# Date 2008-01-16 Time 01:09:08 PST -0800 (1200474548.17 s)
#phil __OFF__

Command line arguments: "../292.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 17997
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 292

-------------------------------------------------------------------------------
  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, 46.6953, 86.822, 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: 3.26, per 1000 atoms: 1.15


================================== 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, 46.6953, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8486 1.97068
Completeness in resolution range: 0.958038
Completeness with d_max=infinity: 0.955049

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8486
                             d_min =   1.9707

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, 46.6953, 86.822, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8486 1.97068
Completeness in resolution range: 0.958038
Completeness with d_max=infinity: 0.955049

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8490 -  4.2163 [2156/2183]  1938   218  10.1%
  bin  2:  4.2163 -  3.3594 [2056/2072]  1854   202   9.8%
  bin  3:  3.3594 -  2.9385 [2040/2059]  1835   205  10.0%
  bin  4:  2.9385 -  2.6715 [2012/2042]  1810   202  10.0%
  bin  5:  2.6715 -  2.4810 [2003/2022]  1799   204  10.2%
  bin  6:  2.4810 -  2.3353 [1989/2014]  1792   197   9.9%
  bin  7:  2.3353 -  2.2187 [1997/2031]  1803   194   9.7%
  bin  8:  2.2187 -  2.1224 [1972/2003]  1772   200  10.1%
  bin  9:  2.1224 -  2.0409 [1974/2015]  1779   195   9.9%
  bin 10:  2.0409 -  1.9707 [1390/2006]  1248   142  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_292/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 26
        2.42 -     3.04: 2226
        3.04 -     3.66: 4729
        3.66 -     4.28: 9113
        4.28 -     4.90: 12442
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.862 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.865 3.040 -x+1,y-1/2,-z+1/2
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.875 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.969 3.040 -x+1,y-1/2,-z+1/2
  ... (remaining 28531 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_292/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_292/model_refine_001.geo

CPU time processing inputs: 9.11


============================ 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 46.69535 86.82195 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 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4383   r_free= 0.4266   ksol= 0.00   Bsol= 0.00   scale= 0.825    |
|                                                                             |
| 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:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.233732                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8490 -  4.7025 0.99   1398  153 0.3618 0.3474      6.5206      6.4925|
|  2:  4.7025 -  3.7523 0.99   1334  154 0.3304 0.3428      6.6331      6.6894|
|  3:  3.7523 -  3.2838 0.99   1322  144 0.3790 0.3578      6.5545      6.5586|
|  4:  3.2838 -  2.9863 0.99   1305  139 0.4221 0.4136      6.4635      6.4226|
|  5:  2.9863 -  2.7737 0.99   1306  148 0.4566 0.4703       6.311      6.3357|
|  6:  2.7737 -  2.6111 0.99   1285  148 0.4610 0.5375      6.2433      6.2325|
|  7:  2.6111 -  2.4810 0.99   1286  145 0.4741 0.4537      6.2103      6.1463|
|  8:  2.4810 -  2.3734 0.98   1298  135 0.4856 0.4515       6.158       6.159|
|  9:  2.3734 -  2.2824 0.98   1273  147 0.4974 0.4811      6.0782      6.1188|
| 10:  2.2824 -  2.2039 0.98   1270  140 0.5035 0.4497      6.1204      6.0038|
| 11:  2.2039 -  2.1352 0.99   1279  142 0.5162 0.4411      6.0414      5.9994|
| 12:  2.1352 -  2.0743 0.97   1263  140 0.5011 0.4597       5.967      5.9882|
| 13:  2.0743 -  2.0198 0.99   1259  139 0.4998 0.4576      5.8737      5.7978|
| 14:  2.0198 -  1.9707 0.58    752   85 0.5137 0.4994      5.8824      5.7628|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8490 -  4.7025  1398   153  0.72  32.64   0.82     0.75      64356.68|
|  2:  4.7025 -  3.7523  1334   154  0.76  29.97   0.92     0.81      80036.81|
|  3:  3.7523 -  3.2838  1322   144  0.69  36.35   0.89     0.79      82568.54|
|  4:  3.2838 -  2.9863  1305   139  0.62  41.96   0.83     0.70      74477.42|
|  5:  2.9863 -  2.7737  1306   148  0.51  51.05   0.77     0.59      67905.65|
|  6:  2.7737 -  2.6111  1285   148  0.47  54.22   0.74     0.53      63108.66|
|  7:  2.6111 -  2.4810  1286   145  0.44  56.46   0.78     0.51      58914.58|
|  8:  2.4810 -  2.3734  1298   135  0.46  55.08   0.76     0.53      50780.18|
|  9:  2.3734 -  2.2824  1273   147  0.48  53.50   0.75     0.58      43930.99|
| 10:  2.2824 -  2.2039  1270   140  0.53  50.32   0.76     0.60      37026.73|
| 11:  2.2039 -  2.1352  1279   142  0.50  51.89   0.76     0.60      34871.01|
| 12:  2.1352 -  2.0743  1263   140  0.49  53.41   0.79     0.59      33505.80|
| 13:  2.0743 -  2.0198  1259   139  0.45  56.28   0.77     0.54      30378.76|
| 14:  2.0198 -  1.9707   752    85  0.45  56.09   0.75     0.46      24432.77|
|alpha:            min =        0.46 max =            0.81 mean =         0.62|
|beta:             min =    24432.77 max =        82568.54 mean =     54511.11|
|figures of merit: min =        0.00 max =            1.00 mean =         0.55|
|phase err.(work): min =        0.00 max =           89.99 mean =        48.09|
|phase err.(test): min =        0.00 max =           89.98 mean =        48.34|
|-----------------------------------------------------------------------------|

============================== 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 = 7.684483              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.111   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.665303              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.859   (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:        2 |
| 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:      175 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      703 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1516 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2667 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3969 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5114 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6616 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7779 |
|-----------------------------------------------------------------------------|
|-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 |       53.373 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.196 |       2.004 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.684)------------------------------------------|
|    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 = 11.684)------------------------------------------|
|    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 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4464   r_free= 0.4335   ksol= 0.00   Bsol= 0.00   scale= 0.793    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.238288                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4301   r_free= 0.4164   ksol= 0.37   Bsol= 20.00   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.41,7.79,8.01,0.00,0.00,0.00); trace/3= 7.74                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.224900                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.212736              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.761   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.656155              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 75.239   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4301      final r-factor (work) = 0.3223          |
| start r-factor (free) = 0.4164      final r-factor (free) = 0.3403          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 75.8861 = 7.21 * 0.50 * 6.2425 + 1.00 * 53.3733                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.0591 = 7.21 * 0.50 * 6.0837 + 1.00 * 0.1189                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3223      final r-factor (work) = 0.2583          |
| start r-factor (free) = 0.3403      final r-factor (free) = 0.2974          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0066 = 0.66 * 1.00 * 6.0837 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8841 = 0.66 * 1.00 * 5.9008 + 1.00 * 0.0123                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.684)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    56.67   10.88    None  None   None       |
|    all(noH): 2823   0      0.00    56.67   10.88    None  None   None       |
|    Sol.    : 438    0      0.00    56.67   27.12    None  None   None       |
|    Mac.    : 2385   0      0.00    55.16   7.89     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 -   5.667: 1158   |   5:    28.337 -  34.004:  103        |
|      1:     5.667 -  11.335:  774   |   6:    34.004 -  39.672:   79        |
|      2:    11.335 -  17.002:  330   |   7:    39.672 -  45.339:   52        |
|      3:    17.002 -  22.670:  169   |   8:    45.339 -  51.007:   26        |
|      4:    22.670 -  28.337:  125   |   9:    51.007 -  56.674:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2583 r_free = 0.2974             target_work(ml) = 5.843         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2579 r_free = 0.2970             target_work(ml) = 5.842         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2579   r_free= 0.2970   ksol= 0.37   Bsol= 20.00   scale= 1.088   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.41,7.79,8.01,0.00,0.00,0.00); trace/3= 7.74                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.841929                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2541   r_free= 0.2926   ksol= 0.34   Bsol= 36.72   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.22,4.38,5.40,0.00,0.00,0.00); trace/3= 4.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.33 A                  |
| x-ray target function (ml) for work reflections: 5.840334                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.443073              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.057   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.352772              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 116.217  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2541      final r-factor (work) = 0.1699          |
| start r-factor (free) = 0.2926      final r-factor (free) = 0.2082          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.2860 = 3.44 * 0.50 * 5.9061 + 1.00 * 0.1185                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.8105 = 3.44 * 0.50 * 5.6628 + 1.00 * 0.0619                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1699      final r-factor (work) = 0.1561          |
| start r-factor (free) = 0.2082      final r-factor (free) = 0.1990          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0099 = 0.35 * 1.00 * 5.6628 + 1.00 * 0.0122                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0693 = 0.35 * 1.00 * 5.4361 + 1.00 * 1.1516                               |
|-----------------------------------------------------------------------------|
| number of iterations = 6       |    number of function evaluations = 6      |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.684)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.34   11.00    None  None   None       |
|    all(noH): 2823   0      0.00    75.34   11.00    None  None   None       |
|    Sol.    : 438    0      0.11    57.39   29.12    None  None   None       |
|    Mac.    : 2385   0      0.00    75.34   7.67     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.534: 1506   |   5:    37.671 -  45.205:   79        |
|      1:     7.534 -  15.068:  682   |   6:    45.205 -  52.739:   34        |
|      2:    15.068 -  22.603:  199   |   7:    52.739 -  60.274:    5        |
|      3:    22.603 -  30.137:  170   |   8:    60.274 -  67.808:    0        |
|      4:    30.137 -  37.671:  147   |   9:    67.808 -  75.342:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1561 r_free = 0.1990             target_work(ml) = 5.410         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1559 r_free = 0.1989             target_work(ml) = 5.409         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1559   r_free= 0.1989   ksol= 0.34   Bsol= 36.72   scale= 1.037   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.22,4.38,5.40,0.00,0.00,0.00); trace/3= 4.67                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.409027                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1550   r_free= 0.1990   ksol= 0.34   Bsol= 36.72   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.80,3.34,4.56,0.00,0.00,0.00); trace/3= 3.57                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.409624                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.594645              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.379  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 20.206552             wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 89.363   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1550      final r-factor (work) = 0.1277          |
| start r-factor (free) = 0.1990      final r-factor (free) = 0.1705          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.1229 = 2.59 * 0.50 * 5.4428 + 1.00 * 0.0619                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.9653 = 2.59 * 0.50 * 5.3226 + 1.00 * 0.0601                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1277      final r-factor (work) = 0.1188          |
| start r-factor (free) = 0.1705      final r-factor (free) = 0.1633          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 107.6875 = 20.21 * 1.00 * 5.3226 + 1.00 * 0.1353                            |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 105.3188 = 20.21 * 1.00 * 5.2114 + 1.00 * 0.0144                            |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.684)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.60   12.02    None  None   None       |
|    all(noH): 2823   0      0.00    78.60   12.02    None  None   None       |
|    Sol.    : 438    0      0.48    73.29   35.31    None  None   None       |
|    Mac.    : 2385   0      0.00    78.60   7.74     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 -   7.860: 1641   |   5:    39.299 -  47.158:   99        |
|      1:     7.860 -  15.720:  564   |   6:    47.158 -  55.018:   79        |
|      2:    15.720 -  23.579:  174   |   7:    55.018 -  62.878:   34        |
|      3:    23.579 -  31.439:  103   |   8:    62.878 -  70.737:   18        |
|      4:    31.439 -  39.299:  106   |   9:    70.737 -  78.597:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1188 r_free = 0.1633             target_work(ml) = 5.190         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1187 r_free = 0.1633             target_work(ml) = 5.190         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1187   r_free= 0.1633   ksol= 0.34   Bsol= 36.72   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.80,3.34,4.56,0.00,0.00,0.00); trace/3= 3.57                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.190289                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1186   r_free= 0.1637   ksol= 0.32   Bsol= 36.72   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.80,3.34,4.56,0.00,0.00,0.00); trace/3= 3.57                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.188744                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.514433              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 128.870  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.121849              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 99.145   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1186      final r-factor (work) = 0.1100          |
| start r-factor (free) = 0.1637      final r-factor (free) = 0.1584          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.2157 = 3.51 * 0.50 * 5.2103 + 1.00 * 0.0601                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.1335 = 3.51 * 0.50 * 5.1570 + 1.00 * 0.0716                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1100      final r-factor (work) = 0.1087          |
| start r-factor (free) = 0.1584      final r-factor (free) = 0.1568          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8003 = 1.12 * 1.00 * 5.1570 + 1.00 * 0.0149                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7868 = 1.12 * 1.00 * 5.1349 + 1.00 * 0.0262                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.684)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.82   11.79    None  None   None       |
|    all(noH): 2823   0      0.00    84.82   11.79    None  None   None       |
|    Sol.    : 438    0      0.72    75.98   34.78    None  None   None       |
|    Mac.    : 2385   0      0.00    84.82   7.56     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 -   8.482: 1752   |   5:    42.410 -  50.893:   92        |
|      1:     8.482 -  16.964:  509   |   6:    50.893 -  59.375:   54        |
|      2:    16.964 -  25.446:  150   |   7:    59.375 -  67.857:   24        |
|      3:    25.446 -  33.928:  128   |   8:    67.857 -  76.339:   10        |
|      4:    33.928 -  42.410:  101   |   9:    76.339 -  84.821:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1087 r_free = 0.1568             target_work(ml) = 5.129         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1087 r_free = 0.1568             target_work(ml) = 5.129         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1087   r_free= 0.1568   ksol= 0.32   Bsol= 36.72   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.80,3.34,4.56,0.00,0.00,0.00); trace/3= 3.57                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.128941                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1087   r_free= 0.1567   ksol= 0.32   Bsol= 40.19   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.67,3.22,4.56,0.00,0.00,0.00); trace/3= 3.48                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.128634                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.129825              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 161.186  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.261400              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.263   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1087      final r-factor (work) = 0.1098          |
| start r-factor (free) = 0.1567      final r-factor (free) = 0.1567          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5396 = 2.13 * 0.50 * 5.1346 + 1.00 * 0.0716                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5263 = 2.13 * 0.50 * 5.1338 + 1.00 * 0.0593                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1098      final r-factor (work) = 0.1104          |
| start r-factor (free) = 0.1567      final r-factor (free) = 0.1556          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3638 = 0.26 * 1.00 * 5.1338 + 1.00 * 0.0219                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3544 = 0.26 * 1.00 * 5.1392 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.684)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.50   11.41    None  None   None       |
|    all(noH): 2823   0      0.00    84.50   11.41    None  None   None       |
|    Sol.    : 438    0      1.02    73.37   33.38    None  None   None       |
|    Mac.    : 2385   0      0.00    84.50   7.37     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 -   8.450: 1798   |   5:    42.249 -  50.699:   79        |
|      1:     8.450 -  16.900:  493   |   6:    50.699 -  59.149:   45        |
|      2:    16.900 -  25.349:  141   |   7:    59.149 -  67.598:   20        |
|      3:    25.349 -  33.799:  123   |   8:    67.598 -  76.048:    8        |
|      4:    33.799 -  42.249:  113   |   9:    76.048 -  84.498:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1104 r_free = 0.1556             target_work(ml) = 5.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1104 r_free = 0.1556             target_work(ml) = 5.134         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1104   r_free= 0.1556   ksol= 0.32   Bsol= 40.19   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.67,3.22,4.56,0.00,0.00,0.00); trace/3= 3.48                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.133872                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8490 -  4.7025 0.99   1398  153 0.0981 0.1258      5.3719      5.5012|
|  2:  4.7025 -  3.7523 0.99   1334  154 0.0849 0.1130      5.4308      5.6314|
|  3:  3.7523 -  3.2838 0.99   1322  144 0.1044 0.1501      5.4622      5.8409|
|  4:  3.2838 -  2.9863 0.99   1305  139 0.1174 0.1577      5.4276      5.5744|
|  5:  2.9863 -  2.7737 0.99   1306  148 0.1290 0.1673      5.3114      5.5399|
|  6:  2.7737 -  2.6111 0.99   1285  148 0.1205 0.1966      5.1961       5.482|
|  7:  2.6111 -  2.4810 0.99   1286  145 0.1239 0.1574      5.1618       5.322|
|  8:  2.4810 -  2.3734 0.98   1298  135 0.1129 0.1677      5.0534      5.3085|
|  9:  2.3734 -  2.2824 0.98   1273  147 0.1196 0.1903      5.0262      5.3411|
| 10:  2.2824 -  2.2039 0.98   1270  140 0.1108 0.1466      4.9447      5.0983|
| 11:  2.2039 -  2.1352 0.99   1279  142 0.1119 0.1792      4.9225      5.2802|
| 12:  2.1352 -  2.0743 0.97   1263  140 0.1125 0.1568      4.8715      5.1492|
| 13:  2.0743 -  2.0198 0.99   1259  139 0.1112 0.1668      4.7715      4.9977|
| 14:  2.0198 -  1.9707 0.58    752   85 0.1031 0.1760      4.6629      4.9573|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8490 -  4.7025  1398   153  0.94   8.92   0.98     0.96       6917.00|
|  2:  4.7025 -  3.7523  1334   154  0.95   7.81   1.02     1.01       8864.62|
|  3:  3.7523 -  3.2838  1322   144  0.94  11.09   1.03     1.02      10183.54|
|  4:  3.2838 -  2.9863  1305   139  0.92  13.07   1.01     1.00       9941.99|
|  5:  2.9863 -  2.7737  1306   148  0.90  15.57   1.00     0.97       8072.27|
|  6:  2.7737 -  2.6111  1285   148  0.90  15.92   0.98     0.96       6878.73|
|  7:  2.6111 -  2.4810  1286   145  0.91  15.40   0.99     0.94       5973.68|
|  8:  2.4810 -  2.3734  1298   135  0.91  14.55   1.00     0.98       5103.13|
|  9:  2.3734 -  2.2824  1273   147  0.91  15.15   1.01     0.99       4877.42|
| 10:  2.2824 -  2.2039  1270   140  0.90  15.54   1.01     0.97       4240.00|
| 11:  2.2039 -  2.1352  1279   142  0.90  15.89   1.00     0.97       4253.71|
| 12:  2.1352 -  2.0743  1263   140  0.91  15.12   1.02     1.02       3839.34|
| 13:  2.0743 -  2.0198  1259   139  0.91  15.44   1.01     0.99       3180.75|
| 14:  2.0198 -  1.9707   752    85  0.92  14.18   0.99     0.96       2483.20|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2483.20 max =        10183.54 mean =      6203.92|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.97 mean =        13.76|
|phase err.(test): min =        0.00 max =           87.84 mean =        13.34|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1104   r_free= 0.1556   ksol= 0.32   Bsol= 43.66   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.84,-0.26,1.10,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.133875                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 14.85 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1104   r_free= 0.1556   ksol= 0.32   Bsol= 43.66   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.84,-0.26,1.10,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.133875                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8490 -  4.7025 0.99   1398  153 0.0981 0.1257      5.3719      5.5011|
|  2:  4.7025 -  3.7523 0.99   1334  154 0.0849 0.1130      5.4306      5.6312|
|  3:  3.7523 -  3.2838 0.99   1322  144 0.1043 0.1500       5.462      5.8404|
|  4:  3.2838 -  2.9863 0.99   1305  139 0.1174 0.1577      5.4276      5.5742|
|  5:  2.9863 -  2.7737 0.99   1306  148 0.1290 0.1673      5.3115      5.5402|
|  6:  2.7737 -  2.6111 0.99   1285  148 0.1205 0.1966      5.1961      5.4818|
|  7:  2.6111 -  2.4810 0.99   1286  145 0.1239 0.1574      5.1618      5.3219|
|  8:  2.4810 -  2.3734 0.98   1298  135 0.1128 0.1677      5.0532      5.3084|
|  9:  2.3734 -  2.2824 0.98   1273  147 0.1196 0.1903      5.0263      5.3411|
| 10:  2.2824 -  2.2039 0.98   1270  140 0.1108 0.1466      4.9448      5.0982|
| 11:  2.2039 -  2.1352 0.99   1279  142 0.1119 0.1792      4.9227      5.2805|
| 12:  2.1352 -  2.0743 0.97   1263  140 0.1124 0.1569      4.8717      5.1499|
| 13:  2.0743 -  2.0198 0.99   1259  139 0.1112 0.1668      4.7717      4.9973|
| 14:  2.0198 -  1.9707 0.58    752   85 0.1031 0.1761      4.6627      4.9577|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8490 -  4.7025  1398   153  0.94   8.92   0.98     0.96       6914.64|
|  2:  4.7025 -  3.7523  1334   154  0.95   7.80   1.02     1.01       8860.90|
|  3:  3.7523 -  3.2838  1322   144  0.94  11.09   1.03     1.02      10176.88|
|  4:  3.2838 -  2.9863  1305   139  0.92  13.07   1.01     1.00       9940.01|
|  5:  2.9863 -  2.7737  1306   148  0.90  15.57   1.00     0.97       8071.57|
|  6:  2.7737 -  2.6111  1285   148  0.90  15.92   0.98     0.96       6879.68|
|  7:  2.6111 -  2.4810  1286   145  0.91  15.40   0.99     0.94       5971.90|
|  8:  2.4810 -  2.3734  1298   135  0.91  14.55   1.00     0.98       5101.51|
|  9:  2.3734 -  2.2824  1273   147  0.91  15.15   1.01     0.99       4875.92|
| 10:  2.2824 -  2.2039  1270   140  0.90  15.55   1.01     0.97       4242.00|
| 11:  2.2039 -  2.1352  1279   142  0.90  15.90   1.00     0.97       4256.79|
| 12:  2.1352 -  2.0743  1263   140  0.91  15.12   1.02     1.02       3841.73|
| 13:  2.0743 -  2.0198  1259   139  0.91  15.45   1.01     0.99       3182.12|
| 14:  2.0198 -  1.9707   752    85  0.92  14.18   0.99     0.96       2483.96|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2483.96 max =        10176.88 mean =      6203.14|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.97 mean =        13.76|
|phase err.(test): min =        0.00 max =           87.84 mean =        13.34|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.684)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.47    87.97   14.88    None  None   None       |
|    all(noH): 2823   0      3.47    87.97   14.88    None  None   None       |
|    Sol.    : 438    0      4.49    76.84   36.85    None  None   None       |
|    Mac.    : 2385   0      3.47    87.97   10.85    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.473 -  11.923: 1798   |   5:    45.722 -  54.172:   79        |
|      1:    11.923 -  20.373:  493   |   6:    54.172 -  62.622:   45        |
|      2:    20.373 -  28.822:  141   |   7:    62.622 -  71.071:   20        |
|      3:    28.822 -  37.272:  123   |   8:    71.071 -  79.521:    8        |
|      4:    37.272 -  45.722:  113   |   9:    79.521 -  87.971:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 300         
Filter by distance & map next to the model:
   mapped sites are within: 0.289 - 5.532
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 293 from: 300
   mapped sites are within: 0.707 - 5.532

peak=   11.684 closest distance to " CB  VAL A 230 " =    1.466
peak=    9.753 closest distance to " CG2 VAL A 296 " =    1.413
peak=    6.785 closest distance to " CG  LEU A   5 " =    1.244
peak=    5.715 closest distance to " NE2 GLN A  11 " =    1.184
peak=    5.566 closest distance to " O   HOH Z 142 " =    1.838
peak=    5.556 closest distance to " CG  PRO A  54 " =    1.329
peak=    5.433 closest distance to " CG  LEU A 228 " =    1.200
peak=    5.394 closest distance to " CD2 LEU A   5 " =    1.153
peak=    5.373 closest distance to " CB  ARG A 275 " =    0.934
peak=    5.090 closest distance to " NH2 ARG A  56 " =    2.105
peak=    5.034 closest distance to " CB  PRO A  54 " =    1.008
peak=    4.937 closest distance to " O   HOH Z 209 " =    2.266
peak=    4.849 closest distance to " CB  GLN A 223 " =    1.507
peak=    4.837 closest distance to " O   HOH Z 346 " =    1.611
peak=    4.789 closest distance to " CB  GLN A 183 " =    1.243
peak=    4.655 closest distance to " CG  PRO A 213 " =    1.241
peak=    4.600 closest distance to " ND2 ASN A 187 " =    1.551
peak=    4.581 closest distance to " O   HOH Z 272 " =    1.847
peak=    4.574 closest distance to " O   HOH Z 232 " =    2.352
peak=    4.529 closest distance to " O   HOH Z 193 " =    1.718
peak=    4.504 closest distance to " C   PRO A 198 " =    1.467
peak=    4.490 closest distance to " O   HOH Z 427 " =    2.958
peak=    4.458 closest distance to " CG  PRO A 243 " =    1.111
peak=    4.456 closest distance to " O   HOH Z 126 " =    1.905
peak=    4.456 closest distance to " CB  ARG A  79 " =    1.399
peak=    4.421 closest distance to " OG  SER A  97 " =    2.926
peak=    4.395 closest distance to " O   SER A  87 " =    2.222
peak=    4.358 closest distance to " CB  SER A  63 " =    1.246
peak=    4.349 closest distance to " O   HOH Z  85 " =    1.432
peak=    4.348 closest distance to " CB  VAL A 230 " =    1.184
peak=    4.321 closest distance to " O   HOH Z 236 " =    2.002
peak=    4.304 closest distance to " O   HOH Z 402 " =    1.429
peak=    4.302 closest distance to " CG  PRO A 198 " =    1.241
peak=    4.273 closest distance to " O   HOH Z  61 " =    1.656
peak=    4.256 closest distance to " OG ASER A 258 " =    3.040
peak=    4.234 closest distance to " CB  VAL A 265 " =    1.289
peak=    4.228 closest distance to " CB  ASN A 148 " =    1.376
peak=    4.224 closest distance to " CB  GLU A 152 " =    1.156
peak=    4.196 closest distance to " O   HOH Z 369 " =    2.195
peak=    4.168 closest distance to " O   HOH Z  78 " =    1.690
peak=    4.129 closest distance to " O   HOH Z 423 " =    1.846
peak=    4.124 closest distance to " O   HOH Z 234 " =    3.572
peak=    4.100 closest distance to " CB  TRP A 266 " =    1.024
peak=    4.068 closest distance to " CB  ASN A  39 " =    0.906
peak=    4.066 closest distance to " O   HOH Z  43 " =    2.049
peak=    4.065 closest distance to " CZ  PHE A 218 " =    1.102
peak=    4.034 closest distance to " CB  VAL A 296 " =    1.029
peak=    4.026 closest distance to " CB  ALA A   9 " =    1.606
peak=    4.016 closest distance to " O   HOH Z  97 " =    2.404
peak=    4.015 closest distance to " O   HOH Z 313 " =    1.906
peak=    4.014 closest distance to " CD2 TRP A 179 " =    1.382
peak=    4.013 closest distance to " O   HOH Z 298 " =    1.708
peak=    4.007 closest distance to " O   HOH Z 250 " =    1.371
peak=    3.999 closest distance to " O   HOH Z 411 " =    3.791
peak=    3.985 closest distance to " CB  SER A   3 " =    1.248
peak=    3.982 closest distance to " O   HOH Z 265 " =    2.334
peak=    3.979 closest distance to " CG1BVAL A  72 " =    1.546
peak=    3.925 closest distance to " O   HOH Z 126 " =    1.926
peak=    3.913 closest distance to " O   HOH Z  97 " =    2.009
peak=    3.913 closest distance to " O   HOH Z  15 " =    2.152
peak=    3.912 closest distance to " O   HOH Z 126 " =    1.697
peak=    3.892 closest distance to " N   ASN A  39 " =    1.144
peak=    3.888 closest distance to " CB  VAL A 202 " =    1.568
peak=    3.882 closest distance to " O   HOH Z 368 " =    2.085
peak=    3.881 closest distance to " CB  SER A  26 " =    1.719
peak=    3.881 closest distance to " O   HOH Z 403 " =    1.686
peak=    3.880 closest distance to " CB  ASN A 187 " =    1.162
peak=    3.877 closest distance to " CB AVAL A  41 " =    1.266
peak=    3.872 closest distance to " O   HOH Z 303 " =    2.083
peak=    3.855 closest distance to " CD2 LEU A 228 " =    1.236
peak=    3.853 closest distance to " O   HOH Z  59 " =    1.824
peak=    3.850 closest distance to " O   HOH Z 203 " =    1.553
peak=    3.828 closest distance to " CA  ASN A 215 " =    1.023
peak=    3.816 closest distance to " O   HOH Z 158 " =    3.158
peak=    3.812 closest distance to " CG  MET A 185 " =    1.157
peak=    3.812 closest distance to " O   HOH Z 124 " =    1.343
peak=    3.810 closest distance to " O   HOH Z 371 " =    2.920
peak=    3.804 closest distance to " O   HOH Z 130 " =    2.686
peak=    3.797 closest distance to " O   HOH Z 273 " =    2.792
peak=    3.791 closest distance to " O   HOH Z 128 " =    2.092
peak=    3.788 closest distance to " N   PHE A 130 " =    1.258
peak=    3.787 closest distance to " OG BSER A 164 " =    2.174
peak=    3.743 closest distance to " CA  PHE A 283 " =    1.152
peak=    3.743 closest distance to " CB  GLU A 277 " =    3.531
peak=    3.740 closest distance to " CG2 VAL A 257 " =    0.845
peak=    3.740 closest distance to " O   HOH Z  44 " =    1.709
peak=    3.736 closest distance to " OD1 ASN A  69 " =    2.574
peak=    3.736 closest distance to " O   HOH Z 261 " =    1.750
peak=    3.730 closest distance to " O   HOH Z  68 " =    2.101
peak=    3.725 closest distance to " O   HOH Z 145 " =    2.162
peak=    3.722 closest distance to " O   HOH Z 248 " =    1.503
peak=    3.721 closest distance to " O   HOH Z 425 " =    1.352
peak=    3.719 closest distance to " CB  THR A  31 " =    1.507
peak=    3.716 closest distance to " CG  LEU A 167 " =    1.216
peak=    3.715 closest distance to " CB  ASN A 142 " =    1.066
peak=    3.705 closest distance to " CB  ASN A 110 " =    1.073
peak=    3.688 closest distance to " O   HOH Z 280 " =    2.980
peak=    3.686 closest distance to " CB  TRP A 179 " =    1.312
peak=    3.682 closest distance to " CB  ALA A 248 " =    1.386
peak=    3.680 closest distance to " O   HOH Z 435 " =    1.960
peak=    3.679 closest distance to " NZ  LYS A 117 " =    2.939
peak=    3.677 closest distance to " CG2 ILE A 120 " =    1.219
peak=    3.662 closest distance to " CA  TYR A  30 " =    0.945
peak=    3.658 closest distance to " O   HOH Z 126 " =    1.492
peak=    3.653 closest distance to " O   HOH Z 128 " =    2.087
peak=    3.646 closest distance to " O  BHOH Z 338 " =    2.399
peak=    3.644 closest distance to " CB  GLU A 128 " =    0.942
peak=    3.643 closest distance to " CD  LYS A 166 " =    1.250
peak=    3.642 closest distance to " CB  GLN A  88 " =    1.151
peak=    3.637 closest distance to " CB  ARG A 190 " =    1.674
peak=    3.628 closest distance to " O   HOH Z 337 " =    3.413
peak=    3.621 closest distance to " O   HOH Z 329 " =    3.957
peak=    3.616 closest distance to " O   HOH Z 180 " =    2.123
peak=    3.614 closest distance to " CB  ARG A 139 " =    0.920
peak=    3.611 closest distance to " O   HOH Z  40 " =    1.430
peak=    3.589 closest distance to " O   HOH Z 130 " =    2.096
peak=    3.589 closest distance to " O   HOH Z 261 " =    1.949
peak=    3.575 closest distance to " O   HOH Z 366 " =    2.871
peak=    3.574 closest distance to " O   HOH Z  10 " =    1.798
peak=    3.566 closest distance to " O   HOH Z   3 " =    1.919
peak=    3.561 closest distance to " O   HOH Z 322 " =    2.152
peak=    3.560 closest distance to " CD  ARG A 269 " =    1.068
peak=    3.555 closest distance to " O   HOH Z 389 " =    1.737
peak=    3.554 closest distance to " O   HOH Z 214 " =    2.255
peak=    3.551 closest distance to " CB  GLN A 278 " =    0.823
peak=    3.547 closest distance to " CG1 ILE A  49 " =    1.521
peak=    3.546 closest distance to " O   HOH Z  80 " =    1.612
peak=    3.535 closest distance to " O   HOH Z 257 " =    2.310
peak=    3.530 closest distance to " O   HOH Z 290 " =    1.008
peak=    3.528 closest distance to " O   HOH Z 193 " =    1.850
peak=    3.520 closest distance to " CA  ALA A  21 " =    1.105
peak=    3.519 closest distance to " O   HOH Z 425 " =    2.078
peak=    3.515 closest distance to " CB  GLU A  46 " =    1.065
peak=    3.514 closest distance to " CA  VAL A  41 " =    0.752
peak=    3.514 closest distance to " NZ  LYS A  48 " =    1.173
peak=    3.513 closest distance to " O   HOH Z 353 " =    2.536
peak=    3.508 closest distance to " O   HOH Z 227 " =    2.137
peak=    3.507 closest distance to " CG2 ILE A  20 " =    1.496
peak=    3.506 closest distance to " CE  LYS A  76 " =    0.881
peak=    3.506 closest distance to " O   HOH Z 344 " =    2.829
peak=    3.501 closest distance to " O   HOH Z 392 " =    2.954
peak=    3.500 closest distance to " O   HOH Z 407 " =    2.429
peak=    3.489 closest distance to " OD2 ASP A 286 " =    2.679
peak=    3.486 closest distance to " CB  ASP A 140 " =    0.953
peak=    3.469 closest distance to " CG AARG A 275 " =    1.151
peak=    3.468 closest distance to " O   HOH Z 417 " =    3.389
peak=    3.461 closest distance to " O   HOH Z 299 " =    4.105
peak=    3.460 closest distance to " O   HOH Z  54 " =    1.598
peak=    3.458 closest distance to " CA  ASP A 162 " =    0.989
peak=    3.457 closest distance to " O   HOH Z  88 " =    2.664
peak=    3.457 closest distance to " CA  ALA A  51 " =    0.959
peak=    3.453 closest distance to " O   HOH Z 422 " =    2.534
peak=    3.452 closest distance to " O   HOH Z 234 " =    1.915
peak=    3.445 closest distance to " O   HOH Z 419 " =    1.894
peak=    3.443 closest distance to " O   HOH Z 164 " =    2.060
peak=    3.433 closest distance to " O   HOH Z 147 " =    1.755
peak=    3.429 closest distance to " O   ASN A  74 " =    1.584
peak=    3.422 closest distance to " CE1 TYR A 186 " =    1.314
peak=    3.419 closest distance to " CA  LYS A 117 " =    1.248
peak=    3.418 closest distance to " CB  ALA A 291 " =    1.258
peak=    3.418 closest distance to " CD2 LEU A 297 " =    1.008
peak=    3.417 closest distance to " O   HOH Z 327 " =    1.484
peak=    3.415 closest distance to " O   HOH Z 148 " =    3.411
peak=    3.413 closest distance to " CE1 HIS A 108 " =    1.141
peak=    3.412 closest distance to " O   HOH Z  21 " =    1.737
peak=    3.408 closest distance to " CB  LEU A 143 " =    1.143
peak=    3.408 closest distance to " CA  ARG A  36 " =    1.020
peak=    3.404 closest distance to " CB  SER A 273 " =    0.885
peak=    3.404 closest distance to " O   ASP A 124 " =    1.165
peak=    3.396 closest distance to " N   ARG A 156 " =    1.308
peak=    3.395 closest distance to " CG1 VAL A 153 " =    0.919
peak=    3.386 closest distance to " O   HOH Z 251 " =    1.455
peak=    3.378 closest distance to " NE2 GLN A  77 " =    3.164
peak=    3.377 closest distance to " CB  LYS A 290 " =    0.982
peak=    3.367 closest distance to " CG  LYS A 119 " =    1.087
peak=    3.365 closest distance to " O   HOH Z 380 " =    1.986
peak=    3.363 closest distance to " CB  HIS A 108 " =    0.827
peak=    3.362 closest distance to " OE1 GLU A   2 " =    2.066
peak=    3.361 closest distance to " O   HOH Z  89 " =    2.309
peak=    3.360 closest distance to " CB  PRO A  90 " =    1.134
peak=    3.357 closest distance to " CD1 LEU A 261 " =    1.183
peak=    3.354 closest distance to " CA  ALA A 233 " =    1.120
peak=    3.349 closest distance to " O   HOH Z  19 " =    2.374
peak=    3.346 closest distance to " CG2 THR A 294 " =    1.623
peak=    3.344 closest distance to " N   SER A 135 " =    1.283
peak=    3.340 closest distance to " O   HOH Z 357 " =    1.837
peak=    3.335 closest distance to " O   HOH Z 368 " =    3.618
peak=    3.334 closest distance to " CA  THR A 264 " =    0.801
peak=    3.334 closest distance to " O   LEU A 228 " =    1.793
peak=    3.332 closest distance to " CA  PHE A  59 " =    0.961
peak=    3.330 closest distance to " CA  ASN A 127 " =    1.049
peak=    3.321 closest distance to " CB  SER A  62 " =    1.337
peak=    3.321 closest distance to " CB  SER A 212 " =    1.250
peak=    3.319 closest distance to " O   HOH Z  78 " =    2.161
peak=    3.317 closest distance to " O   HOH Z 286 " =    2.368
peak=    3.316 closest distance to " CG1 ILE A  33 " =    1.362
peak=    3.315 closest distance to " O   HOH Z 128 " =    2.020
peak=    3.309 closest distance to " N   ASP A 162 " =    1.238
peak=    3.307 closest distance to " O   HOH Z 109 " =    2.454
peak=    3.305 closest distance to " CB  TRP A 150 " =    1.402
peak=    3.298 closest distance to " CA  ALA A 158 " =    1.349
peak=    3.298 closest distance to " O   HOH Z 302 " =    1.907
peak=    3.295 closest distance to " NH1AARG A 145 " =    1.121
peak=    3.294 closest distance to " O   HOH Z 132 " =    2.530
peak=    3.294 closest distance to " O   ASN A  74 " =    2.030
peak=    3.293 closest distance to " CD2 TYR A 186 " =    1.034
peak=    3.288 closest distance to " O   HOH Z 251 " =    1.692
peak=    3.288 closest distance to " O   HOH Z 345 " =    3.211
peak=    3.281 closest distance to " ND2 ASN A 249 " =    0.928
peak=    3.280 closest distance to " O   LYS A 290 " =    2.391
peak=    3.279 closest distance to " O   GLY A  91 " =    1.497
peak=    3.277 closest distance to " CA  SER A  87 " =    0.985
peak=    3.276 closest distance to " O   HOH Z 352 " =    1.327
peak=    3.274 closest distance to " O   HOH Z  88 " =    2.578
peak=    3.268 closest distance to " OE2 GLU A  53 " =    1.950
peak=    3.266 closest distance to " CD1 ILE A  33 " =    1.666
peak=    3.266 closest distance to " CB  PHE A 204 " =    0.846
peak=    3.265 closest distance to " CA  SER A 146 " =    1.804
peak=    3.262 closest distance to " O   HOH Z 426 " =    1.771
peak=    3.262 closest distance to " CB  THR A 157 " =    1.145
peak=    3.261 closest distance to " CB  ASN A 215 " =    1.137
peak=    3.250 closest distance to " O   HOH Z 437 " =    1.806
peak=    3.248 closest distance to " O   HOH Z   1 " =    1.830
peak=    3.245 closest distance to " O   HOH Z 421 " =    1.714
peak=    3.245 closest distance to " O   HOH Z 172 " =    3.520
peak=    3.244 closest distance to " CD BLYS A 290 " =    1.177
peak=    3.244 closest distance to " C   ALA A 299 " =    0.921
peak=    3.243 closest distance to " CB  GLN A 205 " =    1.148
peak=    3.236 closest distance to " CG  GLN A  88 " =    1.061
peak=    3.228 closest distance to " O   TRP A 274 " =    1.837
peak=    3.226 closest distance to " O   HOH Z 336 " =    1.738
peak=    3.225 closest distance to " OG ASER A  99 " =    1.517
peak=    3.223 closest distance to " CA  LYS A 290 " =    1.209
peak=    3.220 closest distance to " O   GLN A 278 " =    1.232
peak=    3.219 closest distance to " O   ALA A   1 " =    1.738
peak=    3.217 closest distance to " O   HOH Z  30 " =    1.405
peak=    3.217 closest distance to " CB  ALA A 114 " =    1.291
peak=    3.206 closest distance to " CA  ASP A 140 " =    1.199
peak=    3.199 closest distance to " O   HOH Z 245 " =    1.401
peak=    3.199 closest distance to " O   HOH Z 424 " =    1.399
peak=    3.196 closest distance to " OG  SER A  62 " =    2.826
peak=    3.195 closest distance to " O   HOH Z 359 " =    3.761
peak=    3.194 closest distance to " O   HOH Z  61 " =    1.541
peak=    3.193 closest distance to " O   HOH Z 263 " =    1.652
peak=    3.191 closest distance to " CG1 ILE A 120 " =    1.131
peak=    3.188 closest distance to " CG BARG A 102 " =    1.724
peak=    3.187 closest distance to " CA  ASN A 217 " =    1.250
peak=    3.187 closest distance to " CB  ILE A  20 " =    1.467
peak=    3.186 closest distance to " CB  ARG A 219 " =    0.989
peak=    3.184 closest distance to " O   HOH Z 141 " =    1.602
peak=    3.184 closest distance to " CB  SER A 216 " =    0.714
peak=    3.183 closest distance to " CD1 ILE A 106 " =    1.167
peak=    3.179 closest distance to " CA  GLN A 194 " =    1.206
peak=    3.179 closest distance to " CA  ILE A 106 " =    0.747
peak=    3.178 closest distance to " CD  LYS A 119 " =    1.708
peak=    3.177 closest distance to " CG2 VAL A 197 " =    1.046
peak=    3.170 closest distance to " CB  ALA A 242 " =    0.842
peak=    3.167 closest distance to " CA  ASP A 191 " =    1.088
peak=    3.165 closest distance to " CG  LEU A 281 " =    1.054
peak=    3.164 closest distance to " O   HOH Z  94 " =    2.033
peak=    3.155 closest distance to " NH1 ARG A  66 " =    1.568
peak=    3.151 closest distance to " CG  LYS A  76 " =    0.902
peak=    3.149 closest distance to " CG2 THR A  18 " =    1.672
peak=    3.144 closest distance to " O   HOH Z 188 " =    2.396
peak=    3.141 closest distance to " O   HOH Z   9 " =    1.790
peak=    3.139 closest distance to " CG  MET A 185 " =    1.039
peak=    3.135 closest distance to " CG1 ILE A 151 " =    1.123
peak=    3.132 closest distance to " NH1 ARG A  14 " =    1.143
peak=    3.129 closest distance to " CG2 VAL A 202 " =    1.128
peak=    3.127 closest distance to " CA  GLY A 267 " =    0.911
peak=    3.126 closest distance to " CG  GLN A  77 " =    2.309
peak=    3.124 closest distance to " CA  ILE A 234 " =    0.887
peak=    3.111 closest distance to " CA  MET A 105 " =    0.948
peak=    3.110 closest distance to " O   SER A 164 " =    1.264
peak=    3.110 closest distance to " O   HOH Z  47 " =    1.739
peak=    3.105 closest distance to " CA  ARG A 102 " =    1.109
peak=    3.101 closest distance to " O   HOH Z 305 " =    3.612
peak=    3.098 closest distance to " O   HOH Z 294 " =    1.494
peak=    3.096 closest distance to " O   HOH Z 282 " =    1.986
peak=    3.094 closest distance to " O   HOH Z 213 " =    2.162
peak=    3.090 closest distance to " O   HOH Z 430 " =    5.532
peak=    3.086 closest distance to " CA  ALA A 291 " =    0.832
peak=    3.075 closest distance to " CD1 LEU A  96 " =    0.707
peak=    3.065 closest distance to " CB  ILE A 120 " =    1.325
peak=    3.058 closest distance to " O   HOH Z 423 " =    2.887
peak=    3.054 closest distance to " OG BSER A 134 " =    3.078
peak=    3.052 closest distance to " NZ  LYS A  48 " =    2.262
peak=    3.050 closest distance to " O   HOH Z 409 " =    3.212
peak=    3.050 closest distance to " O   HOH Z 222 " =    2.419
peak=    3.038 closest distance to " O   HOH Z 183 " =    1.731
peak=    3.030 closest distance to " CB  LEU A 300 " =    0.917
peak=    3.013 closest distance to " O   HOH Z 124 " =    1.966
peak=    3.007 closest distance to " O   HOH Z 238 " =    3.770

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 196         
Filter by distance & map next to the model:
   mapped sites are within: 0.516 - 5.466
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 193 from: 196
   mapped sites are within: 0.735 - 5.466

peak=   -4.581 closest distance to " CD  ARG A  14 " =    3.317
peak=   -4.518 closest distance to " OG BSER A 134 " =    1.158
peak=   -4.455 closest distance to " CD  ARG A 156 " =    2.041
peak=   -4.362 closest distance to " CG  GLN A 223 " =    2.020
peak=   -4.303 closest distance to " C   HIS A 108 " =    1.227
peak=   -4.206 closest distance to " CG  GLN A  58 " =    1.087
peak=   -4.154 closest distance to " O   HOH Z 266 " =    5.180
peak=   -4.152 closest distance to " O   VAL A  67 " =    2.509
peak=   -4.145 closest distance to " CB  PHE A 192 " =    1.958
peak=   -4.141 closest distance to " CB  PRO A 243 " =    2.708
peak=   -4.101 closest distance to " O   HOH Z 351 " =    1.472
peak=   -4.079 closest distance to " O   HOH Z 290 " =    1.172
peak=   -4.060 closest distance to " CG2 VAL A 296 " =    1.905
peak=   -4.034 closest distance to " CD1 LEU A 255 " =    2.794
peak=   -3.990 closest distance to " O   HOH Z 429 " =    1.989
peak=   -3.970 closest distance to " O   HOH Z 166 " =    1.988
peak=   -3.966 closest distance to " CE  MET A 105 " =    2.355
peak=   -3.963 closest distance to " CG2 ILE A  20 " =    2.903
peak=   -3.932 closest distance to " ND2 ASN A  45 " =    1.120
peak=   -3.912 closest distance to " CB  ALA A 248 " =    2.330
peak=   -3.907 closest distance to " O   PRO A 163 " =    2.051
peak=   -3.901 closest distance to " CB  ALA A  43 " =    2.361
peak=   -3.901 closest distance to " ND2 ASN A 187 " =    1.527
peak=   -3.895 closest distance to " O   HOH Z 231 " =    2.139
peak=   -3.894 closest distance to " O   PRO A 198 " =    1.132
peak=   -3.892 closest distance to " O   HOH Z 114 " =    3.084
peak=   -3.854 closest distance to " OXT GLY A 302 " =    2.765
peak=   -3.845 closest distance to " O   HOH Z 394 " =    1.443
peak=   -3.843 closest distance to " O   HOH Z 211 " =    1.571
peak=   -3.829 closest distance to " CG  ASP A 231 " =    0.783
peak=   -3.793 closest distance to " N   GLN A  58 " =    1.970
peak=   -3.779 closest distance to " CB  PRO A 163 " =    2.507
peak=   -3.771 closest distance to " OD2 ASP A 171 " =    2.254
peak=   -3.768 closest distance to " CB  ALA A 161 " =    2.450
peak=   -3.763 closest distance to " CG2 VAL A 296 " =    0.735
peak=   -3.736 closest distance to " CE2 TYR A  30 " =    2.749
peak=   -3.711 closest distance to " O   HOH Z  11 " =    1.873
peak=   -3.706 closest distance to " O   ALA A 161 " =    1.747
peak=   -3.704 closest distance to " CG1 VAL A 112 " =    2.889
peak=   -3.684 closest distance to " O   HOH Z 185 " =    2.418
peak=   -3.681 closest distance to " N   HIS A 115 " =    2.133
peak=   -3.678 closest distance to " C   ILE A 239 " =    2.085
peak=   -3.671 closest distance to " CD1 LEU A 101 " =    2.308
peak=   -3.665 closest distance to " O   HOH Z 389 " =    2.021
peak=   -3.652 closest distance to " CE2 PHE A 218 " =    2.558
peak=   -3.643 closest distance to " CZ3 TRP A 179 " =    1.264
peak=   -3.642 closest distance to " NE2 GLN A  88 " =    1.888
peak=   -3.638 closest distance to " N   THR A 157 " =    1.486
peak=   -3.633 closest distance to " N   ALA A 248 " =    1.618
peak=   -3.627 closest distance to " C   ASP A 231 " =    2.390
peak=   -3.604 closest distance to " CB  ASP A 132 " =    2.391
peak=   -3.599 closest distance to " N   ALA A 226 " =    1.997
peak=   -3.596 closest distance to " CG  TRP A 266 " =    1.929
peak=   -3.580 closest distance to " CG2 THR A 178 " =    2.264
peak=   -3.564 closest distance to " O   SER A 210 " =    1.987
peak=   -3.561 closest distance to " CG1 VAL A 230 " =    1.893
peak=   -3.557 closest distance to " CG  LEU A 228 " =    0.959
peak=   -3.554 closest distance to " CG  PHE A 283 " =    2.642
peak=   -3.542 closest distance to " O   HOH Z 196 " =    2.224
peak=   -3.538 closest distance to " CG  LEU A   5 " =    0.879
peak=   -3.538 closest distance to " CG2 ILE A 263 " =    2.260
peak=   -3.517 closest distance to " C   MET A 188 " =    1.526
peak=   -3.516 closest distance to " CB  ALA A 291 " =    2.247
peak=   -3.497 closest distance to " O   HOH Z  13 " =    1.745
peak=   -3.494 closest distance to " CD  LYS A 289 " =    2.463
peak=   -3.493 closest distance to " NH2 ARG A  79 " =    1.954
peak=   -3.488 closest distance to " O   HOH Z 166 " =    1.530
peak=   -3.486 closest distance to " O   HOH Z 313 " =    1.705
peak=   -3.477 closest distance to " O   SER A  22 " =    2.313
peak=   -3.468 closest distance to " CG1 VAL A 197 " =    2.244
peak=   -3.465 closest distance to " CZ  TYR A 169 " =    1.779
peak=   -3.464 closest distance to " O   HOH Z 423 " =    2.106
peak=   -3.462 closest distance to " O   HOH Z 102 " =    1.724
peak=   -3.458 closest distance to " NH2AARG A 275 " =    4.970
peak=   -3.449 closest distance to " CZ  PHE A  59 " =    1.442
peak=   -3.449 closest distance to " O   HOH Z 139 " =    3.220
peak=   -3.426 closest distance to " OG  SER A   3 " =    1.544
peak=   -3.426 closest distance to " O   HOH Z 103 " =    1.864
peak=   -3.424 closest distance to " O   ALA A  51 " =    1.339
peak=   -3.418 closest distance to " ND2 ASN A 249 " =    2.415
peak=   -3.416 closest distance to " O   HOH Z 198 " =    2.027
peak=   -3.409 closest distance to " CB  ASP A 132 " =    2.291
peak=   -3.408 closest distance to " O   HOH Z  63 " =    1.445
peak=   -3.407 closest distance to " CA  ASP A 298 " =    1.117
peak=   -3.404 closest distance to " O   HOH Z 243 " =    1.885
peak=   -3.401 closest distance to " CG1 VAL A 250 " =    2.734
peak=   -3.401 closest distance to " O   HOH Z 191 " =    5.466
peak=   -3.399 closest distance to " O   HOH Z 407 " =    2.917
peak=   -3.399 closest distance to " CD2 TYR A 293 " =    2.067
peak=   -3.396 closest distance to " CA  GLY A  98 " =    1.818
peak=   -3.392 closest distance to " CE BMET A  47 " =    1.477
peak=   -3.391 closest distance to " ND2 ASN A  39 " =    1.165
peak=   -3.389 closest distance to " NE2 GLN A 278 " =    1.863
peak=   -3.388 closest distance to " CB  ALA A 291 " =    2.169
peak=   -3.388 closest distance to " CD  PRO A 243 " =    2.133
peak=   -3.383 closest distance to " O   HOH Z 265 " =    1.773
peak=   -3.381 closest distance to " O   PRO A 198 " =    1.279
peak=   -3.381 closest distance to " NE2 GLN A  88 " =    1.119
peak=   -3.376 closest distance to " O   PHE A 218 " =    1.646
peak=   -3.358 closest distance to " CA  GLY A 133 " =    1.907
peak=   -3.358 closest distance to " O   ALA A   8 " =    1.940
peak=   -3.348 closest distance to " O   GLY A 196 " =    1.237
peak=   -3.344 closest distance to " O   ILE A 106 " =    2.089
peak=   -3.342 closest distance to " OD1 ASN A 301 " =    2.074
peak=   -3.339 closest distance to " O   HOH Z 295 " =    1.528
peak=   -3.339 closest distance to " O   SER A  95 " =    1.523
peak=   -3.314 closest distance to " CB  SER A 210 " =    1.163
peak=   -3.308 closest distance to " CG1 VAL A 112 " =    2.701
peak=   -3.305 closest distance to " OD1 ASN A  39 " =    2.194
peak=   -3.303 closest distance to " N   THR A  52 " =    1.684
peak=   -3.299 closest distance to " C   GLN A 205 " =    1.916
peak=   -3.296 closest distance to " OH  TYR A 172 " =    1.807
peak=   -3.295 closest distance to " OH  TYR A 247 " =    2.043
peak=   -3.294 closest distance to " O   HOH Z 421 " =    3.093
peak=   -3.285 closest distance to " CA  ASN A 127 " =    1.261
peak=   -3.284 closest distance to " OD2 ASP A 191 " =    1.345
peak=   -3.280 closest distance to " CA  GLY A 241 " =    2.337
peak=   -3.280 closest distance to " O   MET A  40 " =    2.747
peak=   -3.279 closest distance to " O   HOH Z 131 " =    4.110
peak=   -3.279 closest distance to " OG  SER A  97 " =    2.270
peak=   -3.278 closest distance to " CB  ASN A  69 " =    1.176
peak=   -3.274 closest distance to " CB  ASN A  39 " =    2.231
peak=   -3.271 closest distance to " O   HOH Z 165 " =    1.993
peak=   -3.270 closest distance to " OG  SER A  63 " =    1.079
peak=   -3.269 closest distance to " OD1 ASN A 148 " =    1.439
peak=   -3.268 closest distance to " O   HOH Z 100 " =    1.127
peak=   -3.267 closest distance to " O   HOH Z 256 " =    1.353
peak=   -3.263 closest distance to " O   SER A 271 " =    2.155
peak=   -3.261 closest distance to " CA  PRO A 243 " =    2.255
peak=   -3.260 closest distance to " O   HOH Z 372 " =    2.331
peak=   -3.257 closest distance to " O   HOH Z 174 " =    4.209
peak=   -3.253 closest distance to " CD  ARG A 139 " =    1.616
peak=   -3.245 closest distance to " N   ALA A  43 " =    2.629
peak=   -3.244 closest distance to " O   HOH Z 359 " =    3.271
peak=   -3.235 closest distance to " O   VAL A 189 " =    2.596
peak=   -3.231 closest distance to " CA  GLY A 241 " =    3.071
peak=   -3.230 closest distance to " N   ALA A 248 " =    2.228
peak=   -3.228 closest distance to " CD2 LEU A 300 " =    2.863
peak=   -3.228 closest distance to " CE3 TRP A 150 " =    1.980
peak=   -3.221 closest distance to " C   VAL A 265 " =    0.830
peak=   -3.217 closest distance to " CZ  ARG A 259 " =    0.846
peak=   -3.215 closest distance to " CD  PRO A 213 " =    2.088
peak=   -3.215 closest distance to " CD1 ILE A 239 " =    2.295
peak=   -3.209 closest distance to " O   HOH Z  38 " =    1.797
peak=   -3.207 closest distance to " ND2 ASN A 252 " =    1.811
peak=   -3.204 closest distance to " CD1 LEU A 228 " =    2.067
peak=   -3.203 closest distance to " O   HOH Z 134 " =    3.204
peak=   -3.198 closest distance to " CD1 PHE A  59 " =    1.919
peak=   -3.196 closest distance to " CB  ALA A  51 " =    1.932
peak=   -3.189 closest distance to " C   LEU A 222 " =    0.810
peak=   -3.187 closest distance to " N   GLN A  77 " =    1.685
peak=   -3.184 closest distance to " C   LEU A 143 " =    1.071
peak=   -3.182 closest distance to " O   HOH Z 427 " =    1.476
peak=   -3.172 closest distance to " O   HOH Z  47 " =    1.630
peak=   -3.172 closest distance to " CD1 ILE A 199 " =    2.431
peak=   -3.160 closest distance to " O   HOH Z 193 " =    1.699
peak=   -3.150 closest distance to " O   HOH Z 281 " =    2.791
peak=   -3.150 closest distance to " O   ALA A   1 " =    1.657
peak=   -3.147 closest distance to " OE1 GLN A  88 " =    1.055
peak=   -3.147 closest distance to " OG BSER A 134 " =    1.753
peak=   -3.143 closest distance to " OG  SER A 206 " =    1.530
peak=   -3.142 closest distance to " O   HOH Z 369 " =    2.306
peak=   -3.142 closest distance to " CB  TRP A  85 " =    2.638
peak=   -3.140 closest distance to " N   MET A 188 " =    1.865
peak=   -3.139 closest distance to " O   HOH Z 216 " =    1.548
peak=   -3.137 closest distance to " OG  SER A  62 " =    1.521
peak=   -3.133 closest distance to " O   HOH Z 210 " =    1.115
peak=   -3.127 closest distance to " O   HOH Z 149 " =    2.203
peak=   -3.126 closest distance to " N   ASP A 286 " =    2.194
peak=   -3.126 closest distance to " O   GLY A  17 " =    1.264
peak=   -3.119 closest distance to " O   HOH Z 389 " =    1.502
peak=   -3.117 closest distance to " ND2 ASN A  60 " =    1.345
peak=   -3.115 closest distance to " CZ2 TRP A 274 " =    1.048
peak=   -3.112 closest distance to " O   HOH Z 139 " =    5.050
peak=   -3.109 closest distance to " O   HOH Z 346 " =    1.721
peak=   -3.106 closest distance to " O   HOH Z 200 " =    4.476
peak=   -3.101 closest distance to " O   HOH Z 113 " =    2.131
peak=   -3.094 closest distance to " O   HOH Z 374 " =    1.783
peak=   -3.093 closest distance to " CG  ASP A  50 " =    2.222
peak=   -3.089 closest distance to " NH2 ARG A  79 " =    1.586
peak=   -3.088 closest distance to " O   HOH Z 250 " =    1.364
peak=   -3.088 closest distance to " O   HOH Z 371 " =    2.017
peak=   -3.084 closest distance to " CD2 LEU A 300 " =    2.828
peak=   -3.083 closest distance to " O   ARG A  24 " =    1.896
peak=   -3.071 closest distance to " O   ALA A 248 " =    1.692
peak=   -3.070 closest distance to " O   GLY A  80 " =    2.538
peak=   -3.061 closest distance to " O   HOH Z 288 " =    1.277
peak=   -3.048 closest distance to " N   ASP A 171 " =    2.217
peak=   -3.047 closest distance to " CE3 TRP A 274 " =    2.304
peak=   -3.047 closest distance to " CE  LYS A  76 " =    2.787
peak=   -3.037 closest distance to " CG  GLU A   2 " =    2.063
peak=   -3.035 closest distance to " O   HOH Z 353 " =    2.116
peak=   -3.018 closest distance to " OD1 ASN A 249 " =    2.261

================= 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    :  0.4383 0.4266   6.233732e+00   6.212088e+00
   1_bss:  0.4301 0.4164   6.224900e+00   6.197793e+00
   1_xyz:  0.3223 0.3403   6.022808e+00   6.061642e+00
   1_adp:  0.2583 0.2974   5.843218e+00   5.948706e+00
   1_occ:  0.2579 0.2970   5.841929e+00   5.949380e+00
   2_bss:  0.2541 0.2926   5.840334e+00   5.946645e+00
   2_xyz:  0.1699 0.2082   5.483576e+00   5.657251e+00
   2_adp:  0.1561 0.1990   5.409902e+00   5.600701e+00
   2_occ:  0.1559 0.1989   5.409027e+00   5.600345e+00
   3_bss:  0.1550 0.1990   5.409624e+00   5.599352e+00
   3_xyz:  0.1277 0.1705   5.246137e+00   5.462955e+00
   3_adp:  0.1188 0.1633   5.190386e+00   5.419432e+00
   3_occ:  0.1187 0.1633   5.190289e+00   5.419328e+00
   4_bss:  0.1186 0.1637   5.188744e+00   5.417332e+00
   4_xyz:  0.1100 0.1584   5.139440e+00   5.391373e+00
   4_adp:  0.1087 0.1568   5.129165e+00   5.380469e+00
   4_occ:  0.1087 0.1568   5.128941e+00   5.380185e+00
   5_bss:  0.1087 0.1567   5.128634e+00   5.379832e+00
   5_xyz:  0.1098 0.1567   5.135632e+00   5.383465e+00
   5_adp:  0.1104 0.1556   5.134324e+00   5.375731e+00
   5_occ:  0.1104 0.1556   5.133872e+00   5.375220e+00
   5_bss:  0.1104 0.1556   5.133875e+00   5.375196e+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:  0.367  20.001   7.412   7.789   8.013   0.000   0.000   0.000
   1_xyz:  0.367  20.001   7.412   7.789   8.013   0.000   0.000   0.000
   1_adp:  0.367  20.001   7.412   7.789   8.013   0.000   0.000   0.000
   1_occ:  0.367  20.001   7.412   7.789   8.013   0.000   0.000   0.000
   2_bss:  0.338  36.721   4.223   4.382   5.397   0.000   0.000   0.000
   2_xyz:  0.338  36.721   4.223   4.382   5.397   0.000   0.000   0.000
   2_adp:  0.338  36.721   4.223   4.382   5.397   0.000   0.000   0.000
   2_occ:  0.338  36.721   4.223   4.382   5.397   0.000   0.000   0.000
   3_bss:  0.338  36.721   2.798   3.343   4.561   0.000   0.000   0.000
   3_xyz:  0.338  36.721   2.798   3.343   4.561   0.000   0.000   0.000
   3_adp:  0.338  36.721   2.798   3.343   4.561   0.000   0.000   0.000
   3_occ:  0.338  36.721   2.798   3.343   4.561   0.000   0.000   0.000
   4_bss:  0.319  36.721   2.798   3.343   4.561   0.000   0.000   0.000
   4_xyz:  0.319  36.721   2.798   3.343   4.561   0.000   0.000   0.000
   4_adp:  0.319  36.721   2.798   3.343   4.561   0.000   0.000   0.000
   4_occ:  0.319  36.721   2.798   3.343   4.561   0.000   0.000   0.000
   5_bss:  0.322  40.188   2.671   3.216   4.556   0.000   0.000   0.000
   5_xyz:  0.322  40.188   2.671   3.216   4.556   0.000   0.000   0.000
   5_adp:  0.322  40.188   2.671   3.216   4.556   0.000   0.000   0.000
   5_occ:  0.322  40.188   2.671   3.216   4.556   0.000   0.000   0.000
   5_bss:  0.322  43.661  -0.841  -0.263   1.104   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  48.111 0.5459  0.6200    54511.047
   1_bss:  48.013 0.5449  0.7806    51587.084
   1_xyz:  36.527 0.6832  0.9432    31721.059
   1_adp:  29.970 0.7590  1.0311    23134.280
   1_occ:  29.980 0.7588  1.0296    23087.172
   2_bss:  29.698 0.7618  0.9241    22741.297
   2_xyz:  20.189 0.8597  1.0045    11168.346
   2_adp:  18.640 0.8749  1.0188    10005.132
   2_occ:  18.632 0.8749  1.0186     9994.221
   3_bss:  18.597 0.8754  0.9777     9990.893
   3_xyz:  15.615 0.9015  0.9896     7434.491
   3_adp:  14.817 0.9081  0.9883     6790.896
   3_occ:  14.813 0.9082  0.9881     6782.824
   4_bss:  14.794 0.9082  0.9877     6742.747
   4_xyz:  14.162 0.9136  0.9898     6375.469
   4_adp:  13.896 0.9159  0.9863     6250.007
   4_occ:  13.892 0.9159  0.9863     6244.840
   5_bss:  13.884 0.9160  0.9833     6240.616
   5_xyz:  13.904 0.9160  0.9829     6288.004
   5_adp:  13.728 0.9175  0.9817     6209.764
   5_occ:  13.720 0.9175  0.9817     6203.487
   5_bss:  13.721 0.9175  0.9814     6202.704
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3373e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3373e+01
   1_xyz:   1.539  0.011  0.101 17.780  0.006  4.119   1.1895e-01
   1_adp:   1.539  0.011  0.101 17.780  0.006  4.119   1.1895e-01
   1_occ:   1.539  0.011  0.101 17.780  0.006  4.119   1.1895e-01
   2_bss:   1.539  0.011  0.101 17.780  0.006  4.119   1.1895e-01
   2_xyz:   0.990  0.006  0.076 15.934  0.004  4.118   6.1859e-02
   2_adp:   0.990  0.006  0.076 15.934  0.004  4.118   6.1859e-02
   2_occ:   0.990  0.006  0.076 15.934  0.004  4.118   6.1859e-02
   3_bss:   0.990  0.006  0.076 15.934  0.004  4.118   6.1859e-02
   3_xyz:   0.993  0.006  0.077 15.569  0.004  4.110   6.0113e-02
   3_adp:   0.993  0.006  0.077 15.569  0.004  4.110   6.0113e-02
   3_occ:   0.993  0.006  0.077 15.569  0.004  4.110   6.0113e-02
   4_bss:   0.993  0.006  0.077 15.569  0.004  4.110   6.0113e-02
   4_xyz:   1.092  0.009  0.086 15.718  0.004  4.111   7.1628e-02
   4_adp:   1.092  0.009  0.086 15.718  0.004  4.111   7.1628e-02
   4_occ:   1.092  0.009  0.086 15.718  0.004  4.111   7.1628e-02
   5_bss:   1.092  0.009  0.086 15.718  0.004  4.111   7.1628e-02
   5_xyz:   0.976  0.007  0.078 15.377  0.004  4.111   5.9274e-02
   5_adp:   0.976  0.007  0.078 15.377  0.004  4.111   5.9274e-02
   5_occ:   0.976  0.007  0.078 15.377  0.004  4.111   5.9274e-02
   5_bss:   0.976  0.007  0.078 15.377  0.004  4.111   5.9274e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9178e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9178e+00
   1_xyz:  12.961  0.141  0.409 87.875  0.033  2.282   8.7112e-02
   1_adp:  12.961  0.141  0.409 87.875  0.033  2.282   8.7112e-02
   1_occ:  12.961  0.141  0.409 87.875  0.033  2.282   8.7112e-02
   2_bss:  12.961  0.141  0.409 87.875  0.033  2.282   8.7112e-02
   2_xyz:   6.262  0.064  0.345 88.143  0.032  2.304   4.3735e-02
   2_adp:   6.262  0.064  0.345 88.143  0.032  2.304   4.3735e-02
   2_occ:   6.262  0.064  0.345 88.143  0.032  2.304   4.3735e-02
   3_bss:   6.262  0.064  0.345 88.143  0.032  2.304   4.3735e-02
   3_xyz:   6.977  0.044  0.436 82.993  0.029  2.276   4.4478e-02
   3_adp:   6.977  0.044  0.436 82.993  0.029  2.276   4.4478e-02
   3_occ:   6.977  0.044  0.436 82.993  0.029  2.276   4.4478e-02
   4_bss:   6.977  0.044  0.436 82.993  0.029  2.276   4.4478e-02
   4_xyz:   6.790  0.052  0.511 83.219  0.037  2.302   5.7311e-02
   4_adp:   6.790  0.052  0.511 83.219  0.037  2.302   5.7311e-02
   4_occ:   6.790  0.052  0.511 83.219  0.037  2.302   5.7311e-02
   5_bss:   6.790  0.052  0.511 83.219  0.037  2.302   5.7311e-02
   5_xyz:   6.221  0.050  0.416 83.232  0.036  2.343   3.9720e-02
   5_adp:   6.221  0.050  0.416 83.232  0.036  2.343   3.9720e-02
   5_occ:   6.221  0.050  0.416 83.232  0.036  2.343   3.9720e-02
   5_bss:   6.221  0.050  0.416 83.232  0.036  2.343   3.9720e-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:  56.67   0.00  10.88  55.16   0.00   7.89  56.67   0.00  27.12
   1_occ:  56.67   0.00  10.88  55.16   0.00   7.89  56.67   0.00  27.12
   2_bss:  56.67   0.00  10.88  55.16   0.00   7.89  56.67   0.00  27.12
   2_xyz:  56.67   0.00  10.88  55.16   0.00   7.89  56.67   0.00  27.12
   2_adp:  75.34   0.00  11.00  75.34   0.00   7.67  57.39   0.11  29.12
   2_occ:  75.34   0.00  11.00  75.34   0.00   7.67  57.39   0.11  29.12
   3_bss:  75.34   0.00  11.00  75.34   0.00   7.67  57.39   0.11  29.12
   3_xyz:  75.34   0.00  11.00  75.34   0.00   7.67  57.39   0.11  29.12
   3_adp:  78.60   0.00  12.02  78.60   0.00   7.74  73.29   0.48  35.31
   3_occ:  78.60   0.00  12.02  78.60   0.00   7.74  73.29   0.48  35.31
   4_bss:  78.60   0.00  12.02  78.60   0.00   7.74  73.29   0.48  35.31
   4_xyz:  78.60   0.00  12.02  78.60   0.00   7.74  73.29   0.48  35.31
   4_adp:  84.82   0.00  11.79  84.82   0.00   7.56  75.98   0.72  34.78
   4_occ:  84.82   0.00  11.79  84.82   0.00   7.56  75.98   0.72  34.78
   5_bss:  84.82   0.00  11.79  84.82   0.00   7.56  75.98   0.72  34.78
   5_xyz:  84.82   0.00  11.79  84.82   0.00   7.56  75.98   0.72  34.78
   5_adp:  84.50   0.00  11.41  84.50   0.00   7.37  73.37   1.02  33.38
   5_occ:  84.50   0.00  11.41  84.50   0.00   7.37  73.37   1.02  33.38
   5_bss:  87.97   3.47  14.88  87.97   3.47  10.85  76.84   4.49  36.85
------------------------------------------------------------------------
 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:    1.226    0.022    0.403
   1_adp:    1.226    0.022    0.403
   1_occ:    1.226    0.022    0.403
   2_bss:    1.226    0.022    0.403
   2_xyz:    1.509    0.046    0.509
   2_adp:    1.509    0.046    0.509
   2_occ:    1.509    0.046    0.509
   3_bss:    1.509    0.046    0.509
   3_xyz:    1.455    0.057    0.545
   3_adp:    1.455    0.057    0.545
   3_occ:    1.455    0.057    0.545
   4_bss:    1.455    0.057    0.545
   4_xyz:    1.559    0.049    0.562
   4_adp:    1.559    0.049    0.562
   4_occ:    1.559    0.049    0.562
   5_bss:    1.559    0.049    0.562
   5_xyz:    1.623    0.052    0.569
   5_adp:    1.623    0.052    0.569
   5_occ:    1.623    0.052    0.569
   5_bss:    1.623    0.052    0.569
------------------------------------------------------------------------

CPU time actual refinement: 330.73


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_292/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_292/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_292/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_292/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_292/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 330.57 
  Macro-tasks:
    bulk solvent and scale       = 41.93  
    individual site refinement   = 138.35 
    weights calculation          = 32.03  
    collect and process          = 6.64   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 219.07 
  Micro-tasks:
    mask                            = 1.72   
    f_calc                          = 100.17 
    alpha_beta                      = 8.12   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 111.78 
    fmodel                         = 7.44   
    r_factors                      = 0.20   
    phase_errors                   = 11.00  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 241.82 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.598 micro seconds
Total CPU time: 5.73 minutes
from_scatterers_fft:    652 calls, 99.81 s
gradients_fft:          597 calls, 97.78 s

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

# Date 2008-01-16 Time 01:14:51 PST -0800 (1200474891.07 s)
Start R-work = 0.4383, R-free = 0.4266 (no bulk solvent and anisotropic scale)
Final R-work = 0.1288, R-free = 0.1725 (no bulk solvent and anisotropic scale)

Start R-work = 0.4301, R-free = 0.4164
Final R-work = 0.1104, R-free = 0.1556