# Date 2008-01-16 Time 02:02:06 PST -0800 (1200477726.91 s)
#phil __OFF__

Command line arguments: "../659.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 17404
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 659

-------------------------------------------------------------------------------
  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: (70.25, 46.6953, 88.5498, 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: 2.83, per 1000 atoms: 1.00


================================== 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: (70.25, 46.6953, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0929 1.99226
Completeness in resolution range: 0.954862
Completeness with d_max=infinity: 0.951939

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0929
                             d_min =   1.9923

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: (70.25, 46.6953, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0929 1.99226
Completeness in resolution range: 0.954862
Completeness with d_max=infinity: 0.951939

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0933 -  4.2630 [2156/2180]  1937   219  10.2%
  bin  2:  4.2630 -  3.3963 [2062/2082]  1857   205   9.9%
  bin  3:  3.3963 -  2.9707 [2046/2065]  1844   202   9.9%
  bin  4:  2.9707 -  2.7008 [2022/2052]  1819   203  10.0%
  bin  5:  2.7008 -  2.5082 [2000/2019]  1797   203  10.2%
  bin  6:  2.5082 -  2.3609 [2018/2043]  1814   204  10.1%
  bin  7:  2.3609 -  2.2430 [1990/2018]  1792   198   9.9%
  bin  8:  2.2430 -  2.1457 [1975/2011]  1779   196   9.9%
  bin  9:  2.1457 -  2.0633 [1964/2006]  1769   195   9.9%
  bin 10:  2.0633 -  1.9923 [1356/2039]  1222   134   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_659/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: 0.11 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:
        1.45 -     2.14: 9
        2.14 -     2.83: 947
        2.83 -     3.52: 4365
        3.52 -     4.21: 9200
        4.21 -     4.90: 13520
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.452 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.600 3.040 -x+1,y+1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.650 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.690 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.690 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28036 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_659/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_659/model_refine_001.geo

CPU time processing inputs: 8.00


============================ 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 = 70.25 46.69535 88.54975 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: 1.99 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4684   r_free= 0.4556   ksol= 0.00   Bsol= 0.00   scale= 0.793    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.271171                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7547 0.99   1402  154 0.3918 0.3577      6.6028      6.5094|
|  2:  4.7547 -  3.7937 0.99   1349  152 0.3719 0.4024      6.7419      6.8357|
|  3:  3.7937 -  3.3200 0.99   1301  144 0.4239 0.4012      6.6592      6.6305|
|  4:  3.3200 -  3.0191 0.99   1324  149 0.4688 0.4210      6.5265      6.4427|
|  5:  3.0191 -  2.8042 0.99   1296  146 0.4965 0.4380      6.3552      6.3582|
|  6:  2.8042 -  2.6397 0.99   1304  139 0.4860 0.5759      6.2684      6.2306|
|  7:  2.6397 -  2.5082 0.99   1278  148 0.5075 0.4865      6.2254       6.153|
|  8:  2.5082 -  2.3994 0.98   1297  142 0.5243 0.4598      6.1949        6.18|
|  9:  2.3994 -  2.3074 0.98   1264  139 0.4948 0.5566      6.0997      6.1735|
| 10:  2.3074 -  2.2280 1.00   1307  145 0.5304 0.4559      6.1169      6.0538|
| 11:  2.2280 -  2.1586 0.97   1256  143 0.5093 0.5277      6.0272      6.0528|
| 12:  2.1586 -  2.0970 0.98   1278  141 0.5290 0.4797      5.9731      6.0042|
| 13:  2.0970 -  2.0420 0.99   1267  134 0.5088 0.5113      5.8729      5.8166|
| 14:  2.0420 -  1.9923 0.54    707   83 0.5184 0.4877      5.8745      5.7738|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.7547  1402   154  0.72  32.31   0.79     0.75      64198.60|
|  2:  4.7547 -  3.7937  1349   152  0.73  32.18   0.88     0.80      94456.30|
|  3:  3.7937 -  3.3200  1301   144  0.65  39.96   0.84     0.75      99036.74|
|  4:  3.3200 -  3.0191  1324   149  0.56  47.12   0.79     0.64      88895.35|
|  5:  3.0191 -  2.8042  1296   146  0.46  54.85   0.75     0.53      74780.45|
|  6:  2.8042 -  2.6397  1304   139  0.40  59.52   0.72     0.46      70679.23|
|  7:  2.6397 -  2.5082  1278   148  0.38  61.34   0.73     0.44      64732.21|
|  8:  2.5082 -  2.3994  1297   142  0.40  59.97   0.71     0.46      56849.54|
|  9:  2.3994 -  2.3074  1264   139  0.42  58.71   0.74     0.48      50414.76|
| 10:  2.3074 -  2.2280  1307   145  0.41  59.26   0.73     0.48      45412.47|
| 11:  2.2280 -  2.1586  1256   143  0.39  61.00   0.76     0.48      44155.99|
| 12:  2.1586 -  2.0970  1278   141  0.38  61.39   0.74     0.47      39575.77|
| 13:  2.0970 -  2.0420  1267   134  0.37  62.22   0.73     0.45      34777.16|
| 14:  2.0420 -  1.9923   707    83  0.38  61.50   0.75     0.42      29524.82|
|alpha:            min =        0.42 max =            0.80 mean =         0.55|
|beta:             min =    29524.82 max =        99036.74 mean =     62596.02|
|figures of merit: min =        0.00 max =            1.00 mean =         0.48|
|phase err.(work): min =        0.00 max =           89.99 mean =        53.15|
|phase err.(test): min =        0.00 max =           89.84 mean =        53.49|
|-----------------------------------------------------------------------------|

============================== 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 = 11.652450             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.836   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.011022              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.212   (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:        5 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       25 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      164 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      678 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1497 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2591 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3879 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5051 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6496 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7662 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.143 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.836 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.066)------------------------------------------|
|    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 = 12.066)------------------------------------------|
|    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: 1.99 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4756   r_free= 0.4605   ksol= 0.00   Bsol= 0.00   scale= 0.763    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.274713                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4593   r_free= 0.4437   ksol= 0.34   Bsol= 20.00   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.55,7.38,12.44,0.00,0.00,0.00); trace/3= 8.79                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.264223                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.188773             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.822   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.916753              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.848   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4593      final r-factor (work) = 0.3721          |
| start r-factor (free) = 0.4437      final r-factor (free) = 0.3938          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 86.0832 = 10.19 * 0.50 * 6.2696 + 1.00 * 54.1434                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.5459 = 10.19 * 0.50 * 6.1660 + 1.00 * 0.1342                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3721      final r-factor (work) = 0.3217          |
| start r-factor (free) = 0.3938      final r-factor (free) = 0.3692          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6671 = 0.92 * 1.00 * 6.1660 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5713 = 0.92 * 1.00 * 6.0605 + 1.00 * 0.0153                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.066)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    66.06   12.97    None  None   None       |
|    all(noH): 2823   0      0.00    66.06   12.97    None  None   None       |
|    Sol.    : 438    0      0.00    66.06   27.10    None  None   None       |
|    Mac.    : 2385   0      0.00    57.27   10.38    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 -   6.606: 1016   |   5:    33.029 -  39.635:   92        |
|      1:     6.606 -  13.212:  759   |   6:    39.635 -  46.241:   60        |
|      2:    13.212 -  19.817:  427   |   7:    46.241 -  52.846:   34        |
|      3:    19.817 -  26.423:  270   |   8:    52.846 -  59.452:   22        |
|      4:    26.423 -  33.029:  139   |   9:    59.452 -  66.058:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3217 r_free = 0.3692             target_work(ml) = 6.035         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3211 r_free = 0.3702             target_work(ml) = 6.035         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3211   r_free= 0.3702   ksol= 0.34   Bsol= 20.00   scale= 1.103   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.55,7.38,12.44,0.00,0.00,0.00); trace/3= 8.79                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.46 A                  |
| x-ray target function (ml) for work reflections: 6.034758                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3180   r_free= 0.3670   ksol= 0.34   Bsol= 50.00   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.30,3.81,8.79,0.00,0.00,0.00); trace/3= 5.30                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.035345                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.074795              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.480   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.460927              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.433  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3180      final r-factor (work) = 0.2375          |
| start r-factor (free) = 0.3670      final r-factor (free) = 0.2926          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.5293 = 6.07 * 0.50 * 6.0562 + 1.00 * 0.1342                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.0148 = 6.07 * 0.50 * 5.9032 + 1.00 * 0.0845                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2375      final r-factor (work) = 0.2160          |
| start r-factor (free) = 0.2926      final r-factor (free) = 0.2707          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7363 = 0.46 * 1.00 * 5.9032 + 1.00 * 0.0154                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6577 = 0.46 * 1.00 * 5.7411 + 1.00 * 0.0115                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.066)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    67.86   12.68    None  None   None       |
|    all(noH): 2823   0      0.00    67.86   12.68    None  None   None       |
|    Sol.    : 438    0      0.00    67.86   32.15    None  None   None       |
|    Mac.    : 2385   0      0.00    56.64   9.11     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 -   6.786: 1182   |   5:    33.928 -  40.713:  118        |
|      1:     6.786 -  13.571:  775   |   6:    40.713 -  47.499:   74        |
|      2:    13.571 -  20.357:  336   |   7:    47.499 -  54.284:   39        |
|      3:    20.357 -  27.142:  165   |   8:    54.284 -  61.070:   21        |
|      4:    27.142 -  33.928:  109   |   9:    61.070 -  67.855:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2160 r_free = 0.2707             target_work(ml) = 5.708         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2158 r_free = 0.2706             target_work(ml) = 5.707         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2158   r_free= 0.2706   ksol= 0.34   Bsol= 50.00   scale= 1.050   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.30,3.81,8.79,0.00,0.00,0.00); trace/3= 5.30                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.29 A                  |
| x-ray target function (ml) for work reflections: 5.707397                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2142   r_free= 0.2706   ksol= 0.32   Bsol= 57.31   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.05,2.54,5.54,0.00,0.00,0.00); trace/3= 3.38                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.708073                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.594873              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.995  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.433742              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.319  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2142      final r-factor (work) = 0.1582          |
| start r-factor (free) = 0.2706      final r-factor (free) = 0.2120          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.2891 = 4.59 * 0.50 * 5.7475 + 1.00 * 0.0845                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.9043 = 4.59 * 0.50 * 5.5842 + 1.00 * 0.0751                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1582      final r-factor (work) = 0.1422          |
| start r-factor (free) = 0.2120      final r-factor (free) = 0.1971          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.0178 = 1.43 * 1.00 * 5.5842 + 1.00 * 0.0116                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.7482 = 1.43 * 1.00 * 5.3935 + 1.00 * 0.0153                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.066)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.87   13.58    None  None   None       |
|    all(noH): 2823   0      0.00    86.87   13.58    None  None   None       |
|    Sol.    : 438    0      0.82    86.87   39.19    None  None   None       |
|    Mac.    : 2385   0      0.00    79.58   8.88     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.687: 1562   |   5:    43.435 -  52.122:   83        |
|      1:     8.687 -  17.374:  637   |   6:    52.122 -  60.809:   71        |
|      2:    17.374 -  26.061:  187   |   7:    60.809 -  69.496:   46        |
|      3:    26.061 -  34.748:  119   |   8:    69.496 -  78.183:   15        |
|      4:    34.748 -  43.435:   97   |   9:    78.183 -  86.870:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1422 r_free = 0.1971             target_work(ml) = 5.356         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1420 r_free = 0.1968             target_work(ml) = 5.356         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1420   r_free= 0.1968   ksol= 0.32   Bsol= 57.31   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.05,2.54,5.54,0.00,0.00,0.00); trace/3= 3.38                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.355887                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1419   r_free= 0.1965   ksol= 0.33   Bsol= 70.28   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.77,2.17,4.50,0.00,0.00,0.00); trace/3= 2.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.355321                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.940406              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.665  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.326358              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.918  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1419      final r-factor (work) = 0.1257          |
| start r-factor (free) = 0.1965      final r-factor (free) = 0.1771          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.0077 = 2.94 * 0.50 * 5.3956 + 1.00 * 0.0751                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.8740 = 2.94 * 0.50 * 5.3091 + 1.00 * 0.0685                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1257      final r-factor (work) = 0.1237          |
| start r-factor (free) = 0.1771      final r-factor (free) = 0.1717          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7477 = 0.33 * 1.00 * 5.3091 + 1.00 * 0.0150                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7280 = 0.33 * 1.00 * 5.2491 + 1.00 * 0.0149                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.066)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.62   13.03    None  None   None       |
|    all(noH): 2823   0      0.00    85.62   13.03    None  None   None       |
|    Sol.    : 438    0      1.52    85.62   37.54    None  None   None       |
|    Mac.    : 2385   0      0.00    80.12   8.53     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.563: 1609   |   5:    42.812 -  51.375:   86        |
|      1:     8.563 -  17.125:  633   |   6:    51.375 -  59.937:   66        |
|      2:    17.125 -  25.687:  172   |   7:    59.937 -  68.500:   38        |
|      3:    25.687 -  34.250:  101   |   8:    68.500 -  77.062:   12        |
|      4:    34.250 -  42.812:   99   |   9:    77.062 -  85.624:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1237 r_free = 0.1717             target_work(ml) = 5.233         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1236 r_free = 0.1715             target_work(ml) = 5.232         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1236   r_free= 0.1715   ksol= 0.33   Bsol= 70.28   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.77,2.17,4.50,0.00,0.00,0.00); trace/3= 2.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.231837                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1235   r_free= 0.1715   ksol= 0.34   Bsol= 70.28   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.80,2.10,4.17,0.00,0.00,0.00); trace/3= 2.69                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.231675                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.520295              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 138.024  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.397926              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 98.175   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1235      final r-factor (work) = 0.1231          |
| start r-factor (free) = 0.1715      final r-factor (free) = 0.1682          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0581 = 1.52 * 0.50 * 5.2485 + 1.00 * 0.0685                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0327 = 1.52 * 0.50 * 5.2319 + 1.00 * 0.0557                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1231      final r-factor (work) = 0.1224          |
| start r-factor (free) = 0.1682      final r-factor (free) = 0.1680          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0974 = 0.40 * 1.00 * 5.2319 + 1.00 * 0.0155                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0903 = 0.40 * 1.00 * 5.2219 + 1.00 * 0.0123                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.066)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.10   12.88    None  None   None       |
|    all(noH): 2823   0      0.00    86.10   12.88    None  None   None       |
|    Sol.    : 438    0      1.47    86.10   37.15    None  None   None       |
|    Mac.    : 2385   0      0.00    80.73   8.42     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.610: 1632   |   5:    43.052 -  51.662:   86        |
|      1:     8.610 -  17.221:  617   |   6:    51.662 -  60.273:   61        |
|      2:    17.221 -  25.831:  167   |   7:    60.273 -  68.883:   37        |
|      3:    25.831 -  34.442:  107   |   8:    68.883 -  77.493:   10        |
|      4:    34.442 -  43.052:   99   |   9:    77.493 -  86.104:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1224 r_free = 0.1680             target_work(ml) = 5.222         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1224 r_free = 0.1680             target_work(ml) = 5.222         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1224   r_free= 0.1680   ksol= 0.34   Bsol= 70.28   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.80,2.10,4.17,0.00,0.00,0.00); trace/3= 2.69                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.222227                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7547 0.99   1402  154 0.1061 0.1355      5.4497      5.5858|
|  2:  4.7547 -  3.7937 0.99   1349  152 0.0919 0.1231      5.5039      5.7284|
|  3:  3.7937 -  3.3200 0.99   1301  144 0.1156 0.1550      5.5594      5.8613|
|  4:  3.3200 -  3.0191 0.99   1324  149 0.1325 0.1849      5.5201      5.7059|
|  5:  3.0191 -  2.8042 0.99   1296  146 0.1469 0.1666      5.4174      5.5789|
|  6:  2.8042 -  2.6397 0.99   1304  139 0.1335 0.2319      5.2817      5.6027|
|  7:  2.6397 -  2.5082 0.99   1278  148 0.1419 0.1695      5.2657      5.3706|
|  8:  2.5082 -  2.3994 0.98   1297  142 0.1295 0.1716      5.1732      5.4065|
|  9:  2.3994 -  2.3074 0.98   1264  139 0.1295 0.2011      5.1164      5.4263|
| 10:  2.3074 -  2.2280 1.00   1307  145 0.1268 0.1633      5.0358      5.2014|
| 11:  2.2280 -  2.1586 0.97   1256  143 0.1286 0.2000      5.0156      5.3269|
| 12:  2.1586 -  2.0970 0.98   1278  141 0.1295 0.1784      4.9661      5.2778|
| 13:  2.0970 -  2.0420 0.99   1267  134 0.1181 0.1754      4.8245      5.0292|
| 14:  2.0420 -  1.9923 0.54    707   83 0.0990 0.1596      4.6763      4.9377|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.7547  1402   154  0.93   9.98   0.97     0.94       8269.13|
|  2:  4.7547 -  3.7937  1349   152  0.95   8.89   1.01     0.99      10333.19|
|  3:  3.7937 -  3.3200  1301   144  0.92  12.58   1.02     1.02      12192.74|
|  4:  3.3200 -  3.0191  1324   149  0.91  14.73   1.00     0.98      11437.84|
|  5:  3.0191 -  2.8042  1296   146  0.89  17.05   1.00     0.98       9730.52|
|  6:  2.8042 -  2.6397  1304   139  0.89  17.50   0.97     0.94       8105.38|
|  7:  2.6397 -  2.5082  1278   148  0.89  17.18   0.98     0.94       7327.21|
|  8:  2.5082 -  2.3994  1297   142  0.89  16.94   0.99     0.96       6508.50|
|  9:  2.3994 -  2.3074  1264   139  0.90  16.62   1.00     0.95       5818.01|
| 10:  2.3074 -  2.2280  1307   145  0.89  17.00   1.00     0.95       4979.52|
| 11:  2.2280 -  2.1586  1256   143  0.89  17.40   0.99     0.95       4920.00|
| 12:  2.1586 -  2.0970  1278   141  0.89  17.07   1.00     0.99       4530.84|
| 13:  2.0970 -  2.0420  1267   134  0.89  16.99   0.98     0.95       3616.54|
| 14:  2.0420 -  1.9923   707    83  0.92  13.80   0.97     0.94       2627.87|
|alpha:            min =        0.94 max =            1.02 mean =         0.96|
|beta:             min =     2627.87 max =        12192.74 mean =      7362.30|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.95 mean =        15.25|
|phase err.(test): min =        0.00 max =           87.77 mean =        14.71|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1223   r_free= 0.1679   ksol= 0.33   Bsol= 63.61   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.85,-0.59,1.44,-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: 5.221674                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1223   r_free= 0.1679   ksol= 0.33   Bsol= 63.61   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.85,-0.59,1.44,-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: 5.221674                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.7547 0.99   1402  154 0.1046 0.1356      5.4432      5.5812|
|  2:  4.7547 -  3.7937 0.99   1349  152 0.0915 0.1207       5.501      5.7156|
|  3:  3.7937 -  3.3200 0.99   1301  144 0.1154 0.1550      5.5556      5.8636|
|  4:  3.3200 -  3.0191 0.99   1324  149 0.1328 0.1856      5.5222      5.7106|
|  5:  3.0191 -  2.8042 0.99   1296  146 0.1471 0.1668       5.419       5.579|
|  6:  2.8042 -  2.6397 0.99   1304  139 0.1337 0.2326       5.283      5.6052|
|  7:  2.6397 -  2.5082 0.99   1278  148 0.1420 0.1697      5.2667      5.3709|
|  8:  2.5082 -  2.3994 0.98   1297  142 0.1296 0.1719      5.1737      5.4067|
|  9:  2.3994 -  2.3074 0.98   1264  139 0.1295 0.2011      5.1163      5.4267|
| 10:  2.3074 -  2.2280 1.00   1307  145 0.1268 0.1636      5.0356      5.2016|
| 11:  2.2280 -  2.1586 0.97   1256  143 0.1285 0.1998      5.0154      5.3263|
| 12:  2.1586 -  2.0970 0.98   1278  141 0.1295 0.1783      4.9658      5.2779|
| 13:  2.0970 -  2.0420 0.99   1267  134 0.1180 0.1755      4.8245      5.0298|
| 14:  2.0420 -  1.9923 0.54    707   83 0.0991 0.1597      4.6768      4.9378|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0933 -  4.7547  1402   154  0.93  10.17   0.97     0.94       8388.18|
|  2:  4.7547 -  3.7937  1349   152  0.95   8.84   1.01     0.99      10243.58|
|  3:  3.7937 -  3.3200  1301   144  0.93  12.43   1.02     1.02      11987.33|
|  4:  3.3200 -  3.0191  1324   149  0.91  14.76   1.00     0.98      11493.34|
|  5:  3.0191 -  2.8042  1296   146  0.89  17.08   1.00     0.98       9767.92|
|  6:  2.8042 -  2.6397  1304   139  0.89  17.54   0.97     0.94       8128.82|
|  7:  2.6397 -  2.5082  1278   148  0.89  17.20   0.98     0.94       7345.65|
|  8:  2.5082 -  2.3994  1297   142  0.89  16.95   0.99     0.96       6517.50|
|  9:  2.3994 -  2.3074  1264   139  0.90  16.63   1.00     0.95       5821.56|
| 10:  2.3074 -  2.2280  1307   145  0.89  16.99   1.00     0.95       4977.10|
| 11:  2.2280 -  2.1586  1256   143  0.89  17.39   0.99     0.95       4919.00|
| 12:  2.1586 -  2.0970  1278   141  0.89  17.07   1.00     0.99       4529.59|
| 13:  2.0970 -  2.0420  1267   134  0.89  17.00   0.98     0.95       3618.29|
| 14:  2.0420 -  1.9923   707    83  0.92  13.80   0.97     0.94       2629.74|
|alpha:            min =        0.94 max =            1.02 mean =         0.96|
|beta:             min =     2629.74 max =        11987.33 mean =      7360.51|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        15.26|
|phase err.(test): min =        0.00 max =           89.84 mean =        14.71|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.066)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.70    88.80   15.58    None  None   None       |
|    all(noH): 2823   0      2.70    88.80   15.58    None  None   None       |
|    Sol.    : 438    0      4.17    88.80   39.84    None  None   None       |
|    Mac.    : 2385   0      2.70    83.43   11.12    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.697 -  11.307: 1632   |   5:    45.749 -  54.359:   86        |
|      1:    11.307 -  19.917:  617   |   6:    54.359 -  62.969:   61        |
|      2:    19.917 -  28.528:  167   |   7:    62.969 -  71.580:   37        |
|      3:    28.528 -  37.138:  107   |   8:    71.580 -  80.190:   10        |
|      4:    37.138 -  45.749:   99   |   9:    80.190 -  88.800:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 320         
Filter by distance & map next to the model:
   mapped sites are within: 0.247 - 4.533
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 314 from: 320
   mapped sites are within: 0.702 - 4.533

peak=   10.504 closest distance to " CB  VAL A 230 " =    1.433
peak=    7.956 closest distance to " CG2 VAL A 296 " =    1.358
peak=    6.464 closest distance to " CD2 LEU A   5 " =    1.248
peak=    5.487 closest distance to " NE2 GLN A  11 " =    1.143
peak=    5.421 closest distance to " CG  PRO A  54 " =    1.433
peak=    5.283 closest distance to " O   HOH Z 248 " =    1.443
peak=    5.188 closest distance to " CG  LEU A   5 " =    1.248
peak=    5.094 closest distance to " NH2 ARG A  56 " =    2.054
peak=    5.086 closest distance to " CB  GLN A 223 " =    1.472
peak=    5.072 closest distance to " O   HOH Z 142 " =    2.074
peak=    5.015 closest distance to " CB  PRO A  54 " =    1.075
peak=    4.905 closest distance to " O   HOH Z 232 " =    2.209
peak=    4.871 closest distance to " O   HOH Z 127 " =    0.958
peak=    4.820 closest distance to " CB  ASN A 148 " =    1.344
peak=    4.788 closest distance to " CG  LEU A 228 " =    1.211
peak=    4.701 closest distance to " CZ  PHE A 218 " =    1.116
peak=    4.688 closest distance to " O   HOH Z   9 " =    1.833
peak=    4.687 closest distance to " CG  PRO A 198 " =    1.315
peak=    4.672 closest distance to " CB  ASN A 142 " =    1.059
peak=    4.616 closest distance to " O   HOH Z 265 " =    2.096
peak=    4.614 closest distance to " CG  PRO A 243 " =    1.182
peak=    4.597 closest distance to " CD2 LEU A 228 " =    1.342
peak=    4.501 closest distance to " CB  GLN A 183 " =    1.228
peak=    4.483 closest distance to " CB  ASP A 124 " =    0.804
peak=    4.453 closest distance to " O   HOH Z 369 " =    2.317
peak=    4.447 closest distance to " O   HOH Z 313 " =    2.020
peak=    4.368 closest distance to " CZ3 TRP A 266 " =    1.167
peak=    4.353 closest distance to " NH2AARG A 145 " =    1.152
peak=    4.270 closest distance to " O   PRO A 198 " =    1.598
peak=    4.258 closest distance to " O   SER A  87 " =    2.439
peak=    4.253 closest distance to " ND2 ASN A 187 " =    1.650
peak=    4.228 closest distance to " O   HOH Z 425 " =    1.480
peak=    4.180 closest distance to " CB  VAL A 265 " =    1.311
peak=    4.177 closest distance to " CG2 VAL A 257 " =    0.934
peak=    4.152 closest distance to " CB  TYR A 169 " =    0.792
peak=    4.146 closest distance to " O   HOH Z 427 " =    2.940
peak=    4.111 closest distance to " O   HOH Z 126 " =    1.565
peak=    4.095 closest distance to " CG  PRO A 213 " =    1.241
peak=    4.093 closest distance to " CA  SER A  87 " =    0.992
peak=    4.091 closest distance to " CB  ASN A  39 " =    0.918
peak=    4.088 closest distance to " O   HOH Z 251 " =    1.593
peak=    4.086 closest distance to " CB  ARG A 190 " =    1.449
peak=    4.083 closest distance to " CB  ARG A 275 " =    0.923
peak=    4.065 closest distance to " O   HOH Z 346 " =    1.599
peak=    4.065 closest distance to " O   HOH Z 303 " =    2.082
peak=    4.062 closest distance to " N   ASN A  39 " =    1.195
peak=    4.043 closest distance to " CA  ALA A  51 " =    0.975
peak=    4.035 closest distance to " O   HOH Z  43 " =    1.993
peak=    4.026 closest distance to " O   HOH Z  78 " =    1.643
peak=    4.016 closest distance to " CZ  PHE A  38 " =    1.096
peak=    4.009 closest distance to " O   HOH Z  69 " =    0.795
peak=    4.000 closest distance to " CB  PRO A  90 " =    1.111
peak=    3.993 closest distance to " CA  ARG A 195 " =    1.189
peak=    3.993 closest distance to " O  BHOH Z 338 " =    2.371
peak=    3.989 closest distance to " CB  SER A  63 " =    1.212
peak=    3.987 closest distance to " CB  SER A 210 " =    0.787
peak=    3.985 closest distance to " O   HOH Z 353 " =    2.546
peak=    3.975 closest distance to " CB  VAL A 202 " =    1.578
peak=    3.965 closest distance to " CG  LEU A 167 " =    1.223
peak=    3.965 closest distance to " O   HOH Z 188 " =    2.937
peak=    3.944 closest distance to " O   HOH Z 207 " =    1.236
peak=    3.938 closest distance to " O   HOH Z 287 " =    2.101
peak=    3.934 closest distance to " NH1AARG A 145 " =    1.213
peak=    3.926 closest distance to " ND2 ASN A 249 " =    0.907
peak=    3.922 closest distance to " O   HOH Z 126 " =    1.925
peak=    3.905 closest distance to " CB  GLN A  89 " =    1.251
peak=    3.889 closest distance to " O   HOH Z 261 " =    1.908
peak=    3.886 closest distance to " CB  GLU A 277 " =    3.714
peak=    3.875 closest distance to " CB  GLU A  46 " =    0.909
peak=    3.875 closest distance to " CA  VAL A 230 " =    1.151
peak=    3.846 closest distance to " CB  SER A   3 " =    1.342
peak=    3.846 closest distance to " O   HOH Z   7 " =    1.221
peak=    3.845 closest distance to " CD  ARG A 269 " =    0.987
peak=    3.844 closest distance to " O   HOH Z 214 " =    2.369
peak=    3.840 closest distance to " CA  VAL A 296 " =    1.043
peak=    3.832 closest distance to " NE2 HIS A 207 " =    1.099
peak=    3.824 closest distance to " CD2 TRP A 179 " =    1.239
peak=    3.823 closest distance to " CG AARG A 275 " =    1.415
peak=    3.817 closest distance to " O   HOH Z 411 " =    3.880
peak=    3.813 closest distance to " CA  TYR A  30 " =    0.995
peak=    3.812 closest distance to " CD  LYS A 166 " =    1.259
peak=    3.793 closest distance to " N   PHE A 130 " =    1.325
peak=    3.786 closest distance to " CG  GLN A  58 " =    1.092
peak=    3.782 closest distance to " O   HOH Z 211 " =    1.135
peak=    3.781 closest distance to " CB  ARG A  79 " =    1.396
peak=    3.781 closest distance to " CB  ASN A 173 " =    0.998
peak=    3.780 closest distance to " CB  LEU A  83 " =    0.707
peak=    3.774 closest distance to " CA  ILE A 234 " =    0.989
peak=    3.770 closest distance to " CB  TRP A 266 " =    1.061
peak=    3.750 closest distance to " O   HOH Z 112 " =    0.931
peak=    3.743 closest distance to " CB AVAL A  41 " =    1.251
peak=    3.732 closest distance to " O   HOH Z 422 " =    2.637
peak=    3.730 closest distance to " CE  LYS A  76 " =    0.889
peak=    3.728 closest distance to " O   HOH Z 359 " =    1.654
peak=    3.728 closest distance to " CG  MET A 185 " =    1.152
peak=    3.725 closest distance to " O   HOH Z  40 " =    1.702
peak=    3.709 closest distance to " O   HOH Z 365 " =    2.942
peak=    3.702 closest distance to " O   HOH Z 368 " =    2.218
peak=    3.698 closest distance to " O   HOH Z 222 " =    2.418
peak=    3.684 closest distance to " CB  SER A 216 " =    0.891
peak=    3.683 closest distance to " O   HOH Z 193 " =    1.502
peak=    3.680 closest distance to " O   HOH Z 406 " =    1.641
peak=    3.679 closest distance to " O   HOH Z   3 " =    2.082
peak=    3.677 closest distance to " N   ALA A 256 " =    1.139
peak=    3.667 closest distance to " CA  ARG A  36 " =    1.099
peak=    3.659 closest distance to " CB  LYS A 117 " =    1.279
peak=    3.656 closest distance to " CG2 ILE A  20 " =    1.520
peak=    3.655 closest distance to " O  BHOH Z  74 " =    1.219
peak=    3.649 closest distance to " O   HOH Z 193 " =    1.788
peak=    3.646 closest distance to " O   HOH Z 290 " =    1.197
peak=    3.640 closest distance to " O   HOH Z 263 " =    1.687
peak=    3.640 closest distance to " CE3 TRP A 150 " =    1.123
peak=    3.639 closest distance to " CA  VAL A 125 " =    1.244
peak=    3.638 closest distance to " O   HOH Z 193 " =    0.954
peak=    3.637 closest distance to " O   HOH Z 419 " =    1.965
peak=    3.635 closest distance to " CA  ALA A 100 " =    0.899
peak=    3.626 closest distance to " O   PHE A 192 " =    1.326
peak=    3.626 closest distance to " O   HOH Z  92 " =    2.326
peak=    3.618 closest distance to " CB  GLU A 128 " =    0.844
peak=    3.615 closest distance to " CA  LEU A 282 " =    1.181
peak=    3.603 closest distance to " N   GLY A 133 " =    3.755
peak=    3.597 closest distance to " O   HOH Z 238 " =    2.290
peak=    3.595 closest distance to " CB  SER A 212 " =    1.414
peak=    3.592 closest distance to " CG  GLU A  37 " =    0.916
peak=    3.587 closest distance to " O   HOH Z 234 " =    3.769
peak=    3.580 closest distance to " CA  ASP A 162 " =    0.946
peak=    3.570 closest distance to " O   HOH Z 403 " =    1.591
peak=    3.569 closest distance to " CB  THR A  52 " =    0.898
peak=    3.558 closest distance to " OE2 GLU A  53 " =    1.910
peak=    3.556 closest distance to " CB  ASN A 110 " =    1.134
peak=    3.555 closest distance to " NH1 ARG A 138 " =    1.100
peak=    3.555 closest distance to " O   ASN A  74 " =    1.380
peak=    3.554 closest distance to " O   HOH Z 298 " =    1.713
peak=    3.549 closest distance to " CD  LYS A  76 " =    1.962
peak=    3.536 closest distance to " CB  ASP A 140 " =    0.901
peak=    3.534 closest distance to " CA  PHE A 283 " =    1.071
peak=    3.534 closest distance to " CD1 ILE A 199 " =    1.138
peak=    3.533 closest distance to " CD  ARG A 159 " =    0.702
peak=    3.529 closest distance to " CB  TRP A 179 " =    1.469
peak=    3.526 closest distance to " O   HOH Z  61 " =    1.834
peak=    3.517 closest distance to " CG2 ILE A 120 " =    1.261
peak=    3.514 closest distance to " O   HOH Z  21 " =    1.739
peak=    3.514 closest distance to " CB  GLU A 152 " =    1.229
peak=    3.513 closest distance to " O   HOH Z 214 " =    1.337
peak=    3.506 closest distance to " CB  ALA A 114 " =    0.796
peak=    3.502 closest distance to " O   HOH Z  78 " =    2.326
peak=    3.501 closest distance to " CB  SER A 273 " =    0.979
peak=    3.498 closest distance to " OE2 GLU A   2 " =    1.993
peak=    3.494 closest distance to " CA  ILE A 263 " =    1.015
peak=    3.494 closest distance to " CA  TYR A 116 " =    1.450
peak=    3.488 closest distance to " CA  ALA A 160 " =    1.090
peak=    3.483 closest distance to " CG1 ILE A 120 " =    1.067
peak=    3.480 closest distance to " O   HOH Z 272 " =    1.750
peak=    3.476 closest distance to " CB  THR A  31 " =    1.688
peak=    3.466 closest distance to " NH1 ARG A  14 " =    1.047
peak=    3.463 closest distance to " O   HOH Z 371 " =    2.734
peak=    3.463 closest distance to " O   HOH Z 261 " =    1.603
peak=    3.456 closest distance to " O   HOH Z 273 " =    2.963
peak=    3.453 closest distance to " N   SER A 135 " =    1.466
peak=    3.447 closest distance to " O   HOH Z  59 " =    1.931
peak=    3.447 closest distance to " O   HOH Z 153 " =    3.818
peak=    3.446 closest distance to " O   HOH Z  10 " =    1.732
peak=    3.446 closest distance to " CA  ASN A 215 " =    1.020
peak=    3.443 closest distance to " CD1 ILE A  33 " =    1.910
peak=    3.442 closest distance to " O   PHE A  61 " =    1.376
peak=    3.440 closest distance to " O   HOH Z 329 " =    4.241
peak=    3.440 closest distance to " O   HOH Z   4 " =    1.559
peak=    3.437 closest distance to " CB  LEU A 143 " =    1.188
peak=    3.436 closest distance to " OG ASER A 258 " =    3.138
peak=    3.436 closest distance to " O   HOH Z 380 " =    1.685
peak=    3.434 closest distance to " CG1 VAL A 153 " =    0.949
peak=    3.432 closest distance to " CB  SER A  62 " =    1.030
peak=    3.432 closest distance to " O   HOH Z 258 " =    1.144
peak=    3.425 closest distance to " CA  THR A 264 " =    0.845
peak=    3.422 closest distance to " ND2BASN A 224 " =    0.837
peak=    3.420 closest distance to " O   HOH Z 171 " =    4.096
peak=    3.418 closest distance to " CB  PRO A 198 " =    1.053
peak=    3.418 closest distance to " CB  LEU A 300 " =    0.931
peak=    3.411 closest distance to " CD BLYS A 290 " =    1.086
peak=    3.405 closest distance to " C   ALA A 299 " =    0.847
peak=    3.405 closest distance to " CA  ALA A 295 " =    1.110
peak=    3.405 closest distance to " CA  LYS A 117 " =    1.267
peak=    3.404 closest distance to " CB  ARG A 102 " =    1.047
peak=    3.402 closest distance to " CG1 ILE A 151 " =    1.081
peak=    3.398 closest distance to " CG2 ILE A 234 " =    1.053
peak=    3.398 closest distance to " CD1 LEU A  96 " =    1.016
peak=    3.397 closest distance to " CA  ALA A 154 " =    1.081
peak=    3.396 closest distance to " CA  MET A 105 " =    0.958
peak=    3.395 closest distance to " CB  GLN A  88 " =    1.212
peak=    3.389 closest distance to " CA  ASN A 127 " =    1.077
peak=    3.388 closest distance to " O   HOH Z 350 " =    1.631
peak=    3.385 closest distance to " O   HOH Z 368 " =    3.318
peak=    3.381 closest distance to " CB  PRO A 243 " =    1.511
peak=    3.380 closest distance to " OG  SER A 276 " =    1.142
peak=    3.380 closest distance to " O   HOH Z 417 " =    3.304
peak=    3.378 closest distance to " CG2AVAL A  72 " =    1.731
peak=    3.371 closest distance to " O   HOH Z 258 " =    2.003
peak=    3.369 closest distance to " CD  ARG A  66 " =    2.777
peak=    3.360 closest distance to " CB  SER A  26 " =    1.791
peak=    3.359 closest distance to " O   THR A 182 " =    1.407
peak=    3.355 closest distance to " OG1 THR A 279 " =    1.370
peak=    3.353 closest distance to " CB  ASN A 187 " =    1.108
peak=    3.349 closest distance to " CB  ALA A 291 " =    1.063
peak=    3.347 closest distance to " NH2 ARG A  56 " =    1.113
peak=    3.346 closest distance to " O   HOH Z 222 " =    1.220
peak=    3.345 closest distance to " CB  MET A  40 " =    0.797
peak=    3.344 closest distance to " O   HOH Z  68 " =    2.230
peak=    3.343 closest distance to " O   HOH Z 203 " =    1.714
peak=    3.340 closest distance to " OD1 ASN A  69 " =    2.558
peak=    3.335 closest distance to " CB  ASN A 215 " =    1.184
peak=    3.333 closest distance to " O   ASP A 124 " =    1.166
peak=    3.319 closest distance to " O   ILE A  49 " =    1.083
peak=    3.317 closest distance to " NZ  LYS A  48 " =    1.136
peak=    3.314 closest distance to " O   HOH Z 246 " =    1.177
peak=    3.312 closest distance to " O   HOH Z 148 " =    3.613
peak=    3.311 closest distance to " N   SER A 271 " =    1.027
peak=    3.309 closest distance to " CA  ASN A 217 " =    1.247
peak=    3.309 closest distance to " CG2BVAL A 121 " =    0.770
peak=    3.308 closest distance to " CD1 LEU A 261 " =    1.173
peak=    3.308 closest distance to " OG BSER A 134 " =    2.859
peak=    3.306 closest distance to " CB  ALA A 104 " =    0.720
peak=    3.303 closest distance to " O   HOH Z 148 " =    2.214
peak=    3.303 closest distance to " CD1 LEU A 300 " =    1.048
peak=    3.302 closest distance to " N   ARG A 156 " =    1.428
peak=    3.295 closest distance to " CA  ALA A  21 " =    1.113
peak=    3.294 closest distance to " OG  SER A  62 " =    2.911
peak=    3.289 closest distance to " CE3 TRP A  85 " =    1.319
peak=    3.289 closest distance to " O   HOH Z 280 " =    3.065
peak=    3.286 closest distance to " O   HOH Z  80 " =    1.730
peak=    3.286 closest distance to " CB  ARG A 145 " =    0.917
peak=    3.279 closest distance to " CG  LYS A 119 " =    1.054
peak=    3.278 closest distance to " O   HOH Z   1 " =    1.744
peak=    3.277 closest distance to " NZ  LYS A 117 " =    1.275
peak=    3.276 closest distance to " N   GLN A 278 " =    1.448
peak=    3.271 closest distance to " CG1 ILE A  49 " =    1.525
peak=    3.270 closest distance to " CG  MET A 113 " =    1.241
peak=    3.269 closest distance to " OG1 THR A  82 " =    0.943
peak=    3.269 closest distance to " CA  ASN A  74 " =    1.199
peak=    3.267 closest distance to " O   HOH Z 357 " =    2.521
peak=    3.264 closest distance to " O   HOH Z 199 " =    1.555
peak=    3.263 closest distance to " CA  HIS A  86 " =    0.742
peak=    3.261 closest distance to " NH2AARG A 275 " =    3.582
peak=    3.254 closest distance to " CA  ALA A 291 " =    0.839
peak=    3.253 closest distance to " CE1 TYR A 186 " =    1.264
peak=    3.251 closest distance to " CB  ALA A   9 " =    1.649
peak=    3.251 closest distance to " O   HOH Z 293 " =    1.895
peak=    3.247 closest distance to " CB  ALA A 248 " =    1.291
peak=    3.246 closest distance to " O   HOH Z 158 " =    3.198
peak=    3.240 closest distance to " O   HOH Z 244 " =    1.820
peak=    3.229 closest distance to " CD1 LEU A   5 " =    1.445
peak=    3.226 closest distance to " CG2 THR A 221 " =    1.043
peak=    3.225 closest distance to " O   ASN A 284 " =    1.774
peak=    3.224 closest distance to " O   HOH Z 132 " =    2.697
peak=    3.219 closest distance to " CG1 VAL A 296 " =    1.249
peak=    3.219 closest distance to " O   HOH Z 394 " =    3.935
peak=    3.219 closest distance to " CA  ALA A 129 " =    1.425
peak=    3.212 closest distance to " O   HOH Z 389 " =    1.440
peak=    3.206 closest distance to " CG  LEU A 281 " =    1.044
peak=    3.206 closest distance to " NE1 TRP A  92 " =    1.686
peak=    3.204 closest distance to " CA  ARG A 159 " =    1.250
peak=    3.202 closest distance to " O   HOH Z 435 " =    1.830
peak=    3.191 closest distance to " CB  ASP A 298 " =    1.114
peak=    3.189 closest distance to " O   HOH Z  35 " =    4.533
peak=    3.188 closest distance to " CG  PHE A 204 " =    0.978
peak=    3.188 closest distance to " O   HOH Z  88 " =    3.037
peak=    3.188 closest distance to " CB  SER A 146 " =    1.015
peak=    3.187 closest distance to " CA  LEU A  83 " =    1.163
peak=    3.186 closest distance to " CB  PHE A 204 " =    0.867
peak=    3.178 closest distance to " CB  ARG A 156 " =    1.116
peak=    3.177 closest distance to " O   HOH Z 172 " =    3.350
peak=    3.176 closest distance to " CB  HIS A 108 " =    0.813
peak=    3.174 closest distance to " CG  GLN A  77 " =    1.034
peak=    3.171 closest distance to " CG2 THR A 220 " =    0.733
peak=    3.171 closest distance to " O   HOH Z  30 " =    1.468
peak=    3.158 closest distance to " CB  TYR A 247 " =    1.000
peak=    3.157 closest distance to " O   HOH Z 213 " =    2.141
peak=    3.156 closest distance to " CA  ILE A 106 " =    0.754
peak=    3.155 closest distance to " O   HOH Z 294 " =    1.545
peak=    3.149 closest distance to " CB  ASP A 107 " =    1.104
peak=    3.149 closest distance to " CB  TYR A 172 " =    0.824
peak=    3.148 closest distance to " O   HOH Z 337 " =    1.781
peak=    3.144 closest distance to " O   SER A 164 " =    1.452
peak=    3.140 closest distance to " CG BARG A 102 " =    1.856
peak=    3.138 closest distance to " O   HOH Z   1 " =    2.152
peak=    3.136 closest distance to " O   HOH Z 424 " =    2.653
peak=    3.131 closest distance to " O   TYR A 116 " =    1.257
peak=    3.129 closest distance to " O   THR A 251 " =    1.085
peak=    3.128 closest distance to " O   ASP A 200 " =    1.608
peak=    3.126 closest distance to " CA  GLU A 152 " =    0.907
peak=    3.126 closest distance to " CG2 ILE A 263 " =    1.035
peak=    3.124 closest distance to " O   HOH Z 421 " =    2.908
peak=    3.124 closest distance to " CA  ARG A 156 " =    0.964
peak=    3.123 closest distance to " O   HOH Z 133 " =    2.914
peak=    3.122 closest distance to " O   HOH Z 180 " =    2.208
peak=    3.122 closest distance to " OG BSER A 164 " =    2.257
peak=    3.121 closest distance to " N   ALA A 292 " =    0.986
peak=    3.120 closest distance to " CA  LYS A 290 " =    1.203
peak=    3.117 closest distance to " O   THR A 220 " =    1.354
peak=    3.116 closest distance to " CB  TRP A 150 " =    1.313
peak=    3.115 closest distance to " CB  ALA A  43 " =    0.870
peak=    3.111 closest distance to " CG  GLU A  37 " =    1.055
peak=    3.111 closest distance to " CB  ASN A 173 " =    1.238
peak=    3.110 closest distance to " O   HOH Z 305 " =    3.529
peak=    3.101 closest distance to " N   ALA A   7 " =    1.243
peak=    3.096 closest distance to " CA  ARG A 139 " =    1.024
peak=    3.083 closest distance to " CB  ALA A 227 " =    0.996
peak=    3.079 closest distance to " O   LEU A 228 " =    1.979
peak=    3.078 closest distance to " CG  MET A 185 " =    0.951
peak=    3.077 closest distance to " CZ3 TRP A  92 " =    1.319
peak=    3.076 closest distance to " O   HOH Z 343 " =    3.371
peak=    3.073 closest distance to " OE1 GLU A  37 " =    1.164
peak=    3.045 closest distance to " CB  SER A  97 " =    1.266
peak=    3.022 closest distance to " O   HOH Z 437 " =    1.213
peak=    3.004 closest distance to " O   HOH Z 258 " =    1.406

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 200         
Filter by distance & map next to the model:
   mapped sites are within: 0.704 - 5.582
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 200 from: 200
   mapped sites are within: 0.704 - 5.582

peak=   -5.105 closest distance to " CG2 VAL A 230 " =    0.739
peak=   -4.672 closest distance to " O   HOH Z 211 " =    0.704
peak=   -4.436 closest distance to " CD  ARG A  14 " =    3.267
peak=   -4.427 closest distance to " CB  PRO A 243 " =    2.756
peak=   -4.247 closest distance to " O   PRO A 198 " =    1.211
peak=   -4.157 closest distance to " CD  ARG A 156 " =    2.079
peak=   -4.153 closest distance to " CD  GLN A  58 " =    1.010
peak=   -4.144 closest distance to " O   HOH Z 193 " =    1.032
peak=   -4.140 closest distance to " O   VAL A  67 " =    2.493
peak=   -4.104 closest distance to " CZ2 TRP A  92 " =    2.821
peak=   -3.998 closest distance to " CG1 VAL A 112 " =    2.691
peak=   -3.967 closest distance to " CG2 VAL A 202 " =    2.780
peak=   -3.930 closest distance to " O   HOH Z 231 " =    1.992
peak=   -3.922 closest distance to " OG BSER A 134 " =    1.360
peak=   -3.912 closest distance to " C   HIS A 108 " =    1.156
peak=   -3.903 closest distance to " O   HOH Z 394 " =    1.553
peak=   -3.869 closest distance to " CB  PHE A 192 " =    1.985
peak=   -3.860 closest distance to " O   HOH Z 100 " =    0.970
peak=   -3.847 closest distance to " O   HOH Z 106 " =    1.804
peak=   -3.828 closest distance to " O   HOH Z  69 " =    1.652
peak=   -3.827 closest distance to " O   HOH Z 411 " =    5.582
peak=   -3.812 closest distance to " O   HOH Z 166 " =    2.026
peak=   -3.806 closest distance to " CD1 LEU A 101 " =    2.339
peak=   -3.803 closest distance to " O   HOH Z 295 " =    1.539
peak=   -3.777 closest distance to " OE1 GLN A 223 " =    2.258
peak=   -3.738 closest distance to " CB  ALA A 248 " =    2.172
peak=   -3.720 closest distance to " O   PRO A 163 " =    2.009
peak=   -3.717 closest distance to " CA  GLY A 241 " =    2.371
peak=   -3.713 closest distance to " CB  VAL A 230 " =    1.096
peak=   -3.711 closest distance to " O   HOH Z 131 " =    4.006
peak=   -3.699 closest distance to " CE2 TRP A  70 " =    2.234
peak=   -3.698 closest distance to " O   HOH Z 166 " =    2.227
peak=   -3.698 closest distance to " O   HOH Z 351 " =    1.563
peak=   -3.688 closest distance to " CD2 TYR A 293 " =    2.007
peak=   -3.667 closest distance to " OG  SER A  97 " =    2.341
peak=   -3.638 closest distance to " O   HOH Z 149 " =    2.078
peak=   -3.622 closest distance to " CG  TRP A 266 " =    1.889
peak=   -3.618 closest distance to " O   HOH Z 216 " =    1.107
peak=   -3.587 closest distance to " O   HOH Z 290 " =    1.146
peak=   -3.586 closest distance to " CG1 VAL A 112 " =    2.792
peak=   -3.583 closest distance to " O   HOH Z 285 " =    2.074
peak=   -3.582 closest distance to " CE3 TRP A 150 " =    2.225
peak=   -3.581 closest distance to " O   HOH Z 359 " =    2.904
peak=   -3.574 closest distance to " N   THR A  52 " =    1.672
peak=   -3.561 closest distance to " CG2 VAL A 296 " =    0.815
peak=   -3.558 closest distance to " CB  ALA A  43 " =    2.680
peak=   -3.551 closest distance to " O   HOH Z  73 " =    2.388
peak=   -3.546 closest distance to " CB  HIS A  86 " =    1.068
peak=   -3.538 closest distance to " O   HOH Z 133 " =    1.210
peak=   -3.536 closest distance to " CG2 THR A 178 " =    2.486
peak=   -3.535 closest distance to " O   HOH Z 115 " =    1.754
peak=   -3.527 closest distance to " CB  ALA A 161 " =    2.513
peak=   -3.522 closest distance to " CG  ASP A 231 " =    0.811
peak=   -3.521 closest distance to " O   HOH Z 238 " =    0.938
peak=   -3.520 closest distance to " OE1 GLN A  88 " =    1.007
peak=   -3.519 closest distance to " CG  GLU A 277 " =    1.270
peak=   -3.512 closest distance to " CA  VAL A  67 " =    2.996
peak=   -3.510 closest distance to " CE2 TYR A  30 " =    2.654
peak=   -3.502 closest distance to " O   VAL A 189 " =    2.697
peak=   -3.493 closest distance to " O   HOH Z 236 " =    1.392
peak=   -3.490 closest distance to " CA  ASP A 298 " =    1.087
peak=   -3.481 closest distance to " O   HOH Z 127 " =    1.179
peak=   -3.478 closest distance to " CG2 VAL A 296 " =    1.539
peak=   -3.471 closest distance to " O   GLY A  17 " =    1.206
peak=   -3.469 closest distance to " CG1 VAL A 125 " =    1.802
peak=   -3.467 closest distance to " CD2 LEU A 237 " =    2.917
peak=   -3.460 closest distance to " O   HOH Z  52 " =    1.629
peak=   -3.460 closest distance to " CB  GLN A  11 " =    1.721
peak=   -3.448 closest distance to " CG2 VAL A 189 " =    1.853
peak=   -3.444 closest distance to " NE2 GLN A  88 " =    1.064
peak=   -3.436 closest distance to " O   HOH Z 198 " =    1.795
peak=   -3.436 closest distance to " CG2AVAL A  41 " =    2.863
peak=   -3.434 closest distance to " O   HOH Z 276 " =    1.489
peak=   -3.432 closest distance to " O   SER A 271 " =    2.223
peak=   -3.427 closest distance to " O   HOH Z 103 " =    1.704
peak=   -3.424 closest distance to " CG2 ILE A 263 " =    2.429
peak=   -3.412 closest distance to " O   ALA A 227 " =    1.488
peak=   -3.411 closest distance to " CB  ALA A 248 " =    2.336
peak=   -3.409 closest distance to " CA  GLY A 241 " =    3.208
peak=   -3.407 closest distance to " O   HOH Z  11 " =    1.761
peak=   -3.394 closest distance to " ND2 ASN A 249 " =    2.359
peak=   -3.393 closest distance to " C   MET A 188 " =    1.469
peak=   -3.392 closest distance to " O   HOH Z  64 " =    1.557
peak=   -3.391 closest distance to " CB  ALA A 114 " =    2.588
peak=   -3.389 closest distance to " CB  TRP A  85 " =    2.684
peak=   -3.385 closest distance to " OH  TYR A 172 " =    1.851
peak=   -3.382 closest distance to " CD  GLU A 236 " =    1.117
peak=   -3.370 closest distance to " O   HOH Z 147 " =    2.007
peak=   -3.366 closest distance to " CB  GLN A  55 " =    1.239
peak=   -3.362 closest distance to " CA  ASP A  27 " =    2.453
peak=   -3.358 closest distance to " CZ3 TRP A 179 " =    1.241
peak=   -3.356 closest distance to " CD1 LEU A 255 " =    2.935
peak=   -3.354 closest distance to " O   HOH Z 191 " =    5.534
peak=   -3.354 closest distance to " O   HOH Z 176 " =    0.728
peak=   -3.352 closest distance to " CD  PRO A 243 " =    1.951
peak=   -3.352 closest distance to " CD2 HIS A 207 " =    2.208
peak=   -3.351 closest distance to " O   HOH Z 126 " =    1.826
peak=   -3.350 closest distance to " SD  MET A 105 " =    0.978
peak=   -3.349 closest distance to " CE BMET A  47 " =    1.353
peak=   -3.347 closest distance to " O   HOH Z 111 " =    1.602
peak=   -3.347 closest distance to " O   HOH Z 377 " =    2.016
peak=   -3.346 closest distance to " C   ALA A 158 " =    1.338
peak=   -3.346 closest distance to " CA  GLY A  98 " =    2.008
peak=   -3.345 closest distance to " N   SER A 212 " =    1.931
peak=   -3.339 closest distance to " OG  SER A  62 " =    4.264
peak=   -3.336 closest distance to " O   HOH Z 252 " =    3.738
peak=   -3.333 closest distance to " O   HOH Z 256 " =    1.392
peak=   -3.322 closest distance to " ND2 ASN A  45 " =    1.952
peak=   -3.322 closest distance to " O   HOH Z 278 " =    1.136
peak=   -3.322 closest distance to " NE2 GLN A 194 " =    1.897
peak=   -3.321 closest distance to " CE  MET A 105 " =    2.372
peak=   -3.316 closest distance to " CG1 VAL A 112 " =    2.633
peak=   -3.315 closest distance to " O   HOH Z 231 " =    1.492
peak=   -3.315 closest distance to " CG1 VAL A 250 " =    2.744
peak=   -3.313 closest distance to " O   HOH Z  68 " =    1.354
peak=   -3.308 closest distance to " O   HOH Z  44 " =    0.946
peak=   -3.299 closest distance to " O   HOH Z 275 " =    1.501
peak=   -3.298 closest distance to " CD  LYS A 289 " =    2.419
peak=   -3.297 closest distance to " CD2 PHE A 225 " =    1.123
peak=   -3.297 closest distance to " O   HOH Z  60 " =    1.599
peak=   -3.295 closest distance to " CG2 ILE A 151 " =    2.585
peak=   -3.293 closest distance to " O   HOH Z  51 " =    0.857
peak=   -3.293 closest distance to " N   ALA A 226 " =    2.082
peak=   -3.286 closest distance to " O   HOH Z 275 " =    1.801
peak=   -3.277 closest distance to " O   HOH Z 412 " =    4.227
peak=   -3.277 closest distance to " N   ALA A  43 " =    2.614
peak=   -3.276 closest distance to " CD2 LEU A   5 " =    1.055
peak=   -3.267 closest distance to " O   HOH Z 431 " =    1.985
peak=   -3.265 closest distance to " OD1 ASN A 148 " =    1.326
peak=   -3.264 closest distance to " O   HOH Z 411 " =    1.442
peak=   -3.263 closest distance to " O   HOH Z 371 " =    2.388
peak=   -3.261 closest distance to " O   HOH Z 110 " =    1.304
peak=   -3.260 closest distance to " CE3 TRP A  70 " =    1.771
peak=   -3.258 closest distance to " O   HOH Z 144 " =    1.329
peak=   -3.258 closest distance to " O   HOH Z 407 " =    2.848
peak=   -3.257 closest distance to " O   HOH Z 389 " =    1.500
peak=   -3.255 closest distance to " OE1 GLU A  44 " =    1.043
peak=   -3.252 closest distance to " N   ASP A 191 " =    1.154
peak=   -3.250 closest distance to " CD2 PHE A  61 " =    2.079
peak=   -3.249 closest distance to " OG1 THR A  82 " =    1.289
peak=   -3.248 closest distance to " O   HOH Z 390 " =    2.300
peak=   -3.243 closest distance to " CG  GLN A 103 " =    2.399
peak=   -3.241 closest distance to " CD  PRO A 213 " =    2.078
peak=   -3.240 closest distance to " CA  GLY A 203 " =    2.590
peak=   -3.237 closest distance to " N   PHE A  59 " =    1.992
peak=   -3.232 closest distance to " O   HOH Z 219 " =    4.820
peak=   -3.231 closest distance to " NE  ARG A  79 " =    1.103
peak=   -3.226 closest distance to " O   HOH Z  11 " =    2.230
peak=   -3.225 closest distance to " O   HOH Z 138 " =    1.321
peak=   -3.224 closest distance to " CD1 LEU A 228 " =    2.277
peak=   -3.221 closest distance to " CD1 ILE A 151 " =    2.524
peak=   -3.216 closest distance to " CB  ASN A 148 " =    1.852
peak=   -3.212 closest distance to " NZ  LYS A 166 " =    1.258
peak=   -3.206 closest distance to " O   HOH Z 292 " =    1.628
peak=   -3.196 closest distance to " ND2 ASN A 252 " =    2.030
peak=   -3.196 closest distance to " CB  PRO A 163 " =    2.519
peak=   -3.188 closest distance to " ND2 ASN A  45 " =    1.224
peak=   -3.182 closest distance to " CG  LEU A   5 " =    1.330
peak=   -3.181 closest distance to " CD1 ILE A 239 " =    2.311
peak=   -3.181 closest distance to " CZ  PHE A  38 " =    2.571
peak=   -3.177 closest distance to " O   HOH Z 108 " =    1.337
peak=   -3.168 closest distance to " O   HOH Z 185 " =    2.318
peak=   -3.165 closest distance to " C   LEU A 222 " =    1.036
peak=   -3.162 closest distance to " O   GLY A 203 " =    2.521
peak=   -3.162 closest distance to " O   HOH Z 189 " =    2.338
peak=   -3.162 closest distance to " OG BSER A 134 " =    1.909
peak=   -3.157 closest distance to " O   TRP A  70 " =    1.504
peak=   -3.157 closest distance to " O   HOH Z 139 " =    5.266
peak=   -3.152 closest distance to " CE1 TYR A 247 " =    2.637
peak=   -3.152 closest distance to " O   LYS A 289 " =    3.157
peak=   -3.147 closest distance to " O   SER A  22 " =    2.452
peak=   -3.138 closest distance to " CA  GLY A 133 " =    2.291
peak=   -3.129 closest distance to " OD1 ASP A 171 " =    1.537
peak=   -3.128 closest distance to " C   ASP A 270 " =    1.331
peak=   -3.127 closest distance to " O   HOH Z 362 " =    4.762
peak=   -3.117 closest distance to " NH2 ARG A  79 " =    1.478
peak=   -3.117 closest distance to " O   TYR A 186 " =    1.698
peak=   -3.116 closest distance to " O   HOH Z 140 " =    1.330
peak=   -3.112 closest distance to " CZ  PHE A 155 " =    1.047
peak=   -3.111 closest distance to " CB  ASN A  69 " =    1.383
peak=   -3.106 closest distance to " OH  TYR A 247 " =    1.877
peak=   -3.103 closest distance to " CB  TYR A  15 " =    2.259
peak=   -3.101 closest distance to " O   HOH Z 327 " =    1.639
peak=   -3.097 closest distance to " O   ASP A  27 " =    1.763
peak=   -3.091 closest distance to " CG  ARG A 269 " =    2.332
peak=   -3.089 closest distance to " CB  ALA A  10 " =    2.296
peak=   -3.085 closest distance to " O   SER A 276 " =    1.716
peak=   -3.080 closest distance to " O   HOH Z 174 " =    2.463
peak=   -3.064 closest distance to " OG  SER A  63 " =    1.159
peak=   -3.063 closest distance to " CD  GLN A 223 " =    1.272
peak=   -3.059 closest distance to " NH2 ARG A 219 " =    1.678
peak=   -3.057 closest distance to " NE2 GLN A 278 " =    1.708
peak=   -3.056 closest distance to " O   HOH Z  10 " =    1.494
peak=   -3.055 closest distance to " O   HOH Z   9 " =    3.153
peak=   -3.054 closest distance to " O   HOH Z 251 " =    4.955
peak=   -3.050 closest distance to " CA  GLY A 302 " =    2.888
peak=   -3.030 closest distance to " O   ASN A 127 " =    1.461
peak=   -3.018 closest distance to " CD  GLN A  77 " =    1.104
peak=   -3.018 closest distance to " O   HOH Z 357 " =    2.125
peak=   -3.003 closest distance to " CD1 TRP A  70 " =    1.124

================= 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    :  0.4684 0.4556   6.271171e+00   6.250886e+00
   1_bss:  0.4593 0.4437   6.264223e+00   6.236907e+00
   1_xyz:  0.3721 0.3938   6.137530e+00   6.162957e+00
   1_adp:  0.3217 0.3692   6.035395e+00   6.120233e+00
   1_occ:  0.3211 0.3702   6.034758e+00   6.122265e+00
   2_bss:  0.3180 0.3670   6.035345e+00   6.122106e+00
   2_xyz:  0.2375 0.2926   5.785869e+00   5.943838e+00
   2_adp:  0.2160 0.2707   5.708131e+00   5.882513e+00
   2_occ:  0.2158 0.2706   5.707397e+00   5.881847e+00
   3_bss:  0.2142 0.2706   5.708073e+00   5.882739e+00
   3_xyz:  0.1582 0.2120   5.441511e+00   5.655320e+00
   3_adp:  0.1422 0.1971   5.355735e+00   5.586801e+00
   3_occ:  0.1420 0.1968   5.355887e+00   5.587386e+00
   4_bss:  0.1419 0.1965   5.355321e+00   5.587026e+00
   4_xyz:  0.1257 0.1771   5.254880e+00   5.496070e+00
   4_adp:  0.1237 0.1717   5.232562e+00   5.466329e+00
   4_occ:  0.1236 0.1715   5.231837e+00   5.465714e+00
   5_bss:  0.1235 0.1715   5.231675e+00   5.465920e+00
   5_xyz:  0.1231 0.1682   5.225088e+00   5.452758e+00
   5_adp:  0.1224 0.1680   5.222393e+00   5.451395e+00
   5_occ:  0.1224 0.1680   5.222227e+00   5.451314e+00
   5_bss:  0.1223 0.1679   5.221674e+00   5.450753e+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:  0.337  20.000   6.552   7.385  12.435   0.000   0.000   0.000
   1_xyz:  0.337  20.000   6.552   7.385  12.435   0.000   0.000   0.000
   1_adp:  0.337  20.000   6.552   7.385  12.435   0.000   0.000   0.000
   1_occ:  0.337  20.000   6.552   7.385  12.435   0.000   0.000   0.000
   2_bss:  0.340  50.000   3.302   3.805   8.790   0.000   0.000   0.000
   2_xyz:  0.340  50.000   3.302   3.805   8.790   0.000   0.000   0.000
   2_adp:  0.340  50.000   3.302   3.805   8.790   0.000   0.000   0.000
   2_occ:  0.340  50.000   3.302   3.805   8.790   0.000   0.000   0.000
   3_bss:  0.319  57.306   2.053   2.537   5.545   0.000   0.000   0.000
   3_xyz:  0.319  57.306   2.053   2.537   5.545   0.000   0.000   0.000
   3_adp:  0.319  57.306   2.053   2.537   5.545   0.000   0.000   0.000
   3_occ:  0.319  57.306   2.053   2.537   5.545   0.000   0.000   0.000
   4_bss:  0.335  70.276   1.773   2.167   4.502   0.000   0.000   0.000
   4_xyz:  0.335  70.276   1.773   2.167   4.502   0.000   0.000   0.000
   4_adp:  0.335  70.276   1.773   2.167   4.502   0.000   0.000   0.000
   4_occ:  0.335  70.276   1.773   2.167   4.502   0.000   0.000   0.000
   5_bss:  0.338  70.276   1.805   2.100   4.166   0.000   0.000   0.000
   5_xyz:  0.338  70.276   1.805   2.100   4.166   0.000   0.000   0.000
   5_adp:  0.338  70.276   1.805   2.100   4.166   0.000   0.000   0.000
   5_occ:  0.338  70.276   1.805   2.100   4.166   0.000   0.000   0.000
   5_bss:  0.327  63.606  -0.854  -0.587   1.442  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  53.182 0.4813  0.5500    62602.048
   1_bss:  52.626 0.4873  0.7215    60328.013
   1_xyz:  43.705 0.5979  0.8585    43851.999
   1_adp:  39.756 0.6459  0.9589    38258.294
   1_occ:  39.886 0.6443  0.9554    38453.110
   2_bss:  39.690 0.6467  0.8487    38285.202
   2_xyz:  30.054 0.7569  0.9714    22609.479
   2_adp:  27.116 0.7896  0.9963    19288.900
   2_occ:  27.098 0.7898  0.9964    19245.361
   3_bss:  27.007 0.7909  0.9322    19283.323
   3_xyz:  20.315 0.8584  0.9821    11363.759
   3_adp:  18.502 0.8758  0.9850     9852.336
   3_occ:  18.523 0.8756  0.9848     9857.654
   4_bss:  18.463 0.8762  0.9659     9833.617
   4_xyz:  16.355 0.8952  0.9735     8077.109
   4_adp:  15.634 0.9017  0.9711     7630.460
   4_occ:  15.620 0.9018  0.9713     7619.192
   5_bss:  15.615 0.9018  0.9673     7620.343
   5_xyz:  15.240 0.9053  0.9689     7373.284
   5_adp:  15.200 0.9058  0.9646     7365.294
   5_occ:  15.198 0.9058  0.9646     7362.970
   5_bss:  15.206 0.9058  0.9645     7361.177
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.4143e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.4143e+01
   1_xyz:   1.643  0.013  0.105 18.306  0.006  4.111   1.3416e-01
   1_adp:   1.643  0.013  0.105 18.306  0.006  4.111   1.3416e-01
   1_occ:   1.643  0.013  0.105 18.306  0.006  4.111   1.3416e-01
   2_bss:   1.643  0.013  0.105 18.306  0.006  4.111   1.3416e-01
   2_xyz:   1.200  0.009  0.083 16.466  0.005  4.112   8.4470e-02
   2_adp:   1.200  0.009  0.083 16.466  0.005  4.112   8.4470e-02
   2_occ:   1.200  0.009  0.083 16.466  0.005  4.112   8.4470e-02
   3_bss:   1.200  0.009  0.083 16.466  0.005  4.112   8.4470e-02
   3_xyz:   1.128  0.009  0.086 16.181  0.004  4.130   7.5068e-02
   3_adp:   1.128  0.009  0.086 16.181  0.004  4.130   7.5068e-02
   3_occ:   1.128  0.009  0.086 16.181  0.004  4.130   7.5068e-02
   4_bss:   1.128  0.009  0.086 16.181  0.004  4.130   7.5068e-02
   4_xyz:   1.044  0.009  0.081 15.748  0.004  4.114   6.8490e-02
   4_adp:   1.044  0.009  0.081 15.748  0.004  4.114   6.8490e-02
   4_occ:   1.044  0.009  0.081 15.748  0.004  4.114   6.8490e-02
   5_bss:   1.044  0.009  0.081 15.748  0.004  4.114   6.8490e-02
   5_xyz:   0.935  0.007  0.074 15.348  0.003  4.115   5.5742e-02
   5_adp:   0.935  0.007  0.074 15.348  0.003  4.115   5.5742e-02
   5_occ:   0.935  0.007  0.074 15.348  0.003  4.115   5.5742e-02
   5_bss:   0.935  0.007  0.074 15.348  0.003  4.115   5.5742e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0188e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0188e+00
   1_xyz:  13.491  0.164  0.397 86.989  0.035  2.119   9.7876e-02
   1_adp:  13.491  0.164  0.397 86.989  0.035  2.119   9.7876e-02
   1_occ:  13.491  0.164  0.397 86.989  0.035  2.119   9.7876e-02
   2_bss:  13.491  0.164  0.397 86.989  0.035  2.119   9.7876e-02
   2_xyz:   6.990  0.075  0.255 85.696  0.042  2.242   6.1271e-02
   2_adp:   6.990  0.075  0.255 85.696  0.042  2.242   6.1271e-02
   2_occ:   6.990  0.075  0.255 85.696  0.042  2.242   6.1271e-02
   3_bss:   6.990  0.075  0.255 85.696  0.042  2.242   6.1271e-02
   3_xyz:   9.287  0.057  0.422 89.227  0.039  2.272   6.1705e-02
   3_adp:   9.287  0.057  0.422 89.227  0.039  2.272   6.1705e-02
   3_occ:   9.287  0.057  0.422 89.227  0.039  2.272   6.1705e-02
   4_bss:   9.287  0.057  0.422 89.227  0.039  2.272   6.1705e-02
   4_xyz:   6.529  0.051  0.442 85.701  0.042  2.372   4.8729e-02
   4_adp:   6.529  0.051  0.442 85.701  0.042  2.372   4.8729e-02
   4_occ:   6.529  0.051  0.442 85.701  0.042  2.372   4.8729e-02
   5_bss:   6.529  0.051  0.442 85.701  0.042  2.372   4.8729e-02
   5_xyz:   6.963  0.048  0.352 87.116  0.040  2.415   3.1878e-02
   5_adp:   6.963  0.048  0.352 87.116  0.040  2.415   3.1878e-02
   5_occ:   6.963  0.048  0.352 87.116  0.040  2.415   3.1878e-02
   5_bss:   6.963  0.048  0.352 87.116  0.040  2.415   3.1878e-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:  66.06   0.00  12.97  57.27   0.00  10.38  66.06   0.00  27.10
   1_occ:  66.06   0.00  12.97  57.27   0.00  10.38  66.06   0.00  27.10
   2_bss:  66.06   0.00  12.97  57.27   0.00  10.38  66.06   0.00  27.10
   2_xyz:  66.06   0.00  12.97  57.27   0.00  10.38  66.06   0.00  27.10
   2_adp:  67.86   0.00  12.68  56.64   0.00   9.11  67.86   0.00  32.15
   2_occ:  67.86   0.00  12.68  56.64   0.00   9.11  67.86   0.00  32.15
   3_bss:  67.86   0.00  12.68  56.64   0.00   9.11  67.86   0.00  32.15
   3_xyz:  67.86   0.00  12.68  56.64   0.00   9.11  67.86   0.00  32.15
   3_adp:  86.87   0.00  13.58  79.58   0.00   8.88  86.87   0.82  39.19
   3_occ:  86.87   0.00  13.58  79.58   0.00   8.88  86.87   0.82  39.19
   4_bss:  86.87   0.00  13.58  79.58   0.00   8.88  86.87   0.82  39.19
   4_xyz:  86.87   0.00  13.58  79.58   0.00   8.88  86.87   0.82  39.19
   4_adp:  85.62   0.00  13.03  80.12   0.00   8.53  85.62   1.52  37.54
   4_occ:  85.62   0.00  13.03  80.12   0.00   8.53  85.62   1.52  37.54
   5_bss:  85.62   0.00  13.03  80.12   0.00   8.53  85.62   1.52  37.54
   5_xyz:  85.62   0.00  13.03  80.12   0.00   8.53  85.62   1.52  37.54
   5_adp:  86.10   0.00  12.88  80.73   0.00   8.42  86.10   1.47  37.15
   5_occ:  86.10   0.00  12.88  80.73   0.00   8.42  86.10   1.47  37.15
   5_bss:  88.80   2.70  15.58  83.43   2.70  11.12  88.80   4.17  39.84
------------------------------------------------------------------------
 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:    1.256    0.025    0.407
   1_adp:    1.256    0.025    0.407
   1_occ:    1.256    0.025    0.407
   2_bss:    1.256    0.025    0.407
   2_xyz:    1.805    0.045    0.564
   2_adp:    1.805    0.045    0.564
   2_occ:    1.805    0.045    0.564
   3_bss:    1.805    0.045    0.564
   3_xyz:    1.748    0.030    0.639
   3_adp:    1.748    0.030    0.639
   3_occ:    1.748    0.030    0.639
   4_bss:    1.748    0.030    0.639
   4_xyz:    1.921    0.074    0.670
   4_adp:    1.921    0.074    0.670
   4_occ:    1.921    0.074    0.670
   5_bss:    1.921    0.074    0.670
   5_xyz:    1.914    0.062    0.680
   5_adp:    1.914    0.062    0.680
   5_occ:    1.914    0.062    0.680
   5_bss:    1.914    0.062    0.680
------------------------------------------------------------------------

CPU time actual refinement: 284.32


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_659/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_659/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_659/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_659/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_659/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 284.19 
  Macro-tasks:
    bulk solvent and scale       = 34.16  
    individual site refinement   = 119.20 
    weights calculation          = 26.49  
    collect and process          = 5.54   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 185.51 
  Micro-tasks:
    mask                            = 1.94   
    f_calc                          = 86.85  
    alpha_beta                      = 7.07   
    target                          = 1.01   
    gradients_wrt_atomic_parameters = 97.36  
    fmodel                         = 6.33   
    r_factors                      = 0.23   
    phase_errors                   = 8.78   
    foms                           = 0.22   
    TOTAL for micro-tasks          = 209.79 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 3.939 micro seconds
Total CPU time: 4.93 minutes
from_scatterers_fft:    675 calls, 86.50 s
gradients_fft:          620 calls, 85.15 s

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

# Date 2008-01-16 Time 02:07:02 PST -0800 (1200478022.38 s)
Start R-work = 0.4684, R-free = 0.4556 (no bulk solvent and anisotropic scale)
Final R-work = 0.1394, R-free = 0.1840 (no bulk solvent and anisotropic scale)

Start R-work = 0.4593, R-free = 0.4437
Final R-work = 0.1223, R-free = 0.1679