# Date 2008-01-16 Time 01:56:59 PST -0800 (1200477419.41 s)
#phil __OFF__

Command line arguments: "../626.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 23250
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 626

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 45.9914, 88.5498, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.30, per 1000 atoms: 1.17


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 45.9914, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0929 1.96332
Completeness in resolution range: 0.929093
Completeness with d_max=infinity: 0.926369

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0929
                             d_min =   1.9633

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 45.9914, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0929 1.96332
Completeness in resolution range: 0.929093
Completeness with d_max=infinity: 0.926369

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0933 -  4.2023 [2211/2236]  1988   223  10.1%
  bin  2:  4.2023 -  3.3474 [2136/2156]  1927   209   9.8%
  bin  3:  3.3474 -  2.9278 [2091/2110]  1882   209  10.0%
  bin  4:  2.9278 -  2.6617 [2084/2114]  1867   217  10.4%
  bin  5:  2.6617 -  2.4718 [2074/2093]  1868   206   9.9%
  bin  6:  2.4718 -  2.3266 [2057/2082]  1856   201   9.8%
  bin  7:  2.3266 -  2.2105 [2043/2071]  1834   209  10.2%
  bin  8:  2.2105 -  2.1145 [2039/2075]  1830   209  10.3%
  bin  9:  2.1145 -  2.0333 [2008/2081]  1821   187   9.3%
  bin 10:  2.0333 -  1.9633 [ 846/2066]   757    89  10.5%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_626/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: 0.13 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:
        1.51 -     2.19: 22
        2.19 -     2.87: 1200
        2.87 -     3.54: 4463
        3.54 -     4.22: 9207
        4.22 -     4.90: 13373
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.511 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.559 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.574 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  18 " - " O   HOH Z 104 "  1.751 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.784 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28260 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_626/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_626/model_refine_001.geo

CPU time processing inputs: 9.22


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 45.9914 88.54975 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5104   r_free= 0.4995   ksol= 0.00   Bsol= 0.00   scale= 0.768    |
|                                                                             |
| 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:   0.92 A                  |
| x-ray target function (ml) for work reflections: 6.309809                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.6876 0.99   1434  157 0.4356 0.4109      6.6701      6.6477|
|  2:  4.6876 -  3.7393 0.99   1387  157 0.4509 0.4459      6.8676      6.8585|
|  3:  3.7393 -  3.2721 0.99   1356  150 0.4776 0.4194      6.7142      6.6757|
|  4:  3.2721 -  2.9754 0.99   1345  150 0.5170 0.4829      6.5664      6.5131|
|  5:  2.9754 -  2.7636 0.99   1345  149 0.5455 0.5387      6.3751      6.4274|
|  6:  2.7636 -  2.6015 0.99   1338  148 0.5472 0.5592      6.2906      6.2093|
|  7:  2.6015 -  2.4718 0.99   1327  153 0.5353 0.4981      6.2517      6.1902|
|  8:  2.4718 -  2.3646 0.98   1320  149 0.5600 0.5300      6.1844      6.1845|
|  9:  2.3646 -  2.2739 0.98   1303  138 0.5387 0.5700      6.1368       6.206|
| 10:  2.2739 -  2.1957 1.00   1342  149 0.5358 0.5681      6.0841      6.1176|
| 11:  2.1957 -  2.1272 0.98   1314  146 0.5235 0.5370      6.0361      6.0233|
| 12:  2.1272 -  2.0666 0.98   1288  141 0.5443 0.5600      5.9467      5.9688|
| 13:  2.0666 -  2.0123 0.88   1180  132 0.5591 0.5289      5.8956      5.7921|
| 14:  2.0123 -  1.9633 0.26    351   40 0.5259 0.5305      5.8565      5.8718|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0933 -  4.6876  1434   157  0.66  37.38   0.77     0.72      84167.05|
|  2:  4.6876 -  3.7393  1387   157  0.66  38.38   0.84     0.75     125377.46|
|  3:  3.7393 -  3.2721  1356   150  0.53  49.29   0.82     0.67     134438.21|
|  4:  3.2721 -  2.9754  1345   150  0.42  57.81   0.75     0.53     120005.30|
|  5:  2.9754 -  2.7636  1345   149  0.31  66.59   0.70     0.39      96051.92|
|  6:  2.7636 -  2.6015  1338   148  0.27  69.95   0.69     0.32      83603.49|
|  7:  2.6015 -  2.4718  1327   153  0.21  74.28   0.72     0.25      77683.80|
|  8:  2.4718 -  2.3646  1320   149  0.20  75.32   0.70     0.25      70003.47|
|  9:  2.3646 -  2.2739  1303   138  0.17  77.55   0.72     0.21      65965.93|
| 10:  2.2739 -  2.1957  1342   149  0.18  76.61   0.73     0.22      57618.02|
| 11:  2.1957 -  2.1272  1314   146  0.17  77.43   0.75     0.22      56261.92|
| 12:  2.1272 -  2.0666  1288   141  0.19  75.58   0.73     0.26      48693.89|
| 13:  2.0666 -  2.0123  1180   132  0.22  73.88   0.71     0.30      42357.49|
| 14:  2.0123 -  1.9633   351    40  0.32  66.28   0.74     0.36      32241.26|
|alpha:            min =        0.21 max =            0.75 mean =         0.39|
|beta:             min =    32241.26 max =       134438.21 mean =     81455.65|
|figures of merit: min =        0.00 max =            1.00 mean =         0.33|
|phase err.(work): min =        0.00 max =           90.00 mean =        65.00|
|phase err.(test): min =        0.00 max =           89.96 mean =        65.26|
|-----------------------------------------------------------------------------|

============================== 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 = 23.872678             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.748   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.264157              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.786   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       35 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      175 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      691 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1513 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2643 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3920 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5062 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6545 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7715 |
|-----------------------------------------------------------------------------|
|-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 |       53.778 |
| 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  1.196 |       2.150 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.845)------------------------------------------|
|    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 = 11.845)------------------------------------------|
|    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: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5153   r_free= 0.5006   ksol= 0.00   Bsol= 0.00   scale= 0.739    |
|                                                                             |
| 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:   0.87 A                  |
| x-ray target function (ml) for work reflections: 6.310371                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5026   r_free= 0.4874   ksol= 0.36   Bsol= 20.00   scale= 0.959   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.85,8.29,10.99,0.00,0.00,0.00); trace/3= 8.38                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.85 A                  |
| x-ray target function (ml) for work reflections: 6.305083                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 19.148252             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 85.505   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.766813              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.141   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5026      final r-factor (work) = 0.4384          |
| start r-factor (free) = 0.4874      final r-factor (free) = 0.4678          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 114.1128 = 19.15 * 0.50 * 6.3019 + 1.00 * 53.7780                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 60.0212 = 19.15 * 0.50 * 6.2520 + 1.00 * 0.1641                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4384      final r-factor (work) = 0.4027          |
| start r-factor (free) = 0.4678      final r-factor (free) = 0.4672          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.0605 = 1.77 * 1.00 * 6.2520 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.9820 = 1.77 * 1.00 * 6.2044 + 1.00 * 0.0200                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.845)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.55   16.87    None  None   None       |
|    all(noH): 2823   0      0.00    85.55   16.87    None  None   None       |
|    Sol.    : 438    0      0.00    85.55   25.15    None  None   None       |
|    Mac.    : 2385   0      0.00    77.75   15.35    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 -   8.555:  839   |   5:    42.775 -  51.331:   73        |
|      1:     8.555 -  17.110:  817   |   6:    51.331 -  59.886:   40        |
|      2:    17.110 -  25.665:  580   |   7:    59.886 -  68.441:   12        |
|      3:    25.665 -  34.220:  307   |   8:    68.441 -  76.996:    9        |
|      4:    34.220 -  42.775:  143   |   9:    76.996 -  85.551:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4027 r_free = 0.4672             target_work(ml) = 6.197         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4024 r_free = 0.4678             target_work(ml) = 6.197         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4024   r_free= 0.4678   ksol= 0.36   Bsol= 20.00   scale= 1.126   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.85,8.29,10.99,0.00,0.00,0.00); trace/3= 8.38                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.196920                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3998   r_free= 0.4641   ksol= 0.35   Bsol= 43.21   scale= 1.028   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.56,4.34,6.70,0.00,0.00,0.00); trace/3= 4.53                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.72 A                  |
| x-ray target function (ml) for work reflections: 6.199251                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.572833              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.039  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.829447              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.736  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3998      final r-factor (work) = 0.3464          |
| start r-factor (free) = 0.4641      final r-factor (free) = 0.4212          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.8454 = 9.57 * 0.50 * 6.2012 + 1.00 * 0.1641                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.5054 = 9.57 * 0.50 * 6.1444 + 1.00 * 0.0955                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3464      final r-factor (work) = 0.3311          |
| start r-factor (free) = 0.4212      final r-factor (free) = 0.4133          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.1169 = 0.83 * 1.00 * 6.1444 + 1.00 * 0.0204                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.0557 = 0.83 * 1.00 * 6.0783 + 1.00 * 0.0140                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.845)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.45   16.73    None  None   None       |
|    all(noH): 2823   0      0.00    87.45   16.73    None  None   None       |
|    Sol.    : 438    0      0.00    87.45   29.46    None  None   None       |
|    Mac.    : 2385   0      0.00    75.84   14.39    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 -   8.745:  863   |   5:    43.723 -  52.467:   68        |
|      1:     8.745 -  17.489:  862   |   6:    52.467 -  61.212:   30        |
|      2:    17.489 -  26.234:  585   |   7:    61.212 -  69.957:   12        |
|      3:    26.234 -  34.978:  274   |   8:    69.957 -  78.701:    6        |
|      4:    34.978 -  43.723:  122   |   9:    78.701 -  87.446:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3311 r_free = 0.4133             target_work(ml) = 6.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3307 r_free = 0.4139             target_work(ml) = 6.072         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3307   r_free= 0.4139   ksol= 0.35   Bsol= 43.21   scale= 1.077   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.56,4.34,6.70,0.00,0.00,0.00); trace/3= 4.53                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.071895                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3301   r_free= 0.4128   ksol= 0.35   Bsol= 66.38   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.05,1.96,4.20,0.00,0.00,0.00); trace/3= 2.40                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.073403                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.731251              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.420  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.599799              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 158.222  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3301      final r-factor (work) = 0.2665          |
| start r-factor (free) = 0.4128      final r-factor (free) = 0.3409          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.5926 = 7.73 * 0.50 * 6.0785 + 1.00 * 0.0955                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.2793 = 7.73 * 0.50 * 5.9987 + 1.00 * 0.0906                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2665      final r-factor (work) = 0.2428          |
| start r-factor (free) = 0.3409      final r-factor (free) = 0.3205          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.6120 = 0.60 * 1.00 * 5.9987 + 1.00 * 0.0140                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5310 = 0.60 * 1.00 * 5.8661 + 1.00 * 0.0125                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.845)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    88.82   16.13    None  None   None       |
|    all(noH): 2823   0      0.00    88.82   16.13    None  None   None       |
|    Sol.    : 438    0      0.00    88.82   34.46    None  None   None       |
|    Mac.    : 2385   0      0.00    68.51   12.76    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 -   8.883: 1027   |   5:    44.412 -  53.295:   79        |
|      1:     8.883 -  17.765:  854   |   6:    53.295 -  62.177:   25        |
|      2:    17.765 -  26.647:  420   |   7:    62.177 -  71.060:   16        |
|      3:    26.647 -  35.530:  264   |   8:    71.060 -  79.942:    5        |
|      4:    35.530 -  44.412:  132   |   9:    79.942 -  88.825:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2428 r_free = 0.3205             target_work(ml) = 5.834         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2427 r_free = 0.3201             target_work(ml) = 5.834         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2427   r_free= 0.3201   ksol= 0.35   Bsol= 66.38   scale= 1.045   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.05,1.96,4.20,0.00,0.00,0.00); trace/3= 2.40                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.833568                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2429   r_free= 0.3197   ksol= 0.34   Bsol= 60.54   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.27,0.70,2.75,0.00,0.00,0.00); trace/3= 1.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.834261                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.092545              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.359   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 5.106025              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.333  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2429      final r-factor (work) = 0.1990          |
| start r-factor (free) = 0.3197      final r-factor (free) = 0.2650          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.0970 = 4.09 * 0.50 * 5.8674 + 1.00 * 0.0906                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.8457 = 4.09 * 0.50 * 5.7571 + 1.00 * 0.0650                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1990      final r-factor (work) = 0.1797          |
| start r-factor (free) = 0.2650      final r-factor (free) = 0.2484          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 29.4086 = 5.11 * 1.00 * 5.7571 + 1.00 * 0.0124                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 28.6738 = 5.11 * 1.00 * 5.6118 + 1.00 * 0.0200                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.845)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    105.83  17.49    None  None   None       |
|    all(noH): 2823   0      0.00    105.83  17.49    None  None   None       |
|    Sol.    : 438    0      2.03    105.83  47.02    None  None   None       |
|    Mac.    : 2385   0      0.00    92.02   12.06    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.584: 1412   |   5:    52.917 -  63.501:   96        |
|      1:    10.584 -  21.167:  724   |   6:    63.501 -  74.084:   73        |
|      2:    21.167 -  31.750:  230   |   7:    74.084 -  84.668:   26        |
|      3:    31.750 -  42.334:  129   |   8:    84.668 -  95.251:   18        |
|      4:    42.334 -  52.917:  112   |   9:    95.251 - 105.835:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1797 r_free = 0.2484             target_work(ml) = 5.579         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1797 r_free = 0.2481             target_work(ml) = 5.578         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1797   r_free= 0.2481   ksol= 0.34   Bsol= 60.54   scale= 1.025   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.27,0.70,2.75,0.00,0.00,0.00); trace/3= 1.24                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.577553                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1798   r_free= 0.2481   ksol= 0.33   Bsol= 69.43   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.01,0.09,2.37,0.00,0.00,0.00); trace/3= 0.82                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.26 A                  |
| x-ray target function (ml) for work reflections: 5.576585                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.483925              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.522  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.257239              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 112.471  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1798      final r-factor (work) = 0.1554          |
| start r-factor (free) = 0.2481      final r-factor (free) = 0.2171          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.0357 = 2.48 * 0.50 * 5.6125 + 1.00 * 0.0651                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9131 = 2.48 * 0.50 * 5.5200 + 1.00 * 0.0575                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1554      final r-factor (work) = 0.1476          |
| start r-factor (free) = 0.2171      final r-factor (free) = 0.2057          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.4798 = 2.26 * 1.00 * 5.5200 + 1.00 * 0.0198                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.2691 = 2.26 * 1.00 * 5.4276 + 1.00 * 0.0176                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.845)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.51  17.03    None  None   None       |
|    all(noH): 2823   0      0.00    107.51  17.03    None  None   None       |
|    Sol.    : 438    0      3.17    107.51  48.14    None  None   None       |
|    Mac.    : 2385   0      0.00    93.24   11.31    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.751: 1540   |   5:    53.754 -  64.505:   80        |
|      1:    10.751 -  21.502:  676   |   6:    64.505 -  75.256:   73        |
|      2:    21.502 -  32.252:  189   |   7:    75.256 -  86.007:   32        |
|      3:    32.252 -  43.003:  105   |   8:    86.007 -  96.757:   17        |
|      4:    43.003 -  53.754:   99   |   9:    96.757 - 107.508:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1476 r_free = 0.2057             target_work(ml) = 5.400         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1475 r_free = 0.2054             target_work(ml) = 5.399         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1475   r_free= 0.2054   ksol= 0.33   Bsol= 69.43   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.01,0.09,2.37,0.00,0.00,0.00); trace/3= 0.82                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.399016                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.6876 0.99   1434  157 0.1012 0.1403      5.4419      5.6647|
|  2:  4.6876 -  3.7393 0.99   1387  157 0.0981 0.1397      5.5836      5.8257|
|  3:  3.7393 -  3.2721 0.99   1356  150 0.1374 0.1977      5.7058      6.0489|
|  4:  3.2721 -  2.9754 0.99   1345  150 0.1652 0.2224      5.7201      5.8774|
|  5:  2.9754 -  2.7636 0.99   1345  149 0.1762 0.2326      5.5911      5.8411|
|  6:  2.7636 -  2.6015 0.99   1338  148 0.1706 0.2729      5.4882      5.7567|
|  7:  2.6015 -  2.4718 0.99   1327  153 0.1695 0.2049       5.426      5.5416|
|  8:  2.4718 -  2.3646 0.98   1320  149 0.1744 0.2353      5.4007      5.6103|
|  9:  2.3646 -  2.2739 0.98   1303  138 0.1681 0.2499       5.325      5.5837|
| 10:  2.2739 -  2.1957 1.00   1342  149 0.1574 0.2243      5.2222       5.433|
| 11:  2.1957 -  2.1272 0.98   1314  146 0.1565 0.2395      5.1966      5.5438|
| 12:  2.1272 -  2.0666 0.98   1288  141 0.1594 0.2328      5.1478      5.4287|
| 13:  2.0666 -  2.0123 0.88   1180  132 0.1480 0.1912      4.9978      5.1299|
| 14:  2.0123 -  1.9633 0.26    351   40 0.1350 0.2062       4.874      5.1129|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0933 -  4.6876  1434   157  0.93  10.77   0.97     0.94       9186.12|
|  2:  4.6876 -  3.7393  1387   157  0.93  10.67   1.03     1.01      12927.02|
|  3:  3.7393 -  3.2721  1356   150  0.90  16.10   1.06     1.05      17168.34|
|  4:  3.2721 -  2.9754  1345   150  0.86  20.10   1.04     0.99      18563.55|
|  5:  2.9754 -  2.7636  1345   149  0.84  22.51   1.01     0.98      15424.45|
|  6:  2.7636 -  2.6015  1338   148  0.83  23.44   0.98     0.92      13013.36|
|  7:  2.6015 -  2.4718  1327   153  0.84  22.52   1.00     0.95      11307.72|
|  8:  2.4718 -  2.3646  1320   149  0.83  23.51   1.00     0.96      10767.75|
|  9:  2.3646 -  2.2739  1303   138  0.84  22.56   1.00     0.93       9239.92|
| 10:  2.2739 -  2.1957  1342   149  0.84  22.22   1.00     0.95       7807.20|
| 11:  2.1957 -  2.1272  1314   146  0.84  22.56   1.00     0.93       7567.52|
| 12:  2.1272 -  2.0666  1288   141  0.85  21.81   1.00     1.00       6920.46|
| 13:  2.0666 -  2.0123  1180   132  0.85  21.94   0.99     0.94       5161.16|
| 14:  2.0123 -  1.9633   351    40  0.91  16.16   0.99     0.96       3533.62|
|alpha:            min =        0.92 max =            1.05 mean =         0.97|
|beta:             min =     3533.62 max =        18563.55 mean =     11085.20|
|figures of merit: min =        0.00 max =            1.00 mean =         0.86|
|phase err.(work): min =        0.00 max =           89.99 mean =        19.86|
|phase err.(test): min =        0.00 max =           89.71 mean =        19.07|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1478   r_free= 0.2052   ksol= 0.33   Bsol= 70.22   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.75,-0.79,1.54,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.398375                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.09 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1478   r_free= 0.2052   ksol= 0.33   Bsol= 70.22   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.75,-0.79,1.54,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.398375                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0933 -  4.6876 0.99   1434  157 0.1026 0.1376      5.4388      5.6524|
|  2:  4.6876 -  3.7393 0.99   1387  157 0.0985 0.1399      5.5812      5.8279|
|  3:  3.7393 -  3.2721 0.99   1356  150 0.1375 0.1973      5.7049      6.0481|
|  4:  3.2721 -  2.9754 0.99   1345  150 0.1653 0.2223      5.7198       5.876|
|  5:  2.9754 -  2.7636 0.99   1345  149 0.1762 0.2325      5.5906      5.8398|
|  6:  2.7636 -  2.6015 0.99   1338  148 0.1705 0.2733       5.488      5.7575|
|  7:  2.6015 -  2.4718 0.99   1327  153 0.1694 0.2050      5.4261      5.5419|
|  8:  2.4718 -  2.3646 0.98   1320  149 0.1744 0.2352      5.4008      5.6102|
|  9:  2.3646 -  2.2739 0.98   1303  138 0.1680 0.2500       5.325      5.5836|
| 10:  2.2739 -  2.1957 1.00   1342  149 0.1573 0.2243      5.2221      5.4335|
| 11:  2.1957 -  2.1272 0.98   1314  146 0.1564 0.2394      5.1964       5.544|
| 12:  2.1272 -  2.0666 0.98   1288  141 0.1595 0.2332      5.1479      5.4292|
| 13:  2.0666 -  2.0123 0.88   1180  132 0.1480 0.1908      4.9973      5.1287|
| 14:  2.0123 -  1.9633 0.26    351   40 0.1350 0.2056      4.8732      5.1112|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0933 -  4.6876  1434   157  0.93  10.53   0.96     0.94       8888.11|
|  2:  4.6876 -  3.7393  1387   157  0.93  10.57   1.03     1.01      12753.25|
|  3:  3.7393 -  3.2721  1356   150  0.90  16.10   1.06     1.05      17134.92|
|  4:  3.2721 -  2.9754  1345   150  0.86  20.06   1.04     0.99      18516.11|
|  5:  2.9754 -  2.7636  1345   149  0.84  22.49   1.01     0.97      15408.77|
|  6:  2.7636 -  2.6015  1338   148  0.83  23.44   0.98     0.92      13017.67|
|  7:  2.6015 -  2.4718  1327   153  0.84  22.53   1.00     0.95      11313.48|
|  8:  2.4718 -  2.3646  1320   149  0.83  23.51   1.00     0.95      10765.66|
|  9:  2.3646 -  2.2739  1303   138  0.84  22.56   1.00     0.93       9242.00|
| 10:  2.2739 -  2.1957  1342   149  0.84  22.21   1.00     0.95       7808.49|
| 11:  2.1957 -  2.1272  1314   146  0.84  22.55   1.00     0.93       7568.52|
| 12:  2.1272 -  2.0666  1288   141  0.85  21.82   1.00     1.00       6921.63|
| 13:  2.0666 -  2.0123  1180   132  0.85  21.93   0.99     0.93       5153.12|
| 14:  2.0123 -  1.9633   351    40  0.91  16.09   0.98     0.96       3519.46|
|alpha:            min =        0.92 max =            1.05 mean =         0.96|
|beta:             min =     3519.46 max =        18516.11 mean =     11040.10|
|figures of merit: min =        0.00 max =            1.00 mean =         0.86|
|phase err.(work): min =        0.00 max =           89.87 mean =        19.83|
|phase err.(test): min =        0.00 max =           89.58 mean =        19.01|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.845)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.80    108.30  17.82    None  None   None       |
|    all(noH): 2823   0      0.80    108.30  17.82    None  None   None       |
|    Sol.    : 438    0      3.96    108.30  48.94    None  None   None       |
|    Mac.    : 2385   0      0.80    94.04   12.11    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.796 -  11.547: 1540   |   5:    54.550 -  65.301:   80        |
|      1:    11.547 -  22.297:  676   |   6:    65.301 -  76.052:   73        |
|      2:    22.297 -  33.048:  189   |   7:    76.052 -  86.802:   32        |
|      3:    33.048 -  43.799:  105   |   8:    86.802 -  97.553:   17        |
|      4:    43.799 -  54.550:   99   |   9:    97.553 - 108.304:   12        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 356         
Filter by distance & map next to the model:
   mapped sites are within: 0.256 - 4.878
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 353 from: 356
   mapped sites are within: 0.758 - 4.878

peak=    7.679 closest distance to " CB  VAL A 230 " =    1.427
peak=    7.626 closest distance to " O   HOH Z 103 " =    1.353
peak=    7.362 closest distance to " O   HOH Z 130 " =    1.836
peak=    7.180 closest distance to " CB  VAL A 296 " =    1.535
peak=    6.761 closest distance to " O  BHOH Z  74 " =    1.088
peak=    6.690 closest distance to " CD2 LEU A   5 " =    1.477
peak=    5.774 closest distance to " NH1 ARG A 138 " =    1.099
peak=    5.768 closest distance to " CG  ARG A 138 " =    1.225
peak=    5.698 closest distance to " O   HOH Z 246 " =    1.700
peak=    5.548 closest distance to " CD1AILE A 234 " =    1.033
peak=    5.472 closest distance to " O   HOH Z 245 " =    1.101
peak=    5.257 closest distance to " CB  VAL A 230 " =    1.330
peak=    5.244 closest distance to " O   HOH Z  70 " =    1.191
peak=    5.222 closest distance to " O   HOH Z 127 " =    1.312
peak=    5.182 closest distance to " O   HOH Z 385 " =    1.169
peak=    5.180 closest distance to " C   GLN A  73 " =    1.075
peak=    5.100 closest distance to " C   PRO A 198 " =    1.473
peak=    5.096 closest distance to " O   HOH Z 105 " =    1.294
peak=    5.088 closest distance to " C   VAL A  72 " =    1.071
peak=    5.073 closest distance to " O   HOH Z 268 " =    1.135
peak=    5.035 closest distance to " CB  SER A 216 " =    1.148
peak=    4.992 closest distance to " OD1 ASN A  69 " =    1.190
peak=    4.977 closest distance to " O   HOH Z  63 " =    1.608
peak=    4.950 closest distance to " O   HOH Z 330 " =    1.168
peak=    4.894 closest distance to " O   HOH Z 425 " =    1.668
peak=    4.876 closest distance to " O   HOH Z 331 " =    1.280
peak=    4.860 closest distance to " CD  ARG A 138 " =    0.997
peak=    4.848 closest distance to " O   HOH Z 258 " =    1.463
peak=    4.816 closest distance to " O   HOH Z 110 " =    0.953
peak=    4.808 closest distance to " NE2 GLN A  11 " =    1.125
peak=    4.777 closest distance to " O   HOH Z  46 " =    1.244
peak=    4.746 closest distance to " CG  PRO A  54 " =    1.527
peak=    4.703 closest distance to " CB  SER A  63 " =    1.451
peak=    4.697 closest distance to " O   HOH Z 415 " =    1.158
peak=    4.687 closest distance to " O   HOH Z 427 " =    2.188
peak=    4.647 closest distance to " O   HOH Z  69 " =    1.618
peak=    4.635 closest distance to " NH2 ARG A  56 " =    2.179
peak=    4.627 closest distance to " CG  PRO A 243 " =    1.175
peak=    4.569 closest distance to " CG  ARG A 138 " =    1.183
peak=    4.566 closest distance to " O   HOH Z  65 " =    1.903
peak=    4.557 closest distance to " O   HOH Z 222 " =    1.605
peak=    4.541 closest distance to " O   HOH Z 287 " =    1.871
peak=    4.534 closest distance to " O   HOH Z 422 " =    1.086
peak=    4.486 closest distance to " O   HOH Z  66 " =    1.090
peak=    4.472 closest distance to " O   HOH Z 255 " =    0.970
peak=    4.403 closest distance to " O   HOH Z 417 " =    2.088
peak=    4.363 closest distance to " O   HOH Z 207 " =    1.190
peak=    4.354 closest distance to " N   TYR A  15 " =    1.099
peak=    4.316 closest distance to " CG2 ILE A 120 " =    1.199
peak=    4.315 closest distance to " O   HOH Z 112 " =    1.141
peak=    4.306 closest distance to " O   HOH Z 263 " =    1.282
peak=    4.300 closest distance to " CZ  PHE A 218 " =    1.136
peak=    4.272 closest distance to " O   HOH Z  39 " =    1.607
peak=    4.260 closest distance to " CG2 ILE A 234 " =    1.000
peak=    4.244 closest distance to " O   HOH Z 414 " =    1.571
peak=    4.224 closest distance to " O   HOH Z   7 " =    2.109
peak=    4.208 closest distance to " O   HOH Z 427 " =    1.203
peak=    4.156 closest distance to " CZ3 TRP A 266 " =    1.267
peak=    4.149 closest distance to " CB  LYS A 117 " =    1.307
peak=    4.147 closest distance to " O   HOH Z 375 " =    1.184
peak=    4.141 closest distance to " CB  ASN A 148 " =    1.481
peak=    4.105 closest distance to " O   HOH Z 124 " =    1.413
peak=    4.100 closest distance to " CZ  PHE A  38 " =    1.177
peak=    4.083 closest distance to " O   HOH Z  21 " =    1.403
peak=    4.077 closest distance to " O   HOH Z  59 " =    1.939
peak=    4.073 closest distance to " O   HOH Z 146 " =    1.489
peak=    4.063 closest distance to " CB  PRO A  54 " =    1.236
peak=    4.058 closest distance to " CD2 LEU A 228 " =    1.280
peak=    4.050 closest distance to " O   HOH Z 232 " =    2.214
peak=    4.046 closest distance to " CB  ALA A  10 " =    1.072
peak=    4.032 closest distance to " O   HOH Z 418 " =    1.091
peak=    4.027 closest distance to " CG  LEU A 228 " =    1.050
peak=    4.023 closest distance to " C   HIS A 115 " =    0.961
peak=    4.022 closest distance to " O   HOH Z 139 " =    1.198
peak=    4.017 closest distance to " CG  PRO A 198 " =    1.313
peak=    4.012 closest distance to " O   HOH Z 278 " =    1.050
peak=    4.011 closest distance to " CB  MET A  40 " =    1.029
peak=    4.003 closest distance to " O   HOH Z  52 " =    0.991
peak=    3.991 closest distance to " O   HOH Z 437 " =    2.261
peak=    3.974 closest distance to " O   HOH Z 298 " =    1.722
peak=    3.973 closest distance to " O   HOH Z 147 " =    1.471
peak=    3.936 closest distance to " CE3 TRP A 274 " =    1.317
peak=    3.923 closest distance to " O   HOH Z 316 " =    3.049
peak=    3.913 closest distance to " O   HOH Z 143 " =    2.143
peak=    3.907 closest distance to " O   HOH Z 374 " =    1.356
peak=    3.907 closest distance to " CB  ASN A  39 " =    0.940
peak=    3.906 closest distance to " O   HOH Z 359 " =    1.391
peak=    3.888 closest distance to " O   HOH Z 350 " =    1.503
peak=    3.887 closest distance to " CG BARG A 275 " =    1.325
peak=    3.871 closest distance to " ND2BASN A 224 " =    0.990
peak=    3.868 closest distance to " O   HOH Z 365 " =    3.249
peak=    3.864 closest distance to " CB  SER A  62 " =    1.296
peak=    3.862 closest distance to " O   HOH Z   9 " =    2.721
peak=    3.853 closest distance to " CB  SER A   3 " =    1.488
peak=    3.846 closest distance to " O   HOH Z 368 " =    1.172
peak=    3.833 closest distance to " CB  ARG A 275 " =    1.139
peak=    3.820 closest distance to " O   HOH Z 342 " =    0.994
peak=    3.807 closest distance to " CA  CYS A 201 " =    1.073
peak=    3.799 closest distance to " O   HOH Z  66 " =    2.385
peak=    3.792 closest distance to " O   HOH Z 369 " =    2.087
peak=    3.783 closest distance to " NH2 ARG A 269 " =    0.945
peak=    3.781 closest distance to " O   HOH Z 357 " =    2.280
peak=    3.772 closest distance to " O   HOH Z  53 " =    2.217
peak=    3.770 closest distance to " O   HOH Z  24 " =    1.829
peak=    3.764 closest distance to " N   GLN A 122 " =    0.758
peak=    3.763 closest distance to " CB  ASN A 142 " =    1.034
peak=    3.762 closest distance to " O   HOH Z  78 " =    1.868
peak=    3.756 closest distance to " CA  ILE A 234 " =    1.052
peak=    3.754 closest distance to " O   HOH Z 182 " =    1.227
peak=    3.747 closest distance to " O   HOH Z  30 " =    1.328
peak=    3.745 closest distance to " O   HOH Z  61 " =    1.762
peak=    3.745 closest distance to " CB  ARG A 138 " =    1.033
peak=    3.740 closest distance to " CE2 PHE A  16 " =    0.831
peak=    3.740 closest distance to " O   HOH Z 193 " =    1.705
peak=    3.739 closest distance to " CD1 LEU A   5 " =    1.399
peak=    3.730 closest distance to " O   HOH Z 101 " =    0.930
peak=    3.730 closest distance to " O   HOH Z 424 " =    1.120
peak=    3.729 closest distance to " O   HOH Z  26 " =    1.657
peak=    3.724 closest distance to " O   HOH Z 343 " =    2.769
peak=    3.723 closest distance to " O   HOH Z 225 " =    1.858
peak=    3.721 closest distance to " CD  GLN A  77 " =    1.229
peak=    3.720 closest distance to " O   HOH Z 303 " =    2.080
peak=    3.719 closest distance to " O   HOH Z 293 " =    1.509
peak=    3.717 closest distance to " N   PHE A  59 " =    0.842
peak=    3.717 closest distance to " OE1 GLN A 240 " =    1.598
peak=    3.714 closest distance to " O   HOH Z 148 " =    1.679
peak=    3.712 closest distance to " C   PRO A  54 " =    0.924
peak=    3.705 closest distance to " N   GLN A 278 " =    0.963
peak=    3.701 closest distance to " CG  ASP A  65 " =    1.048
peak=    3.698 closest distance to " NH2AARG A 190 " =    1.835
peak=    3.695 closest distance to " NZ  LYS A 119 " =    2.865
peak=    3.695 closest distance to " O   HOH Z 143 " =    1.649
peak=    3.694 closest distance to " CB  GLN A 223 " =    1.427
peak=    3.689 closest distance to " CB  ASP A 107 " =    1.104
peak=    3.688 closest distance to " O   HOH Z  80 " =    1.609
peak=    3.687 closest distance to " CG2 THR A 221 " =    1.238
peak=    3.682 closest distance to " O   HOH Z  77 " =    1.255
peak=    3.679 closest distance to " O   HOH Z 380 " =    1.827
peak=    3.675 closest distance to " O   HOH Z 153 " =    3.722
peak=    3.669 closest distance to " O   TYR A 116 " =    0.982
peak=    3.667 closest distance to " CB  ARG A  79 " =    0.898
peak=    3.661 closest distance to " CB  PRO A 213 " =    1.282
peak=    3.660 closest distance to " CG  LEU A   5 " =    1.151
peak=    3.656 closest distance to " O   HOH Z  49 " =    1.407
peak=    3.653 closest distance to " O   HOH Z 389 " =    1.794
peak=    3.648 closest distance to " O   HOH Z 119 " =    1.664
peak=    3.648 closest distance to " N   ARG A 156 " =    1.278
peak=    3.648 closest distance to " O   HOH Z 272 " =    1.855
peak=    3.646 closest distance to " NH1AARG A 145 " =    1.063
peak=    3.643 closest distance to " O   GLN A  55 " =    0.830
peak=    3.643 closest distance to " CB  ASN A 110 " =    1.091
peak=    3.641 closest distance to " NH2AARG A 190 " =    2.027
peak=    3.637 closest distance to " O   HOH Z 238 " =    1.307
peak=    3.637 closest distance to " O   HOH Z 180 " =    2.226
peak=    3.633 closest distance to " O   HOH Z 428 " =    1.243
peak=    3.629 closest distance to " O   HOH Z 360 " =    1.223
peak=    3.627 closest distance to " O   HOH Z 411 " =    3.190
peak=    3.622 closest distance to " CA  TRP A 150 " =    0.981
peak=    3.619 closest distance to " O   HOH Z  91 " =    2.409
peak=    3.608 closest distance to " CB  THR A  52 " =    0.999
peak=    3.603 closest distance to " O   HOH Z  43 " =    1.323
peak=    3.596 closest distance to " CA  ARG A  36 " =    0.988
peak=    3.596 closest distance to " C   ASN A 209 " =    1.593
peak=    3.591 closest distance to " N   GLN A  73 " =    1.011
peak=    3.591 closest distance to " O   HOH Z 392 " =    1.264
peak=    3.585 closest distance to " O   HOH Z 124 " =    1.882
peak=    3.581 closest distance to " CB  ALA A  43 " =    0.952
peak=    3.569 closest distance to " CB  TYR A 169 " =    0.783
peak=    3.565 closest distance to " CB  SER A 276 " =    1.177
peak=    3.545 closest distance to " O   HOH Z 329 " =    4.368
peak=    3.544 closest distance to " O   HOH Z 403 " =    1.595
peak=    3.543 closest distance to " O   HOH Z  92 " =    1.211
peak=    3.542 closest distance to " O   HOH Z 216 " =    3.586
peak=    3.542 closest distance to " O   HOH Z  49 " =    2.660
peak=    3.540 closest distance to " CA  GLY A  80 " =    0.865
peak=    3.538 closest distance to " O   HOH Z 201 " =    1.685
peak=    3.537 closest distance to " O   HOH Z 362 " =    1.963
peak=    3.535 closest distance to " O   HOH Z  20 " =    1.749
peak=    3.528 closest distance to " O   HOH Z 419 " =    1.725
peak=    3.518 closest distance to " CG1 VAL A 296 " =    1.257
peak=    3.517 closest distance to " ND2 ASN A 249 " =    0.766
peak=    3.516 closest distance to " O   HOH Z  88 " =    3.305
peak=    3.514 closest distance to " O   HOH Z 126 " =    1.967
peak=    3.512 closest distance to " O   HOH Z 220 " =    1.488
peak=    3.510 closest distance to " O   HOH Z 389 " =    2.416
peak=    3.510 closest distance to " CD  LYS A  76 " =    1.834
peak=    3.504 closest distance to " O   HOH Z 159 " =    0.889
peak=    3.502 closest distance to " OD1 ASN A  45 " =    1.436
peak=    3.494 closest distance to " O   HOH Z 361 " =    2.582
peak=    3.492 closest distance to " OD1 ASP A 200 " =    1.555
peak=    3.491 closest distance to " OG  SER A 146 " =    0.893
peak=    3.488 closest distance to " CG2 VAL A 257 " =    0.894
peak=    3.487 closest distance to " CA  VAL A 125 " =    1.078
peak=    3.486 closest distance to " O   HOH Z 181 " =    2.307
peak=    3.479 closest distance to " CB  TRP A 179 " =    1.450
peak=    3.479 closest distance to " CG  GLN A  58 " =    1.361
peak=    3.477 closest distance to " CB  ALA A 114 " =    1.549
peak=    3.474 closest distance to " O   HOH Z 353 " =    2.412
peak=    3.473 closest distance to " CB  THR A  31 " =    1.516
peak=    3.473 closest distance to " O   HOH Z 203 " =    1.981
peak=    3.472 closest distance to " O   HOH Z   4 " =    2.151
peak=    3.468 closest distance to " O   HOH Z 158 " =    2.753
peak=    3.468 closest distance to " CG  ARG A 156 " =    1.350
peak=    3.463 closest distance to " O   HOH Z 422 " =    2.448
peak=    3.455 closest distance to " CB  PRO A  90 " =    1.030
peak=    3.453 closest distance to " CB  GLU A 277 " =    3.588
peak=    3.451 closest distance to " CD  ARG A  66 " =    2.208
peak=    3.446 closest distance to " N   TRP A  70 " =    0.868
peak=    3.444 closest distance to " O   HOH Z 423 " =    2.158
peak=    3.441 closest distance to " CB  LEU A 237 " =    0.989
peak=    3.441 closest distance to " N   GLU A   2 " =    1.575
peak=    3.440 closest distance to " N   ASP A 162 " =    1.055
peak=    3.437 closest distance to " O   HOH Z 236 " =    1.537
peak=    3.435 closest distance to " O   HOH Z 123 " =    1.186
peak=    3.429 closest distance to " O   HOH Z 410 " =    1.482
peak=    3.428 closest distance to " CG BARG A 102 " =    2.070
peak=    3.424 closest distance to " CG2 ILE A  20 " =    1.647
peak=    3.422 closest distance to " O   HOH Z 373 " =    1.562
peak=    3.420 closest distance to " CB  ALA A 233 " =    0.963
peak=    3.419 closest distance to " O   HOH Z 193 " =    1.653
peak=    3.414 closest distance to " O   HOH Z 172 " =    2.332
peak=    3.404 closest distance to " O   HOH Z 211 " =    1.356
peak=    3.402 closest distance to " O   HOH Z 132 " =    2.226
peak=    3.400 closest distance to " O   HOH Z 274 " =    2.550
peak=    3.400 closest distance to " O   HOH Z 320 " =    0.929
peak=    3.395 closest distance to " CA  ALA A 160 " =    1.126
peak=    3.393 closest distance to " CB  ALA A 114 " =    0.819
peak=    3.390 closest distance to " C   PHE A 208 " =    0.868
peak=    3.383 closest distance to " C   ASN A 301 " =    1.008
peak=    3.383 closest distance to " NH2BARG A 190 " =    1.170
peak=    3.382 closest distance to " CB  ASN A 215 " =    1.275
peak=    3.380 closest distance to " O   HOH Z  85 " =    2.738
peak=    3.378 closest distance to " CD  LYS A 119 " =    1.731
peak=    3.378 closest distance to " CD2 TRP A 179 " =    1.414
peak=    3.374 closest distance to " CA  ALA A  51 " =    1.078
peak=    3.372 closest distance to " NH2AARG A 102 " =    0.919
peak=    3.369 closest distance to " N   VAL A 296 " =    1.833
peak=    3.369 closest distance to " CA  GLY A 136 " =    1.062
peak=    3.368 closest distance to " O   HOH Z 403 " =    1.337
peak=    3.360 closest distance to " O   HOH Z 361 " =    1.458
peak=    3.360 closest distance to " CA  ARG A 195 " =    1.353
peak=    3.359 closest distance to " O   HOH Z  40 " =    1.436
peak=    3.359 closest distance to " CE3 TRP A  85 " =    1.340
peak=    3.358 closest distance to " CD1 LEU A 300 " =    1.055
peak=    3.356 closest distance to " O   HOH Z  83 " =    1.135
peak=    3.355 closest distance to " OG  SER A 276 " =    1.086
peak=    3.340 closest distance to " CB  TYR A  30 " =    1.424
peak=    3.340 closest distance to " N   TYR A 186 " =    1.599
peak=    3.337 closest distance to " N   PHE A 130 " =    1.378
peak=    3.335 closest distance to " NE2 GLN A  73 " =    1.579
peak=    3.334 closest distance to " CA  ASP A 124 " =    0.792
peak=    3.334 closest distance to " OG BSER A 212 " =    2.477
peak=    3.333 closest distance to " O   HOH Z 368 " =    2.913
peak=    3.332 closest distance to " ND2 ASN A 176 " =    0.864
peak=    3.329 closest distance to " NE1 TRP A 274 " =    1.014
peak=    3.326 closest distance to " N   ALA A 165 " =    1.283
peak=    3.320 closest distance to " CD  GLU A   2 " =    2.038
peak=    3.314 closest distance to " O   HOH Z 296 " =    1.131
peak=    3.312 closest distance to " CB  SER A 141 " =    1.206
peak=    3.312 closest distance to " CB  MET A  47 " =    1.091
peak=    3.311 closest distance to " O   HOH Z   1 " =    1.773
peak=    3.308 closest distance to " O   HOH Z  71 " =    1.579
peak=    3.308 closest distance to " CB  VAL A 202 " =    1.676
peak=    3.301 closest distance to " O   HOH Z 213 " =    1.818
peak=    3.296 closest distance to " O   HOH Z 328 " =    1.537
peak=    3.286 closest distance to " CG2 VAL A 202 " =    1.277
peak=    3.285 closest distance to " O   HOH Z  76 " =    1.444
peak=    3.283 closest distance to " CD1 LEU A 228 " =    1.681
peak=    3.283 closest distance to " O   HOH Z 425 " =    2.042
peak=    3.282 closest distance to " OD1 ASN A 148 " =    1.949
peak=    3.281 closest distance to " NZ  LYS A  48 " =    1.891
peak=    3.281 closest distance to " O   HOH Z 132 " =    2.467
peak=    3.277 closest distance to " C   LEU A  25 " =    1.043
peak=    3.276 closest distance to " CG  GLN A  11 " =    2.237
peak=    3.276 closest distance to " O   HOH Z 368 " =    4.130
peak=    3.274 closest distance to " O   HOH Z 218 " =    1.708
peak=    3.273 closest distance to " CG  GLN A  89 " =    1.616
peak=    3.272 closest distance to " O   HOH Z 368 " =    1.726
peak=    3.271 closest distance to " CB  ALA A 248 " =    1.998
peak=    3.270 closest distance to " CA  LEU A 222 " =    1.207
peak=    3.269 closest distance to " CE  MET A  93 " =    1.546
peak=    3.268 closest distance to " O   ASN A 142 " =    1.033
peak=    3.255 closest distance to " O   HOH Z  42 " =    1.360
peak=    3.252 closest distance to " O   HOH Z 106 " =    1.642
peak=    3.251 closest distance to " O   HOH Z 116 " =    1.121
peak=    3.249 closest distance to " OG  SER A 135 " =    1.175
peak=    3.246 closest distance to " CB  TRP A 266 " =    1.056
peak=    3.245 closest distance to " O   HOH Z 158 " =    1.146
peak=    3.245 closest distance to " CB  SER A 210 " =    1.040
peak=    3.244 closest distance to " CA  VAL A 153 " =    0.969
peak=    3.244 closest distance to " CB  ASP A 124 " =    0.883
peak=    3.243 closest distance to " CB  GLN A 183 " =    1.176
peak=    3.242 closest distance to " CA  ARG A 156 " =    1.048
peak=    3.226 closest distance to " O   THR A 294 " =    1.082
peak=    3.226 closest distance to " CA  CYS A 260 " =    1.360
peak=    3.225 closest distance to " O   HOH Z 162 " =    1.327
peak=    3.225 closest distance to " O   HOH Z  11 " =    1.042
peak=    3.224 closest distance to " CG2 THR A 264 " =    1.145
peak=    3.216 closest distance to " CA  ARG A 102 " =    1.098
peak=    3.214 closest distance to " O   HOH Z 409 " =    4.878
peak=    3.214 closest distance to " CA  TYR A  30 " =    1.096
peak=    3.209 closest distance to " N   ARG A 139 " =    1.097
peak=    3.209 closest distance to " O   HOH Z  78 " =    2.103
peak=    3.208 closest distance to " OD2 ASP A 286 " =    2.737
peak=    3.205 closest distance to " CE2 PHE A 192 " =    1.508
peak=    3.205 closest distance to " CB  GLU A 175 " =    1.065
peak=    3.199 closest distance to " CD2 LEU A 143 " =    1.328
peak=    3.199 closest distance to " CG  LEU A 167 " =    1.341
peak=    3.190 closest distance to " NZ  LYS A 117 " =    2.922
peak=    3.185 closest distance to " NH2AARG A 145 " =    1.179
peak=    3.185 closest distance to " CG  PRO A  90 " =    1.743
peak=    3.183 closest distance to " OG BSER A  99 " =    3.053
peak=    3.181 closest distance to " O  BHOH Z 338 " =    2.501
peak=    3.179 closest distance to " N   ASN A  74 " =    1.055
peak=    3.173 closest distance to " CB  ALA A 131 " =    1.462
peak=    3.173 closest distance to " CE AMET A  47 " =    1.554
peak=    3.171 closest distance to " O   HOH Z 344 " =    1.166
peak=    3.166 closest distance to " O   HOH Z  40 " =    2.069
peak=    3.161 closest distance to " NZ  LYS A 166 " =    0.895
peak=    3.161 closest distance to " CD  ARG A 159 " =    0.798
peak=    3.159 closest distance to " CA  ALA A 129 " =    1.157
peak=    3.158 closest distance to " OG ASER A 212 " =    1.457
peak=    3.150 closest distance to " O   HOH Z 113 " =    1.935
peak=    3.150 closest distance to " CG2 VAL A 268 " =    0.894
peak=    3.147 closest distance to " NZ BLYS A 290 " =    1.002
peak=    3.144 closest distance to " CE  LYS A  76 " =    0.978
peak=    3.142 closest distance to " CD  ARG A 195 " =    3.617
peak=    3.141 closest distance to " CE3 TRP A 150 " =    1.180
peak=    3.129 closest distance to " O   HOH Z 326 " =    3.184
peak=    3.129 closest distance to " N   SER A  97 " =    0.855
peak=    3.128 closest distance to " O   HOH Z 104 " =    1.814
peak=    3.119 closest distance to " O   HOH Z 369 " =    1.243
peak=    3.116 closest distance to " O   HOH Z  94 " =    1.397
peak=    3.115 closest distance to " N   ILE A 109 " =    1.412
peak=    3.114 closest distance to " CB  PHE A  61 " =    1.173
peak=    3.111 closest distance to " O   HOH Z 371 " =    2.988
peak=    3.108 closest distance to " O   PHE A  59 " =    0.820
peak=    3.098 closest distance to " CD ALYS A 290 " =    1.026
peak=    3.097 closest distance to " CB  VAL A 265 " =    1.310
peak=    3.094 closest distance to " O   HOH Z   7 " =    3.084
peak=    3.094 closest distance to " O   HOH Z 380 " =    1.463
peak=    3.087 closest distance to " CG2 THR A  42 " =    1.370
peak=    3.082 closest distance to " NE AARG A 275 " =    1.842
peak=    3.079 closest distance to " CE  MET A  40 " =    1.118
peak=    3.076 closest distance to " OG ASER A 212 " =    1.911
peak=    3.071 closest distance to " CG2 VAL A 232 " =    1.756
peak=    3.068 closest distance to " O   HOH Z  67 " =    1.208
peak=    3.066 closest distance to " O   HOH Z 116 " =    1.744
peak=    3.057 closest distance to " CG BARG A 275 " =    1.207
peak=    3.052 closest distance to " OD1 ASP A 238 " =    0.979
peak=    3.050 closest distance to " CB  LEU A 300 " =    1.001
peak=    3.021 closest distance to " CD1 LEU A   5 " =    0.925
peak=    3.011 closest distance to " O   HOH Z 238 " =    1.960

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 219         
Filter by distance & map next to the model:
   mapped sites are within: 0.602 - 5.750
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 217 from: 219
   mapped sites are within: 0.769 - 5.750

peak=   -6.249 closest distance to " CD  ARG A 138 " =    1.168
peak=   -4.942 closest distance to " CB  GLN A  55 " =    1.068
peak=   -4.454 closest distance to " O   PRO A 198 " =    1.128
peak=   -4.407 closest distance to " CG2 VAL A 230 " =    0.828
peak=   -4.381 closest distance to " CB  VAL A 230 " =    0.976
peak=   -4.324 closest distance to " OE1 GLU A 277 " =    2.256
peak=   -4.268 closest distance to " O   HOH Z 268 " =    0.936
peak=   -4.181 closest distance to " CA  ASP A  27 " =    2.450
peak=   -4.121 closest distance to " O   HOH Z  69 " =    1.786
peak=   -4.119 closest distance to " OG  SER A  97 " =    2.037
peak=   -4.052 closest distance to " O   HOH Z 147 " =    1.872
peak=   -4.043 closest distance to " O  BHOH Z  74 " =    0.867
peak=   -3.991 closest distance to " OG  SER A  87 " =    1.929
peak=   -3.974 closest distance to " OG BSER A 134 " =    1.570
peak=   -3.948 closest distance to " CG  MET A 105 " =    0.951
peak=   -3.905 closest distance to " CG  ARG A 259 " =    2.415
peak=   -3.893 closest distance to " O   HOH Z 216 " =    1.560
peak=   -3.888 closest distance to " O   HOH Z 415 " =    0.918
peak=   -3.867 closest distance to " CG  ARG A 219 " =    2.368
peak=   -3.851 closest distance to " O   THR A 178 " =    0.925
peak=   -3.847 closest distance to " CD2 TYR A 293 " =    1.784
peak=   -3.841 closest distance to " O   HOH Z 128 " =    2.472
peak=   -3.837 closest distance to " N   PRO A  54 " =    1.005
peak=   -3.822 closest distance to " O   TYR A 172 " =    1.603
peak=   -3.811 closest distance to " NE2 GLN A 223 " =    1.545
peak=   -3.810 closest distance to " CD  PRO A 213 " =    2.297
peak=   -3.807 closest distance to " O   SER A 135 " =    1.557
peak=   -3.796 closest distance to " CA  HIS A 207 " =    1.119
peak=   -3.792 closest distance to " O   HOH Z 276 " =    1.253
peak=   -3.788 closest distance to " C   GLU A   2 " =    2.053
peak=   -3.786 closest distance to " CG  PRO A 243 " =    1.681
peak=   -3.778 closest distance to " O   HOH Z 105 " =    2.296
peak=   -3.745 closest distance to " CD2 TYR A 116 " =    2.264
peak=   -3.739 closest distance to " CA  GLY A 241 " =    2.346
peak=   -3.739 closest distance to " CG2 ILE A 120 " =    1.251
peak=   -3.738 closest distance to " O   HOH Z  60 " =    1.667
peak=   -3.730 closest distance to " N   THR A 157 " =    1.515
peak=   -3.721 closest distance to " O   HOH Z   9 " =    2.164
peak=   -3.721 closest distance to " O   HOH Z 165 " =    2.250
peak=   -3.694 closest distance to " N   ALA A  84 " =    1.604
peak=   -3.691 closest distance to " O   HOH Z 411 " =    5.041
peak=   -3.689 closest distance to " C   ASN A 285 " =    2.225
peak=   -3.686 closest distance to " O   HOH Z 245 " =    1.645
peak=   -3.685 closest distance to " O   HOH Z 134 " =    4.353
peak=   -3.679 closest distance to " CD1 TYR A 214 " =    1.678
peak=   -3.678 closest distance to " O   SER A  22 " =    2.579
peak=   -3.670 closest distance to " CG1 VAL A 125 " =    2.333
peak=   -3.660 closest distance to " N   GLU A 277 " =    1.538
peak=   -3.637 closest distance to " O   HOH Z 257 " =    1.163
peak=   -3.629 closest distance to " CA  ASN A 127 " =    1.335
peak=   -3.607 closest distance to " O   HOH Z 245 " =    0.897
peak=   -3.606 closest distance to " OD1 ASN A  69 " =    0.799
peak=   -3.593 closest distance to " O   HOH Z 131 " =    3.862
peak=   -3.588 closest distance to " O   HOH Z 300 " =    1.046
peak=   -3.579 closest distance to " CD1 PHE A  59 " =    1.295
peak=   -3.577 closest distance to " O   HOH Z 435 " =    2.325
peak=   -3.575 closest distance to " CE2 TYR A  30 " =    2.529
peak=   -3.568 closest distance to " CB  ASP A 132 " =    2.609
peak=   -3.565 closest distance to " CB  ALA A   9 " =    2.546
peak=   -3.558 closest distance to " O   ALA A  51 " =    1.259
peak=   -3.552 closest distance to " CA  HIS A  86 " =    2.098
peak=   -3.545 closest distance to " CG1 ILE A 234 " =    1.268
peak=   -3.545 closest distance to " C   ILE A 239 " =    2.020
peak=   -3.544 closest distance to " O   HOH Z 163 " =    1.918
peak=   -3.541 closest distance to " CE2 PHE A 218 " =    2.557
peak=   -3.540 closest distance to " CZ2 TRP A  92 " =    2.728
peak=   -3.526 closest distance to " O   HOH Z  20 " =    1.620
peak=   -3.525 closest distance to " O   HOH Z 177 " =    2.445
peak=   -3.525 closest distance to " CD2 LEU A 167 " =    1.862
peak=   -3.523 closest distance to " CD  LYS A 166 " =    2.459
peak=   -3.521 closest distance to " OG  SER A  28 " =    1.884
peak=   -3.517 closest distance to " O   SER A  28 " =    1.287
peak=   -3.517 closest distance to " CG1 VAL A 265 " =    2.484
peak=   -3.501 closest distance to " O   HOH Z 352 " =    1.540
peak=   -3.492 closest distance to " CB  ALA A   7 " =    2.083
peak=   -3.492 closest distance to " O   ILE A  49 " =    1.545
peak=   -3.490 closest distance to " O   HOH Z  53 " =    1.678
peak=   -3.485 closest distance to " O   HOH Z 407 " =    2.762
peak=   -3.484 closest distance to " O   HOH Z 174 " =    2.944
peak=   -3.484 closest distance to " NE1 TRP A 177 " =    1.838
peak=   -3.484 closest distance to " O   HOH Z  52 " =    1.500
peak=   -3.480 closest distance to " O   HOH Z  22 " =    2.889
peak=   -3.478 closest distance to " O   HOH Z  64 " =    1.223
peak=   -3.476 closest distance to " O   HOH Z  39 " =    0.778
peak=   -3.474 closest distance to " OD2 ASP A 171 " =    1.690
peak=   -3.474 closest distance to " CD1 ILE A  33 " =    1.964
peak=   -3.470 closest distance to " NE1 TRP A 179 " =    1.268
peak=   -3.467 closest distance to " CA  ILE A 120 " =    1.204
peak=   -3.467 closest distance to " O   ALA A  10 " =    1.514
peak=   -3.463 closest distance to " O   ARG A 156 " =    1.425
peak=   -3.459 closest distance to " C   VAL A  72 " =    0.769
peak=   -3.458 closest distance to " C   HIS A 108 " =    1.434
peak=   -3.452 closest distance to " OH  TYR A 247 " =    1.388
peak=   -3.449 closest distance to " OD2 ASP A 171 " =    2.413
peak=   -3.446 closest distance to " O   HOH Z 117 " =    1.081
peak=   -3.431 closest distance to " CA  GLY A  80 " =    1.295
peak=   -3.423 closest distance to " O   HOH Z 244 " =    1.464
peak=   -3.417 closest distance to " O   HOH Z  67 " =    1.327
peak=   -3.415 closest distance to " CG  LEU A 281 " =    1.867
peak=   -3.410 closest distance to " O   HOH Z 385 " =    1.502
peak=   -3.407 closest distance to " CD  ARG A  14 " =    3.079
peak=   -3.394 closest distance to " NH2BARG A 102 " =    0.891
peak=   -3.387 closest distance to " O   ASN A  69 " =    0.941
peak=   -3.387 closest distance to " O   HOH Z 183 " =    2.076
peak=   -3.386 closest distance to " CD1 TRP A  85 " =    1.130
peak=   -3.385 closest distance to " CZ3 TRP A 274 " =    2.242
peak=   -3.382 closest distance to " CB  ALA A 129 " =    2.575
peak=   -3.375 closest distance to " N   LYS A 290 " =    1.156
peak=   -3.371 closest distance to " O   HOH Z 149 " =    1.479
peak=   -3.370 closest distance to " O   HOH Z  24 " =    1.049
peak=   -3.370 closest distance to " OE1 GLN A 144 " =    1.340
peak=   -3.370 closest distance to " O   HOH Z 359 " =    3.178
peak=   -3.367 closest distance to " N   SER A 206 " =    2.094
peak=   -3.363 closest distance to " O   HOH Z  68 " =    1.705
peak=   -3.362 closest distance to " CB  ALA A 161 " =    1.487
peak=   -3.355 closest distance to " C   PHE A  59 " =    0.911
peak=   -3.353 closest distance to " O   HOH Z 193 " =    0.840
peak=   -3.350 closest distance to " NH2 ARG A 195 " =    2.416
peak=   -3.344 closest distance to " OD1 ASP A 107 " =    1.320
peak=   -3.343 closest distance to " ND2 ASN A  69 " =    1.827
peak=   -3.341 closest distance to " CG  GLN A  88 " =    1.183
peak=   -3.340 closest distance to " CD1 TYR A 247 " =    2.491
peak=   -3.330 closest distance to " O   HOH Z 286 " =    1.481
peak=   -3.327 closest distance to " O   HOH Z 111 " =    1.899
peak=   -3.327 closest distance to " NH2 ARG A  79 " =    2.336
peak=   -3.327 closest distance to " O   HOH Z 200 " =    3.604
peak=   -3.320 closest distance to " CA  GLN A  58 " =    1.020
peak=   -3.317 closest distance to " O   HOH Z 159 " =    1.142
peak=   -3.316 closest distance to " OD1 ASP A 191 " =    1.855
peak=   -3.316 closest distance to " OE2 GLU A 152 " =    1.283
peak=   -3.315 closest distance to " CB  ALA A 114 " =    2.469
peak=   -3.314 closest distance to " CB  PHE A  61 " =    1.284
peak=   -3.313 closest distance to " O   ALA A 256 " =    1.896
peak=   -3.306 closest distance to " CG1 VAL A 125 " =    2.149
peak=   -3.304 closest distance to " O   LYS A 193 " =    1.519
peak=   -3.303 closest distance to " CG2AVAL A  41 " =    2.821
peak=   -3.303 closest distance to " O   LYS A  76 " =    1.196
peak=   -3.302 closest distance to " O   HOH Z 292 " =    1.637
peak=   -3.299 closest distance to " CD1 LEU A   5 " =    2.174
peak=   -3.296 closest distance to " CA  GLY A 133 " =    1.968
peak=   -3.294 closest distance to " O   HOH Z 181 " =    1.259
peak=   -3.294 closest distance to " O   PRO A 163 " =    1.722
peak=   -3.291 closest distance to " CG1 VAL A 126 " =    2.657
peak=   -3.288 closest distance to " O   GLU A  44 " =    1.746
peak=   -3.284 closest distance to " O   HOH Z 144 " =    1.021
peak=   -3.282 closest distance to " O   HOH Z 100 " =    0.926
peak=   -3.281 closest distance to " NH2AARG A 275 " =    5.178
peak=   -3.280 closest distance to " C   SER A 135 " =    1.268
peak=   -3.280 closest distance to " O   HOH Z 389 " =    1.141
peak=   -3.279 closest distance to " ND2 ASN A 285 " =    2.235
peak=   -3.277 closest distance to " CB  TYR A  68 " =    1.056
peak=   -3.276 closest distance to " ND2 ASN A  39 " =    1.574
peak=   -3.273 closest distance to " O   HOH Z 179 " =    1.833
peak=   -3.265 closest distance to " CG2BVAL A  72 " =    2.219
peak=   -3.262 closest distance to " CA  MET A 113 " =    1.128
peak=   -3.260 closest distance to " O   HOH Z 368 " =    2.102
peak=   -3.258 closest distance to " CB  ALA A  43 " =    2.664
peak=   -3.254 closest distance to " CG1BVAL A  72 " =    2.540
peak=   -3.252 closest distance to " CB  HIS A  81 " =    1.123
peak=   -3.252 closest distance to " OG ASER A 134 " =    1.236
peak=   -3.252 closest distance to " NE2 GLN A 194 " =    1.930
peak=   -3.251 closest distance to " CB  ALA A 248 " =    2.003
peak=   -3.250 closest distance to " O   GLY A 203 " =    2.357
peak=   -3.249 closest distance to " CZ  TYR A 169 " =    2.006
peak=   -3.242 closest distance to " O   HOH Z 389 " =    2.653
peak=   -3.242 closest distance to " CA  ASN A 110 " =    1.016
peak=   -3.239 closest distance to " O   VAL A 174 " =    2.217
peak=   -3.237 closest distance to " O   HOH Z  70 " =    0.994
peak=   -3.231 closest distance to " O   HOH Z 368 " =    1.106
peak=   -3.228 closest distance to " O   HOH Z 133 " =    1.472
peak=   -3.222 closest distance to " CB  HIS A  86 " =    1.053
peak=   -3.216 closest distance to " O   HOH Z 121 " =    3.977
peak=   -3.214 closest distance to " C   ARG A 269 " =    1.282
peak=   -3.212 closest distance to " CG  LEU A   5 " =    0.970
peak=   -3.207 closest distance to " OE1 GLN A  88 " =    1.195
peak=   -3.205 closest distance to " O   HOH Z 350 " =    2.043
peak=   -3.205 closest distance to " O   HOH Z   1 " =    3.543
peak=   -3.189 closest distance to " CB  SER A  62 " =    5.636
peak=   -3.188 closest distance to " CA  GLY A 203 " =    2.632
peak=   -3.188 closest distance to " OD2 ASP A 272 " =    1.592
peak=   -3.183 closest distance to " O   HOH Z 255 " =    1.362
peak=   -3.182 closest distance to " CD2 LEU A 222 " =    2.035
peak=   -3.173 closest distance to " O   ILE A 234 " =    1.480
peak=   -3.167 closest distance to " O   TRP A  70 " =    1.471
peak=   -3.165 closest distance to " O   GLN A 240 " =    3.246
peak=   -3.164 closest distance to " CB  SER A  62 " =    5.750
peak=   -3.162 closest distance to " C   LEU A 222 " =    1.424
peak=   -3.162 closest distance to " NE2 GLN A  11 " =    1.681
peak=   -3.159 closest distance to " O   GLY A  80 " =    2.499
peak=   -3.154 closest distance to " C   ALA A   9 " =    1.206
peak=   -3.145 closest distance to " CG2 THR A 178 " =    2.271
peak=   -3.145 closest distance to " CA  GLY A  57 " =    2.152
peak=   -3.141 closest distance to " O   HOH Z 131 " =    1.325
peak=   -3.139 closest distance to " O   HOH Z  32 " =    2.015
peak=   -3.138 closest distance to " CE1 TYR A 186 " =    2.184
peak=   -3.137 closest distance to " O   ARG A 219 " =    2.140
peak=   -3.134 closest distance to " N   ALA A  19 " =    2.188
peak=   -3.134 closest distance to " CZ  ARG A 259 " =    0.889
peak=   -3.132 closest distance to " O   HOH Z 236 " =    1.248
peak=   -3.129 closest distance to " OD2 ASP A  50 " =    1.589
peak=   -3.124 closest distance to " O   HOH Z 339 " =    1.680
peak=   -3.119 closest distance to " OE1 GLU A  44 " =    1.975
peak=   -3.117 closest distance to " O   HOH Z  41 " =    0.866
peak=   -3.112 closest distance to " CG1BVAL A  41 " =    2.144
peak=   -3.106 closest distance to " O   HOH Z 339 " =    1.804
peak=   -3.104 closest distance to " O   HOH Z  83 " =    1.549
peak=   -3.102 closest distance to " O   HOH Z  66 " =    1.081
peak=   -3.096 closest distance to " OG  SER A  63 " =    1.521
peak=   -3.094 closest distance to " CA  GLY A  57 " =    2.162
peak=   -3.080 closest distance to " O   HOH Z 135 " =    2.096
peak=   -3.075 closest distance to " O   HOH Z 165 " =    1.596
peak=   -3.072 closest distance to " O   HOH Z 328 " =    1.104
peak=   -3.068 closest distance to " CG2 VAL A 197 " =    2.449
peak=   -3.062 closest distance to " O   ARG A  79 " =    1.082
peak=   -3.040 closest distance to " CG2 VAL A 202 " =    2.690
peak=   -3.039 closest distance to " CG2 ILE A 234 " =    1.499
peak=   -3.018 closest distance to " O   HOH Z  13 " =    1.660

================= 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    :  0.5104 0.4995   6.309809e+00   6.295255e+00
   1_bss:  0.5026 0.4874   6.305083e+00   6.289414e+00
   1_xyz:  0.4384 0.4678   6.238809e+00   6.262981e+00
   1_adp:  0.4027 0.4672   6.197060e+00   6.260658e+00
   1_occ:  0.4024 0.4678   6.196920e+00   6.261006e+00
   2_bss:  0.3998 0.4641   6.199251e+00   6.261382e+00
   2_xyz:  0.3464 0.4212   6.092123e+00   6.198269e+00
   2_adp:  0.3311 0.4133   6.071652e+00   6.186789e+00
   2_occ:  0.3307 0.4139   6.071895e+00   6.187445e+00
   3_bss:  0.3301 0.4128   6.073403e+00   6.188487e+00
   3_xyz:  0.2665 0.3409   5.897746e+00   6.062077e+00
   3_adp:  0.2428 0.3205   5.834128e+00   6.014546e+00
   3_occ:  0.2427 0.3201   5.833568e+00   6.014181e+00
   4_bss:  0.2429 0.3197   5.834261e+00   6.014332e+00
   4_xyz:  0.1990 0.2650   5.656670e+00   5.862505e+00
   4_adp:  0.1797 0.2484   5.578519e+00   5.803619e+00
   4_occ:  0.1797 0.2481   5.577553e+00   5.802532e+00
   5_bss:  0.1798 0.2481   5.576585e+00   5.801461e+00
   5_xyz:  0.1554 0.2171   5.446454e+00   5.683777e+00
   5_adp:  0.1476 0.2057   5.399794e+00   5.634307e+00
   5_occ:  0.1475 0.2054   5.399016e+00   5.633295e+00
   5_bss:  0.1478 0.2052   5.398375e+00   5.632272e+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:  0.362  20.000   5.848   8.290  10.991   0.000   0.000   0.000
   1_xyz:  0.362  20.000   5.848   8.290  10.991   0.000   0.000   0.000
   1_adp:  0.362  20.000   5.848   8.290  10.991   0.000   0.000   0.000
   1_occ:  0.362  20.000   5.848   8.290  10.991   0.000   0.000   0.000
   2_bss:  0.349  43.214   2.565   4.343   6.696   0.000   0.000   0.000
   2_xyz:  0.349  43.214   2.565   4.343   6.696   0.000   0.000   0.000
   2_adp:  0.349  43.214   2.565   4.343   6.696   0.000   0.000   0.000
   2_occ:  0.349  43.214   2.565   4.343   6.696   0.000   0.000   0.000
   3_bss:  0.354  66.381   1.053   1.962   4.196   0.000   0.000   0.000
   3_xyz:  0.354  66.381   1.053   1.962   4.196   0.000   0.000   0.000
   3_adp:  0.354  66.381   1.053   1.962   4.196   0.000   0.000   0.000
   3_occ:  0.354  66.381   1.053   1.962   4.196   0.000   0.000   0.000
   4_bss:  0.337  60.539   0.272   0.698   2.754   0.000   0.000   0.000
   4_xyz:  0.337  60.539   0.272   0.698   2.754   0.000   0.000   0.000
   4_adp:  0.337  60.539   0.272   0.698   2.754   0.000   0.000   0.000
   4_occ:  0.337  60.539   0.272   0.698   2.754   0.000   0.000   0.000
   5_bss:  0.328  69.426   0.006   0.088   2.372   0.000   0.000   0.000
   5_xyz:  0.328  69.426   0.006   0.088   2.372   0.000   0.000   0.000
   5_adp:  0.328  69.426   0.006   0.088   2.372   0.000   0.000   0.000
   5_occ:  0.328  69.426   0.006   0.088   2.372   0.000   0.000   0.000
   5_bss:  0.328  70.222  -0.752  -0.788   1.540  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  65.025 0.3276  0.3948    81462.996
   1_bss:  63.669 0.3450  0.5290    80015.892
   1_xyz:  57.303 0.4266  0.6408    68412.976
   1_adp:  56.397 0.4379  0.7406    67480.094
   1_occ:  56.537 0.4361  0.7367    67722.825
   2_bss:  56.432 0.4374  0.6511    67520.720
   2_xyz:  47.588 0.5490  0.8136    51471.241
   2_adp:  46.585 0.5615  0.8380    49732.382
   2_occ:  46.689 0.5602  0.8355    49837.319
   3_bss:  46.557 0.5619  0.7785    49777.658
   3_xyz:  36.970 0.6767  0.9183    32356.026
   3_adp:  33.470 0.7181  0.9419    28018.608
   3_occ:  33.459 0.7182  0.9417    27964.314
   4_bss:  33.410 0.7187  0.9048    27945.991
   4_xyz:  26.939 0.7900  0.9637    18614.452
   4_adp:  24.838 0.8123  0.9615    16141.236
   4_occ:  24.800 0.8126  0.9614    16079.533
   5_bss:  24.735 0.8131  0.9472    16003.749
   5_xyz:  21.277 0.8484  0.9694    12298.530
   5_adp:  19.812 0.8633  0.9655    11117.001
   5_occ:  19.783 0.8635  0.9655    11086.016
   5_bss:  19.746 0.8638  0.9649    11040.924
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3778e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3778e+01
   1_xyz:   1.837  0.015  0.112 18.725  0.007  4.105   1.6414e-01
   1_adp:   1.837  0.015  0.112 18.725  0.007  4.105   1.6414e-01
   1_occ:   1.837  0.015  0.112 18.725  0.007  4.105   1.6414e-01
   2_bss:   1.837  0.015  0.112 18.725  0.007  4.105   1.6414e-01
   2_xyz:   1.227  0.009  0.080 16.864  0.005  4.123   9.5523e-02
   2_adp:   1.227  0.009  0.080 16.864  0.005  4.123   9.5523e-02
   2_occ:   1.227  0.009  0.080 16.864  0.005  4.123   9.5523e-02
   3_bss:   1.227  0.009  0.080 16.864  0.005  4.123   9.5523e-02
   3_xyz:   1.190  0.009  0.088 16.042  0.006  4.116   9.0602e-02
   3_adp:   1.190  0.009  0.088 16.042  0.006  4.116   9.0602e-02
   3_occ:   1.190  0.009  0.088 16.042  0.006  4.116   9.0602e-02
   4_bss:   1.190  0.009  0.088 16.042  0.006  4.116   9.0602e-02
   4_xyz:   1.017  0.007  0.076 15.883  0.004  4.127   6.5003e-02
   4_adp:   1.017  0.007  0.076 15.883  0.004  4.127   6.5003e-02
   4_occ:   1.017  0.007  0.076 15.883  0.004  4.127   6.5003e-02
   5_bss:   1.017  0.007  0.076 15.883  0.004  4.127   6.5003e-02
   5_xyz:   0.937  0.006  0.069 15.494  0.003  4.122   5.7469e-02
   5_adp:   0.937  0.006  0.069 15.494  0.003  4.122   5.7469e-02
   5_occ:   0.937  0.006  0.069 15.494  0.003  4.122   5.7469e-02
   5_bss:   0.937  0.006  0.069 15.494  0.003  4.122   5.7469e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9692e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9692e+00
   1_xyz:  14.555  0.203  0.444 85.324  0.036  2.038   1.0998e-01
   1_adp:  14.555  0.203  0.444 85.324  0.036  2.038   1.0998e-01
   1_occ:  14.555  0.203  0.444 85.324  0.036  2.038   1.0998e-01
   2_bss:  14.555  0.203  0.444 85.324  0.036  2.038   1.0998e-01
   2_xyz:   7.757  0.084  0.290 80.189  0.045  2.101   6.0479e-02
   2_adp:   7.757  0.084  0.290 80.189  0.045  2.101   6.0479e-02
   2_occ:   7.757  0.084  0.290 80.189  0.045  2.101   6.0479e-02
   3_bss:   7.757  0.084  0.290 80.189  0.045  2.101   6.0479e-02
   3_xyz:   8.476  0.048  0.359 85.508  0.052  2.201   1.1921e-01
   3_adp:   8.476  0.048  0.359 85.508  0.052  2.201   1.1921e-01
   3_occ:   8.476  0.048  0.359 85.508  0.052  2.201   1.1921e-01
   4_bss:   8.476  0.048  0.359 85.508  0.052  2.201   1.1921e-01
   4_xyz:   6.533  0.062  0.253 89.920  0.048  2.341   5.6668e-02
   4_adp:   6.533  0.062  0.253 89.920  0.048  2.341   5.6668e-02
   4_occ:   6.533  0.062  0.253 89.920  0.048  2.341   5.6668e-02
   5_bss:   6.533  0.062  0.253 89.920  0.048  2.341   5.6668e-02
   5_xyz:   6.179  0.041  0.218 84.243  0.036  2.324   6.8363e-02
   5_adp:   6.179  0.041  0.218 84.243  0.036  2.324   6.8363e-02
   5_occ:   6.179  0.041  0.218 84.243  0.036  2.324   6.8363e-02
   5_bss:   6.179  0.041  0.218 84.243  0.036  2.324   6.8363e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  85.55   0.00  16.87  77.75   0.00  15.35  85.55   0.00  25.15
   1_occ:  85.55   0.00  16.87  77.75   0.00  15.35  85.55   0.00  25.15
   2_bss:  85.55   0.00  16.87  77.75   0.00  15.35  85.55   0.00  25.15
   2_xyz:  85.55   0.00  16.87  77.75   0.00  15.35  85.55   0.00  25.15
   2_adp:  87.45   0.00  16.73  75.84   0.00  14.39  87.45   0.00  29.46
   2_occ:  87.45   0.00  16.73  75.84   0.00  14.39  87.45   0.00  29.46
   3_bss:  87.45   0.00  16.73  75.84   0.00  14.39  87.45   0.00  29.46
   3_xyz:  87.45   0.00  16.73  75.84   0.00  14.39  87.45   0.00  29.46
   3_adp:  88.82   0.00  16.13  68.51   0.00  12.76  88.82   0.00  34.46
   3_occ:  88.82   0.00  16.13  68.51   0.00  12.76  88.82   0.00  34.46
   4_bss:  88.82   0.00  16.13  68.51   0.00  12.76  88.82   0.00  34.46
   4_xyz:  88.82   0.00  16.13  68.51   0.00  12.76  88.82   0.00  34.46
   4_adp: 105.83   0.00  17.49  92.02   0.00  12.06 105.83   2.03  47.02
   4_occ: 105.83   0.00  17.49  92.02   0.00  12.06 105.83   2.03  47.02
   5_bss: 105.83   0.00  17.49  92.02   0.00  12.06 105.83   2.03  47.02
   5_xyz: 105.83   0.00  17.49  92.02   0.00  12.06 105.83   2.03  47.02
   5_adp: 107.51   0.00  17.03  93.24   0.00  11.31 107.51   3.17  48.14
   5_occ: 107.51   0.00  17.03  93.24   0.00  11.31 107.51   3.17  48.14
   5_bss: 108.30   0.80  17.82  94.04   0.80  12.11 108.30   3.96  48.94
------------------------------------------------------------------------
 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:    1.321    0.026    0.419
   1_adp:    1.321    0.026    0.419
   1_occ:    1.321    0.026    0.419
   2_bss:    1.321    0.026    0.419
   2_xyz:    1.852    0.057    0.567
   2_adp:    1.852    0.057    0.567
   2_occ:    1.852    0.057    0.567
   3_bss:    1.852    0.057    0.567
   3_xyz:    1.836    0.037    0.718
   3_adp:    1.836    0.037    0.718
   3_occ:    1.836    0.037    0.718
   4_bss:    1.836    0.037    0.718
   4_xyz:    1.728    0.012    0.814
   4_adp:    1.728    0.012    0.814
   4_occ:    1.728    0.012    0.814
   5_bss:    1.728    0.012    0.814
   5_xyz:    1.809    0.033    0.862
   5_adp:    1.809    0.033    0.862
   5_occ:    1.809    0.033    0.862
   5_bss:    1.809    0.033    0.862
------------------------------------------------------------------------

CPU time actual refinement: 337.90


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_626/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_626/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_626/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_626/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_626/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 337.75 
  Macro-tasks:
    bulk solvent and scale       = 42.42  
    individual site refinement   = 136.98 
    weights calculation          = 32.55  
    collect and process          = 6.39   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 218.47 
  Micro-tasks:
    mask                            = 3.04   
    f_calc                          = 104.57 
    alpha_beta                      = 8.42   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 113.63 
    fmodel                         = 7.18   
    r_factors                      = 0.28   
    phase_errors                   = 9.88   
    foms                           = 0.24   
    TOTAL for micro-tasks          = 248.39 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.822 micro seconds
Total CPU time: 5.86 minutes
from_scatterers_fft:    620 calls, 104.27 s
gradients_fft:          565 calls, 100.99 s

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

# Date 2008-01-16 Time 02:02:50 PST -0800 (1200477770.96 s)
Start R-work = 0.5104, R-free = 0.4995 (no bulk solvent and anisotropic scale)
Final R-work = 0.1630, R-free = 0.2203 (no bulk solvent and anisotropic scale)

Start R-work = 0.5026, R-free = 0.4874
Final R-work = 0.1478, R-free = 0.2052