 " =    2.918
peak=   -3.189 closest distance to " O   HOH Z 220 " =    1.051
peak=   -3.189 closest distance to " C   GLY A  23 " =    1.826
peak=   -3.186 closest distance to " N   ALA A  84 " =    1.575
peak=   -3.182 closest distance to " OG1 THR A  52 " =    2.556
peak=   -3.179 closest distance to " ND2 ASN A  60 " =    1.206
peak=   -3.177 closest distance to " CD1 TRP A 274 " =    1.434
peak=   -3.171 closest distance to " O   HOH Z  65 " =    0.951
peak=   -3.165 closest distance to " O   HOH Z 155 " =    1.101
peak=   -3.165 closest distance to " CE  MET A  93 " =    1.133
peak=   -3.157 closest distance to " O   HOH Z  20 " =    2.464
peak=   -3.154 closest distance to " O   HOH Z 210 " =    2.001
peak=   -3.147 closest distance to " O   HOH Z 234 " =    4.746
peak=   -3.138 closest distance to " CA  ARG A  56 " =    1.280
peak=   -3.130 closest distance to " O   LEU A 143 " =    1.430
peak=   -3.130 closest distance to " NE2 GLN A  58 " =    4.636
peak=   -3.127 closest distance to " O   HOH Z 211 " =    1.090
peak=   -3.114 closest distance to " CG  TRP A 266 " =    1.404
peak=   -3.112 closest distance to " O   ASP A 191 " =    1.527
peak=   -3.107 closest distance to " O   TRP A  92 " =    1.775
peak=   -3.101 closest distance to " OG  SER A  87 " =    1.568
peak=   -3.099 closest distance to " CG  ASP A 231 " =    0.772
peak=   -3.093 closest distance to " O   VAL A 197 " =    1.040
peak=   -3.092 closest distance to " O   HOH Z 158 " =    2.153
peak=   -3.088 closest distance to " CE  LYS A  76 " =    2.897
peak=   -3.074 closest distance to " O   HOH Z  97 " =    1.484
peak=   -3.074 closest distance to " NH1BARG A 145 " =    4.984
peak=   -3.070 closest distance to " O   HOH Z 385 " =    1.964
peak=   -3.062 closest distance to " N   ALA A   1 " =    1.770
peak=   -3.056 closest distance to " NH1 ARG A 269 " =    1.525
peak=   -3.029 closest distance to " C   VAL A 265 " =    0.904

================= 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    :  0.4980 0.4894   6.295656e+00   6.291371e+00
   1_bss:  0.4894 0.4780   6.290983e+00   6.282767e+00
   1_xyz:  0.4281 0.4472   6.220415e+00   6.244715e+00
   1_adp:  0.3886 0.4443   6.172898e+00   6.242415e+00
   1_occ:  0.3883 0.4448   6.172617e+00   6.242358e+00
   2_bss:  0.3870 0.4415   6.172970e+00   6.240924e+00
   2_xyz:  0.3245 0.3854   6.038221e+00   6.156367e+00
   2_adp:  0.3088 0.3690   6.005804e+00   6.132940e+00
   2_occ:  0.3088 0.3691   6.005721e+00   6.133114e+00
   3_bss:  0.3079 0.3685   6.006809e+00   6.134339e+00
   3_xyz:  0.2289 0.2887   5.761655e+00   5.938346e+00
   3_adp:  0.1986 0.2709   5.662032e+00   5.883159e+00
   3_occ:  0.1985 0.2708   5.661172e+00   5.882431e+00
   4_bss:  0.1982 0.2691   5.657854e+00   5.877635e+00
   4_xyz:  0.1648 0.2273   5.497329e+00   5.731479e+00
   4_adp:  0.1547 0.2086   5.429967e+00   5.648559e+00
   4_occ:  0.1544 0.2080   5.428685e+00   5.647129e+00
   5_bss:  0.1545 0.2083   5.428225e+00   5.647014e+00
   5_xyz:  0.1344 0.1811   5.293840e+00   5.521819e+00
   5_adp:  0.1290 0.1758   5.261269e+00   5.493520e+00
   5_occ:  0.1289 0.1755   5.260464e+00   5.492370e+00
   5_bss:  0.1289 0.1754   5.260284e+00   5.492307e+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:  0.389  20.000   5.445   7.860   8.004   0.000   0.000   0.000
   1_xyz:  0.389  20.000   5.445   7.860   8.004   0.000   0.000   0.000
   1_adp:  0.389  20.000   5.445   7.860   8.004   0.000   0.000   0.000
   1_occ:  0.389  20.000   5.445   7.860   8.004   0.000   0.000   0.000
   2_bss:  0.348  33.915   2.963   4.270   5.520   0.000   0.000   0.000
   2_xyz:  0.348  33.915   2.963   4.270   5.520   0.000   0.000   0.000
   2_adp:  0.348  33.915   2.963   4.270   5.520   0.000   0.000   0.000
   2_occ:  0.348  33.915   2.963   4.270   5.520   0.000   0.000   0.000
   3_bss:  0.324  36.221   1.770   2.174   3.402   0.000   0.000   0.000
   3_xyz:  0.324  36.221   1.770   2.174   3.402   0.000   0.000   0.000
   3_adp:  0.324  36.221   1.770   2.174   3.402   0.000   0.000   0.000
   3_occ:  0.324  36.221   1.770   2.174   3.402   0.000   0.000   0.000
   4_bss:  0.325  45.041   1.093   0.946   2.018   0.000   0.000   0.000
   4_xyz:  0.325  45.041   1.093   0.946   2.018   0.000   0.000   0.000
   4_adp:  0.325  45.041   1.093   0.946   2.018   0.000   0.000   0.000
   4_occ:  0.325  45.041   1.093   0.946   2.018   0.000   0.000   0.000
   5_bss:  0.319  40.252   0.739   0.503   1.415   0.000   0.000   0.000
   5_xyz:  0.319  40.252   0.739   0.503   1.415   0.000   0.000   0.000
   5_adp:  0.319  40.252   0.739   0.503   1.415   0.000   0.000   0.000
   5_occ:  0.319  40.252   0.739   0.503   1.415   0.000   0.000   0.000
   5_bss:  0.319  40.951  -0.100  -0.333   0.433   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  61.701 0.3719  0.4506    78214.713
   1_bss:  61.911 0.3674  0.5373    75142.137
   1_xyz:  53.933 0.4695  0.6770    61321.249
   1_adp:  53.062 0.4807  0.7609    60832.491
   1_occ:  53.191 0.4791  0.7577    61020.398
   2_bss:  52.938 0.4821  0.6933    60554.019
   2_xyz:  43.135 0.6034  0.8581    42622.750
   2_adp:  40.542 0.6351  0.9080    38957.955
   2_occ:  40.566 0.6348  0.9073    38984.708
   3_bss:  40.489 0.6357  0.8524    39022.812
   3_xyz:  29.883 0.7588  0.9813    22338.391
   3_adp:  27.303 0.7872  0.9900    19417.384
   3_occ:  27.273 0.7875  0.9901    19368.438
   4_bss:  27.055 0.7896  0.9530    19055.206
   4_xyz:  22.458 0.8371  0.9858    13446.941
   4_adp:  19.953 0.8627  0.9935    11322.955
   4_occ:  19.914 0.8631  0.9934    11279.100
   5_bss:  19.905 0.8631  0.9761    11262.090
   5_xyz:  16.816 0.8912  0.9923     8416.790
   5_adp:  16.073 0.8981  0.9916     7961.493
   5_occ:  16.049 0.8983  0.9916     7936.189
   5_bss:  16.044 0.8984  0.9848     7934.838
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.087   5.3031e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.087   5.3031e+01
   1_xyz:   1.655  0.013  0.104 18.412  0.006  4.107   1.3842e-01
   1_adp:   1.655  0.013  0.104 18.412  0.006  4.107   1.3842e-01
   1_occ:   1.655  0.013  0.104 18.412  0.006  4.107   1.3842e-01
   2_bss:   1.655  0.013  0.104 18.412  0.006  4.107   1.3842e-01
   2_xyz:   1.148  0.008  0.078 16.232  0.005  4.120   8.2297e-02
   2_adp:   1.148  0.008  0.078 16.232  0.005  4.120   8.2297e-02
   2_occ:   1.148  0.008  0.078 16.232  0.005  4.120   8.2297e-02
   3_bss:   1.148  0.008  0.078 16.232  0.005  4.120   8.2297e-02
   3_xyz:   1.202  0.009  0.085 16.200  0.005  4.117   8.2770e-02
   3_adp:   1.202  0.009  0.085 16.200  0.005  4.117   8.2770e-02
   3_occ:   1.202  0.009  0.085 16.200  0.005  4.117   8.2770e-02
   4_bss:   1.202  0.009  0.085 16.200  0.005  4.117   8.2770e-02
   4_xyz:   0.871  0.005  0.064 15.287  0.003  4.118   5.3341e-02
   4_adp:   0.871  0.005  0.064 15.287  0.003  4.118   5.3341e-02
   4_occ:   0.871  0.005  0.064 15.287  0.003  4.118   5.3341e-02
   5_bss:   0.871  0.005  0.064 15.287  0.003  4.118   5.3341e-02
   5_xyz:   0.936  0.005  0.068 15.179  0.003  4.113   5.4485e-02
   5_adp:   0.936  0.005  0.068 15.179  0.003  4.113   5.4485e-02
   5_occ:   0.936  0.005  0.068 15.179  0.003  4.113   5.4485e-02
   5_bss:   0.936  0.005  0.068 15.179  0.003  4.113   5.4485e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.8726e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.8726e+00
   1_xyz:  12.862  0.165  0.426 84.437  0.049  2.110   9.2354e-02
   1_adp:  12.862  0.165  0.426 84.437  0.049  2.110   9.2354e-02
   1_occ:  12.862  0.165  0.426 84.437  0.049  2.110   9.2354e-02
   2_bss:  12.862  0.165  0.426 84.437  0.049  2.110   9.2354e-02
   2_xyz:   7.878  0.085  0.339 77.754  0.039  2.269   4.6244e-02
   2_adp:   7.878  0.085  0.339 77.754  0.039  2.269   4.6244e-02
   2_occ:   7.878  0.085  0.339 77.754  0.039  2.269   4.6244e-02
   3_bss:   7.878  0.085  0.339 77.754  0.039  2.269   4.6244e-02
   3_xyz:   8.385  0.066  0.332 85.578  0.045  2.255   7.1724e-02
   3_adp:   8.385  0.066  0.332 85.578  0.045  2.255   7.1724e-02
   3_occ:   8.385  0.066  0.332 85.578  0.045  2.255   7.1724e-02
   4_bss:   8.385  0.066  0.332 85.578  0.045  2.255   7.1724e-02
   4_xyz:   6.552  0.046  0.273 88.162  0.023  2.425   7.9619e-02
   4_adp:   6.552  0.046  0.273 88.162  0.023  2.425   7.9619e-02
   4_occ:   6.552  0.046  0.273 88.162  0.023  2.425   7.9619e-02
   5_bss:   6.552  0.046  0.273 88.162  0.023  2.425   7.9619e-02
   5_xyz:   6.583  0.048  0.334 81.315  0.030  2.316   3.1698e-02
   5_adp:   6.583  0.048  0.334 81.315  0.030  2.316   3.1698e-02
   5_occ:   6.583  0.048  0.334 81.315  0.030  2.316   3.1698e-02
   5_bss:   6.583  0.048  0.334 81.315  0.030  2.316   3.1698e-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: 108.43   0.00  15.49  99.38   0.00  13.62 108.43   0.00  25.70
   1_occ: 108.43   0.00  15.49  99.38   0.00  13.62 108.43   0.00  25.70
   2_bss: 108.43   0.00  15.49  99.38   0.00  13.62 108.43   0.00  25.70
   2_xyz: 108.43   0.00  15.49  99.38   0.00  13.62 108.43   0.00  25.70
   2_adp: 105.28   0.00  15.21 100.17   0.00  12.59 105.28   0.00  29.45
   2_occ: 105.28   0.00  15.21 100.17   0.00  12.59 105.28   0.00  29.45
   3_bss: 105.28   0.00  15.21 100.17   0.00  12.59 105.28   0.00  29.45
   3_xyz: 105.28   0.00  15.21 100.17   0.00  12.59 105.28   0.00  29.45
   3_adp: 112.48   0.00  16.37 112.48   0.00  11.61 109.20   1.07  42.26
   3_occ: 112.48   0.00  16.37 112.48   0.00  11.61 109.20   1.07  42.26
   4_bss: 112.48   0.00  16.37 112.48   0.00  11.61 109.20   1.07  42.26
   4_xyz: 112.48   0.00  16.37 112.48   0.00  11.61 109.20   1.07  42.26
   4_adp: 110.16   0.00  15.38 110.16   0.00  10.58 104.82   3.03  41.52
   4_occ: 110.16   0.00  15.38 110.16   0.00  10.58 104.82   3.03  41.52
   5_bss: 110.16   0.00  15.38 110.16   0.00  10.58 104.82   3.03  41.52
   5_xyz: 110.16   0.00  15.38 110.16   0.00  10.58 104.82   3.03  41.52
   5_adp: 112.15   0.00  15.25 112.15   0.00  10.35 104.95   3.50  41.98
   5_occ: 112.15   0.00  15.25 112.15   0.00  10.35 104.95   3.50  41.98
   5_bss: 112.85   0.70  15.95 112.85   0.70  11.05 105.65   4.20  42.67
------------------------------------------------------------------------
 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:    1.239    0.018    0.404
   1_adp:    1.239    0.018    0.404
   1_occ:    1.239    0.018    0.404
   2_bss:    1.239    0.018    0.404
   2_xyz:    1.711    0.027    0.546
   2_adp:    1.711    0.027    0.546
   2_occ:    1.711    0.027    0.546
   3_bss:    1.711    0.027    0.546
   3_xyz:    1.583    0.042    0.703
   3_adp:    1.583    0.042    0.703
   3_occ:    1.583    0.042    0.703
   4_bss:    1.583    0.042    0.703
   4_xyz:    1.846    0.074    0.760
   4_adp:    1.846    0.074    0.760
   4_occ:    1.846    0.074    0.760
   5_bss:    1.846    0.074    0.760
   5_xyz:    1.951    0.082    0.802
   5_adp:    1.951    0.082    0.802
   5_occ:    1.951    0.082    0.802
   5_bss:    1.951    0.082    0.802
------------------------------------------------------------------------

CPU time actual refinement: 347.82


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_748/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_748/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_748/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_748/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_748/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 347.67 
  Macro-tasks:
    bulk solvent and scale       = 40.93  
    individual site refinement   = 140.63 
    weights calculation          = 33.06  
    collect and process          = 6.29   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 221.04 
  Micro-tasks:
    mask                            = 2.41   
    f_calc                          = 112.22 
    alpha_beta                      = 7.85   
    target                          = 1.07   
    gradients_wrt_atomic_parameters = 119.94 
    fmodel                         = 6.88   
    r_factors                      = 0.34   
    phase_errors                   = 10.17  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 261.17 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.971 micro seconds
Total CPU time: 6.02 minutes
from_scatterers_fft:    634 calls, 111.92 s
gradients_fft:          579 calls, 107.32 s

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

# Date 2008-01-16 Time 02:20:15 PST -0800 (1200478815.49 s)
Start R-work = 0.4980, R-free = 0.4894 (no bulk solvent and anisotropic scale)
Final R-work = 0.1442, R-free = 0.1917 (no bulk solvent and anisotropic scale)

Start R-work = 0.4894, R-free = 0.4780
Final R-work = 0.1289, R-free = 0.1754