# Date 2008-01-16 Time 00:46:00 PST -0800 (1200473160.46 s)
#phil __OFF__

Command line arguments: "../154.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 2583
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 154

-------------------------------------------------------------------------------
  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: (68.845, 46.4607, 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: 3.27, 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: (68.845, 46.4607, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6737 1.95113
Completeness in resolution range: 0.967501
Completeness with d_max=infinity: 0.964453

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.6737
                             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: (68.845, 46.4607, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.6737 1.95113
Completeness in resolution range: 0.967501
Completeness with d_max=infinity: 0.964453

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.6741 -  4.1744 [2122/2149]  1910   212  10.0%
  bin  2:  4.1744 -  3.3260 [2036/2052]  1832   204  10.0%
  bin  3:  3.3260 -  2.9093 [2019/2038]  1816   203  10.1%
  bin  4:  2.9093 -  2.6450 [1997/2027]  1799   198   9.9%
  bin  5:  2.6450 -  2.4563 [1977/1996]  1779   198  10.0%
  bin  6:  2.4563 -  2.3121 [1974/2010]  1782   192   9.7%
  bin  7:  2.3121 -  2.1967 [1969/2002]  1765   204  10.4%
  bin  8:  2.1967 -  2.1014 [1954/1988]  1758   196  10.0%
  bin  9:  2.1014 -  2.0207 [1943/1971]  1752   191   9.8%
  bin 10:  2.0207 -  1.9511 [1598/2014]  1437   161  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_154/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: 0.15 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:
        0.88 -     1.68: 11
        1.68 -     2.49: 87
        2.49 -     3.29: 3781
        3.29 -     4.10: 9713
        4.10 -     4.90: 15576
  Warning: very small nonbonded interaction distances.
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  52 " - " O   HOH Z 183 "  0.880 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.292 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.319 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.485 3.040 -x+1/2,-y+1,z+1/2
  " OD2 ASP A 107 " - " OG ASER A 216 "  1.554 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 29163 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_154/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_154/model_refine_001.geo

CPU time processing inputs: 9.37


============================ 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 = 68.845 46.4607 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 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5043   r_free= 0.4938   ksol= 0.00   Bsol= 0.00   scale= 0.794    |
|                                                                             |
| 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: 6.298316                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6741 -  4.6556 0.99   1376  155 0.4151 0.4239      6.6205       6.664|
|  2:  4.6556 -  3.7150 0.99   1336  144 0.4478 0.4373      6.8376      6.8414|
|  3:  3.7150 -  3.2512 0.99   1301  148 0.4700 0.4477       6.721      6.7921|
|  4:  3.2512 -  2.9566 0.99   1292  143 0.4798 0.4980       6.556      6.5189|
|  5:  2.9566 -  2.7462 0.99   1285  140 0.5350 0.5345      6.4078      6.3739|
|  6:  2.7462 -  2.5852 0.99   1280  145 0.5327 0.5523      6.3015      6.2707|
|  7:  2.5852 -  2.4563 0.99   1266  140 0.5315 0.4872      6.2588      6.1816|
|  8:  2.4563 -  2.3499 0.98   1277  140 0.5452 0.5426      6.2053      6.2052|
|  9:  2.3499 -  2.2597 0.98   1277  144 0.5457 0.5325       6.126      6.1543|
| 10:  2.2597 -  2.1820 0.98   1236  133 0.5601 0.5021      6.1317      6.0996|
| 11:  2.1820 -  2.1140 1.00   1274  148 0.5474 0.5494      6.0569      6.0965|
| 12:  2.1140 -  2.0537 0.97   1252  131 0.5370 0.4675      5.9963      6.0144|
| 13:  2.0537 -  1.9998 0.98   1238  142 0.5524 0.5115      5.8951      5.8665|
| 14:  1.9998 -  1.9511 0.73    940  106 0.5399 0.5416        5.86      5.7753|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6741 -  4.6556  1376   155  0.62  40.67   0.79     0.67      93011.56|
|  2:  4.6556 -  3.7150  1336   144  0.62  41.81   0.86     0.71     138992.27|
|  3:  3.7150 -  3.2512  1301   148  0.52  50.43   0.85     0.66     145052.71|
|  4:  3.2512 -  2.9566  1292   143  0.44  56.32   0.81     0.56     121770.76|
|  5:  2.9566 -  2.7462  1285   140  0.38  61.69   0.72     0.47      92506.98|
|  6:  2.7462 -  2.5852  1280   145  0.35  63.85   0.72     0.42      77478.00|
|  7:  2.5852 -  2.4563  1266   140  0.32  66.17   0.73     0.37      70624.47|
|  8:  2.4563 -  2.3499  1277   140  0.31  66.78   0.74     0.38      63371.68|
|  9:  2.3499 -  2.2597  1277   144  0.30  67.25   0.73     0.38      57919.07|
| 10:  2.2597 -  2.1820  1236   133  0.33  65.03   0.75     0.41      50782.32|
| 11:  2.1820 -  2.1140  1274   148  0.29  68.06   0.77     0.38      49009.28|
| 12:  2.1140 -  2.0537  1252   131  0.29  68.36   0.76     0.37      45934.79|
| 13:  2.0537 -  1.9998  1238   142  0.25  71.40   0.74     0.33      40492.07|
| 14:  1.9998 -  1.9511   940   106  0.26  70.51   0.74     0.30      32049.09|
|alpha:            min =        0.30 max =            0.71 mean =         0.46|
|beta:             min =    32049.09 max =       145052.71 mean =     78561.07|
|figures of merit: min =        0.00 max =            1.00 mean =         0.38|
|phase err.(work): min =        0.00 max =           89.99 mean =        60.89|
|phase err.(test): min =        0.00 max =           89.99 mean =        61.37|
|-----------------------------------------------------------------------------|

============================== 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 = 22.214830             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.680   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.721106              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 83.263   (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 |  0.443 -  0.889:        1 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  0.889 -  1.335:        2 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.335 -  1.780:       19 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  1.780 -  2.226:      153 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.226 -  2.672:      798 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.672 -  3.117:     2025 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.117 -  3.563:     3718 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.563 -  4.009:     5586 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.009 -  4.454:     7535 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.454 -  4.900:     9352 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       52.547 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.085    4.900  0.443 |       3.228 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.227)------------------------------------------|
|    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 = 11.227)------------------------------------------|
|    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 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5086   r_free= 0.4979   ksol= 0.00   Bsol= 0.00   scale= 0.762    |
|                                                                             |
| 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: 6.298801                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4961   r_free= 0.4861   ksol= 0.39   Bsol= 6.92   scale= 0.985    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.02,8.15,9.08,0.00,0.00,0.00); trace/3= 8.08                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.84 A                  |
| x-ray target function (ml) for work reflections: 6.292055                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 17.493830             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.780   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.559697              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.798   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4961      final r-factor (work) = 0.4260          |
| start r-factor (free) = 0.4861      final r-factor (free) = 0.4406          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 107.6133 = 17.49 * 0.50 * 6.2955 + 1.00 * 52.5474                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 54.6687 = 17.49 * 0.50 * 6.2311 + 1.00 * 0.1655                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4260      final r-factor (work) = 0.3852          |
| start r-factor (free) = 0.4406      final r-factor (free) = 0.4407          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.7330 = 1.56 * 1.00 * 6.2311 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.6421 = 1.56 * 1.00 * 6.1693 + 1.00 * 0.0198                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.227)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.36   14.74    None  None   None       |
|    all(noH): 2823   0      0.00    85.36   14.74    None  None   None       |
|    Sol.    : 438    0      0.00    85.36   25.66    None  None   None       |
|    Mac.    : 2385   0      0.00    77.01   12.74    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.536: 1065   |   5:    42.681 -  51.217:   69        |
|      1:     8.536 -  17.072:  799   |   6:    51.217 -  59.753:   29        |
|      2:    17.072 -  25.609:  487   |   7:    59.753 -  68.289:    9        |
|      3:    25.609 -  34.145:  234   |   8:    68.289 -  76.826:    7        |
|      4:    34.145 -  42.681:  122   |   9:    76.826 -  85.362:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3852 r_free = 0.4407             target_work(ml) = 6.158         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3846 r_free = 0.4405             target_work(ml) = 6.157         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3846   r_free= 0.4405   ksol= 0.39   Bsol= 6.92   scale= 1.115    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.02,8.15,9.08,0.00,0.00,0.00); trace/3= 8.08                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.157327                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3816   r_free= 0.4370   ksol= 0.35   Bsol= 23.91   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.45,4.13,5.69,0.00,0.00,0.00); trace/3= 4.42                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.157038                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.208984              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.470   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.672918              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.643  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3816      final r-factor (work) = 0.3004          |
| start r-factor (free) = 0.4370      final r-factor (free) = 0.3596          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.5441 = 9.21 * 0.50 * 6.1632 + 1.00 * 0.1655                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.0468 = 9.21 * 0.50 * 6.0701 + 1.00 * 0.0971                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3004      final r-factor (work) = 0.2766          |
| start r-factor (free) = 0.3596      final r-factor (free) = 0.3375          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1119 = 0.67 * 1.00 * 6.0701 + 1.00 * 0.0273                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0353 = 0.67 * 1.00 * 5.9392 + 1.00 * 0.0387                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.227)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.23   14.62    None  None   None       |
|    all(noH): 2823   0      0.00    91.23   14.62    None  None   None       |
|    Sol.    : 438    0      0.00    90.36   31.96    None  None   None       |
|    Mac.    : 2385   0      0.00    91.23   11.43    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.123: 1264   |   5:    45.616 -  54.739:   59        |
|      1:     9.123 -  18.246:  761   |   6:    54.739 -  63.862:   34        |
|      2:    18.246 -  27.369:  364   |   7:    63.862 -  72.985:    9        |
|      3:    27.369 -  36.493:  199   |   8:    72.985 -  82.108:    2        |
|      4:    36.493 -  45.616:  128   |   9:    82.108 -  91.231:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2766 r_free = 0.3375             target_work(ml) = 5.917         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2763 r_free = 0.3378             target_work(ml) = 5.917         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2763   r_free= 0.3378   ksol= 0.35   Bsol= 23.91   scale= 1.075   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.45,4.13,5.69,0.00,0.00,0.00); trace/3= 4.42                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.916694                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2741   r_free= 0.3372   ksol= 0.33   Bsol= 32.58   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.69,2.10,3.31,0.00,0.00,0.00); trace/3= 2.37                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.914236                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.223686              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.996   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.885601              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.266   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2741      final r-factor (work) = 0.2077          |
| start r-factor (free) = 0.3372      final r-factor (free) = 0.2605          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.6382 = 4.22 * 0.50 * 5.9385 + 1.00 * 0.0971                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.3287 = 4.22 * 0.50 * 5.8053 + 1.00 * 0.0688                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2077      final r-factor (work) = 0.1848          |
| start r-factor (free) = 0.2605      final r-factor (free) = 0.2449          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1580 = 0.89 * 1.00 * 5.8053 + 1.00 * 0.0169                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9942 = 0.89 * 1.00 * 5.6212 + 1.00 * 0.0160                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.227)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    102.99  15.11    None  None   None       |
|    all(noH): 2823   0      0.00    102.99  15.11    None  None   None       |
|    Sol.    : 438    0      2.09    87.26   39.43    None  None   None       |
|    Mac.    : 2385   0      0.00    102.99  10.64    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.299: 1545   |   5:    51.493 -  61.792:   79        |
|      1:    10.299 -  20.597:  656   |   6:    61.792 -  72.091:   41        |
|      2:    20.597 -  30.896:  211   |   7:    72.091 -  82.389:   10        |
|      3:    30.896 -  41.195:  142   |   8:    82.389 -  92.688:    3        |
|      4:    41.195 -  51.493:  133   |   9:    92.688 - 102.987:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1848 r_free = 0.2449             target_work(ml) = 5.582         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1844 r_free = 0.2446             target_work(ml) = 5.582         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1844   r_free= 0.2446   ksol= 0.33   Bsol= 32.58   scale= 1.048   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.69,2.10,3.31,0.00,0.00,0.00); trace/3= 2.37                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.581591                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1841   r_free= 0.2442   ksol= 0.31   Bsol= 30.59   scale= 1.022   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.85,1.35,2.17,0.00,0.00,0.00); trace/3= 1.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.577950                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.572087              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.312  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.161401              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 108.267  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1841      final r-factor (work) = 0.1450          |
| start r-factor (free) = 0.2442      final r-factor (free) = 0.1950          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.1117 = 3.57 * 0.50 * 5.6230 + 1.00 * 0.0688                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8529 = 3.57 * 0.50 * 5.4803 + 1.00 * 0.0648                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1450      final r-factor (work) = 0.1376          |
| start r-factor (free) = 0.1950      final r-factor (free) = 0.1808          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8987 = 0.16 * 1.00 * 5.4803 + 1.00 * 0.0142                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8771 = 0.16 * 1.00 * 5.3415 + 1.00 * 0.0150                               |
|-----------------------------------------------------------------------------|
| number of iterations = 12      |    number of function evaluations = 17     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.227)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    100.19  14.58    None  None   None       |
|    all(noH): 2823   0      0.00    100.19  14.58    None  None   None       |
|    Sol.    : 438    0      3.80    85.28   38.36    None  None   None       |
|    Mac.    : 2385   0      0.00    100.19  10.21    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 -  10.019: 1645   |   5:    50.095 -  60.114:   82        |
|      1:    10.019 -  20.038:  619   |   6:    60.114 -  70.133:   42        |
|      2:    20.038 -  30.057:  163   |   7:    70.133 -  80.152:    8        |
|      3:    30.057 -  40.076:  143   |   8:    80.152 -  90.171:    4        |
|      4:    40.076 -  50.095:  114   |   9:    90.171 - 100.189:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1376 r_free = 0.1808             target_work(ml) = 5.297         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1373 r_free = 0.1804             target_work(ml) = 5.295         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1373   r_free= 0.1804   ksol= 0.31   Bsol= 30.59   scale= 1.033   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.85,1.35,2.17,0.00,0.00,0.00); trace/3= 1.46                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.295343                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1372   r_free= 0.1796   ksol= 0.31   Bsol= 31.38   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.38,0.90,1.53,0.00,0.00,0.00); trace/3= 0.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.294662                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.589338              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 121.868  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.386852              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 93.130   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1372      final r-factor (work) = 0.1280          |
| start r-factor (free) = 0.1796      final r-factor (free) = 0.1697          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3097 = 1.59 * 0.50 * 5.3416 + 1.00 * 0.0648                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2379 = 1.59 * 0.50 * 5.2628 + 1.00 * 0.0557                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1280      final r-factor (work) = 0.1237          |
| start r-factor (free) = 0.1697      final r-factor (free) = 0.1674          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0475 = 0.39 * 1.00 * 5.2628 + 1.00 * 0.0115                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0295 = 0.39 * 1.00 * 5.2203 + 1.00 * 0.0100                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.227)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.45   14.45    None  None   None       |
|    all(noH): 2823   0      0.00    95.45   14.45    None  None   None       |
|    Sol.    : 438    0      3.29    88.60   38.93    None  None   None       |
|    Mac.    : 2385   0      0.00    95.45   9.95     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.546: 1596   |   5:    47.727 -  57.273:   85        |
|      1:     9.546 -  19.091:  670   |   6:    57.273 -  66.818:   58        |
|      2:    19.091 -  28.636:  156   |   7:    66.818 -  76.364:   14        |
|      3:    28.636 -  38.182:  119   |   8:    76.364 -  85.909:    7        |
|      4:    38.182 -  47.727:  113   |   9:    85.909 -  95.455:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1237 r_free = 0.1674             target_work(ml) = 5.213         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1236 r_free = 0.1673             target_work(ml) = 5.212         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1236   r_free= 0.1673   ksol= 0.31   Bsol= 31.38   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.38,0.90,1.53,0.00,0.00,0.00); trace/3= 0.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.212265                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6741 -  4.6556 0.99   1376  155 0.1081 0.1294      5.4467      5.5592|
|  2:  4.6556 -  3.7150 0.99   1336  144 0.0977 0.1304      5.5304      5.7785|
|  3:  3.7150 -  3.2512 0.99   1301  148 0.1202 0.1478        5.57      5.8133|
|  4:  3.2512 -  2.9566 0.99   1292  143 0.1384 0.1760       5.543      5.6975|
|  5:  2.9566 -  2.7462 0.99   1285  140 0.1379 0.1691      5.3582      5.4941|
|  6:  2.7462 -  2.5852 0.99   1280  145 0.1315 0.1922      5.2578      5.4835|
|  7:  2.5852 -  2.4563 0.99   1266  140 0.1310 0.1766      5.1998      5.4137|
|  8:  2.4563 -  2.3499 0.98   1277  140 0.1285 0.1776      5.1508      5.3821|
|  9:  2.3499 -  2.2597 0.98   1277  144 0.1282 0.1883      5.0806      5.3411|
| 10:  2.2597 -  2.1820 0.98   1236  133 0.1232 0.1812      5.0309      5.2143|
| 11:  2.1820 -  2.1140 1.00   1274  148 0.1270 0.1866      4.9909      5.3583|
| 12:  2.1140 -  2.0537 0.97   1252  131 0.1224 0.1742      4.9532      5.1949|
| 13:  2.0537 -  1.9998 0.98   1238  142 0.1266 0.1968       4.886      5.1475|
| 14:  1.9998 -  1.9511 0.73    940  106 0.1199 0.1916      4.7984      5.0395|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6741 -  4.6556  1376   155  0.94   9.47   0.99     0.97       7652.08|
|  2:  4.6556 -  3.7150  1336   144  0.95   8.56   1.04     1.02       9838.70|
|  3:  3.7150 -  3.2512  1301   148  0.92  12.53   1.05     1.04      11800.73|
|  4:  3.2512 -  2.9566  1292   143  0.92  14.10   1.03     1.03      11196.45|
|  5:  2.9566 -  2.7462  1285   140  0.90  15.85   1.01     0.97       8438.74|
|  6:  2.7462 -  2.5852  1280   145  0.90  16.34   0.99     0.96       7381.00|
|  7:  2.5852 -  2.4563  1266   140  0.90  16.32   1.00     0.97       6533.18|
|  8:  2.4563 -  2.3499  1277   140  0.90  16.19   1.01     0.98       5986.17|
|  9:  2.3499 -  2.2597  1277   144  0.90  16.16   1.02     1.01       5348.44|
| 10:  2.2597 -  2.1820  1236   133  0.90  16.42   1.03     1.00       4942.28|
| 11:  2.1820 -  2.1140  1274   148  0.90  16.66   1.02     0.98       4628.00|
| 12:  2.1140 -  2.0537  1252   131  0.90  16.46   1.03     1.01       4530.42|
| 13:  2.0537 -  1.9998  1238   142  0.89  17.55   1.03     1.02       4025.63|
| 14:  1.9998 -  1.9511   940   106  0.89  17.27   1.02     0.99       3383.98|
|alpha:            min =        0.96 max =            1.04 mean =         1.00|
|beta:             min =     3383.98 max =        11800.73 mean =      6941.04|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.88 mean =        14.88|
|phase err.(test): min =        0.00 max =           89.36 mean =        14.39|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1236   r_free= 0.1672   ksol= 0.32   Bsol= 32.18   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.56,-0.04,0.60,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.212430                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.67 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1236   r_free= 0.1672   ksol= 0.32   Bsol= 32.18   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.56,-0.04,0.60,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.212430                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.6741 -  4.6556 0.99   1376  155 0.1083 0.1294      5.4495      5.5622|
|  2:  4.6556 -  3.7150 0.99   1336  144 0.0975 0.1300      5.5294      5.7755|
|  3:  3.7150 -  3.2512 0.99   1301  148 0.1200 0.1476      5.5688      5.8123|
|  4:  3.2512 -  2.9566 0.99   1292  143 0.1384 0.1761      5.5426      5.6978|
|  5:  2.9566 -  2.7462 0.99   1285  140 0.1379 0.1690      5.3581       5.494|
|  6:  2.7462 -  2.5852 0.99   1280  145 0.1315 0.1923      5.2579      5.4838|
|  7:  2.5852 -  2.4563 0.99   1266  140 0.1311 0.1766      5.2001      5.4136|
|  8:  2.4563 -  2.3499 0.98   1277  140 0.1285 0.1777       5.151      5.3826|
|  9:  2.3499 -  2.2597 0.98   1277  144 0.1282 0.1883      5.0809      5.3412|
| 10:  2.2597 -  2.1820 0.98   1236  133 0.1233 0.1813      5.0311      5.2147|
| 11:  2.1820 -  2.1140 1.00   1274  148 0.1270 0.1867      4.9911      5.3584|
| 12:  2.1140 -  2.0537 0.97   1252  131 0.1224 0.1742      4.9534      5.1951|
| 13:  2.0537 -  1.9998 0.98   1238  142 0.1266 0.1969      4.8861      5.1476|
| 14:  1.9998 -  1.9511 0.73    940  106 0.1199 0.1917      4.7987      5.0396|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.6741 -  4.6556  1376   155  0.94   9.49   0.99     0.97       7719.61|
|  2:  4.6556 -  3.7150  1336   144  0.95   8.57   1.04     1.02       9847.33|
|  3:  3.7150 -  3.2512  1301   148  0.92  12.51   1.05     1.04      11765.29|
|  4:  3.2512 -  2.9566  1292   143  0.92  14.08   1.03     1.03      11182.46|
|  5:  2.9566 -  2.7462  1285   140  0.90  15.85   1.01     0.97       8438.21|
|  6:  2.7462 -  2.5852  1280   145  0.90  16.33   0.99     0.96       7379.90|
|  7:  2.5852 -  2.4563  1266   140  0.90  16.32   1.00     0.97       6535.90|
|  8:  2.4563 -  2.3499  1277   140  0.90  16.20   1.01     0.98       5990.33|
|  9:  2.3499 -  2.2597  1277   144  0.90  16.17   1.02     1.01       5352.52|
| 10:  2.2597 -  2.1820  1236   133  0.90  16.42   1.03     1.00       4944.82|
| 11:  2.1820 -  2.1140  1274   148  0.90  16.66   1.02     0.98       4629.37|
| 12:  2.1140 -  2.0537  1252   131  0.90  16.46   1.03     1.01       4531.73|
| 13:  2.0537 -  1.9998  1238   142  0.89  17.55   1.03     1.02       4027.07|
| 14:  1.9998 -  1.9511   940   106  0.89  17.28   1.02     0.99       3385.78|
|alpha:            min =        0.96 max =            1.04 mean =         1.00|
|beta:             min =     3385.78 max =        11765.29 mean =      6944.57|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.95 mean =        14.88|
|phase err.(test): min =        0.00 max =           89.46 mean =        14.39|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.227)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.94    96.39   15.39    None  None   None       |
|    all(noH): 2823   0      0.94    96.39   15.39    None  None   None       |
|    Sol.    : 438    0      4.23    89.54   39.87    None  None   None       |
|    Mac.    : 2385   0      0.94    96.39   10.89    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:     0.938 -  10.483: 1596   |   5:    48.665 -  58.211:   85        |
|      1:    10.483 -  20.029:  670   |   6:    58.211 -  67.756:   58        |
|      2:    20.029 -  29.574:  156   |   7:    67.756 -  77.301:   14        |
|      3:    29.574 -  39.120:  119   |   8:    77.301 -  86.847:    7        |
|      4:    39.120 -  48.665:  113   |   9:    86.847 -  96.392:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 325         
Filter by distance & map next to the model:
   mapped sites are within: 0.736 - 5.968
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 325 from: 325
   mapped sites are within: 0.736 - 5.968

peak=   10.982 closest distance to " CB  VAL A 230 " =    1.434
peak=   10.917 closest distance to " CB  VAL A 296 " =    1.552
peak=    7.108 closest distance to " CG  ARG A 138 " =    1.137
peak=    6.808 closest distance to " O   HOH Z 199 " =    1.735
peak=    6.139 closest distance to " O   HOH Z 236 " =    1.720
peak=    6.117 closest distance to " O   HOH Z 142 " =    1.851
peak=    5.928 closest distance to " O   HOH Z 278 " =    2.042
peak=    5.738 closest distance to " O   HOH Z 279 " =    1.164
peak=    5.704 closest distance to " O   HOH Z 193 " =    1.769
peak=    5.667 closest distance to " CD2 LEU A   5 " =    1.338
peak=    5.442 closest distance to " CD1AILE A 234 " =    1.014
peak=    5.217 closest distance to " CG  LEU A   5 " =    1.257
peak=    5.177 closest distance to " O   HOH Z  78 " =    1.559
peak=    5.176 closest distance to " O   HOH Z 124 " =    1.704
peak=    5.116 closest distance to " CB  ASN A 187 " =    2.064
peak=    5.085 closest distance to " CB  ARG A 275 " =    1.028
peak=    5.063 closest distance to " O   HOH Z 130 " =    1.038
peak=    5.051 closest distance to " NE2 GLN A  11 " =    1.122
peak=    4.985 closest distance to " CG  PRO A 213 " =    1.318
peak=    4.919 closest distance to " O   HOH Z 188 " =    1.236
peak=    4.871 closest distance to " CG  GLN A  11 " =    2.136
peak=    4.812 closest distance to " O   HOH Z 263 " =    1.544
peak=    4.784 closest distance to " O   HOH Z 427 " =    2.569
peak=    4.768 closest distance to " O   HOH Z 138 " =    0.970
peak=    4.754 closest distance to " O   HOH Z 214 " =    1.430
peak=    4.729 closest distance to " CA  GLY A 241 " =    3.677
peak=    4.720 closest distance to " O   HOH Z 120 " =    1.092
peak=    4.714 closest distance to " O   HOH Z 132 " =    1.534
peak=    4.711 closest distance to " NH2 ARG A  56 " =    2.044
peak=    4.711 closest distance to " CD2 LEU A 228 " =    1.185
peak=    4.694 closest distance to " NE2 GLN A  55 " =    1.361
peak=    4.626 closest distance to " O   HOH Z 232 " =    2.150
peak=    4.617 closest distance to " O   HOH Z 134 " =    1.569
peak=    4.577 closest distance to " O   HOH Z   5 " =    1.418
peak=    4.567 closest distance to " CG AARG A 275 " =    1.182
peak=    4.562 closest distance to " O   HOH Z  59 " =    1.692
peak=    4.554 closest distance to " O   HOH Z  97 " =    1.676
peak=    4.545 closest distance to " NH1 ARG A 138 " =    1.088
peak=    4.539 closest distance to " CG  PRO A 198 " =    1.250
peak=    4.493 closest distance to " O   HOH Z 227 " =    1.892
peak=    4.469 closest distance to " CB  VAL A 265 " =    1.268
peak=    4.465 closest distance to " CB  VAL A 230 " =    1.084
peak=    4.463 closest distance to " CB  ARG A 102 " =    0.839
peak=    4.425 closest distance to " O   SER A  87 " =    2.339
peak=    4.409 closest distance to " O   HOH Z 148 " =    1.790
peak=    4.389 closest distance to " O   HOH Z 202 " =    1.387
peak=    4.350 closest distance to " O   HOH Z 192 " =    1.705
peak=    4.340 closest distance to " O   HOH Z 276 " =    1.460
peak=    4.331 closest distance to " O   HOH Z 108 " =    1.310
peak=    4.325 closest distance to " O   HOH Z 291 " =    1.374
peak=    4.323 closest distance to " O   HOH Z 344 " =    1.328
peak=    4.322 closest distance to " O   HOH Z 423 " =    1.366
peak=    4.315 closest distance to " O   HOH Z 326 " =    1.337
peak=    4.309 closest distance to " O   HOH Z 316 " =    2.501
peak=    4.282 closest distance to " O   HOH Z 406 " =    1.225
peak=    4.278 closest distance to " O   HOH Z 284 " =    1.464
peak=    4.257 closest distance to " O   HOH Z 260 " =    1.580
peak=    4.255 closest distance to " O   HOH Z   7 " =    1.385
peak=    4.253 closest distance to " O   HOH Z 272 " =    1.820
peak=    4.244 closest distance to " NZ  LYS A 117 " =    3.448
peak=    4.231 closest distance to " CG2 VAL A 257 " =    0.908
peak=    4.224 closest distance to " O   HOH Z 143 " =    1.402
peak=    4.189 closest distance to " CG  GLN A  77 " =    1.014
peak=    4.162 closest distance to " CB  SER A   3 " =    1.234
peak=    4.161 closest distance to " CB  GLN A 223 " =    1.592
peak=    4.142 closest distance to " O   HOH Z 249 " =    1.180
peak=    4.130 closest distance to " O   PRO A 198 " =    1.240
peak=    4.119 closest distance to " O   HOH Z 147 " =    1.341
peak=    4.110 closest distance to " NH1 ARG A  14 " =    1.013
peak=    4.101 closest distance to " O   HOH Z 117 " =    1.720
peak=    4.093 closest distance to " O   HOH Z 414 " =    1.278
peak=    4.088 closest distance to " O   HOH Z 100 " =    1.117
peak=    4.086 closest distance to " CB  ASN A 148 " =    1.337
peak=    4.085 closest distance to " O   HOH Z  69 " =    1.160
peak=    4.072 closest distance to " O   HOH Z 117 " =    1.301
peak=    4.054 closest distance to " O   HOH Z   9 " =    1.094
peak=    4.034 closest distance to " O   HOH Z  44 " =    1.906
peak=    4.019 closest distance to " O   HOH Z 217 " =    1.540
peak=    4.012 closest distance to " CG1BVAL A  72 " =    1.361
peak=    4.008 closest distance to " O   HOH Z  97 " =    2.155
peak=    4.004 closest distance to " O   HOH Z 357 " =    1.841
peak=    3.995 closest distance to " O   HOH Z 344 " =    2.603
peak=    3.970 closest distance to " NE1 TRP A 274 " =    0.960
peak=    3.963 closest distance to " CB  SER A  26 " =    1.598
peak=    3.955 closest distance to " O   HOH Z  89 " =    1.604
peak=    3.954 closest distance to " O   HOH Z   9 " =    2.100
peak=    3.933 closest distance to " O   HOH Z  85 " =    1.290
peak=    3.929 closest distance to " O   HOH Z  11 " =    1.309
peak=    3.903 closest distance to " CA  TYR A  30 " =    1.096
peak=    3.859 closest distance to " O   HOH Z  80 " =    1.659
peak=    3.853 closest distance to " O   HOH Z 250 " =    1.479
peak=    3.853 closest distance to " OD2 ASP A 286 " =    2.355
peak=    3.851 closest distance to " O   HOH Z 189 " =    2.309
peak=    3.850 closest distance to " O   HOH Z 303 " =    2.157
peak=    3.847 closest distance to " O   HOH Z 322 " =    2.048
peak=    3.830 closest distance to " O   HOH Z 289 " =    1.498
peak=    3.823 closest distance to " O   HOH Z 108 " =    1.649
peak=    3.821 closest distance to " CG  PRO A 243 " =    1.258
peak=    3.819 closest distance to " CB  TRP A 179 " =    1.138
peak=    3.798 closest distance to " O   HOH Z  43 " =    1.661
peak=    3.796 closest distance to " CB  TYR A  30 " =    1.714
peak=    3.793 closest distance to " CB  VAL A 202 " =    1.619
peak=    3.787 closest distance to " O   HOH Z  95 " =    1.630
peak=    3.778 closest distance to " OE1 GLU A   2 " =    2.069
peak=    3.775 closest distance to " CB  LEU A 255 " =    0.839
peak=    3.765 closest distance to " O   HOH Z 137 " =    1.562
peak=    3.763 closest distance to " O   HOH Z  43 " =    1.177
peak=    3.748 closest distance to " O   HOH Z 247 " =    1.266
peak=    3.739 closest distance to " NE2 GLN A  58 " =    5.600
peak=    3.737 closest distance to " O   HOH Z  63 " =    2.105
peak=    3.730 closest distance to " NE2 GLN A 223 " =    1.626
peak=    3.730 closest distance to " O   HOH Z 280 " =    1.624
peak=    3.724 closest distance to " CG  LEU A 228 " =    1.250
peak=    3.714 closest distance to " OG  SER A  62 " =    2.892
peak=    3.714 closest distance to " CG1 VAL A 153 " =    0.873
peak=    3.707 closest distance to " O   HOH Z 366 " =    2.628
peak=    3.706 closest distance to " O   HOH Z 287 " =    1.556
peak=    3.705 closest distance to " O   HOH Z 176 " =    1.543
peak=    3.705 closest distance to " CG2 THR A 221 " =    1.209
peak=    3.693 closest distance to " CB  GLN A 183 " =    1.282
peak=    3.689 closest distance to " CB  PRO A 198 " =    0.987
peak=    3.686 closest distance to " CG  ASN A  60 " =    1.121
peak=    3.684 closest distance to " O   HOH Z  59 " =    2.149
peak=    3.683 closest distance to " O   HOH Z 302 " =    1.719
peak=    3.671 closest distance to " CG  LEU A 167 " =    1.041
peak=    3.655 closest distance to " CB  GLU A 128 " =    1.175
peak=    3.648 closest distance to " CB  ASN A 148 " =    1.875
peak=    3.646 closest distance to " CB  SER A 216 " =    0.915
peak=    3.644 closest distance to " CD  ARG A 269 " =    1.097
peak=    3.640 closest distance to " CA  ALA A  21 " =    1.073
peak=    3.638 closest distance to " N   TRP A 177 " =    1.500
peak=    3.631 closest distance to " O   HOH Z 403 " =    2.041
peak=    3.631 closest distance to " O   HOH Z 214 " =    1.802
peak=    3.621 closest distance to " O   HOH Z 345 " =    2.991
peak=    3.620 closest distance to " CA  ASN A 284 " =    1.005
peak=    3.619 closest distance to " O   HOH Z 402 " =    1.414
peak=    3.615 closest distance to " CB  GLN A  88 " =    1.333
peak=    3.605 closest distance to " O   HOH Z 234 " =    3.378
peak=    3.594 closest distance to " O   HOH Z 395 " =    1.475
peak=    3.592 closest distance to " CA  VAL A  41 " =    0.827
peak=    3.590 closest distance to " O   HOH Z  61 " =    1.591
peak=    3.582 closest distance to " O   HOH Z 368 " =    2.113
peak=    3.579 closest distance to " CA  GLN A 194 " =    1.083
peak=    3.573 closest distance to " CB BVAL A  41 " =    1.181
peak=    3.571 closest distance to " O   HOH Z 347 " =    0.915
peak=    3.565 closest distance to " O   SER A 164 " =    1.308
peak=    3.562 closest distance to " O   HOH Z 130 " =    2.486
peak=    3.562 closest distance to " CA  VAL A 126 " =    1.089
peak=    3.557 closest distance to " O   HOH Z 361 " =    1.538
peak=    3.549 closest distance to " O   HOH Z 193 " =    1.953
peak=    3.548 closest distance to " O   HOH Z 213 " =    1.782
peak=    3.542 closest distance to " CG1BVAL A 121 " =    1.062
peak=    3.535 closest distance to " CB  ALA A   9 " =    1.538
peak=    3.535 closest distance to " O   HOH Z  58 " =    1.733
peak=    3.534 closest distance to " O   HOH Z 156 " =    2.937
peak=    3.528 closest distance to " O   HOH Z  80 " =    2.100
peak=    3.522 closest distance to " O   HOH Z 261 " =    1.681
peak=    3.521 closest distance to " CG  GLN A  88 " =    1.049
peak=    3.519 closest distance to " O   HOH Z 249 " =    1.726
peak=    3.517 closest distance to " NH2BARG A 190 " =    1.462
peak=    3.510 closest distance to " O   HOH Z 209 " =    2.154
peak=    3.510 closest distance to " O   HOH Z 152 " =    2.734
peak=    3.509 closest distance to " CB  GLN A 278 " =    0.822
peak=    3.505 closest distance to " CG  MET A 188 " =    1.328
peak=    3.504 closest distance to " O   HOH Z  66 " =    2.088
peak=    3.500 closest distance to " CZ AARG A 102 " =    1.488
peak=    3.495 closest distance to " ND1 HIS A  81 " =    1.246
peak=    3.488 closest distance to " O   HOH Z 136 " =    1.103
peak=    3.482 closest distance to " O   HOH Z 112 " =    1.057
peak=    3.481 closest distance to " O   HOH Z 435 " =    1.953
peak=    3.477 closest distance to " O   HOH Z 234 " =    2.060
peak=    3.477 closest distance to " CD  GLN A 194 " =    1.463
peak=    3.476 closest distance to " CB  GLU A 152 " =    1.212
peak=    3.472 closest distance to " O   HOH Z 245 " =    1.422
peak=    3.471 closest distance to " CB  ARG A  79 " =    1.371
peak=    3.471 closest distance to " O   HOH Z 233 " =    1.542
peak=    3.467 closest distance to " CD1 ILE A  33 " =    1.610
peak=    3.465 closest distance to " O   HOH Z 392 " =    1.871
peak=    3.465 closest distance to " CA  ASN A 127 " =    1.123
peak=    3.465 closest distance to " O   HOH Z  68 " =    2.664
peak=    3.464 closest distance to " CD1 LEU A 228 " =    1.534
peak=    3.462 closest distance to " O   HOH Z 128 " =    2.042
peak=    3.455 closest distance to " CA  LEU A 282 " =    1.278
peak=    3.454 closest distance to " O   HOH Z 392 " =    2.839
peak=    3.454 closest distance to " NH2BARG A 145 " =    1.516
peak=    3.452 closest distance to " CA  ILE A 234 " =    0.952
peak=    3.444 closest distance to " O   HOH Z 366 " =    1.926
peak=    3.440 closest distance to " CB  ARG A 138 " =    1.421
peak=    3.436 closest distance to " O   SER A  26 " =    1.570
peak=    3.432 closest distance to " CE BMET A  47 " =    1.223
peak=    3.431 closest distance to " CB  TYR A 169 " =    0.736
peak=    3.430 closest distance to " CG  GLN A  77 " =    2.190
peak=    3.430 closest distance to " O   HOH Z 145 " =    1.570
peak=    3.427 closest distance to " O   HOH Z 118 " =    2.038
peak=    3.413 closest distance to " O   HOH Z 203 " =    1.569
peak=    3.410 closest distance to " O   HOH Z 196 " =    1.465
peak=    3.407 closest distance to " C   ALA A 299 " =    0.954
peak=    3.406 closest distance to " CD2 TYR A  30 " =    0.904
peak=    3.406 closest distance to " CA  SER A  99 " =    0.738
peak=    3.405 closest distance to " CE  MET A  93 " =    1.437
peak=    3.399 closest distance to " O   HOH Z 172 " =    3.723
peak=    3.397 closest distance to " O   HOH Z  10 " =    1.669
peak=    3.396 closest distance to " CA  PRO A 163 " =    1.004
peak=    3.396 closest distance to " O   HOH Z  13 " =    1.703
peak=    3.393 closest distance to " O   HOH Z 113 " =    1.839
peak=    3.390 closest distance to " CB  ASN A  60 " =    0.902
peak=    3.388 closest distance to " O   HOH Z 430 " =    1.801
peak=    3.387 closest distance to " O   HOH Z   1 " =    1.601
peak=    3.383 closest distance to " O   HOH Z 423 " =    1.674
peak=    3.382 closest distance to " CE AMET A  47 " =    1.136
peak=    3.373 closest distance to " O   HOH Z 191 " =    1.699
peak=    3.368 closest distance to " O   HOH Z 193 " =    1.898
peak=    3.364 closest distance to " O   HOH Z  47 " =    1.503
peak=    3.364 closest distance to " CB  ALA A 114 " =    1.390
peak=    3.358 closest distance to " O   HOH Z 128 " =    2.027
peak=    3.346 closest distance to " CG2 ILE A 120 " =    1.374
peak=    3.344 closest distance to " OD1 ASN A  69 " =    2.878
peak=    3.340 closest distance to " O   HOH Z 222 " =    2.200
peak=    3.337 closest distance to " O   HOH Z  61 " =    1.503
peak=    3.337 closest distance to " CA  ALA A  51 " =    1.035
peak=    3.335 closest distance to " O   HOH Z  20 " =    1.804
peak=    3.334 closest distance to " CA  ARG A 275 " =    1.113
peak=    3.332 closest distance to " O   HOH Z 227 " =    2.271
peak=    3.330 closest distance to " O   HOH Z 222 " =    2.256
peak=    3.329 closest distance to " CD AARG A 145 " =    1.029
peak=    3.328 closest distance to " O   HOH Z 267 " =    2.042
peak=    3.326 closest distance to " O   HOH Z 144 " =    2.027
peak=    3.324 closest distance to " O   HOH Z 184 " =    1.165
peak=    3.318 closest distance to " OG ASER A 134 " =    1.603
peak=    3.316 closest distance to " O   HOH Z 172 " =    5.968
peak=    3.311 closest distance to " O   HOH Z 298 " =    1.791
peak=    3.310 closest distance to " O   HOH Z  88 " =    2.260
peak=    3.304 closest distance to " CG1 ILE A  33 " =    1.409
peak=    3.301 closest distance to " CA  PHE A 283 " =    1.066
peak=    3.295 closest distance to " N   GLN A 278 " =    1.047
peak=    3.293 closest distance to " O   HOH Z 123 " =    1.094
peak=    3.292 closest distance to " CG2 THR A 294 " =    1.629
peak=    3.291 closest distance to " O   HOH Z 183 " =    1.692
peak=    3.287 closest distance to " OG1 THR A 294 " =    2.372
peak=    3.285 closest distance to " O   HOH Z 380 " =    1.648
peak=    3.285 closest distance to " CD1 LEU A   5 " =    1.801
peak=    3.278 closest distance to " O   HOH Z 426 " =    2.989
peak=    3.278 closest distance to " O   HOH Z 109 " =    2.175
peak=    3.275 closest distance to " O   HOH Z 284 " =    2.653
peak=    3.274 closest distance to " CA  ARG A  66 " =    0.923
peak=    3.272 closest distance to " CA  LYS A 117 " =    1.234
peak=    3.266 closest distance to " CG  ARG A  66 " =    0.976
peak=    3.262 closest distance to " O   HOH Z  54 " =    1.488
peak=    3.261 closest distance to " CB  MET A  47 " =    1.654
peak=    3.257 closest distance to " O   HOH Z 285 " =    1.636
peak=    3.257 closest distance to " O   HOH Z 389 " =    1.362
peak=    3.256 closest distance to " O   HOH Z 343 " =    1.479
peak=    3.256 closest distance to " CB  ARG A 269 " =    0.911
peak=    3.255 closest distance to " O   HOH Z 148 " =    3.136
peak=    3.252 closest distance to " O   HOH Z 422 " =    2.414
peak=    3.249 closest distance to " CB  THR A  52 " =    1.367
peak=    3.246 closest distance to " CD2 TRP A 179 " =    1.426
peak=    3.246 closest distance to " NE2 GLN A  58 " =    1.765
peak=    3.245 closest distance to " O   HOH Z  12 " =    1.816
peak=    3.245 closest distance to " N   TYR A  15 " =    1.030
peak=    3.243 closest distance to " CB  ALA A  34 " =    0.983
peak=    3.241 closest distance to " O   HOH Z 380 " =    3.401
peak=    3.239 closest distance to " CB  PRO A 198 " =    1.682
peak=    3.238 closest distance to " N   PHE A 130 " =    1.380
peak=    3.237 closest distance to " CE  LYS A 119 " =    1.155
peak=    3.236 closest distance to " O   HOH Z 389 " =    1.494
peak=    3.235 closest distance to " CB  TRP A 266 " =    1.073
peak=    3.228 closest distance to " O   HOH Z 269 " =    3.334
peak=    3.228 closest distance to " O   HOH Z 273 " =    0.966
peak=    3.225 closest distance to " NH2 ARG A 219 " =    1.911
peak=    3.225 closest distance to " OH  TYR A 116 " =    1.080
peak=    3.221 closest distance to " O   HOH Z 374 " =    2.420
peak=    3.220 closest distance to " O   HOH Z 369 " =    2.116
peak=    3.220 closest distance to " CE  MET A  40 " =    1.084
peak=    3.217 closest distance to " N   GLY A 111 " =    1.218
peak=    3.216 closest distance to " CB  ALA A 248 " =    1.279
peak=    3.210 closest distance to " CG  MET A 185 " =    1.307
peak=    3.207 closest distance to " O   HOH Z 408 " =    1.612
peak=    3.205 closest distance to " NH1BARG A 145 " =    1.387
peak=    3.202 closest distance to " NH1BARG A 190 " =    1.924
peak=    3.195 closest distance to " NH2 ARG A 156 " =    1.088
peak=    3.195 closest distance to " CE1 PHE A  61 " =    1.218
peak=    3.193 closest distance to " O   HOH Z 106 " =    2.293
peak=    3.192 closest distance to " CA  LEU A 101 " =    1.399
peak=    3.191 closest distance to " N   GLU A 236 " =    0.909
peak=    3.191 closest distance to " N   ASN A  39 " =    1.136
peak=    3.190 closest distance to " O   HOH Z 244 " =    1.609
peak=    3.188 closest distance to " O   HOH Z 253 " =    1.488
peak=    3.188 closest distance to " CB  SER A  63 " =    1.274
peak=    3.188 closest distance to " O   HOH Z 299 " =    4.604
peak=    3.187 closest distance to " ND1 HIS A  81 " =    1.394
peak=    3.186 closest distance to " CA  ASN A 215 " =    1.021
peak=    3.185 closest distance to " CE3 TRP A 274 " =    2.332
peak=    3.184 closest distance to " O   HOH Z 345 " =    1.670
peak=    3.184 closest distance to " CB  HIS A 108 " =    0.885
peak=    3.176 closest distance to " CB  ALA A   1 " =    4.410
peak=    3.174 closest distance to " O   HOH Z 411 " =    1.821
peak=    3.172 closest distance to " OD1 ASP A 286 " =    1.361
peak=    3.170 closest distance to " CB  ASP A 200 " =    1.033
peak=    3.169 closest distance to " O   HOH Z 371 " =    1.469
peak=    3.160 closest distance to " CB  ASN A 215 " =    0.944
peak=    3.152 closest distance to " O   HOH Z 356 " =    1.380
peak=    3.148 closest distance to " O   HOH Z  63 " =    2.306
peak=    3.148 closest distance to " O   PRO A 213 " =    1.467
peak=    3.141 closest distance to " CB  PRO A  54 " =    0.906
peak=    3.137 closest distance to " O   HOH Z 155 " =    1.517
peak=    3.137 closest distance to " CA  THR A 264 " =    0.854
peak=    3.135 closest distance to " O   HOH Z 371 " =    2.315
peak=    3.130 closest distance to " O   HOH Z 375 " =    1.065
peak=    3.120 closest distance to " CZ2 TRP A 274 " =    1.780
peak=    3.116 closest distance to " CB  ALA A   1 " =    1.018
peak=    3.104 closest distance to " O   HOH Z 118 " =    5.532
peak=    3.078 closest distance to " CA  LYS A  48 " =    1.279
peak=    3.076 closest distance to " CG  LYS A 119 " =    1.112
peak=    3.074 closest distance to " CB  ASN A  69 " =    1.499
peak=    3.065 closest distance to " CA  GLY A  80 " =    0.783
peak=    3.056 closest distance to " O   GLN A  58 " =    1.395
peak=    3.053 closest distance to " O   HOH Z 359 " =    1.171
peak=    3.051 closest distance to " CG  LYS A  76 " =    1.445
peak=    3.048 closest distance to " O   HOH Z 406 " =    1.387
peak=    3.045 closest distance to " NH1AARG A 145 " =    0.841
peak=    3.042 closest distance to " OE2 GLU A  53 " =    2.051
peak=    3.035 closest distance to " CG AARG A 102 " =    2.255
peak=    3.029 closest distance to " O   HOH Z 156 " =    2.387
peak=    3.020 closest distance to " CB  LEU A 228 " =    1.447

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 194         
Filter by distance & map next to the model:
   mapped sites are within: 0.762 - 5.690
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 194 from: 194
   mapped sites are within: 0.762 - 5.690

peak=   -4.384 closest distance to " CG2 VAL A 230 " =    0.762
peak=   -4.379 closest distance to " SG  CYS A 254 " =    3.149
peak=   -4.330 closest distance to " C   HIS A 108 " =    1.085
peak=   -4.231 closest distance to " N   GLN A  58 " =    1.021
peak=   -4.207 closest distance to " NH2 ARG A  79 " =    1.959
peak=   -4.193 closest distance to " CG  ARG A 138 " =    0.847
peak=   -4.180 closest distance to " CA  GLY A  23 " =    1.767
peak=   -4.161 closest distance to " CD  ARG A 138 " =    1.350
peak=   -4.149 closest distance to " CG2 THR A   4 " =    1.866
peak=   -4.135 closest distance to " C   ASP A 231 " =    2.411
peak=   -4.128 closest distance to " O   HOH Z 138 " =    0.926
peak=   -4.121 closest distance to " O   HOH Z 164 " =    5.690
peak=   -4.066 closest distance to " O   ALA A 161 " =    1.428
peak=   -4.003 closest distance to " O   PRO A 163 " =    1.931
peak=   -3.970 closest distance to " CD  ARG A 156 " =    2.009
peak=   -3.950 closest distance to " N   MET A 188 " =    1.906
peak=   -3.947 closest distance to " CD  GLN A  88 " =    1.093
peak=   -3.943 closest distance to " CE2 TYR A  30 " =    2.909
peak=   -3.918 closest distance to " NE1 TRP A 274 " =    1.110
peak=   -3.891 closest distance to " OG ASER A 134 " =    1.168
peak=   -3.858 closest distance to " OD1 ASN A 249 " =    1.118
peak=   -3.852 closest distance to " O   HOH Z 266 " =    4.345
peak=   -3.792 closest distance to " O   ASN A 187 " =    1.289
peak=   -3.791 closest distance to " O   HOH Z 290 " =    1.030
peak=   -3.787 closest distance to " O   HOH Z  11 " =    1.993
peak=   -3.785 closest distance to " O   HOH Z  93 " =    1.481
peak=   -3.782 closest distance to " N   HIS A 115 " =    1.915
peak=   -3.782 closest distance to " O   ILE A  49 " =    1.754
peak=   -3.761 closest distance to " O   HOH Z 423 " =    2.211
peak=   -3.743 closest distance to " O   ALA A  51 " =    1.184
peak=   -3.736 closest distance to " O   HOH Z  69 " =    1.543
peak=   -3.725 closest distance to " OG BSER A 134 " =    1.237
peak=   -3.721 closest distance to " OG BSER A  99 " =    0.992
peak=   -3.720 closest distance to " O   HOH Z 250 " =    1.327
peak=   -3.717 closest distance to " O   HOH Z  98 " =    1.608
peak=   -3.708 closest distance to " CA  VAL A  67 " =    2.705
peak=   -3.695 closest distance to " CG  ASP A 231 " =    0.805
peak=   -3.693 closest distance to " O   HOH Z 419 " =    1.011
peak=   -3.678 closest distance to " CG  PHE A 283 " =    2.482
peak=   -3.669 closest distance to " O   HOH Z 191 " =    4.885
peak=   -3.663 closest distance to " N   GLN A  77 " =    1.487
peak=   -3.663 closest distance to " O   HOH Z 407 " =    2.670
peak=   -3.652 closest distance to " OG  SER A   3 " =    1.209
peak=   -3.641 closest distance to " O   HOH Z 388 " =    1.958
peak=   -3.633 closest distance to " N   ALA A 248 " =    1.663
peak=   -3.627 closest distance to " O   ALA A 100 " =    2.475
peak=   -3.626 closest distance to " CD  GLU A 152 " =    2.261
peak=   -3.620 closest distance to " O   HOH Z 197 " =    5.003
peak=   -3.611 closest distance to " OD1 ASP A 200 " =    1.111
peak=   -3.610 closest distance to " C   ASN A 285 " =    1.996
peak=   -3.601 closest distance to " CB  TYR A  15 " =    2.077
peak=   -3.594 closest distance to " N   GLN A  58 " =    2.218
peak=   -3.593 closest distance to " OD2 ASP A  50 " =    1.387
peak=   -3.583 closest distance to " C   ALA A 158 " =    1.044
peak=   -3.581 closest distance to " CD1 LEU A 101 " =    2.240
peak=   -3.579 closest distance to " OG1 THR A 246 " =    1.159
peak=   -3.573 closest distance to " CD1 LEU A 255 " =    2.768
peak=   -3.563 closest distance to " CE2 PHE A 218 " =    2.670
peak=   -3.556 closest distance to " CB  ALA A 248 " =    1.948
peak=   -3.555 closest distance to " CG1 ILE A 234 " =    1.895
peak=   -3.546 closest distance to " O   THR A 182 " =    1.165
peak=   -3.541 closest distance to " O   HOH Z  88 " =    2.122
peak=   -3.540 closest distance to " O   PRO A 198 " =    1.162
peak=   -3.538 closest distance to " O   SER A  22 " =    1.452
peak=   -3.532 closest distance to " CA  GLY A 133 " =    1.791
peak=   -3.523 closest distance to " O   HOH Z 198 " =    1.706
peak=   -3.519 closest distance to " CD  LYS A 289 " =    2.552
peak=   -3.518 closest distance to " OD2 ASP A 191 " =    1.404
peak=   -3.515 closest distance to " N   GLN A 122 " =    1.299
peak=   -3.507 closest distance to " CG  PRO A 198 " =    1.745
peak=   -3.496 closest distance to " O   HOH Z 193 " =    2.233
peak=   -3.487 closest distance to " O   HOH Z 166 " =    1.650
peak=   -3.482 closest distance to " CD1 ILE A 239 " =    2.523
peak=   -3.467 closest distance to " CD  PRO A 198 " =    1.267
peak=   -3.462 closest distance to " O   SER A  22 " =    2.358
peak=   -3.458 closest distance to " CA  TYR A  68 " =    2.733
peak=   -3.458 closest distance to " O   HOH Z 427 " =    1.577
peak=   -3.437 closest distance to " O   HOH Z 165 " =    2.127
peak=   -3.428 closest distance to " O   HOH Z 192 " =    1.053
peak=   -3.428 closest distance to " O   HOH Z 426 " =    2.099
peak=   -3.422 closest distance to " CG  PRO A 243 " =    1.338
peak=   -3.419 closest distance to " CG  ASP A  50 " =    2.077
peak=   -3.417 closest distance to " O   HOH Z   9 " =    1.447
peak=   -3.417 closest distance to " O   SER A 135 " =    1.577
peak=   -3.413 closest distance to " O   HOH Z  56 " =    1.807
peak=   -3.413 closest distance to " O   HOH Z 368 " =    2.384
peak=   -3.400 closest distance to " O   SER A 146 " =    0.801
peak=   -3.389 closest distance to " O   HOH Z 377 " =    0.882
peak=   -3.388 closest distance to " CB  ALA A  43 " =    2.115
peak=   -3.386 closest distance to " O   HOH Z 220 " =    1.182
peak=   -3.383 closest distance to " O   HOH Z 188 " =    4.279
peak=   -3.380 closest distance to " CB  ALA A  51 " =    1.854
peak=   -3.376 closest distance to " O   SER A 273 " =    1.519
peak=   -3.369 closest distance to " ND2 ASN A  45 " =    0.913
peak=   -3.369 closest distance to " O   HOH Z 193 " =    1.716
peak=   -3.365 closest distance to " O   HOH Z 153 " =    1.564
peak=   -3.359 closest distance to " O   HOH Z  63 " =    1.055
peak=   -3.354 closest distance to " O   MET A  40 " =    2.589
peak=   -3.352 closest distance to " O   HOH Z 103 " =    1.702
peak=   -3.352 closest distance to " ND2 ASN A  39 " =    1.168
peak=   -3.342 closest distance to " CB  ALA A 244 " =    2.077
peak=   -3.340 closest distance to " O   HOH Z 137 " =    1.430
peak=   -3.337 closest distance to " O   HOH Z 364 " =    2.887
peak=   -3.336 closest distance to " CE2 TYR A 116 " =    3.033
peak=   -3.335 closest distance to " O   MET A 188 " =    1.533
peak=   -3.334 closest distance to " O   HOH Z 116 " =    1.152
peak=   -3.334 closest distance to " O   GLN A  89 " =    1.248
peak=   -3.332 closest distance to " CD1 LEU A 228 " =    1.944
peak=   -3.325 closest distance to " O   HOH Z 351 " =    1.440
peak=   -3.325 closest distance to " CA  VAL A  67 " =    2.614
peak=   -3.323 closest distance to " CG  GLN A  11 " =    2.042
peak=   -3.321 closest distance to " CG  ARG A 219 " =    2.150
peak=   -3.321 closest distance to " O   HOH Z 274 " =    2.728
peak=   -3.318 closest distance to " OE1 GLN A  88 " =    1.101
peak=   -3.317 closest distance to " CE  LYS A  76 " =    2.935
peak=   -3.310 closest distance to " O   SER A  99 " =    1.394
peak=   -3.308 closest distance to " O   ALA A   8 " =    1.807
peak=   -3.308 closest distance to " O   HOH Z 365 " =    1.325
peak=   -3.303 closest distance to " CG  PHE A  59 " =    2.139
peak=   -3.302 closest distance to " O   LEU A 228 " =    2.245
peak=   -3.300 closest distance to " ND2 ASN A 187 " =    1.661
peak=   -3.295 closest distance to " O   ASN A 215 " =    1.462
peak=   -3.289 closest distance to " NE2 GLN A  58 " =    1.876
peak=   -3.289 closest distance to " CG  PRO A 163 " =    2.819
peak=   -3.287 closest distance to " OD1 ASN A 301 " =    1.813
peak=   -3.284 closest distance to " O   HOH Z 410 " =    2.242
peak=   -3.283 closest distance to " OE2 GLU A   2 " =    1.166
peak=   -3.280 closest distance to " OG1 THR A  82 " =    1.305
peak=   -3.279 closest distance to " CG1 VAL A 296 " =    1.956
peak=   -3.276 closest distance to " OH  TYR A 169 " =    0.895
peak=   -3.275 closest distance to " O   ASN A  69 " =    1.238
peak=   -3.273 closest distance to " OD1 ASP A 191 " =    1.451
peak=   -3.269 closest distance to " CA  GLY A  35 " =    2.162
peak=   -3.267 closest distance to " O   HOH Z 171 " =    1.277
peak=   -3.260 closest distance to " O   HOH Z 385 " =    1.655
peak=   -3.258 closest distance to " ND2 ASN A 217 " =    2.297
peak=   -3.256 closest distance to " OG1 THR A 178 " =    1.114
peak=   -3.252 closest distance to " O   THR A 220 " =    1.582
peak=   -3.249 closest distance to " O   HOH Z 352 " =    1.104
peak=   -3.242 closest distance to " O   GLY A  98 " =    2.097
peak=   -3.240 closest distance to " OG1 THR A 246 " =    1.984
peak=   -3.235 closest distance to " O   HOH Z 392 " =    0.804
peak=   -3.233 closest distance to " O   HOH Z 231 " =    1.922
peak=   -3.225 closest distance to " O   HOH Z 210 " =    0.801
peak=   -3.220 closest distance to " O   HOH Z 131 " =    3.874
peak=   -3.220 closest distance to " O   HOH Z 139 " =    3.705
peak=   -3.219 closest distance to " C   LEU A 143 " =    1.061
peak=   -3.215 closest distance to " O   HOH Z 175 " =    1.039
peak=   -3.213 closest distance to " C   ASN A 217 " =    1.473
peak=   -3.212 closest distance to " O   HOH Z 430 " =    1.844
peak=   -3.211 closest distance to " OD1 ASN A 176 " =    1.094
peak=   -3.211 closest distance to " NH2AARG A 275 " =    4.835
peak=   -3.209 closest distance to " O   HOH Z 100 " =    1.402
peak=   -3.209 closest distance to " CA  ASP A  27 " =    2.380
peak=   -3.208 closest distance to " O   HOH Z 372 " =    2.381
peak=   -3.203 closest distance to " CB  SER A 273 " =    1.807
peak=   -3.200 closest distance to " O   HOH Z 414 " =    2.443
peak=   -3.200 closest distance to " O   GLY A  57 " =    1.560
peak=   -3.197 closest distance to " O   HOH Z  68 " =    2.011
peak=   -3.195 closest distance to " O   VAL A 125 " =    2.021
peak=   -3.190 closest distance to " O   HOH Z  97 " =    1.500
peak=   -3.188 closest distance to " CG  LEU A 228 " =    1.137
peak=   -3.186 closest distance to " O   GLN A 183 " =    1.372
peak=   -3.168 closest distance to " CB  ASP A 132 " =    2.006
peak=   -3.166 closest distance to " O   HOH Z 313 " =    1.491
peak=   -3.159 closest distance to " CG  PRO A 213 " =    0.944
peak=   -3.157 closest distance to " CB  ALA A 114 " =    2.265
peak=   -3.157 closest distance to " C   ILE A 239 " =    2.132
peak=   -3.145 closest distance to " CG2 THR A 279 " =    2.030
peak=   -3.144 closest distance to " OG  SER A  63 " =    1.387
peak=   -3.142 closest distance to " C   ARG A 269 " =    1.332
peak=   -3.132 closest distance to " N   VAL A 189 " =    1.602
peak=   -3.132 closest distance to " CZ  PHE A 130 " =    0.893
peak=   -3.124 closest distance to " O   HOH Z 256 " =    1.311
peak=   -3.120 closest distance to " CG  GLN A  58 " =    1.160
peak=   -3.120 closest distance to " CB  ILE A  33 " =    2.869
peak=   -3.117 closest distance to " CD2 LEU A 237 " =    2.838
peak=   -3.113 closest distance to " C   ARG A 190 " =    1.196
peak=   -3.112 closest distance to " O   HOH Z 438 " =    0.938
peak=   -3.109 closest distance to " N   SER A 276 " =    1.077
peak=   -3.106 closest distance to " O   HOH Z 210 " =    2.052
peak=   -3.091 closest distance to " O   HOH Z 260 " =    1.196
peak=   -3.090 closest distance to " N   GLN A  88 " =    1.631
peak=   -3.089 closest distance to " O   HOH Z 140 " =    1.846
peak=   -3.086 closest distance to " CA  GLY A 133 " =    1.676
peak=   -3.086 closest distance to " CG  GLN A 223 " =    2.032
peak=   -3.080 closest distance to " CD1 LEU A  96 " =    2.085
peak=   -3.074 closest distance to " OD2 ASP A 270 " =    1.163
peak=   -3.070 closest distance to " O   HOH Z 130 " =    0.788
peak=   -3.064 closest distance to " OG  SER A   3 " =    1.588
peak=   -3.063 closest distance to " CG AARG A 102 " =    1.709
peak=   -3.055 closest distance to " CE1 TYR A 247 " =    2.330
peak=   -3.030 closest distance to " O   HOH Z 407 " =    3.129
peak=   -3.016 closest distance to " O   HOH Z 437 " =    1.782

================= 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    :  0.5043 0.4938   6.298316e+00   6.291030e+00
   1_bss:  0.4961 0.4861   6.292055e+00   6.281470e+00
   1_xyz:  0.4260 0.4406   6.213938e+00   6.238611e+00
   1_adp:  0.3852 0.4407   6.157946e+00   6.227621e+00
   1_occ:  0.3846 0.4405   6.157327e+00   6.227825e+00
   2_bss:  0.3816 0.4370   6.157038e+00   6.225943e+00
   2_xyz:  0.3004 0.3596   5.974401e+00   6.100401e+00
   2_adp:  0.2766 0.3375   5.916530e+00   6.061187e+00
   2_occ:  0.2763 0.3378   5.916694e+00   6.061685e+00
   3_bss:  0.2741 0.3372   5.914236e+00   6.060644e+00
   3_xyz:  0.2077 0.2605   5.671714e+00   5.858839e+00
   3_adp:  0.1848 0.2449   5.582422e+00   5.792355e+00
   3_occ:  0.1844 0.2446   5.581591e+00   5.791473e+00
   4_bss:  0.1841 0.2442   5.577950e+00   5.787853e+00
   4_xyz:  0.1450 0.1950   5.362802e+00   5.591110e+00
   4_adp:  0.1376 0.1808   5.297371e+00   5.508874e+00
   4_occ:  0.1373 0.1804   5.295343e+00   5.505861e+00
   5_bss:  0.1372 0.1796   5.294662e+00   5.503865e+00
   5_xyz:  0.1280 0.1697   5.237039e+00   5.451230e+00
   5_adp:  0.1237 0.1674   5.212713e+00   5.434801e+00
   5_occ:  0.1236 0.1673   5.212265e+00   5.434363e+00
   5_bss:  0.1236 0.1672   5.212430e+00   5.434422e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.386   6.923   7.022   8.148   9.084   0.000   0.000   0.000
   1_xyz:  0.386   6.923   7.022   8.148   9.084   0.000   0.000   0.000
   1_adp:  0.386   6.923   7.022   8.148   9.084   0.000   0.000   0.000
   1_occ:  0.386   6.923   7.022   8.148   9.084   0.000   0.000   0.000
   2_bss:  0.354  23.909   3.454   4.132   5.687   0.000   0.000   0.000
   2_xyz:  0.354  23.909   3.454   4.132   5.687   0.000   0.000   0.000
   2_adp:  0.354  23.909   3.454   4.132   5.687   0.000   0.000   0.000
   2_occ:  0.354  23.909   3.454   4.132   5.687   0.000   0.000   0.000
   3_bss:  0.334  32.584   1.691   2.102   3.311   0.000   0.000   0.000
   3_xyz:  0.334  32.584   1.691   2.102   3.311   0.000   0.000   0.000
   3_adp:  0.334  32.584   1.691   2.102   3.311   0.000   0.000   0.000
   3_occ:  0.334  32.584   1.691   2.102   3.311   0.000   0.000   0.000
   4_bss:  0.305  30.591   0.851   1.348   2.171   0.000   0.000   0.000
   4_xyz:  0.305  30.591   0.851   1.348   2.171   0.000   0.000   0.000
   4_adp:  0.305  30.591   0.851   1.348   2.171   0.000   0.000   0.000
   4_occ:  0.305  30.591   0.851   1.348   2.171   0.000   0.000   0.000
   5_bss:  0.308  31.385   0.377   0.903   1.533   0.000   0.000   0.000
   5_xyz:  0.308  31.385   0.377   0.903   1.533   0.000   0.000   0.000
   5_adp:  0.308  31.385   0.377   0.903   1.533   0.000   0.000   0.000
   5_occ:  0.308  31.385   0.377   0.903   1.533   0.000   0.000   0.000
   5_bss:  0.316  32.181  -0.561  -0.035   0.596   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  60.936 0.3827  0.4628    78554.361
   1_bss:  61.740 0.3702  0.5589    75715.296
   1_xyz:  52.468 0.4891  0.7300    60068.680
   1_adp:  50.646 0.5122  0.8268    57826.506
   1_occ:  50.666 0.5119  0.8256    57796.912
   2_bss:  50.335 0.5158  0.7335    57255.246
   2_xyz:  38.737 0.6571  0.9173    35399.295
   2_adp:  35.665 0.6935  0.9620    31064.737
   2_occ:  35.697 0.6932  0.9615    31153.646
   3_bss:  35.524 0.6950  0.8947    30903.024
   3_xyz:  26.385 0.7964  0.9885    17729.108
   3_adp:  23.703 0.8254  1.0060    15233.068
   3_occ:  23.689 0.8256  1.0059    15219.763
   4_bss:  23.504 0.8272  0.9727    14957.212
   4_xyz:  18.484 0.8760  1.0011     9629.804
   4_adp:  16.462 0.8947  1.0128     8250.336
   4_occ:  16.400 0.8952  1.0128     8188.821
   5_bss:  16.361 0.8955  0.9939     8140.465
   5_xyz:  15.197 0.9054  0.9976     7196.749
   5_adp:  14.839 0.9084  0.9958     6947.951
   5_occ:  14.830 0.9085  0.9958     6940.716
   5_bss:  14.832 0.9085  0.9958     6944.238
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.085   5.2547e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.085   5.2547e+01
   1_xyz:   1.825  0.015  0.113 18.531  0.007  4.103   1.6550e-01
   1_adp:   1.825  0.015  0.113 18.531  0.007  4.103   1.6550e-01
   1_occ:   1.825  0.015  0.113 18.531  0.007  4.103   1.6550e-01
   2_bss:   1.825  0.015  0.113 18.531  0.007  4.103   1.6550e-01
   2_xyz:   1.248  0.009  0.085 16.905  0.006  4.103   9.7136e-02
   2_adp:   1.248  0.009  0.085 16.905  0.006  4.103   9.7136e-02
   2_occ:   1.248  0.009  0.085 16.905  0.006  4.103   9.7136e-02
   3_bss:   1.248  0.009  0.085 16.905  0.006  4.103   9.7136e-02
   3_xyz:   1.056  0.007  0.071 16.101  0.004  4.115   6.8811e-02
   3_adp:   1.056  0.007  0.071 16.101  0.004  4.115   6.8811e-02
   3_occ:   1.056  0.007  0.071 16.101  0.004  4.115   6.8811e-02
   4_bss:   1.056  0.007  0.071 16.101  0.004  4.115   6.8811e-02
   4_xyz:   1.036  0.006  0.072 15.944  0.004  4.106   6.4832e-02
   4_adp:   1.036  0.006  0.072 15.944  0.004  4.106   6.4832e-02
   4_occ:   1.036  0.006  0.072 15.944  0.004  4.106   6.4832e-02
   5_bss:   1.036  0.006  0.072 15.944  0.004  4.106   6.4832e-02
   5_xyz:   0.932  0.005  0.065 15.826  0.003  4.107   5.5749e-02
   5_adp:   0.932  0.005  0.065 15.826  0.003  4.107   5.5749e-02
   5_occ:   0.932  0.005  0.065 15.826  0.003  4.107   5.5749e-02
   5_bss:   0.932  0.005  0.065 15.826  0.003  4.107   5.5749e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.443   6.8014e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.443   6.8014e+00
   1_xyz:  15.410  0.182  0.524 83.878  0.054  2.199   1.1151e-01
   1_adp:  15.410  0.182  0.524 83.878  0.054  2.199   1.1151e-01
   1_occ:  15.410  0.182  0.524 83.878  0.054  2.199   1.1151e-01
   2_bss:  15.410  0.182  0.524 83.878  0.054  2.199   1.1151e-01
   2_xyz:   9.169  0.094  0.425 74.271  0.054  2.175   8.2902e-02
   2_adp:   9.169  0.094  0.425 74.271  0.054  2.175   8.2902e-02
   2_occ:   9.169  0.094  0.425 74.271  0.054  2.175   8.2902e-02
   3_bss:   9.169  0.094  0.425 74.271  0.054  2.175   8.2902e-02
   3_xyz:   6.539  0.058  0.288 85.874  0.023  2.299   8.1500e-02
   3_adp:   6.539  0.058  0.288 85.874  0.023  2.299   8.1500e-02
   3_occ:   6.539  0.058  0.288 85.874  0.023  2.299   8.1500e-02
   4_bss:   6.539  0.058  0.288 85.874  0.023  2.299   8.1500e-02
   4_xyz:   7.522  0.042  0.260 82.581  0.025  2.298   4.4329e-02
   4_adp:   7.522  0.042  0.260 82.581  0.025  2.298   4.4329e-02
   4_occ:   7.522  0.042  0.260 82.581  0.025  2.298   4.4329e-02
   5_bss:   7.522  0.042  0.260 82.581  0.025  2.298   4.4329e-02
   5_xyz:   7.232  0.033  0.207 85.411  0.026  2.361   3.4057e-02
   5_adp:   7.232  0.033  0.207 85.411  0.026  2.361   3.4057e-02
   5_occ:   7.232  0.033  0.207 85.411  0.026  2.361   3.4057e-02
   5_bss:   7.232  0.033  0.207 85.411  0.026  2.361   3.4057e-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:  85.36   0.00  14.74  77.01   0.00  12.74  85.36   0.00  25.66
   1_occ:  85.36   0.00  14.74  77.01   0.00  12.74  85.36   0.00  25.66
   2_bss:  85.36   0.00  14.74  77.01   0.00  12.74  85.36   0.00  25.66
   2_xyz:  85.36   0.00  14.74  77.01   0.00  12.74  85.36   0.00  25.66
   2_adp:  91.23   0.00  14.62  91.23   0.00  11.43  90.36   0.00  31.96
   2_occ:  91.23   0.00  14.62  91.23   0.00  11.43  90.36   0.00  31.96
   3_bss:  91.23   0.00  14.62  91.23   0.00  11.43  90.36   0.00  31.96
   3_xyz:  91.23   0.00  14.62  91.23   0.00  11.43  90.36   0.00  31.96
   3_adp: 102.99   0.00  15.11 102.99   0.00  10.64  87.26   2.09  39.43
   3_occ: 102.99   0.00  15.11 102.99   0.00  10.64  87.26   2.09  39.43
   4_bss: 102.99   0.00  15.11 102.99   0.00  10.64  87.26   2.09  39.43
   4_xyz: 102.99   0.00  15.11 102.99   0.00  10.64  87.26   2.09  39.43
   4_adp: 100.19   0.00  14.58 100.19   0.00  10.21  85.28   3.80  38.36
   4_occ: 100.19   0.00  14.58 100.19   0.00  10.21  85.28   3.80  38.36
   5_bss: 100.19   0.00  14.58 100.19   0.00  10.21  85.28   3.80  38.36
   5_xyz: 100.19   0.00  14.58 100.19   0.00  10.21  85.28   3.80  38.36
   5_adp:  95.45   0.00  14.45  95.45   0.00   9.95  88.60   3.29  38.93
   5_occ:  95.45   0.00  14.45  95.45   0.00   9.95  88.60   3.29  38.93
   5_bss:  96.39   0.94  15.39  96.39   0.94  10.89  89.54   4.23  39.87
------------------------------------------------------------------------
 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:    1.284    0.021    0.426
   1_adp:    1.284    0.021    0.426
   1_occ:    1.284    0.021    0.426
   2_bss:    1.284    0.021    0.426
   2_xyz:    1.632    0.042    0.607
   2_adp:    1.632    0.042    0.607
   2_occ:    1.632    0.042    0.607
   3_bss:    1.632    0.042    0.607
   3_xyz:    1.648    0.021    0.715
   3_adp:    1.648    0.021    0.715
   3_occ:    1.648    0.021    0.715
   4_bss:    1.648    0.021    0.715
   4_xyz:    1.748    0.055    0.791
   4_adp:    1.748    0.055    0.791
   4_occ:    1.748    0.055    0.791
   5_bss:    1.748    0.055    0.791
   5_xyz:    1.821    0.080    0.807
   5_adp:    1.821    0.080    0.807
   5_occ:    1.821    0.080    0.807
   5_bss:    1.821    0.080    0.807
------------------------------------------------------------------------

CPU time actual refinement: 342.83


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_154/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_154/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_154/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_154/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_154/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 342.67 
  Macro-tasks:
    bulk solvent and scale       = 47.05  
    individual site refinement   = 140.60 
    weights calculation          = 32.51  
    collect and process          = 6.46   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 226.74 
  Micro-tasks:
    mask                            = 2.43   
    f_calc                          = 105.02 
    alpha_beta                      = 8.08   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 114.24 
    fmodel                         = 7.55   
    r_factors                      = 0.43   
    phase_errors                   = 10.06  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 249.20 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.844 micro seconds
Total CPU time: 5.94 minutes
from_scatterers_fft:    629 calls, 104.60 s
gradients_fft:          573 calls, 101.29 s

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

# Date 2008-01-16 Time 00:51:56 PST -0800 (1200473516.90 s)
Start R-work = 0.5043, R-free = 0.4938 (no bulk solvent and anisotropic scale)
Final R-work = 0.1402, R-free = 0.1838 (no bulk solvent and anisotropic scale)

Start R-work = 0.4961, R-free = 0.4861
Final R-work = 0.1236, R-free = 0.1672