# Date 2008-01-16 Time 01:10:13 PST -0800 (1200474613.56 s)
#phil __OFF__

Command line arguments: "../316.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 15282
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 316

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (69.1963, 47.1647, 87.6859, 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: 3.32, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.1647, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8871 1.97081
Completeness in resolution range: 0.939881
Completeness with d_max=infinity: 0.937004

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8871
                             d_min =   1.9708

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (69.1963, 47.1647, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8871 1.97081
Completeness in resolution range: 0.939881
Completeness with d_max=infinity: 0.937004

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8875 -  4.2168 [2195/2223]  1974   221  10.1%
  bin  2:  4.2168 -  3.3597 [2096/2115]  1883   213  10.2%
  bin  3:  3.3597 -  2.9387 [2074/2094]  1873   201   9.7%
  bin  4:  2.9387 -  2.6717 [2056/2081]  1849   207  10.1%
  bin  5:  2.6717 -  2.4811 [2028/2048]  1824   204  10.1%
  bin  6:  2.4811 -  2.3354 [2041/2088]  1835   206  10.1%
  bin  7:  2.3354 -  2.2189 [2020/2052]  1821   199   9.9%
  bin  8:  2.2189 -  2.1226 [2018/2053]  1808   210  10.4%
  bin  9:  2.1226 -  2.0411 [2011/2041]  1815   196   9.7%
  bin 10:  2.0411 -  1.9708 [1050/2047]   948   102   9.7%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_316/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: 0.15 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:
        1.63 -     2.29: 16
        2.29 -     2.94: 1608
        2.94 -     3.59: 4463
        3.59 -     4.25: 9188
        4.25 -     4.90: 12988
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.634 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  43 " - " O   HOH Z 169 "  1.676 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.682 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " NH1 ARG A  24 " - " O   GLY A  91 "  1.806 3.120 -x+1,y+1/2,-z+1/2
  ... (remaining 28258 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_316/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_316/model_refine_001.geo

CPU time processing inputs: 9.84


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 69.19625 47.16465 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4603   r_free= 0.4451   ksol= 0.00   Bsol= 0.00   scale= 0.805    |
|                                                                             |
| 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:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.261040                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8875 -  4.7031 0.99   1421  158 0.3673 0.3594      6.5531      6.5423|
|  2:  4.7031 -  3.7527 0.99   1378  152 0.3575 0.3934        6.69       6.806|
|  3:  3.7527 -  3.2841 0.99   1331  150 0.4197 0.3761       6.628      6.5887|
|  4:  3.2841 -  2.9865 0.99   1346  141 0.4443 0.4514      6.4807      6.4586|
|  5:  2.9865 -  2.7739 0.99   1299  154 0.4872 0.4472      6.3411      6.3544|
|  6:  2.7739 -  2.6113 0.98   1331  145 0.4878 0.5366      6.2605      6.2042|
|  7:  2.6113 -  2.4811 0.99   1297  146 0.4916 0.4896      6.2124      6.1304|
|  8:  2.4811 -  2.3736 0.98   1320  143 0.5150 0.4411      6.1805      6.1498|
|  9:  2.3736 -  2.2825 0.98   1306  145 0.5225 0.4802       6.119      6.1229|
| 10:  2.2825 -  2.2040 0.98   1297  142 0.5267 0.4593      6.1149      6.0447|
| 11:  2.2040 -  2.1353 0.99   1298  153 0.5124 0.5350      6.0104      6.0508|
| 12:  2.1353 -  2.0745 0.98   1297  140 0.5233 0.4730      5.9589      5.9586|
| 13:  2.0745 -  2.0200 0.96   1264  132 0.5230 0.4951      5.8846      5.8174|
| 14:  2.0200 -  1.9708 0.35    445   58 0.5230 0.4268      5.9105      5.6737|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8875 -  4.7031  1421   158  0.72  32.41   0.81     0.73      63521.99|
|  2:  4.7031 -  3.7527  1378   152  0.73  32.52   0.90     0.78      90915.93|
|  3:  3.7527 -  3.2841  1331   150  0.65  39.63   0.84     0.75      95424.18|
|  4:  3.2841 -  2.9865  1346   141  0.57  46.16   0.81     0.66      84519.41|
|  5:  2.9865 -  2.7739  1299   154  0.47  53.96   0.75     0.56      72737.49|
|  6:  2.7739 -  2.6113  1331   145  0.44  57.11   0.73     0.50      66712.18|
|  7:  2.6113 -  2.4811  1297   146  0.43  57.50   0.76     0.49      59914.34|
|  8:  2.4811 -  2.3736  1320   143  0.46  55.28   0.73     0.53      49943.86|
|  9:  2.3736 -  2.2825  1306   145  0.49  53.25   0.72     0.58      43926.62|
| 10:  2.2825 -  2.2040  1297   142  0.49  53.30   0.74     0.56      39409.70|
| 11:  2.2040 -  2.1353  1298   153  0.43  58.04   0.75     0.53      41136.72|
| 12:  2.1353 -  2.0745  1297   140  0.40  60.46   0.76     0.50      38933.95|
| 13:  2.0745 -  2.0200  1264   132  0.40  59.89   0.73     0.50      33328.84|
| 14:  2.0200 -  1.9708   445    58  0.51  51.42   0.76     0.51      22344.68|
|alpha:            min =        0.49 max =            0.78 mean =         0.59|
|beta:             min =    22344.68 max =        95424.18 mean =     59426.02|
|figures of merit: min =        0.00 max =            1.00 mean =         0.52|
|phase err.(work): min =        0.00 max =           89.93 mean =        50.50|
|phase err.(test): min =        0.00 max =           89.91 mean =        50.80|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.772151              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.025   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.783802              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.127   (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:       26 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      173 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      693 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1505 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2632 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3903 |
| 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:     6593 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7705 |
|-----------------------------------------------------------------------------|
|-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 |   4.090    4.900  1.196 |       1.996 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.881)------------------------------------------|
|    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 = 11.881)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4665   r_free= 0.4448   ksol= 0.00   Bsol= 0.00   scale= 0.775    |
|                                                                             |
| 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:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.264637                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4504   r_free= 0.4350   ksol= 0.34   Bsol= 20.00   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.50,8.06,10.35,0.00,0.00,0.00); trace/3= 8.64                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.252095                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.136545              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.414   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.770607              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 74.434   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4504      final r-factor (work) = 0.3516          |
| start r-factor (free) = 0.4350      final r-factor (free) = 0.3712          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 82.3945 = 9.14 * 0.50 * 6.2642 + 1.00 * 53.7781                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 28.1373 = 9.14 * 0.50 * 6.1302 + 1.00 * 0.1330                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3516      final r-factor (work) = 0.2988          |
| start r-factor (free) = 0.3712      final r-factor (free) = 0.3395          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7383 = 0.77 * 1.00 * 6.1302 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6325 = 0.77 * 1.00 * 5.9932 + 1.00 * 0.0141                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.881)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    64.48   11.99    None  None   None       |
|    all(noH): 2823   0      0.00    64.48   11.99    None  None   None       |
|    Sol.    : 438    0      0.00    64.48   27.29    None  None   None       |
|    Mac.    : 2385   0      0.00    58.03   9.18     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.448: 1120   |   5:    32.238 -  38.686:   78        |
|      1:     6.448 -  12.895:  753   |   6:    38.686 -  45.134:   60        |
|      2:    12.895 -  19.343:  399   |   7:    45.134 -  51.581:   36        |
|      3:    19.343 -  25.791:  225   |   8:    51.581 -  58.029:   20        |
|      4:    25.791 -  32.238:  126   |   9:    58.029 -  64.477:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2988 r_free = 0.3395             target_work(ml) = 5.957         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2984 r_free = 0.3405             target_work(ml) = 5.957         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2984   r_free= 0.3405   ksol= 0.34   Bsol= 20.00   scale= 1.104   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.50,8.06,10.35,0.00,0.00,0.00); trace/3= 8.64                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.956778                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2938   r_free= 0.3361   ksol= 0.33   Bsol= 43.07   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.79,4.19,6.60,0.00,0.00,0.00); trace/3= 4.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.957186                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.893077              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.116   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.385624              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 116.946  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2938      final r-factor (work) = 0.1966          |
| start r-factor (free) = 0.3361      final r-factor (free) = 0.2404          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.8024 = 4.89 * 0.50 * 5.9960 + 1.00 * 0.1330                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.2336 = 4.89 * 0.50 * 5.7877 + 1.00 * 0.0738                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1966      final r-factor (work) = 0.1737          |
| start r-factor (free) = 0.2404      final r-factor (free) = 0.2218          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2592 = 0.39 * 1.00 * 5.7877 + 1.00 * 0.0274                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1892 = 0.39 * 1.00 * 5.5456 + 1.00 * 0.0507                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.881)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    72.38   12.29    None  None   None       |
|    all(noH): 2823   0      0.00    72.38   12.29    None  None   None       |
|    Sol.    : 438    0      0.51    66.98   33.50    None  None   None       |
|    Mac.    : 2385   0      0.00    72.38   8.39     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 -   7.238: 1385   |   5:    36.190 -  43.428:   88        |
|      1:     7.238 -  14.476:  751   |   6:    43.428 -  50.666:   77        |
|      2:    14.476 -  21.714:  213   |   7:    50.666 -  57.904:   44        |
|      3:    21.714 -  28.952:  110   |   8:    57.904 -  65.142:   17        |
|      4:    28.952 -  36.190:  134   |   9:    65.142 -  72.380:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1737 r_free = 0.2218             target_work(ml) = 5.509         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1735 r_free = 0.2217             target_work(ml) = 5.509         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1735   r_free= 0.2217   ksol= 0.33   Bsol= 43.07   scale= 1.046   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.79,4.19,6.60,0.00,0.00,0.00); trace/3= 4.86                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.508767                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1715   r_free= 0.2203   ksol= 0.32   Bsol= 50.69   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.02,2.95,4.42,0.00,0.00,0.00); trace/3= 3.13                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.22 A                  |
| x-ray target function (ml) for work reflections: 5.507294                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.915629              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.743   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.177132              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.201   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1715      final r-factor (work) = 0.1400          |
| start r-factor (free) = 0.2203      final r-factor (free) = 0.1819          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3988 = 1.92 * 0.50 * 5.5596 + 1.00 * 0.0737                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2495 = 1.92 * 0.50 * 5.4216 + 1.00 * 0.0567                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1400      final r-factor (work) = 0.1330          |
| start r-factor (free) = 0.1819      final r-factor (free) = 0.1765          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.4015 = 1.18 * 1.00 * 5.4216 + 1.00 * 0.0196                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2528 = 1.18 * 1.00 * 5.2960 + 1.00 * 0.0188                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.881)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.82   13.05    None  None   None       |
|    all(noH): 2823   0      0.00    85.82   13.05    None  None   None       |
|    Sol.    : 438    0      0.98    78.91   37.83    None  None   None       |
|    Mac.    : 2385   0      0.00    85.82   8.50     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 -   8.582: 1627   |   5:    42.911 -  51.493:   89        |
|      1:     8.582 -  17.164:  595   |   6:    51.493 -  60.075:   71        |
|      2:    17.164 -  25.746:  170   |   7:    60.075 -  68.657:   38        |
|      3:    25.746 -  34.329:  108   |   8:    68.657 -  77.239:   15        |
|      4:    34.329 -  42.911:  105   |   9:    77.239 -  85.821:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1330 r_free = 0.1765             target_work(ml) = 5.286         |
| occupancies: max = 1.00  min = 0.03   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1328 r_free = 0.1767             target_work(ml) = 5.285         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1328   r_free= 0.1767   ksol= 0.32   Bsol= 50.69   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.02,2.95,4.42,0.00,0.00,0.00); trace/3= 3.13                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.285322                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1329   r_free= 0.1770   ksol= 0.33   Bsol= 54.45   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.77,2.70,4.07,0.00,0.00,0.00); trace/3= 2.85                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.286322                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.011899              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 125.126  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.259035              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 101.670  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1329      final r-factor (work) = 0.1203          |
| start r-factor (free) = 0.1770      final r-factor (free) = 0.1661          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3845 = 2.01 * 0.50 * 5.2964 + 1.00 * 0.0567                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3364 = 2.01 * 0.50 * 5.2444 + 1.00 * 0.0608                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1203      final r-factor (work) = 0.1198          |
| start r-factor (free) = 0.1661      final r-factor (free) = 0.1625          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3756 = 0.26 * 1.00 * 5.2444 + 1.00 * 0.0171                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3620 = 0.26 * 1.00 * 5.2139 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.881)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.02   12.50    None  None   None       |
|    all(noH): 2823   0      0.00    85.02   12.50    None  None   None       |
|    Sol.    : 438    0      1.18    77.74   35.94    None  None   None       |
|    Mac.    : 2385   0      0.00    85.02   8.20     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 -   8.502: 1667   |   5:    42.508 -  51.010:   79        |
|      1:     8.502 -  17.003:  590   |   6:    51.010 -  59.511:   63        |
|      2:    17.003 -  25.505:  150   |   7:    59.511 -  68.013:   33        |
|      3:    25.505 -  34.006:  121   |   8:    68.013 -  76.514:   10        |
|      4:    34.006 -  42.508:  106   |   9:    76.514 -  85.016:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1198 r_free = 0.1625             target_work(ml) = 5.201         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1197 r_free = 0.1624             target_work(ml) = 5.201         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1197   r_free= 0.1624   ksol= 0.33   Bsol= 54.45   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.77,2.70,4.07,0.00,0.00,0.00); trace/3= 2.85                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.200716                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1197   r_free= 0.1624   ksol= 0.33   Bsol= 54.45   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.80,2.69,4.03,0.00,0.00,0.00); trace/3= 2.84                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.200756                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.819085              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 143.378  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.611329              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 160.096  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1197      final r-factor (work) = 0.1169          |
| start r-factor (free) = 0.1624      final r-factor (free) = 0.1596          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8031 = 1.82 * 0.50 * 5.2136 + 1.00 * 0.0611                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.7794 = 1.82 * 0.50 * 5.1901 + 1.00 * 0.0588                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1169      final r-factor (work) = 0.1161          |
| start r-factor (free) = 0.1596      final r-factor (free) = 0.1598          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1842 = 0.61 * 1.00 * 5.1901 + 1.00 * 0.0113                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1775 = 0.61 * 1.00 * 5.1778 + 1.00 * 0.0121                               |
|-----------------------------------------------------------------------------|
| number of iterations = 9       |    number of function evaluations = 12     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.881)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.27   12.43    None  None   None       |
|    all(noH): 2823   0      0.00    85.27   12.43    None  None   None       |
|    Sol.    : 438    0      1.01    78.00   35.93    None  None   None       |
|    Mac.    : 2385   0      0.00    85.27   8.12     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.527: 1684   |   5:    42.635 -  51.161:   80        |
|      1:     8.527 -  17.054:  574   |   6:    51.161 -  59.688:   65        |
|      2:    17.054 -  25.581:  151   |   7:    59.688 -  68.215:   30        |
|      3:    25.581 -  34.108:  120   |   8:    68.215 -  76.742:   10        |
|      4:    34.108 -  42.635:  105   |   9:    76.742 -  85.269:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1161 r_free = 0.1598             target_work(ml) = 5.180         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1161 r_free = 0.1598             target_work(ml) = 5.179         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1161   r_free= 0.1598   ksol= 0.33   Bsol= 54.45   scale= 0.998   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.80,2.69,4.03,0.00,0.00,0.00); trace/3= 2.84                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.179291                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8875 -  4.7031 0.99   1421  158 0.1033 0.1338      5.4236      5.5737|
|  2:  4.7031 -  3.7527 0.99   1378  152 0.0874 0.1104      5.4505      5.6446|
|  3:  3.7527 -  3.2841 0.99   1331  150 0.1098 0.1530      5.4908      5.8369|
|  4:  3.2841 -  2.9865 0.99   1346  141 0.1229 0.1615      5.4599      5.6269|
|  5:  2.9865 -  2.7739 0.99   1299  154 0.1372 0.1561      5.3495      5.5085|
|  6:  2.7739 -  2.6113 0.98   1331  145 0.1288 0.2133      5.2366      5.5375|
|  7:  2.6113 -  2.4811 0.99   1297  146 0.1332 0.1630      5.2142      5.3381|
|  8:  2.4811 -  2.3736 0.98   1320  143 0.1184 0.1720      5.1041      5.3554|
|  9:  2.3736 -  2.2825 0.98   1306  145 0.1245 0.2046      5.0634       5.403|
| 10:  2.2825 -  2.2040 0.98   1297  142 0.1184 0.1538      4.9836      5.1188|
| 11:  2.2040 -  2.1353 0.99   1298  153 0.1214 0.1880        4.96      5.3291|
| 12:  2.1353 -  2.0745 0.98   1297  140 0.1165 0.1660      4.8954      5.1165|
| 13:  2.0745 -  2.0200 0.96   1264  132 0.1155 0.1668      4.8001      4.9974|
| 14:  2.0200 -  1.9708 0.35    445   58 0.1025 0.1885       4.687      4.9779|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8875 -  4.7031  1421   158  0.94   9.55   0.98     0.95       7788.14|
|  2:  4.7031 -  3.7527  1378   152  0.95   8.22   1.01     1.00       9265.60|
|  3:  3.7527 -  3.2841  1331   150  0.93  11.62   1.02     1.02      10517.76|
|  4:  3.2841 -  2.9865  1346   141  0.92  13.68   1.01     1.00      10444.59|
|  5:  2.9865 -  2.7739  1299   154  0.90  16.20   0.99     0.97       8585.10|
|  6:  2.7739 -  2.6113  1331   145  0.89  17.03   0.98     0.95       7404.32|
|  7:  2.6113 -  2.4811  1297   146  0.90  16.13   0.98     0.94       6573.60|
|  8:  2.4811 -  2.3736  1320   143  0.90  15.86   1.00     0.96       5834.11|
|  9:  2.3736 -  2.2825  1306   145  0.90  16.48   1.00     0.97       5313.67|
| 10:  2.2825 -  2.2040  1297   142  0.90  16.33   0.99     0.95       4590.91|
| 11:  2.2040 -  2.1353  1298   153  0.90  16.84   0.99     0.95       4547.42|
| 12:  2.1353 -  2.0745  1297   140  0.90  16.17   1.00     0.99       4093.55|
| 13:  2.0745 -  2.0200  1264   132  0.90  16.60   0.99     0.97       3451.38|
| 14:  2.0200 -  1.9708   445    58  0.92  14.32   0.97     0.93       2640.37|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2640.37 max =        10517.76 mean =      6736.82|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.90 mean =        14.59|
|phase err.(test): min =        0.00 max =           89.93 mean =        14.13|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1161   r_free= 0.1598   ksol= 0.32   Bsol= 55.55   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.04,-0.16,1.20,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.179291                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1161   r_free= 0.1598   ksol= 0.32   Bsol= 55.55   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-1.04,-0.16,1.20,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.179291                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8875 -  4.7031 0.99   1421  158 0.1031 0.1338      5.4221      5.5729|
|  2:  4.7031 -  3.7527 0.99   1378  152 0.0873 0.1104        5.45       5.644|
|  3:  3.7527 -  3.2841 0.99   1331  150 0.1098 0.1530      5.4906      5.8369|
|  4:  3.2841 -  2.9865 0.99   1346  141 0.1229 0.1616      5.4602      5.6274|
|  5:  2.9865 -  2.7739 0.99   1299  154 0.1372 0.1562      5.3499       5.509|
|  6:  2.7739 -  2.6113 0.98   1331  145 0.1288 0.2134       5.237       5.538|
|  7:  2.6113 -  2.4811 0.99   1297  146 0.1333 0.1631      5.2146      5.3386|
|  8:  2.4811 -  2.3736 0.98   1320  143 0.1184 0.1720      5.1043      5.3555|
|  9:  2.3736 -  2.2825 0.98   1306  145 0.1245 0.2045      5.0635      5.4029|
| 10:  2.2825 -  2.2040 0.98   1297  142 0.1184 0.1538      4.9838      5.1191|
| 11:  2.2040 -  2.1353 0.99   1298  153 0.1214 0.1880      4.9601      5.3292|
| 12:  2.1353 -  2.0745 0.98   1297  140 0.1165 0.1660      4.8954      5.1166|
| 13:  2.0745 -  2.0200 0.96   1264  132 0.1156 0.1667      4.8001      4.9973|
| 14:  2.0200 -  1.9708 0.35    445   58 0.1025 0.1885      4.6871      4.9781|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8875 -  4.7031  1421   158  0.94   9.55   0.98     0.95       7767.74|
|  2:  4.7031 -  3.7527  1378   152  0.95   8.20   1.01     1.00       9253.97|
|  3:  3.7527 -  3.2841  1331   150  0.93  11.62   1.02     1.02      10514.37|
|  4:  3.2841 -  2.9865  1346   141  0.92  13.69   1.01     1.00      10452.57|
|  5:  2.9865 -  2.7739  1299   154  0.90  16.21   1.00     0.97       8593.92|
|  6:  2.7739 -  2.6113  1331   145  0.89  17.04   0.98     0.95       7412.50|
|  7:  2.6113 -  2.4811  1297   146  0.90  16.14   0.98     0.94       6579.10|
|  8:  2.4811 -  2.3736  1320   143  0.90  15.87   1.00     0.97       5836.27|
|  9:  2.3736 -  2.2825  1306   145  0.90  16.49   1.01     0.98       5315.22|
| 10:  2.2825 -  2.2040  1297   142  0.90  16.33   0.99     0.95       4591.93|
| 11:  2.2040 -  2.1353  1298   153  0.90  16.84   0.99     0.95       4549.65|
| 12:  2.1353 -  2.0745  1297   140  0.90  16.18   1.01     1.00       4094.68|
| 13:  2.0745 -  2.0200  1264   132  0.90  16.60   0.99     0.98       3451.80|
| 14:  2.0200 -  1.9708   445    58  0.92  14.32   0.97     0.93       2640.62|
|alpha:            min =        0.93 max =            1.02 mean =         0.97|
|beta:             min =     2640.62 max =        10514.37 mean =      6736.93|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.84 mean =        14.59|
|phase err.(test): min =        0.00 max =           89.89 mean =        14.13|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.881)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.89    88.16   15.32    None  None   None       |
|    all(noH): 2823   0      2.89    88.16   15.32    None  None   None       |
|    Sol.    : 438    0      3.90    80.89   38.82    None  None   None       |
|    Mac.    : 2385   0      2.89    88.16   11.01    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.890 -  11.417: 1684   |   5:    45.524 -  54.051:   80        |
|      1:    11.417 -  19.944:  574   |   6:    54.051 -  62.578:   65        |
|      2:    19.944 -  28.471:  151   |   7:    62.578 -  71.105:   30        |
|      3:    28.471 -  36.998:  120   |   8:    71.105 -  79.632:   10        |
|      4:    36.998 -  45.524:  105   |   9:    79.632 -  88.159:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 297         
Filter by distance & map next to the model:
   mapped sites are within: 0.215 - 4.245
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 292 from: 297
   mapped sites are within: 0.713 - 4.245

peak=   11.192 closest distance to " CB  VAL A 230 " =    1.476
peak=    6.032 closest distance to " CG  LEU A   5 " =    1.269
peak=    5.528 closest distance to " CG2 VAL A 296 " =    1.070
peak=    5.517 closest distance to " CD2 LEU A   5 " =    1.188
peak=    5.390 closest distance to " CG  PRO A  54 " =    1.335
peak=    5.324 closest distance to " NH2 ARG A  56 " =    2.147
peak=    5.233 closest distance to " CB  VAL A 296 " =    1.078
peak=    5.226 closest distance to " CB  GLN A 223 " =    1.497
peak=    5.198 closest distance to " CB  ARG A 275 " =    0.939
peak=    5.173 closest distance to " NE2 GLN A  11 " =    1.091
peak=    5.074 closest distance to " CG1 VAL A 296 " =    1.195
peak=    5.005 closest distance to " O   HOH Z 142 " =    1.773
peak=    4.952 closest distance to " CG  LEU A 228 " =    1.212
peak=    4.911 closest distance to " O   HOH Z 232 " =    2.290
peak=    4.882 closest distance to " CB  PRO A  54 " =    1.033
peak=    4.804 closest distance to " O   HOH Z 402 " =    1.468
peak=    4.634 closest distance to " O   HOH Z 248 " =    1.242
peak=    4.512 closest distance to " O   HOH Z 209 " =    2.304
peak=    4.506 closest distance to " CG  PRO A 243 " =    1.163
peak=    4.500 closest distance to " O   HOH Z 346 " =    1.574
peak=    4.478 closest distance to " CG  PRO A 198 " =    1.209
peak=    4.433 closest distance to " O   SER A  87 " =    2.315
peak=    4.423 closest distance to " CB  SER A  63 " =    1.196
peak=    4.391 closest distance to " CZ  PHE A 218 " =    1.176
peak=    4.366 closest distance to " O   HOH Z 126 " =    1.911
peak=    4.361 closest distance to " CD2 TRP A 179 " =    1.286
peak=    4.358 closest distance to " CG  PRO A 213 " =    1.234
peak=    4.335 closest distance to " O   HOH Z 251 " =    1.543
peak=    4.325 closest distance to " CB  GLN A 183 " =    1.268
peak=    4.323 closest distance to " O   HOH Z 403 " =    1.704
peak=    4.323 closest distance to " O   HOH Z  61 " =    1.770
peak=    4.295 closest distance to " O   HOH Z 427 " =    2.992
peak=    4.293 closest distance to " O   HOH Z 265 " =    2.114
peak=    4.290 closest distance to " CB  VAL A 230 " =    1.176
peak=    4.284 closest distance to " CB  ASN A 148 " =    1.403
peak=    4.254 closest distance to " O   HOH Z  43 " =    2.110
peak=    4.245 closest distance to " O   HOH Z  85 " =    1.455
peak=    4.225 closest distance to " CB  ARG A  79 " =    1.387
peak=    4.218 closest distance to " O   HOH Z 188 " =    2.833
peak=    4.202 closest distance to " CB  GLU A 277 " =    3.654
peak=    4.195 closest distance to " CB  GLU A 152 " =    1.115
peak=    4.187 closest distance to " O   HOH Z 313 " =    1.850
peak=    4.161 closest distance to " O   HOH Z 272 " =    1.876
peak=    4.142 closest distance to " O   HOH Z  63 " =    1.964
peak=    4.128 closest distance to " O   HOH Z 303 " =    2.114
peak=    4.123 closest distance to " O   HOH Z 287 " =    1.866
peak=    4.113 closest distance to " O   HOH Z 193 " =    1.598
peak=    4.101 closest distance to " CA  TYR A  30 " =    0.951
peak=    4.100 closest distance to " CA  ALA A  51 " =    0.955
peak=    4.098 closest distance to " CB  ARG A 190 " =    1.759
peak=    4.091 closest distance to " ND2 ASN A 187 " =    1.655
peak=    4.085 closest distance to " CD2 LEU A 228 " =    1.320
peak=    4.076 closest distance to " CB  ASN A 142 " =    1.145
peak=    4.058 closest distance to " O   HOH Z 411 " =    3.969
peak=    4.044 closest distance to " O   HOH Z 369 " =    2.357
peak=    4.029 closest distance to " O   HOH Z  78 " =    1.679
peak=    4.022 closest distance to " N   ASN A  39 " =    1.187
peak=    4.012 closest distance to " O   HOH Z 359 " =    1.531
peak=    4.000 closest distance to " O   HOH Z 422 " =    2.573
peak=    3.987 closest distance to " C   PRO A 198 " =    1.528
peak=    3.962 closest distance to " CA  ARG A  36 " =    1.021
peak=    3.952 closest distance to " O   HOH Z 130 " =    2.692
peak=    3.940 closest distance to " O   HOH Z  59 " =    2.108
peak=    3.936 closest distance to " CB  SER A  26 " =    1.842
peak=    3.934 closest distance to " O   HOH Z 234 " =    3.730
peak=    3.927 closest distance to " ND2 ASN A 249 " =    0.936
peak=    3.924 closest distance to " O   HOH Z 214 " =    2.620
peak=    3.896 closest distance to " CA  ARG A 195 " =    1.195
peak=    3.892 closest distance to " CB  TRP A 266 " =    1.090
peak=    3.887 closest distance to " O   HOH Z 128 " =    1.315
peak=    3.885 closest distance to " O   HOH Z  97 " =    2.331
peak=    3.885 closest distance to " CD  ARG A 269 " =    1.040
peak=    3.883 closest distance to " O   HOH Z  80 " =    1.901
peak=    3.880 closest distance to " OG ASER A 258 " =    3.100
peak=    3.867 closest distance to " O   HOH Z 298 " =    1.733
peak=    3.859 closest distance to " CB  ASN A  39 " =    0.914
peak=    3.856 closest distance to " O   HOH Z 423 " =    1.825
peak=    3.854 closest distance to " O   HOH Z 126 " =    1.539
peak=    3.841 closest distance to " O   ASN A  74 " =    1.479
peak=    3.839 closest distance to " O   HOH Z 368 " =    2.274
peak=    3.831 closest distance to " CZ  PHE A  38 " =    1.127
peak=    3.821 closest distance to " CB  VAL A 202 " =    1.529
peak=    3.812 closest distance to " O   HOH Z 365 " =    2.745
peak=    3.806 closest distance to " CD  LYS A  76 " =    2.058
peak=    3.805 closest distance to " CB  VAL A 265 " =    1.311
peak=    3.795 closest distance to " CB  ALA A   9 " =    1.618
peak=    3.790 closest distance to " CB  GLU A  46 " =    1.024
peak=    3.783 closest distance to " O   HOH Z 280 " =    2.959
peak=    3.772 closest distance to " CE  LYS A  76 " =    0.947
peak=    3.768 closest distance to " CB  THR A  31 " =    1.513
peak=    3.762 closest distance to " CB  ASN A 187 " =    1.296
peak=    3.745 closest distance to " CD1 LEU A  96 " =    0.717
peak=    3.741 closest distance to " CD  LYS A 166 " =    1.359
peak=    3.736 closest distance to " O   HOH Z 124 " =    1.174
peak=    3.735 closest distance to " O   HOH Z 158 " =    3.134
peak=    3.732 closest distance to " CB  ASN A 110 " =    1.092
peak=    3.724 closest distance to " O   HOH Z 261 " =    2.334
peak=    3.722 closest distance to " CG2 VAL A 257 " =    0.869
peak=    3.720 closest distance to " CB  GLU A 128 " =    1.042
peak=    3.707 closest distance to " CD2 LEU A 297 " =    0.987
peak=    3.703 closest distance to " O   HOH Z 273 " =    3.015
peak=    3.702 closest distance to " CB  ARG A  79 " =    0.914
peak=    3.701 closest distance to " CG  MET A 185 " =    1.186
peak=    3.698 closest distance to " CG2 ILE A  20 " =    1.452
peak=    3.692 closest distance to " OG BSER A 164 " =    2.210
peak=    3.688 closest distance to " O   HOH Z 371 " =    3.037
peak=    3.684 closest distance to " O   HOH Z  40 " =    1.798
peak=    3.676 closest distance to " O   HOH Z 406 " =    1.396
peak=    3.668 closest distance to " CD  ARG A 159 " =    0.739
peak=    3.654 closest distance to " CB  TRP A 179 " =    1.390
peak=    3.653 closest distance to " O   HOH Z 154 " =    1.505
peak=    3.652 closest distance to " CG BARG A 102 " =    1.789
peak=    3.648 closest distance to " CG  LEU A 167 " =    1.236
peak=    3.635 closest distance to " CG  GLN A  58 " =    0.778
peak=    3.635 closest distance to " CB  THR A  52 " =    0.860
peak=    3.632 closest distance to " O   HOH Z  97 " =    2.049
peak=    3.619 closest distance to " N   PHE A 130 " =    1.306
peak=    3.601 closest distance to " CB  SER A   3 " =    1.228
peak=    3.601 closest distance to " O   HOH Z 188 " =    1.243
peak=    3.591 closest distance to " O   ASP A 124 " =    1.170
peak=    3.584 closest distance to " O  BHOH Z 338 " =    2.376
peak=    3.582 closest distance to " CG1 ILE A  49 " =    1.540
peak=    3.569 closest distance to " CA  TYR A 116 " =    1.552
peak=    3.559 closest distance to " CA  VAL A  41 " =    0.806
peak=    3.558 closest distance to " O   HOH Z 250 " =    1.339
peak=    3.552 closest distance to " CZ3 TRP A 266 " =    1.091
peak=    3.551 closest distance to " O   HOH Z 353 " =    2.700
peak=    3.551 closest distance to " N   ASP A 162 " =    1.253
peak=    3.550 closest distance to " O   HOH Z 258 " =    2.214
peak=    3.549 closest distance to " CB BVAL A  41 " =    1.135
peak=    3.547 closest distance to " O   HOH Z  68 " =    2.126
peak=    3.538 closest distance to " O   HOH Z  88 " =    2.670
peak=    3.537 closest distance to " O   HOH Z 128 " =    2.584
peak=    3.529 closest distance to " CB  SER A 273 " =    0.904
peak=    3.516 closest distance to " O   HOH Z 187 " =    2.280
peak=    3.512 closest distance to " CG2AVAL A 121 " =    2.260
peak=    3.512 closest distance to " CB  ALA A 114 " =    1.127
peak=    3.511 closest distance to " O   HOH Z 425 " =    1.367
peak=    3.509 closest distance to " O   HOH Z  19 " =    1.902
peak=    3.509 closest distance to " O   HOH Z  44 " =    1.976
peak=    3.509 closest distance to " O   HOH Z 130 " =    0.931
peak=    3.491 closest distance to " CD  LYS A 119 " =    1.986
peak=    3.490 closest distance to " CB  ASP A 140 " =    1.138
peak=    3.490 closest distance to " CB  PRO A 198 " =    1.097
peak=    3.488 closest distance to " N   SER A 135 " =    1.391
peak=    3.478 closest distance to " O   HOH Z  21 " =    1.800
peak=    3.474 closest distance to " O   HOH Z 227 " =    1.427
peak=    3.468 closest distance to " CB  GLN A  89 " =    1.231
peak=    3.467 closest distance to " CG2 ILE A 120 " =    1.277
peak=    3.463 closest distance to " CB  PHE A 204 " =    0.875
peak=    3.460 closest distance to " NZ  LYS A  48 " =    1.077
peak=    3.460 closest distance to " CG2 ILE A 234 " =    0.986
peak=    3.453 closest distance to " O   HOH Z 368 " =    3.479
peak=    3.439 closest distance to " CB  PRO A  90 " =    1.043
peak=    3.434 closest distance to " O   HOH Z 141 " =    1.616
peak=    3.431 closest distance to " NE2 GLN A  77 " =    3.280
peak=    3.426 closest distance to " O   HOH Z 345 " =    3.144
peak=    3.426 closest distance to " NH1AARG A 145 " =    1.314
peak=    3.424 closest distance to " CE1 TYR A 186 " =    1.265
peak=    3.422 closest distance to " CA  SER A  87 " =    0.997
peak=    3.421 closest distance to " OG  SER A 276 " =    1.427
peak=    3.418 closest distance to " CA  ASN A 217 " =    1.223
peak=    3.413 closest distance to " CG1 VAL A 153 " =    0.929
peak=    3.413 closest distance to " CA  ALA A 160 " =    0.949
peak=    3.412 closest distance to " NE2 HIS A 207 " =    1.128
peak=    3.409 closest distance to " CG AARG A 275 " =    1.214
peak=    3.406 closest distance to " O   HOH Z  88 " =    3.564
peak=    3.399 closest distance to " CB  HIS A 108 " =    0.844
peak=    3.399 closest distance to " CB  ASN A 215 " =    1.200
peak=    3.397 closest distance to " CB  ARG A 139 " =    0.953
peak=    3.396 closest distance to " O   HOH Z 238 " =    0.829
peak=    3.395 closest distance to " O   HOH Z 293 " =    1.850
peak=    3.395 closest distance to " CD2 TYR A 186 " =    1.105
peak=    3.395 closest distance to " O   LEU A 228 " =    1.819
peak=    3.391 closest distance to " O   HOH Z 172 " =    3.701
peak=    3.388 closest distance to " CA  ASN A 215 " =    0.989
peak=    3.388 closest distance to " CD1 ILE A 199 " =    1.108
peak=    3.386 closest distance to " O   HOH Z 407 " =    2.630
peak=    3.384 closest distance to " O   HOH Z 145 " =    2.431
peak=    3.383 closest distance to " NZ  LYS A 117 " =    2.942
peak=    3.381 closest distance to " O   HOH Z 329 " =    4.086
peak=    3.375 closest distance to " CB  PRO A 243 " =    1.178
peak=    3.372 closest distance to " CG  PHE A 204 " =    0.927
peak=    3.370 closest distance to " CB  LEU A  83 " =    0.722
peak=    3.367 closest distance to " CB  ALA A 248 " =    1.365
peak=    3.367 closest distance to " O   HOH Z 102 " =    1.239
peak=    3.366 closest distance to " O   HOH Z 246 " =    1.304
peak=    3.356 closest distance to " O   HOH Z 392 " =    2.698
peak=    3.354 closest distance to " CA  LYS A 117 " =    1.294
peak=    3.354 closest distance to " CB  SER A  62 " =    0.869
peak=    3.354 closest distance to " CA  ALA A 295 " =    1.041
peak=    3.350 closest distance to " O   HOH Z 322 " =    1.990
peak=    3.349 closest distance to " N   ARG A 156 " =    1.405
peak=    3.346 closest distance to " O   HOH Z 173 " =    2.283
peak=    3.346 closest distance to " CA  MET A 105 " =    1.024
peak=    3.344 closest distance to " OD1 ASN A  69 " =    2.455
peak=    3.343 closest distance to " CA  LYS A 290 " =    1.183
peak=    3.342 closest distance to " CB  ASP A 124 " =    0.760
peak=    3.338 closest distance to " O   HOH Z 435 " =    1.996
peak=    3.337 closest distance to " O   HOH Z  49 " =    0.946
peak=    3.331 closest distance to " NH2BARG A 190 " =    1.730
peak=    3.331 closest distance to " O   TRP A 274 " =    1.799
peak=    3.324 closest distance to " O   HOH Z 417 " =    3.302
peak=    3.322 closest distance to " CA  ALA A 291 " =    0.808
peak=    3.318 closest distance to " CG  GLU A  37 " =    0.928
peak=    3.317 closest distance to " CB  ALA A 295 " =    1.278
peak=    3.317 closest distance to " O   HOH Z  54 " =    1.558
peak=    3.317 closest distance to " O   HOH Z 380 " =    1.876
peak=    3.310 closest distance to " CA  LEU A 282 " =    1.238
peak=    3.307 closest distance to " CB  TRP A 150 " =    1.409
peak=    3.306 closest distance to " O   HOH Z 294 " =    1.594
peak=    3.298 closest distance to " CA  VAL A 125 " =    1.087
peak=    3.290 closest distance to " CB  ASP A 298 " =    1.156
peak=    3.285 closest distance to " O   HOH Z  35 " =    2.327
peak=    3.284 closest distance to " O   HOH Z 180 " =    2.142
peak=    3.283 closest distance to " O   HOH Z 299 " =    4.245
peak=    3.282 closest distance to " O   HOH Z 344 " =    2.891
peak=    3.280 closest distance to " CG2AVAL A  72 " =    1.761
peak=    3.279 closest distance to " O   HOH Z 216 " =    3.251
peak=    3.276 closest distance to " O   HOH Z 383 " =    1.914
peak=    3.274 closest distance to " O   HOH Z 337 " =    3.502
peak=    3.273 closest distance to " CB  THR A 235 " =    1.271
peak=    3.272 closest distance to " O   HOH Z   4 " =    1.468
peak=    3.267 closest distance to " O   HOH Z  15 " =    2.131
peak=    3.267 closest distance to " CB  GLN A  88 " =    1.198
peak=    3.262 closest distance to " CA  ALA A  21 " =    1.043
peak=    3.257 closest distance to " O   HOH Z  63 " =    2.056
peak=    3.256 closest distance to " N   ALA A 256 " =    1.034
peak=    3.252 closest distance to " OE1 GLU A   2 " =    2.151
peak=    3.247 closest distance to " C   ALA A 299 " =    0.887
peak=    3.246 closest distance to " CB  ARG A 138 " =    0.849
peak=    3.246 closest distance to " O   PRO A 213 " =    1.397
peak=    3.241 closest distance to " CG  MET A 185 " =    0.998
peak=    3.235 closest distance to " CE3 TRP A 150 " =    1.052
peak=    3.234 closest distance to " CB  ARG A 219 " =    1.009
peak=    3.233 closest distance to " O   HOH Z 421 " =    1.827
peak=    3.231 closest distance to " O   HOH Z 148 " =    3.387
peak=    3.230 closest distance to " O   HOH Z 389 " =    1.795
peak=    3.227 closest distance to " O   ARG A  56 " =    2.993
peak=    3.227 closest distance to " O   SER A 164 " =    1.242
peak=    3.226 closest distance to " O   ALA A 165 " =    1.540
peak=    3.218 closest distance to " O   HOH Z 233 " =    1.639
peak=    3.212 closest distance to " O   HOH Z 183 " =    1.832
peak=    3.212 closest distance to " CB  TYR A 247 " =    1.024
peak=    3.211 closest distance to " O   HOH Z  88 " =    2.831
peak=    3.210 closest distance to " O   HOH Z  48 " =    1.615
peak=    3.210 closest distance to " CZ3 TRP A  85 " =    0.913
peak=    3.209 closest distance to " O   HOH Z 236 " =    1.456
peak=    3.206 closest distance to " CA  ASP A 162 " =    1.047
peak=    3.206 closest distance to " OG1 THR A 294 " =    1.673
peak=    3.199 closest distance to " O   HOH Z 244 " =    1.606
peak=    3.194 closest distance to " O   GLN A  88 " =    1.676
peak=    3.192 closest distance to " CB  SER A 212 " =    1.324
peak=    3.190 closest distance to " O   HOH Z 162 " =    1.441
peak=    3.188 closest distance to " O   GLN A 194 " =    1.457
peak=    3.188 closest distance to " CA  ASP A 191 " =    1.213
peak=    3.186 closest distance to " O   HOH Z  94 " =    2.246
peak=    3.185 closest distance to " O   THR A 182 " =    1.393
peak=    3.178 closest distance to " CA  ASP A 149 " =    1.129
peak=    3.175 closest distance to " CB  ASN A 173 " =    1.111
peak=    3.174 closest distance to " CA  ILE A 106 " =    0.745
peak=    3.174 closest distance to " CD1 ILE A  33 " =    1.722
peak=    3.171 closest distance to " O   HOH Z 350 " =    1.574
peak=    3.167 closest distance to " O   HOH Z 361 " =    3.551
peak=    3.166 closest distance to " O   HOH Z 337 " =    1.734
peak=    3.165 closest distance to " O   HOH Z  10 " =    1.727
peak=    3.161 closest distance to " CB  SER A  62 " =    1.188
peak=    3.156 closest distance to " CA  ILE A 234 " =    0.939
peak=    3.156 closest distance to " CB  ALA A 104 " =    0.713
peak=    3.153 closest distance to " OG  SER A  62 " =    2.738
peak=    3.149 closest distance to " CB  LYS A 117 " =    1.180
peak=    3.149 closest distance to " OE2 GLU A  53 " =    2.006
peak=    3.148 closest distance to " O   HOH Z   3 " =    1.709
peak=    3.129 closest distance to " CB  ALA A 242 " =    0.842
peak=    3.128 closest distance to " O   PHE A 192 " =    1.377
peak=    3.118 closest distance to " CB  SER A 288 " =    1.509
peak=    3.109 closest distance to " O   HOH Z 325 " =    2.106
peak=    3.107 closest distance to " O   PRO A 198 " =    1.347
peak=    3.106 closest distance to " O   HOH Z 420 " =    2.034
peak=    3.100 closest distance to " CG  LEU A 281 " =    1.036
peak=    3.093 closest distance to " O   GLY A  91 " =    1.400
peak=    3.085 closest distance to " O   HOH Z 133 " =    2.848
peak=    3.085 closest distance to " CB  ASP A 132 " =    1.015
peak=    3.076 closest distance to " O   HOH Z 201 " =    3.181
peak=    3.076 closest distance to " O   HOH Z 410 " =    3.020
peak=    3.065 closest distance to " CD  ARG A  66 " =    2.723
peak=    3.063 closest distance to " O   ASP A 124 " =    1.753
peak=    3.059 closest distance to " CA  ARG A 102 " =    1.117
peak=    3.056 closest distance to " O   HOH Z  83 " =    1.483
peak=    3.039 closest distance to " O   HOH Z 285 " =    2.581
peak=    3.038 closest distance to " CE  LYS A 119 " =    0.952
peak=    3.035 closest distance to " CG2 ILE A 106 " =    0.837

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 200         
Filter by distance & map next to the model:
   mapped sites are within: 0.698 - 5.583
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 197 from: 200
   mapped sites are within: 0.793 - 5.583

peak=   -4.954 closest distance to " CD  GLN A  58 " =    1.034
peak=   -4.795 closest distance to " SG  CYS A 254 " =    3.323
peak=   -4.318 closest distance to " OG BSER A 134 " =    1.366
peak=   -4.262 closest distance to " C   HIS A 108 " =    1.178
peak=   -4.244 closest distance to " CD  ARG A 156 " =    2.061
peak=   -4.242 closest distance to " CD1 LEU A 101 " =    2.382
peak=   -4.242 closest distance to " CB  PHE A 192 " =    2.025
peak=   -4.128 closest distance to " O   VAL A  67 " =    2.577
peak=   -4.096 closest distance to " O   HOH Z 266 " =    5.574
peak=   -4.088 closest distance to " OE1 GLN A 223 " =    2.310
peak=   -4.076 closest distance to " O   HOH Z 193 " =    1.246
peak=   -4.069 closest distance to " O   HOH Z 166 " =    1.910
peak=   -4.031 closest distance to " NE2 GLN A  88 " =    1.038
peak=   -4.030 closest distance to " O   HOH Z 394 " =    1.623
peak=   -4.021 closest distance to " CA  VAL A  67 " =    2.869
peak=   -4.011 closest distance to " CB  PRO A 243 " =    2.714
peak=   -4.001 closest distance to " O   PRO A 163 " =    2.197
peak=   -4.001 closest distance to " O   HOH Z 351 " =    1.437
peak=   -3.948 closest distance to " O   HOH Z 196 " =    2.141
peak=   -3.928 closest distance to " O   PRO A 198 " =    1.179
peak=   -3.872 closest distance to " CG1 VAL A 112 " =    2.688
peak=   -3.866 closest distance to " CD2 TYR A 293 " =    1.924
peak=   -3.850 closest distance to " O   HOH Z 231 " =    2.223
peak=   -3.838 closest distance to " O   HOH Z 290 " =    1.159
peak=   -3.833 closest distance to " CB  ALA A 248 " =    2.292
peak=   -3.833 closest distance to " CD2 LEU A 237 " =    2.707
peak=   -3.832 closest distance to " CE3 TRP A 150 " =    2.058
peak=   -3.817 closest distance to " OXT GLY A 302 " =    2.879
peak=   -3.815 closest distance to " CE2 TYR A  30 " =    2.774
peak=   -3.804 closest distance to " ND2 ASN A  45 " =    1.080
peak=   -3.803 closest distance to " O   HOH Z 211 " =    1.506
peak=   -3.791 closest distance to " CA  GLY A 241 " =    2.416
peak=   -3.773 closest distance to " O   ALA A 227 " =    1.338
peak=   -3.758 closest distance to " CA  ASP A 298 " =    1.092
peak=   -3.755 closest distance to " CB  ALA A 248 " =    2.142
peak=   -3.738 closest distance to " ND2 ASN A 187 " =    1.509
peak=   -3.732 closest distance to " CG1 VAL A 296 " =    1.065
peak=   -3.700 closest distance to " ND2 ASN A 249 " =    2.317
peak=   -3.693 closest distance to " O   SER A 271 " =    2.111
peak=   -3.689 closest distance to " CE  MET A 105 " =    2.269
peak=   -3.670 closest distance to " CG2 VAL A 296 " =    1.291
peak=   -3.670 closest distance to " O   HOH Z 103 " =    1.783
peak=   -3.661 closest distance to " CB  ALA A 161 " =    2.522
peak=   -3.645 closest distance to " O   HOH Z 114 " =    3.204
peak=   -3.644 closest distance to " CG  ASP A 231 " =    0.793
peak=   -3.642 closest distance to " NE2 GLN A  11 " =    1.773
peak=   -3.641 closest distance to " O   HOH Z 407 " =    2.869
peak=   -3.630 closest distance to " N   ALA A 226 " =    1.936
peak=   -3.619 closest distance to " CB  ALA A  43 " =    2.491
peak=   -3.617 closest distance to " CG  LEU A   5 " =    0.880
peak=   -3.614 closest distance to " CD1 ILE A 199 " =    2.409
peak=   -3.591 closest distance to " O   HOH Z 191 " =    5.583
peak=   -3.588 closest distance to " NH2AARG A 275 " =    4.926
peak=   -3.587 closest distance to " O   HOH Z 216 " =    1.241
peak=   -3.583 closest distance to " OG  SER A  97 " =    2.336
peak=   -3.560 closest distance to " CG2 THR A 178 " =    2.381
peak=   -3.553 closest distance to " CZ3 TRP A 179 " =    1.296
peak=   -3.552 closest distance to " O   ASN A  45 " =    1.931
peak=   -3.546 closest distance to " O   HOH Z 154 " =    1.586
peak=   -3.534 closest distance to " CZ2 TRP A  92 " =    2.842
peak=   -3.532 closest distance to " CD1 LEU A 255 " =    2.749
peak=   -3.527 closest distance to " CG  TRP A 266 " =    1.852
peak=   -3.525 closest distance to " NE  ARG A  66 " =    4.251
peak=   -3.524 closest distance to " OD1 ASN A 249 " =    2.494
peak=   -3.485 closest distance to " O   HOH Z 165 " =    1.954
peak=   -3.484 closest distance to " CA  GLY A 133 " =    2.300
peak=   -3.477 closest distance to " O   HOH Z 174 " =    3.903
peak=   -3.476 closest distance to " CG2 ILE A 263 " =    2.331
peak=   -3.473 closest distance to " O   HOH Z 131 " =    4.109
peak=   -3.470 closest distance to " CG  GLU A 277 " =    1.253
peak=   -3.466 closest distance to " O   HOH Z 431 " =    1.950
peak=   -3.462 closest distance to " O   HOH Z 102 " =    1.567
peak=   -3.446 closest distance to " N   THR A  52 " =    1.674
peak=   -3.435 closest distance to " O   HOH Z 252 " =    3.835
peak=   -3.430 closest distance to " O   HOH Z 423 " =    2.229
peak=   -3.426 closest distance to " CD1 PHE A  59 " =    2.061
peak=   -3.421 closest distance to " CA  ASN A 127 " =    1.294
peak=   -3.415 closest distance to " O   HOH Z 421 " =    3.348
peak=   -3.415 closest distance to " O   HOH Z 136 " =    2.625
peak=   -3.409 closest distance to " CB  TRP A  85 " =    2.606
peak=   -3.399 closest distance to " O   HOH Z 371 " =    2.252
peak=   -3.396 closest distance to " O   GLY A 196 " =    1.247
peak=   -3.388 closest distance to " O   HOH Z 275 " =    1.831
peak=   -3.388 closest distance to " N   THR A 157 " =    1.479
peak=   -3.372 closest distance to " C   MET A 188 " =    1.413
peak=   -3.372 closest distance to " O   HOH Z 123 " =    2.600
peak=   -3.369 closest distance to " O   HOH Z  13 " =    1.750
peak=   -3.363 closest distance to " O   MET A  40 " =    2.836
peak=   -3.360 closest distance to " CZ  TYR A 169 " =    1.839
peak=   -3.357 closest distance to " CE2 PHE A  61 " =    2.628
peak=   -3.352 closest distance to " N   SER A 276 " =    1.389
peak=   -3.350 closest distance to " O   SER A 210 " =    1.875
peak=   -3.350 closest distance to " O   VAL A 189 " =    2.697
peak=   -3.343 closest distance to " O   HOH Z 285 " =    1.889
peak=   -3.336 closest distance to " CE BMET A  47 " =    1.340
peak=   -3.332 closest distance to " CB  ASP A 132 " =    2.310
peak=   -3.330 closest distance to " CB  SER A 210 " =    1.071
peak=   -3.328 closest distance to " OXT GLY A 302 " =    3.392
peak=   -3.326 closest distance to " O   HOH Z 295 " =    1.534
peak=   -3.325 closest distance to " O   HOH Z 243 " =    1.986
peak=   -3.322 closest distance to " O   TRP A  92 " =    1.976
peak=   -3.322 closest distance to " CG1 VAL A 112 " =    2.554
peak=   -3.321 closest distance to " CB  ALA A  10 " =    2.307
peak=   -3.320 closest distance to " CA  GLY A 133 " =    1.920
peak=   -3.316 closest distance to " C   SER A 206 " =    1.514
peak=   -3.314 closest distance to " NE2 GLN A  88 " =    1.969
peak=   -3.311 closest distance to " O   GLY A  80 " =    2.528
peak=   -3.309 closest distance to " O   HOH Z 372 " =    2.238
peak=   -3.306 closest distance to " O   HOH Z  11 " =    1.926
peak=   -3.303 closest distance to " O   ARG A  24 " =    2.059
peak=   -3.300 closest distance to " O   ILE A 106 " =    1.793
peak=   -3.297 closest distance to " O   HOH Z 374 " =    1.908
peak=   -3.297 closest distance to " O   HOH Z 177 " =    1.778
peak=   -3.296 closest distance to " O   HOH Z 283 " =    2.336
peak=   -3.296 closest distance to " CG  ARG A 269 " =    2.229
peak=   -3.295 closest distance to " CD1 ILE A 239 " =    2.300
peak=   -3.295 closest distance to " O   ASN A 187 " =    1.577
peak=   -3.294 closest distance to " ND2 ASN A  39 " =    1.168
peak=   -3.291 closest distance to " O   HOH Z 128 " =    2.305
peak=   -3.284 closest distance to " CG1 VAL A 230 " =    1.864
peak=   -3.282 closest distance to " N   ALA A 248 " =    1.721
peak=   -3.279 closest distance to " ND2 ASN A  69 " =    1.931
peak=   -3.277 closest distance to " CG2 VAL A 189 " =    1.998
peak=   -3.276 closest distance to " O   HOH Z 429 " =    2.035
peak=   -3.265 closest distance to " O   HOH Z 359 " =    2.896
peak=   -3.262 closest distance to " O   HOH Z  19 " =    2.360
peak=   -3.256 closest distance to " O   HOH Z 275 " =    1.392
peak=   -3.252 closest distance to " CD1 TRP A  70 " =    1.791
peak=   -3.247 closest distance to " CD  ARG A 139 " =    1.680
peak=   -3.247 closest distance to " OD2 ASP A  50 " =    2.199
peak=   -3.245 closest distance to " CE3 TRP A 274 " =    2.323
peak=   -3.237 closest distance to " O   PHE A 218 " =    1.606
peak=   -3.234 closest distance to " O   HOH Z 128 " =    1.338
peak=   -3.234 closest distance to " CB  PRO A 163 " =    2.506
peak=   -3.233 closest distance to " C   ASN A 285 " =    2.310
peak=   -3.233 closest distance to " O   HOH Z 111 " =    4.463
peak=   -3.229 closest distance to " O   HOH Z  52 " =    1.668
peak=   -3.224 closest distance to " O   HOH Z 397 " =    1.145
peak=   -3.218 closest distance to " NH2 ARG A  79 " =    1.544
peak=   -3.217 closest distance to " CD2 PHE A 225 " =    1.088
peak=   -3.215 closest distance to " CB  ASN A  39 " =    2.320
peak=   -3.215 closest distance to " O   VAL A 174 " =    2.130
peak=   -3.210 closest distance to " CG  GLU A  53 " =    1.597
peak=   -3.208 closest distance to " N   HIS A 115 " =    2.242
peak=   -3.206 closest distance to " O   GLY A  80 " =    2.470
peak=   -3.203 closest distance to " O   HOH Z 357 " =    2.107
peak=   -3.203 closest distance to " O   HOH Z  38 " =    1.869
peak=   -3.200 closest distance to " CD  PRO A 243 " =    2.058
peak=   -3.199 closest distance to " CD2 PHE A  61 " =    2.136
peak=   -3.197 closest distance to " CZ  PHE A  38 " =    2.092
peak=   -3.191 closest distance to " O   HOH Z 426 " =    1.705
peak=   -3.190 closest distance to " O   ALA A   1 " =    1.665
peak=   -3.190 closest distance to " O   HOH Z 185 " =    2.435
peak=   -3.189 closest distance to " OG ASER A 134 " =    1.340
peak=   -3.188 closest distance to " OE1 GLN A 183 " =    1.537
peak=   -3.186 closest distance to " O   HOH Z 116 " =    1.447
peak=   -3.185 closest distance to " O   HOH Z 251 " =    5.125
peak=   -3.184 closest distance to " CG1 VAL A  78 " =    2.540
peak=   -3.179 closest distance to " CG1BVAL A  72 " =    2.301
peak=   -3.173 closest distance to " N   GLN A  58 " =    1.952
peak=   -3.171 closest distance to " CA  VAL A 296 " =    0.968
peak=   -3.171 closest distance to " O   HOH Z 166 " =    1.622
peak=   -3.170 closest distance to " O   HOH Z 111 " =    1.969
peak=   -3.168 closest distance to " O   HOH Z 174 " =    2.377
peak=   -3.167 closest distance to " CB  PRO A 280 " =    2.150
peak=   -3.162 closest distance to " O   HOH Z 236 " =    1.691
peak=   -3.152 closest distance to " N   PHE A  59 " =    1.942
peak=   -3.149 closest distance to " CB  ASP A 132 " =    2.402
peak=   -3.147 closest distance to " N   ALA A 248 " =    2.356
peak=   -3.144 closest distance to " C   ALA A 158 " =    1.344
peak=   -3.144 closest distance to " CG  MET A 105 " =    0.898
peak=   -3.140 closest distance to " O   HOH Z 198 " =    1.944
peak=   -3.139 closest distance to " CA  GLY A 241 " =    3.106
peak=   -3.133 closest distance to " O   HOH Z 392 " =    1.926
peak=   -3.132 closest distance to " O   ALA A  51 " =    1.205
peak=   -3.131 closest distance to " O   ASN A 252 " =    1.357
peak=   -3.129 closest distance to " CD2 HIS A 207 " =    2.478
peak=   -3.127 closest distance to " O   SER A 276 " =    1.682
peak=   -3.120 closest distance to " O   HOH Z 340 " =    1.846
peak=   -3.119 closest distance to " O   HOH Z  10 " =    1.432
peak=   -3.116 closest distance to " CB  VAL A 296 " =    1.012
peak=   -3.111 closest distance to " CB  TYR A  15 " =    2.186
peak=   -3.107 closest distance to " N   SER A   3 " =    2.259
peak=   -3.106 closest distance to " CB  ALA A   9 " =    2.546
peak=   -3.106 closest distance to " O   HOH Z 110 " =    1.509
peak=   -3.105 closest distance to " CB  ALA A 291 " =    2.185
peak=   -3.103 closest distance to " CB  ALA A 291 " =    2.175
peak=   -3.103 closest distance to " O   HOH Z   6 " =    1.617
peak=   -3.102 closest distance to " CE1 TYR A 247 " =    2.617
peak=   -3.100 closest distance to " O   HOH Z  60 " =    1.865
peak=   -3.087 closest distance to " CG1 VAL A 197 " =    2.211
peak=   -3.072 closest distance to " NE2 GLN A 240 " =    1.610
peak=   -3.068 closest distance to " O   HOH Z 109 " =    1.021
peak=   -3.062 closest distance to " O   HOH Z 111 " =    2.266
peak=   -3.047 closest distance to " O   HOH Z  71 " =    2.314
peak=   -3.041 closest distance to " O   HOH Z 139 " =    5.012
peak=   -3.020 closest distance to " CG1 VAL A  78 " =    3.206

================= 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    :  0.4603 0.4451   6.261040e+00   6.239361e+00
   1_bss:  0.4504 0.4350   6.252095e+00   6.230697e+00
   1_xyz:  0.3516 0.3712   6.086220e+00   6.121552e+00
   1_adp:  0.2988 0.3395   5.957460e+00   6.051612e+00
   1_occ:  0.2984 0.3405   5.956778e+00   6.053667e+00
   2_bss:  0.2938 0.3361   5.957186e+00   6.052879e+00
   2_xyz:  0.1966 0.2404   5.608915e+00   5.773252e+00
   2_adp:  0.1737 0.2218   5.509000e+00   5.696663e+00
   2_occ:  0.1735 0.2217   5.508767e+00   5.696882e+00
   3_bss:  0.1715 0.2203   5.507294e+00   5.694226e+00
   3_xyz:  0.1400 0.1819   5.321623e+00   5.521689e+00
   3_adp:  0.1330 0.1765   5.285575e+00   5.499067e+00
   3_occ:  0.1328 0.1767   5.285322e+00   5.499106e+00
   4_bss:  0.1329 0.1770   5.286322e+00   5.499495e+00
   4_xyz:  0.1203 0.1661   5.214503e+00   5.444249e+00
   4_adp:  0.1198 0.1625   5.201245e+00   5.421252e+00
   4_occ:  0.1197 0.1624   5.200716e+00   5.420815e+00
   5_bss:  0.1197 0.1624   5.200756e+00   5.420902e+00
   5_xyz:  0.1169 0.1596   5.181485e+00   5.406333e+00
   5_adp:  0.1161 0.1598   5.179614e+00   5.408368e+00
   5_occ:  0.1161 0.1598   5.179291e+00   5.408018e+00
   5_bss:  0.1161 0.1598   5.179291e+00   5.408088e+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:  0.343  20.001   7.497   8.062  10.353   0.000   0.000   0.000
   1_xyz:  0.343  20.001   7.497   8.062  10.353   0.000   0.000   0.000
   1_adp:  0.343  20.001   7.497   8.062  10.353   0.000   0.000   0.000
   1_occ:  0.343  20.001   7.497   8.062  10.353   0.000   0.000   0.000
   2_bss:  0.334  43.071   3.792   4.186   6.596   0.000   0.000   0.000
   2_xyz:  0.334  43.071   3.792   4.186   6.596   0.000   0.000   0.000
   2_adp:  0.334  43.071   3.792   4.186   6.596   0.000   0.000   0.000
   2_occ:  0.334  43.071   3.792   4.186   6.596   0.000   0.000   0.000
   3_bss:  0.319  50.688   2.018   2.947   4.415   0.000   0.000   0.000
   3_xyz:  0.319  50.688   2.018   2.947   4.415   0.000   0.000   0.000
   3_adp:  0.319  50.688   2.018   2.947   4.415   0.000   0.000   0.000
   3_occ:  0.319  50.688   2.018   2.947   4.415   0.000   0.000   0.000
   4_bss:  0.328  54.454   1.774   2.702   4.072   0.000   0.000   0.000
   4_xyz:  0.328  54.454   1.774   2.702   4.072   0.000   0.000   0.000
   4_adp:  0.328  54.454   1.774   2.702   4.072   0.000   0.000   0.000
   4_occ:  0.328  54.454   1.774   2.702   4.072   0.000   0.000   0.000
   5_bss:  0.329  54.454   1.797   2.690   4.030   0.000   0.000   0.000
   5_xyz:  0.329  54.454   1.797   2.690   4.030   0.000   0.000   0.000
   5_adp:  0.329  54.454   1.797   2.690   4.030   0.000   0.000   0.000
   5_occ:  0.329  54.454   1.797   2.690   4.030   0.000   0.000   0.000
   5_bss:  0.324  55.550  -1.038  -0.163   1.201   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  50.534 0.5155  0.5913    59417.895
   1_bss:  50.281 0.5172  0.7727    57617.612
   1_xyz:  40.525 0.6356  0.9133    37988.290
   1_adp:  35.255 0.6986  1.0169    30735.003
   1_occ:  35.352 0.6975  1.0143    30905.603
   2_bss:  35.120 0.7002  0.8906    30708.557
   2_xyz:  23.820 0.8234  1.0039    14698.332
   2_adp:  21.474 0.8475  1.0215    12627.949
   2_occ:  21.489 0.8474  1.0213    12620.340
   3_bss:  21.361 0.8485  0.9596    12489.227
   3_xyz:  17.052 0.8891  0.9812     8531.656
   3_adp:  16.485 0.8943  0.9795     8132.646
   3_occ:  16.493 0.8942  0.9793     8133.783
   4_bss:  16.506 0.8942  0.9695     8160.693
   4_xyz:  15.381 0.9037  0.9738     7257.329
   4_adp:  14.885 0.9080  0.9728     6978.133
   4_occ:  14.875 0.9081  0.9728     6970.806
   5_bss:  14.874 0.9081  0.9725     6971.947
   5_xyz:  14.533 0.9110  0.9739     6723.488
   5_adp:  14.553 0.9109  0.9701     6744.638
   5_occ:  14.545 0.9109  0.9700     6735.876
   5_bss:  14.547 0.9109  0.9717     6735.985
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3778e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3778e+01
   1_xyz:   1.646  0.013  0.106 17.882  0.006  4.110   1.3303e-01
   1_adp:   1.646  0.013  0.106 17.882  0.006  4.110   1.3303e-01
   1_occ:   1.646  0.013  0.106 17.882  0.006  4.110   1.3303e-01
   2_bss:   1.646  0.013  0.106 17.882  0.006  4.110   1.3303e-01
   2_xyz:   1.104  0.008  0.077 16.064  0.004  4.127   7.3831e-02
   2_adp:   1.104  0.008  0.077 16.064  0.004  4.127   7.3831e-02
   2_occ:   1.104  0.008  0.077 16.064  0.004  4.127   7.3831e-02
   3_bss:   1.104  0.008  0.077 16.064  0.004  4.127   7.3831e-02
   3_xyz:   0.959  0.006  0.073 15.716  0.003  4.126   5.6681e-02
   3_adp:   0.959  0.006  0.073 15.716  0.003  4.126   5.6681e-02
   3_occ:   0.959  0.006  0.073 15.716  0.003  4.126   5.6681e-02
   4_bss:   0.959  0.006  0.073 15.716  0.003  4.126   5.6681e-02
   4_xyz:   1.000  0.007  0.079 15.514  0.004  4.132   6.0757e-02
   4_adp:   1.000  0.007  0.079 15.514  0.004  4.132   6.0757e-02
   4_occ:   1.000  0.007  0.079 15.514  0.004  4.132   6.0757e-02
   5_bss:   1.000  0.007  0.079 15.514  0.004  4.132   6.0757e-02
   5_xyz:   0.988  0.007  0.078 15.252  0.003  4.120   5.8772e-02
   5_adp:   0.988  0.007  0.078 15.252  0.003  4.120   5.8772e-02
   5_occ:   0.988  0.007  0.078 15.252  0.003  4.120   5.8772e-02
   5_bss:   0.988  0.007  0.078 15.252  0.003  4.120   5.8772e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9702e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9702e+00
   1_xyz:  14.053  0.161  0.447 86.021  0.045  2.266   1.0035e-01
   1_adp:  14.053  0.161  0.447 86.021  0.045  2.266   1.0035e-01
   1_occ:  14.053  0.161  0.447 86.021  0.045  2.266   1.0035e-01
   2_bss:  14.053  0.161  0.447 86.021  0.045  2.266   1.0035e-01
   2_xyz:   6.910  0.089  0.290 82.034  0.039  2.290   9.2967e-02
   2_adp:   6.910  0.089  0.290 82.034  0.039  2.290   9.2967e-02
   2_occ:   6.910  0.089  0.290 82.034  0.039  2.290   9.2967e-02
   3_bss:   6.910  0.089  0.290 82.034  0.039  2.290   9.2967e-02
   3_xyz:   7.409  0.049  0.305 82.014  0.041  2.333   3.2799e-02
   3_adp:   7.409  0.049  0.305 82.014  0.041  2.333   3.2799e-02
   3_occ:   7.409  0.049  0.305 82.014  0.041  2.333   3.2799e-02
   4_bss:   7.409  0.049  0.305 82.014  0.041  2.333   3.2799e-02
   4_xyz:   6.813  0.041  0.401 81.839  0.036  2.354   3.8995e-02
   4_adp:   6.813  0.041  0.401 81.839  0.036  2.354   3.8995e-02
   4_occ:   6.813  0.041  0.401 81.839  0.036  2.354   3.8995e-02
   5_bss:   6.813  0.041  0.401 81.839  0.036  2.354   3.8995e-02
   5_xyz:   6.990  0.047  0.398 81.658  0.035  2.350   3.4627e-02
   5_adp:   6.990  0.047  0.398 81.658  0.035  2.350   3.4627e-02
   5_occ:   6.990  0.047  0.398 81.658  0.035  2.350   3.4627e-02
   5_bss:   6.990  0.047  0.398 81.658  0.035  2.350   3.4627e-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:  64.48   0.00  11.99  58.03   0.00   9.18  64.48   0.00  27.29
   1_occ:  64.48   0.00  11.99  58.03   0.00   9.18  64.48   0.00  27.29
   2_bss:  64.48   0.00  11.99  58.03   0.00   9.18  64.48   0.00  27.29
   2_xyz:  64.48   0.00  11.99  58.03   0.00   9.18  64.48   0.00  27.29
   2_adp:  72.38   0.00  12.29  72.38   0.00   8.39  66.98   0.51  33.50
   2_occ:  72.38   0.00  12.29  72.38   0.00   8.39  66.98   0.51  33.50
   3_bss:  72.38   0.00  12.29  72.38   0.00   8.39  66.98   0.51  33.50
   3_xyz:  72.38   0.00  12.29  72.38   0.00   8.39  66.98   0.51  33.50
   3_adp:  85.82   0.00  13.05  85.82   0.00   8.50  78.91   0.98  37.83
   3_occ:  85.82   0.00  13.05  85.82   0.00   8.50  78.91   0.98  37.83
   4_bss:  85.82   0.00  13.05  85.82   0.00   8.50  78.91   0.98  37.83
   4_xyz:  85.82   0.00  13.05  85.82   0.00   8.50  78.91   0.98  37.83
   4_adp:  85.02   0.00  12.50  85.02   0.00   8.20  77.74   1.18  35.94
   4_occ:  85.02   0.00  12.50  85.02   0.00   8.20  77.74   1.18  35.94
   5_bss:  85.02   0.00  12.50  85.02   0.00   8.20  77.74   1.18  35.94
   5_xyz:  85.02   0.00  12.50  85.02   0.00   8.20  77.74   1.18  35.94
   5_adp:  85.27   0.00  12.43  85.27   0.00   8.12  78.00   1.01  35.93
   5_occ:  85.27   0.00  12.43  85.27   0.00   8.12  78.00   1.01  35.93
   5_bss:  88.16   2.89  15.32  88.16   2.89  11.01  80.89   3.90  38.82
------------------------------------------------------------------------
 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:    1.273    0.026    0.411
   1_adp:    1.273    0.026    0.411
   1_occ:    1.273    0.026    0.411
   2_bss:    1.273    0.026    0.411
   2_xyz:    1.702    0.036    0.557
   2_adp:    1.702    0.036    0.557
   2_occ:    1.702    0.036    0.557
   3_bss:    1.702    0.036    0.557
   3_xyz:    1.717    0.044    0.586
   3_adp:    1.717    0.044    0.586
   3_occ:    1.717    0.044    0.586
   4_bss:    1.717    0.044    0.586
   4_xyz:    1.833    0.054    0.616
   4_adp:    1.833    0.054    0.616
   4_occ:    1.833    0.054    0.616
   5_bss:    1.833    0.054    0.616
   5_xyz:    1.851    0.050    0.627
   5_adp:    1.851    0.050    0.627
   5_occ:    1.851    0.050    0.627
   5_bss:    1.851    0.050    0.627
------------------------------------------------------------------------

CPU time actual refinement: 327.52


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_316/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_316/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_316/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_316/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_316/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 327.37 
  Macro-tasks:
    bulk solvent and scale       = 42.17  
    individual site refinement   = 127.96 
    weights calculation          = 32.60  
    collect and process          = 6.56   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 209.41 
  Micro-tasks:
    mask                            = 1.82   
    f_calc                          = 100.24 
    alpha_beta                      = 8.26   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 109.00 
    fmodel                         = 7.30   
    r_factors                      = 0.16   
    phase_errors                   = 10.53  
    foms                           = 0.27   
    TOTAL for micro-tasks          = 238.72 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.679 micro seconds
Total CPU time: 5.69 minutes
from_scatterers_fft:    640 calls, 99.94 s
gradients_fft:          584 calls, 96.23 s

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

# Date 2008-01-16 Time 01:15:54 PST -0800 (1200474954.78 s)
Start R-work = 0.4603, R-free = 0.4451 (no bulk solvent and anisotropic scale)
Final R-work = 0.1334, R-free = 0.1753 (no bulk solvent and anisotropic scale)

Start R-work = 0.4504, R-free = 0.4350
Final R-work = 0.1161, R-free = 0.1598