# Date 2008-01-16 Time 02:25:06 PST -0800 (1200479106.40 s)
#phil __OFF__

Command line arguments: "../817.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 24270
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 817

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 47.6339, 85.5261, 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: (70.6012, 47.6339, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.007 1.9813
Completeness in resolution range: 0.949954
Completeness with d_max=infinity: 0.947015

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0070
                             d_min =   1.9813

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.6339, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.007 1.9813
Completeness in resolution range: 0.949954
Completeness with d_max=infinity: 0.947015

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0074 -  4.2395 [2171/2199]  1955   216   9.9%
  bin  2:  4.2395 -  3.3776 [2066/2089]  1859   207  10.0%
  bin  3:  3.3776 -  2.9544 [2051/2073]  1843   208  10.1%
  bin  4:  2.9544 -  2.6859 [2043/2062]  1846   197   9.6%
  bin  5:  2.6859 -  2.4944 [2028/2057]  1819   209  10.3%
  bin  6:  2.4944 -  2.3479 [1998/2039]  1802   196   9.8%
  bin  7:  2.3479 -  2.2307 [1982/2017]  1780   202  10.2%
  bin  8:  2.2307 -  2.1339 [2007/2046]  1810   197   9.8%
  bin  9:  2.1339 -  2.0519 [1995/2026]  1798   197   9.9%
  bin 10:  2.0519 -  1.9813 [1248/2013]  1118   130  10.4%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_817/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 19
        2.42 -     3.04: 2184
        3.04 -     3.66: 4658
        3.66 -     4.28: 8968
        4.28 -     4.90: 12379
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.902 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  1.927 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  1.964 3.040 -x+1/2,-y+1,z-1/2
  " O   TYR A 214 " - " O   HOH Z 204 "  2.092 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 28203 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_817/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_817/model_refine_001.geo

CPU time processing inputs: 9.26


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 47.63395 85.5261 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: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4618   r_free= 0.4510   ksol= 0.00   Bsol= 0.00   scale= 0.803    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.263199                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0074 -  4.7285 0.99   1403  154 0.3800 0.3624      6.5616      6.5047|
|  2:  4.7285 -  3.7728 0.99   1363  150 0.3697 0.4006      6.7387      6.7951|
|  3:  3.7728 -  3.3017 0.99   1318  154 0.4192 0.3719      6.6367      6.5997|
|  4:  3.3017 -  3.0024 0.99   1327  141 0.4413 0.4139      6.4932      6.4085|
|  5:  3.0024 -  2.7887 0.99   1301  148 0.4911 0.4943       6.362      6.4074|
|  6:  2.7887 -  2.6252 0.98   1296  146 0.4879 0.5148      6.2554       6.195|
|  7:  2.6252 -  2.4944 0.99   1314  144 0.4863 0.4133      6.2362      6.1486|
|  8:  2.4944 -  2.3862 0.99   1281  144 0.5079 0.4940      6.1637      6.1736|
|  9:  2.3862 -  2.2947 0.98   1299  140 0.5269 0.5082      6.1268      6.1114|
| 10:  2.2947 -  2.2158 0.98   1271  141 0.5021 0.5284      6.0951      6.1187|
| 11:  2.2158 -  2.1467 0.98   1285  146 0.5063 0.4683      6.0309      6.0393|
| 12:  2.1467 -  2.0855 0.99   1278  139 0.5259 0.5643      5.9714      6.0065|
| 13:  2.0855 -  2.0307 0.97   1266  137 0.5287 0.4971      5.8762      5.8455|
| 14:  2.0307 -  1.9813 0.49    628   75 0.5488 0.5026      5.8375      5.7264|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0074 -  4.7285  1403   154  0.72  32.89   0.81     0.74      65676.68|
|  2:  4.7285 -  3.7728  1363   150  0.74  32.17   0.90     0.78      88974.72|
|  3:  3.7728 -  3.3017  1318   154  0.65  39.81   0.84     0.75      94766.12|
|  4:  3.3017 -  3.0024  1327   141  0.57  45.96   0.81     0.65      84607.59|
|  5:  3.0024 -  2.7887  1301   148  0.48  53.52   0.75     0.56      73059.21|
|  6:  2.7887 -  2.6252  1296   146  0.47  54.42   0.75     0.54      62176.97|
|  7:  2.6252 -  2.4944  1314   144  0.49  53.18   0.74     0.54      55112.89|
|  8:  2.4944 -  2.3862  1281   144  0.46  55.51   0.73     0.53      50688.43|
|  9:  2.3862 -  2.2947  1299   140  0.41  59.45   0.72     0.47      49487.05|
| 10:  2.2947 -  2.2158  1271   141  0.38  61.42   0.77     0.44      47675.29|
| 11:  2.2158 -  2.1467  1285   146  0.35  64.08   0.77     0.41      45677.08|
| 12:  2.1467 -  2.0855  1278   139  0.33  65.14   0.75     0.41      43009.67|
| 13:  2.0855 -  2.0307  1266   137  0.31  67.23   0.72     0.38      37318.60|
| 14:  2.0307 -  1.9813   628    75  0.32  65.90   0.72     0.36      29772.83|
|alpha:            min =        0.36 max =            0.78 mean =         0.55|
|beta:             min =    29772.83 max =        94766.12 mean =     60581.83|
|figures of merit: min =        0.00 max =            1.00 mean =         0.49|
|phase err.(work): min =        0.00 max =           90.00 mean =        52.86|
|phase err.(test): min =        0.00 max =           89.85 mean =        52.86|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.149657             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.218   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.951071              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.292   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      168 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      680 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1516 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2593 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3891 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5073 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6520 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7742 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.894 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.093    4.900  1.196 |       1.771 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.018)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.018)------------------------------------------|
|    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: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4686   r_free= 0.4588   ksol= 0.00   Bsol= 0.00   scale= 0.772    |
|                                                                             |
| 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:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.265332                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4539   r_free= 0.4413   ksol= 0.30   Bsol= 20.00   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.69,10.71,7.47,0.00,0.00,0.00); trace/3= 8.29                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.258743                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.362382             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.157   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.872227              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.843   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4539      final r-factor (work) = 0.3624          |
| start r-factor (free) = 0.4413      final r-factor (free) = 0.3868          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 86.3559 = 10.36 * 0.50 * 6.2653 + 1.00 * 53.8941                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.9822 = 10.36 * 0.50 * 6.1462 + 1.00 * 0.1375                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3624      final r-factor (work) = 0.3108          |
| start r-factor (free) = 0.3868      final r-factor (free) = 0.3516          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3752 = 0.87 * 1.00 * 6.1462 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2775 = 0.87 * 1.00 * 6.0339 + 1.00 * 0.0145                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.018)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.19   12.00    None  None   None       |
|    all(noH): 2823   0      0.00    90.19   12.00    None  None   None       |
|    Sol.    : 438    0      0.00    90.19   27.32    None  None   None       |
|    Mac.    : 2385   0      0.00    80.28   9.18     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 -   9.019: 1562   |   5:    45.093 -  54.112:   43        |
|      1:     9.019 -  18.037:  650   |   6:    54.112 -  63.130:   17        |
|      2:    18.037 -  27.056:  304   |   7:    63.130 -  72.149:    9        |
|      3:    27.056 -  36.075:  150   |   8:    72.149 -  81.168:    2        |
|      4:    36.075 -  45.093:   83   |   9:    81.168 -  90.186:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3108 r_free = 0.3516             target_work(ml) = 6.002         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3105 r_free = 0.3512             target_work(ml) = 6.001         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3105   r_free= 0.3512   ksol= 0.30   Bsol= 20.00   scale= 1.081   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.69,10.71,7.47,0.00,0.00,0.00); trace/3= 8.29                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.43 A                  |
| x-ray target function (ml) for work reflections: 6.000818                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3081   r_free= 0.3460   ksol= 0.31   Bsol= 45.27   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.50,6.79,4.70,0.00,0.00,0.00); trace/3= 5.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 6.002338                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.148184              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.763   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.444189              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 118.969  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3081      final r-factor (work) = 0.2231          |
| start r-factor (free) = 0.3460      final r-factor (free) = 0.2711          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.6669 = 5.15 * 0.50 * 6.0330 + 1.00 * 0.1375                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.1348 = 5.15 * 0.50 * 5.8492 + 1.00 * 0.0783                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2231      final r-factor (work) = 0.2028          |
| start r-factor (free) = 0.2711      final r-factor (free) = 0.2530          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6138 = 0.44 * 1.00 * 5.8492 + 1.00 * 0.0157                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5367 = 0.44 * 1.00 * 5.6851 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.018)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.89   12.40    None  None   None       |
|    all(noH): 2823   0      0.00    84.89   12.40    None  None   None       |
|    Sol.    : 438    0      1.11    84.89   32.66    None  None   None       |
|    Mac.    : 2385   0      0.00    80.90   8.68     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.489: 1543   |   5:    42.444 -  50.933:   97        |
|      1:     8.489 -  16.978:  665   |   6:    50.933 -  59.421:   39        |
|      2:    16.978 -  25.466:  211   |   7:    59.421 -  67.910:   14        |
|      3:    25.466 -  33.955:  137   |   8:    67.910 -  76.399:    4        |
|      4:    33.955 -  42.444:  109   |   9:    76.399 -  84.888:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2028 r_free = 0.2530             target_work(ml) = 5.655         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2027 r_free = 0.2531             target_work(ml) = 5.655         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2027   r_free= 0.2531   ksol= 0.31   Bsol= 45.27   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.50,6.79,4.70,0.00,0.00,0.00); trace/3= 5.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.654639                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2013   r_free= 0.2522   ksol= 0.31   Bsol= 45.27   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.42,4.22,3.50,0.00,0.00,0.00); trace/3= 3.38                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.28 A                  |
| x-ray target function (ml) for work reflections: 5.653956                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.566504              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.554  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.260509              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.179  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2013      final r-factor (work) = 0.1447          |
| start r-factor (free) = 0.2522      final r-factor (free) = 0.1844          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.0704 = 4.57 * 0.50 * 5.6900 + 1.00 * 0.0785                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.6750 = 4.57 * 0.50 * 5.5205 + 1.00 * 0.0704                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1447      final r-factor (work) = 0.1342          |
| start r-factor (free) = 0.1844      final r-factor (free) = 0.1754          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4495 = 0.26 * 1.00 * 5.5205 + 1.00 * 0.0114                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.4131 = 0.26 * 1.00 * 5.3060 + 1.00 * 0.0308                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.018)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.47   12.34    None  None   None       |
|    all(noH): 2823   0      0.00    82.47   12.34    None  None   None       |
|    Sol.    : 438    0      1.53    82.47   33.97    None  None   None       |
|    Mac.    : 2385   0      0.00    81.00   8.37     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 -   8.247: 1593   |   5:    41.236 -  49.484:  111        |
|      1:     8.247 -  16.495:  636   |   6:    49.484 -  57.731:   41        |
|      2:    16.495 -  24.742:  169   |   7:    57.731 -  65.978:   19        |
|      3:    24.742 -  32.989:  122   |   8:    65.978 -  74.225:    6        |
|      4:    32.989 -  41.236:  122   |   9:    74.225 -  82.472:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1342 r_free = 0.1754             target_work(ml) = 5.283         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1340 r_free = 0.1753             target_work(ml) = 5.282         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1340   r_free= 0.1753   ksol= 0.31   Bsol= 45.27   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.42,4.22,3.50,0.00,0.00,0.00); trace/3= 3.38                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.281899                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1340   r_free= 0.1751   ksol= 0.32   Bsol= 45.27   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.01,3.13,3.04,0.00,0.00,0.00); trace/3= 2.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.283420                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.766129              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 113.386  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.357201              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.546   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1340      final r-factor (work) = 0.1245          |
| start r-factor (free) = 0.1751      final r-factor (free) = 0.1665          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7598 = 1.77 * 0.50 * 5.3103 + 1.00 * 0.0704                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.6954 = 1.77 * 0.50 * 5.2531 + 1.00 * 0.0565                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1245      final r-factor (work) = 0.1207          |
| start r-factor (free) = 0.1665      final r-factor (free) = 0.1662          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 17.6674 = 3.36 * 1.00 * 5.2531 + 1.00 * 0.0315                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 17.6311 = 3.36 * 1.00 * 5.2128 + 1.00 * 0.1305                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.018)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.63  13.05    None  None   None       |
|    all(noH): 2823   0      0.00    107.63  13.05    None  None   None       |
|    Sol.    : 438    0      1.07    82.35   37.76    None  None   None       |
|    Mac.    : 2385   0      0.00    107.63  8.51     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.763: 1883   |   5:    53.815 -  64.578:   72        |
|      1:    10.763 -  21.526:  457   |   6:    64.578 -  75.341:   25        |
|      2:    21.526 -  32.289:  150   |   7:    75.341 -  86.104:   10        |
|      3:    32.289 -  43.052:  110   |   8:    86.104 -  96.867:    3        |
|      4:    43.052 -  53.815:  111   |   9:    96.867 - 107.630:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1207 r_free = 0.1662             target_work(ml) = 5.212         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1205 r_free = 0.1661             target_work(ml) = 5.212         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1205   r_free= 0.1661   ksol= 0.32   Bsol= 45.27   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.01,3.13,3.04,0.00,0.00,0.00); trace/3= 2.73                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.211587                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1205   r_free= 0.1660   ksol= 0.32   Bsol= 45.27   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.15,3.01,3.13,0.00,0.00,0.00); trace/3= 2.76                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.211506                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.523400              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 139.888  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.936706              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.180   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1205      final r-factor (work) = 0.1205          |
| start r-factor (free) = 0.1660      final r-factor (free) = 0.1660          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0267 = 1.52 * 0.50 * 5.2123 + 1.00 * 0.0565                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0266 = 1.52 * 0.50 * 5.2115 + 1.00 * 0.0570                               |
|-----------------------------------------------------------------------------|
| number of iterations = 1       |    number of function evaluations = 1      |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1205      final r-factor (work) = 0.1210          |
| start r-factor (free) = 0.1660      final r-factor (free) = 0.1659          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.2201 = 1.94 * 1.00 * 5.2115 + 1.00 * 0.1269                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.1092 = 1.94 * 1.00 * 5.2121 + 1.00 * 0.0148                              |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 8      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.018)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.05   12.96    None  None   None       |
|    all(noH): 2823   0      0.00    99.05   12.96    None  None   None       |
|    Sol.    : 438    0      1.15    82.67   37.67    None  None   None       |
|    Mac.    : 2385   0      0.00    99.05   8.42     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.905: 1818   |   5:    49.526 -  59.432:   88        |
|      1:     9.905 -  19.811:  486   |   6:    59.432 -  69.337:   37        |
|      2:    19.811 -  29.716:  151   |   7:    69.337 -  79.242:   20        |
|      3:    29.716 -  39.621:  112   |   8:    79.242 -  89.147:    7        |
|      4:    39.621 -  49.526:  103   |   9:    89.147 -  99.053:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1210 r_free = 0.1659             target_work(ml) = 5.211         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1210 r_free = 0.1659             target_work(ml) = 5.211         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1210   r_free= 0.1659   ksol= 0.32   Bsol= 45.27   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.15,3.01,3.13,0.00,0.00,0.00); trace/3= 2.76                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.211355                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0074 -  4.7285 0.99   1403  154 0.1000 0.1298      5.3926      5.5275|
|  2:  4.7285 -  3.7728 0.99   1363  150 0.0882 0.1124      5.4527      5.6614|
|  3:  3.7728 -  3.3017 0.99   1318  154 0.1127 0.1593      5.5289      5.8852|
|  4:  3.3017 -  3.0024 0.99   1327  141 0.1328 0.1653      5.5109      5.6875|
|  5:  3.0024 -  2.7887 0.99   1301  148 0.1457 0.1726      5.4077      5.5282|
|  6:  2.7887 -  2.6252 0.98   1296  146 0.1363 0.2115      5.2897      5.5625|
|  7:  2.6252 -  2.4944 0.99   1314  144 0.1356 0.1773      5.2342      5.4588|
|  8:  2.4944 -  2.3862 0.99   1281  144 0.1266 0.1786      5.1328      5.3346|
|  9:  2.3862 -  2.2947 0.98   1299  140 0.1282 0.1952      5.1051      5.3857|
| 10:  2.2947 -  2.2158 0.98   1271  141 0.1280 0.1900      5.0528      5.2927|
| 11:  2.2158 -  2.1467 0.98   1285  146 0.1259 0.1782      5.0057      5.2833|
| 12:  2.1467 -  2.0855 0.99   1278  139 0.1212 0.1762      4.9273       5.183|
| 13:  2.0855 -  2.0307 0.97   1266  137 0.1274 0.1903      4.8605      5.1336|
| 14:  2.0307 -  1.9813 0.49    628   75 0.1188 0.1912      4.7739      4.9914|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0074 -  4.7285  1403   154  0.94   9.19   0.97     0.95       7360.91|
|  2:  4.7285 -  3.7728  1363   150  0.95   8.33   1.01     0.99       9196.69|
|  3:  3.7728 -  3.3017  1318   154  0.93  12.05   1.02     1.02      11452.32|
|  4:  3.3017 -  3.0024  1327   141  0.91  14.77   1.00     0.97      11134.73|
|  5:  3.0024 -  2.7887  1301   148  0.89  17.37   0.99     0.97       9546.58|
|  6:  2.7887 -  2.6252  1296   146  0.89  16.99   0.98     0.96       8054.82|
|  7:  2.6252 -  2.4944  1314   144  0.90  16.36   0.99     0.95       6836.67|
|  8:  2.4944 -  2.3862  1281   144  0.89  16.94   0.99     0.96       6191.00|
|  9:  2.3862 -  2.2947  1299   140  0.90  16.86   0.99     0.96       5781.82|
| 10:  2.2947 -  2.2158  1271   141  0.89  17.37   0.98     0.94       5220.85|
| 11:  2.2158 -  2.1467  1285   146  0.89  17.25   0.99     0.94       4775.14|
| 12:  2.1467 -  2.0855  1278   139  0.91  15.83   0.98     0.97       4261.15|
| 13:  2.0855 -  2.0307  1266   137  0.88  18.10   0.99     0.98       3895.46|
| 14:  2.0307 -  1.9813   628    75  0.89  16.92   0.97     0.93       3178.57|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     3178.57 max =        11452.32 mean =      7099.35|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        15.17|
|phase err.(test): min =        0.00 max =           89.56 mean =        14.56|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1209   r_free= 0.1659   ksol= 0.32   Bsol= 53.76   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.58,0.19,0.39,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.211276                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1209   r_free= 0.1659   ksol= 0.32   Bsol= 53.76   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.58,0.19,0.39,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.211276                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0074 -  4.7285 0.99   1403  154 0.1002 0.1303      5.3943       5.531|
|  2:  4.7285 -  3.7728 0.99   1363  150 0.0887 0.1131      5.4567      5.6677|
|  3:  3.7728 -  3.3017 0.99   1318  154 0.1129 0.1595      5.5313      5.8856|
|  4:  3.3017 -  3.0024 0.99   1327  141 0.1327 0.1652      5.5102      5.6876|
|  5:  3.0024 -  2.7887 0.99   1301  148 0.1454 0.1722      5.4055      5.5262|
|  6:  2.7887 -  2.6252 0.98   1296  146 0.1360 0.2111      5.2881      5.5609|
|  7:  2.6252 -  2.4944 0.99   1314  144 0.1354 0.1778      5.2331      5.4594|
|  8:  2.4944 -  2.3862 0.99   1281  144 0.1264 0.1780       5.132      5.3325|
|  9:  2.3862 -  2.2947 0.98   1299  140 0.1282 0.1954      5.1047      5.3857|
| 10:  2.2947 -  2.2158 0.98   1271  141 0.1280 0.1898      5.0521      5.2918|
| 11:  2.2158 -  2.1467 0.98   1285  146 0.1258 0.1782       5.005      5.2826|
| 12:  2.1467 -  2.0855 0.99   1278  139 0.1212 0.1764       4.927      5.1833|
| 13:  2.0855 -  2.0307 0.97   1266  137 0.1275 0.1903        4.86      5.1328|
| 14:  2.0307 -  1.9813 0.49    628   75 0.1187 0.1910      4.7729      4.9897|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0074 -  4.7285  1403   154  0.94   9.24   0.97     0.95       7403.11|
|  2:  4.7285 -  3.7728  1363   150  0.95   8.40   1.01     1.00       9277.41|
|  3:  3.7728 -  3.3017  1318   154  0.93  12.11   1.03     1.02      11550.68|
|  4:  3.3017 -  3.0024  1327   141  0.91  14.78   1.00     0.98      11126.37|
|  5:  3.0024 -  2.7887  1301   148  0.89  17.34   1.00     0.97       9513.84|
|  6:  2.7887 -  2.6252  1296   146  0.89  16.95   0.99     0.96       8027.91|
|  7:  2.6252 -  2.4944  1314   144  0.90  16.35   0.99     0.96       6825.15|
|  8:  2.4944 -  2.3862  1281   144  0.89  16.94   1.00     0.97       6182.36|
|  9:  2.3862 -  2.2947  1299   140  0.90  16.85   1.00     0.96       5773.39|
| 10:  2.2947 -  2.2158  1271   141  0.89  17.35   0.99     0.95       5210.44|
| 11:  2.2158 -  2.1467  1285   146  0.89  17.23   0.99     0.95       4766.47|
| 12:  2.1467 -  2.0855  1278   139  0.91  15.82   0.99     0.97       4257.72|
| 13:  2.0855 -  2.0307  1266   137  0.88  18.09   1.00     0.99       3887.97|
| 14:  2.0307 -  1.9813   628    75  0.89  16.90   0.98     0.94       3168.83|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     3168.83 max =        11550.68 mean =      7106.65|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        15.17|
|phase err.(test): min =        0.00 max =           89.90 mean =        14.56|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.018)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.91    101.96  15.87    None  None   None       |
|    all(noH): 2823   0      2.91    101.96  15.87    None  None   None       |
|    Sol.    : 438    0      4.06    85.58   40.58    None  None   None       |
|    Mac.    : 2385   0      2.91    101.96  11.33    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.912 -  12.817: 1818   |   5:    52.438 -  62.343:   88        |
|      1:    12.817 -  22.722:  486   |   6:    62.343 -  72.249:   37        |
|      2:    22.722 -  32.628:  151   |   7:    72.249 -  82.154:   20        |
|      3:    32.628 -  42.533:  112   |   8:    82.154 -  92.059:    7        |
|      4:    42.533 -  52.438:  103   |   9:    92.059 - 101.964:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 346         
Filter by distance & map next to the model:
   mapped sites are within: 0.141 - 5.560
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 340 from: 346
   mapped sites are within: 0.721 - 5.560

peak=    9.372 closest distance to " CG2 VAL A 230 " =    1.346
peak=    7.665 closest distance to " CG2 VAL A 296 " =    1.189
peak=    6.237 closest distance to " CG  LEU A   5 " =    1.198
peak=    5.886 closest distance to " NH2 ARG A  56 " =    2.306
peak=    5.399 closest distance to " O   HOH Z 120 " =    1.080
peak=    5.227 closest distance to " CG  PRO A  54 " =    1.214
peak=    5.217 closest distance to " CB  VAL A 230 " =    1.212
peak=    5.209 closest distance to " CB  GLN A 223 " =    1.399
peak=    5.162 closest distance to " O   HOH Z 247 " =    1.497
peak=    5.151 closest distance to " CG  PRO A 198 " =    1.237
peak=    5.145 closest distance to " CD1AILE A 234 " =    1.018
peak=    5.074 closest distance to " CB  PRO A  54 " =    0.951
peak=    4.947 closest distance to " CG  LEU A 228 " =    1.223
peak=    4.941 closest distance to " CB  SER A  63 " =    1.304
peak=    4.746 closest distance to " CA  TYR A  30 " =    1.000
peak=    4.726 closest distance to " CB  ARG A 275 " =    0.902
peak=    4.602 closest distance to " O   HOH Z 102 " =    1.386
peak=    4.560 closest distance to " O   HOH Z 403 " =    1.811
peak=    4.548 closest distance to " C   PRO A 198 " =    1.477
peak=    4.539 closest distance to " O   HOH Z  48 " =    1.801
peak=    4.522 closest distance to " CB  GLN A 183 " =    1.254
peak=    4.520 closest distance to " O   HOH Z 316 " =    2.697
peak=    4.504 closest distance to " CG  PRO A 213 " =    1.277
peak=    4.446 closest distance to " O   HOH Z 124 " =    1.325
peak=    4.428 closest distance to " O   HOH Z 433 " =    1.581
peak=    4.374 closest distance to " CB  TYR A 169 " =    0.787
peak=    4.360 closest distance to " O   HOH Z 130 " =    2.845
peak=    4.346 closest distance to " CB  GLU A 128 " =    1.190
peak=    4.343 closest distance to " O   HOH Z 402 " =    1.558
peak=    4.333 closest distance to " O   HOH Z  80 " =    1.934
peak=    4.329 closest distance to " O   HOH Z 279 " =    1.241
peak=    4.304 closest distance to " O   HOH Z 232 " =    2.282
peak=    4.279 closest distance to " CG  PRO A 280 " =    0.818
peak=    4.277 closest distance to " CB  VAL A 296 " =    1.016
peak=    4.265 closest distance to " CG  PRO A  90 " =    1.145
peak=    4.220 closest distance to " O   HOH Z 411 " =    3.452
peak=    4.217 closest distance to " O   HOH Z  63 " =    1.940
peak=    4.214 closest distance to " O   HOH Z 128 " =    1.703
peak=    4.178 closest distance to " CD  ARG A 159 " =    0.828
peak=    4.164 closest distance to " O   HOH Z  91 " =    2.409
peak=    4.148 closest distance to " CD2 LEU A 228 " =    1.249
peak=    4.128 closest distance to " O   HOH Z 371 " =    3.241
peak=    4.118 closest distance to " O   HOH Z 193 " =    1.777
peak=    4.099 closest distance to " O   HOH Z  40 " =    1.851
peak=    4.098 closest distance to " O   HOH Z 272 " =    1.969
peak=    4.088 closest distance to " NH2 ARG A 156 " =    1.106
peak=    4.087 closest distance to " O   HOH Z  44 " =    2.335
peak=    4.086 closest distance to " NE2 GLN A  11 " =    0.981
peak=    4.067 closest distance to " O   HOH Z 298 " =    1.924
peak=    4.046 closest distance to " O   HOH Z 234 " =    3.706
peak=    4.043 closest distance to " CA  VAL A  41 " =    0.835
peak=    4.037 closest distance to " CB  TRP A 179 " =    1.322
peak=    4.034 closest distance to " CA  ALA A  21 " =    1.278
peak=    4.022 closest distance to " CG1 ILE A  33 " =    1.334
peak=    4.017 closest distance to " O   HOH Z 389 " =    1.878
peak=    4.016 closest distance to " CB  PRO A  54 " =    1.368
peak=    4.015 closest distance to " O   HOH Z 126 " =    1.541
peak=    3.991 closest distance to " O   HOH Z 134 " =    1.630
peak=    3.983 closest distance to " C   SER A  32 " =    1.063
peak=    3.982 closest distance to " O   HOH Z 332 " =    1.625
peak=    3.948 closest distance to " O   HOH Z 263 " =    1.590
peak=    3.934 closest distance to " O   HOH Z 423 " =    1.734
peak=    3.933 closest distance to " O   HOH Z  48 " =    2.029
peak=    3.930 closest distance to " NZ  LYS A 117 " =    3.083
peak=    3.930 closest distance to " CB  ASN A 148 " =    1.296
peak=    3.927 closest distance to " O   HOH Z  97 " =    2.025
peak=    3.925 closest distance to " CD  ARG A 269 " =    1.080
peak=    3.923 closest distance to " O   HOH Z 345 " =    3.198
peak=    3.916 closest distance to " CB  TRP A 266 " =    1.053
peak=    3.905 closest distance to " O   HOH Z 112 " =    1.567
peak=    3.904 closest distance to " CG2 THR A 221 " =    1.091
peak=    3.899 closest distance to " O   HOH Z 346 " =    1.526
peak=    3.870 closest distance to " O   HOH Z 245 " =    1.381
peak=    3.863 closest distance to " CB  SER A   3 " =    1.260
peak=    3.858 closest distance to " O   HOH Z  20 " =    1.625
peak=    3.841 closest distance to " O   HOH Z   4 " =    1.646
peak=    3.840 closest distance to " O   HOH Z 394 " =    1.548
peak=    3.839 closest distance to " O   HOH Z 142 " =    1.386
peak=    3.838 closest distance to " O   HOH Z 132 " =    2.688
peak=    3.834 closest distance to " O   HOH Z 369 " =    2.235
peak=    3.834 closest distance to " O   ASP A 124 " =    1.180
peak=    3.798 closest distance to " OE1 GLN A  11 " =    1.864
peak=    3.792 closest distance to " OE1 GLU A   2 " =    2.068
peak=    3.787 closest distance to " CB  GLU A 277 " =    3.708
peak=    3.784 closest distance to " O   HOH Z 357 " =    2.052
peak=    3.783 closest distance to " OD1 ASN A  69 " =    2.568
peak=    3.782 closest distance to " O   HOH Z 395 " =    1.540
peak=    3.769 closest distance to " CB  ARG A 190 " =    1.769
peak=    3.766 closest distance to " O   HOH Z  11 " =    1.333
peak=    3.765 closest distance to " O   HOH Z 210 " =    1.013
peak=    3.762 closest distance to " O   GLY A  23 " =    2.439
peak=    3.754 closest distance to " CG  PRO A 243 " =    1.148
peak=    3.753 closest distance to " O   HOH Z 425 " =    1.354
peak=    3.752 closest distance to " CB  PRO A 198 " =    1.104
peak=    3.751 closest distance to " O   HOH Z 214 " =    2.468
peak=    3.748 closest distance to " O   HOH Z 236 " =    1.863
peak=    3.747 closest distance to " O   HOH Z 163 " =    1.497
peak=    3.745 closest distance to " CZ  PHE A 218 " =    1.221
peak=    3.744 closest distance to " CD2 LEU A   5 " =    1.148
peak=    3.742 closest distance to " O   HOH Z  61 " =    1.516
peak=    3.733 closest distance to " CD BLYS A 290 " =    0.984
peak=    3.728 closest distance to " CB  GLU A 152 " =    1.112
peak=    3.724 closest distance to " O   HOH Z 404 " =    1.565
peak=    3.723 closest distance to " CE1 TYR A 186 " =    1.311
peak=    3.720 closest distance to " O   HOH Z  54 " =    2.247
peak=    3.719 closest distance to " O   HOH Z  15 " =    2.281
peak=    3.712 closest distance to " O   HOH Z  68 " =    1.666
peak=    3.712 closest distance to " CA  GLY A  80 " =    1.009
peak=    3.708 closest distance to " O   HOH Z 280 " =    2.956
peak=    3.708 closest distance to " O   HOH Z 203 " =    1.701
peak=    3.702 closest distance to " CG1 VAL A 153 " =    1.006
peak=    3.701 closest distance to " O   HOH Z 431 " =    1.041
peak=    3.697 closest distance to " O   HOH Z 406 " =    1.607
peak=    3.687 closest distance to " CG1BVAL A  72 " =    1.714
peak=    3.683 closest distance to " O   HOH Z 193 " =    2.215
peak=    3.676 closest distance to " OG1 THR A 294 " =    2.232
peak=    3.675 closest distance to " O   HOH Z 189 " =    2.727
peak=    3.671 closest distance to " CB  ALA A 100 " =    1.313
peak=    3.657 closest distance to " O   HOH Z 344 " =    2.964
peak=    3.656 closest distance to " CA  ASN A 176 " =    1.092
peak=    3.652 closest distance to " CB  SER A 141 " =    1.124
peak=    3.648 closest distance to " O   HOH Z  88 " =    3.129
peak=    3.647 closest distance to " O   HOH Z 303 " =    2.207
peak=    3.639 closest distance to " O   HOH Z 295 " =    1.571
peak=    3.635 closest distance to " CB  ALA A 291 " =    1.333
peak=    3.632 closest distance to " O   HOH Z  78 " =    1.762
peak=    3.631 closest distance to " O   HOH Z  78 " =    2.138
peak=    3.618 closest distance to " O  BHOH Z  74 " =    1.262
peak=    3.616 closest distance to " O   HOH Z 108 " =    2.519
peak=    3.606 closest distance to " CG  ARG A  66 " =    0.972
peak=    3.606 closest distance to " CA  ASP A 191 " =    0.815
peak=    3.604 closest distance to " N   ASN A  39 " =    1.240
peak=    3.603 closest distance to " CB  VAL A 265 " =    1.242
peak=    3.602 closest distance to " CD1 LEU A 300 " =    1.126
peak=    3.594 closest distance to " CD  LYS A 119 " =    1.858
peak=    3.594 closest distance to " CG  MET A 185 " =    1.179
peak=    3.593 closest distance to " CB  LEU A 228 " =    1.401
peak=    3.578 closest distance to " O   HOH Z 427 " =    2.981
peak=    3.566 closest distance to " CA  ARG A 195 " =    1.172
peak=    3.563 closest distance to " O   HOH Z 368 " =    2.128
peak=    3.562 closest distance to " CD1 LEU A  96 " =    0.738
peak=    3.561 closest distance to " CB BVAL A  41 " =    1.235
peak=    3.558 closest distance to " O   HOH Z 133 " =    1.678
peak=    3.553 closest distance to " CB  SER A  28 " =    1.276
peak=    3.552 closest distance to " O   HOH Z 437 " =    2.130
peak=    3.549 closest distance to " O   HOH Z 426 " =    1.545
peak=    3.539 closest distance to " O   HOH Z 131 " =    2.517
peak=    3.538 closest distance to " CB  SER A  62 " =    0.779
peak=    3.534 closest distance to " O   GLY A  91 " =    1.238
peak=    3.524 closest distance to " O   HOH Z  97 " =    2.584
peak=    3.522 closest distance to " O   HOH Z 126 " =    1.875
peak=    3.521 closest distance to " CB  ALA A 137 " =    1.291
peak=    3.520 closest distance to " O   HOH Z 280 " =    2.525
peak=    3.516 closest distance to " O   HOH Z 423 " =    3.136
peak=    3.515 closest distance to " O   HOH Z 383 " =    2.048
peak=    3.509 closest distance to " O   GLN A 278 " =    1.311
peak=    3.508 closest distance to " CE  LYS A 119 " =    1.171
peak=    3.506 closest distance to " N   TYR A 247 " =    1.233
peak=    3.503 closest distance to " O   HOH Z 387 " =    2.916
peak=    3.502 closest distance to " CB  ASN A 187 " =    1.492
peak=    3.501 closest distance to " O   HOH Z 133 " =    2.330
peak=    3.501 closest distance to " O   HOH Z  85 " =    1.078
peak=    3.498 closest distance to " O   THR A  31 " =    1.562
peak=    3.497 closest distance to " CB  ALA A 242 " =    1.013
peak=    3.494 closest distance to " CB  ARG A  79 " =    1.341
peak=    3.492 closest distance to " CA  LYS A 117 " =    1.284
peak=    3.488 closest distance to " CG1BVAL A 121 " =    1.251
peak=    3.488 closest distance to " O   HOH Z 197 " =    1.965
peak=    3.487 closest distance to " O   HOH Z 417 " =    3.273
peak=    3.481 closest distance to " CE1 HIS A 108 " =    1.146
peak=    3.479 closest distance to " O   HOH Z 422 " =    2.620
peak=    3.478 closest distance to " NZ  LYS A  76 " =    1.594
peak=    3.474 closest distance to " O   HOH Z 185 " =    1.739
peak=    3.466 closest distance to " O   HOH Z 130 " =    1.145
peak=    3.464 closest distance to " O   HOH Z  44 " =    1.787
peak=    3.462 closest distance to " O   HOH Z 414 " =    1.503
peak=    3.459 closest distance to " CG BARG A 102 " =    1.949
peak=    3.458 closest distance to " O   HOH Z 261 " =    1.803
peak=    3.456 closest distance to " N   SER A 164 " =    1.059
peak=    3.455 closest distance to " CA  ALA A  51 " =    1.095
peak=    3.447 closest distance to " CG  ARG A 138 " =    1.213
peak=    3.445 closest distance to " CB  SER A 216 " =    0.866
peak=    3.443 closest distance to " O   HOH Z 136 " =    1.323
peak=    3.433 closest distance to " O   HOH Z 104 " =    3.102
peak=    3.428 closest distance to " NH2BARG A 145 " =    2.045
peak=    3.421 closest distance to " O   HOH Z 301 " =    1.888
peak=    3.416 closest distance to " N   LYS A 166 " =    0.983
peak=    3.416 closest distance to " CD1 LEU A 101 " =    1.236
peak=    3.414 closest distance to " CA  ASP A 140 " =    1.213
peak=    3.411 closest distance to " O   HOH Z 227 " =    1.683
peak=    3.406 closest distance to " CG1 VAL A 296 " =    1.168
peak=    3.404 closest distance to " CG AARG A 275 " =    1.143
peak=    3.402 closest distance to " CA  VAL A 125 " =    1.563
peak=    3.399 closest distance to " O   HOH Z 248 " =    1.760
peak=    3.398 closest distance to " O   HOH Z 355 " =    1.838
peak=    3.397 closest distance to " CB  ASP A 124 " =    0.726
peak=    3.395 closest distance to " O   HOH Z 189 " =    3.059
peak=    3.394 closest distance to " O   HOH Z 128 " =    1.970
peak=    3.393 closest distance to " CD  LYS A 166 " =    1.423
peak=    3.388 closest distance to " OE1 GLN A  55 " =    1.360
peak=    3.378 closest distance to " O   HOH Z 420 " =    2.125
peak=    3.373 closest distance to " O   HOH Z 327 " =    2.598
peak=    3.372 closest distance to " CA  LEU A 282 " =    1.215
peak=    3.370 closest distance to " O   HOH Z 214 " =    1.299
peak=    3.369 closest distance to " OD2 ASP A 286 " =    2.883
peak=    3.366 closest distance to " OG BSER A 258 " =    3.393
peak=    3.364 closest distance to " CD2 LEU A 255 " =    1.279
peak=    3.363 closest distance to " CA  MET A  40 " =    1.130
peak=    3.361 closest distance to " CB  ALA A   9 " =    1.582
peak=    3.359 closest distance to " CB  ASN A 142 " =    1.164
peak=    3.358 closest distance to " NH1 ARG A  14 " =    1.182
peak=    3.357 closest distance to " CB  GLN A  58 " =    1.028
peak=    3.354 closest distance to " O   HOH Z 236 " =    1.747
peak=    3.354 closest distance to " CB  GLN A  88 " =    1.272
peak=    3.352 closest distance to " CB  ASN A  39 " =    0.817
peak=    3.352 closest distance to " O   HOH Z 109 " =    2.411
peak=    3.349 closest distance to " NH2 ARG A  79 " =    1.334
peak=    3.342 closest distance to " O   HOH Z 146 " =    1.373
peak=    3.337 closest distance to " CZ  PHE A  38 " =    1.285
peak=    3.336 closest distance to " CA  ALA A 295 " =    1.107
peak=    3.333 closest distance to " CG  MET A 188 " =    0.937
peak=    3.331 closest distance to " OD1 ASN A 217 " =    1.737
peak=    3.326 closest distance to " O   HOH Z 166 " =    1.546
peak=    3.321 closest distance to " O   MET A 105 " =    1.864
peak=    3.321 closest distance to " CD1 LEU A   5 " =    1.392
peak=    3.318 closest distance to " CD2 TRP A 179 " =    1.383
peak=    3.318 closest distance to " ND1 HIS A  81 " =    1.543
peak=    3.314 closest distance to " O   HOH Z 116 " =    1.782
peak=    3.311 closest distance to " CB  MET A  40 " =    0.721
peak=    3.307 closest distance to " CA  ARG A 275 " =    1.859
peak=    3.306 closest distance to " CA  THR A 246 " =    1.067
peak=    3.306 closest distance to " O   GLY A  57 " =    2.443
peak=    3.305 closest distance to " O   ALA A 158 " =    1.316
peak=    3.304 closest distance to " CB  VAL A 202 " =    1.478
peak=    3.302 closest distance to " CB  PRO A 243 " =    1.109
peak=    3.301 closest distance to " CD2 LEU A 297 " =    0.828
peak=    3.298 closest distance to " CB  SER A 273 " =    0.865
peak=    3.289 closest distance to " CD1 TRP A 266 " =    1.203
peak=    3.287 closest distance to " O   HOH Z  54 " =    1.478
peak=    3.283 closest distance to " CG1 ILE A  49 " =    1.685
peak=    3.283 closest distance to " CG2 VAL A 202 " =    1.178
peak=    3.280 closest distance to " O   HOH Z 427 " =    3.077
peak=    3.278 closest distance to " N   VAL A 126 " =    1.529
peak=    3.277 closest distance to " OG BSER A 164 " =    2.075
peak=    3.274 closest distance to " CG  GLN A  58 " =    2.558
peak=    3.274 closest distance to " CA  ALA A 160 " =    0.891
peak=    3.273 closest distance to " CG2 VAL A 197 " =    1.209
peak=    3.272 closest distance to " O   HOH Z 114 " =    1.188
peak=    3.267 closest distance to " O   HOH Z 281 " =    4.478
peak=    3.266 closest distance to " NZ  LYS A 166 " =    3.057
peak=    3.265 closest distance to " O   HOH Z 158 " =    3.105
peak=    3.264 closest distance to " NZ  LYS A 193 " =    1.229
peak=    3.262 closest distance to " CA  MET A 105 " =    1.195
peak=    3.262 closest distance to " CA  GLN A  73 " =    1.405
peak=    3.261 closest distance to " O   HOH Z 374 " =    2.647
peak=    3.257 closest distance to " CZ  PHE A 192 " =    1.153
peak=    3.256 closest distance to " NZ  LYS A 181 " =    1.009
peak=    3.256 closest distance to " CA  VAL A 126 " =    0.906
peak=    3.252 closest distance to " ND2 ASN A 110 " =    1.554
peak=    3.252 closest distance to " O   HOH Z 141 " =    1.522
peak=    3.250 closest distance to " CG2 ILE A 106 " =    0.915
peak=    3.246 closest distance to " CG2 VAL A  78 " =    0.950
peak=    3.246 closest distance to " CA  SER A  87 " =    0.973
peak=    3.246 closest distance to " CA  ALA A 291 " =    0.952
peak=    3.244 closest distance to " O   HOH Z  21 " =    1.812
peak=    3.243 closest distance to " OG  SER A  97 " =    2.617
peak=    3.243 closest distance to " NH1AARG A 145 " =    1.089
peak=    3.233 closest distance to " O   ASP A 200 " =    1.690
peak=    3.232 closest distance to " CD1 LEU A 222 " =    0.722
peak=    3.232 closest distance to " O   HOH Z 366 " =    3.027
peak=    3.231 closest distance to " OG  SER A 206 " =    1.190
peak=    3.229 closest distance to " CA  ILE A 263 " =    0.986
peak=    3.228 closest distance to " O   HOH Z 420 " =    5.560
peak=    3.228 closest distance to " O   HOH Z   1 " =    2.048
peak=    3.227 closest distance to " CA  ALA A 158 " =    1.130
peak=    3.226 closest distance to " CB  LEU A 143 " =    1.191
peak=    3.221 closest distance to " O   HOH Z 155 " =    2.968
peak=    3.220 closest distance to " O   HOH Z 298 " =    5.084
peak=    3.219 closest distance to " CB  TYR A 247 " =    0.985
peak=    3.211 closest distance to " O   ALA A 165 " =    1.363
peak=    3.210 closest distance to " O   HOH Z  48 " =    2.064
peak=    3.207 closest distance to " O   HOH Z 329 " =    2.726
peak=    3.204 closest distance to " OG  SER A  62 " =    3.000
peak=    3.204 closest distance to " CA  ARG A  36 " =    1.112
peak=    3.203 closest distance to " CD  GLU A 152 " =    0.849
peak=    3.200 closest distance to " CB  MET A  47 " =    1.236
peak=    3.200 closest distance to " CG2AVAL A 121 " =    2.016
peak=    3.198 closest distance to " O   HOH Z 336 " =    1.750
peak=    3.198 closest distance to " O   HOH Z 155 " =    1.511
peak=    3.197 closest distance to " O   HOH Z 258 " =    2.371
peak=    3.195 closest distance to " CB  ALA A 248 " =    1.469
peak=    3.195 closest distance to " O   HOH Z 329 " =    3.673
peak=    3.194 closest distance to " CA  THR A 264 " =    0.793
peak=    3.192 closest distance to " O   HOH Z 409 " =    3.553
peak=    3.189 closest distance to " O   THR A 251 " =    1.229
peak=    3.185 closest distance to " CG2 ILE A 120 " =    1.222
peak=    3.183 closest distance to " O   HOH Z 435 " =    1.954
peak=    3.179 closest distance to " CB  ASP A 140 " =    0.817
peak=    3.178 closest distance to " NZ  LYS A 117 " =    1.557
peak=    3.177 closest distance to " NE2 HIS A 115 " =    0.903
peak=    3.173 closest distance to " CA  ASP A 162 " =    1.150
peak=    3.170 closest distance to " CB  GLU A 175 " =    1.279
peak=    3.166 closest distance to " CB  ALA A  71 " =    1.230
peak=    3.166 closest distance to " O   HOH Z  90 " =    3.381
peak=    3.164 closest distance to " OG  SER A 245 " =    1.567
peak=    3.164 closest distance to " OG  SER A  22 " =    2.841
peak=    3.163 closest distance to " C   ALA A 299 " =    0.986
peak=    3.161 closest distance to " O   HOH Z 207 " =    2.386
peak=    3.156 closest distance to " O   HOH Z 222 " =    3.132
peak=    3.155 closest distance to " CA  LEU A 101 " =    1.432
peak=    3.150 closest distance to " O   HOH Z 273 " =    2.885
peak=    3.149 closest distance to " O   HOH Z 368 " =    3.421
peak=    3.148 closest distance to " O   HOH Z  49 " =    1.013
peak=    3.144 closest distance to " O   HOH Z 240 " =    2.001
peak=    3.144 closest distance to " O   HOH Z  89 " =    3.582
peak=    3.139 closest distance to " O   HOH Z 152 " =    2.320
peak=    3.136 closest distance to " CB  ARG A 139 " =    0.865
peak=    3.134 closest distance to " CG2 VAL A 296 " =    1.608
peak=    3.133 closest distance to " CB  ALA A 256 " =    1.124
peak=    3.131 closest distance to " CG  GLN A  11 " =    1.329
peak=    3.129 closest distance to " O   HOH Z 261 " =    1.815
peak=    3.116 closest distance to " O   HOH Z 221 " =    1.151
peak=    3.115 closest distance to " CA  GLN A  88 " =    1.156
peak=    3.109 closest distance to " O   HOH Z  57 " =    1.369
peak=    3.103 closest distance to " O   HOH Z 421 " =    2.077
peak=    3.097 closest distance to " CG2 VAL A 268 " =    0.961
peak=    3.089 closest distance to " O   HOH Z  50 " =    1.946
peak=    3.086 closest distance to " NH2BARG A 102 " =    0.984
peak=    3.082 closest distance to " OH  TYR A 116 " =    1.185
peak=    3.076 closest distance to " O   HOH Z 313 " =    1.757
peak=    3.065 closest distance to " O   HOH Z 175 " =    3.600
peak=    3.062 closest distance to " CG2 ILE A 234 " =    0.971
peak=    3.061 closest distance to " O   HOH Z 277 " =    2.668
peak=    3.057 closest distance to " O   HOH Z 162 " =    1.770
peak=    3.054 closest distance to " O   HOH Z 145 " =    2.606
peak=    3.036 closest distance to " CZ3 TRP A  85 " =    0.905
peak=    3.033 closest distance to " O   HOH Z 147 " =    1.762
peak=    3.025 closest distance to " CG1 ILE A 120 " =    1.011
peak=    3.017 closest distance to " O   HOH Z 353 " =    2.720
peak=    3.007 closest distance to " O   HOH Z 193 " =    1.538

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 213         
Filter by distance & map next to the model:
   mapped sites are within: 0.829 - 5.543
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 211 from: 213
   mapped sites are within: 0.829 - 5.543

peak=   -4.952 closest distance to " CG2 VAL A 230 " =    0.907
peak=   -4.560 closest distance to " O   HOH Z 166 " =    1.636
peak=   -4.458 closest distance to " NH2 ARG A  66 " =    1.261
peak=   -4.378 closest distance to " O   HOH Z 184 " =    1.171
peak=   -4.297 closest distance to " CD  ARG A 156 " =    2.073
peak=   -4.219 closest distance to " O   HOH Z 266 " =    4.711
peak=   -4.200 closest distance to " CG2BVAL A  41 " =    2.667
peak=   -4.168 closest distance to " CB  ALA A 161 " =    2.654
peak=   -4.149 closest distance to " N   ALA A 226 " =    2.107
peak=   -4.148 closest distance to " CA  SER A 164 " =    2.068
peak=   -4.141 closest distance to " O   HOH Z  13 " =    1.634
peak=   -4.055 closest distance to " O   HOH Z 210 " =    0.850
peak=   -4.048 closest distance to " O   HOH Z 165 " =    2.000
peak=   -4.045 closest distance to " CE2 TYR A  30 " =    2.744
peak=   -4.041 closest distance to " O   HOH Z  52 " =    2.093
peak=   -4.035 closest distance to " CD1 PHE A  59 " =    1.978
peak=   -4.025 closest distance to " OXT GLY A 302 " =    2.907
peak=   -3.988 closest distance to " CG  ASP A 231 " =    0.849
peak=   -3.943 closest distance to " O   HOH Z 426 " =    1.717
peak=   -3.933 closest distance to " O   HOH Z 351 " =    1.531
peak=   -3.919 closest distance to " C   THR A 279 " =    1.207
peak=   -3.911 closest distance to " CA  ASP A 298 " =    0.979
peak=   -3.902 closest distance to " CG  GLU A  53 " =    1.406
peak=   -3.888 closest distance to " CG  ASP A  50 " =    2.213
peak=   -3.876 closest distance to " C   HIS A 108 " =    1.231
peak=   -3.868 closest distance to " O   HOH Z 103 " =    1.817
peak=   -3.859 closest distance to " O   HOH Z 407 " =    3.213
peak=   -3.850 closest distance to " CA  GLY A 203 " =    2.212
peak=   -3.844 closest distance to " OG  SER A  97 " =    2.305
peak=   -3.809 closest distance to " O   HOH Z 380 " =    4.832
peak=   -3.800 closest distance to " C   ALA A 158 " =    1.220
peak=   -3.784 closest distance to " O   HOH Z 252 " =    4.066
peak=   -3.770 closest distance to " CD2 LEU A 237 " =    2.659
peak=   -3.763 closest distance to " N   THR A 235 " =    1.279
peak=   -3.740 closest distance to " CG  ARG A 269 " =    2.266
peak=   -3.727 closest distance to " CB  ALA A 248 " =    2.016
peak=   -3.714 closest distance to " O   HOH Z 151 " =    1.353
peak=   -3.706 closest distance to " CD2 LEU A 167 " =    1.677
peak=   -3.697 closest distance to " SG  CYS A 254 " =    3.292
peak=   -3.678 closest distance to " O   VAL A  67 " =    2.583
peak=   -3.675 closest distance to " OE1 GLN A 223 " =    2.404
peak=   -3.659 closest distance to " O   HOH Z 292 " =    4.291
peak=   -3.647 closest distance to " O   HOH Z 222 " =    1.382
peak=   -3.634 closest distance to " O   HOH Z 385 " =    3.863
peak=   -3.633 closest distance to " CG  GLU A   2 " =    1.699
peak=   -3.622 closest distance to " C   SER A 206 " =    1.572
peak=   -3.621 closest distance to " CD2 LEU A 300 " =    2.758
peak=   -3.621 closest distance to " O   HOH Z  10 " =    1.560
peak=   -3.615 closest distance to " O   HOH Z 166 " =    2.524
peak=   -3.613 closest distance to " N   ALA A  43 " =    2.563
peak=   -3.607 closest distance to " O   HOH Z 189 " =    2.108
peak=   -3.600 closest distance to " CG  PRO A 243 " =    1.689
peak=   -3.598 closest distance to " CD  GLN A  58 " =    1.209
peak=   -3.591 closest distance to " N   GLN A  58 " =    1.622
peak=   -3.575 closest distance to " O   HOH Z 231 " =    1.943
peak=   -3.569 closest distance to " O   HOH Z  71 " =    1.371
peak=   -3.556 closest distance to " O   ALA A   7 " =    1.620
peak=   -3.549 closest distance to " OG ASER A 134 " =    1.193
peak=   -3.536 closest distance to " ND2 ASN A  45 " =    0.988
peak=   -3.528 closest distance to " ND2 ASN A  60 " =    1.485
peak=   -3.518 closest distance to " C   ASN A 187 " =    1.900
peak=   -3.515 closest distance to " ND2 ASN A  60 " =    1.597
peak=   -3.515 closest distance to " O   HOH Z 377 " =    1.254
peak=   -3.502 closest distance to " O   TRP A  92 " =    1.880
peak=   -3.502 closest distance to " C   ASN A 285 " =    2.415
peak=   -3.494 closest distance to " CG1 VAL A 296 " =    1.281
peak=   -3.485 closest distance to " CB  ALA A 227 " =    2.286
peak=   -3.481 closest distance to " O   HOH Z 423 " =    2.209
peak=   -3.476 closest distance to " CA  ASN A 127 " =    0.932
peak=   -3.466 closest distance to " O   HOH Z 252 " =    1.285
peak=   -3.466 closest distance to " O   HOH Z  19 " =    2.168
peak=   -3.464 closest distance to " CD1 LEU A 228 " =    2.369
peak=   -3.464 closest distance to " O   SER A 271 " =    2.100
peak=   -3.464 closest distance to " CE BMET A  47 " =    1.712
peak=   -3.459 closest distance to " CD1 LEU A 101 " =    2.626
peak=   -3.455 closest distance to " O   GLY A 196 " =    1.007
peak=   -3.436 closest distance to " CG2 THR A 182 " =    2.349
peak=   -3.430 closest distance to " O   PRO A 198 " =    1.267
peak=   -3.429 closest distance to " CG1 VAL A 265 " =    2.393
peak=   -3.421 closest distance to " OD1 ASN A 148 " =    1.552
peak=   -3.413 closest distance to " CD  ARG A 195 " =    4.941
peak=   -3.406 closest distance to " O   HOH Z 348 " =    2.279
peak=   -3.406 closest distance to " O   HOH Z 353 " =    2.309
peak=   -3.405 closest distance to " CE3 TRP A 150 " =    2.171
peak=   -3.398 closest distance to " C   GLY A 133 " =    1.199
peak=   -3.398 closest distance to " CB  TYR A  15 " =    2.315
peak=   -3.393 closest distance to " CA  VAL A 197 " =    1.040
peak=   -3.392 closest distance to " O   HOH Z 246 " =    1.448
peak=   -3.387 closest distance to " CG  GLU A 277 " =    1.253
peak=   -3.386 closest distance to " O   HOH Z 191 " =    5.543
peak=   -3.373 closest distance to " O   HOH Z  65 " =    1.240
peak=   -3.373 closest distance to " CG2 THR A   4 " =    1.829
peak=   -3.368 closest distance to " OG BSER A 134 " =    1.382
peak=   -3.364 closest distance to " O   HOH Z 418 " =    1.608
peak=   -3.363 closest distance to " CA  GLY A 133 " =    2.313
peak=   -3.361 closest distance to " O   ALA A 256 " =    1.402
peak=   -3.356 closest distance to " O   HOH Z 290 " =    1.178
peak=   -3.356 closest distance to " O   HOH Z  11 " =    1.505
peak=   -3.355 closest distance to " O   HOH Z 118 " =    4.266
peak=   -3.349 closest distance to " O   HOH Z 388 " =    1.886
peak=   -3.349 closest distance to " CD1 LEU A  25 " =    2.502
peak=   -3.348 closest distance to " CD  GLU A 236 " =    1.049
peak=   -3.346 closest distance to " CD  GLN A 223 " =    1.616
peak=   -3.344 closest distance to " O   HOH Z 234 " =    4.187
peak=   -3.342 closest distance to " CA  SER A 276 " =    1.393
peak=   -3.342 closest distance to " O   VAL A 189 " =    2.430
peak=   -3.338 closest distance to " O   GLY A 211 " =    1.550
peak=   -3.336 closest distance to " O   HOH Z  43 " =    1.644
peak=   -3.334 closest distance to " NE2 GLN A  88 " =    1.008
peak=   -3.334 closest distance to " OG  SER A  32 " =    1.140
peak=   -3.332 closest distance to " CB  ASP A 162 " =    2.408
peak=   -3.328 closest distance to " O   HOH Z 308 " =    1.658
peak=   -3.318 closest distance to " O   HOH Z 150 " =    1.686
peak=   -3.316 closest distance to " O   HOH Z 132 " =    1.110
peak=   -3.311 closest distance to " CH2 TRP A 179 " =    1.249
peak=   -3.310 closest distance to " O   HOH Z 174 " =    2.074
peak=   -3.301 closest distance to " ND2BASN A 224 " =    1.799
peak=   -3.300 closest distance to " O   HOH Z 185 " =    2.262
peak=   -3.299 closest distance to " CB  PRO A 243 " =    2.733
peak=   -3.299 closest distance to " O   HOH Z 111 " =    1.335
peak=   -3.293 closest distance to " O   HOH Z 118 " =    2.992
peak=   -3.292 closest distance to " CA  GLY A 133 " =    1.980
peak=   -3.290 closest distance to " CG  TRP A 266 " =    1.751
peak=   -3.289 closest distance to " CG1 VAL A 112 " =    2.584
peak=   -3.288 closest distance to " OG BSER A 134 " =    1.725
peak=   -3.287 closest distance to " NZ  LYS A 119 " =    3.696
peak=   -3.286 closest distance to " NE2 GLN A 103 " =    1.743
peak=   -3.279 closest distance to " O   HOH Z  94 " =    2.213
peak=   -3.278 closest distance to " CD2 PHE A  61 " =    1.934
peak=   -3.275 closest distance to " O   HOH Z 283 " =    2.042
peak=   -3.275 closest distance to " NH2AARG A 275 " =    5.075
peak=   -3.274 closest distance to " O   ALA A 161 " =    1.629
peak=   -3.267 closest distance to " CD  ARG A 139 " =    1.585
peak=   -3.265 closest distance to " CE  MET A 105 " =    2.140
peak=   -3.265 closest distance to " O   HOH Z   6 " =    2.085
peak=   -3.261 closest distance to " CG1 VAL A 112 " =    2.672
peak=   -3.261 closest distance to " OG1 THR A  82 " =    1.683
peak=   -3.249 closest distance to " O   VAL A 125 " =    2.316
peak=   -3.245 closest distance to " CB  SER A 245 " =    2.323
peak=   -3.243 closest distance to " C   GLY A  91 " =    1.379
peak=   -3.239 closest distance to " O   HOH Z 198 " =    2.132
peak=   -3.237 closest distance to " OG  SER A  62 " =    1.572
peak=   -3.224 closest distance to " NH1 ARG A 195 " =    2.635
peak=   -3.224 closest distance to " O   HOH Z 311 " =    3.762
peak=   -3.219 closest distance to " ND2 ASN A 252 " =    1.757
peak=   -3.216 closest distance to " O   HOH Z 151 " =    1.889
peak=   -3.216 closest distance to " O   HOH Z 231 " =    1.598
peak=   -3.212 closest distance to " OD1 ASN A 187 " =    1.609
peak=   -3.210 closest distance to " O  BHOH Z 338 " =    1.346
peak=   -3.209 closest distance to " CG2 VAL A 112 " =    2.584
peak=   -3.208 closest distance to " O   HOH Z 350 " =    1.764
peak=   -3.204 closest distance to " O   VAL A 197 " =    1.355
peak=   -3.203 closest distance to " O   HOH Z 397 " =    1.118
peak=   -3.200 closest distance to " O   GLY A  80 " =    2.456
peak=   -3.199 closest distance to " NE1 TRP A 266 " =    2.197
peak=   -3.199 closest distance to " O   HOH Z 221 " =    1.248
peak=   -3.197 closest distance to " O   HOH Z 396 " =    1.582
peak=   -3.193 closest distance to " CD  PRO A 243 " =    1.879
peak=   -3.189 closest distance to " CB  ALA A 291 " =    2.312
peak=   -3.187 closest distance to " O   HOH Z 301 " =    2.400
peak=   -3.187 closest distance to " O   HOH Z 389 " =    1.665
peak=   -3.182 closest distance to " OXT GLY A 302 " =    3.526
peak=   -3.175 closest distance to " OD1 ASN A 249 " =    1.171
peak=   -3.174 closest distance to " CE  MET A 105 " =    1.992
peak=   -3.173 closest distance to " O   HOH Z 423 " =    1.139
peak=   -3.169 closest distance to " CG1 VAL A 197 " =    2.301
peak=   -3.165 closest distance to " CE2 TRP A  85 " =    1.003
peak=   -3.160 closest distance to " CD2 TYR A 247 " =    2.337
peak=   -3.159 closest distance to " CA  GLY A 241 " =    2.249
peak=   -3.157 closest distance to " CG  MET A 105 " =    0.829
peak=   -3.157 closest distance to " OG  SER A  87 " =    1.595
peak=   -3.156 closest distance to " O   HOH Z  60 " =    2.380
peak=   -3.155 closest distance to " O   SER A 210 " =    1.960
peak=   -3.154 closest distance to " OH  TYR A 169 " =    1.023
peak=   -3.151 closest distance to " CB  TRP A  85 " =    2.463
peak=   -3.146 closest distance to " SG  CYS A 168 " =    1.001
peak=   -3.145 closest distance to " O   LYS A 289 " =    1.045
peak=   -3.144 closest distance to " N   GLY A  17 " =    1.605
peak=   -3.139 closest distance to " O   HOH Z 297 " =    2.834
peak=   -3.139 closest distance to " CZ  TYR A 169 " =    1.773
peak=   -3.137 closest distance to " OXT GLY A 302 " =    3.401
peak=   -3.135 closest distance to " OD1 ASN A 249 " =    2.067
peak=   -3.130 closest distance to " O   HOH Z 365 " =    1.859
peak=   -3.129 closest distance to " CG2 VAL A 189 " =    2.093
peak=   -3.127 closest distance to " SG  CYS A 260 " =    2.549
peak=   -3.126 closest distance to " O   ALA A 100 " =    2.221
peak=   -3.125 closest distance to " O   HOH Z  97 " =    1.254
peak=   -3.125 closest distance to " O   HOH Z 171 " =    2.177
peak=   -3.124 closest distance to " O   HOH Z 200 " =    1.498
peak=   -3.124 closest distance to " CG  GLN A  11 " =    1.658
peak=   -3.123 closest distance to " O   HOH Z 409 " =    5.232
peak=   -3.120 closest distance to " CB  ASN A  39 " =    2.101
peak=   -3.116 closest distance to " CD1 ILE A 263 " =    2.325
peak=   -3.115 closest distance to " CE3 TRP A  70 " =    1.669
peak=   -3.112 closest distance to " OE1 GLN A  88 " =    0.906
peak=   -3.110 closest distance to " CD2 PHE A 192 " =    2.099
peak=   -3.109 closest distance to " CA  GLY A 241 " =    3.138
peak=   -3.108 closest distance to " CB  ALA A  10 " =    2.131
peak=   -3.099 closest distance to " CB  ALA A  43 " =    2.592
peak=   -3.098 closest distance to " O   HOH Z  44 " =    2.122
peak=   -3.097 closest distance to " OG  SER A  26 " =    1.297
peak=   -3.097 closest distance to " O   HOH Z 324 " =    2.156
peak=   -3.096 closest distance to " O   HOH Z 427 " =    1.465
peak=   -3.088 closest distance to " CZ3 TRP A 266 " =    1.612
peak=   -3.070 closest distance to " CB  LEU A 167 " =    2.147
peak=   -3.069 closest distance to " O   HOH Z 298 " =    2.797
peak=   -3.055 closest distance to " CG1 VAL A  78 " =    2.525
peak=   -3.048 closest distance to " C   GLU A  46 " =    1.013
peak=   -3.040 closest distance to " NH2 ARG A 159 " =    2.318
peak=   -3.013 closest distance to " CD  GLN A  88 " =    0.918
peak=   -3.004 closest distance to " CG2 VAL A 296 " =    1.134

================= 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    :  0.4618 0.4510   6.263199e+00   6.244728e+00
   1_bss:  0.4539 0.4413   6.258743e+00   6.233895e+00
   1_xyz:  0.3624 0.3868   6.112405e+00   6.151614e+00
   1_adp:  0.3108 0.3516   6.001635e+00   6.091568e+00
   1_occ:  0.3105 0.3512   6.000818e+00   6.091374e+00
   2_bss:  0.3081 0.3460   6.002338e+00   6.090110e+00
   2_xyz:  0.2231 0.2711   5.731102e+00   5.883924e+00
   2_adp:  0.2028 0.2530   5.655017e+00   5.823730e+00
   2_occ:  0.2027 0.2531   5.654639e+00   5.823993e+00
   3_bss:  0.2013 0.2522   5.653956e+00   5.822063e+00
   3_xyz:  0.1447 0.1844   5.342568e+00   5.546435e+00
   3_adp:  0.1342 0.1754   5.282685e+00   5.496198e+00
   3_occ:  0.1340 0.1753   5.281899e+00   5.495558e+00
   4_bss:  0.1340 0.1751   5.283420e+00   5.495668e+00
   4_xyz:  0.1245 0.1665   5.228737e+00   5.448766e+00
   4_adp:  0.1207 0.1662   5.212157e+00   5.445274e+00
   4_occ:  0.1205 0.1661   5.211587e+00   5.444944e+00
   5_bss:  0.1205 0.1660   5.211506e+00   5.444891e+00
   5_xyz:  0.1205 0.1660   5.211506e+00   5.444891e+00
   5_adp:  0.1210 0.1659   5.211317e+00   5.442930e+00
   5_occ:  0.1210 0.1659   5.211355e+00   5.443072e+00
   5_bss:  0.1209 0.1659   5.211276e+00   5.443272e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  20.000   6.692  10.706   7.469   0.000   0.000   0.000
   1_xyz:  0.300  20.000   6.692  10.706   7.469   0.000   0.000   0.000
   1_adp:  0.300  20.000   6.692  10.706   7.469   0.000   0.000   0.000
   1_occ:  0.300  20.000   6.692  10.706   7.469   0.000   0.000   0.000
   2_bss:  0.308  45.269   3.498   6.792   4.702   0.000   0.000   0.000
   2_xyz:  0.308  45.269   3.498   6.792   4.702   0.000   0.000   0.000
   2_adp:  0.308  45.269   3.498   6.792   4.702   0.000   0.000   0.000
   2_occ:  0.308  45.269   3.498   6.792   4.702   0.000   0.000   0.000
   3_bss:  0.314  45.269   2.420   4.222   3.501   0.000   0.000   0.000
   3_xyz:  0.314  45.269   2.420   4.222   3.501   0.000   0.000   0.000
   3_adp:  0.314  45.269   2.420   4.222   3.501   0.000   0.000   0.000
   3_occ:  0.314  45.269   2.420   4.222   3.501   0.000   0.000   0.000
   4_bss:  0.317  45.269   2.014   3.130   3.043   0.000   0.000   0.000
   4_xyz:  0.317  45.269   2.014   3.130   3.043   0.000   0.000   0.000
   4_adp:  0.317  45.269   2.014   3.130   3.043   0.000   0.000   0.000
   4_occ:  0.317  45.269   2.014   3.130   3.043   0.000   0.000   0.000
   5_bss:  0.317  45.269   2.154   3.011   3.128   0.000   0.000   0.000
   5_xyz:  0.317  45.269   2.154   3.011   3.128   0.000   0.000   0.000
   5_adp:  0.317  45.269   2.154   3.011   3.128   0.000   0.000   0.000
   5_occ:  0.317  45.269   2.154   3.011   3.128   0.000   0.000   0.000
   5_bss:  0.320  53.760  -0.583   0.194   0.388   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  52.863 0.4852  0.5509    60585.577
   1_bss:  53.130 0.4794  0.6903    58569.973
   1_xyz:  43.345 0.6009  0.8497    42007.717
   1_adp:  37.392 0.6735  0.9665    33726.219
   1_occ:  37.400 0.6734  0.9658    33706.615
   2_bss:  37.149 0.6764  0.8648    33429.614
   2_xyz:  27.891 0.7803  0.9716    19424.210
   2_adp:  25.300 0.8087  0.9925    16788.167
   2_occ:  25.319 0.8084  0.9921    16794.769
   3_bss:  25.204 0.8096  0.9387    16710.590
   3_xyz:  17.455 0.8850  0.9896     8653.767
   3_adp:  16.312 0.8955  0.9940     7917.483
   3_occ:  16.299 0.8956  0.9940     7907.566
   4_bss:  16.310 0.8955  0.9710     7931.066
   4_xyz:  15.240 0.9051  0.9728     7183.340
   4_adp:  15.161 0.9058  0.9679     7122.487
   4_occ:  15.162 0.9058  0.9676     7123.562
   5_bss:  15.157 0.9058  0.9691     7123.240
   5_xyz:  15.157 0.9058  0.9691     7123.240
   5_adp:  15.109 0.9062  0.9653     7098.070
   5_occ:  15.111 0.9062  0.9652     7099.914
   5_bss:  15.113 0.9062  0.9705     7107.243
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.093   5.3894e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.093   5.3894e+01
   1_xyz:   1.678  0.013  0.108 17.946  0.007  4.112   1.3747e-01
   1_adp:   1.678  0.013  0.108 17.946  0.007  4.112   1.3747e-01
   1_occ:   1.678  0.013  0.108 17.946  0.007  4.112   1.3747e-01
   2_bss:   1.678  0.013  0.108 17.946  0.007  4.112   1.3747e-01
   2_xyz:   1.156  0.008  0.077 16.167  0.005  4.131   7.8330e-02
   2_adp:   1.156  0.008  0.077 16.167  0.005  4.131   7.8330e-02
   2_occ:   1.156  0.008  0.077 16.167  0.005  4.131   7.8330e-02
   3_bss:   1.156  0.008  0.077 16.167  0.005  4.131   7.8330e-02
   3_xyz:   1.098  0.008  0.082 15.302  0.004  4.132   7.0438e-02
   3_adp:   1.098  0.008  0.082 15.302  0.004  4.132   7.0438e-02
   3_occ:   1.098  0.008  0.082 15.302  0.004  4.132   7.0438e-02
   4_bss:   1.098  0.008  0.082 15.302  0.004  4.132   7.0438e-02
   4_xyz:   0.971  0.006  0.077 15.099  0.004  4.134   5.6533e-02
   4_adp:   0.971  0.006  0.077 15.099  0.004  4.134   5.6533e-02
   4_occ:   0.971  0.006  0.077 15.099  0.004  4.134   5.6533e-02
   5_bss:   0.971  0.006  0.077 15.099  0.004  4.134   5.6533e-02
   5_xyz:   0.971  0.006  0.077 15.099  0.004  4.115   5.6964e-02
   5_adp:   0.971  0.006  0.077 15.099  0.004  4.115   5.6964e-02
   5_occ:   0.971  0.006  0.077 15.099  0.004  4.115   5.6964e-02
   5_bss:   0.971  0.006  0.077 15.099  0.004  4.115   5.6964e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9872e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9872e+00
   1_xyz:  15.131  0.161  0.525 88.854  0.049  2.306   1.0201e-01
   1_adp:  15.131  0.161  0.525 88.854  0.049  2.306   1.0201e-01
   1_occ:  15.131  0.161  0.525 88.854  0.049  2.306   1.0201e-01
   2_bss:  15.131  0.161  0.525 88.854  0.049  2.306   1.0201e-01
   2_xyz:   8.112  0.115  0.281 86.519  0.043  2.144   7.9051e-02
   2_adp:   8.112  0.115  0.281 86.519  0.043  2.144   7.9051e-02
   2_occ:   8.112  0.115  0.281 86.519  0.043  2.144   7.9051e-02
   3_bss:   8.112  0.115  0.281 86.519  0.043  2.144   7.9051e-02
   3_xyz:   7.383  0.064  0.464 83.805  0.041  2.323   7.1189e-02
   3_adp:   7.383  0.064  0.464 83.805  0.041  2.323   7.1189e-02
   3_occ:   7.383  0.064  0.464 83.805  0.041  2.323   7.1189e-02
   4_bss:   7.383  0.064  0.464 83.805  0.041  2.323   7.1189e-02
   4_xyz:   6.822  0.040  0.469 82.540  0.031  2.329   3.5671e-02
   4_adp:   6.822  0.040  0.469 82.540  0.031  2.329   3.5671e-02
   4_occ:   6.822  0.040  0.469 82.540  0.031  2.329   3.5671e-02
   5_bss:   6.822  0.040  0.469 82.540  0.031  2.329   3.5671e-02
   5_xyz:   6.822  0.040  0.469 82.540  0.031  2.329   3.5943e-02
   5_adp:   6.822  0.040  0.469 82.540  0.031  2.329   3.5943e-02
   5_occ:   6.822  0.040  0.469 82.540  0.031  2.329   3.5943e-02
   5_bss:   6.822  0.040  0.469 82.540  0.031  2.329   3.5943e-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:  90.19   0.00  12.00  80.28   0.00   9.18  90.19   0.00  27.32
   1_occ:  90.19   0.00  12.00  80.28   0.00   9.18  90.19   0.00  27.32
   2_bss:  90.19   0.00  12.00  80.28   0.00   9.18  90.19   0.00  27.32
   2_xyz:  90.19   0.00  12.00  80.28   0.00   9.18  90.19   0.00  27.32
   2_adp:  84.89   0.00  12.40  80.90   0.00   8.68  84.89   1.11  32.66
   2_occ:  84.89   0.00  12.40  80.90   0.00   8.68  84.89   1.11  32.66
   3_bss:  84.89   0.00  12.40  80.90   0.00   8.68  84.89   1.11  32.66
   3_xyz:  84.89   0.00  12.40  80.90   0.00   8.68  84.89   1.11  32.66
   3_adp:  82.47   0.00  12.34  81.00   0.00   8.37  82.47   1.53  33.97
   3_occ:  82.47   0.00  12.34  81.00   0.00   8.37  82.47   1.53  33.97
   4_bss:  82.47   0.00  12.34  81.00   0.00   8.37  82.47   1.53  33.97
   4_xyz:  82.47   0.00  12.34  81.00   0.00   8.37  82.47   1.53  33.97
   4_adp: 107.63   0.00  13.05 107.63   0.00   8.51  82.35   1.07  37.76
   4_occ: 107.63   0.00  13.05 107.63   0.00   8.51  82.35   1.07  37.76
   5_bss: 107.63   0.00  13.05 107.63   0.00   8.51  82.35   1.07  37.76
   5_xyz: 107.63   0.00  13.05 107.63   0.00   8.51  82.35   1.07  37.76
   5_adp:  99.05   0.00  12.96  99.05   0.00   8.42  82.67   1.15  37.67
   5_occ:  99.05   0.00  12.96  99.05   0.00   8.42  82.67   1.15  37.67
   5_bss: 101.96   2.91  15.87 101.96   2.91  11.33  85.58   4.06  40.58
------------------------------------------------------------------------
 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:    1.167    0.015    0.413
   1_adp:    1.167    0.015    0.413
   1_occ:    1.167    0.015    0.413
   2_bss:    1.167    0.015    0.413
   2_xyz:    1.610    0.026    0.570
   2_adp:    1.610    0.026    0.570
   2_occ:    1.610    0.026    0.570
   3_bss:    1.610    0.026    0.570
   3_xyz:    1.552    0.038    0.643
   3_adp:    1.552    0.038    0.643
   3_occ:    1.552    0.038    0.643
   4_bss:    1.552    0.038    0.643
   4_xyz:    1.710    0.053    0.670
   4_adp:    1.710    0.053    0.670
   4_occ:    1.710    0.053    0.670
   5_bss:    1.710    0.053    0.670
   5_xyz:    1.710    0.053    0.670
   5_adp:    1.710    0.053    0.670
   5_occ:    1.710    0.053    0.670
   5_bss:    1.710    0.053    0.670
------------------------------------------------------------------------

CPU time actual refinement: 318.41


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_817/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_817/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_817/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_817/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_817/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 318.26 
  Macro-tasks:
    bulk solvent and scale       = 40.39  
    individual site refinement   = 122.31 
    weights calculation          = 32.24  
    collect and process          = 6.66   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 201.74 
  Micro-tasks:
    mask                            = 1.79   
    f_calc                          = 96.80  
    alpha_beta                      = 8.51   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 104.98 
    fmodel                         = 7.10   
    r_factors                      = 0.31   
    phase_errors                   = 10.87  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 231.82 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.619 micro seconds
Total CPU time: 5.53 minutes
from_scatterers_fft:    613 calls, 96.35 s
gradients_fft:          557 calls, 93.00 s

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

# Date 2008-01-16 Time 02:30:37 PST -0800 (1200479437.22 s)
Start R-work = 0.4618, R-free = 0.4510 (no bulk solvent and anisotropic scale)
Final R-work = 0.1369, R-free = 0.1820 (no bulk solvent and anisotropic scale)

Start R-work = 0.4539, R-free = 0.4413
Final R-work = 0.1209, R-free = 0.1659