# Date 2008-01-16 Time 02:38:11 PST -0800 (1200479891.24 s)
#phil __OFF__

Command line arguments: "../912.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 11779
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 912

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.9525, 46.93, 88.5498, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.25, 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: (70.9525, 46.93, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2039 2.00248
Completeness in resolution range: 0.954909
Completeness with d_max=infinity: 0.951985

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.2039
                             d_min =   2.0025

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.93, 88.5498, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.2039 2.00248
Completeness in resolution range: 0.954909
Completeness with d_max=infinity: 0.951985

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.2043 -  4.2850 [2155/2179]  1936   219  10.2%
  bin  2:  4.2850 -  3.4138 [2061/2081]  1856   205   9.9%
  bin  3:  3.4138 -  2.9860 [2046/2065]  1844   202   9.9%
  bin  4:  2.9860 -  2.7147 [2019/2049]  1816   203  10.1%
  bin  5:  2.7147 -  2.5210 [2010/2029]  1809   201  10.0%
  bin  6:  2.5210 -  2.3730 [2001/2026]  1798   203  10.1%
  bin  7:  2.3730 -  2.2546 [2003/2031]  1803   200  10.0%
  bin  8:  2.2546 -  2.1567 [1968/2004]  1773   195   9.9%
  bin  9:  2.1567 -  2.0739 [1962/2004]  1771   191   9.7%
  bin 10:  2.0739 -  2.0025 [1364/2046]  1224   140  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_912/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.74 -     2.37: 10
        2.37 -     3.00: 1921
        3.00 -     3.64: 4509
        3.64 -     4.27: 8945
        4.27 -     4.90: 12441
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.741 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  95 " - " O   HOH Z  50 "  1.834 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.834 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.957 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 27821 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_912/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_912/model_refine_001.geo

CPU time processing inputs: 9.02


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.9525 46.93 88.54975 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.00 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4707   r_free= 0.4646   ksol= 0.00   Bsol= 0.00   scale= 0.786    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.272968                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2043 -  4.7794 0.99   1396  154 0.3941 0.3559      6.6117      6.5023|
|  2:  4.7794 -  3.8133 0.99   1348  153 0.3775 0.4106      6.7542      6.8647|
|  3:  3.8133 -  3.3370 0.99   1311  141 0.4307 0.4041      6.6663      6.6371|
|  4:  3.3370 -  3.0346 0.99   1315  151 0.4613 0.4115        6.52      6.4221|
|  5:  3.0346 -  2.8186 0.99   1307  143 0.5001 0.4796      6.3658      6.3934|
|  6:  2.8186 -  2.6533 0.99   1298  144 0.4907 0.5659      6.2673      6.2135|
|  7:  2.6533 -  2.5210 0.99   1286  144 0.5116 0.5139      6.2275      6.2078|
|  8:  2.5210 -  2.4118 0.98   1278  141 0.5300 0.4557      6.1958      6.1335|
|  9:  2.4118 -  2.3192 0.98   1281  144 0.4988 0.6021      6.0992       6.176|
| 10:  2.3192 -  2.2395 1.00   1293  142 0.5253 0.4860      6.1134      6.0832|
| 11:  2.2395 -  2.1696 0.98   1278  138 0.5106 0.4824      6.0241       6.054|
| 12:  2.1696 -  2.1078 0.98   1254  144 0.5155 0.4718      5.9705       5.986|
| 13:  2.1078 -  2.0524 0.99   1288  139 0.5193 0.5352      5.8721      5.8353|
| 14:  2.0524 -  2.0025 0.53    697   81 0.5271 0.5125      5.8763      5.7629|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2043 -  4.7794  1396   154  0.72  32.12   0.79     0.75      63466.98|
|  2:  4.7794 -  3.8133  1348   153  0.73  32.38   0.87     0.79      94807.91|
|  3:  3.8133 -  3.3370  1311   141  0.64  40.47   0.82     0.74     100488.42|
|  4:  3.3370 -  3.0346  1315   151  0.55  48.07   0.79     0.62      91751.09|
|  5:  3.0346 -  2.8186  1307   143  0.45  56.11   0.74     0.52      77221.97|
|  6:  2.8186 -  2.6533  1298   144  0.40  60.13   0.72     0.44      71608.68|
|  7:  2.6533 -  2.5210  1286   144  0.37  62.09   0.73     0.42      65025.12|
|  8:  2.5210 -  2.4118  1278   141  0.38  61.32   0.72     0.43      57344.80|
|  9:  2.4118 -  2.3192  1281   144  0.39  60.66   0.73     0.45      52161.12|
| 10:  2.3192 -  2.2395  1293   142  0.39  60.70   0.73     0.45      46846.71|
| 11:  2.2395 -  2.1696  1278   138  0.38  61.89   0.75     0.46      45067.17|
| 12:  2.1696 -  2.1078  1254   144  0.37  62.12   0.74     0.45      40580.10|
| 13:  2.1078 -  2.0524  1288   139  0.35  64.11   0.71     0.43      35607.18|
| 14:  2.0524 -  2.0025   697    81  0.37  62.46   0.71     0.39      30046.04|
|alpha:            min =        0.39 max =            0.79 mean =         0.53|
|beta:             min =    30046.04 max =       100488.42 mean =     63656.20|
|figures of merit: min =        0.00 max =            1.00 mean =         0.47|
|phase err.(work): min =        0.00 max =           89.97 mean =        54.09|
|phase err.(test): min =        0.00 max =           89.96 mean =        54.39|
|-----------------------------------------------------------------------------|

============================== 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 = 12.859551             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.857   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.108931              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.094   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       24 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      163 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      675 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1485 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2557 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3859 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4998 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6473 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7576 |
|-----------------------------------------------------------------------------|
|-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 |       54.494 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.707 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.276)------------------------------------------|
|    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 = 12.276)------------------------------------------|
|    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: 2.00 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4766   r_free= 0.4658   ksol= 0.00   Bsol= 0.00   scale= 0.758    |
|                                                                             |
| 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:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.275574                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4617   r_free= 0.4515   ksol= 0.33   Bsol= 30.30   scale= 0.985   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.11,6.65,12.11,0.00,0.00,0.00); trace/3= 8.62                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.266404                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.600572             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.719   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.008345              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.161   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4617      final r-factor (work) = 0.3730          |
| start r-factor (free) = 0.4515      final r-factor (free) = 0.4009          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 90.8749 = 11.60 * 0.50 * 6.2722 + 1.00 * 54.4943                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 35.9138 = 11.60 * 0.50 * 6.1673 + 1.00 * 0.1416                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3730      final r-factor (work) = 0.3238          |
| start r-factor (free) = 0.4009      final r-factor (free) = 0.3752          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.2332 = 1.01 * 1.00 * 6.1673 + 1.00 * 0.0145                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.1337 = 1.01 * 1.00 * 6.0673 + 1.00 * 0.0158                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.276)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.82   13.07    None  None   None       |
|    all(noH): 2823   0      0.00    77.82   13.07    None  None   None       |
|    Sol.    : 438    0      0.00    77.82   27.89    None  None   None       |
|    Mac.    : 2385   0      0.00    72.37   10.35    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.783: 1220   |   5:    38.912 -  46.695:   65        |
|      1:     7.783 -  15.565:  737   |   6:    46.695 -  54.477:   49        |
|      2:    15.565 -  23.348:  398   |   7:    54.477 -  62.260:   25        |
|      3:    23.348 -  31.130:  208   |   8:    62.260 -  70.042:    6        |
|      4:    31.130 -  38.912:  111   |   9:    70.042 -  77.825:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3238 r_free = 0.3752             target_work(ml) = 6.038         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3235 r_free = 0.3764             target_work(ml) = 6.038         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3235   r_free= 0.3764   ksol= 0.33   Bsol= 30.30   scale= 1.085   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.11,6.65,12.11,0.00,0.00,0.00); trace/3= 8.62                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.48 A                  |
| x-ray target function (ml) for work reflections: 6.037725                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3214   r_free= 0.3730   ksol= 0.31   Bsol= 46.50   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.11,3.87,8.74,0.00,0.00,0.00); trace/3= 5.57                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 6.038716                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.580967              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.411   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.441232              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 132.749  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3214      final r-factor (work) = 0.2413          |
| start r-factor (free) = 0.3730      final r-factor (free) = 0.2991          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 20.0881 = 6.58 * 0.50 * 6.0619 + 1.00 * 0.1416                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 19.5496 = 6.58 * 0.50 * 5.9153 + 1.00 * 0.0853                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2413      final r-factor (work) = 0.2198          |
| start r-factor (free) = 0.2991      final r-factor (free) = 0.2743          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6263 = 0.44 * 1.00 * 5.9153 + 1.00 * 0.0163                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5563 = 0.44 * 1.00 * 5.7547 + 1.00 * 0.0172                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.276)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.19   12.66    None  None   None       |
|    all(noH): 2823   0      0.00    93.19   12.66    None  None   None       |
|    Sol.    : 438    0      0.00    77.23   32.68    None  None   None       |
|    Mac.    : 2385   0      0.00    93.19   8.99     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 -   9.319: 1587   |   5:    46.595 -  55.915:   72        |
|      1:     9.319 -  18.638:  635   |   6:    55.915 -  65.234:   18        |
|      2:    18.638 -  27.957:  244   |   7:    65.234 -  74.553:    3        |
|      3:    27.957 -  37.276:  146   |   8:    74.553 -  83.872:    2        |
|      4:    37.276 -  46.595:  115   |   9:    83.872 -  93.191:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2198 r_free = 0.2743             target_work(ml) = 5.722         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2196 r_free = 0.2740             target_work(ml) = 5.722         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2196   r_free= 0.2740   ksol= 0.31   Bsol= 46.50   scale= 1.044   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.11,3.87,8.74,0.00,0.00,0.00); trace/3= 5.57                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.721986                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2181   r_free= 0.2740   ksol= 0.32   Bsol= 63.54   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.49,2.70,5.58,0.00,0.00,0.00); trace/3= 3.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.31 A                  |
| x-ray target function (ml) for work reflections: 5.723808                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.135731              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.318  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.724780              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 106.502  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2181      final r-factor (work) = 0.1646          |
| start r-factor (free) = 0.2740      final r-factor (free) = 0.2166          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.9993 = 4.14 * 0.50 * 5.7614 + 1.00 * 0.0855                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.6673 = 4.14 * 0.50 * 5.6069 + 1.00 * 0.0729                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1646      final r-factor (work) = 0.1497          |
| start r-factor (free) = 0.2166      final r-factor (free) = 0.2042          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.6947 = 1.72 * 1.00 * 5.6069 + 1.00 * 0.0240                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.4127 = 1.72 * 1.00 * 5.4277 + 1.00 * 0.0511                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.276)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    115.60  13.84    None  None   None       |
|    all(noH): 2823   0      0.00    115.60  13.84    None  None   None       |
|    Sol.    : 438    0      0.54    96.50   40.50    None  None   None       |
|    Mac.    : 2385   0      0.00    115.60  8.95     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 -  11.560: 1868   |   5:    57.801 -  69.361:   68        |
|      1:    11.560 -  23.121:  468   |   6:    69.361 -  80.922:   33        |
|      2:    23.121 -  34.681:  151   |   7:    80.922 -  92.482:    4        |
|      3:    34.681 -  46.241:  116   |   8:    92.482 - 104.042:    2        |
|      4:    46.241 -  57.801:  112   |   9:   104.042 - 115.602:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1497 r_free = 0.2042             target_work(ml) = 5.400         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1495 r_free = 0.2043             target_work(ml) = 5.400         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1495   r_free= 0.2043   ksol= 0.32   Bsol= 63.54   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.49,2.70,5.58,0.00,0.00,0.00); trace/3= 3.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.399778                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1493   r_free= 0.2040   ksol= 0.33   Bsol= 75.17   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.15,2.35,4.52,0.00,0.00,0.00); trace/3= 3.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.399310                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.986963              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 116.194  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.465744              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 95.502   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1493      final r-factor (work) = 0.1348          |
| start r-factor (free) = 0.2040      final r-factor (free) = 0.1859          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.4666 = 1.99 * 0.50 * 5.4291 + 1.00 * 0.0729                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3867 = 1.99 * 0.50 * 5.3591 + 1.00 * 0.0626                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1348      final r-factor (work) = 0.1328          |
| start r-factor (free) = 0.1859      final r-factor (free) = 0.1810          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.5199 = 0.47 * 1.00 * 5.3591 + 1.00 * 0.0239                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4869 = 0.47 * 1.00 * 5.3091 + 1.00 * 0.0142                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.276)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    99.33   13.21    None  None   None       |
|    all(noH): 2823   0      0.00    99.33   13.21    None  None   None       |
|    Sol.    : 438    0      0.91    99.33   38.73    None  None   None       |
|    Mac.    : 2385   0      0.00    80.45   8.53     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 -   9.933: 1769   |   5:    49.665 -  59.599:   90        |
|      1:     9.933 -  19.866:  536   |   6:    59.599 -  69.532:   39        |
|      2:    19.866 -  29.799:  146   |   7:    69.532 -  79.465:   24        |
|      3:    29.799 -  39.732:  117   |   8:    79.465 -  89.398:    4        |
|      4:    39.732 -  49.665:   94   |   9:    89.398 -  99.331:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1328 r_free = 0.1810             target_work(ml) = 5.294         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1327 r_free = 0.1809             target_work(ml) = 5.293         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1327   r_free= 0.1809   ksol= 0.33   Bsol= 75.17   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.15,2.35,4.52,0.00,0.00,0.00); trace/3= 3.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.293177                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1327   r_free= 0.1809   ksol= 0.33   Bsol= 68.76   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.22,2.37,4.30,0.00,0.00,0.00); trace/3= 2.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.292956                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.359027              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 111.096  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.539961              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.837  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1327      final r-factor (work) = 0.1198          |
| start r-factor (free) = 0.1809      final r-factor (free) = 0.1696          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9786 = 3.36 * 0.50 * 5.3087 + 1.00 * 0.0626                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9094 = 3.36 * 0.50 * 5.2504 + 1.00 * 0.0913                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1198      final r-factor (work) = 0.1185          |
| start r-factor (free) = 0.1696      final r-factor (free) = 0.1685          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8492 = 0.54 * 1.00 * 5.2504 + 1.00 * 0.0141                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8266 = 0.54 * 1.00 * 5.2095 + 1.00 * 0.0137                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.276)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    101.73  12.97    None  None   None       |
|    all(noH): 2823   0      0.00    101.73  12.97    None  None   None       |
|    Sol.    : 438    0      1.00    101.73  37.97    None  None   None       |
|    Mac.    : 2385   0      0.00    82.29   8.37     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 -  10.173: 1836   |   5:    50.864 -  61.037:   86        |
|      1:    10.173 -  20.346:  486   |   6:    61.037 -  71.210:   27        |
|      2:    20.346 -  30.518:  140   |   7:    71.210 -  81.382:   18        |
|      3:    30.518 -  40.691:  131   |   8:    81.382 -  91.555:    4        |
|      4:    40.691 -  50.864:   92   |   9:    91.555 - 101.728:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1185 r_free = 0.1685             target_work(ml) = 5.205         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1184 r_free = 0.1685             target_work(ml) = 5.205         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1184   r_free= 0.1685   ksol= 0.33   Bsol= 68.76   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.22,2.37,4.30,0.00,0.00,0.00); trace/3= 2.96                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.204857                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2043 -  4.7794 0.99   1396  154 0.1009 0.1384      5.4148      5.5823|
|  2:  4.7794 -  3.8133 0.99   1348  153 0.0854 0.1200      5.4566      5.6998|
|  3:  3.8133 -  3.3370 0.99   1311  141 0.1117 0.1541      5.5284      5.8662|
|  4:  3.3370 -  3.0346 0.99   1315  151 0.1288 0.1876      5.5055      5.7092|
|  5:  3.0346 -  2.8186 0.99   1307  143 0.1451 0.1754      5.4046      5.5986|
|  6:  2.8186 -  2.6533 0.99   1298  144 0.1310 0.2219      5.2744        5.58|
|  7:  2.6533 -  2.5210 0.99   1286  144 0.1357 0.1686      5.2429      5.3866|
|  8:  2.5210 -  2.4118 0.98   1278  141 0.1255 0.1712      5.1517      5.4065|
|  9:  2.4118 -  2.3192 0.98   1281  144 0.1280 0.1965      5.1129      5.3816|
| 10:  2.3192 -  2.2395 1.00   1293  142 0.1225 0.1715      5.0257      5.2214|
| 11:  2.2395 -  2.1696 0.98   1278  138 0.1223 0.1905      4.9993      5.3154|
| 12:  2.1696 -  2.1078 0.98   1254  144 0.1185 0.1852      4.9265      5.2603|
| 13:  2.1078 -  2.0524 0.99   1288  139 0.1202 0.1798      4.8301      5.0694|
| 14:  2.0524 -  2.0025 0.53    697   81 0.1052 0.1669      4.7165      4.9572|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2043 -  4.7794  1396   154  0.94   9.58   0.97     0.95       7904.21|
|  2:  4.7794 -  3.8133  1348   153  0.95   8.54   1.00     0.99       9925.65|
|  3:  3.8133 -  3.3370  1311   141  0.93  12.26   1.02     1.02      11745.39|
|  4:  3.3370 -  3.0346  1315   151  0.91  14.64   1.00     0.98      11566.62|
|  5:  3.0346 -  2.8186  1307   143  0.89  17.25   1.00     0.97       9667.61|
|  6:  2.8186 -  2.6533  1298   144  0.89  17.34   0.97     0.94       8079.30|
|  7:  2.6533 -  2.5210  1286   144  0.89  17.14   0.98     0.95       7294.46|
|  8:  2.5210 -  2.4118  1278   141  0.89  16.83   0.99     0.96       6321.92|
|  9:  2.4118 -  2.3192  1281   144  0.90  16.84   1.00     0.96       5990.05|
| 10:  2.3192 -  2.2395  1293   142  0.89  17.32   1.00     0.96       5107.80|
| 11:  2.2395 -  2.1696  1278   138  0.89  17.40   0.99     0.94       4877.51|
| 12:  2.1696 -  2.1078  1254   144  0.90  16.80   1.00     0.99       4435.63|
| 13:  2.1078 -  2.0524  1288   139  0.89  17.57   0.98     0.96       3727.98|
| 14:  2.0524 -  2.0025   697    81  0.91  14.79   0.96     0.93       2840.20|
|alpha:            min =        0.93 max =            1.02 mean =         0.96|
|beta:             min =     2840.20 max =        11745.39 mean =      7286.42|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.97 mean =        15.26|
|phase err.(test): min =        0.00 max =           88.76 mean =        14.55|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1183   r_free= 0.1682   ksol= 0.33   Bsol= 67.15   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.68,-0.59,1.27,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.203954                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1183   r_free= 0.1682   ksol= 0.33   Bsol= 67.15   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.68,-0.59,1.27,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.203954                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.2043 -  4.7794 0.99   1396  154 0.1006 0.1352      5.4035       5.561|
|  2:  4.7794 -  3.8133 0.99   1348  153 0.0858 0.1191      5.4558      5.6951|
|  3:  3.8133 -  3.3370 0.99   1311  141 0.1117 0.1537      5.5267      5.8668|
|  4:  3.3370 -  3.0346 0.99   1315  151 0.1287 0.1884      5.5063      5.7124|
|  5:  3.0346 -  2.8186 0.99   1307  143 0.1450 0.1746      5.4058      5.5979|
|  6:  2.8186 -  2.6533 0.99   1298  144 0.1310 0.2219      5.2747      5.5801|
|  7:  2.6533 -  2.5210 0.99   1286  144 0.1358 0.1687      5.2433      5.3871|
|  8:  2.5210 -  2.4118 0.98   1278  141 0.1255 0.1717      5.1524      5.4068|
|  9:  2.4118 -  2.3192 0.98   1281  144 0.1279 0.1965      5.1127      5.3825|
| 10:  2.3192 -  2.2395 1.00   1293  142 0.1225 0.1716      5.0259      5.2215|
| 11:  2.2395 -  2.1696 0.98   1278  138 0.1222 0.1903      4.9988      5.3149|
| 12:  2.1696 -  2.1078 0.98   1254  144 0.1184 0.1849       4.926      5.2593|
| 13:  2.1078 -  2.0524 0.99   1288  139 0.1200 0.1801      4.8299      5.0699|
| 14:  2.0524 -  2.0025 0.53    697   81 0.1053 0.1669      4.7171      4.9574|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.2043 -  4.7794  1396   154  0.94   9.62   0.97     0.94       7724.05|
|  2:  4.7794 -  3.8133  1348   153  0.95   8.44   1.00     0.99       9744.66|
|  3:  3.8133 -  3.3370  1311   141  0.93  12.16   1.02     1.02      11630.90|
|  4:  3.3370 -  3.0346  1315   151  0.91  14.66   1.00     0.98      11608.44|
|  5:  3.0346 -  2.8186  1307   143  0.89  17.25   1.00     0.97       9693.53|
|  6:  2.8186 -  2.6533  1298   144  0.89  17.36   0.97     0.95       8093.70|
|  7:  2.6533 -  2.5210  1286   144  0.89  17.15   0.98     0.95       7297.25|
|  8:  2.5210 -  2.4118  1278   141  0.89  16.85   0.99     0.96       6333.64|
|  9:  2.4118 -  2.3192  1281   144  0.90  16.86   1.00     0.96       5999.42|
| 10:  2.3192 -  2.2395  1293   142  0.89  17.32   1.00     0.96       5107.72|
| 11:  2.2395 -  2.1696  1278   138  0.89  17.39   0.99     0.94       4872.36|
| 12:  2.1696 -  2.1078  1254   144  0.90  16.79   1.00     0.99       4430.43|
| 13:  2.1078 -  2.0524  1288   139  0.89  17.56   0.99     0.96       3727.19|
| 14:  2.0524 -  2.0025   697    81  0.91  14.80   0.97     0.94       2843.19|
|alpha:            min =        0.94 max =            1.02 mean =         0.97|
|beta:             min =     2843.19 max =        11630.90 mean =      7256.95|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.88 mean =        15.25|
|phase err.(test): min =        0.00 max =           88.68 mean =        14.55|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.276)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.99    104.72  15.96    None  None   None       |
|    all(noH): 2823   0      2.99    104.72  15.96    None  None   None       |
|    Sol.    : 438    0      3.99    104.72  40.96    None  None   None       |
|    Mac.    : 2385   0      2.99    85.28   11.36    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.991 -  13.164: 1836   |   5:    53.855 -  64.028:   86        |
|      1:    13.164 -  23.337:  486   |   6:    64.028 -  74.201:   27        |
|      2:    23.337 -  33.510:  140   |   7:    74.201 -  84.374:   18        |
|      3:    33.510 -  43.682:  131   |   8:    84.374 -  94.546:    4        |
|      4:    43.682 -  53.855:   92   |   9:    94.546 - 104.719:    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)= 328         
Filter by distance & map next to the model:
   mapped sites are within: 0.280 - 4.929
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 323 from: 328
   mapped sites are within: 0.702 - 4.929

peak=   10.427 closest distance to " CB  VAL A 230 " =    1.453
peak=    5.821 closest distance to " CD2 LEU A   5 " =    1.174
peak=    5.573 closest distance to " CG  LEU A   5 " =    1.243
peak=    5.456 closest distance to " NE2 GLN A  11 " =    1.098
peak=    5.360 closest distance to " CG  LEU A 228 " =    1.193
peak=    5.274 closest distance to " O   HOH Z 142 " =    2.049
peak=    5.103 closest distance to " NH2 ARG A  56 " =    2.146
peak=    4.978 closest distance to " CB  GLN A 223 " =    1.494
peak=    4.946 closest distance to " CB  GLN A 183 " =    1.261
peak=    4.941 closest distance to " O   HOH Z 369 " =    2.089
peak=    4.857 closest distance to " NH1 ARG A 138 " =    1.080
peak=    4.836 closest distance to " CB  VAL A 296 " =    1.075
peak=    4.777 closest distance to " O   HOH Z 425 " =    1.557
peak=    4.759 closest distance to " CG2 VAL A 296 " =    1.043
peak=    4.588 closest distance to " O   HOH Z 265 " =    2.060
peak=    4.580 closest distance to " CZ  PHE A 218 " =    1.138
peak=    4.571 closest distance to " O   HOH Z   9 " =    1.603
peak=    4.553 closest distance to " O   HOH Z 248 " =    1.447
peak=    4.426 closest distance to " O   HOH Z 427 " =    3.005
peak=    4.423 closest distance to " CB  ASN A 148 " =    1.465
peak=    4.392 closest distance to " O   HOH Z 368 " =    2.265
peak=    4.376 closest distance to " O   HOH Z 232 " =    2.242
peak=    4.354 closest distance to " O   HOH Z 207 " =    1.310
peak=    4.334 closest distance to " CZ3 TRP A 266 " =    1.151
peak=    4.323 closest distance to " O   SER A  87 " =    2.319
peak=    4.286 closest distance to " CB  ASP A 124 " =    0.802
peak=    4.267 closest distance to " CB  ASN A 142 " =    1.085
peak=    4.257 closest distance to " CG  ARG A 138 " =    0.957
peak=    4.223 closest distance to " O   HOH Z 303 " =    2.134
peak=    4.209 closest distance to " CG  PRO A 243 " =    1.130
peak=    4.202 closest distance to " NH2AARG A 145 " =    1.144
peak=    4.201 closest distance to " CG  MET A 185 " =    1.249
peak=    4.156 closest distance to " CB  GLU A 277 " =    3.708
peak=    4.144 closest distance to " O   HOH Z 313 " =    1.858
peak=    4.138 closest distance to " CB  SER A  63 " =    1.214
peak=    4.123 closest distance to " CA  ALA A  51 " =    0.986
peak=    4.111 closest distance to " O   HOH Z 290 " =    1.306
peak=    4.081 closest distance to " CB  ARG A 190 " =    1.517
peak=    4.079 closest distance to " O   HOH Z 127 " =    1.171
peak=    4.071 closest distance to " O   HOH Z 126 " =    1.665
peak=    4.068 closest distance to " O   HOH Z 126 " =    1.953
peak=    4.063 closest distance to " O   PRO A 198 " =    1.566
peak=    4.058 closest distance to " NH1AARG A 145 " =    1.171
peak=    4.052 closest distance to " O   HOH Z 287 " =    2.039
peak=    4.040 closest distance to " CD2 LEU A 228 " =    1.191
peak=    4.029 closest distance to " O   HOH Z 411 " =    3.730
peak=    4.026 closest distance to " O   HOH Z 346 " =    1.614
peak=    3.996 closest distance to " ND2 ASN A 187 " =    1.556
peak=    3.985 closest distance to " CG2 ILE A 234 " =    1.047
peak=    3.974 closest distance to " O   HOH Z 359 " =    1.734
peak=    3.965 closest distance to " O   HOH Z 193 " =    1.917
peak=    3.958 closest distance to " O   HOH Z 188 " =    2.885
peak=    3.957 closest distance to " O   HOH Z 251 " =    1.619
peak=    3.951 closest distance to " CG AARG A 275 " =    1.347
peak=    3.949 closest distance to " CD  LYS A 166 " =    1.363
peak=    3.941 closest distance to " O   HOH Z  76 " =    1.299
peak=    3.940 closest distance to " CG  PRO A 198 " =    1.272
peak=    3.939 closest distance to " CG  PRO A 213 " =    1.204
peak=    3.921 closest distance to " CE  LYS A  76 " =    0.931
peak=    3.916 closest distance to " CB  ASN A  39 " =    0.927
peak=    3.896 closest distance to " CD  ARG A 159 " =    0.750
peak=    3.876 closest distance to " CB  GLN A  89 " =    1.164
peak=    3.873 closest distance to " CG  LEU A 167 " =    1.216
peak=    3.863 closest distance to " CB  VAL A 265 " =    1.341
peak=    3.853 closest distance to " CB  TRP A 266 " =    1.063
peak=    3.840 closest distance to " O   HOH Z 214 " =    2.580
peak=    3.837 closest distance to " CA  TYR A 116 " =    1.365
peak=    3.830 closest distance to " CA  ARG A 195 " =    1.244
peak=    3.830 closest distance to " O   HOH Z 406 " =    1.544
peak=    3.822 closest distance to " O   HOH Z 112 " =    0.914
peak=    3.822 closest distance to " O   HOH Z 298 " =    1.848
peak=    3.820 closest distance to " CG1 VAL A 296 " =    1.255
peak=    3.818 closest distance to " CB  ARG A 275 " =    0.968
peak=    3.799 closest distance to " O   HOH Z 158 " =    3.126
peak=    3.796 closest distance to " CB  VAL A 230 " =    1.208
peak=    3.792 closest distance to " CB  VAL A 202 " =    1.588
peak=    3.789 closest distance to " O   HOH Z 261 " =    1.810
peak=    3.787 closest distance to " CD  ARG A  66 " =    2.455
peak=    3.786 closest distance to " CB  SER A 212 " =    1.269
peak=    3.776 closest distance to " O   HOH Z 365 " =    2.952
peak=    3.749 closest distance to " O   HOH Z 199 " =    1.565
peak=    3.739 closest distance to " CB  GLU A  46 " =    0.918
peak=    3.739 closest distance to " N   PHE A 130 " =    1.267
peak=    3.733 closest distance to " CG  GLN A  58 " =    1.057
peak=    3.732 closest distance to " O  BHOH Z 338 " =    2.347
peak=    3.724 closest distance to " N   ALA A 256 " =    1.180
peak=    3.713 closest distance to " O   HOH Z  80 " =    1.726
peak=    3.706 closest distance to " CG2 THR A 221 " =    1.089
peak=    3.699 closest distance to " O   HOH Z 193 " =    1.618
peak=    3.698 closest distance to " CB  ARG A  79 " =    1.517
peak=    3.695 closest distance to " CD2 TRP A 179 " =    1.244
peak=    3.693 closest distance to " O   PHE A 192 " =    1.447
peak=    3.692 closest distance to " CA  TYR A  30 " =    0.995
peak=    3.688 closest distance to " CB  LEU A  83 " =    0.752
peak=    3.688 closest distance to " O   HOH Z 145 " =    1.355
peak=    3.685 closest distance to " O   HOH Z  78 " =    1.639
peak=    3.681 closest distance to " CA  LEU A 282 " =    1.100
peak=    3.679 closest distance to " O   HOH Z 422 " =    2.623
peak=    3.677 closest distance to " O   HOH Z 214 " =    1.293
peak=    3.670 closest distance to " O   HOH Z  19 " =    2.351
peak=    3.668 closest distance to " CA  ALA A 295 " =    1.163
peak=    3.662 closest distance to " O   HOH Z 273 " =    2.815
peak=    3.661 closest distance to " CD1 ILE A  33 " =    1.859
peak=    3.657 closest distance to " O   HOH Z 238 " =    2.256
peak=    3.653 closest distance to " CB  SER A  62 " =    0.925
peak=    3.648 closest distance to " OE2 GLU A  53 " =    2.086
peak=    3.646 closest distance to " CB  GLU A 152 " =    1.187
peak=    3.625 closest distance to " CD1AILE A 234 " =    0.950
peak=    3.624 closest distance to " CG  GLU A  37 " =    1.036
peak=    3.622 closest distance to " O   HOH Z  59 " =    2.226
peak=    3.620 closest distance to " CB  PRO A  90 " =    1.232
peak=    3.618 closest distance to " O   HOH Z 353 " =    2.614
peak=    3.612 closest distance to " O   HOH Z 213 " =    1.945
peak=    3.591 closest distance to " CB  TRP A 150 " =    1.363
peak=    3.590 closest distance to " CB  LEU A 143 " =    1.278
peak=    3.584 closest distance to " O   ASP A 124 " =    1.186
peak=    3.583 closest distance to " CB  ALA A   9 " =    1.696
peak=    3.579 closest distance to " O   HOH Z 227 " =    1.799
peak=    3.579 closest distance to " O   HOH Z 368 " =    3.472
peak=    3.570 closest distance to " CG2 VAL A 257 " =    0.901
peak=    3.563 closest distance to " O   HOH Z 130 " =    1.075
peak=    3.548 closest distance to " CB  GLN A  88 " =    1.249
peak=    3.543 closest distance to " O   HOH Z 184 " =    1.442
peak=    3.535 closest distance to " O   ASP A 200 " =    1.629
peak=    3.533 closest distance to " CB  ASP A 140 " =    0.934
peak=    3.531 closest distance to " CB  GLU A 128 " =    1.003
peak=    3.528 closest distance to " CD1 LEU A 300 " =    1.081
peak=    3.524 closest distance to " O   HOH Z  49 " =    1.040
peak=    3.520 closest distance to " ND2BASN A 224 " =    0.853
peak=    3.519 closest distance to " CG2 ILE A  20 " =    1.545
peak=    3.519 closest distance to " O   MET A 105 " =    1.597
peak=    3.518 closest distance to " O   HOH Z   4 " =    1.630
peak=    3.514 closest distance to " O   HOH Z  30 " =    1.502
peak=    3.513 closest distance to " CG AARG A 102 " =    1.197
peak=    3.512 closest distance to " CD  ARG A 269 " =    0.978
peak=    3.511 closest distance to " O   HOH Z 180 " =    2.187
peak=    3.511 closest distance to " OD1 ASN A  69 " =    2.596
peak=    3.508 closest distance to " O   HOH Z  68 " =    2.125
peak=    3.507 closest distance to " CB  SER A 216 " =    0.915
peak=    3.506 closest distance to " CA  ASP A 162 " =    0.924
peak=    3.505 closest distance to " CB  SER A   3 " =    1.451
peak=    3.504 closest distance to " O   HOH Z 222 " =    2.300
peak=    3.504 closest distance to " O   HOH Z  43 " =    2.013
peak=    3.499 closest distance to " O   HOH Z 166 " =    3.768
peak=    3.496 closest distance to " O   HOH Z 350 " =    1.581
peak=    3.496 closest distance to " CB  THR A  82 " =    1.242
peak=    3.481 closest distance to " O   ASN A 284 " =    1.866
peak=    3.479 closest distance to " O   HOH Z 272 " =    1.826
peak=    3.475 closest distance to " CA  VAL A 125 " =    1.163
peak=    3.474 closest distance to " O   HOH Z 148 " =    3.508
peak=    3.472 closest distance to " O   HOH Z 102 " =    1.262
peak=    3.471 closest distance to " O   HOH Z 234 " =    3.599
peak=    3.465 closest distance to " O   HOH Z  88 " =    3.433
peak=    3.464 closest distance to " CD ALYS A 290 " =    1.046
peak=    3.461 closest distance to " OG  SER A 276 " =    1.309
peak=    3.457 closest distance to " O   HOH Z  88 " =    3.654
peak=    3.457 closest distance to " CA  ALA A  21 " =    1.177
peak=    3.454 closest distance to " CA  ALA A 160 " =    1.110
peak=    3.454 closest distance to " O   HOH Z 261 " =    1.807
peak=    3.449 closest distance to " O   HOH Z 316 " =    3.149
peak=    3.446 closest distance to " O   HOH Z 329 " =    4.272
peak=    3.442 closest distance to " O   HOH Z  40 " =    1.762
peak=    3.438 closest distance to " OE1 GLN A  55 " =    1.437
peak=    3.435 closest distance to " O   HOH Z  69 " =    0.759
peak=    3.435 closest distance to " O   HOH Z 368 " =    4.076
peak=    3.430 closest distance to " O   HOH Z   3 " =    1.959
peak=    3.428 closest distance to " CB  TRP A 179 " =    1.369
peak=    3.425 closest distance to " O   HOH Z  61 " =    1.776
peak=    3.419 closest distance to " CB  PRO A 243 " =    1.572
peak=    3.419 closest distance to " CA  ALA A 291 " =    0.868
peak=    3.413 closest distance to " O   HOH Z 357 " =    2.778
peak=    3.412 closest distance to " CA  SER A  87 " =    0.939
peak=    3.407 closest distance to " CE1 TYR A 186 " =    1.220
peak=    3.404 closest distance to " O   ALA A 165 " =    1.462
peak=    3.403 closest distance to " CA  ARG A  36 " =    1.162
peak=    3.401 closest distance to " NH2 ARG A  56 " =    1.141
peak=    3.400 closest distance to " CB  LYS A 117 " =    1.208
peak=    3.393 closest distance to " O   HOH Z 211 " =    1.287
peak=    3.384 closest distance to " CD1 LEU A   5 " =    1.397
peak=    3.381 closest distance to " OG1 THR A 279 " =    1.477
peak=    3.381 closest distance to " CE3 TRP A 150 " =    1.069
peak=    3.373 closest distance to " CZ3 TRP A  92 " =    1.344
peak=    3.371 closest distance to " O   HOH Z 258 " =    2.030
peak=    3.365 closest distance to " CG BARG A 102 " =    1.858
peak=    3.363 closest distance to " O   HOH Z 203 " =    1.658
peak=    3.359 closest distance to " O   HOH Z 329 " =    3.059
peak=    3.359 closest distance to " OG  SER A  62 " =    3.023
peak=    3.359 closest distance to " N   ASN A  39 " =    1.319
peak=    3.359 closest distance to " CA  ASN A  74 " =    1.261
peak=    3.355 closest distance to " CB  ALA A   1 " =    4.929
peak=    3.353 closest distance to " CA  MET A 105 " =    0.906
peak=    3.351 closest distance to " CB  PRO A  54 " =    0.762
peak=    3.351 closest distance to " O   HOH Z 371 " =    2.825
peak=    3.350 closest distance to " CB  THR A  52 " =    0.906
peak=    3.349 closest distance to " CB AVAL A  41 " =    1.287
peak=    3.348 closest distance to " O   HOH Z 133 " =    2.856
peak=    3.344 closest distance to " CA  ASP A 140 " =    1.546
peak=    3.341 closest distance to " CB  ASP A 298 " =    1.160
peak=    3.339 closest distance to " OE2 GLU A   2 " =    2.026
peak=    3.338 closest distance to " CA  ALA A 129 " =    1.409
peak=    3.337 closest distance to " CA  GLY A 267 " =    0.889
peak=    3.336 closest distance to " CD1 LEU A  96 " =    1.120
peak=    3.333 closest distance to " CA  ALA A 100 " =    0.845
peak=    3.331 closest distance to " O   HOH Z 183 " =    1.295
peak=    3.331 closest distance to " O   HOH Z  85 " =    2.200
peak=    3.328 closest distance to " NZ  LYS A 117 " =    1.353
peak=    3.328 closest distance to " CA  LYS A 117 " =    1.260
peak=    3.326 closest distance to " CB  SER A  26 " =    1.794
peak=    3.322 closest distance to " CG1 ILE A 120 " =    1.074
peak=    3.318 closest distance to " O   HOH Z 112 " =    1.190
peak=    3.318 closest distance to " O   HOH Z 222 " =    1.273
peak=    3.315 closest distance to " NE2 GLN A  77 " =    3.383
peak=    3.314 closest distance to " OG BSER A 164 " =    2.271
peak=    3.314 closest distance to " CG2 ILE A 120 " =    1.309
peak=    3.314 closest distance to " ND1 HIS A  81 " =    1.808
peak=    3.310 closest distance to " NE2 HIS A 207 " =    1.233
peak=    3.307 closest distance to " CB  SER A 288 " =    1.455
peak=    3.304 closest distance to " O   ASN A  74 " =    1.456
peak=    3.298 closest distance to " CA  THR A 264 " =    0.798
peak=    3.296 closest distance to " CZ  PHE A  38 " =    1.204
peak=    3.295 closest distance to " CA  ALA A 158 " =    1.169
peak=    3.294 closest distance to " CB  THR A  31 " =    1.600
peak=    3.291 closest distance to " CB  TYR A  30 " =    1.153
peak=    3.290 closest distance to " CD  GLN A 240 " =    1.553
peak=    3.288 closest distance to " O   HOH Z 116 " =    1.785
peak=    3.288 closest distance to " CG1 VAL A 153 " =    0.957
peak=    3.285 closest distance to " O   HOH Z 280 " =    3.007
peak=    3.283 closest distance to " CA  ASP A 191 " =    1.299
peak=    3.282 closest distance to " O   HOH Z 299 " =    4.385
peak=    3.280 closest distance to " O   HOH Z  10 " =    1.786
peak=    3.280 closest distance to " O   HOH Z  21 " =    1.710
peak=    3.279 closest distance to " O   ALA A 158 " =    1.387
peak=    3.277 closest distance to " CE3 TRP A  85 " =    1.146
peak=    3.272 closest distance to " O   HOH Z  35 " =    4.615
peak=    3.270 closest distance to " CB  ASN A 110 " =    1.172
peak=    3.269 closest distance to " O   HOH Z 172 " =    3.874
peak=    3.268 closest distance to " O   HOH Z 258 " =    1.188
peak=    3.263 closest distance to " O   HOH Z 147 " =    1.681
peak=    3.260 closest distance to " CG1 ILE A 151 " =    1.191
peak=    3.260 closest distance to " CA  ASP A 124 " =    0.740
peak=    3.260 closest distance to " CD  LYS A  76 " =    1.853
peak=    3.248 closest distance to " ND1 HIS A  86 " =    1.630
peak=    3.245 closest distance to " O   HOH Z   1 " =    1.950
peak=    3.245 closest distance to " CG  PHE A 204 " =    0.877
peak=    3.245 closest distance to " CB  ASN A 187 " =    1.121
peak=    3.244 closest distance to " O   HOH Z 148 " =    2.129
peak=    3.244 closest distance to " O   HOH Z 417 " =    3.226
peak=    3.244 closest distance to " OH  TYR A 247 " =    1.210
peak=    3.244 closest distance to " CD  LYS A 119 " =    2.185
peak=    3.239 closest distance to " O   HOH Z 285 " =    2.110
peak=    3.236 closest distance to " CA  ARG A 139 " =    1.112
peak=    3.236 closest distance to " CB  VAL A 257 " =    0.816
peak=    3.234 closest distance to " O   ILE A  49 " =    1.172
peak=    3.229 closest distance to " CD1 ILE A 199 " =    1.059
peak=    3.227 closest distance to " O   HOH Z   1 " =    1.661
peak=    3.226 closest distance to " CG  MET A 185 " =    0.963
peak=    3.222 closest distance to " CA  ARG A 159 " =    1.174
peak=    3.222 closest distance to " CA  ILE A 234 " =    0.993
peak=    3.222 closest distance to " CB  ASN A 215 " =    1.241
peak=    3.221 closest distance to " O   HOH Z 185 " =    1.917
peak=    3.220 closest distance to " OG  SER A  62 " =    2.826
peak=    3.217 closest distance to " O   HOH Z 171 " =    4.071
peak=    3.215 closest distance to " CB  ALA A 227 " =    0.980
peak=    3.215 closest distance to " CB  ALA A 104 " =    0.787
peak=    3.215 closest distance to " CB  ALA A 248 " =    1.100
peak=    3.212 closest distance to " CG1 ILE A  49 " =    1.538
peak=    3.211 closest distance to " O   HOH Z 133 " =    1.091
peak=    3.207 closest distance to " OG  SER A 245 " =    1.706
peak=    3.207 closest distance to " NH2AARG A 275 " =    3.263
peak=    3.205 closest distance to " CB  TYR A 116 " =    0.934
peak=    3.202 closest distance to " NZ  LYS A 117 " =    3.364
peak=    3.201 closest distance to " O   HOH Z 188 " =    1.880
peak=    3.199 closest distance to " OG  SER A 135 " =    1.195
peak=    3.192 closest distance to " O   HOH Z 263 " =    1.706
peak=    3.190 closest distance to " ND2 ASN A 249 " =    0.855
peak=    3.188 closest distance to " O   HOH Z 391 " =    2.956
peak=    3.180 closest distance to " O   HOH Z 215 " =    2.989
peak=    3.173 closest distance to " CA  ALA A 184 " =    1.088
peak=    3.170 closest distance to " CB  VAL A 268 " =    0.893
peak=    3.169 closest distance to " CB  ASP A 171 " =    1.175
peak=    3.169 closest distance to " O   LEU A 228 " =    1.986
peak=    3.165 closest distance to " CB  PHE A 283 " =    0.702
peak=    3.161 closest distance to " CB  ALA A  43 " =    0.851
peak=    3.156 closest distance to " O   THR A 251 " =    1.238
peak=    3.154 closest distance to " O   HOH Z  63 " =    1.711
peak=    3.149 closest distance to " CA  GLN A  94 " =    0.755
peak=    3.145 closest distance to " ND2 ASN A 249 " =    1.859
peak=    3.144 closest distance to " O   HOH Z 109 " =    2.891
peak=    3.142 closest distance to " CG  ARG A 159 " =    0.976
peak=    3.136 closest distance to " O   ASN A 209 " =    1.314
peak=    3.131 closest distance to " O   HOH Z  97 " =    2.111
peak=    3.130 closest distance to " O   HOH Z 305 " =    3.305
peak=    3.127 closest distance to " O   HOH Z 313 " =    1.473
peak=    3.123 closest distance to " O   HOH Z 193 " =    1.168
peak=    3.121 closest distance to " O   HOH Z 128 " =    2.183
peak=    3.119 closest distance to " CG2AVAL A  72 " =    1.764
peak=    3.119 closest distance to " OD2 ASP A  65 " =    2.899
peak=    3.115 closest distance to " O  BHOH Z  74 " =    1.306
peak=    3.113 closest distance to " O   HOH Z 337 " =    1.711
peak=    3.110 closest distance to " O   HOH Z 124 " =    2.163
peak=    3.104 closest distance to " CG1 VAL A 174 " =    1.080
peak=    3.103 closest distance to " CG  MET A 113 " =    1.821
peak=    3.100 closest distance to " CZ  PHE A 192 " =    0.996
peak=    3.100 closest distance to " CB  ASN A 285 " =    0.998
peak=    3.098 closest distance to " O   HOH Z  61 " =    1.572
peak=    3.094 closest distance to " N   ASP A 162 " =    1.284
peak=    3.091 closest distance to " O   HOH Z 141 " =    1.558
peak=    3.090 closest distance to " CB  GLU A  37 " =    0.909
peak=    3.088 closest distance to " CA  ASN A 127 " =    1.088
peak=    3.087 closest distance to " O   HOH Z  28 " =    1.444
peak=    3.078 closest distance to " O   THR A 182 " =    1.469
peak=    3.076 closest distance to " CB  ASN A 173 " =    0.973
peak=    3.074 closest distance to " CZ3 TRP A  85 " =    1.074
peak=    3.071 closest distance to " O   HOH Z 423 " =    1.785
peak=    3.067 closest distance to " O   HOH Z 403 " =    1.580
peak=    3.065 closest distance to " CA  ARG A 102 " =    1.160
peak=    3.060 closest distance to " CG  GLN A  55 " =    2.430
peak=    3.057 closest distance to " CB  PHE A 204 " =    0.938
peak=    3.053 closest distance to " O   HOH Z 345 " =    3.492
peak=    3.036 closest distance to " N   ASN A 127 " =    1.330
peak=    3.018 closest distance to " O   HOH Z 371 " =    3.350
peak=    3.017 closest distance to " OD2 ASP A  50 " =    2.963
peak=    2.988 closest distance to " N   GLY A 133 " =    3.793

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 212         
Filter by distance & map next to the model:
   mapped sites are within: 0.538 - 5.651
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 210 from: 212
   mapped sites are within: 0.727 - 5.651

peak=   -5.003 closest distance to " CG2 VAL A 230 " =    0.727
peak=   -4.472 closest distance to " CD  ARG A  14 " =    3.260
peak=   -4.454 closest distance to " O   HOH Z 162 " =    2.717
peak=   -4.376 closest distance to " O   HOH Z 193 " =    1.088
peak=   -4.264 closest distance to " CD  GLN A  58 " =    0.982
peak=   -4.126 closest distance to " CG1 VAL A 296 " =    1.231
peak=   -4.119 closest distance to " CZ2 TRP A  92 " =    2.829
peak=   -4.103 closest distance to " O   HOH Z 411 " =    5.439
peak=   -4.061 closest distance to " CD  ARG A 156 " =    2.119
peak=   -4.045 closest distance to " O   HOH Z 127 " =    1.050
peak=   -4.032 closest distance to " CA  ASP A 298 " =    1.064
peak=   -4.031 closest distance to " OE1 GLN A  88 " =    0.997
peak=   -4.024 closest distance to " O   HOH Z 196 " =    2.407
peak=   -3.999 closest distance to " CG  GLN A 223 " =    2.306
peak=   -3.954 closest distance to " O   HOH Z 100 " =    0.942
peak=   -3.924 closest distance to " O   HOH Z 216 " =    0.985
peak=   -3.917 closest distance to " CB  VAL A 230 " =    1.194
peak=   -3.914 closest distance to " O   PRO A 198 " =    1.294
peak=   -3.907 closest distance to " CG1 VAL A 112 " =    2.667
peak=   -3.901 closest distance to " CD1 LEU A 101 " =    2.436
peak=   -3.897 closest distance to " O   HOH Z 231 " =    2.017
peak=   -3.878 closest distance to " CG2 VAL A 296 " =    1.107
peak=   -3.858 closest distance to " O   HOH Z 133 " =    1.043
peak=   -3.856 closest distance to " O   VAL A  67 " =    2.757
peak=   -3.851 closest distance to " O   HOH Z 359 " =    2.910
peak=   -3.842 closest distance to " CG2AVAL A  41 " =    2.820
peak=   -3.839 closest distance to " CA  GLY A 241 " =    2.382
peak=   -3.828 closest distance to " CG1 VAL A 250 " =    2.734
peak=   -3.794 closest distance to " OG  SER A  97 " =    2.300
peak=   -3.790 closest distance to " CD  GLN A  55 " =    1.137
peak=   -3.785 closest distance to " O   HOH Z 166 " =    1.820
peak=   -3.778 closest distance to " CE3 TRP A  70 " =    1.800
peak=   -3.771 closest distance to " O   HOH Z 394 " =    1.566
peak=   -3.767 closest distance to " O   HOH Z  73 " =    2.407
peak=   -3.758 closest distance to " CB  HIS A  86 " =    1.147
peak=   -3.747 closest distance to " CE2 TYR A  30 " =    2.630
peak=   -3.738 closest distance to " C   ALA A 158 " =    1.352
peak=   -3.737 closest distance to " CB  ALA A 161 " =    2.618
peak=   -3.723 closest distance to " CG2 VAL A 202 " =    2.770
peak=   -3.722 closest distance to " OG BSER A 134 " =    1.389
peak=   -3.717 closest distance to " O   HOH Z 183 " =    1.277
peak=   -3.706 closest distance to " O   HOH Z 295 " =    1.590
peak=   -3.703 closest distance to " O   HOH Z 238 " =    0.892
peak=   -3.702 closest distance to " CE3 TRP A 150 " =    2.336
peak=   -3.671 closest distance to " C   HIS A 108 " =    1.238
peak=   -3.657 closest distance to " CD  PRO A 213 " =    2.113
peak=   -3.646 closest distance to " CD1 LEU A 228 " =    2.382
peak=   -3.645 closest distance to " O   GLY A  80 " =    2.678
peak=   -3.640 closest distance to " CD2 TYR A 293 " =    2.020
peak=   -3.640 closest distance to " O   HOH Z 149 " =    2.101
peak=   -3.637 closest distance to " CG1 VAL A 112 " =    2.783
peak=   -3.629 closest distance to " CE BMET A  47 " =    1.353
peak=   -3.622 closest distance to " O   VAL A 189 " =    2.687
peak=   -3.617 closest distance to " OG  SER A 141 " =    1.785
peak=   -3.615 closest distance to " CD1 ILE A  33 " =    2.612
peak=   -3.609 closest distance to " CG2 THR A 178 " =    2.419
peak=   -3.592 closest distance to " CE2 TRP A  70 " =    2.316
peak=   -3.583 closest distance to " CD1 ILE A 151 " =    2.542
peak=   -3.570 closest distance to " CD2 PHE A 225 " =    1.171
peak=   -3.567 closest distance to " C   LEU A 143 " =    1.167
peak=   -3.564 closest distance to " O   HOH Z  68 " =    1.355
peak=   -3.563 closest distance to " CG  ARG A 269 " =    2.289
peak=   -3.562 closest distance to " O   HOH Z 377 " =    1.965
peak=   -3.561 closest distance to " O   HOH Z 232 " =    1.947
peak=   -3.557 closest distance to " N   THR A  52 " =    1.661
peak=   -3.556 closest distance to " O   HOH Z  52 " =    1.598
peak=   -3.550 closest distance to " O   HOH Z 252 " =    3.826
peak=   -3.539 closest distance to " O   SER A 271 " =    2.169
peak=   -3.539 closest distance to " O   HOH Z 103 " =    1.759
peak=   -3.538 closest distance to " O   VAL A  67 " =    2.857
peak=   -3.535 closest distance to " O   HOH Z 106 " =    1.829
peak=   -3.530 closest distance to " O   HOH Z 351 " =    1.686
peak=   -3.526 closest distance to " O   HOH Z 115 " =    1.713
peak=   -3.522 closest distance to " CD2 LEU A 167 " =    1.842
peak=   -3.520 closest distance to " O   HOH Z  11 " =    1.737
peak=   -3.518 closest distance to " N   ALA A  43 " =    2.732
peak=   -3.513 closest distance to " O   HOH Z 198 " =    2.056
peak=   -3.512 closest distance to " CB  TRP A  85 " =    2.738
peak=   -3.512 closest distance to " CG  TRP A 266 " =    1.806
peak=   -3.507 closest distance to " OG  SER A  62 " =    4.330
peak=   -3.495 closest distance to " CG2 VAL A 189 " =    1.987
peak=   -3.488 closest distance to " O   HOH Z  44 " =    0.898
peak=   -3.481 closest distance to " CD  GLN A  88 " =    0.913
peak=   -3.479 closest distance to " O   PRO A 163 " =    2.138
peak=   -3.478 closest distance to " CG  GLU A 277 " =    1.282
peak=   -3.470 closest distance to " C   MET A 188 " =    1.482
peak=   -3.469 closest distance to " O   HOH Z 236 " =    1.342
peak=   -3.468 closest distance to " O   HOH Z 290 " =    1.313
peak=   -3.463 closest distance to " O   ALA A 227 " =    1.391
peak=   -3.462 closest distance to " O   HOH Z 131 " =    3.986
peak=   -3.433 closest distance to " O   HOH Z 128 " =    2.633
peak=   -3.425 closest distance to " O   GLY A  17 " =    1.254
peak=   -3.418 closest distance to " CA  GLY A 241 " =    3.233
peak=   -3.412 closest distance to " CG2BVAL A  41 " =    1.872
peak=   -3.405 closest distance to " CD2 PHE A  61 " =    2.056
peak=   -3.402 closest distance to " OD1 ASP A 171 " =    1.672
peak=   -3.402 closest distance to " O   HOH Z 110 " =    1.210
peak=   -3.397 closest distance to " CD  LYS A 289 " =    2.411
peak=   -3.396 closest distance to " CD1 PHE A  59 " =    2.107
peak=   -3.394 closest distance to " O   HOH Z 177 " =    1.949
peak=   -3.388 closest distance to " OH  TYR A 247 " =    1.865
peak=   -3.385 closest distance to " CB  ALA A  43 " =    2.687
peak=   -3.385 closest distance to " CH2 TRP A 179 " =    1.208
peak=   -3.384 closest distance to " CB  TYR A  15 " =    2.249
peak=   -3.377 closest distance to " CA  GLY A 133 " =    2.265
peak=   -3.366 closest distance to " N   ASP A 171 " =    2.533
peak=   -3.364 closest distance to " NE2 GLN A  11 " =    1.696
peak=   -3.360 closest distance to " CB  PHE A 192 " =    1.979
peak=   -3.355 closest distance to " CG  ARG A 259 " =    2.419
peak=   -3.355 closest distance to " O   GLY A 211 " =    1.345
peak=   -3.351 closest distance to " CG2 ILE A 263 " =    2.465
peak=   -3.351 closest distance to " O   GLN A 240 " =    2.613
peak=   -3.348 closest distance to " O   HOH Z 102 " =    1.589
peak=   -3.346 closest distance to " O   HOH Z  93 " =    2.271
peak=   -3.345 closest distance to " CA  ASP A  27 " =    2.541
peak=   -3.343 closest distance to " CD1 LEU A   5 " =    2.555
peak=   -3.340 closest distance to " NE  ARG A  66 " =    4.075
peak=   -3.340 closest distance to " ND2 ASN A  45 " =    2.202
peak=   -3.339 closest distance to " CD  GLN A 223 " =    1.382
peak=   -3.334 closest distance to " OG  SER A  87 " =    1.549
peak=   -3.334 closest distance to " O   HOH Z 111 " =    1.652
peak=   -3.329 closest distance to " O   HOH Z 431 " =    1.930
peak=   -3.327 closest distance to " O   HOH Z 389 " =    1.548
peak=   -3.325 closest distance to " O   HOH Z  10 " =    1.586
peak=   -3.325 closest distance to " O   HOH Z  43 " =    1.651
peak=   -3.322 closest distance to " CG1 VAL A 125 " =    1.914
peak=   -3.321 closest distance to " O   HOH Z  11 " =    2.188
peak=   -3.321 closest distance to " O   HOH Z 100 " =    1.326
peak=   -3.320 closest distance to " CB  PRO A 163 " =    2.443
peak=   -3.319 closest distance to " NE2 GLN A  88 " =    1.132
peak=   -3.318 closest distance to " O   HOH Z  60 " =    2.024
peak=   -3.311 closest distance to " N   ALA A 226 " =    2.133
peak=   -3.310 closest distance to " OG  SER A  28 " =    2.092
peak=   -3.309 closest distance to " OD1 ASN A 148 " =    1.443
peak=   -3.308 closest distance to " O   HOH Z 407 " =    2.954
peak=   -3.305 closest distance to " O   HOH Z 435 " =    2.889
peak=   -3.302 closest distance to " O   SER A 210 " =    1.798
peak=   -3.299 closest distance to " O   HOH Z 145 " =    0.910
peak=   -3.293 closest distance to " OG ASER A 134 " =    1.391
peak=   -3.280 closest distance to " O   HOH Z 251 " =    4.943
peak=   -3.279 closest distance to " CG  PRO A 163 " =    2.212
peak=   -3.279 closest distance to " O   HOH Z 434 " =    1.611
peak=   -3.273 closest distance to " O   HOH Z  60 " =    1.566
peak=   -3.268 closest distance to " CA  GLY A  98 " =    2.046
peak=   -3.268 closest distance to " O   HOH Z 405 " =    4.526
peak=   -3.262 closest distance to " ND2 ASN A 249 " =    2.490
peak=   -3.259 closest distance to " O   ASP A  27 " =    1.901
peak=   -3.256 closest distance to " N   PHE A  59 " =    1.915
peak=   -3.248 closest distance to " O   HOH Z 275 " =    1.649
peak=   -3.243 closest distance to " CB  HIS A  81 " =    1.021
peak=   -3.241 closest distance to " CG  GLU A  53 " =    1.508
peak=   -3.240 closest distance to " O   HOH Z 285 " =    2.059
peak=   -3.237 closest distance to " O   HOH Z 411 " =    1.569
peak=   -3.236 closest distance to " O   HOH Z 100 " =    0.749
peak=   -3.235 closest distance to " O   HOH Z 371 " =    1.424
peak=   -3.235 closest distance to " O   HOH Z 185 " =    2.410
peak=   -3.234 closest distance to " CB  ALA A 248 " =    2.138
peak=   -3.233 closest distance to " O   PHE A 218 " =    1.656
peak=   -3.232 closest distance to " O   TYR A 186 " =    1.801
peak=   -3.231 closest distance to " O   HOH Z 189 " =    2.512
peak=   -3.230 closest distance to " C   ARG A 269 " =    1.508
peak=   -3.229 closest distance to " CG  MET A 105 " =    1.006
peak=   -3.229 closest distance to " O   HOH Z  17 " =    1.530
peak=   -3.219 closest distance to " CE2 PHE A  61 " =    2.668
peak=   -3.215 closest distance to " CA  GLY A 203 " =    2.608
peak=   -3.212 closest distance to " C   LEU A 222 " =    1.098
peak=   -3.202 closest distance to " CE1 TYR A 247 " =    2.597
peak=   -3.202 closest distance to " O   HOH Z 191 " =    5.651
peak=   -3.201 closest distance to " CD2 LEU A 237 " =    2.786
peak=   -3.200 closest distance to " ND2 ASN A  69 " =    1.935
peak=   -3.194 closest distance to " O   GLY A  80 " =    2.353
peak=   -3.191 closest distance to " N   LYS A 166 " =    1.938
peak=   -3.191 closest distance to " OG BSER A 134 " =    1.845
peak=   -3.191 closest distance to " O   HOH Z 138 " =    1.286
peak=   -3.191 closest distance to " CD  PRO A 243 " =    2.106
peak=   -3.189 closest distance to " NE2 GLN A 194 " =    1.927
peak=   -3.185 closest distance to " O   HOH Z 286 " =    1.803
peak=   -3.184 closest distance to " N   SER A 276 " =    1.476
peak=   -3.183 closest distance to " OG1 THR A  82 " =    2.111
peak=   -3.183 closest distance to " O   HOH Z 231 " =    1.266
peak=   -3.183 closest distance to " O   HOH Z 147 " =    1.913
peak=   -3.178 closest distance to " O   HOH Z 350 " =    1.919
peak=   -3.177 closest distance to " O   HOH Z 144 " =    1.148
peak=   -3.169 closest distance to " O   SER A 276 " =    1.680
peak=   -3.169 closest distance to " O   HOH Z  64 " =    1.604
peak=   -3.167 closest distance to " O   HOH Z 426 " =    1.732
peak=   -3.161 closest distance to " O   HOH Z 371 " =    2.395
peak=   -3.159 closest distance to " CG1 VAL A  67 " =    2.926
peak=   -3.156 closest distance to " O   HOH Z 357 " =    2.137
peak=   -3.153 closest distance to " CE  MET A 105 " =    2.377
peak=   -3.141 closest distance to " CG1 VAL A 197 " =    2.428
peak=   -3.131 closest distance to " CD2 LEU A   5 " =    1.155
peak=   -3.130 closest distance to " CD1 TYR A 247 " =    2.445
peak=   -3.122 closest distance to " O   HOH Z 390 " =    2.141
peak=   -3.121 closest distance to " O   HOH Z 312 " =    1.680
peak=   -3.120 closest distance to " O   HOH Z  78 " =    1.988
peak=   -3.118 closest distance to " N   ALA A 248 " =    1.783
peak=   -3.115 closest distance to " OXT GLY A 302 " =    3.215
peak=   -3.113 closest distance to " NE2 GLN A 240 " =    1.661
peak=   -3.110 closest distance to " NH2 ARG A 219 " =    1.712
peak=   -3.101 closest distance to " O   HOH Z 136 " =    2.631
peak=   -3.100 closest distance to " O   ALA A  51 " =    1.328
peak=   -3.091 closest distance to " O   HOH Z   9 " =    3.150
peak=   -3.089 closest distance to " N   ALA A 248 " =    2.400
peak=   -3.089 closest distance to " NH2AARG A 275 " =    5.326
peak=   -3.080 closest distance to " O   HOH Z 140 " =    1.520
peak=   -3.080 closest distance to " O   HOH Z 219 " =    4.664
peak=   -3.075 closest distance to " CZ3 TRP A 177 " =    1.087
peak=   -3.040 closest distance to " CA  SER A  62 " =    2.527
peak=   -3.027 closest distance to " ND2 ASN A  60 " =    1.197

================= 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    :  0.4707 0.4646   6.272968e+00   6.254960e+00
   1_bss:  0.4617 0.4515   6.266404e+00   6.243605e+00
   1_xyz:  0.3730 0.4009   6.138900e+00   6.174412e+00
   1_adp:  0.3238 0.3752   6.038465e+00   6.130671e+00
   1_occ:  0.3235 0.3764   6.037725e+00   6.132529e+00
   2_bss:  0.3214 0.3730   6.038716e+00   6.131172e+00
   2_xyz:  0.2413 0.2991   5.798738e+00   5.954172e+00
   2_adp:  0.2198 0.2743   5.722466e+00   5.891214e+00
   2_occ:  0.2196 0.2740   5.721986e+00   5.891315e+00
   3_bss:  0.2181 0.2740   5.723808e+00   5.892775e+00
   3_xyz:  0.1646 0.2166   5.470725e+00   5.679157e+00
   3_adp:  0.1497 0.2042   5.399578e+00   5.626060e+00
   3_occ:  0.1495 0.2043   5.399778e+00   5.627101e+00
   4_bss:  0.1493 0.2040   5.399310e+00   5.626148e+00
   4_xyz:  0.1348 0.1859   5.314585e+00   5.545099e+00
   4_adp:  0.1328 0.1810   5.293660e+00   5.515983e+00
   4_occ:  0.1327 0.1809   5.293177e+00   5.515474e+00
   5_bss:  0.1327 0.1809   5.292956e+00   5.515387e+00
   5_xyz:  0.1198 0.1696   5.214672e+00   5.457936e+00
   5_adp:  0.1185 0.1685   5.204953e+00   5.449907e+00
   5_occ:  0.1184 0.1685   5.204857e+00   5.450053e+00
   5_bss:  0.1183 0.1682   5.203954e+00   5.448337e+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:  0.327  30.302   7.106   6.654  12.105   0.000   0.000   0.000
   1_xyz:  0.327  30.302   7.106   6.654  12.105   0.000   0.000   0.000
   1_adp:  0.327  30.302   7.106   6.654  12.105   0.000   0.000   0.000
   1_occ:  0.327  30.302   7.106   6.654  12.105   0.000   0.000   0.000
   2_bss:  0.313  46.498   4.111   3.868   8.737   0.000   0.000   0.000
   2_xyz:  0.313  46.498   4.111   3.868   8.737   0.000   0.000   0.000
   2_adp:  0.313  46.498   4.111   3.868   8.737   0.000   0.000   0.000
   2_occ:  0.313  46.498   4.111   3.868   8.737   0.000   0.000   0.000
   3_bss:  0.317  63.542   2.488   2.698   5.575   0.000   0.000   0.000
   3_xyz:  0.317  63.542   2.488   2.698   5.575   0.000   0.000   0.000
   3_adp:  0.317  63.542   2.488   2.698   5.575   0.000   0.000   0.000
   3_occ:  0.317  63.542   2.488   2.698   5.575   0.000   0.000   0.000
   4_bss:  0.334  75.173   2.150   2.349   4.520   0.000   0.000   0.000
   4_xyz:  0.334  75.173   2.150   2.349   4.520   0.000   0.000   0.000
   4_adp:  0.334  75.173   2.150   2.349   4.520   0.000   0.000   0.000
   4_occ:  0.334  75.173   2.150   2.349   4.520   0.000   0.000   0.000
   5_bss:  0.330  68.759   2.224   2.368   4.301   0.000   0.000   0.000
   5_xyz:  0.330  68.759   2.224   2.368   4.301   0.000   0.000   0.000
   5_adp:  0.330  68.759   2.224   2.368   4.301   0.000   0.000   0.000
   5_occ:  0.330  68.759   2.224   2.368   4.301   0.000   0.000   0.000
   5_bss:  0.326  67.155  -0.681  -0.592   1.273  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  54.123 0.4691  0.5321    63656.875
   1_bss:  53.102 0.4815  0.7062    61496.362
   1_xyz:  45.263 0.5784  0.8218    45891.576
   1_adp:  40.738 0.6339  0.9262    39475.374
   1_occ:  40.807 0.6331  0.9243    39600.185
   2_bss:  40.608 0.6353  0.8338    39257.860
   2_xyz:  30.607 0.7507  0.9617    23499.736
   2_adp:  27.644 0.7839  0.9876    19946.304
   2_occ:  27.678 0.7834  0.9868    19941.321
   3_bss:  27.644 0.7840  0.9213    20080.074
   3_xyz:  20.854 0.8533  0.9728    11973.131
   3_adp:  19.368 0.8679  0.9763    10666.666
   3_occ:  19.405 0.8675  0.9758    10681.212
   4_bss:  19.357 0.8679  0.9563    10651.623
   4_xyz:  17.441 0.8857  0.9632     8907.832
   4_adp:  16.711 0.8926  0.9607     8428.207
   4_occ:  16.699 0.8927  0.9608     8416.593
   5_bss:  16.692 0.8927  0.9595     8412.247
   5_xyz:  15.394 0.9039  0.9679     7418.094
   5_adp:  15.187 0.9058  0.9646     7291.889
   5_occ:  15.190 0.9057  0.9645     7286.423
   5_bss:  15.182 0.9057  0.9652     7256.968
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.4494e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.4494e+01
   1_xyz:   1.691  0.014  0.108 18.325  0.006  4.111   1.4162e-01
   1_adp:   1.691  0.014  0.108 18.325  0.006  4.111   1.4162e-01
   1_occ:   1.691  0.014  0.108 18.325  0.006  4.111   1.4162e-01
   2_bss:   1.691  0.014  0.108 18.325  0.006  4.111   1.4162e-01
   2_xyz:   1.216  0.009  0.083 16.747  0.005  4.132   8.5339e-02
   2_adp:   1.216  0.009  0.083 16.747  0.005  4.132   8.5339e-02
   2_occ:   1.216  0.009  0.083 16.747  0.005  4.132   8.5339e-02
   3_bss:   1.216  0.009  0.083 16.747  0.005  4.132   8.5339e-02
   3_xyz:   1.092  0.009  0.082 16.442  0.004  4.133   7.2935e-02
   3_adp:   1.092  0.009  0.082 16.442  0.004  4.133   7.2935e-02
   3_occ:   1.092  0.009  0.082 16.442  0.004  4.133   7.2935e-02
   4_bss:   1.092  0.009  0.082 16.442  0.004  4.133   7.2935e-02
   4_xyz:   0.993  0.007  0.076 15.983  0.003  4.140   6.2601e-02
   4_adp:   0.993  0.007  0.076 15.983  0.003  4.140   6.2601e-02
   4_occ:   0.993  0.007  0.076 15.983  0.003  4.140   6.2601e-02
   5_bss:   0.993  0.007  0.076 15.983  0.003  4.140   6.2601e-02
   5_xyz:   1.223  0.012  0.095 15.953  0.004  4.116   9.1256e-02
   5_adp:   1.223  0.012  0.095 15.953  0.004  4.116   9.1256e-02
   5_occ:   1.223  0.012  0.095 15.953  0.004  4.116   9.1256e-02
   5_bss:   1.223  0.012  0.095 15.953  0.004  4.116   9.1256e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0654e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0654e+00
   1_xyz:  14.131  0.162  0.423 86.593  0.036  2.175   1.0619e-01
   1_adp:  14.131  0.162  0.423 86.593  0.036  2.175   1.0619e-01
   1_occ:  14.131  0.162  0.423 86.593  0.036  2.175   1.0619e-01
   2_bss:  14.131  0.162  0.423 86.593  0.036  2.175   1.0619e-01
   2_xyz:   6.839  0.074  0.250 88.637  0.051  2.276   5.4758e-02
   2_adp:   6.839  0.074  0.250 88.637  0.051  2.276   5.4758e-02
   2_occ:   6.839  0.074  0.250 88.637  0.051  2.276   5.4758e-02
   3_bss:   6.839  0.074  0.250 88.637  0.051  2.276   5.4758e-02
   3_xyz:   7.696  0.053  0.301 89.314  0.038  2.356   5.4435e-02
   3_adp:   7.696  0.053  0.301 89.314  0.038  2.356   5.4435e-02
   3_occ:   7.696  0.053  0.301 89.314  0.038  2.356   5.4435e-02
   4_bss:   7.696  0.053  0.301 89.314  0.038  2.356   5.4435e-02
   4_xyz:   7.581  0.047  0.282 82.752  0.037  2.444   6.6874e-02
   4_adp:   7.581  0.047  0.282 82.752  0.037  2.444   6.6874e-02
   4_occ:   7.581  0.047  0.282 82.752  0.037  2.444   6.6874e-02
   5_bss:   7.581  0.047  0.282 82.752  0.037  2.444   6.6874e-02
   5_xyz:   8.520  0.064  0.565 83.520  0.041  2.278   6.8112e-02
   5_adp:   8.520  0.064  0.565 83.520  0.041  2.278   6.8112e-02
   5_occ:   8.520  0.064  0.565 83.520  0.041  2.278   6.8112e-02
   5_bss:   8.520  0.064  0.565 83.520  0.041  2.278   6.8112e-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:  77.82   0.00  13.07  72.37   0.00  10.35  77.82   0.00  27.89
   1_occ:  77.82   0.00  13.07  72.37   0.00  10.35  77.82   0.00  27.89
   2_bss:  77.82   0.00  13.07  72.37   0.00  10.35  77.82   0.00  27.89
   2_xyz:  77.82   0.00  13.07  72.37   0.00  10.35  77.82   0.00  27.89
   2_adp:  93.19   0.00  12.66  93.19   0.00   8.99  77.23   0.00  32.68
   2_occ:  93.19   0.00  12.66  93.19   0.00   8.99  77.23   0.00  32.68
   3_bss:  93.19   0.00  12.66  93.19   0.00   8.99  77.23   0.00  32.68
   3_xyz:  93.19   0.00  12.66  93.19   0.00   8.99  77.23   0.00  32.68
   3_adp: 115.60   0.00  13.84 115.60   0.00   8.95  96.50   0.54  40.50
   3_occ: 115.60   0.00  13.84 115.60   0.00   8.95  96.50   0.54  40.50
   4_bss: 115.60   0.00  13.84 115.60   0.00   8.95  96.50   0.54  40.50
   4_xyz: 115.60   0.00  13.84 115.60   0.00   8.95  96.50   0.54  40.50
   4_adp:  99.33   0.00  13.21  80.45   0.00   8.53  99.33   0.91  38.73
   4_occ:  99.33   0.00  13.21  80.45   0.00   8.53  99.33   0.91  38.73
   5_bss:  99.33   0.00  13.21  80.45   0.00   8.53  99.33   0.91  38.73
   5_xyz:  99.33   0.00  13.21  80.45   0.00   8.53  99.33   0.91  38.73
   5_adp: 101.73   0.00  12.97  82.29   0.00   8.37 101.73   1.00  37.97
   5_occ: 101.73   0.00  12.97  82.29   0.00   8.37 101.73   1.00  37.97
   5_bss: 104.72   2.99  15.96  85.28   2.99  11.36 104.72   3.99  40.96
------------------------------------------------------------------------
 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:    1.257    0.011    0.413
   1_adp:    1.257    0.011    0.413
   1_occ:    1.257    0.011    0.413
   2_bss:    1.257    0.011    0.413
   2_xyz:    1.827    0.049    0.569
   2_adp:    1.827    0.049    0.569
   2_occ:    1.827    0.049    0.569
   3_bss:    1.827    0.049    0.569
   3_xyz:    1.770    0.073    0.633
   3_adp:    1.770    0.073    0.633
   3_occ:    1.770    0.073    0.633
   4_bss:    1.770    0.073    0.633
   4_xyz:    1.953    0.074    0.668
   4_adp:    1.953    0.074    0.668
   4_occ:    1.953    0.074    0.668
   5_bss:    1.953    0.074    0.668
   5_xyz:    1.949    0.075    0.684
   5_adp:    1.949    0.075    0.684
   5_occ:    1.949    0.075    0.684
   5_bss:    1.949    0.075    0.684
------------------------------------------------------------------------

CPU time actual refinement: 330.47


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_912/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_912/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_912/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_912/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_912/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 330.32 
  Macro-tasks:
    bulk solvent and scale       = 40.89  
    individual site refinement   = 134.82 
    weights calculation          = 31.05  
    collect and process          = 6.44   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 213.30 
  Micro-tasks:
    mask                            = 2.26   
    f_calc                          = 101.45 
    alpha_beta                      = 8.25   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 112.57 
    fmodel                         = 6.95   
    r_factors                      = 0.23   
    phase_errors                   = 10.76  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 243.90 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.622 micro seconds
Total CPU time: 5.73 minutes
from_scatterers_fft:    669 calls, 101.13 s
gradients_fft:          614 calls,  99.04 s

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

# Date 2008-01-16 Time 02:43:53 PST -0800 (1200480233.66 s)
Start R-work = 0.4707, R-free = 0.4646 (no bulk solvent and anisotropic scale)
Final R-work = 0.1354, R-free = 0.1839 (no bulk solvent and anisotropic scale)

Start R-work = 0.4617, R-free = 0.4515
Final R-work = 0.1183, R-free = 0.1682