# Date 2008-01-16 Time 02:22:11 PST -0800 (1200478931.97 s)
#phil __OFF__

Command line arguments: "../806.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 19154
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 806

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.6012, 47.3993, 85.5261, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.37, per 1000 atoms: 1.19


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.3993, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.007 1.98123
Completeness in resolution range: 0.955188
Completeness with d_max=infinity: 0.952217

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0070
                             d_min =   1.9812

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.6012, 47.3993, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.007 1.98123
Completeness in resolution range: 0.955188
Completeness with d_max=infinity: 0.952217

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0074 -  4.2394 [2151/2179]  1939   212   9.9%
  bin  2:  4.2394 -  3.3775 [2063/2082]  1854   209  10.1%
  bin  3:  3.3775 -  2.9543 [2048/2068]  1843   205  10.0%
  bin  4:  2.9543 -  2.6859 [2033/2058]  1835   198   9.7%
  bin  5:  2.6859 -  2.4943 [2011/2030]  1807   204  10.1%
  bin  6:  2.4943 -  2.3478 [1999/2045]  1798   201  10.1%
  bin  7:  2.3478 -  2.2306 [1975/2008]  1775   200  10.1%
  bin  8:  2.2306 -  2.1338 [1991/2026]  1792   199  10.0%
  bin  9:  2.1338 -  2.0519 [1992/2022]  1798   194   9.7%
  bin 10:  2.0519 -  1.9812 [1326/1990]  1189   137  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_806/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 17
        2.42 -     3.04: 2184
        3.04 -     3.66: 4664
        3.66 -     4.28: 8984
        4.28 -     4.90: 12377
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.001 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  2.098 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 206 " - " O   HOH Z 342 "  2.144 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A 246 " - " O   HOH Z 201 "  2.174 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 28221 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_806/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_806/model_refine_001.geo

CPU time processing inputs: 9.85


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.60125 47.3993 85.5261 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4423   r_free= 0.4324   ksol= 0.00   Bsol= 0.00   scale= 0.816    |
|                                                                             |
| 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:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.238344                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0074 -  4.7284 0.99   1393  154 0.3680 0.3431      6.5337      6.4569|
|  2:  4.7284 -  3.7727 0.99   1360  148 0.3415 0.3710      6.6765      6.7261|
|  3:  3.7727 -  3.3016 0.99   1308  153 0.3884 0.3631      6.5832      6.5767|
|  4:  3.3016 -  3.0023 0.99   1326  143 0.4155 0.3969      6.4576      6.3649|
|  5:  3.0023 -  2.7886 0.99   1303  145 0.4633 0.4785       6.332      6.3855|
|  6:  2.7886 -  2.6251 0.98   1284  143 0.4693 0.5018      6.2281      6.1924|
|  7:  2.6251 -  2.4943 0.99   1304  142 0.4786 0.4168      6.2293      6.1268|
|  8:  2.4943 -  2.3862 0.98   1272  147 0.4862 0.4647      6.1514      6.1294|
|  9:  2.3862 -  2.2946 0.98   1299  143 0.5049 0.5004      6.1084      6.1204|
| 10:  2.2946 -  2.2157 0.98   1273  136 0.4921 0.5093      6.0888      6.1009|
| 11:  2.2157 -  2.1466 0.99   1268  146 0.4951 0.4395      6.0169       6.022|
| 12:  2.1466 -  2.0854 0.98   1273  138 0.5134 0.5337      5.9677      6.0056|
| 13:  2.0854 -  2.0307 0.97   1266  141 0.5151 0.5068       5.874      5.8344|
| 14:  2.0307 -  1.9812 0.55    701   80 0.5253 0.4756       5.825      5.7414|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0074 -  4.7284  1393   154  0.74  31.06   0.81     0.75      58810.31|
|  2:  4.7284 -  3.7727  1360   148  0.77  29.48   0.91     0.81      77616.79|
|  3:  3.7727 -  3.3016  1308   153  0.68  36.68   0.86     0.78      82213.50|
|  4:  3.3016 -  3.0023  1326   143  0.62  42.06   0.83     0.69      73791.65|
|  5:  3.0023 -  2.7886  1303   145  0.53  49.82   0.77     0.61      65308.32|
|  6:  2.7886 -  2.6251  1284   143  0.51  50.98   0.76     0.58      56873.61|
|  7:  2.6251 -  2.4943  1304   142  0.53  49.70   0.76     0.58      50604.18|
|  8:  2.4943 -  2.3862  1272   147  0.51  51.22   0.75     0.58      45831.35|
|  9:  2.3862 -  2.2946  1299   143  0.48  53.49   0.74     0.55      42808.94|
| 10:  2.2946 -  2.2157  1273   136  0.46  55.18   0.78     0.53      42022.20|
| 11:  2.2157 -  2.1466  1268   146  0.42  58.37   0.77     0.49      40313.40|
| 12:  2.1466 -  2.0854  1273   138  0.38  61.60   0.77     0.46      40280.66|
| 13:  2.0854 -  2.0307  1266   141  0.36  63.43   0.74     0.43      34763.29|
| 14:  2.0307 -  1.9812   701    80  0.40  59.80   0.73     0.45      27261.73|
|alpha:            min =        0.43 max =            0.81 mean =         0.60|
|beta:             min =    27261.73 max =        82213.50 mean =     53879.24|
|figures of merit: min =        0.00 max =            1.00 mean =         0.54|
|phase err.(work): min =        0.00 max =           89.95 mean =        48.88|
|phase err.(test): min =        0.00 max =           89.81 mean =        48.87|
|-----------------------------------------------------------------------------|

============================== 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 = 8.830850              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.195   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.723923              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.936   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       22 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      163 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      685 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1512 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2614 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3893 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5079 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6543 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7718 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.855 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.708 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.975)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.975)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4496   r_free= 0.4390   ksol= 0.00   Bsol= 0.00   scale= 0.786    |
|                                                                             |
| 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:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.242227                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4340   r_free= 0.4227   ksol= 0.34   Bsol= 20.00   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.22,9.67,8.06,0.00,0.00,0.00); trace/3= 8.32                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.236031                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.196066              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.484   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.704464              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.068   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4340      final r-factor (work) = 0.3296          |
| start r-factor (free) = 0.4227      final r-factor (free) = 0.3579          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 79.4542 = 8.20 * 0.50 * 6.2467 + 1.00 * 53.8550                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 25.0874 = 8.20 * 0.50 * 6.0909 + 1.00 * 0.1266                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3296      final r-factor (work) = 0.2724          |
| start r-factor (free) = 0.3579      final r-factor (free) = 0.3118          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3052 = 0.70 * 1.00 * 6.0909 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1952 = 0.70 * 1.00 * 5.9380 + 1.00 * 0.0121                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.975)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    65.96   10.87    None  None   None       |
|    all(noH): 2823   0      0.00    65.96   10.87    None  None   None       |
|    Sol.    : 438    0      0.00    65.96   27.20    None  None   None       |
|    Mac.    : 2385   0      0.00    63.49   7.87     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 -   6.596: 1362   |   5:    32.978 -  39.574:   85        |
|      1:     6.596 -  13.191:  718   |   6:    39.574 -  46.170:   66        |
|      2:    13.191 -  19.787:  267   |   7:    46.170 -  52.765:   29        |
|      3:    19.787 -  26.383:  170   |   8:    52.765 -  59.361:    6        |
|      4:    26.383 -  32.978:  113   |   9:    59.361 -  65.957:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2724 r_free = 0.3118             target_work(ml) = 5.887         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2719 r_free = 0.3117             target_work(ml) = 5.886         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2719   r_free= 0.3117   ksol= 0.34   Bsol= 20.00   scale= 1.085   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.22,9.67,8.06,0.00,0.00,0.00); trace/3= 8.32                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.34 A                  |
| x-ray target function (ml) for work reflections: 5.886149                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2680   r_free= 0.3066   ksol= 0.32   Bsol= 45.60   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.87,5.75,5.10,0.00,0.00,0.00); trace/3= 4.90                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.885345                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.168912              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.232   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.385834              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.968  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2680      final r-factor (work) = 0.1792          |
| start r-factor (free) = 0.3066      final r-factor (free) = 0.2215          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.5141 = 4.17 * 0.50 * 5.9428 + 1.00 * 0.1266                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.9615 = 4.17 * 0.50 * 5.7068 + 1.00 * 0.0659                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1792      final r-factor (work) = 0.1613          |
| start r-factor (free) = 0.2215      final r-factor (free) = 0.2046          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2140 = 0.39 * 1.00 * 5.7068 + 1.00 * 0.0122                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1246 = 0.39 * 1.00 * 5.4788 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.975)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    71.67   11.50    None  None   None       |
|    all(noH): 2823   0      0.00    71.67   11.50    None  None   None       |
|    Sol.    : 438    0      0.91    66.69   32.39    None  None   None       |
|    Mac.    : 2385   0      0.00    71.67   7.66     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.168: 1513   |   5:    35.837 -  43.005:  106        |
|      1:     7.168 -  14.335:  669   |   6:    43.005 -  50.172:   89        |
|      2:    14.335 -  21.502:  194   |   7:    50.172 -  57.340:   28        |
|      3:    21.502 -  28.670:  103   |   8:    57.340 -  64.507:   13        |
|      4:    28.670 -  35.837:  105   |   9:    64.507 -  71.675:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1613 r_free = 0.2046             target_work(ml) = 5.442         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1611 r_free = 0.2046             target_work(ml) = 5.441         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1611   r_free= 0.2046   ksol= 0.32   Bsol= 45.60   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.87,5.75,5.10,0.00,0.00,0.00); trace/3= 4.90                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.441257                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1599   r_free= 0.2033   ksol= 0.32   Bsol= 45.60   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.81,3.87,3.93,0.00,0.00,0.00); trace/3= 3.54                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.441711                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.064779              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.210  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.449328              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.185  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1599      final r-factor (work) = 0.1310          |
| start r-factor (free) = 0.2033      final r-factor (free) = 0.1700          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7320 = 2.06 * 0.50 * 5.4881 + 1.00 * 0.0661                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5886 = 2.06 * 0.50 * 5.3559 + 1.00 * 0.0592                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1310      final r-factor (work) = 0.1252          |
| start r-factor (free) = 0.1700      final r-factor (free) = 0.1649          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4172 = 0.45 * 1.00 * 5.3559 + 1.00 * 0.0106                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3650 = 0.45 * 1.00 * 5.2375 + 1.00 * 0.0116                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.975)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.06   11.83    None  None   None       |
|    all(noH): 2823   0      0.00    77.06   11.83    None  None   None       |
|    Sol.    : 438    0      0.84    68.86   34.34    None  None   None       |
|    Mac.    : 2385   0      0.00    77.06   7.69     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.706: 1621   |   5:    38.531 -  46.237:  100        |
|      1:     7.706 -  15.412:  599   |   6:    46.237 -  53.943:   84        |
|      2:    15.412 -  23.118:  168   |   7:    53.943 -  61.649:   30        |
|      3:    23.118 -  30.825:  100   |   8:    61.649 -  69.355:   11        |
|      4:    30.825 -  38.531:  105   |   9:    69.355 -  77.061:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1252 r_free = 0.1649             target_work(ml) = 5.225         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1251 r_free = 0.1649             target_work(ml) = 5.224         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1251   r_free= 0.1649   ksol= 0.32   Bsol= 45.60   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.81,3.87,3.93,0.00,0.00,0.00); trace/3= 3.54                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.224342                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1254   r_free= 0.1655   ksol= 0.32   Bsol= 47.28   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.63,3.37,3.63,0.00,0.00,0.00); trace/3= 3.21                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.226504                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.477728              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.976  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.491610              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.773  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1254      final r-factor (work) = 0.1151          |
| start r-factor (free) = 0.1655      final r-factor (free) = 0.1589          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.5492 = 2.48 * 0.50 * 5.2387 + 1.00 * 0.0592                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.4954 = 2.48 * 0.50 * 5.1888 + 1.00 * 0.0672                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1151      final r-factor (work) = 0.1141          |
| start r-factor (free) = 0.1589      final r-factor (free) = 0.1588          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5624 = 0.49 * 1.00 * 5.1888 + 1.00 * 0.0115                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5498 = 0.49 * 1.00 * 5.1626 + 1.00 * 0.0118                               |
|-----------------------------------------------------------------------------|
| number of iterations = 20      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.975)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.07   11.77    None  None   None       |
|    all(noH): 2823   0      0.00    79.07   11.77    None  None   None       |
|    Sol.    : 438    0      0.79    69.36   34.26    None  None   None       |
|    Mac.    : 2385   0      0.00    79.07   7.64     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.907: 1667   |   5:    39.533 -  47.440:   99        |
|      1:     7.907 -  15.813:  565   |   6:    47.440 -  55.346:   77        |
|      2:    15.813 -  23.720:  165   |   7:    55.346 -  63.253:   26        |
|      3:    23.720 -  31.627:  112   |   8:    63.253 -  71.160:    9        |
|      4:    31.627 -  39.533:   98   |   9:    71.160 -  79.066:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1141 r_free = 0.1588             target_work(ml) = 5.163         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1140 r_free = 0.1589             target_work(ml) = 5.163         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1140   r_free= 0.1589   ksol= 0.32   Bsol= 47.28   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.63,3.37,3.63,0.00,0.00,0.00); trace/3= 3.21                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.162926                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1140   r_free= 0.1589   ksol= 0.32   Bsol= 46.65   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.72,3.31,3.67,0.00,0.00,0.00); trace/3= 3.23                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.162861                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.298525              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 147.794  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.658769              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.563  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1140      final r-factor (work) = 0.1123          |
| start r-factor (free) = 0.1589      final r-factor (free) = 0.1580          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.0002 = 2.30 * 0.50 * 5.1625 + 1.00 * 0.0672                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.9913 = 2.30 * 0.50 * 5.1573 + 1.00 * 0.0642                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1123      final r-factor (work) = 0.1119          |
| start r-factor (free) = 0.1580      final r-factor (free) = 0.1584          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4092 = 0.66 * 1.00 * 5.1573 + 1.00 * 0.0117                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.4065 = 0.66 * 1.00 * 5.1525 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 19     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.975)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.71   11.72    None  None   None       |
|    all(noH): 2823   0      0.00    80.71   11.72    None  None   None       |
|    Sol.    : 438    0      0.89    69.10   34.22    None  None   None       |
|    Mac.    : 2385   0      0.00    80.71   7.59     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.071: 1699   |   5:    40.353 -  48.424:   88        |
|      1:     8.071 -  16.141:  547   |   6:    48.424 -  56.494:   70        |
|      2:    16.141 -  24.212:  155   |   7:    56.494 -  64.565:   21        |
|      3:    24.212 -  32.282:  116   |   8:    64.565 -  72.635:   10        |
|      4:    32.282 -  40.353:  112   |   9:    72.635 -  80.706:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1119 r_free = 0.1584             target_work(ml) = 5.155         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1119 r_free = 0.1586             target_work(ml) = 5.155         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1119   r_free= 0.1586   ksol= 0.32   Bsol= 46.65   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.72,3.31,3.67,0.00,0.00,0.00); trace/3= 3.23                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.155237                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0074 -  4.7284 0.99   1393  154 0.1000 0.1303      5.3837      5.5233|
|  2:  4.7284 -  3.7727 0.99   1360  148 0.0862 0.1113      5.4381      5.6516|
|  3:  3.7727 -  3.3016 0.99   1308  153 0.1055 0.1517      5.4772      5.8637|
|  4:  3.3016 -  3.0023 0.99   1326  143 0.1215 0.1535      5.4547      5.5959|
|  5:  3.0023 -  2.7886 0.99   1303  145 0.1313 0.1730      5.3366      5.5187|
|  6:  2.7886 -  2.6251 0.98   1284  143 0.1238 0.1970      5.2249       5.503|
|  7:  2.6251 -  2.4943 0.99   1304  142 0.1233 0.1667      5.1693      5.3771|
|  8:  2.4943 -  2.3862 0.98   1272  147 0.1175 0.1707      5.0807      5.3244|
|  9:  2.3862 -  2.2946 0.98   1299  143 0.1182 0.1805      5.0443      5.3298|
| 10:  2.2946 -  2.2157 0.98   1273  136 0.1133 0.1755      4.9741      5.2363|
| 11:  2.2157 -  2.1466 0.99   1268  146 0.1136 0.1730      4.9387      5.2763|
| 12:  2.1466 -  2.0854 0.98   1273  138 0.1075 0.1636      4.8642      5.1138|
| 13:  2.0854 -  2.0307 0.97   1266  141 0.1167 0.1826      4.8089      5.0954|
| 14:  2.0307 -  1.9812 0.55    701   80 0.1084 0.1791        4.71      4.9526|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0074 -  4.7284  1393   154  0.94   8.73   0.98     0.95       6971.47|
|  2:  4.7284 -  3.7727  1360   148  0.95   7.93   1.01     0.99       8919.78|
|  3:  3.7727 -  3.3016  1308   153  0.93  11.48   1.02     1.02      10686.78|
|  4:  3.3016 -  3.0023  1326   143  0.92  13.99   1.00     0.98      10461.56|
|  5:  3.0023 -  2.7886  1303   145  0.89  16.51   0.99     0.96       8622.29|
|  6:  2.7886 -  2.6251  1284   143  0.90  16.32   0.98     0.95       7411.52|
|  7:  2.6251 -  2.4943  1304   142  0.91  15.40   0.99     0.95       6294.22|
|  8:  2.4943 -  2.3862  1272   147  0.90  15.68   0.99     0.96       5559.54|
|  9:  2.3862 -  2.2946  1299   143  0.91  15.66   1.00     0.97       5149.00|
| 10:  2.2946 -  2.2157  1273   136  0.90  16.05   0.99     0.96       4601.29|
| 11:  2.2157 -  2.1466  1268   146  0.90  16.27   0.99     0.96       4355.20|
| 12:  2.1466 -  2.0854  1273   138  0.92  14.81   1.00     0.97       3885.79|
| 13:  2.0854 -  2.0307  1266   141  0.90  16.85   0.99     0.99       3554.41|
| 14:  2.0307 -  1.9812   701    80  0.90  16.12   0.98     0.94       2867.85|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2867.85 max =        10686.78 mean =      6537.06|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.88 mean =        14.29|
|phase err.(test): min =        0.00 max =           89.31 mean =        13.77|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1119   r_free= 0.1586   ksol= 0.32   Bsol= 49.98   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.49,0.04,0.45,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.155279                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.01 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1119   r_free= 0.1586   ksol= 0.32   Bsol= 49.98   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.49,0.04,0.45,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.155279                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0074 -  4.7284 0.99   1393  154 0.1000 0.1304      5.3842       5.524|
|  2:  4.7284 -  3.7727 0.99   1360  148 0.0863 0.1113      5.4385      5.6517|
|  3:  3.7727 -  3.3016 0.99   1308  153 0.1055 0.1518      5.4773       5.864|
|  4:  3.3016 -  3.0023 0.99   1326  143 0.1215 0.1535      5.4547      5.5959|
|  5:  3.0023 -  2.7886 0.99   1303  145 0.1313 0.1730      5.3365      5.5185|
|  6:  2.7886 -  2.6251 0.98   1284  143 0.1238 0.1970      5.2247      5.5026|
|  7:  2.6251 -  2.4943 0.99   1304  142 0.1233 0.1668      5.1694      5.3776|
|  8:  2.4943 -  2.3862 0.98   1272  147 0.1175 0.1706      5.0807       5.324|
|  9:  2.3862 -  2.2946 0.98   1299  143 0.1181 0.1804      5.0443      5.3299|
| 10:  2.2946 -  2.2157 0.98   1273  136 0.1132 0.1755      4.9742      5.2365|
| 11:  2.2157 -  2.1466 0.99   1268  146 0.1135 0.1730      4.9387      5.2762|
| 12:  2.1466 -  2.0854 0.98   1273  138 0.1075 0.1636      4.8641      5.1143|
| 13:  2.0854 -  2.0307 0.97   1266  141 0.1167 0.1826      4.8088       5.095|
| 14:  2.0307 -  1.9812 0.55    701   80 0.1084 0.1789      4.7098      4.9519|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0074 -  4.7284  1393   154  0.94   8.74   0.98     0.95       6979.96|
|  2:  4.7284 -  3.7727  1360   148  0.95   7.95   1.01     1.00       8926.97|
|  3:  3.7727 -  3.3016  1308   153  0.93  11.48   1.02     1.02      10691.96|
|  4:  3.3016 -  3.0023  1326   143  0.92  14.00   1.00     0.98      10460.38|
|  5:  3.0023 -  2.7886  1303   145  0.89  16.51   0.99     0.96       8617.79|
|  6:  2.7886 -  2.6251  1284   143  0.90  16.32   0.98     0.96       7408.29|
|  7:  2.6251 -  2.4943  1304   142  0.91  15.40   0.99     0.96       6293.55|
|  8:  2.4943 -  2.3862  1272   147  0.90  15.69   0.99     0.96       5560.18|
|  9:  2.3862 -  2.2946  1299   143  0.91  15.66   1.00     0.97       5150.48|
| 10:  2.2946 -  2.2157  1273   136  0.90  16.05   1.00     0.96       4601.64|
| 11:  2.2157 -  2.1466  1268   146  0.90  16.27   1.00     0.96       4355.04|
| 12:  2.1466 -  2.0854  1273   138  0.92  14.82   1.00     0.98       3885.99|
| 13:  2.0854 -  2.0307  1266   141  0.90  16.85   1.00     0.99       3553.15|
| 14:  2.0307 -  1.9812   701    80  0.90  16.12   0.98     0.94       2865.21|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2865.21 max =        10691.96 mean =      6537.95|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.88 mean =        14.29|
|phase err.(test): min =        0.00 max =           89.31 mean =        13.77|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.975)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.33    84.04   15.05    None  None   None       |
|    all(noH): 2823   0      3.33    84.04   15.05    None  None   None       |
|    Sol.    : 438    0      4.22    72.43   37.55    None  None   None       |
|    Mac.    : 2385   0      3.33    84.04   10.92    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:     3.330 -  11.401: 1699   |   5:    43.683 -  51.754:   88        |
|      1:    11.401 -  19.471:  547   |   6:    51.754 -  59.824:   70        |
|      2:    19.471 -  27.542:  155   |   7:    59.824 -  67.895:   21        |
|      3:    27.542 -  35.613:  116   |   8:    67.895 -  75.966:   10        |
|      4:    35.613 -  43.683:  112   |   9:    75.966 -  84.036:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 318         
Filter by distance & map next to the model:
   mapped sites are within: 0.418 - 5.746
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 308 from: 318
   mapped sites are within: 0.755 - 5.746

peak=   10.516 closest distance to " CG2 VAL A 230 " =    1.426
peak=    7.174 closest distance to " CG2 VAL A 296 " =    1.110
peak=    6.309 closest distance to " CG  LEU A   5 " =    1.206
peak=    6.149 closest distance to " NH2 ARG A  56 " =    2.285
peak=    5.616 closest distance to " CG  LEU A 228 " =    1.193
peak=    5.527 closest distance to " CG  PRO A  54 " =    1.262
peak=    5.524 closest distance to " CB  GLN A 223 " =    1.421
peak=    5.286 closest distance to " CB  VAL A 296 " =    1.102
peak=    5.184 closest distance to " CB  SER A  63 " =    1.273
peak=    4.865 closest distance to " CB  ARG A 275 " =    0.897
peak=    4.860 closest distance to " CB  PRO A  54 " =    0.924
peak=    4.824 closest distance to " CD2 LEU A   5 " =    1.133
peak=    4.794 closest distance to " CB  VAL A 230 " =    1.236
peak=    4.671 closest distance to " CG  PRO A 213 " =    1.212
peak=    4.658 closest distance to " CB  GLN A 183 " =    1.316
peak=    4.554 closest distance to " O   HOH Z 232 " =    2.307
peak=    4.552 closest distance to " O   HOH Z 272 " =    1.904
peak=    4.517 closest distance to " O   HOH Z 126 " =    1.862
peak=    4.468 closest distance to " O   SER A  87 " =    2.284
peak=    4.435 closest distance to " O   HOH Z 316 " =    2.996
peak=    4.419 closest distance to " CG  PRO A 198 " =    1.199
peak=    4.403 closest distance to " O   HOH Z 298 " =    1.852
peak=    4.382 closest distance to " NE2 GLN A  11 " =    1.090
peak=    4.378 closest distance to " C   PRO A 198 " =    1.492
peak=    4.375 closest distance to " CG  PRO A 243 " =    1.167
peak=    4.374 closest distance to " OD1 ASN A  69 " =    2.623
peak=    4.348 closest distance to " CB  GLU A 128 " =    1.046
peak=    4.341 closest distance to " O   HOH Z  48 " =    1.599
peak=    4.337 closest distance to " CB  SER A   3 " =    1.288
peak=    4.326 closest distance to " CB  GLU A 152 " =    1.136
peak=    4.294 closest distance to " O   HOH Z 423 " =    1.814
peak=    4.285 closest distance to " O   HOH Z 369 " =    2.170
peak=    4.277 closest distance to " O   HOH Z 403 " =    1.717
peak=    4.215 closest distance to " O   HOH Z 368 " =    2.246
peak=    4.205 closest distance to " CB  TRP A 179 " =    1.359
peak=    4.205 closest distance to " CB  GLU A 277 " =    3.608
peak=    4.120 closest distance to " O   HOH Z 236 " =    1.873
peak=    4.113 closest distance to " O   HOH Z 193 " =    1.809
peak=    4.105 closest distance to " CB  ASN A 148 " =    1.316
peak=    4.075 closest distance to " O   HOH Z 303 " =    2.089
peak=    4.069 closest distance to " NH2 ARG A 156 " =    1.132
peak=    4.065 closest distance to " CB  ARG A  79 " =    1.406
peak=    4.029 closest distance to " CA  TYR A  30 " =    0.905
peak=    4.022 closest distance to " O   HOH Z 280 " =    2.941
peak=    4.015 closest distance to " O   HOH Z 265 " =    2.420
peak=    4.008 closest distance to " CA  ALA A  21 " =    1.248
peak=    4.008 closest distance to " O   HOH Z 427 " =    3.009
peak=    3.993 closest distance to " CG1BVAL A  72 " =    1.691
peak=    3.986 closest distance to " O   TRP A 274 " =    1.904
peak=    3.984 closest distance to " CB  TRP A 266 " =    0.977
peak=    3.979 closest distance to " ND2 ASN A 249 " =    1.961
peak=    3.976 closest distance to " ND2 ASN A 187 " =    1.506
peak=    3.970 closest distance to " OD2 ASP A 286 " =    2.858
peak=    3.966 closest distance to " O   HOH Z 142 " =    1.587
peak=    3.962 closest distance to " O   HOH Z 234 " =    3.615
peak=    3.940 closest distance to " CB  VAL A 265 " =    1.287
peak=    3.933 closest distance to " O   HOH Z  78 " =    1.636
peak=    3.928 closest distance to " O   HOH Z 158 " =    3.068
peak=    3.916 closest distance to " O   HOH Z  20 " =    1.646
peak=    3.909 closest distance to " CD2 LEU A 228 " =    1.160
peak=    3.904 closest distance to " CB  ARG A 139 " =    0.892
peak=    3.899 closest distance to " CA  ALA A  51 " =    1.002
peak=    3.870 closest distance to " O   HOH Z  44 " =    2.295
peak=    3.870 closest distance to " O   HOH Z 346 " =    1.507
peak=    3.869 closest distance to " CB  ASN A  39 " =    0.883
peak=    3.866 closest distance to " O   HOH Z  97 " =    2.038
peak=    3.859 closest distance to " O   HOH Z  43 " =    2.083
peak=    3.851 closest distance to " NZ  LYS A 117 " =    3.221
peak=    3.831 closest distance to " O   HOH Z 203 " =    1.809
peak=    3.830 closest distance to " O   HOH Z 371 " =    3.305
peak=    3.826 closest distance to " O   HOH Z  80 " =    1.718
peak=    3.823 closest distance to " O   HOH Z 345 " =    3.204
peak=    3.809 closest distance to " CB  ARG A 190 " =    1.595
peak=    3.801 closest distance to " O   HOH Z 344 " =    2.826
peak=    3.793 closest distance to " O   HOH Z 411 " =    3.729
peak=    3.784 closest distance to " O   HOH Z  15 " =    2.150
peak=    3.783 closest distance to " CD  ARG A 159 " =    0.787
peak=    3.769 closest distance to " O   HOH Z  48 " =    1.613
peak=    3.754 closest distance to " O   HOH Z 426 " =    1.505
peak=    3.754 closest distance to " CD  LYS A 166 " =    1.327
peak=    3.749 closest distance to " O   HOH Z 247 " =    1.309
peak=    3.736 closest distance to " CZ  PHE A 218 " =    1.085
peak=    3.729 closest distance to " CG2 THR A 221 " =    1.119
peak=    3.728 closest distance to " O   HOH Z  63 " =    1.554
peak=    3.726 closest distance to " O   HOH Z 402 " =    1.503
peak=    3.726 closest distance to " O   HOH Z 189 " =    2.630
peak=    3.719 closest distance to " CG1 ILE A  33 " =    1.300
peak=    3.714 closest distance to " CA  LYS A 117 " =    1.293
peak=    3.712 closest distance to " O   HOH Z  61 " =    1.600
peak=    3.708 closest distance to " O   HOH Z  97 " =    2.571
peak=    3.706 closest distance to " CE1 TYR A 186 " =    1.250
peak=    3.703 closest distance to " O   HOH Z 193 " =    2.156
peak=    3.703 closest distance to " O   MET A 105 " =    1.837
peak=    3.703 closest distance to " CB  VAL A 202 " =    1.575
peak=    3.702 closest distance to " OG BSER A 164 " =    2.230
peak=    3.694 closest distance to " O   HOH Z 130 " =    2.248
peak=    3.691 closest distance to " O   HOH Z  88 " =    3.130
peak=    3.691 closest distance to " CA  THR A 221 " =    0.911
peak=    3.685 closest distance to " O   HOH Z 329 " =    3.815
peak=    3.681 closest distance to " O   HOH Z 124 " =    1.302
peak=    3.672 closest distance to " CD1 LEU A 300 " =    1.174
peak=    3.671 closest distance to " O   HOH Z  54 " =    1.624
peak=    3.668 closest distance to " O   HOH Z 245 " =    1.396
peak=    3.658 closest distance to " CB  LEU A 143 " =    1.162
peak=    3.654 closest distance to " CB  ASP A 140 " =    0.849
peak=    3.653 closest distance to " O   HOH Z 135 " =    1.876
peak=    3.646 closest distance to " O   HOH Z 102 " =    1.280
peak=    3.638 closest distance to " O   HOH Z 133 " =    1.640
peak=    3.630 closest distance to " O   HOH Z 261 " =    2.125
peak=    3.623 closest distance to " O   HOH Z 197 " =    2.810
peak=    3.621 closest distance to " O   HOH Z 134 " =    1.479
peak=    3.621 closest distance to " CB  ALA A 248 " =    1.454
peak=    3.621 closest distance to " N   ASN A  39 " =    1.205
peak=    3.619 closest distance to " CA  ASP A 191 " =    0.875
peak=    3.618 closest distance to " O   HOH Z 261 " =    1.992
peak=    3.614 closest distance to " CB  ALA A 291 " =    1.362
peak=    3.610 closest distance to " CB  ALA A   9 " =    1.631
peak=    3.608 closest distance to " O   HOH Z 133 " =    2.356
peak=    3.606 closest distance to " O   HOH Z 126 " =    1.599
peak=    3.605 closest distance to " O   HOH Z 263 " =    1.652
peak=    3.599 closest distance to " O   HOH Z 214 " =    2.296
peak=    3.590 closest distance to " CD  ARG A 269 " =    0.963
peak=    3.588 closest distance to " CB AVAL A  41 " =    1.100
peak=    3.586 closest distance to " O   HOH Z 273 " =    2.743
peak=    3.575 closest distance to " O   HOH Z 112 " =    1.623
peak=    3.572 closest distance to " CA  THR A 264 " =    0.761
peak=    3.570 closest distance to " CA  VAL A  41 " =    0.829
peak=    3.569 closest distance to " O   HOH Z 128 " =    2.155
peak=    3.561 closest distance to " CE1 HIS A 108 " =    1.155
peak=    3.561 closest distance to " O   HOH Z 420 " =    2.052
peak=    3.558 closest distance to " CG  ARG A  66 " =    2.801
peak=    3.555 closest distance to " CB  ASN A 187 " =    1.351
peak=    3.552 closest distance to " NZ  LYS A 166 " =    3.086
peak=    3.551 closest distance to " CG1 VAL A 153 " =    0.930
peak=    3.549 closest distance to " CZ  PHE A 192 " =    0.995
peak=    3.544 closest distance to " NH1AARG A 145 " =    1.051
peak=    3.543 closest distance to " O   HOH Z  21 " =    1.678
peak=    3.541 closest distance to " O   HOH Z  40 " =    1.642
peak=    3.539 closest distance to " CA  ARG A 195 " =    1.223
peak=    3.534 closest distance to " CB  ARG A  79 " =    0.893
peak=    3.529 closest distance to " O   HOH Z 271 " =    2.630
peak=    3.520 closest distance to " O   HOH Z 250 " =    1.360
peak=    3.514 closest distance to " O   HOH Z 295 " =    1.512
peak=    3.504 closest distance to " O   HOH Z 172 " =    3.868
peak=    3.500 closest distance to " CB  TRP A 150 " =    1.417
peak=    3.500 closest distance to " O   HOH Z  59 " =    2.326
peak=    3.496 closest distance to " CA  ASP A 140 " =    1.230
peak=    3.483 closest distance to " O   HOH Z 248 " =    1.736
peak=    3.482 closest distance to " CG1 ILE A  49 " =    1.492
peak=    3.481 closest distance to " CD BLYS A 290 " =    0.999
peak=    3.477 closest distance to " O   HOH Z 313 " =    1.822
peak=    3.470 closest distance to " O   HOH Z 383 " =    2.043
peak=    3.461 closest distance to " O   ALA A 158 " =    1.353
peak=    3.458 closest distance to " O   HOH Z 327 " =    2.466
peak=    3.454 closest distance to " CA  ASN A 215 " =    1.319
peak=    3.448 closest distance to " O   HOH Z 227 " =    1.634
peak=    3.446 closest distance to " O   HOH Z 425 " =    2.069
peak=    3.445 closest distance to " CG BARG A 102 " =    1.861
peak=    3.443 closest distance to " O   HOH Z 128 " =    2.117
peak=    3.443 closest distance to " CB  LEU A 228 " =    1.317
peak=    3.441 closest distance to " CD2 HIS A  81 " =    1.070
peak=    3.438 closest distance to " CB  ASN A 142 " =    1.115
peak=    3.436 closest distance to " N   VAL A 126 " =    1.383
peak=    3.435 closest distance to " CB  SER A 216 " =    0.755
peak=    3.432 closest distance to " O   HOH Z 250 " =    1.405
peak=    3.432 closest distance to " CA  ALA A 295 " =    1.075
peak=    3.426 closest distance to " CA  GLY A 267 " =    0.774
peak=    3.419 closest distance to " CB  SER A 212 " =    1.182
peak=    3.419 closest distance to " O   HOH Z 422 " =    2.725
peak=    3.415 closest distance to " CB  MET A  40 " =    0.850
peak=    3.412 closest distance to " ND1 HIS A  81 " =    1.591
peak=    3.412 closest distance to " CG2 ILE A  20 " =    1.448
peak=    3.412 closest distance to " O   HOH Z  68 " =    2.085
peak=    3.411 closest distance to " CB  THR A 157 " =    1.143
peak=    3.407 closest distance to " CB  ALA A 295 " =    1.241
peak=    3.405 closest distance to " O   HOH Z 180 " =    2.135
peak=    3.404 closest distance to " CA  ARG A  36 " =    1.102
peak=    3.403 closest distance to " CA  ALA A 158 " =    1.212
peak=    3.393 closest distance to " NZ  LYS A  76 " =    1.301
peak=    3.393 closest distance to " O   HOH Z 147 " =    1.754
peak=    3.392 closest distance to " O   HOH Z  68 " =    1.633
peak=    3.389 closest distance to " CG1 VAL A 296 " =    1.205
peak=    3.387 closest distance to " N   ARG A 190 " =    1.079
peak=    3.383 closest distance to " O   HOH Z 366 " =    3.035
peak=    3.383 closest distance to " O   HOH Z 357 " =    1.998
peak=    3.382 closest distance to " CD2 TRP A 179 " =    1.386
peak=    3.374 closest distance to " CB  HIS A 108 " =    0.805
peak=    3.369 closest distance to " O   HOH Z 407 " =    2.714
peak=    3.369 closest distance to " O   HOH Z 281 " =    4.607
peak=    3.369 closest distance to " CA  MET A  40 " =    1.120
peak=    3.366 closest distance to " O   GLN A 278 " =    1.241
peak=    3.360 closest distance to " N   SER A 135 " =    1.423
peak=    3.359 closest distance to " CA  ASN A 176 " =    1.077
peak=    3.358 closest distance to " OG  SER A  22 " =    2.833
peak=    3.358 closest distance to " O   HOH Z 368 " =    3.595
peak=    3.356 closest distance to " O   HOH Z  78 " =    2.128
peak=    3.352 closest distance to " O   ASP A 124 " =    1.122
peak=    3.351 closest distance to " CG  MET A 185 " =    1.159
peak=    3.349 closest distance to " CG  GLN A  77 " =    2.307
peak=    3.346 closest distance to " CD2 LEU A 255 " =    1.509
peak=    3.346 closest distance to " CB  LYS A 117 " =    1.149
peak=    3.345 closest distance to " O   ALA A 165 " =    1.412
peak=    3.345 closest distance to " CG  GLN A  58 " =    2.778
peak=    3.335 closest distance to " CB  SER A  26 " =    1.672
peak=    3.334 closest distance to " O   HOH Z  85 " =    1.330
peak=    3.331 closest distance to " CG  MET A 185 " =    1.146
peak=    3.326 closest distance to " OD1 ASN A 217 " =    1.687
peak=    3.321 closest distance to " O   HOH Z 423 " =    3.197
peak=    3.318 closest distance to " CG AARG A 275 " =    1.207
peak=    3.317 closest distance to " O   HOH Z 132 " =    2.733
peak=    3.315 closest distance to " OG1 THR A 294 " =    2.334
peak=    3.312 closest distance to " NH2BARG A 145 " =    2.176
peak=    3.302 closest distance to " ND2 ASN A 110 " =    1.663
peak=    3.295 closest distance to " NH2 ARG A  79 " =    1.321
peak=    3.293 closest distance to " CA  SER A  87 " =    1.015
peak=    3.288 closest distance to " CA  GLN A 194 " =    1.232
peak=    3.287 closest distance to " CD1 ILE A 106 " =    1.049
peak=    3.285 closest distance to " O   HOH Z 425 " =    1.278
peak=    3.280 closest distance to " O   HOH Z 421 " =    1.721
peak=    3.278 closest distance to " CB  GLN A  88 " =    1.219
peak=    3.277 closest distance to " CD2 LEU A 297 " =    0.864
peak=    3.276 closest distance to " O   HOH Z 419 " =    1.652
peak=    3.275 closest distance to " O   HOH Z  49 " =    2.651
peak=    3.275 closest distance to " O   HOH Z 279 " =    2.210
peak=    3.273 closest distance to " CB  GLN A 278 " =    0.875
peak=    3.273 closest distance to " CB  SER A 273 " =    0.809
peak=    3.273 closest distance to " CG  LEU A 167 " =    1.138
peak=    3.272 closest distance to " CA  VAL A 126 " =    0.942
peak=    3.268 closest distance to " O   HOH Z 193 " =    1.566
peak=    3.265 closest distance to " OD1 ASP A 231 " =    1.860
peak=    3.264 closest distance to " CB  THR A  31 " =    1.680
peak=    3.264 closest distance to " CG2 ILE A 120 " =    1.246
peak=    3.260 closest distance to " O   HOH Z 227 " =    2.075
peak=    3.255 closest distance to " CB  MET A  47 " =    1.114
peak=    3.253 closest distance to " CD1 LEU A   5 " =    1.445
peak=    3.252 closest distance to " CB  GLU A  46 " =    1.063
peak=    3.249 closest distance to " O   HOH Z 417 " =    3.151
peak=    3.246 closest distance to " O   HOH Z 406 " =    1.523
peak=    3.245 closest distance to " C   ALA A 299 " =    0.933
peak=    3.244 closest distance to " CG2 THR A 220 " =    0.882
peak=    3.241 closest distance to " O   HOH Z 291 " =    1.547
peak=    3.239 closest distance to " CD1 ILE A  33 " =    1.590
peak=    3.235 closest distance to " O   HOH Z 116 " =    1.848
peak=    3.232 closest distance to " OE1 GLU A   2 " =    2.071
peak=    3.231 closest distance to " CA  LEU A 282 " =    1.094
peak=    3.229 closest distance to " O   HOH Z 437 " =    2.111
peak=    3.225 closest distance to " O   HOH Z 359 " =    3.855
peak=    3.219 closest distance to " O   HOH Z 209 " =    2.416
peak=    3.217 closest distance to " CB  ALA A 248 " =    1.067
peak=    3.217 closest distance to " O   HOH Z 155 " =    3.174
peak=    3.217 closest distance to " CD  LYS A 119 " =    1.903
peak=    3.217 closest distance to " O   HOH Z 374 " =    2.676
peak=    3.216 closest distance to " CA  ASP A 162 " =    1.146
peak=    3.216 closest distance to " OD1 ASP A 286 " =    1.749
peak=    3.213 closest distance to " NH2AARG A 275 " =    3.681
peak=    3.212 closest distance to " C   TYR A 214 " =    1.432
peak=    3.209 closest distance to " CA  ALA A 233 " =    1.421
peak=    3.208 closest distance to " CB  ALA A 242 " =    0.921
peak=    3.205 closest distance to " ND1 HIS A  86 " =    1.623
peak=    3.202 closest distance to " O   HOH Z 435 " =    1.863
peak=    3.201 closest distance to " O   HOH Z 282 " =    2.022
peak=    3.200 closest distance to " CG2 ILE A 234 " =    2.068
peak=    3.195 closest distance to " CG1 VAL A 174 " =    1.162
peak=    3.190 closest distance to " O   ALA A   1 " =    1.524
peak=    3.184 closest distance to " CB  LEU A 255 " =    0.765
peak=    3.180 closest distance to " CA  ALA A 291 " =    0.910
peak=    3.175 closest distance to " O   HOH Z 227 " =    1.520
peak=    3.173 closest distance to " O   HOH Z   9 " =    2.125
peak=    3.169 closest distance to " CG2 VAL A 202 " =    1.160
peak=    3.168 closest distance to " CA  ASN A 217 " =    1.314
peak=    3.167 closest distance to " O   HOH Z 302 " =    1.842
peak=    3.163 closest distance to " CA  LYS A 290 " =    1.266
peak=    3.163 closest distance to " CB  ASN A 215 " =    1.152
peak=    3.163 closest distance to " CG2 VAL A 257 " =    0.862
peak=    3.161 closest distance to " O   HOH Z  46 " =    1.494
peak=    3.159 closest distance to " O   HOH Z 404 " =    2.300
peak=    3.157 closest distance to " CB  ASN A 224 " =    1.037
peak=    3.149 closest distance to " CA  ALA A 154 " =    0.991
peak=    3.145 closest distance to " O   HOH Z  10 " =    1.750
peak=    3.144 closest distance to " CA  ALA A 160 " =    0.850
peak=    3.144 closest distance to " O   HOH Z  61 " =    1.551
peak=    3.143 closest distance to " OD2 ASP A 200 " =    1.360
peak=    3.142 closest distance to " CA  ILE A 106 " =    0.784
peak=    3.141 closest distance to " O   HOH Z  90 " =    3.286
peak=    3.137 closest distance to " O   HOH Z 256 " =    2.324
peak=    3.135 closest distance to " CB  ILE A 120 " =    1.424
peak=    3.131 closest distance to " O   HOH Z 327 " =    1.731
peak=    3.127 closest distance to " NE AARG A 190 " =    2.089
peak=    3.127 closest distance to " CB  PRO A 243 " =    1.214
peak=    3.126 closest distance to " O   HOH Z 387 " =    3.110
peak=    3.125 closest distance to " CZ3 TRP A  85 " =    0.956
peak=    3.121 closest distance to " O   THR A  31 " =    1.516
peak=    3.120 closest distance to " O   HOH Z 109 " =    2.581
peak=    3.118 closest distance to " O   HOH Z 329 " =    2.702
peak=    3.116 closest distance to " O   HOH Z 251 " =    1.705
peak=    3.116 closest distance to " O   HOH Z 128 " =    1.847
peak=    3.111 closest distance to " O   HOH Z 367 " =    3.414
peak=    3.102 closest distance to " O   HOH Z 420 " =    5.746
peak=    3.085 closest distance to " O   HOH Z 406 " =    1.539
peak=    3.079 closest distance to " CB  ALA A 100 " =    1.258
peak=    3.073 closest distance to " CG2 ILE A 234 " =    0.867
peak=    3.067 closest distance to " CA  THR A 221 " =    1.442
peak=    3.055 closest distance to " O   HOH Z 391 " =    3.030
peak=    3.052 closest distance to " O   HOH Z 417 " =    2.221
peak=    3.050 closest distance to " CG  GLN A  89 " =    1.542
peak=    3.040 closest distance to " O   HOH Z  40 " =    2.459
peak=    3.038 closest distance to " O   HOH Z 123 " =    2.240
peak=    3.032 closest distance to " O   HOH Z 353 " =    2.774

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 209         
Filter by distance & map next to the model:
   mapped sites are within: 0.677 - 5.517
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 207 from: 209
   mapped sites are within: 0.796 - 5.517

peak=   -5.462 closest distance to " CG2 VAL A 230 " =    0.796
peak=   -4.661 closest distance to " CD  ARG A 156 " =    2.024
peak=   -4.633 closest distance to " CG2BVAL A  41 " =    2.583
peak=   -4.450 closest distance to " O   HOH Z 266 " =    4.721
peak=   -4.245 closest distance to " SG  CYS A 254 " =    3.239
peak=   -4.242 closest distance to " O   HOH Z 196 " =    2.209
peak=   -4.107 closest distance to " CB  ALA A 161 " =    2.573
peak=   -4.082 closest distance to " CE2 TYR A  30 " =    2.764
peak=   -4.064 closest distance to " C   HIS A 108 " =    1.190
peak=   -4.042 closest distance to " CG  ASP A 231 " =    0.852
peak=   -4.041 closest distance to " O   PRO A 163 " =    2.131
peak=   -4.028 closest distance to " O   HOH Z 290 " =    1.091
peak=   -3.992 closest distance to " OG  SER A  97 " =    2.280
peak=   -3.972 closest distance to " CD2 LEU A 300 " =    2.783
peak=   -3.958 closest distance to " NH2 ARG A  66 " =    1.654
peak=   -3.955 closest distance to " OE1 GLN A 223 " =    2.074
peak=   -3.951 closest distance to " O   HOH Z 166 " =    1.844
peak=   -3.904 closest distance to " O   HOH Z  37 " =    1.888
peak=   -3.858 closest distance to " OXT GLY A 302 " =    2.892
peak=   -3.857 closest distance to " CD1 LEU A 101 " =    2.493
peak=   -3.837 closest distance to " O   HOH Z 351 " =    1.535
peak=   -3.827 closest distance to " N   ALA A  43 " =    2.523
peak=   -3.822 closest distance to " NH2AARG A 275 " =    5.117
peak=   -3.801 closest distance to " CZ3 TRP A 179 " =    1.234
peak=   -3.799 closest distance to " OG ASER A 134 " =    1.306
peak=   -3.794 closest distance to " O   HOH Z  52 " =    1.593
peak=   -3.791 closest distance to " CG1 VAL A 250 " =    2.756
peak=   -3.790 closest distance to " O   HOH Z 292 " =    4.447
peak=   -3.782 closest distance to " O   HOH Z  11 " =    1.902
peak=   -3.745 closest distance to " CB  PRO A 243 " =    2.663
peak=   -3.731 closest distance to " CD  GLN A  58 " =    1.143
peak=   -3.726 closest distance to " C   ALA A 158 " =    1.286
peak=   -3.717 closest distance to " O   HOH Z 231 " =    2.001
peak=   -3.713 closest distance to " O   ALA A 256 " =    1.613
peak=   -3.704 closest distance to " OG BSER A 134 " =    1.226
peak=   -3.702 closest distance to " ND2 ASN A  45 " =    1.019
peak=   -3.700 closest distance to " O   HOH Z  17 " =    1.417
peak=   -3.693 closest distance to " O   HOH Z 166 " =    1.588
peak=   -3.677 closest distance to " CD  LYS A 289 " =    2.518
peak=   -3.673 closest distance to " O   HOH Z  13 " =    1.505
peak=   -3.672 closest distance to " O   HOH Z 407 " =    3.083
peak=   -3.662 closest distance to " O   HOH Z  19 " =    2.109
peak=   -3.659 closest distance to " O   HOH Z 426 " =    1.727
peak=   -3.649 closest distance to " N   GLN A  58 " =    1.729
peak=   -3.646 closest distance to " N   ALA A 226 " =    2.096
peak=   -3.629 closest distance to " N   THR A 235 " =    1.346
peak=   -3.628 closest distance to " O   HOH Z 118 " =    3.205
peak=   -3.628 closest distance to " O   HOH Z 353 " =    2.180
peak=   -3.627 closest distance to " CB  ALA A 248 " =    2.002
peak=   -3.624 closest distance to " CD  ARG A 139 " =    1.619
peak=   -3.623 closest distance to " CG  LEU A 101 " =    2.452
peak=   -3.617 closest distance to " CA  ASP A 298 " =    1.036
peak=   -3.613 closest distance to " O   HOH Z 283 " =    1.980
peak=   -3.601 closest distance to " O   HOH Z 389 " =    1.799
peak=   -3.596 closest distance to " O   HOH Z  43 " =    1.628
peak=   -3.591 closest distance to " CB  PRO A 280 " =    2.150
peak=   -3.574 closest distance to " CD1 PHE A  59 " =    1.880
peak=   -3.564 closest distance to " CE3 TRP A 150 " =    2.081
peak=   -3.558 closest distance to " CD1 LEU A 228 " =    2.309
peak=   -3.553 closest distance to " CD1 LEU A  25 " =    2.469
peak=   -3.552 closest distance to " NE2 GLN A  88 " =    2.019
peak=   -3.547 closest distance to " O   HOH Z 311 " =    3.672
peak=   -3.543 closest distance to " CE  MET A 105 " =    2.083
peak=   -3.543 closest distance to " N   THR A 157 " =    1.528
peak=   -3.540 closest distance to " CG1 VAL A 112 " =    2.649
peak=   -3.538 closest distance to " CG  ARG A 269 " =    2.337
peak=   -3.530 closest distance to " OG BSER A 134 " =    1.792
peak=   -3.527 closest distance to " CG2 ILE A 263 " =    2.371
peak=   -3.525 closest distance to " ND2 ASN A 187 " =    1.705
peak=   -3.522 closest distance to " O   VAL A 189 " =    2.615
peak=   -3.513 closest distance to " O   HOH Z 185 " =    2.371
peak=   -3.504 closest distance to " O   VAL A 125 " =    2.267
peak=   -3.490 closest distance to " OG  SER A  62 " =    1.612
peak=   -3.489 closest distance to " CG2 VAL A 296 " =    1.441
peak=   -3.482 closest distance to " OD1 ASN A 148 " =    1.523
peak=   -3.471 closest distance to " CE2 PHE A 218 " =    2.659
peak=   -3.470 closest distance to " CE BMET A  47 " =    1.939
peak=   -3.467 closest distance to " O   HOH Z 165 " =    1.975
peak=   -3.466 closest distance to " CG1 VAL A 112 " =    2.875
peak=   -3.465 closest distance to " O   VAL A  67 " =    2.570
peak=   -3.461 closest distance to " O   GLY A 196 " =    1.090
peak=   -3.460 closest distance to " O   HOH Z 222 " =    1.480
peak=   -3.457 closest distance to " CB  PRO A 163 " =    2.617
peak=   -3.454 closest distance to " CB  ALA A  43 " =    2.454
peak=   -3.447 closest distance to " O   ALA A 161 " =    1.728
peak=   -3.445 closest distance to " CD1 LEU A 101 " =    2.634
peak=   -3.439 closest distance to " O   HOH Z 262 " =    2.785
peak=   -3.423 closest distance to " O   HOH Z  10 " =    1.554
peak=   -3.422 closest distance to " CB  ALA A 248 " =    2.329
peak=   -3.421 closest distance to " C   SER A 206 " =    1.522
peak=   -3.420 closest distance to " CG  PHE A 283 " =    2.794
peak=   -3.418 closest distance to " N   MET A 105 " =    2.657
peak=   -3.415 closest distance to " NE2 GLN A 103 " =    1.734
peak=   -3.405 closest distance to " N   SER A 212 " =    1.946
peak=   -3.404 closest distance to " CG  TRP A 266 " =    1.868
peak=   -3.399 closest distance to " CB  TYR A  15 " =    2.251
peak=   -3.396 closest distance to " CG  GLU A  53 " =    1.553
peak=   -3.394 closest distance to " OG  SER A  26 " =    1.317
peak=   -3.392 closest distance to " CA  GLY A 203 " =    2.351
peak=   -3.392 closest distance to " CB  ASN A  39 " =    2.191
peak=   -3.390 closest distance to " O   HOH Z 431 " =    1.746
peak=   -3.388 closest distance to " OG  SER A  87 " =    1.436
peak=   -3.386 closest distance to " O   HOH Z 136 " =    2.079
peak=   -3.381 closest distance to " CG1 VAL A 296 " =    1.366
peak=   -3.376 closest distance to " CG2 VAL A 112 " =    2.590
peak=   -3.374 closest distance to " O   LYS A 117 " =    1.744
peak=   -3.368 closest distance to " CB  ALA A 291 " =    2.169
peak=   -3.366 closest distance to " N   SER A 276 " =    1.374
peak=   -3.357 closest distance to " CA  GLY A 133 " =    1.995
peak=   -3.352 closest distance to " C   ASN A 285 " =    2.444
peak=   -3.350 closest distance to " OD1 ASN A 187 " =    1.606
peak=   -3.348 closest distance to " C   MET A 188 " =    1.509
peak=   -3.346 closest distance to " CD1 PHE A  59 " =    2.295
peak=   -3.338 closest distance to " CB  ALA A  10 " =    2.261
peak=   -3.335 closest distance to " O   HOH Z 234 " =    4.180
peak=   -3.331 closest distance to " O   HOH Z 423 " =    2.222
peak=   -3.328 closest distance to " CD2 LEU A 167 " =    1.748
peak=   -3.328 closest distance to " O   HOH Z 102 " =    1.572
peak=   -3.328 closest distance to " CZ  PHE A  59 " =    1.679
peak=   -3.326 closest distance to " CG  GLU A 277 " =    1.109
peak=   -3.321 closest distance to " C   ASN A 187 " =    1.915
peak=   -3.320 closest distance to " O   SER A  95 " =    1.601
peak=   -3.317 closest distance to " O   HOH Z 275 " =    1.488
peak=   -3.309 closest distance to " CD2 TYR A 293 " =    2.066
peak=   -3.305 closest distance to " CZ  TYR A 169 " =    1.746
peak=   -3.302 closest distance to " O   HOH Z 252 " =    3.957
peak=   -3.295 closest distance to " O   HOH Z 241 " =    1.289
peak=   -3.284 closest distance to " CB  ALA A 291 " =    2.286
peak=   -3.283 closest distance to " O   SER A 258 " =    1.914
peak=   -3.283 closest distance to " O   PRO A 198 " =    1.244
peak=   -3.276 closest distance to " NE1 TRP A 266 " =    2.314
peak=   -3.271 closest distance to " CB  ASN A  69 " =    1.117
peak=   -3.270 closest distance to " O   HOH Z  38 " =    1.607
peak=   -3.266 closest distance to " NH1 ARG A 195 " =    2.600
peak=   -3.265 closest distance to " OG  SER A 206 " =    1.677
peak=   -3.261 closest distance to " C   LEU A 143 " =    1.049
peak=   -3.257 closest distance to " O   SER A 271 " =    2.050
peak=   -3.257 closest distance to " O   HOH Z 253 " =    3.937
peak=   -3.256 closest distance to " NH2 ARG A  79 " =    1.980
peak=   -3.253 closest distance to " O   HOH Z 174 " =    2.271
peak=   -3.250 closest distance to " O   HOH Z 435 " =    2.709
peak=   -3.250 closest distance to " CA  GLY A 241 " =    3.001
peak=   -3.248 closest distance to " CA  GLY A 133 " =    2.257
peak=   -3.248 closest distance to " CG  MET A 105 " =    0.890
peak=   -3.247 closest distance to " O   VAL A 197 " =    1.370
peak=   -3.241 closest distance to " O   GLY A 211 " =    1.454
peak=   -3.234 closest distance to " N   ASP A 171 " =    2.368
peak=   -3.233 closest distance to " C   THR A 279 " =    1.168
peak=   -3.230 closest distance to " ND2 ASN A  60 " =    1.474
peak=   -3.228 closest distance to " CG1 VAL A  78 " =    2.530
peak=   -3.227 closest distance to " O   HOH Z 193 " =    1.799
peak=   -3.222 closest distance to " CA  PRO A 243 " =    2.510
peak=   -3.220 closest distance to " CB  PHE A 192 " =    1.834
peak=   -3.220 closest distance to " O   HOH Z 265 " =    2.135
peak=   -3.214 closest distance to " C   ASP A 231 " =    2.654
peak=   -3.210 closest distance to " O   HOH Z  60 " =    2.196
peak=   -3.208 closest distance to " CB  ASP A 132 " =    2.287
peak=   -3.206 closest distance to " OXT GLY A 302 " =    3.396
peak=   -3.203 closest distance to " O   HOH Z 372 " =    2.317
peak=   -3.200 closest distance to " O   HOH Z  90 " =    1.683
peak=   -3.198 closest distance to " CG  ASP A  50 " =    2.382
peak=   -3.196 closest distance to " O   PRO A 198 " =    1.318
peak=   -3.194 closest distance to " O   HOH Z 150 " =    1.835
peak=   -3.189 closest distance to " N   ALA A 248 " =    1.630
peak=   -3.189 closest distance to " O   HOH Z  15 " =    1.574
peak=   -3.186 closest distance to " O   HOH Z  44 " =    2.166
peak=   -3.182 closest distance to " O   HOH Z 353 " =    2.128
peak=   -3.180 closest distance to " CD1 TYR A 247 " =    2.298
peak=   -3.179 closest distance to " CA  ASN A 127 " =    1.063
peak=   -3.170 closest distance to " CG  LEU A 228 " =    0.960
peak=   -3.168 closest distance to " O   LEU A 167 " =    1.506
peak=   -3.167 closest distance to " C   GLN A 205 " =    1.992
peak=   -3.165 closest distance to " O   HOH Z 350 " =    1.781
peak=   -3.163 closest distance to " O   HOH Z 232 " =    1.790
peak=   -3.159 closest distance to " CA  GLY A 241 " =    2.292
peak=   -3.159 closest distance to " CA  GLY A  98 " =    2.036
peak=   -3.157 closest distance to " OD2 ASP A 171 " =    2.251
peak=   -3.156 closest distance to " O   HOH Z 211 " =    1.623
peak=   -3.156 closest distance to " O   HOH Z 191 " =    5.517
peak=   -3.153 closest distance to " O   HOH Z 128 " =    2.480
peak=   -3.150 closest distance to " OG1 THR A  82 " =    1.448
peak=   -3.148 closest distance to " ND2BASN A 224 " =    1.677
peak=   -3.148 closest distance to " SG ACYS A 201 " =    2.293
peak=   -3.143 closest distance to " O   ILE A 234 " =    1.251
peak=   -3.139 closest distance to " C   LEU A 222 " =    0.876
peak=   -3.139 closest distance to " O   HOH Z 295 " =    1.431
peak=   -3.137 closest distance to " OD2 ASP A 171 " =    1.791
peak=   -3.123 closest distance to " CG1 VAL A 197 " =    2.290
peak=   -3.123 closest distance to " NE2 GLN A 194 " =    1.724
peak=   -3.118 closest distance to " O   HOH Z 123 " =    2.330
peak=   -3.117 closest distance to " CB  ALA A  51 " =    1.868
peak=   -3.115 closest distance to " O   HOH Z 414 " =    1.449
peak=   -3.112 closest distance to " O   HOH Z 348 " =    2.307
peak=   -3.099 closest distance to " CG  GLU A   2 " =    1.754
peak=   -3.089 closest distance to " O   HOH Z 266 " =    4.885
peak=   -3.085 closest distance to " O   HOH Z 313 " =    1.953
peak=   -3.083 closest distance to " CD  GLN A  88 " =    0.852
peak=   -3.083 closest distance to " O   HOH Z 111 " =    2.329
peak=   -3.066 closest distance to " O   HOH Z 189 " =    1.689
peak=   -3.062 closest distance to " CE  MET A  93 " =    1.254
peak=   -3.059 closest distance to " CD  ARG A 195 " =    5.089
peak=   -3.045 closest distance to " O   HOH Z   6 " =    1.832
peak=   -3.040 closest distance to " O   HOH Z 175 " =    4.447
peak=   -3.034 closest distance to " O   HOH Z 313 " =    1.102
peak=   -3.032 closest distance to " CG1 VAL A 296 " =    1.301
peak=   -3.031 closest distance to " CG  ASN A 301 " =    2.034
peak=   -3.019 closest distance to " O   GLY A  80 " =    2.600

================= 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    :  0.4423 0.4324   6.238344e+00   6.219286e+00
   1_bss:  0.4340 0.4227   6.236031e+00   6.207220e+00
   1_xyz:  0.3296 0.3579   6.042231e+00   6.094477e+00
   1_adp:  0.2724 0.3118   5.886979e+00   5.993803e+00
   1_occ:  0.2719 0.3117   5.886149e+00   5.993955e+00
   2_bss:  0.2680 0.3066   5.885345e+00   5.989815e+00
   2_xyz:  0.1792 0.2215   5.533268e+00   5.711417e+00
   2_adp:  0.1613 0.2046   5.441671e+00   5.635232e+00
   2_occ:  0.1611 0.2046   5.441257e+00   5.635272e+00
   3_bss:  0.1599 0.2033   5.441711e+00   5.634817e+00
   3_xyz:  0.1310 0.1700   5.258549e+00   5.468335e+00
   3_adp:  0.1252 0.1649   5.224711e+00   5.442652e+00
   3_occ:  0.1251 0.1649   5.224342e+00   5.442491e+00
   4_bss:  0.1254 0.1655   5.226504e+00   5.444663e+00
   4_xyz:  0.1151 0.1589   5.167178e+00   5.404100e+00
   4_adp:  0.1141 0.1588   5.162797e+00   5.402972e+00
   4_occ:  0.1140 0.1589   5.162926e+00   5.403384e+00
   5_bss:  0.1140 0.1589   5.162861e+00   5.403356e+00
   5_xyz:  0.1123 0.1580   5.154684e+00   5.398704e+00
   5_adp:  0.1119 0.1584   5.154942e+00   5.401577e+00
   5_occ:  0.1119 0.1586   5.155237e+00   5.402136e+00
   5_bss:  0.1119 0.1586   5.155279e+00   5.402167e+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:  0.340  20.001   7.218   9.666   8.061   0.000   0.000   0.000
   1_xyz:  0.340  20.001   7.218   9.666   8.061   0.000   0.000   0.000
   1_adp:  0.340  20.001   7.218   9.666   8.061   0.000   0.000   0.000
   1_occ:  0.340  20.001   7.218   9.666   8.061   0.000   0.000   0.000
   2_bss:  0.320  45.603   3.865   5.745   5.104   0.000   0.000   0.000
   2_xyz:  0.320  45.603   3.865   5.745   5.104   0.000   0.000   0.000
   2_adp:  0.320  45.603   3.865   5.745   5.104   0.000   0.000   0.000
   2_occ:  0.320  45.603   3.865   5.745   5.104   0.000   0.000   0.000
   3_bss:  0.322  45.603   2.812   3.870   3.935   0.000   0.000   0.000
   3_xyz:  0.322  45.603   2.812   3.870   3.935   0.000   0.000   0.000
   3_adp:  0.322  45.603   2.812   3.870   3.935   0.000   0.000   0.000
   3_occ:  0.322  45.603   2.812   3.870   3.935   0.000   0.000   0.000
   4_bss:  0.323  47.277   2.635   3.374   3.627   0.000   0.000   0.000
   4_xyz:  0.323  47.277   2.635   3.374   3.627   0.000   0.000   0.000
   4_adp:  0.323  47.277   2.635   3.374   3.627   0.000   0.000   0.000
   4_occ:  0.323  47.277   2.635   3.374   3.627   0.000   0.000   0.000
   5_bss:  0.321  46.646   2.719   3.305   3.672   0.000   0.000   0.000
   5_xyz:  0.321  46.646   2.719   3.305   3.672   0.000   0.000   0.000
   5_adp:  0.321  46.646   2.719   3.305   3.672   0.000   0.000   0.000
   5_occ:  0.321  46.646   2.719   3.305   3.672   0.000   0.000   0.000
   5_bss:  0.321  49.976  -0.489   0.036   0.453   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  48.883 0.5355  0.6013    53879.996
   1_bss:  48.999 0.5314  0.7612    51752.763
   1_xyz:  38.818 0.6552  0.9191    34793.664
   1_adp:  31.917 0.7367  1.0191    25505.846
   1_occ:  31.951 0.7363  1.0178    25517.145
   2_bss:  31.706 0.7389  0.9048    25180.493
   2_xyz:  21.786 0.8437  0.9967    12560.885
   2_adp:  19.606 0.8656  1.0111    10672.799
   2_occ:  19.609 0.8655  1.0109    10673.019
   3_bss:  19.585 0.8658  0.9627    10682.397
   3_xyz:  15.635 0.9013  0.9824     7378.584
   3_adp:  15.034 0.9067  0.9853     7060.320
   3_occ:  15.026 0.9068  0.9853     7058.684
   4_bss:  15.062 0.9066  0.9734     7114.760
   4_xyz:  14.309 0.9127  0.9746     6576.282
   4_adp:  14.273 0.9131  0.9716     6577.765
   4_occ:  14.276 0.9131  0.9715     6586.119
   5_bss:  14.274 0.9131  0.9723     6585.772
   5_xyz:  14.165 0.9140  0.9727     6499.462
   5_adp:  14.229 0.9135  0.9694     6529.146
   5_occ:  14.236 0.9134  0.9693     6537.296
   5_bss:  14.238 0.9134  0.9727     6538.187
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.3855e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.3855e+01
   1_xyz:   1.604  0.012  0.105 17.830  0.006  4.112   1.2656e-01
   1_adp:   1.604  0.012  0.105 17.830  0.006  4.112   1.2656e-01
   1_occ:   1.604  0.012  0.105 17.830  0.006  4.112   1.2656e-01
   2_bss:   1.604  0.012  0.105 17.830  0.006  4.112   1.2656e-01
   2_xyz:   1.025  0.007  0.074 16.115  0.004  4.128   6.5905e-02
   2_adp:   1.025  0.007  0.074 16.115  0.004  4.128   6.5905e-02
   2_occ:   1.025  0.007  0.074 16.115  0.004  4.128   6.5905e-02
   3_bss:   1.025  0.007  0.074 16.115  0.004  4.128   6.5905e-02
   3_xyz:   0.984  0.006  0.076 15.495  0.003  4.126   5.9161e-02
   3_adp:   0.984  0.006  0.076 15.495  0.003  4.126   5.9161e-02
   3_occ:   0.984  0.006  0.076 15.495  0.003  4.126   5.9161e-02
   4_bss:   0.984  0.006  0.076 15.495  0.003  4.126   5.9161e-02
   4_xyz:   1.057  0.008  0.085 15.683  0.004  4.113   6.7156e-02
   4_adp:   1.057  0.008  0.085 15.683  0.004  4.113   6.7156e-02
   4_occ:   1.057  0.008  0.085 15.683  0.004  4.113   6.7156e-02
   5_bss:   1.057  0.008  0.085 15.683  0.004  4.113   6.7156e-02
   5_xyz:   1.027  0.008  0.082 15.369  0.004  4.114   6.4189e-02
   5_adp:   1.027  0.008  0.082 15.369  0.004  4.114   6.4189e-02
   5_occ:   1.027  0.008  0.082 15.369  0.004  4.114   6.4189e-02
   5_bss:   1.027  0.008  0.082 15.369  0.004  4.114   6.4189e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9826e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9826e+00
   1_xyz:  14.147  0.152  0.483 88.225  0.048  2.269   9.5640e-02
   1_adp:  14.147  0.152  0.483 88.225  0.048  2.269   9.5640e-02
   1_occ:  14.147  0.152  0.483 88.225  0.048  2.269   9.5640e-02
   2_bss:  14.147  0.152  0.483 88.225  0.048  2.269   9.5640e-02
   2_xyz:   6.927  0.061  0.251 89.413  0.028  2.246   7.0381e-02
   2_adp:   6.927  0.061  0.251 89.413  0.028  2.246   7.0381e-02
   2_occ:   6.927  0.061  0.251 89.413  0.028  2.246   7.0381e-02
   3_bss:   6.927  0.061  0.251 89.413  0.028  2.246   7.0381e-02
   3_xyz:   6.590  0.042  0.459 80.955  0.039  2.371   6.5530e-02
   3_adp:   6.590  0.042  0.459 80.955  0.039  2.371   6.5530e-02
   3_occ:   6.590  0.042  0.459 80.955  0.039  2.371   6.5530e-02
   4_bss:   6.590  0.042  0.459 80.955  0.039  2.371   6.5530e-02
   4_xyz:   7.182  0.043  0.609 83.389  0.041  2.348   4.6248e-02
   4_adp:   7.182  0.043  0.609 83.389  0.041  2.348   4.6248e-02
   4_occ:   7.182  0.043  0.609 83.389  0.041  2.348   4.6248e-02
   5_bss:   7.182  0.043  0.609 83.389  0.041  2.348   4.6248e-02
   5_xyz:   7.116  0.047  0.571 81.981  0.039  2.359   4.4412e-02
   5_adp:   7.116  0.047  0.571 81.981  0.039  2.359   4.4412e-02
   5_occ:   7.116  0.047  0.571 81.981  0.039  2.359   4.4412e-02
   5_bss:   7.116  0.047  0.571 81.981  0.039  2.359   4.4412e-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:  65.96   0.00  10.87  63.49   0.00   7.87  65.96   0.00  27.20
   1_occ:  65.96   0.00  10.87  63.49   0.00   7.87  65.96   0.00  27.20
   2_bss:  65.96   0.00  10.87  63.49   0.00   7.87  65.96   0.00  27.20
   2_xyz:  65.96   0.00  10.87  63.49   0.00   7.87  65.96   0.00  27.20
   2_adp:  71.67   0.00  11.50  71.67   0.00   7.66  66.69   0.91  32.39
   2_occ:  71.67   0.00  11.50  71.67   0.00   7.66  66.69   0.91  32.39
   3_bss:  71.67   0.00  11.50  71.67   0.00   7.66  66.69   0.91  32.39
   3_xyz:  71.67   0.00  11.50  71.67   0.00   7.66  66.69   0.91  32.39
   3_adp:  77.06   0.00  11.83  77.06   0.00   7.69  68.86   0.84  34.34
   3_occ:  77.06   0.00  11.83  77.06   0.00   7.69  68.86   0.84  34.34
   4_bss:  77.06   0.00  11.83  77.06   0.00   7.69  68.86   0.84  34.34
   4_xyz:  77.06   0.00  11.83  77.06   0.00   7.69  68.86   0.84  34.34
   4_adp:  79.07   0.00  11.77  79.07   0.00   7.64  69.36   0.79  34.26
   4_occ:  79.07   0.00  11.77  79.07   0.00   7.64  69.36   0.79  34.26
   5_bss:  79.07   0.00  11.77  79.07   0.00   7.64  69.36   0.79  34.26
   5_xyz:  79.07   0.00  11.77  79.07   0.00   7.64  69.36   0.79  34.26
   5_adp:  80.71   0.00  11.72  80.71   0.00   7.59  69.10   0.89  34.22
   5_occ:  80.71   0.00  11.72  80.71   0.00   7.59  69.10   0.89  34.22
   5_bss:  84.04   3.33  15.05  84.04   3.33  10.92  72.43   4.22  37.55
------------------------------------------------------------------------
 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:    1.187    0.024    0.409
   1_adp:    1.187    0.024    0.409
   1_occ:    1.187    0.024    0.409
   2_bss:    1.187    0.024    0.409
   2_xyz:    1.503    0.028    0.537
   2_adp:    1.503    0.028    0.537
   2_occ:    1.503    0.028    0.537
   3_bss:    1.503    0.028    0.537
   3_xyz:    1.558    0.024    0.570
   3_adp:    1.558    0.024    0.570
   3_occ:    1.558    0.024    0.570
   4_bss:    1.558    0.024    0.570
   4_xyz:    1.599    0.059    0.593
   4_adp:    1.599    0.059    0.593
   4_occ:    1.599    0.059    0.593
   5_bss:    1.599    0.059    0.593
   5_xyz:    1.674    0.056    0.605
   5_adp:    1.674    0.056    0.605
   5_occ:    1.674    0.056    0.605
   5_bss:    1.674    0.056    0.605
------------------------------------------------------------------------

CPU time actual refinement: 325.10


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_806/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_806/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_806/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_806/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_806/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 324.94 
  Macro-tasks:
    bulk solvent and scale       = 41.49  
    individual site refinement   = 136.45 
    weights calculation          = 31.50  
    collect and process          = 6.38   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 215.92 
  Micro-tasks:
    mask                            = 1.78   
    f_calc                          = 97.99  
    alpha_beta                      = 8.08   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 109.92 
    fmodel                         = 7.44   
    r_factors                      = 0.23   
    phase_errors                   = 10.57  
    foms                           = 0.21   
    TOTAL for micro-tasks          = 237.39 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.503 micro seconds
Total CPU time: 5.65 minutes
from_scatterers_fft:    660 calls, 97.70 s
gradients_fft:          604 calls, 95.86 s

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

# Date 2008-01-16 Time 02:27:49 PST -0800 (1200479269.10 s)
Start R-work = 0.4423, R-free = 0.4324 (no bulk solvent and anisotropic scale)
Final R-work = 0.1286, R-free = 0.1741 (no bulk solvent and anisotropic scale)

Start R-work = 0.4340, R-free = 0.4227
Final R-work = 0.1119, R-free = 0.1586