# Date 2008-01-16 Time 01:10:29 PST -0800 (1200474629.28 s)
#phil __OFF__

Command line arguments: "../323.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 22752
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 323

-------------------------------------------------------------------------------
  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: (69.1963, 47.3993, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.27, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.3993, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8295 1.97064
Completeness in resolution range: 0.953932
Completeness with d_max=infinity: 0.950968

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8295
                             d_min =   1.9706

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: (69.1963, 47.3993, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8295 1.97064
Completeness in resolution range: 0.953932
Completeness with d_max=infinity: 0.950968

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8299 -  4.2161 [2168/2196]  1950   218  10.1%
  bin  2:  4.2161 -  3.3593 [2054/2077]  1850   204   9.9%
  bin  3:  3.3593 -  2.9384 [2050/2072]  1845   205  10.0%
  bin  4:  2.9384 -  2.6714 [2028/2047]  1825   203  10.0%
  bin  5:  2.6714 -  2.4809 [2008/2037]  1798   210  10.5%
  bin  6:  2.4809 -  2.3352 [1999/2041]  1810   189   9.5%
  bin  7:  2.3352 -  2.2187 [1991/2027]  1792   199  10.0%
  bin  8:  2.2187 -  2.1224 [1987/2024]  1784   203  10.2%
  bin  9:  2.1224 -  2.0409 [1967/1999]  1776   191   9.7%
  bin 10:  2.0409 -  1.9706 [1337/2015]  1200   137  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_323/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:
        1.60 -     2.26: 14
        2.26 -     2.92: 1502
        2.92 -     3.58: 4513
        3.58 -     4.24: 9245
        4.24 -     4.90: 13172
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.601 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.797 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.843 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  81 " - " O   HOH Z 186 "  1.915 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28441 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_323/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_323/model_refine_001.geo

CPU time processing inputs: 9.12


============================ 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 = 69.19625 47.3993 85.95805 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: 1.97 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4555   r_free= 0.4424   ksol= 0.00   Bsol= 0.00   scale= 0.814    |
|                                                                             |
| 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:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.252745                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8299 -  4.7022 0.99   1400  157 0.3718 0.3603      6.5369      6.5663|
|  2:  4.7022 -  3.7522 0.99   1351  150 0.3581 0.3627      6.7013      6.7216|
|  3:  3.7522 -  3.2837 0.99   1325  150 0.4063 0.3817      6.6096      6.6296|
|  4:  3.2837 -  2.9862 0.99   1312  134 0.4310 0.3960      6.4692       6.384|
|  5:  2.9862 -  2.7736 0.98   1292  149 0.4830 0.4821      6.3505      6.3879|
|  6:  2.7736 -  2.6110 0.98   1295  143 0.4792 0.5277       6.254       6.192|
|  7:  2.6110 -  2.4809 0.99   1293  157 0.4888 0.4600      6.2347      6.1515|
|  8:  2.4809 -  2.3734 0.99   1311  128 0.5020 0.4729      6.1612      6.1551|
|  9:  2.3734 -  2.2823 0.98   1277  147 0.5031 0.5335      6.0979      6.1496|
| 10:  2.2823 -  2.2038 0.98   1262  143 0.5144 0.4799      6.1147      6.0652|
| 11:  2.2038 -  2.1351 0.98   1286  146 0.5128 0.4774       6.022      6.0321|
| 12:  2.1351 -  2.0743 0.99   1281  137 0.5298 0.5302      5.9743      6.0112|
| 13:  2.0743 -  2.0198 0.97   1260  133 0.5269 0.5121      5.8953      5.8404|
| 14:  2.0198 -  1.9706 0.54    685   85 0.5186 0.4756      5.8592      5.7305|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8299 -  4.7022  1400   157  0.70  34.36   0.81     0.71      68697.73|
|  2:  4.7022 -  3.7522  1351   150  0.73  32.22   0.91     0.78      89150.29|
|  3:  3.7522 -  3.2837  1325   150  0.66  38.46   0.87     0.76      90704.02|
|  4:  3.2837 -  2.9862  1312   134  0.61  43.20   0.82     0.69      76614.51|
|  5:  2.9862 -  2.7736  1292   149  0.51  51.42   0.75     0.59      68312.41|
|  6:  2.7736 -  2.6110  1295   143  0.48  53.88   0.75     0.54      61373.54|
|  7:  2.6110 -  2.4809  1293   157  0.45  55.74   0.76     0.51      58026.23|
|  8:  2.4809 -  2.3734  1311   128  0.45  55.71   0.75     0.52      50490.99|
|  9:  2.3734 -  2.2823  1277   147  0.44  56.60   0.75     0.52      46904.24|
| 10:  2.2823 -  2.2038  1262   143  0.45  55.79   0.76     0.53      42200.98|
| 11:  2.2038 -  2.1351  1286   146  0.42  58.68   0.75     0.51      41786.34|
| 12:  2.1351 -  2.0743  1281   137  0.39  60.89   0.77     0.50      40043.89|
| 13:  2.0743 -  2.0198  1260   133  0.39  61.20   0.75     0.47      33990.96|
| 14:  2.0198 -  1.9706   685    85  0.45  56.26   0.73     0.47      23437.93|
|alpha:            min =        0.47 max =            0.78 mean =         0.59|
|beta:             min =    23437.93 max =        90704.02 mean =     58046.02|
|figures of merit: min =        0.00 max =            1.00 mean =         0.51|
|phase err.(work): min =        0.00 max =           89.95 mean =        50.62|
|phase err.(test): min =        0.00 max =           89.95 mean =        50.56|
|-----------------------------------------------------------------------------|

============================== 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 = 9.382354              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.378   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.791143              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.150   (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 |  1.103 -  1.483:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.483 -  1.862:       10 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.862 -  2.242:      127 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.242 -  2.622:      607 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.622 -  3.002:     1427 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.002 -  3.381:     2536 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.381 -  3.761:     3959 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.761 -  4.141:     5201 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.141 -  4.520:     6674 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.520 -  4.900:     7918 |
|-----------------------------------------------------------------------------|
|-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 |       53.532 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.103 |       2.055 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.743)------------------------------------------|
|    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 = 11.743)------------------------------------------|
|    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: 1.97 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4625   r_free= 0.4510   ksol= 0.00   Bsol= 0.00   scale= 0.783    |
|                                                                             |
| 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:   0.66 A                  |
| x-ray target function (ml) for work reflections: 6.255488                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4464   r_free= 0.4366   ksol= 0.36   Bsol= 19.80   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.75,9.51,7.83,0.00,0.00,0.00); trace/3= 8.36                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.244270                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.134128              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.884   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.823425              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.096   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4464      final r-factor (work) = 0.3442          |
| start r-factor (free) = 0.4366      final r-factor (free) = 0.3657          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 82.1236 = 9.13 * 0.50 * 6.2605 + 1.00 * 53.5316                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.0848 = 9.13 * 0.50 * 6.1204 + 1.00 * 0.1324                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3442      final r-factor (work) = 0.2886          |
| start r-factor (free) = 0.3657      final r-factor (free) = 0.3242          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0540 = 0.82 * 1.00 * 6.1204 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.9350 = 0.82 * 1.00 * 5.9768 + 1.00 * 0.0135                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.743)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    68.45   11.53    None  None   None       |
|    all(noH): 2823   0      0.00    68.45   11.53    None  None   None       |
|    Sol.    : 438    0      0.00    68.45   27.15    None  None   None       |
|    Mac.    : 2385   0      0.00    64.26   8.67     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 -   6.845: 1285   |   5:    34.224 -  41.068:   96        |
|      1:     6.845 -  13.690:  736   |   6:    41.068 -  47.913:   44        |
|      2:    13.690 -  20.534:  320   |   7:    47.913 -  54.758:   28        |
|      3:    20.534 -  27.379:  173   |   8:    54.758 -  61.603:   11        |
|      4:    27.379 -  34.224:  123   |   9:    61.603 -  68.447:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2886 r_free = 0.3242             target_work(ml) = 5.933         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2881 r_free = 0.3241             target_work(ml) = 5.932         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2881   r_free= 0.3241   ksol= 0.36   Bsol= 19.80   scale= 1.097   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.75,9.51,7.83,0.00,0.00,0.00); trace/3= 8.36                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.36 A                  |
| x-ray target function (ml) for work reflections: 5.931784                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2841   r_free= 0.3199   ksol= 0.33   Bsol= 35.89   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.21,5.64,4.88,0.00,0.00,0.00); trace/3= 4.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.931502                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.453037              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.448   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.359083              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.260  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2841      final r-factor (work) = 0.1981          |
| start r-factor (free) = 0.3199      final r-factor (free) = 0.2374          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.4560 = 3.45 * 0.50 * 5.9794 + 1.00 * 0.1324                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.0229 = 3.45 * 0.50 * 5.7680 + 1.00 * 0.0642                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1981      final r-factor (work) = 0.1799          |
| start r-factor (free) = 0.2374      final r-factor (free) = 0.2219          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0857 = 0.36 * 1.00 * 5.7680 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0134 = 0.36 * 1.00 * 5.5687 + 1.00 * 0.0138                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.743)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.30   11.83    None  None   None       |
|    all(noH): 2823   0      0.00    72.30   11.83    None  None   None       |
|    Sol.    : 438    0      1.61    63.55   31.89    None  None   None       |
|    Mac.    : 2385   0      0.00    72.30   8.14     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 -   7.230: 1437   |   5:    36.148 -  43.378:   91        |
|      1:     7.230 -  14.459:  711   |   6:    43.378 -  50.608:   79        |
|      2:    14.459 -  21.689:  213   |   7:    50.608 -  57.837:   32        |
|      3:    21.689 -  28.919:  128   |   8:    57.837 -  65.067:   15        |
|      4:    28.919 -  36.148:  112   |   9:    65.067 -  72.297:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1799 r_free = 0.2219             target_work(ml) = 5.536         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1798 r_free = 0.2217             target_work(ml) = 5.536         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1798   r_free= 0.2217   ksol= 0.33   Bsol= 35.89   scale= 1.042   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.21,5.64,4.88,0.00,0.00,0.00); trace/3= 4.91                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.536006                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1781   r_free= 0.2213   ksol= 0.32   Bsol= 35.89   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.46,3.87,3.95,0.00,0.00,0.00); trace/3= 3.43                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.534742                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.814435              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.857  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.200309              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 109.216  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1781      final r-factor (work) = 0.1331          |
| start r-factor (free) = 0.2213      final r-factor (free) = 0.1716          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9102 = 2.81 * 0.50 * 5.5756 + 1.00 * 0.0641                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6755 = 2.81 * 0.50 * 5.4105 + 1.00 * 0.0617                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1331      final r-factor (work) = 0.1265          |
| start r-factor (free) = 0.1716      final r-factor (free) = 0.1626          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1111 = 0.20 * 1.00 * 5.4105 + 1.00 * 0.0273                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0607 = 0.20 * 1.00 * 5.2486 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.743)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.22   11.79    None  None   None       |
|    all(noH): 2823   0      0.00    72.22   11.79    None  None   None       |
|    Sol.    : 438    0      1.63    63.15   32.78    None  None   None       |
|    Mac.    : 2385   0      0.00    72.22   7.94     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 -   7.222: 1496   |   5:    36.111 -  43.333:  110        |
|      1:     7.222 -  14.445:  688   |   6:    43.333 -  50.556:   70        |
|      2:    14.445 -  21.667:  181   |   7:    50.556 -  57.778:   35        |
|      3:    21.667 -  28.889:  111   |   8:    57.778 -  65.000:   14        |
|      4:    28.889 -  36.111:  113   |   9:    65.000 -  72.222:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1265 r_free = 0.1626             target_work(ml) = 5.222         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1263 r_free = 0.1624             target_work(ml) = 5.221         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1263   r_free= 0.1624   ksol= 0.32   Bsol= 35.89   scale= 1.016   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.46,3.87,3.95,0.00,0.00,0.00); trace/3= 3.43                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.221098                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1265   r_free= 0.1621   ksol= 0.33   Bsol= 42.62   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.99,3.15,3.55,0.00,0.00,0.00); trace/3= 2.90                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.222146                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.488488              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 126.779  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.326147              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 113.786  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1265      final r-factor (work) = 0.1200          |
| start r-factor (free) = 0.1621      final r-factor (free) = 0.1582          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9703 = 1.49 * 0.50 * 5.2518 + 1.00 * 0.0617                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.9231 = 1.49 * 0.50 * 5.1976 + 1.00 * 0.0548                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1200      final r-factor (work) = 0.1177          |
| start r-factor (free) = 0.1582      final r-factor (free) = 0.1580          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7052 = 0.33 * 1.00 * 5.1976 + 1.00 * 0.0101                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.7088 = 0.33 * 1.00 * 5.1776 + 1.00 * 0.0201                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.743)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.47   11.97    None  None   None       |
|    all(noH): 2823   0      0.00    76.47   11.97    None  None   None       |
|    Sol.    : 438    0      1.26    65.82   33.90    None  None   None       |
|    Mac.    : 2385   0      0.00    76.47   7.94     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 -   7.647: 1588   |   5:    38.234 -  45.881:  102        |
|      1:     7.647 -  15.294:  634   |   6:    45.881 -  53.527:   67        |
|      2:    15.294 -  22.940:  158   |   7:    53.527 -  61.174:   34        |
|      3:    22.940 -  30.587:  114   |   8:    61.174 -  68.821:   11        |
|      4:    30.587 -  38.234:  109   |   9:    68.821 -  76.468:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1177 r_free = 0.1580             target_work(ml) = 5.177         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1176 r_free = 0.1580             target_work(ml) = 5.176         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1176   r_free= 0.1580   ksol= 0.33   Bsol= 42.62   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.99,3.15,3.55,0.00,0.00,0.00); trace/3= 2.90                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.175872                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1176   r_free= 0.1580   ksol= 0.33   Bsol= 42.62   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.97,3.03,3.55,0.00,0.00,0.00); trace/3= 2.85                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.175852                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.076098              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 125.888  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.830020              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.701   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1176      final r-factor (work) = 0.1122          |
| start r-factor (free) = 0.1580      final r-factor (free) = 0.1551          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4288 = 2.08 * 0.50 * 5.1770 + 1.00 * 0.0548                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4147 = 2.08 * 0.50 * 5.1547 + 1.00 * 0.0639                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1122      final r-factor (work) = 0.1110          |
| start r-factor (free) = 0.1551      final r-factor (free) = 0.1560          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3309 = 0.83 * 1.00 * 5.1547 + 1.00 * 0.0524                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2774 = 0.83 * 1.00 * 5.1386 + 1.00 * 0.0123                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.743)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.62   12.14    None  None   None       |
|    all(noH): 2823   0      0.00    83.62   12.14    None  None   None       |
|    Sol.    : 438    0      1.11    73.64   34.87    None  None   None       |
|    Mac.    : 2385   0      0.00    83.62   7.96     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 -   8.362: 1684   |   5:    41.811 -  50.173:   94        |
|      1:     8.362 -  16.724:  567   |   6:    50.173 -  58.535:   56        |
|      2:    16.724 -  25.086:  162   |   7:    58.535 -  66.897:   26        |
|      3:    25.086 -  33.448:  108   |   8:    66.897 -  75.259:    8        |
|      4:    33.448 -  41.811:  113   |   9:    75.259 -  83.621:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1110 r_free = 0.1560             target_work(ml) = 5.143         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1110 r_free = 0.1560             target_work(ml) = 5.143         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1110   r_free= 0.1560   ksol= 0.33   Bsol= 42.62   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.97,3.03,3.55,0.00,0.00,0.00); trace/3= 2.85                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.142680                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8299 -  4.7022 0.99   1400  157 0.0994 0.1285      5.3791      5.5311|
|  2:  4.7022 -  3.7522 0.99   1351  150 0.0849 0.1091      5.4282      5.6353|
|  3:  3.7522 -  3.2837 0.99   1325  150 0.1050 0.1489       5.465      5.8275|
|  4:  3.2837 -  2.9862 0.99   1312  134 0.1186 0.1549      5.4346      5.6116|
|  5:  2.9862 -  2.7736 0.98   1292  149 0.1315 0.1623      5.3204      5.4807|
|  6:  2.7736 -  2.6110 0.98   1295  143 0.1241 0.1989       5.218      5.4932|
|  7:  2.6110 -  2.4809 0.99   1293  157 0.1196 0.1607      5.1534      5.3765|
|  8:  2.4809 -  2.3734 0.99   1311  128 0.1160 0.1718      5.0772      5.3181|
|  9:  2.3734 -  2.2823 0.98   1277  147 0.1171 0.1840        5.02      5.3162|
| 10:  2.2823 -  2.2038 0.98   1262  143 0.1116 0.1656      4.9621      5.1745|
| 11:  2.2038 -  2.1351 0.98   1286  146 0.1132 0.1711      4.9222      5.2459|
| 12:  2.1351 -  2.0743 0.99   1281  137 0.1094 0.1668      4.8491      5.1418|
| 13:  2.0743 -  2.0198 0.97   1260  133 0.1095 0.1687      4.7851       5.021|
| 14:  2.0198 -  1.9706 0.54    685   85 0.1110 0.1795       4.723      4.9611|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8299 -  4.7022  1400   157  0.94   8.85   0.98     0.96       6941.89|
|  2:  4.7022 -  3.7522  1351   150  0.95   7.83   1.02     1.00       8810.31|
|  3:  3.7522 -  3.2837  1325   150  0.94  11.09   1.03     1.02      10293.50|
|  4:  3.2837 -  2.9862  1312   134  0.92  13.54   1.01     1.00      10102.45|
|  5:  2.9862 -  2.7736  1292   149  0.90  15.95   0.99     0.96       8194.29|
|  6:  2.7736 -  2.6110  1295   143  0.90  16.34   0.97     0.94       7093.45|
|  7:  2.6110 -  2.4809  1293   157  0.91  15.22   0.98     0.95       6083.67|
|  8:  2.4809 -  2.3734  1311   128  0.91  15.05   1.00     0.97       5453.86|
|  9:  2.3734 -  2.2823  1277   147  0.91  15.63   1.00     0.98       4931.21|
| 10:  2.2823 -  2.2038  1262   143  0.90  15.90   0.99     0.96       4489.62|
| 11:  2.2038 -  2.1351  1286   146  0.90  15.90   1.00     0.96       4269.95|
| 12:  2.1351 -  2.0743  1281   137  0.91  14.94   1.01     0.99       3734.01|
| 13:  2.0743 -  2.0198  1260   133  0.91  15.74   1.00     0.99       3367.43|
| 14:  2.0198 -  1.9706   685    85  0.90  16.14   0.98     0.93       2905.04|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2905.04 max =        10293.50 mean =      6340.00|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.92 mean =        14.02|
|phase err.(test): min =        0.00 max =           88.41 mean =        13.53|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1110   r_free= 0.1560   ksol= 0.32   Bsol= 46.32   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.87,0.16,0.71,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.142625                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.83 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1110   r_free= 0.1560   ksol= 0.32   Bsol= 46.32   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.87,0.16,0.71,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.142625                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8299 -  4.7022 0.99   1400  157 0.0994 0.1285      5.3788      5.5316|
|  2:  4.7022 -  3.7522 0.99   1351  150 0.0851 0.1092      5.4292      5.6362|
|  3:  3.7522 -  3.2837 0.99   1325  150 0.1051 0.1489      5.4655      5.8277|
|  4:  3.2837 -  2.9862 0.99   1312  134 0.1186 0.1547      5.4345      5.6113|
|  5:  2.9862 -  2.7736 0.98   1292  149 0.1314 0.1623        5.32      5.4802|
|  6:  2.7736 -  2.6110 0.98   1295  143 0.1241 0.1988      5.2176      5.4926|
|  7:  2.6110 -  2.4809 0.99   1293  157 0.1196 0.1607       5.153      5.3766|
|  8:  2.4809 -  2.3734 0.99   1311  128 0.1160 0.1717       5.077      5.3178|
|  9:  2.3734 -  2.2823 0.98   1277  147 0.1171 0.1840      5.0199      5.3162|
| 10:  2.2823 -  2.2038 0.98   1262  143 0.1116 0.1657      4.9621      5.1747|
| 11:  2.2038 -  2.1351 0.98   1286  146 0.1131 0.1711      4.9221      5.2458|
| 12:  2.1351 -  2.0743 0.99   1281  137 0.1094 0.1669       4.849      5.1419|
| 13:  2.0743 -  2.0198 0.97   1260  133 0.1096 0.1687       4.785      5.0207|
| 14:  2.0198 -  1.9706 0.54    685   85 0.1110 0.1794      4.7229      4.9606|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8299 -  4.7022  1400   157  0.94   8.84   0.98     0.96       6932.02|
|  2:  4.7022 -  3.7522  1351   150  0.95   7.84   1.02     1.00       8819.07|
|  3:  3.7522 -  3.2837  1325   150  0.94  11.10   1.03     1.02      10311.49|
|  4:  3.2837 -  2.9862  1312   134  0.92  13.54   1.01     1.00      10099.14|
|  5:  2.9862 -  2.7736  1292   149  0.90  15.95   1.00     0.97       8185.48|
|  6:  2.7736 -  2.6110  1295   143  0.90  16.33   0.98     0.94       7086.18|
|  7:  2.6110 -  2.4809  1293   157  0.91  15.21   0.99     0.96       6078.93|
|  8:  2.4809 -  2.3734  1311   128  0.91  15.05   1.00     0.98       5451.65|
|  9:  2.3734 -  2.2823  1277   147  0.91  15.63   1.01     0.98       4930.21|
| 10:  2.2823 -  2.2038  1262   143  0.90  15.90   1.00     0.97       4488.95|
| 11:  2.2038 -  2.1351  1286   146  0.90  15.90   1.00     0.97       4269.38|
| 12:  2.1351 -  2.0743  1281   137  0.91  14.94   1.01     1.00       3733.11|
| 13:  2.0743 -  2.0198  1260   133  0.91  15.74   1.00     1.00       3365.49|
| 14:  2.0198 -  1.9706   685    85  0.90  16.13   0.98     0.94       2902.00|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2902.00 max =        10311.49 mean =      6338.82|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.88 mean =        14.02|
|phase err.(test): min =        0.00 max =           88.41 mean =        13.53|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.743)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.99    86.62   15.13    None  None   None       |
|    all(noH): 2823   0      2.99    86.62   15.13    None  None   None       |
|    Sol.    : 438    0      4.10    76.64   37.86    None  None   None       |
|    Mac.    : 2385   0      2.99    86.62   10.96    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.994 -  11.356: 1684   |   5:    44.805 -  53.167:   94        |
|      1:    11.356 -  19.718:  567   |   6:    53.167 -  61.529:   56        |
|      2:    19.718 -  28.081:  162   |   7:    61.529 -  69.891:   26        |
|      3:    28.081 -  36.443:  108   |   8:    69.891 -  78.253:    8        |
|      4:    36.443 -  44.805:  113   |   9:    78.253 -  86.615:    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)= 302         
Filter by distance & map next to the model:
   mapped sites are within: 0.289 - 4.817
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 299 from: 302
   mapped sites are within: 0.704 - 4.817

peak=   11.296 closest distance to " CB  VAL A 230 " =    1.443
peak=    7.510 closest distance to " CG2 VAL A 296 " =    1.161
peak=    6.273 closest distance to " CG  LEU A   5 " =    1.165
peak=    5.580 closest distance to " NH2 ARG A  56 " =    2.208
peak=    5.377 closest distance to " CB  VAL A 296 " =    1.051
peak=    5.273 closest distance to " CG  PRO A  54 " =    1.271
peak=    5.238 closest distance to " CG  LEU A 228 " =    1.143
peak=    5.092 closest distance to " CB  ARG A 275 " =    0.934
peak=    5.056 closest distance to " CB  GLN A 223 " =    1.382
peak=    4.938 closest distance to " O   HOH Z 209 " =    2.321
peak=    4.927 closest distance to " O   HOH Z 193 " =    1.754
peak=    4.923 closest distance to " CD2 LEU A   5 " =    1.111
peak=    4.893 closest distance to " CB  SER A  63 " =    1.181
peak=    4.795 closest distance to " CB  GLN A 183 " =    1.317
peak=    4.772 closest distance to " CG  PRO A 213 " =    1.233
peak=    4.771 closest distance to " NE2 GLN A  11 " =    1.036
peak=    4.765 closest distance to " O   HOH Z 142 " =    1.697
peak=    4.743 closest distance to " O   HOH Z 402 " =    1.498
peak=    4.718 closest distance to " O   HOH Z 126 " =    1.917
peak=    4.705 closest distance to " O   HOH Z  85 " =    1.479
peak=    4.659 closest distance to " O   SER A  87 " =    2.240
peak=    4.654 closest distance to " O   HOH Z 124 " =    1.422
peak=    4.646 closest distance to " CB  PRO A  54 " =    0.929
peak=    4.609 closest distance to " O   HOH Z 232 " =    2.299
peak=    4.600 closest distance to " CB  VAL A 230 " =    1.148
peak=    4.527 closest distance to " O   HOH Z 298 " =    1.809
peak=    4.490 closest distance to " C   PRO A 198 " =    1.464
peak=    4.489 closest distance to " O   HOH Z 346 " =    1.549
peak=    4.387 closest distance to " O   HOH Z 423 " =    1.823
peak=    4.371 closest distance to " O   HOH Z 102 " =    1.335
peak=    4.364 closest distance to " O   HOH Z 403 " =    1.797
peak=    4.354 closest distance to " CB  GLU A 152 " =    1.128
peak=    4.348 closest distance to " O   HOH Z  97 " =    1.912
peak=    4.337 closest distance to " O   HOH Z 234 " =    3.586
peak=    4.334 closest distance to " O   HOH Z 272 " =    1.889
peak=    4.295 closest distance to " O   HOH Z  59 " =    2.243
peak=    4.261 closest distance to " CB  SER A   3 " =    1.253
peak=    4.237 closest distance to " CG  PRO A 198 " =    1.166
peak=    4.235 closest distance to " O   HOH Z  63 " =    2.233
peak=    4.231 closest distance to " O   HOH Z 414 " =    1.597
peak=    4.212 closest distance to " O   HOH Z 316 " =    2.937
peak=    4.204 closest distance to " CA  TYR A  30 " =    0.934
peak=    4.191 closest distance to " O   HOH Z 236 " =    1.880
peak=    4.171 closest distance to " CG  PRO A 243 " =    1.171
peak=    4.171 closest distance to " O   HOH Z  80 " =    1.791
peak=    4.167 closest distance to " CB  ASN A 148 " =    1.453
peak=    4.157 closest distance to " CB  TYR A 169 " =    0.712
peak=    4.151 closest distance to " O   HOH Z 368 " =    2.253
peak=    4.150 closest distance to " CD2 LEU A 228 " =    1.196
peak=    4.079 closest distance to " CB  ARG A  79 " =    1.351
peak=    4.065 closest distance to " CB  GLU A 277 " =    3.573
peak=    4.053 closest distance to " O   HOH Z  97 " =    2.430
peak=    4.043 closest distance to " O   HOH Z 126 " =    1.994
peak=    4.041 closest distance to " O   HOH Z  54 " =    1.602
peak=    4.040 closest distance to " N   ASN A  39 " =    1.223
peak=    4.020 closest distance to " ND2 ASN A 187 " =    1.580
peak=    4.006 closest distance to " CD2 TRP A 179 " =    1.400
peak=    3.998 closest distance to " CB  TRP A 179 " =    1.256
peak=    3.996 closest distance to " O   HOH Z 203 " =    1.656
peak=    3.989 closest distance to " O   HOH Z 327 " =    1.577
peak=    3.988 closest distance to " O   HOH Z 284 " =    2.917
peak=    3.979 closest distance to " O   HOH Z 369 " =    2.409
peak=    3.963 closest distance to " O   HOH Z  48 " =    1.696
peak=    3.953 closest distance to " CG1BVAL A  72 " =    1.690
peak=    3.944 closest distance to " O   HOH Z  40 " =    1.723
peak=    3.943 closest distance to " OD1 ASN A  69 " =    2.517
peak=    3.939 closest distance to " CB  GLU A 128 " =    1.150
peak=    3.934 closest distance to " CA  ALA A  21 " =    1.168
peak=    3.930 closest distance to " CA  ALA A  51 " =    1.029
peak=    3.928 closest distance to " O   HOH Z  61 " =    1.659
peak=    3.926 closest distance to " O   HOH Z 130 " =    2.732
peak=    3.926 closest distance to " O   HOH Z 411 " =    3.756
peak=    3.925 closest distance to " NZ  LYS A 117 " =    2.945
peak=    3.901 closest distance to " O   HOH Z 371 " =    3.269
peak=    3.898 closest distance to " CB  ALA A 248 " =    1.370
peak=    3.880 closest distance to " O   HOH Z 345 " =    2.917
peak=    3.876 closest distance to " O   HOH Z 248 " =    1.646
peak=    3.875 closest distance to " O   HOH Z  54 " =    2.300
peak=    3.873 closest distance to " O   HOH Z 137 " =    1.723
peak=    3.870 closest distance to " O   HOH Z  15 " =    2.084
peak=    3.861 closest distance to " O   HOH Z 189 " =    2.537
peak=    3.843 closest distance to " O   HOH Z 357 " =    1.963
peak=    3.834 closest distance to " O   HOH Z 128 " =    2.283
peak=    3.823 closest distance to " CB  TRP A 266 " =    1.010
peak=    3.817 closest distance to " CG2 ILE A  20 " =    1.389
peak=    3.813 closest distance to " CG1 ILE A  33 " =    1.262
peak=    3.808 closest distance to " O   HOH Z 303 " =    2.121
peak=    3.792 closest distance to " O   HOH Z 245 " =    1.421
peak=    3.791 closest distance to " O   HOH Z 344 " =    2.934
peak=    3.787 closest distance to " CA  LYS A 117 " =    1.295
peak=    3.784 closest distance to " O   HOH Z 427 " =    2.753
peak=    3.782 closest distance to " CD  ARG A 269 " =    1.025
peak=    3.782 closest distance to " O   HOH Z  43 " =    2.236
peak=    3.773 closest distance to " O   HOH Z 154 " =    1.473
peak=    3.773 closest distance to " CB  ASN A  39 " =    0.865
peak=    3.768 closest distance to " O   HOH Z 389 " =    1.893
peak=    3.768 closest distance to " O   HOH Z 227 " =    1.656
peak=    3.763 closest distance to " CG  ARG A  66 " =    0.972
peak=    3.758 closest distance to " CB  SER A  26 " =    1.739
peak=    3.756 closest distance to " O   HOH Z 158 " =    3.062
peak=    3.751 closest distance to " CB  ARG A 190 " =    1.722
peak=    3.751 closest distance to " O   HOH Z 214 " =    2.571
peak=    3.746 closest distance to " CB  ALA A   9 " =    1.567
peak=    3.743 closest distance to " CD  LYS A 166 " =    1.369
peak=    3.731 closest distance to " CA  VAL A  41 " =    0.823
peak=    3.715 closest distance to " O   TRP A 274 " =    1.934
peak=    3.712 closest distance to " CD1AILE A 234 " =    0.934
peak=    3.709 closest distance to " CB  ARG A 139 " =    0.885
peak=    3.708 closest distance to " O   HOH Z 421 " =    1.711
peak=    3.693 closest distance to " O   HOH Z 250 " =    1.377
peak=    3.682 closest distance to " O   HOH Z 422 " =    2.556
peak=    3.680 closest distance to " O   HOH Z  44 " =    1.952
peak=    3.676 closest distance to " CZ  PHE A 218 " =    1.116
peak=    3.671 closest distance to " O   HOH Z  78 " =    1.612
peak=    3.666 closest distance to " O   HOH Z 128 " =    1.882
peak=    3.666 closest distance to " O   HOH Z 426 " =    1.493
peak=    3.663 closest distance to " O   HOH Z 193 " =    2.064
peak=    3.661 closest distance to " CB  ARG A  79 " =    0.886
peak=    3.660 closest distance to " CB  ALA A 295 " =    1.158
peak=    3.652 closest distance to " OD2 ASP A 298 " =    3.923
peak=    3.649 closest distance to " O   HOH Z 197 " =    2.859
peak=    3.648 closest distance to " CG2 ILE A 120 " =    1.254
peak=    3.639 closest distance to " CB  VAL A 265 " =    1.256
peak=    3.638 closest distance to " OG1 THR A 294 " =    2.305
peak=    3.635 closest distance to " O   HOH Z 416 " =    2.789
peak=    3.630 closest distance to " O   HOH Z 130 " =    2.275
peak=    3.626 closest distance to " O   ASP A 124 " =    1.364
peak=    3.622 closest distance to " O   HOH Z 273 " =    2.839
peak=    3.605 closest distance to " CB AVAL A  41 " =    1.098
peak=    3.600 closest distance to " O   HOH Z 134 " =    1.402
peak=    3.592 closest distance to " CG  GLN A  58 " =    2.743
peak=    3.585 closest distance to " OE1 GLU A   2 " =    2.142
peak=    3.579 closest distance to " O   HOH Z 366 " =    2.865
peak=    3.577 closest distance to " NH2 ARG A 156 " =    1.071
peak=    3.570 closest distance to " O   ALA A 165 " =    1.386
peak=    3.570 closest distance to " CB  THR A  31 " =    1.549
peak=    3.567 closest distance to " CD1 LEU A  96 " =    0.704
peak=    3.567 closest distance to " O   HOH Z 250 " =    1.507
peak=    3.557 closest distance to " O   GLY A  91 " =    1.557
peak=    3.557 closest distance to " CA  ASP A 140 " =    1.177
peak=    3.554 closest distance to " CB  VAL A 202 " =    1.503
peak=    3.547 closest distance to " O   HOH Z 247 " =    1.301
peak=    3.542 closest distance to " O   HOH Z 263 " =    1.684
peak=    3.526 closest distance to " O   HOH Z 417 " =    3.211
peak=    3.514 closest distance to " OD1 ASP A 286 " =    1.727
peak=    3.510 closest distance to " NH2BARG A 145 " =    2.058
peak=    3.504 closest distance to " CG BARG A 102 " =    1.808
peak=    3.499 closest distance to " O   HOH Z 147 " =    1.745
peak=    3.493 closest distance to " NH1BARG A 190 " =    2.124
peak=    3.493 closest distance to " O   HOH Z 261 " =    1.855
peak=    3.490 closest distance to " CG  GLN A  77 " =    2.311
peak=    3.484 closest distance to " O   HOH Z 313 " =    1.796
peak=    3.478 closest distance to " N   SER A 135 " =    1.353
peak=    3.467 closest distance to " CA  ASN A 215 " =    1.146
peak=    3.464 closest distance to " CD  ARG A 159 " =    0.729
peak=    3.463 closest distance to " CA  ARG A  36 " =    1.013
peak=    3.456 closest distance to " CG AARG A 275 " =    1.145
peak=    3.454 closest distance to " O   HOH Z 299 " =    4.278
peak=    3.452 closest distance to " NH2 ARG A  79 " =    1.290
peak=    3.449 closest distance to " OG BSER A 164 " =    2.171
peak=    3.447 closest distance to " CE1 TYR A 186 " =    1.264
peak=    3.444 closest distance to " O   HOH Z  47 " =    1.654
peak=    3.444 closest distance to " CB  ASP A 140 " =    1.024
peak=    3.442 closest distance to " O   HOH Z 419 " =    1.666
peak=    3.441 closest distance to " O   HOH Z  68 " =    2.178
peak=    3.436 closest distance to " CG2 THR A 221 " =    1.238
peak=    3.435 closest distance to " NZ  LYS A  76 " =    1.838
peak=    3.432 closest distance to " CG2 ILE A 234 " =    1.010
peak=    3.431 closest distance to " O   HOH Z 383 " =    1.994
peak=    3.426 closest distance to " O   HOH Z  88 " =    2.680
peak=    3.420 closest distance to " OE1 GLN A  11 " =    1.738
peak=    3.418 closest distance to " O   HOH Z 345 " =    1.589
peak=    3.418 closest distance to " CD  LYS A 119 " =    1.943
peak=    3.417 closest distance to " O   HOH Z 435 " =    1.954
peak=    3.416 closest distance to " CB  ASN A 142 " =    1.168
peak=    3.411 closest distance to " O   HOH Z 261 " =    2.259
peak=    3.405 closest distance to " CG  MET A 185 " =    1.131
peak=    3.404 closest distance to " O   HOH Z 112 " =    1.675
peak=    3.396 closest distance to " O   HOH Z 209 " =    2.409
peak=    3.394 closest distance to " O   HOH Z 425 " =    2.014
peak=    3.393 closest distance to " O   HOH Z 406 " =    1.503
peak=    3.392 closest distance to " C   ILE A 106 " =    1.872
peak=    3.392 closest distance to " O   HOH Z 367 " =    3.398
peak=    3.390 closest distance to " N   ASP A 162 " =    1.277
peak=    3.386 closest distance to " O   HOH Z 423 " =    3.292
peak=    3.384 closest distance to " O   HOH Z 155 " =    3.140
peak=    3.381 closest distance to " CB  ASN A 110 " =    1.140
peak=    3.372 closest distance to " OD2 ASP A 286 " =    2.743
peak=    3.366 closest distance to " O   HOH Z 359 " =    1.310
peak=    3.365 closest distance to " O   HOH Z 109 " =    2.276
peak=    3.352 closest distance to " CE1 HIS A 108 " =    1.106
peak=    3.349 closest distance to " CA  ASP A 191 " =    1.131
peak=    3.349 closest distance to " CG1 ILE A  49 " =    1.477
peak=    3.349 closest distance to " O   HOH Z 420 " =    1.936
peak=    3.341 closest distance to " CE  LYS A 119 " =    1.037
peak=    3.340 closest distance to " CA  ALA A 158 " =    1.338
peak=    3.339 closest distance to " CD2 TYR A  30 " =    0.834
peak=    3.338 closest distance to " NH2AARG A 275 " =    3.625
peak=    3.335 closest distance to " O   HOH Z 374 " =    2.509
peak=    3.332 closest distance to " O   HOH Z 251 " =    1.692
peak=    3.330 closest distance to " NH1AARG A 145 " =    1.129
peak=    3.329 closest distance to " CB  TRP A 150 " =    1.473
peak=    3.328 closest distance to " O   HOH Z 180 " =    2.187
peak=    3.327 closest distance to " CB  GLU A  46 " =    1.064
peak=    3.323 closest distance to " OG  SER A 276 " =    1.410
peak=    3.319 closest distance to " CZ3 TRP A  85 " =    0.963
peak=    3.319 closest distance to " CD BLYS A 290 " =    1.096
peak=    3.318 closest distance to " O   HOH Z  88 " =    3.011
peak=    3.315 closest distance to " O   HOH Z 329 " =    3.912
peak=    3.310 closest distance to " CB  THR A  52 " =    0.872
peak=    3.308 closest distance to " O   HOH Z  49 " =    2.379
peak=    3.306 closest distance to " O   HOH Z 404 " =    2.208
peak=    3.303 closest distance to " ND2 ASN A 110 " =    1.566
peak=    3.298 closest distance to " O   HOH Z 280 " =    2.659
peak=    3.298 closest distance to " O   HOH Z 188 " =    2.200
peak=    3.297 closest distance to " O   HOH Z  21 " =    1.724
peak=    3.290 closest distance to " NZ  LYS A 119 " =    1.547
peak=    3.289 closest distance to " CD1 LEU A 228 " =    1.762
peak=    3.288 closest distance to " O   HOH Z 408 " =    1.488
peak=    3.287 closest distance to " O   HOH Z 185 " =    1.699
peak=    3.285 closest distance to " CA  ASN A 176 " =    1.105
peak=    3.279 closest distance to " CB  PRO A 198 " =    1.077
peak=    3.279 closest distance to " OG  SER A  62 " =    2.796
peak=    3.279 closest distance to " O   HOH Z  35 " =    2.279
peak=    3.269 closest distance to " CB  GLN A 205 " =    1.186
peak=    3.263 closest distance to " CD2 LEU A 297 " =    0.909
peak=    3.262 closest distance to " O   HOH Z 163 " =    1.336
peak=    3.262 closest distance to " CD2 HIS A  81 " =    1.006
peak=    3.257 closest distance to " CG1 VAL A 296 " =    1.197
peak=    3.257 closest distance to " O   HOH Z 411 " =    1.722
peak=    3.253 closest distance to " CA  ARG A 195 " =    1.290
peak=    3.252 closest distance to " O   HOH Z 123 " =    2.134
peak=    3.246 closest distance to " O   HOH Z 227 " =    2.137
peak=    3.245 closest distance to " CD1 ILE A 106 " =    1.149
peak=    3.243 closest distance to " O   HOH Z 437 " =    2.001
peak=    3.234 closest distance to " CZ  PHE A  38 " =    1.330
peak=    3.226 closest distance to " O   HOH Z 189 " =    2.601
peak=    3.222 closest distance to " CA  ALA A  84 " =    1.300
peak=    3.221 closest distance to " CA  ALA A 291 " =    0.881
peak=    3.219 closest distance to " CA  ASP A 162 " =    1.132
peak=    3.215 closest distance to " CG2 ILE A 234 " =    2.100
peak=    3.213 closest distance to " O   HOH Z 261 " =    1.932
peak=    3.213 closest distance to " CB  HIS A 108 " =    0.846
peak=    3.212 closest distance to " O   HOH Z 380 " =    1.881
peak=    3.207 closest distance to " O   HOH Z 162 " =    2.016
peak=    3.206 closest distance to " OG1 THR A 294 " =    1.643
peak=    3.205 closest distance to " CB  MET A  47 " =    1.145
peak=    3.199 closest distance to " CB  ASN A 215 " =    1.077
peak=    3.198 closest distance to " O   HOH Z 350 " =    1.794
peak=    3.193 closest distance to " CG  LEU A 167 " =    1.170
peak=    3.192 closest distance to " O   HOH Z 271 " =    2.507
peak=    3.189 closest distance to " O   HOH Z 438 " =    2.020
peak=    3.185 closest distance to " CB  ALA A 100 " =    1.130
peak=    3.183 closest distance to " N   VAL A 126 " =    1.387
peak=    3.181 closest distance to " CB  THR A 157 " =    1.163
peak=    3.180 closest distance to " CD  GLN A 194 " =    1.492
peak=    3.175 closest distance to " OH  TYR A 116 " =    1.086
peak=    3.175 closest distance to " O   HOH Z 313 " =    1.729
peak=    3.173 closest distance to " O   HOH Z 299 " =    2.209
peak=    3.168 closest distance to " O   HOH Z 361 " =    3.203
peak=    3.168 closest distance to " O   HOH Z 279 " =    2.086
peak=    3.168 closest distance to " CA  ALA A 160 " =    0.848
peak=    3.163 closest distance to " CZ2 TRP A 150 " =    1.149
peak=    3.159 closest distance to " CG  LYS A  76 " =    1.105
peak=    3.159 closest distance to " NH1 ARG A 138 " =    1.285
peak=    3.158 closest distance to " OG  SER A  22 " =    2.673
peak=    3.158 closest distance to " CB  SER A 141 " =    1.064
peak=    3.155 closest distance to " N   PHE A 130 " =    1.369
peak=    3.151 closest distance to " CA  SER A 146 " =    1.920
peak=    3.150 closest distance to " O   HOH Z  28 " =    2.137
peak=    3.150 closest distance to " O   HOH Z   4 " =    1.524
peak=    3.149 closest distance to " CD1 LEU A 300 " =    1.271
peak=    3.141 closest distance to " CG2 VAL A 257 " =    0.787
peak=    3.137 closest distance to " O   HOH Z 132 " =    2.571
peak=    3.136 closest distance to " CG2AVAL A 121 " =    2.163
peak=    3.135 closest distance to " CA  LYS A 290 " =    1.119
peak=    3.129 closest distance to " O   HOH Z 417 " =    2.293
peak=    3.125 closest distance to " CA  VAL A 126 " =    1.051
peak=    3.121 closest distance to " CG  MET A 185 " =    0.984
peak=    3.118 closest distance to " O   HOH Z 301 " =    1.943
peak=    3.114 closest distance to " O   HOH Z 298 " =    4.817
peak=    3.099 closest distance to " O   HOH Z 406 " =    1.243
peak=    3.097 closest distance to " CB  ALA A 291 " =    1.332
peak=    3.096 closest distance to " O   HOH Z  61 " =    1.514
peak=    3.092 closest distance to " CA  MET A 105 " =    1.074
peak=    3.089 closest distance to " CG1 VAL A 153 " =    0.937
peak=    3.088 closest distance to " CA  GLY A  80 " =    0.840
peak=    3.084 closest distance to " O   ILE A  33 " =    1.225
peak=    3.083 closest distance to " CB  PHE A 204 " =    0.745
peak=    3.078 closest distance to " OD1 ASP A 231 " =    1.923
peak=    3.076 closest distance to " O   HOH Z 148 " =    3.236
peak=    3.071 closest distance to " CB  LYS A 290 " =    1.146
peak=    3.070 closest distance to " O   HOH Z  66 " =    2.051
peak=    3.064 closest distance to " C   ALA A 299 " =    0.932
peak=    3.062 closest distance to " CG2 THR A  42 " =    0.915
peak=    3.062 closest distance to " OE2 GLU A  53 " =    2.041
peak=    3.053 closest distance to " NZ  LYS A 166 " =    3.001
peak=    3.014 closest distance to " OG BSER A 164 " =    1.884
peak=    2.992 closest distance to " O   HOH Z 286 " =    2.436

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 198         
Filter by distance & map next to the model:
   mapped sites are within: 0.760 - 5.524
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 197 from: 198
   mapped sites are within: 0.760 - 5.524

peak=   -4.829 closest distance to " CG2 VAL A 230 " =    0.760
peak=   -4.645 closest distance to " O   HOH Z 266 " =    4.847
peak=   -4.594 closest distance to " CD  ARG A 156 " =    2.052
peak=   -4.548 closest distance to " SG  CYS A 254 " =    3.254
peak=   -4.360 closest distance to " O   PRO A 163 " =    2.085
peak=   -4.339 closest distance to " C   HIS A 108 " =    1.226
peak=   -4.325 closest distance to " CD  GLN A  58 " =    1.202
peak=   -4.298 closest distance to " OXT GLY A 302 " =    2.799
peak=   -4.288 closest distance to " CG2BVAL A  41 " =    2.590
peak=   -4.172 closest distance to " OG BSER A 134 " =    1.276
peak=   -4.157 closest distance to " CD2 TYR A  30 " =    2.762
peak=   -4.147 closest distance to " CD1 LEU A 101 " =    2.430
peak=   -4.092 closest distance to " O   HOH Z 166 " =    1.723
peak=   -4.055 closest distance to " CD2 PHE A 192 " =    2.045
peak=   -4.018 closest distance to " ND2 ASN A 187 " =    1.550
peak=   -3.977 closest distance to " O   HOH Z 290 " =    1.050
peak=   -3.959 closest distance to " O   HOH Z 231 " =    2.214
peak=   -3.905 closest distance to " ND2 ASN A  45 " =    1.036
peak=   -3.893 closest distance to " CG  GLN A 223 " =    2.154
peak=   -3.890 closest distance to " O   HOH Z 114 " =    3.226
peak=   -3.877 closest distance to " O   HOH Z  13 " =    1.682
peak=   -3.866 closest distance to " O   HOH Z 351 " =    1.511
peak=   -3.854 closest distance to " CB  ALA A 161 " =    2.557
peak=   -3.819 closest distance to " CG2 VAL A 296 " =    1.222
peak=   -3.813 closest distance to " N   ALA A 248 " =    1.723
peak=   -3.804 closest distance to " O   ASN A  45 " =    1.879
peak=   -3.797 closest distance to " O   VAL A  67 " =    2.801
peak=   -3.781 closest distance to " O   HOH Z 426 " =    1.782
peak=   -3.773 closest distance to " O   HOH Z  44 " =    2.208
peak=   -3.759 closest distance to " OG  SER A  97 " =    2.295
peak=   -3.756 closest distance to " CB  ALA A 248 " =    2.314
peak=   -3.744 closest distance to " CA  ASP A 298 " =    1.048
peak=   -3.742 closest distance to " O   PHE A 218 " =    1.655
peak=   -3.739 closest distance to " O   SER A 210 " =    1.948
peak=   -3.737 closest distance to " CZ3 TRP A 179 " =    1.318
peak=   -3.729 closest distance to " O   HOH Z  37 " =    1.875
peak=   -3.690 closest distance to " O   HOH Z 423 " =    2.133
peak=   -3.673 closest distance to " CG  ASP A 231 " =    0.852
peak=   -3.671 closest distance to " CG1 VAL A 112 " =    2.711
peak=   -3.667 closest distance to " CB  ALA A 291 " =    2.381
peak=   -3.636 closest distance to " O   HOH Z 165 " =    1.986
peak=   -3.615 closest distance to " CB  PRO A 243 " =    2.622
peak=   -3.607 closest distance to " O   HOH Z 196 " =    2.103
peak=   -3.607 closest distance to " CB  PRO A 163 " =    2.569
peak=   -3.606 closest distance to " NH2 ARG A  66 " =    1.624
peak=   -3.603 closest distance to " O   HOH Z 377 " =    2.170
peak=   -3.601 closest distance to " O   GLY A  80 " =    2.442
peak=   -3.592 closest distance to " NE2 GLN A  88 " =    1.918
peak=   -3.592 closest distance to " CD  ARG A 139 " =    1.682
peak=   -3.583 closest distance to " O   HOH Z 407 " =    2.841
peak=   -3.578 closest distance to " O   VAL A 125 " =    2.322
peak=   -3.576 closest distance to " CB  ALA A 248 " =    2.018
peak=   -3.576 closest distance to " O   ALA A 256 " =    1.571
peak=   -3.574 closest distance to " N   ALA A 226 " =    1.957
peak=   -3.571 closest distance to " ND2 ASN A  39 " =    1.125
peak=   -3.563 closest distance to " OD1 ASN A  39 " =    2.118
peak=   -3.561 closest distance to " OG  SER A   3 " =    1.621
peak=   -3.556 closest distance to " OG ASER A 134 " =    1.263
peak=   -3.550 closest distance to " O   HOH Z 166 " =    1.763
peak=   -3.544 closest distance to " N   THR A 235 " =    1.337
peak=   -3.538 closest distance to " N   GLN A  58 " =    1.810
peak=   -3.527 closest distance to " CE  LYS A 166 " =    3.059
peak=   -3.522 closest distance to " CE3 TRP A 150 " =    2.058
peak=   -3.521 closest distance to " O   HOH Z  88 " =    4.268
peak=   -3.517 closest distance to " O   HOH Z 150 " =    2.203
peak=   -3.514 closest distance to " NE2 GLN A  88 " =    1.071
peak=   -3.508 closest distance to " CG2 ILE A 263 " =    2.275
peak=   -3.504 closest distance to " CE  MET A 105 " =    2.229
peak=   -3.503 closest distance to " NH2AARG A 275 " =    4.857
peak=   -3.501 closest distance to " CD  LYS A 289 " =    2.444
peak=   -3.501 closest distance to " NH2 ARG A  79 " =    2.002
peak=   -3.500 closest distance to " O   HOH Z  11 " =    1.831
peak=   -3.496 closest distance to " CB  GLN A  11 " =    1.910
peak=   -3.493 closest distance to " O   HOH Z 353 " =    2.127
peak=   -3.491 closest distance to " O   GLY A  75 " =    1.802
peak=   -3.484 closest distance to " CD2 LEU A 237 " =    2.702
peak=   -3.472 closest distance to " C   THR A 279 " =    1.200
peak=   -3.461 closest distance to " CD1 PHE A  59 " =    2.174
peak=   -3.457 closest distance to " CZ  TYR A 169 " =    1.805
peak=   -3.454 closest distance to " O   TRP A  92 " =    1.912
peak=   -3.451 closest distance to " O   HOH Z  60 " =    2.166
peak=   -3.441 closest distance to " CD1 PHE A  59 " =    1.981
peak=   -3.441 closest distance to " O   HOH Z 234 " =    3.979
peak=   -3.437 closest distance to " N   SER A 276 " =    1.360
peak=   -3.436 closest distance to " CD2 TYR A 293 " =    2.012
peak=   -3.432 closest distance to " CD2 LEU A 300 " =    2.785
peak=   -3.426 closest distance to " C   MET A 188 " =    1.540
peak=   -3.421 closest distance to " N   THR A 157 " =    1.510
peak=   -3.421 closest distance to " OG BSER A 134 " =    1.698
peak=   -3.420 closest distance to " O   HOH Z 301 " =    2.327
peak=   -3.411 closest distance to " CG  ASP A 132 " =    2.322
peak=   -3.411 closest distance to " CG  GLU A  53 " =    1.529
peak=   -3.411 closest distance to " OD2 ASP A 191 " =    1.435
peak=   -3.410 closest distance to " CD1 LEU A  25 " =    2.505
peak=   -3.410 closest distance to " O   HOH Z 431 " =    1.897
peak=   -3.403 closest distance to " O   HOH Z 136 " =    2.246
peak=   -3.398 closest distance to " O   HOH Z 193 " =    1.681
peak=   -3.398 closest distance to " CD1 LEU A 255 " =    2.709
peak=   -3.395 closest distance to " C   ALA A 158 " =    1.271
peak=   -3.394 closest distance to " OG BSER A 210 " =    1.294
peak=   -3.394 closest distance to " O   HOH Z 389 " =    1.769
peak=   -3.383 closest distance to " O   HOH Z  97 " =    1.178
peak=   -3.375 closest distance to " O   HOH Z  17 " =    1.260
peak=   -3.375 closest distance to " O   HOH Z 131 " =    4.048
peak=   -3.374 closest distance to " O   MET A  40 " =    2.731
peak=   -3.371 closest distance to " ND2 ASN A  69 " =    1.729
peak=   -3.370 closest distance to " C   GLN A 205 " =    1.860
peak=   -3.370 closest distance to " CE2 PHE A 218 " =    2.655
peak=   -3.358 closest distance to " CG1 VAL A 112 " =    2.838
peak=   -3.358 closest distance to " CD1 TYR A 247 " =    2.571
peak=   -3.353 closest distance to " CB  ASP A 231 " =    2.478
peak=   -3.346 closest distance to " N   ALA A  43 " =    2.779
peak=   -3.345 closest distance to " O   HOH Z 427 " =    1.464
peak=   -3.344 closest distance to " O   HOH Z  92 " =    1.742
peak=   -3.341 closest distance to " CG1 VAL A  78 " =    2.662
peak=   -3.338 closest distance to " CG  ASP A  50 " =    2.410
peak=   -3.336 closest distance to " NH2 ARG A  66 " =    4.971
peak=   -3.335 closest distance to " N   ALA A 248 " =    2.246
peak=   -3.333 closest distance to " O   PRO A 198 " =    1.259
peak=   -3.333 closest distance to " CD2 LEU A 167 " =    1.711
peak=   -3.327 closest distance to " O   HOH Z  15 " =    1.517
peak=   -3.326 closest distance to " O   GLY A 196 " =    1.066
peak=   -3.324 closest distance to " O   HOH Z 126 " =    1.849
peak=   -3.314 closest distance to " CA  GLY A  23 " =    1.873
peak=   -3.313 closest distance to " NE2 GLN A 194 " =    1.774
peak=   -3.313 closest distance to " O   ASN A 187 " =    1.536
peak=   -3.311 closest distance to " OD1 ASN A 148 " =    1.496
peak=   -3.307 closest distance to " O   HOH Z 283 " =    1.875
peak=   -3.306 closest distance to " CG  GLU A 277 " =    1.093
peak=   -3.305 closest distance to " O   HOH Z  11 " =    1.995
peak=   -3.302 closest distance to " O   HOH Z 369 " =    2.259
peak=   -3.299 closest distance to " OXT GLY A 302 " =    3.383
peak=   -3.291 closest distance to " CA  GLY A 133 " =    1.932
peak=   -3.287 closest distance to " N   MET A 105 " =    3.040
peak=   -3.285 closest distance to " CE BMET A  47 " =    1.482
peak=   -3.284 closest distance to " O   HOH Z 139 " =    5.134
peak=   -3.281 closest distance to " OG1 THR A  82 " =    1.378
peak=   -3.280 closest distance to " O   HOH Z  19 " =    2.071
peak=   -3.275 closest distance to " O   ALA A 161 " =    1.740
peak=   -3.275 closest distance to " O   SER A 271 " =    1.940
peak=   -3.273 closest distance to " O   VAL A 174 " =    2.054
peak=   -3.269 closest distance to " O   HOH Z 185 " =    2.407
peak=   -3.260 closest distance to " O   ALA A  51 " =    1.278
peak=   -3.253 closest distance to " CB  ALA A 291 " =    2.171
peak=   -3.252 closest distance to " O   LEU A 167 " =    1.584
peak=   -3.245 closest distance to " O   HOH Z 422 " =    1.604
peak=   -3.241 closest distance to " CG  TRP A 266 " =    2.087
peak=   -3.236 closest distance to " O   HOH Z 211 " =    1.630
peak=   -3.235 closest distance to " C   SER A 206 " =    1.548
peak=   -3.232 closest distance to " O   VAL A 189 " =    2.622
peak=   -3.231 closest distance to " NH1 ARG A 195 " =    2.591
peak=   -3.230 closest distance to " O   HOH Z 198 " =    2.063
peak=   -3.227 closest distance to " CB  ASP A 132 " =    2.386
peak=   -3.227 closest distance to " CA  GLY A 203 " =    2.335
peak=   -3.223 closest distance to " CA  TYR A  68 " =    3.110
peak=   -3.221 closest distance to " CZ  PHE A  59 " =    1.580
peak=   -3.216 closest distance to " N   THR A  52 " =    1.686
peak=   -3.214 closest distance to " O   HOH Z 339 " =    1.775
peak=   -3.213 closest distance to " OD2 ASP A 171 " =    2.340
peak=   -3.213 closest distance to " CD1 LEU A 228 " =    2.085
peak=   -3.213 closest distance to " O   HOH Z   6 " =    1.818
peak=   -3.211 closest distance to " O   PRO A 198 " =    1.290
peak=   -3.208 closest distance to " CA  GLY A 133 " =    2.266
peak=   -3.196 closest distance to " CG  PHE A 283 " =    2.667
peak=   -3.196 closest distance to " O   HOH Z  52 " =    1.703
peak=   -3.194 closest distance to " CG1 VAL A 230 " =    1.853
peak=   -3.191 closest distance to " O   HOH Z 313 " =    1.247
peak=   -3.191 closest distance to " OG  SER A  62 " =    1.418
peak=   -3.159 closest distance to " O   ASP A 171 " =    1.965
peak=   -3.157 closest distance to " CG2 THR A 221 " =    2.267
peak=   -3.157 closest distance to " O   ALA A 160 " =    1.450
peak=   -3.155 closest distance to " O   HOH Z 197 " =    5.125
peak=   -3.151 closest distance to " OD1 ASN A 301 " =    1.951
peak=   -3.148 closest distance to " CB  SER A 210 " =    1.222
peak=   -3.148 closest distance to " CG  GLU A   2 " =    1.778
peak=   -3.143 closest distance to " O   HOH Z 372 " =    2.260
peak=   -3.143 closest distance to " O   HOH Z 174 " =    4.242
peak=   -3.140 closest distance to " O   HOH Z  71 " =    1.593
peak=   -3.139 closest distance to " O   HOH Z 139 " =    3.261
peak=   -3.138 closest distance to " O   HOH Z 191 " =    5.524
peak=   -3.132 closest distance to " O   HOH Z 250 " =    1.326
peak=   -3.120 closest distance to " O   GLY A  80 " =    2.542
peak=   -3.104 closest distance to " O   ASN A 301 " =    1.496
peak=   -3.103 closest distance to " CB  PHE A 208 " =    2.308
peak=   -3.100 closest distance to " CG  ARG A 269 " =    2.199
peak=   -3.097 closest distance to " OG  SER A  63 " =    1.168
peak=   -3.094 closest distance to " O   GLY A  80 " =    2.596
peak=   -3.092 closest distance to " O   HOH Z 295 " =    1.420
peak=   -3.088 closest distance to " O   ARG A  24 " =    1.960
peak=   -3.087 closest distance to " N   HIS A 115 " =    2.055
peak=   -3.071 closest distance to " CG2 VAL A 189 " =    1.979
peak=   -3.057 closest distance to " O   HOH Z  47 " =    1.599
peak=   -3.051 closest distance to " O   HOH Z 407 " =    3.465
peak=   -3.050 closest distance to " O   HOH Z  61 " =    1.589
peak=   -3.046 closest distance to " O   LYS A 117 " =    1.606
peak=   -3.037 closest distance to " O   HOH Z 389 " =    4.919
peak=   -3.023 closest distance to " OD1 ASP A 200 " =    1.408

================= 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    :  0.4555 0.4424   6.252745e+00   6.237540e+00
   1_bss:  0.4464 0.4366   6.244270e+00   6.229577e+00
   1_xyz:  0.3442 0.3657   6.071327e+00   6.114935e+00
   1_adp:  0.2886 0.3242   5.932831e+00   6.030537e+00
   1_occ:  0.2881 0.3241   5.931784e+00   6.030186e+00
   2_bss:  0.2841 0.3199   5.931502e+00   6.027660e+00
   2_xyz:  0.1981 0.2374   5.618145e+00   5.777719e+00
   2_adp:  0.1799 0.2219   5.536474e+00   5.707522e+00
   2_occ:  0.1798 0.2217   5.536006e+00   5.707534e+00
   3_bss:  0.1781 0.2213   5.534742e+00   5.705942e+00
   3_xyz:  0.1331 0.1716   5.273745e+00   5.478107e+00
   3_adp:  0.1265 0.1626   5.222127e+00   5.424016e+00
   3_occ:  0.1263 0.1624   5.221098e+00   5.423124e+00
   4_bss:  0.1265 0.1621   5.222146e+00   5.420030e+00
   4_xyz:  0.1200 0.1582   5.186887e+00   5.399986e+00
   4_adp:  0.1177 0.1580   5.176585e+00   5.397160e+00
   4_occ:  0.1176 0.1580   5.175872e+00   5.396775e+00
   5_bss:  0.1176 0.1580   5.175852e+00   5.396775e+00
   5_xyz:  0.1122 0.1551   5.143930e+00   5.379016e+00
   5_adp:  0.1110 0.1560   5.142872e+00   5.384525e+00
   5_occ:  0.1110 0.1560   5.142680e+00   5.384372e+00
   5_bss:  0.1110 0.1560   5.142625e+00   5.384357e+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:  0.359  19.797   7.749   9.514   7.825   0.000   0.000   0.000
   1_xyz:  0.359  19.797   7.749   9.514   7.825   0.000   0.000   0.000
   1_adp:  0.359  19.797   7.749   9.514   7.825   0.000   0.000   0.000
   1_occ:  0.359  19.797   7.749   9.514   7.825   0.000   0.000   0.000
   2_bss:  0.330  35.886   4.214   5.644   4.878   0.000   0.000   0.000
   2_xyz:  0.330  35.886   4.214   5.644   4.878   0.000   0.000   0.000
   2_adp:  0.330  35.886   4.214   5.644   4.878   0.000   0.000   0.000
   2_occ:  0.330  35.886   4.214   5.644   4.878   0.000   0.000   0.000
   3_bss:  0.320  35.886   2.458   3.873   3.953   0.000   0.000   0.000
   3_xyz:  0.320  35.886   2.458   3.873   3.953   0.000   0.000   0.000
   3_adp:  0.320  35.886   2.458   3.873   3.953   0.000   0.000   0.000
   3_occ:  0.320  35.886   2.458   3.873   3.953   0.000   0.000   0.000
   4_bss:  0.327  42.620   1.990   3.150   3.553   0.000   0.000   0.000
   4_xyz:  0.327  42.620   1.990   3.150   3.553   0.000   0.000   0.000
   4_adp:  0.327  42.620   1.990   3.150   3.553   0.000   0.000   0.000
   4_occ:  0.327  42.620   1.990   3.150   3.553   0.000   0.000   0.000
   5_bss:  0.327  42.620   1.966   3.033   3.550   0.000   0.000   0.000
   5_xyz:  0.327  42.620   1.966   3.033   3.550   0.000   0.000   0.000
   5_adp:  0.327  42.620   1.966   3.033   3.550   0.000   0.000   0.000
   5_occ:  0.327  42.620   1.966   3.033   3.550   0.000   0.000   0.000
   5_bss:  0.325  46.322  -0.869   0.161   0.708   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  50.613 0.5145  0.5851    58039.653
   1_bss:  50.818 0.5098  0.7460    56036.657
   1_xyz:  40.416 0.6365  0.9087    37274.468
   1_adp:  33.913 0.7142  1.0198    28526.984
   1_occ:  33.891 0.7145  1.0191    28493.763
   2_bss:  33.632 0.7173  0.9035    28108.473
   2_xyz:  23.964 0.8215  0.9968    14780.602
   2_adp:  21.667 0.8454  1.0159    12665.408
   2_occ:  21.667 0.8454  1.0155    12655.511
   3_bss:  21.615 0.8459  0.9624    12598.748
   3_xyz:  16.071 0.8973  0.9937     7620.427
   3_adp:  14.895 0.9077  0.9994     6924.016
   3_occ:  14.878 0.9078  0.9995     6910.862
   4_bss:  14.833 0.9082  0.9806     6891.253
   4_xyz:  14.328 0.9126  0.9807     6571.283
   4_adp:  14.239 0.9135  0.9786     6532.555
   4_occ:  14.226 0.9136  0.9785     6529.384
   5_bss:  14.223 0.9136  0.9769     6529.313
   5_xyz:  13.868 0.9163  0.9781     6295.636
   5_adp:  13.975 0.9155  0.9741     6340.350
   5_occ:  13.968 0.9156  0.9740     6338.694
   5_bss:  13.967 0.9156  0.9792     6337.513
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3532e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3532e+01
   1_xyz:   1.639  0.013  0.107 17.938  0.006  4.109   1.3235e-01
   1_adp:   1.639  0.013  0.107 17.938  0.006  4.109   1.3235e-01
   1_occ:   1.639  0.013  0.107 17.938  0.006  4.109   1.3235e-01
   2_bss:   1.639  0.013  0.107 17.938  0.006  4.109   1.3235e-01
   2_xyz:   1.020  0.007  0.074 16.011  0.004  4.120   6.4239e-02
   2_adp:   1.020  0.007  0.074 16.011  0.004  4.120   6.4239e-02
   2_occ:   1.020  0.007  0.074 16.011  0.004  4.120   6.4239e-02
   3_bss:   1.020  0.007  0.074 16.011  0.004  4.120   6.4239e-02
   3_xyz:   1.024  0.006  0.079 15.563  0.004  4.124   6.1664e-02
   3_adp:   1.024  0.006  0.079 15.563  0.004  4.124   6.1664e-02
   3_occ:   1.024  0.006  0.079 15.563  0.004  4.124   6.1664e-02
   4_bss:   1.024  0.006  0.079 15.563  0.004  4.124   6.1664e-02
   4_xyz:   0.940  0.006  0.075 15.377  0.003  4.118   5.4799e-02
   4_adp:   0.940  0.006  0.075 15.377  0.003  4.118   5.4799e-02
   4_occ:   0.940  0.006  0.075 15.377  0.003  4.118   5.4799e-02
   5_bss:   0.940  0.006  0.075 15.377  0.003  4.118   5.4799e-02
   5_xyz:   1.043  0.007  0.083 15.421  0.004  4.120   6.3890e-02
   5_adp:   1.043  0.007  0.083 15.421  0.004  4.120   6.3890e-02
   5_occ:   1.043  0.007  0.083 15.421  0.004  4.120   6.3890e-02
   5_bss:   1.043  0.007  0.083 15.421  0.004  4.120   6.3890e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.103   6.9380e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.103   6.9380e+00
   1_xyz:  15.088  0.160  0.517 85.451  0.041  2.317   9.7983e-02
   1_adp:  15.088  0.160  0.517 85.451  0.041  2.317   9.7983e-02
   1_occ:  15.088  0.160  0.517 85.451  0.041  2.317   9.7983e-02
   2_bss:  15.088  0.160  0.517 85.451  0.041  2.317   9.7983e-02
   2_xyz:   6.679  0.085  0.231 82.719  0.035  2.269   5.4970e-02
   2_adp:   6.679  0.085  0.231 82.719  0.035  2.269   5.4970e-02
   2_occ:   6.679  0.085  0.231 82.719  0.035  2.269   5.4970e-02
   3_bss:   6.679  0.085  0.231 82.719  0.035  2.269   5.4970e-02
   3_xyz:   6.732  0.045  0.535 82.717  0.037  2.291   3.9861e-02
   3_adp:   6.732  0.045  0.535 82.717  0.037  2.291   3.9861e-02
   3_occ:   6.732  0.045  0.535 82.717  0.037  2.291   3.9861e-02
   4_bss:   6.732  0.045  0.535 82.717  0.037  2.291   3.9861e-02
   4_xyz:   6.377  0.038  0.473 82.750  0.034  2.325   4.5236e-02
   4_adp:   6.377  0.038  0.473 82.750  0.034  2.325   4.5236e-02
   4_occ:   6.377  0.038  0.473 82.750  0.034  2.325   4.5236e-02
   5_bss:   6.377  0.038  0.473 82.750  0.034  2.325   4.5236e-02
   5_xyz:   7.267  0.048  0.618 82.541  0.037  2.312   3.9946e-02
   5_adp:   7.267  0.048  0.618 82.541  0.037  2.312   3.9946e-02
   5_occ:   7.267  0.048  0.618 82.541  0.037  2.312   3.9946e-02
   5_bss:   7.267  0.048  0.618 82.541  0.037  2.312   3.9946e-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:  68.45   0.00  11.53  64.26   0.00   8.67  68.45   0.00  27.15
   1_occ:  68.45   0.00  11.53  64.26   0.00   8.67  68.45   0.00  27.15
   2_bss:  68.45   0.00  11.53  64.26   0.00   8.67  68.45   0.00  27.15
   2_xyz:  68.45   0.00  11.53  64.26   0.00   8.67  68.45   0.00  27.15
   2_adp:  72.30   0.00  11.83  72.30   0.00   8.14  63.55   1.61  31.89
   2_occ:  72.30   0.00  11.83  72.30   0.00   8.14  63.55   1.61  31.89
   3_bss:  72.30   0.00  11.83  72.30   0.00   8.14  63.55   1.61  31.89
   3_xyz:  72.30   0.00  11.83  72.30   0.00   8.14  63.55   1.61  31.89
   3_adp:  72.22   0.00  11.79  72.22   0.00   7.94  63.15   1.63  32.78
   3_occ:  72.22   0.00  11.79  72.22   0.00   7.94  63.15   1.63  32.78
   4_bss:  72.22   0.00  11.79  72.22   0.00   7.94  63.15   1.63  32.78
   4_xyz:  72.22   0.00  11.79  72.22   0.00   7.94  63.15   1.63  32.78
   4_adp:  76.47   0.00  11.97  76.47   0.00   7.94  65.82   1.26  33.90
   4_occ:  76.47   0.00  11.97  76.47   0.00   7.94  65.82   1.26  33.90
   5_bss:  76.47   0.00  11.97  76.47   0.00   7.94  65.82   1.26  33.90
   5_xyz:  76.47   0.00  11.97  76.47   0.00   7.94  65.82   1.26  33.90
   5_adp:  83.62   0.00  12.14  83.62   0.00   7.96  73.64   1.11  34.87
   5_occ:  83.62   0.00  12.14  83.62   0.00   7.96  73.64   1.11  34.87
   5_bss:  86.62   2.99  15.13  86.62   2.99  10.96  76.64   4.10  37.86
------------------------------------------------------------------------
 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:    1.198    0.019    0.412
   1_adp:    1.198    0.019    0.412
   1_occ:    1.198    0.019    0.412
   2_bss:    1.198    0.019    0.412
   2_xyz:    1.668    0.049    0.536
   2_adp:    1.668    0.049    0.536
   2_occ:    1.668    0.049    0.536
   3_bss:    1.668    0.049    0.536
   3_xyz:    1.616    0.033    0.596
   3_adp:    1.616    0.033    0.596
   3_occ:    1.616    0.033    0.596
   4_bss:    1.616    0.033    0.596
   4_xyz:    1.756    0.058    0.614
   4_adp:    1.756    0.058    0.614
   4_occ:    1.756    0.058    0.614
   5_bss:    1.756    0.058    0.614
   5_xyz:    1.812    0.051    0.627
   5_adp:    1.812    0.051    0.627
   5_occ:    1.812    0.051    0.627
   5_bss:    1.812    0.051    0.627
------------------------------------------------------------------------

CPU time actual refinement: 328.12


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_323/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_323/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_323/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_323/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_323/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 327.97 
  Macro-tasks:
    bulk solvent and scale       = 41.38  
    individual site refinement   = 128.25 
    weights calculation          = 32.87  
    collect and process          = 6.60   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 209.20 
  Micro-tasks:
    mask                            = 1.84   
    f_calc                          = 101.00 
    alpha_beta                      = 8.21   
    target                          = 1.20   
    gradients_wrt_atomic_parameters = 109.60 
    fmodel                         = 6.94   
    r_factors                      = 0.22   
    phase_errors                   = 10.82  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 240.10 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.701 micro seconds
Total CPU time: 5.69 minutes
from_scatterers_fft:    628 calls, 100.58 s
gradients_fft:          572 calls,  97.02 s

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

# Date 2008-01-16 Time 01:16:11 PST -0800 (1200474971.76 s)
Start R-work = 0.4555, R-free = 0.4424 (no bulk solvent and anisotropic scale)
Final R-work = 0.1289, R-free = 0.1718 (no bulk solvent and anisotropic scale)

Start R-work = 0.4464, R-free = 0.4366
Final R-work = 0.1110, R-free = 0.1560