# Date 2008-01-16 Time 02:01:58 PST -0800 (1200477718.11 s)
#phil __OFF__

Command line arguments: "../654.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = blackbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 17035
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 654

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 46.6953, 86.39, 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: 2.75, per 1000 atoms: 0.97


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.6953, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.994 1.99157
Completeness in resolution range: 0.978227
Completeness with d_max=infinity: 0.975159

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9940
                             d_min =   1.9916

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.6953, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.994 1.99157
Completeness in resolution range: 0.978227
Completeness with d_max=infinity: 0.975159

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9944 -  4.2610 [2102/2126]  1892   210  10.0%
  bin  2:  4.2610 -  3.3950 [2027/2047]  1823   204  10.1%
  bin  3:  3.3950 -  2.9696 [1992/2011]  1794   198   9.9%
  bin  4:  2.9696 -  2.6998 [1963/1993]  1765   198  10.1%
  bin  5:  2.6998 -  2.5073 [1977/1996]  1782   195   9.9%
  bin  6:  2.5073 -  2.3600 [1958/1983]  1758   200  10.2%
  bin  7:  2.3600 -  2.2423 [1940/1968]  1748   192   9.9%
  bin  8:  2.2423 -  2.1449 [1932/1968]  1739   193  10.0%
  bin  9:  2.1449 -  2.0626 [1915/1957]  1724   191  10.0%
  bin 10:  2.0626 -  1.9916 [1783/1976]  1605   178  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_654/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.15 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 8
        2.42 -     3.04: 2213
        3.04 -     3.66: 4670
        3.66 -     4.28: 9084
        4.28 -     4.90: 12372
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " NH1BARG A 275 " - " O  BHOH Z 338 "  2.341 3.120
  " OE1 GLN A  55 " - " O   HOH Z 403 "  2.382 3.040 -x+1,y-1/2,-z+1/2
  " NH2BARG A 275 " - " O   HOH Z 335 "  2.406 3.120
  ... (remaining 28342 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_654/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_654/model_refine_001.geo

CPU time processing inputs: 7.87


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 46.69535 86.39 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.99 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4095   r_free= 0.3950   ksol= 0.00   Bsol= 0.00   scale= 0.837    |
|                                                                             |
| 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:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.192961                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9944 -  4.7522 0.99   1374  152 0.3532 0.3362      6.4943      6.4342|
|  2:  4.7522 -  3.7921 0.99   1303  146 0.2987 0.2954      6.5711      6.5634|
|  3:  3.7921 -  3.3186 0.99   1287  144 0.3371 0.3179      6.4839      6.4983|
|  4:  3.3186 -  3.0179 0.99   1284  143 0.3847 0.3375      6.4114      6.2953|
|  5:  3.0179 -  2.8031 0.99   1267  138 0.4237 0.4368      6.2756      6.3282|
|  6:  2.8031 -  2.6388 0.99   1272  143 0.4299 0.4967      6.2061      6.1893|
|  7:  2.6388 -  2.5073 0.99   1269  139 0.4584 0.4265      6.1805      6.1372|
|  8:  2.5073 -  2.3986 0.98   1248  141 0.4645 0.4460      6.1398      6.1514|
|  9:  2.3986 -  2.3066 0.98   1255  138 0.4418 0.4508      6.0568      6.0376|
| 10:  2.3066 -  2.2273 1.00   1237  141 0.4765 0.4282      6.0974      6.0102|
| 11:  2.2273 -  2.1578 0.97   1254  135 0.4822 0.4004      6.0242      5.9407|
| 12:  2.1578 -  2.0963 0.98   1246  140 0.4661 0.4718      5.9533      5.9827|
| 13:  2.0963 -  2.0413 0.99   1243  136 0.4737 0.4756      5.8639      5.8769|
| 14:  2.0413 -  1.9916 0.86   1091  123 0.4874 0.4550      5.8332      5.7161|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9944 -  4.7522  1374   152  0.74  30.23   0.82     0.77      55602.16|
|  2:  4.7522 -  3.7921  1303   146  0.80  25.80   0.93     0.85      62692.84|
|  3:  3.7921 -  3.3186  1287   144  0.75  30.90   0.90     0.83      63159.00|
|  4:  3.3186 -  3.0179  1284   143  0.70  35.59   0.85     0.75      57803.01|
|  5:  3.0179 -  2.8031  1267   138  0.60  43.78   0.80     0.67      54269.81|
|  6:  2.8031 -  2.6388  1272   143  0.56  46.87   0.77     0.62      51618.53|
|  7:  2.6388 -  2.5073  1269   139  0.54  49.07   0.77     0.60      48559.91|
|  8:  2.5073 -  2.3986  1248   141  0.54  48.71   0.78     0.62      43770.41|
|  9:  2.3986 -  2.3066  1255   138  0.58  46.11   0.77     0.63      36568.22|
| 10:  2.3066 -  2.2273  1237   141  0.59  45.35   0.79     0.65      31760.62|
| 11:  2.2273 -  2.1578  1254   135  0.57  46.38   0.78     0.65      29788.56|
| 12:  2.1578 -  2.0963  1246   140  0.52  50.43   0.81     0.61      30830.37|
| 13:  2.0963 -  2.0413  1243   136  0.49  53.11   0.78     0.56      28376.52|
| 14:  2.0413 -  1.9916  1091   123  0.51  51.44   0.75     0.54      22522.59|
|alpha:            min =        0.54 max =            0.85 mean =         0.67|
|beta:             min =    22522.59 max =        63159.00 mean =     44529.33|
|figures of merit: min =        0.00 max =            1.00 mean =         0.61|
|phase err.(work): min =        0.00 max =           89.97 mean =        42.87|
|phase err.(test): min =        0.00 max =           89.76 mean =        43.08|
|-----------------------------------------------------------------------------|

============================== 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 = 6.139219              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 72.343   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.501656              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.816   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      168 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      682 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1503 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2646 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3922 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5102 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6559 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7736 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.688 |
| 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 |       1.670 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.860)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

|-Occupancies statistics------------------------------------------------------|
| occupancies: max = 1.00   min = 0.30   number of occupancies < 0.1 = 0      |
|-----------------------------------------------------------------------------|

                ----------Modify initial isotropic ADP----------               

Randomizing
|-ADP statistics (Wilson B = 11.860)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4191   r_free= 0.4049   ksol= 0.00   Bsol= 0.00   scale= 0.804    |
|                                                                             |
| 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:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.201754                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4011   r_free= 0.3849   ksol= 0.36   Bsol= 20.00   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.34,8.54,8.21,0.00,0.00,0.00); trace/3= 8.03                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.52 A                  |
| x-ray target function (ml) for work reflections: 6.188786                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.826398              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 74.538   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.500065              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 75.813   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4011      final r-factor (work) = 0.2857          |
| start r-factor (free) = 0.3849      final r-factor (free) = 0.3060          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 71.7969 = 5.83 * 0.50 * 6.2161 + 1.00 * 53.6882                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.5930 = 5.83 * 0.50 * 6.0028 + 1.00 * 0.1056                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2857      final r-factor (work) = 0.2081          |
| start r-factor (free) = 0.3060      final r-factor (free) = 0.2368          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0166 = 0.50 * 1.00 * 6.0028 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8902 = 0.50 * 1.00 * 5.7584 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.860)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    50.57   9.73     None  None   None       |
|    all(noH): 2823   0      0.00    50.57   9.73     None  None   None       |
|    Sol.    : 438    0      0.00    50.57   26.40    None  None   None       |
|    Mac.    : 2385   0      0.00    42.10   6.67     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   5.057: 1188   |   5:    25.283 -  30.339:  120        |
|      1:     5.057 -  10.113:  801   |   6:    30.339 -  35.396:  108        |
|      2:    10.113 -  15.170:  261   |   7:    35.396 -  40.452:   69        |
|      3:    15.170 -  20.226:  145   |   8:    40.452 -  45.509:   20        |
|      4:    20.226 -  25.283:  105   |   9:    45.509 -  50.565:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2081 r_free = 0.2368             target_work(ml) = 5.635         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2075 r_free = 0.2366             target_work(ml) = 5.633         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2075   r_free= 0.2366   ksol= 0.36   Bsol= 20.00   scale= 1.088   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.34,8.54,8.21,0.00,0.00,0.00); trace/3= 8.03                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.633432                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2011   r_free= 0.2292   ksol= 0.34   Bsol= 36.68   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.13,4.61,5.40,0.00,0.00,0.00); trace/3= 4.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.628033                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.250577              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 92.444   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.238835              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 112.282  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2011      final r-factor (work) = 0.1392          |
| start r-factor (free) = 0.2292      final r-factor (free) = 0.1755          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4942 = 3.25 * 0.50 * 5.7769 + 1.00 * 0.1051                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9148 = 3.25 * 0.50 * 5.4451 + 1.00 * 0.0650                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1392      final r-factor (work) = 0.1273          |
| start r-factor (free) = 0.1755      final r-factor (free) = 0.1657          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3108 = 0.24 * 1.00 * 5.4451 + 1.00 * 0.0104                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.2649 = 0.24 * 1.00 * 5.2570 + 1.00 * 0.0093                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.860)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    51.69   10.19    None  None   None       |
|    all(noH): 2823   0      0.00    51.69   10.19    None  None   None       |
|    Sol.    : 438    0      0.00    51.69   29.56    None  None   None       |
|    Mac.    : 2385   0      0.00    48.48   6.64     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   5.169: 1299   |   5:    25.845 -  31.014:   94        |
|      1:     5.169 -  10.338:  703   |   6:    31.014 -  36.183:   89        |
|      2:    10.338 -  15.507:  277   |   7:    36.183 -  41.352:   98        |
|      3:    15.507 -  20.676:  110   |   8:    41.352 -  46.521:   57        |
|      4:    20.676 -  25.845:   78   |   9:    46.521 -  51.690:   18        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1273 r_free = 0.1657             target_work(ml) = 5.227         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1272 r_free = 0.1655             target_work(ml) = 5.226         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1272   r_free= 0.1655   ksol= 0.34   Bsol= 36.68   scale= 1.021   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.13,4.61,5.40,0.00,0.00,0.00); trace/3= 4.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.226440                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1270   r_free= 0.1651   ksol= 0.33   Bsol= 36.68   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.45,3.75,4.83,0.00,0.00,0.00); trace/3= 4.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.226610                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.137275              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 119.821  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.605651              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.315  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1270      final r-factor (work) = 0.1164          |
| start r-factor (free) = 0.1651      final r-factor (free) = 0.1571          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6862 = 2.14 * 0.50 * 5.2602 + 1.00 * 0.0650                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.6035 = 2.14 * 0.50 * 5.1858 + 1.00 * 0.0617                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1164      final r-factor (work) = 0.1125          |
| start r-factor (free) = 0.1571      final r-factor (free) = 0.1562          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 18.7076 = 3.61 * 1.00 * 5.1858 + 1.00 * 0.0092                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 18.5752 = 3.61 * 1.00 * 5.1474 + 1.00 * 0.0155                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.860)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    71.68   11.09    None  None   None       |
|    all(noH): 2823   0      0.00    71.68   11.09    None  None   None       |
|    Sol.    : 438    0      0.00    71.40   33.71    None  None   None       |
|    Mac.    : 2385   0      0.00    71.68   6.94     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.168: 1663   |   5:    35.842 -  43.010:   86        |
|      1:     7.168 -  14.337:  538   |   6:    43.010 -  50.178:   76        |
|      2:    14.337 -  21.505:  168   |   7:    50.178 -  57.347:   55        |
|      3:    21.505 -  28.673:  101   |   8:    57.347 -  64.515:   25        |
|      4:    28.673 -  35.842:  102   |   9:    64.515 -  71.683:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1125 r_free = 0.1562             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1124 r_free = 0.1562             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1124   r_free= 0.1562   ksol= 0.33   Bsol= 36.68   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.45,3.75,4.83,0.00,0.00,0.00); trace/3= 4.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.145175                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1124   r_free= 0.1561   ksol= 0.32   Bsol= 41.96   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.52,3.75,4.91,0.00,0.00,0.00); trace/3= 4.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.144097                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.615672              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 148.745  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.425586              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 101.856  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1124      final r-factor (work) = 0.1120          |
| start r-factor (free) = 0.1561      final r-factor (free) = 0.1571          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2196 = 1.62 * 0.50 * 5.1470 + 1.00 * 0.0617                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2103 = 1.62 * 0.50 * 5.1430 + 1.00 * 0.0557                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1120      final r-factor (work) = 0.1123          |
| start r-factor (free) = 0.1571      final r-factor (free) = 0.1558          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2064 = 0.43 * 1.00 * 5.1430 + 1.00 * 0.0177                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2222 = 0.43 * 1.00 * 5.1468 + 1.00 * 0.0318                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.860)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.12   10.83    None  None   None       |
|    all(noH): 2823   0      0.00    76.12   10.83    None  None   None       |
|    Sol.    : 438    0      0.34    68.58   32.52    None  None   None       |
|    Mac.    : 2385   0      0.00    76.12   6.85     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.612: 1733   |   5:    38.058 -  45.670:   94        |
|      1:     7.612 -  15.223:  517   |   6:    45.670 -  53.282:   61        |
|      2:    15.223 -  22.835:  145   |   7:    53.282 -  60.893:   33        |
|      3:    22.835 -  30.447:  113   |   8:    60.893 -  68.505:   12        |
|      4:    30.447 -  38.058:  110   |   9:    68.505 -  76.117:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1123 r_free = 0.1558             target_work(ml) = 5.143         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1122 r_free = 0.1558             target_work(ml) = 5.143         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1122   r_free= 0.1558   ksol= 0.32   Bsol= 41.96   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.52,3.75,4.91,0.00,0.00,0.00); trace/3= 4.06                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.142733                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1122   r_free= 0.1558   ksol= 0.32   Bsol= 41.96   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.53,3.76,4.93,0.00,0.00,0.00); trace/3= 4.08                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.142740                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.040309              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 149.588  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.017007              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 97.334   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1122      final r-factor (work) = 0.1097          |
| start r-factor (free) = 0.1558      final r-factor (free) = 0.1551          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3059 = 2.04 * 0.50 * 5.1465 + 1.00 * 0.0557                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2980 = 2.04 * 0.50 * 5.1331 + 1.00 * 0.0615                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1097      final r-factor (work) = 0.1092          |
| start r-factor (free) = 0.1551      final r-factor (free) = 0.1557          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2423 = 1.02 * 1.00 * 5.1331 + 1.00 * 0.0219                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2287 = 1.02 * 1.00 * 5.1283 + 1.00 * 0.0132                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 24     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.860)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.63   10.89    None  None   None       |
|    all(noH): 2823   0      0.00    80.63   10.89    None  None   None       |
|    Sol.    : 438    0      0.15    70.98   32.97    None  None   None       |
|    Mac.    : 2385   0      0.00    80.63   6.84     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.063: 1780   |   5:    40.314 -  48.376:   91        |
|      1:     8.063 -  16.125:  488   |   6:    48.376 -  56.439:   57        |
|      2:    16.125 -  24.188:  146   |   7:    56.439 -  64.502:   20        |
|      3:    24.188 -  32.251:  118   |   8:    64.502 -  72.564:   10        |
|      4:    32.251 -  40.314:  110   |   9:    72.564 -  80.627:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1092 r_free = 0.1557             target_work(ml) = 5.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1092 r_free = 0.1557             target_work(ml) = 5.131         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1092   r_free= 0.1557   ksol= 0.32   Bsol= 41.96   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.53,3.76,4.93,0.00,0.00,0.00); trace/3= 4.08                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.131269                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9944 -  4.7522 0.99   1374  152 0.0995 0.1293      5.3825      5.5129|
|  2:  4.7522 -  3.7921 0.99   1303  146 0.0842 0.1138      5.4309      5.6439|
|  3:  3.7921 -  3.3186 0.99   1287  144 0.1034 0.1476      5.4666      5.8339|
|  4:  3.3186 -  3.0179 0.99   1284  143 0.1169 0.1547      5.4382      5.5817|
|  5:  3.0179 -  2.8031 0.99   1267  138 0.1273 0.1694      5.3164      5.5466|
|  6:  2.8031 -  2.6388 0.99   1272  143 0.1162 0.1866      5.1926      5.4771|
|  7:  2.6388 -  2.5073 0.99   1269  139 0.1232 0.1540       5.151      5.3205|
|  8:  2.5073 -  2.3986 0.98   1248  141 0.1138 0.1738      5.0695       5.378|
|  9:  2.3986 -  2.3066 0.98   1255  138 0.1140 0.1746      5.0319      5.2521|
| 10:  2.3066 -  2.2273 1.00   1237  141 0.1083 0.1700      4.9557      5.2517|
| 11:  2.2273 -  2.1578 0.97   1254  135 0.1113 0.1615      4.9278       5.209|
| 12:  2.1578 -  2.0963 0.98   1246  140 0.1113 0.1753      4.8709      5.2529|
| 13:  2.0963 -  2.0413 0.99   1243  136 0.1114 0.1582      4.8016      5.0256|
| 14:  2.0413 -  1.9916 0.86   1091  123 0.1028 0.1864      4.6816      4.9833|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9944 -  4.7522  1374   152  0.94   9.03   0.98     0.96       7130.75|
|  2:  4.7522 -  3.7921  1303   146  0.95   7.86   1.02     1.00       9011.06|
|  3:  3.7921 -  3.3186  1287   144  0.94  10.95   1.03     1.02      10218.23|
|  4:  3.3186 -  3.0179  1284   143  0.92  13.07   1.01     0.99      10088.73|
|  5:  3.0179 -  2.8031  1267   138  0.90  15.48   1.00     0.97       8261.98|
|  6:  2.8031 -  2.6388  1272   143  0.90  15.65   0.99     0.96       6943.14|
|  7:  2.6388 -  2.5073  1269   139  0.91  15.41   0.99     0.96       6047.48|
|  8:  2.5073 -  2.3986  1248   141  0.91  14.66   0.99     0.97       5244.58|
|  9:  2.3986 -  2.3066  1255   138  0.91  15.30   1.01     0.98       5062.06|
| 10:  2.3066 -  2.2273  1237   141  0.91  15.09   1.00     0.96       4314.23|
| 11:  2.2273 -  2.1578  1254   135  0.90  16.07   1.00     0.97       4328.42|
| 12:  2.1578 -  2.0963  1246   140  0.91  15.10   1.01     1.00       3855.76|
| 13:  2.0963 -  2.0413  1243   136  0.91  15.66   1.00     0.99       3409.63|
| 14:  2.0413 -  1.9916  1091   123  0.91  14.84   0.98     0.94       2674.25|
|alpha:            min =        0.94 max =            1.02 mean =         0.98|
|beta:             min =     2674.25 max =        10218.23 mean =      6253.00|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.81|
|phase err.(test): min =        0.00 max =           89.80 mean =        13.38|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1092   r_free= 0.1557   ksol= 0.32   Bsol= 46.09   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.54,-0.33,0.86,-0.00,0.00,0.00); trace/3= -0.00                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.131282                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 14.99 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1092   r_free= 0.1557   ksol= 0.32   Bsol= 46.09   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.54,-0.33,0.86,-0.00,0.00,0.00); trace/3= -0.00                          |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.131282                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9944 -  4.7522 0.99   1374  152 0.0996 0.1294      5.3827      5.5132|
|  2:  4.7522 -  3.7921 0.99   1303  146 0.0842 0.1138      5.4311      5.6439|
|  3:  3.7921 -  3.3186 0.99   1287  144 0.1034 0.1477      5.4666       5.834|
|  4:  3.3186 -  3.0179 0.99   1284  143 0.1168 0.1547      5.4382      5.5817|
|  5:  3.0179 -  2.8031 0.99   1267  138 0.1273 0.1694      5.3163      5.5465|
|  6:  2.8031 -  2.6388 0.99   1272  143 0.1162 0.1865      5.1925       5.477|
|  7:  2.6388 -  2.5073 0.99   1269  139 0.1232 0.1540       5.151      5.3205|
|  8:  2.5073 -  2.3986 0.98   1248  141 0.1138 0.1738      5.0695       5.378|
|  9:  2.3986 -  2.3066 0.98   1255  138 0.1140 0.1746      5.0319       5.252|
| 10:  2.3066 -  2.2273 1.00   1237  141 0.1083 0.1700      4.9557       5.252|
| 11:  2.2273 -  2.1578 0.97   1254  135 0.1113 0.1615      4.9278       5.209|
| 12:  2.1578 -  2.0963 0.98   1246  140 0.1113 0.1753      4.8709      5.2528|
| 13:  2.0963 -  2.0413 0.99   1243  136 0.1114 0.1582      4.8016      5.0256|
| 14:  2.0413 -  1.9916 0.86   1091  123 0.1029 0.1864      4.6815      4.9831|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.9944 -  4.7522  1374   152  0.94   9.04   0.98     0.96       7135.57|
|  2:  4.7522 -  3.7921  1303   146  0.95   7.86   1.02     1.00       9014.53|
|  3:  3.7921 -  3.3186  1287   144  0.94  10.95   1.03     1.02      10219.19|
|  4:  3.3186 -  3.0179  1284   143  0.92  13.07   1.01     0.99      10087.92|
|  5:  3.0179 -  2.8031  1267   138  0.90  15.48   1.00     0.97       8259.90|
|  6:  2.8031 -  2.6388  1272   143  0.90  15.65   0.99     0.96       6941.99|
|  7:  2.6388 -  2.5073  1269   139  0.91  15.41   0.99     0.96       6047.22|
|  8:  2.5073 -  2.3986  1248   141  0.91  14.66   0.99     0.97       5244.34|
|  9:  2.3986 -  2.3066  1255   138  0.91  15.30   1.01     0.99       5062.64|
| 10:  2.3066 -  2.2273  1237   141  0.91  15.09   1.00     0.96       4314.05|
| 11:  2.2273 -  2.1578  1254   135  0.90  16.07   1.00     0.97       4328.99|
| 12:  2.1578 -  2.0963  1246   140  0.91  15.10   1.02     1.00       3855.76|
| 13:  2.0963 -  2.0413  1243   136  0.91  15.66   1.01     0.99       3409.18|
| 14:  2.0413 -  1.9916  1091   123  0.91  14.84   0.99     0.95       2673.03|
|alpha:            min =        0.95 max =            1.02 mean =         0.98|
|beta:             min =     2673.03 max =        10219.19 mean =      6253.34|
|figures of merit: min =        0.00 max =            1.00 mean =         0.92|
|phase err.(work): min =        0.00 max =           89.98 mean =        13.81|
|phase err.(test): min =        0.00 max =           89.80 mean =        13.38|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.860)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      4.13    84.76   15.02    None  None   None       |
|    all(noH): 2823   0      4.13    84.76   15.02    None  None   None       |
|    Sol.    : 438    0      4.28    75.11   37.10    None  None   None       |
|    Mac.    : 2385   0      4.13    84.76   10.97    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:     4.132 -  12.195: 1780   |   5:    44.446 -  52.508:   91        |
|      1:    12.195 -  20.257:  488   |   6:    52.508 -  60.571:   57        |
|      2:    20.257 -  28.320:  146   |   7:    60.571 -  68.634:   20        |
|      3:    28.320 -  36.383:  118   |   8:    68.634 -  76.696:   10        |
|      4:    36.383 -  44.446:  110   |   9:    76.696 -  84.759:    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)= 314         
Filter by distance & map next to the model:
   mapped sites are within: 0.300 - 4.754
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 303 from: 314
   mapped sites are within: 0.732 - 4.754

peak=   11.142 closest distance to " CG2 VAL A 230 " =    1.449
peak=    7.746 closest distance to " CG2 VAL A 296 " =    1.158
peak=    6.395 closest distance to " CG  LEU A   5 " =    1.193
peak=    5.726 closest distance to " CD2 LEU A   5 " =    1.195
peak=    5.655 closest distance to " CG  LEU A 228 " =    1.150
peak=    5.581 closest distance to " NH2 ARG A  56 " =    2.196
peak=    5.442 closest distance to " NE2 GLN A  11 " =    1.178
peak=    5.270 closest distance to " CB  GLN A 223 " =    1.466
peak=    5.205 closest distance to " O   HOH Z 142 " =    1.812
peak=    5.128 closest distance to " CB  GLN A 183 " =    1.261
peak=    5.072 closest distance to " CB  VAL A 296 " =    1.050
peak=    4.889 closest distance to " CB  VAL A 230 " =    1.126
peak=    4.872 closest distance to " O   HOH Z 232 " =    2.304
peak=    4.846 closest distance to " CB  ARG A 275 " =    0.920
peak=    4.645 closest distance to " O   HOH Z 427 " =    2.958
peak=    4.644 closest distance to " CG  PRO A 213 " =    1.217
peak=    4.641 closest distance to " CB  SER A  63 " =    1.261
peak=    4.617 closest distance to " O   HOH Z 126 " =    1.949
peak=    4.595 closest distance to " O   HOH Z  61 " =    1.705
peak=    4.511 closest distance to " C   PRO A 198 " =    1.475
peak=    4.455 closest distance to " O   HOH Z 209 " =    2.267
peak=    4.438 closest distance to " CB  GLU A 152 " =    1.238
peak=    4.373 closest distance to " ND2 ASN A 187 " =    1.518
peak=    4.369 closest distance to " O   HOH Z 346 " =    1.614
peak=    4.368 closest distance to " O   SER A  87 " =    2.294
peak=    4.360 closest distance to " OG ASER A 258 " =    3.076
peak=    4.349 closest distance to " O   HOH Z  43 " =    1.960
peak=    4.324 closest distance to " CB  ASN A 148 " =    1.369
peak=    4.279 closest distance to " O   HOH Z 203 " =    1.737
peak=    4.276 closest distance to " O   HOH Z 265 " =    2.505
peak=    4.276 closest distance to " CG  PRO A 243 " =    1.106
peak=    4.247 closest distance to " O   HOH Z 158 " =    3.141
peak=    4.223 closest distance to " CD2 LEU A 228 " =    1.148
peak=    4.204 closest distance to " O   HOH Z 272 " =    1.868
peak=    4.198 closest distance to " O   HOH Z 298 " =    1.793
peak=    4.191 closest distance to " O   HOH Z 193 " =    1.750
peak=    4.186 closest distance to " CB  SER A   3 " =    1.281
peak=    4.176 closest distance to " CB  TRP A 266 " =    1.015
peak=    4.157 closest distance to " OD1 ASN A  69 " =    2.630
peak=    4.134 closest distance to " O   HOH Z  78 " =    1.780
peak=    4.132 closest distance to " CG  PRO A 198 " =    1.216
peak=    4.127 closest distance to " CB  VAL A 265 " =    1.350
peak=    4.126 closest distance to " O   HOH Z 236 " =    1.923
peak=    4.120 closest distance to " O   HOH Z   9 " =    2.243
peak=    4.097 closest distance to " CB  ARG A  79 " =    1.375
peak=    4.087 closest distance to " CA  TYR A  30 " =    0.952
peak=    4.078 closest distance to " O   HOH Z 369 " =    2.191
peak=    4.073 closest distance to " CB  ALA A   9 " =    1.576
peak=    4.051 closest distance to " O   HOH Z 189 " =    2.759
peak=    4.050 closest distance to " CZ  PHE A 218 " =    1.129
peak=    4.035 closest distance to " O   HOH Z 303 " =    2.093
peak=    4.024 closest distance to " O   HOH Z 423 " =    1.776
peak=    4.018 closest distance to " O   HOH Z 261 " =    2.108
peak=    3.959 closest distance to " CB  ASP A 140 " =    0.936
peak=    3.943 closest distance to " CG1BVAL A  72 " =    1.606
peak=    3.893 closest distance to " CB  GLU A 128 " =    0.986
peak=    3.881 closest distance to " O   HOH Z 248 " =    1.582
peak=    3.872 closest distance to " O   HOH Z 234 " =    3.569
peak=    3.845 closest distance to " CG2 VAL A 257 " =    0.835
peak=    3.842 closest distance to " CB  PRO A  54 " =    0.808
peak=    3.811 closest distance to " O   HOH Z 250 " =    1.391
peak=    3.811 closest distance to " O   HOH Z 368 " =    2.093
peak=    3.808 closest distance to " CB  ARG A 190 " =    1.632
peak=    3.807 closest distance to " CB  GLU A 277 " =    3.590
peak=    3.802 closest distance to " CB  VAL A 202 " =    1.612
peak=    3.799 closest distance to " O   HOH Z 425 " =    2.129
peak=    3.796 closest distance to " CB  ASN A  39 " =    0.912
peak=    3.786 closest distance to " CB  TRP A 179 " =    1.367
peak=    3.769 closest distance to " CG  ARG A  66 " =    2.756
peak=    3.766 closest distance to " O   HOH Z 126 " =    1.981
peak=    3.763 closest distance to " O   HOH Z 435 " =    2.016
peak=    3.757 closest distance to " CB  ASN A 142 " =    1.103
peak=    3.753 closest distance to " O   HOH Z  97 " =    1.990
peak=    3.750 closest distance to " O   HOH Z 411 " =    3.758
peak=    3.743 closest distance to " O   HOH Z 402 " =    1.368
peak=    3.742 closest distance to " O   HOH Z 389 " =    1.864
peak=    3.742 closest distance to " OG BSER A 164 " =    2.195
peak=    3.721 closest distance to " O   HOH Z 403 " =    1.666
peak=    3.719 closest distance to " O   HOH Z 193 " =    1.568
peak=    3.698 closest distance to " O   HOH Z 280 " =    2.975
peak=    3.695 closest distance to " CB  THR A 157 " =    1.135
peak=    3.693 closest distance to " O   HOH Z  78 " =    2.126
peak=    3.693 closest distance to " CA  ALA A 158 " =    1.291
peak=    3.689 closest distance to " CD BLYS A 290 " =    1.121
peak=    3.689 closest distance to " O   HOH Z 371 " =    2.993
peak=    3.684 closest distance to " CB  HIS A 108 " =    0.833
peak=    3.682 closest distance to " N   PHE A 130 " =    1.276
peak=    3.679 closest distance to " O   HOH Z 193 " =    1.942
peak=    3.679 closest distance to " CB  ALA A 248 " =    1.497
peak=    3.678 closest distance to " CB  LEU A 143 " =    1.185
peak=    3.676 closest distance to " O   HOH Z  59 " =    1.888
peak=    3.675 closest distance to " N   ASN A  39 " =    1.188
peak=    3.671 closest distance to " O   HOH Z 425 " =    1.336
peak=    3.667 closest distance to " CA  ASN A 215 " =    1.128
peak=    3.660 closest distance to " CA  PHE A 283 " =    1.235
peak=    3.648 closest distance to " CB  ALA A 291 " =    1.440
peak=    3.645 closest distance to " CA  ALA A  21 " =    1.130
peak=    3.643 closest distance to " OD2 ASP A 286 " =    2.757
peak=    3.639 closest distance to " O   HOH Z 147 " =    1.738
peak=    3.633 closest distance to " O   HOH Z 392 " =    3.194
peak=    3.633 closest distance to " O   HOH Z 426 " =    1.641
peak=    3.631 closest distance to " CB  ARG A 139 " =    0.907
peak=    3.627 closest distance to " O   HOH Z 214 " =    2.122
peak=    3.621 closest distance to " O   HOH Z 145 " =    2.045
peak=    3.614 closest distance to " CB AVAL A  41 " =    1.224
peak=    3.612 closest distance to " NH1AARG A 145 " =    1.076
peak=    3.611 closest distance to " CG1 VAL A 153 " =    0.951
peak=    3.605 closest distance to " CA  ALA A  51 " =    0.924
peak=    3.599 closest distance to " O   HOH Z 313 " =    1.802
peak=    3.580 closest distance to " CB  THR A  31 " =    1.647
peak=    3.559 closest distance to " CG  LEU A 167 " =    1.173
peak=    3.553 closest distance to " O   HOH Z  88 " =    2.940
peak=    3.541 closest distance to " O   HOH Z 132 " =    2.669
peak=    3.533 closest distance to " O   HOH Z 305 " =    3.579
peak=    3.531 closest distance to " CB  SER A 212 " =    1.170
peak=    3.525 closest distance to " CB  ASN A 110 " =    1.106
peak=    3.519 closest distance to " O   HOH Z  66 " =    2.153
peak=    3.518 closest distance to " O   HOH Z 417 " =    3.208
peak=    3.516 closest distance to " O   MET A 105 " =    1.873
peak=    3.515 closest distance to " CE  LYS A  76 " =    0.877
peak=    3.515 closest distance to " O   HOH Z 344 " =    3.059
peak=    3.514 closest distance to " O   GLN A 278 " =    1.301
peak=    3.514 closest distance to " O   HOH Z  10 " =    1.782
peak=    3.513 closest distance to " CB  SER A 216 " =    0.827
peak=    3.507 closest distance to " CB  THR A  82 " =    1.347
peak=    3.505 closest distance to " CD1 LEU A 228 " =    2.030
peak=    3.504 closest distance to " O   HOH Z 245 " =    1.351
peak=    3.501 closest distance to " O   HOH Z 273 " =    2.705
peak=    3.500 closest distance to " O   HOH Z  21 " =    1.702
peak=    3.498 closest distance to " CB  LYS A 290 " =    1.009
peak=    3.494 closest distance to " O   HOH Z 172 " =    3.546
peak=    3.491 closest distance to " CB  LEU A 228 " =    1.288
peak=    3.489 closest distance to " CG2 ILE A  20 " =    1.608
peak=    3.483 closest distance to " CD1 LEU A 300 " =    1.293
peak=    3.479 closest distance to " CD2 TRP A 179 " =    1.372
peak=    3.475 closest distance to " CG1 ILE A  49 " =    1.377
peak=    3.469 closest distance to " O   HOH Z  19 " =    2.462
peak=    3.468 closest distance to " CG2 THR A 221 " =    1.251
peak=    3.468 closest distance to " O   HOH Z 234 " =    1.831
peak=    3.466 closest distance to " O   HOH Z 290 " =    1.032
peak=    3.464 closest distance to " O   HOH Z 437 " =    1.852
peak=    3.456 closest distance to " O   HOH Z 112 " =    1.694
peak=    3.455 closest distance to " CA  TYR A  30 " =    1.062
peak=    3.452 closest distance to " CB  SER A  26 " =    1.715
peak=    3.445 closest distance to " CA  VAL A  41 " =    0.784
peak=    3.442 closest distance to " CG1 ILE A  33 " =    1.260
peak=    3.441 closest distance to " CB  VAL A 268 " =    0.840
peak=    3.440 closest distance to " ND2 ASN A 110 " =    1.674
peak=    3.439 closest distance to " CB  ASN A 224 " =    1.068
peak=    3.437 closest distance to " O   HOH Z 285 " =    2.856
peak=    3.436 closest distance to " NH2 ARG A 156 " =    1.125
peak=    3.436 closest distance to " O   HOH Z 353 " =    2.595
peak=    3.428 closest distance to " O   HOH Z  48 " =    1.608
peak=    3.428 closest distance to " CB  ILE A  20 " =    1.426
peak=    3.423 closest distance to " CG2 ILE A 120 " =    1.255
peak=    3.413 closest distance to " NZ  LYS A 117 " =    3.232
peak=    3.413 closest distance to " CA  THR A 264 " =    0.751
peak=    3.412 closest distance to " O   HOH Z 128 " =    2.058
peak=    3.410 closest distance to " OG1 THR A 294 " =    2.418
peak=    3.408 closest distance to " O   ASP A 124 " =    1.075
peak=    3.406 closest distance to " CA  SER A  87 " =    0.979
peak=    3.400 closest distance to " N   SER A 135 " =    1.320
peak=    3.399 closest distance to " CG BARG A 275 " =    1.413
peak=    3.395 closest distance to " O   HOH Z 128 " =    2.267
peak=    3.393 closest distance to " CA  LYS A 117 " =    1.225
peak=    3.393 closest distance to " CD1 ILE A  33 " =    1.668
peak=    3.384 closest distance to " O   HOH Z 109 " =    2.573
peak=    3.382 closest distance to " O   HOH Z 263 " =    1.631
peak=    3.382 closest distance to " CG  MET A 185 " =    1.201
peak=    3.377 closest distance to " N   ARG A 156 " =    1.299
peak=    3.376 closest distance to " CA  ARG A  36 " =    1.021
peak=    3.376 closest distance to " CB  LYS A 117 " =    1.253
peak=    3.371 closest distance to " O   HOH Z 329 " =    3.937
peak=    3.371 closest distance to " O   HOH Z 407 " =    2.365
peak=    3.367 closest distance to " O   HOH Z 251 " =    1.525
peak=    3.366 closest distance to " CE1 TYR A 186 " =    1.305
peak=    3.360 closest distance to " CA  ARG A 195 " =    1.188
peak=    3.359 closest distance to " NE2 GLN A  77 " =    3.199
peak=    3.358 closest distance to " O   HOH Z 299 " =    4.203
peak=    3.356 closest distance to " O   HOH Z 145 " =    3.714
peak=    3.352 closest distance to " CG  MET A 185 " =    1.077
peak=    3.351 closest distance to " CD1 ILE A 106 " =    0.984
peak=    3.350 closest distance to " CD2 LEU A   5 " =    0.732
peak=    3.346 closest distance to " O   HOH Z 422 " =    2.599
peak=    3.345 closest distance to " O   HOH Z 124 " =    1.249
peak=    3.343 closest distance to " CB  MET A  40 " =    0.822
peak=    3.342 closest distance to " CD2 LEU A 255 " =    1.640
peak=    3.337 closest distance to " NZ  LYS A  48 " =    1.279
peak=    3.325 closest distance to " CB  GLU A  46 " =    1.030
peak=    3.325 closest distance to " CA  SER A 146 " =    1.732
peak=    3.325 closest distance to " CB  ALA A 295 " =    1.222
peak=    3.325 closest distance to " O   HOH Z   3 " =    1.869
peak=    3.324 closest distance to " O   HOH Z 261 " =    1.515
peak=    3.322 closest distance to " CD  LYS A 166 " =    1.273
peak=    3.318 closest distance to " CG  GLN A  88 " =    1.064
peak=    3.314 closest distance to " O   HOH Z 130 " =    2.179
peak=    3.314 closest distance to " CG2 VAL A 197 " =    1.026
peak=    3.312 closest distance to " CB  GLN A  88 " =    1.187
peak=    3.312 closest distance to " O   HOH Z 180 " =    2.126
peak=    3.305 closest distance to " O   HOH Z 303 " =    1.747
peak=    3.304 closest distance to " O   HOH Z   1 " =    1.828
peak=    3.303 closest distance to " O   HOH Z  97 " =    2.604
peak=    3.303 closest distance to " CB  ALA A  34 " =    0.880
peak=    3.303 closest distance to " CA  ALA A 291 " =    0.882
peak=    3.300 closest distance to " CG  MET A 113 " =    1.250
peak=    3.297 closest distance to " O   HOH Z 175 " =    2.132
peak=    3.296 closest distance to " CB  ALA A 242 " =    0.806
peak=    3.290 closest distance to " O   HOH Z 189 " =    2.762
peak=    3.290 closest distance to " CD  LYS A 119 " =    1.495
peak=    3.289 closest distance to " CB  TRP A 150 " =    1.397
peak=    3.287 closest distance to " O   HOH Z  40 " =    1.878
peak=    3.285 closest distance to " O   HOH Z  61 " =    1.558
peak=    3.281 closest distance to " O   HOH Z 345 " =    3.330
peak=    3.278 closest distance to " O   HOH Z 128 " =    1.890
peak=    3.277 closest distance to " O  BHOH Z 338 " =    2.398
peak=    3.273 closest distance to " OG BSER A 134 " =    2.981
peak=    3.272 closest distance to " O   HOH Z  44 " =    1.687
peak=    3.271 closest distance to " CB  SER A 273 " =    0.853
peak=    3.270 closest distance to " O   HOH Z 409 " =    3.197
peak=    3.268 closest distance to " CG1 ILE A 151 " =    1.020
peak=    3.268 closest distance to " CB  ALA A 233 " =    1.379
peak=    3.268 closest distance to " CB  LYS A 290 " =    1.244
peak=    3.268 closest distance to " CA  THR A 221 " =    0.973
peak=    3.267 closest distance to " NH2AARG A 275 " =    3.609
peak=    3.265 closest distance to " O   ARG A  56 " =    2.802
peak=    3.263 closest distance to " O   HOH Z 148 " =    3.345
peak=    3.261 closest distance to " OG  SER A  22 " =    2.837
peak=    3.258 closest distance to " CD1 LEU A  96 " =    0.741
peak=    3.258 closest distance to " CG  GLN A  77 " =    2.209
peak=    3.250 closest distance to " O   HOH Z 227 " =    2.220
peak=    3.247 closest distance to " O   HOH Z 133 " =    2.598
peak=    3.244 closest distance to " O   HOH Z 282 " =    1.942
peak=    3.242 closest distance to " N   GLN A 278 " =    1.190
peak=    3.240 closest distance to " O   HOH Z 368 " =    3.551
peak=    3.240 closest distance to " O   HOH Z 291 " =    1.517
peak=    3.234 closest distance to " CB  GLN A 205 " =    1.130
peak=    3.231 closest distance to " O   HOH Z 359 " =    3.708
peak=    3.230 closest distance to " O   HOH Z 133 " =    1.510
peak=    3.225 closest distance to " O   HOH Z 279 " =    2.164
peak=    3.224 closest distance to " N   ASP A 162 " =    1.240
peak=    3.217 closest distance to " O   HOH Z 313 " =    1.621
peak=    3.215 closest distance to " CD  ARG A 195 " =    3.501
peak=    3.215 closest distance to " O   TRP A 274 " =    1.856
peak=    3.213 closest distance to " CA  ASP A 162 " =    1.037
peak=    3.213 closest distance to " N   VAL A 126 " =    1.332
peak=    3.208 closest distance to " CG2 THR A 294 " =    1.726
peak=    3.207 closest distance to " CA  LEU A 282 " =    1.131
peak=    3.205 closest distance to " O   HOH Z 222 " =    2.506
peak=    3.201 closest distance to " CA  TYR A 116 " =    1.401
peak=    3.199 closest distance to " CA  ALA A 154 " =    1.003
peak=    3.196 closest distance to " O   HOH Z 419 " =    1.901
peak=    3.196 closest distance to " CA  MET A 105 " =    0.978
peak=    3.194 closest distance to " CB  GLN A 278 " =    0.852
peak=    3.187 closest distance to " O   HOH Z 336 " =    1.861
peak=    3.187 closest distance to " CB  ASN A 215 " =    1.185
peak=    3.178 closest distance to " O   HOH Z 173 " =    2.153
peak=    3.178 closest distance to " CB  TYR A 116 " =    0.817
peak=    3.176 closest distance to " CA  ALA A 233 " =    1.142
peak=    3.168 closest distance to " NH2BARG A 145 " =    2.022
peak=    3.167 closest distance to " O   HOH Z 325 " =    2.180
peak=    3.166 closest distance to " CA  VAL A 126 " =    0.887
peak=    3.164 closest distance to " ND1 HIS A  86 " =    1.790
peak=    3.160 closest distance to " O   HOH Z 366 " =    3.017
peak=    3.157 closest distance to " O   HOH Z 423 " =    2.899
peak=    3.155 closest distance to " O   HOH Z 368 " =    2.729
peak=    3.155 closest distance to " O   HOH Z 213 " =    2.376
peak=    3.148 closest distance to " N   ASN A 127 " =    1.227
peak=    3.144 closest distance to " CA  ASN A 127 " =    1.059
peak=    3.143 closest distance to " OE2 GLU A  53 " =    1.993
peak=    3.141 closest distance to " O   HOH Z  30 " =    1.338
peak=    3.138 closest distance to " CG  LYS A  76 " =    0.973
peak=    3.138 closest distance to " O   HOH Z 384 " =    3.221
peak=    3.132 closest distance to " CD1 ILE A 263 " =    1.285
peak=    3.125 closest distance to " CG1 VAL A 174 " =    1.121
peak=    3.123 closest distance to " O   HOH Z 171 " =    2.273
peak=    3.122 closest distance to " NZ  LYS A  76 " =    1.513
peak=    3.120 closest distance to " O   HOH Z  85 " =    2.159
peak=    3.117 closest distance to " CB  GLU A 277 " =    3.733
peak=    3.117 closest distance to " ND1 HIS A  81 " =    1.718
peak=    3.116 closest distance to " O   HOH Z 116 " =    1.708
peak=    3.115 closest distance to " CB  MET A  47 " =    1.074
peak=    3.113 closest distance to " O   HOH Z 187 " =    2.278
peak=    3.109 closest distance to " O   HOH Z 339 " =    2.138
peak=    3.106 closest distance to " O   HOH Z 302 " =    1.938
peak=    3.103 closest distance to " O   ALA A   1 " =    1.713
peak=    3.102 closest distance to " O   HOH Z 350 " =    1.598
peak=    3.101 closest distance to " O   HOH Z   2 " =    1.502
peak=    3.098 closest distance to " O   HOH Z  89 " =    2.309
peak=    3.095 closest distance to " C   ALA A 299 " =    0.938
peak=    3.090 closest distance to " CG  ARG A 159 " =    0.930
peak=    3.087 closest distance to " CG  GLN A  89 " =    1.500
peak=    3.087 closest distance to " O   HOH Z 201 " =    3.150
peak=    3.084 closest distance to " O   HOH Z   9 " =    2.046
peak=    3.081 closest distance to " O   HOH Z  40 " =    1.486
peak=    3.078 closest distance to " CG2 VAL A 202 " =    1.153
peak=    3.076 closest distance to " O   HOH Z 154 " =    2.097
peak=    3.074 closest distance to " CB  ALA A   1 " =    4.754
peak=    3.070 closest distance to " CA  GLN A 194 " =    1.253
peak=    3.068 closest distance to " CG  GLN A 278 " =    1.267
peak=    3.066 closest distance to " O   HOH Z 213 " =    1.846
peak=    3.066 closest distance to " O   ALA A 158 " =    1.381
peak=    3.040 closest distance to " O   HOH Z 357 " =    1.897
peak=    3.000 closest distance to " N   GLY A 133 " =    3.702

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 203         
Filter by distance & map next to the model:
   mapped sites are within: 0.545 - 5.490
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 201 from: 203
   mapped sites are within: 0.771 - 5.490

peak=   -5.176 closest distance to " CG2 VAL A 230 " =    0.784
peak=   -4.440 closest distance to " OG BSER A 134 " =    1.190
peak=   -4.420 closest distance to " CD  ARG A 156 " =    2.008
peak=   -4.319 closest distance to " CB  PRO A 243 " =    2.654
peak=   -4.317 closest distance to " O   HOH Z 266 " =    5.082
peak=   -4.297 closest distance to " SG  CYS A 254 " =    3.311
peak=   -4.295 closest distance to " CG  GLN A 223 " =    1.986
peak=   -4.263 closest distance to " CG2 VAL A 296 " =    1.354
peak=   -4.182 closest distance to " C   HIS A 108 " =    1.219
peak=   -4.124 closest distance to " CB  PHE A 192 " =    1.948
peak=   -3.995 closest distance to " O   HOH Z 290 " =    1.181
peak=   -3.991 closest distance to " O   HOH Z 114 " =    3.016
peak=   -3.987 closest distance to " CD  GLN A  58 " =    1.110
peak=   -3.975 closest distance to " CE2 TYR A  30 " =    2.752
peak=   -3.968 closest distance to " CA  VAL A  67 " =    2.740
peak=   -3.945 closest distance to " O   PRO A 163 " =    2.087
peak=   -3.932 closest distance to " O   HOH Z 231 " =    2.058
peak=   -3.922 closest distance to " O   HOH Z 389 " =    1.995
peak=   -3.914 closest distance to " O   ILE A 109 " =    2.596
peak=   -3.903 closest distance to " O   VAL A  67 " =    2.630
peak=   -3.891 closest distance to " CB  ALA A 248 " =    2.067
peak=   -3.853 closest distance to " CB  ALA A  43 " =    2.506
peak=   -3.849 closest distance to " O   HOH Z 435 " =    2.847
peak=   -3.848 closest distance to " OD1 ASN A 187 " =    1.594
peak=   -3.844 closest distance to " O   HOH Z 196 " =    2.221
peak=   -3.806 closest distance to " ND2 ASN A  45 " =    1.607
peak=   -3.789 closest distance to " O   HOH Z 351 " =    1.483
peak=   -3.785 closest distance to " CG  ASP A 231 " =    0.794
peak=   -3.785 closest distance to " CE2 PHE A 218 " =    2.541
peak=   -3.775 closest distance to " CG1 VAL A 112 " =    2.618
peak=   -3.775 closest distance to " O   HOH Z 185 " =    2.368
peak=   -3.766 closest distance to " CB  ALA A 291 " =    2.298
peak=   -3.761 closest distance to " CE  MET A 105 " =    2.318
peak=   -3.761 closest distance to " CG1 VAL A 112 " =    2.851
peak=   -3.754 closest distance to " O   HOH Z 166 " =    1.947
peak=   -3.741 closest distance to " CB  ALA A 291 " =    2.207
peak=   -3.725 closest distance to " OXT GLY A 302 " =    2.876
peak=   -3.716 closest distance to " N   ALA A  43 " =    2.431
peak=   -3.704 closest distance to " O   HOH Z  11 " =    1.932
peak=   -3.702 closest distance to " CB  ALA A 248 " =    2.388
peak=   -3.681 closest distance to " CZ3 TRP A 179 " =    1.207
peak=   -3.679 closest distance to " O   HOH Z 394 " =    1.520
peak=   -3.666 closest distance to " O   HOH Z 407 " =    3.038
peak=   -3.634 closest distance to " N   ALA A 226 " =    2.065
peak=   -3.633 closest distance to " CG  TRP A 266 " =    1.895
peak=   -3.596 closest distance to " ND2 ASN A  45 " =    1.160
peak=   -3.590 closest distance to " CB  ASP A 132 " =    2.305
peak=   -3.582 closest distance to " ND2 ASN A 187 " =    1.469
peak=   -3.579 closest distance to " CD  ARG A 139 " =    1.602
peak=   -3.575 closest distance to " CA  GLY A 241 " =    3.102
peak=   -3.571 closest distance to " O   PRO A 198 " =    1.230
peak=   -3.570 closest distance to " NH2 ARG A  79 " =    1.999
peak=   -3.562 closest distance to " O   HOH Z  44 " =    2.255
peak=   -3.551 closest distance to " C   MET A 188 " =    1.390
peak=   -3.551 closest distance to " N   THR A 157 " =    1.468
peak=   -3.542 closest distance to " CE BMET A  47 " =    1.656
peak=   -3.539 closest distance to " NH2AARG A 275 " =    5.252
peak=   -3.538 closest distance to " CG2 VAL A 296 " =    1.808
peak=   -3.535 closest distance to " O   VAL A 189 " =    2.583
peak=   -3.525 closest distance to " O   HOH Z  38 " =    1.693
peak=   -3.522 closest distance to " CB  PRO A 163 " =    2.557
peak=   -3.521 closest distance to " CZ  PHE A  59 " =    1.509
peak=   -3.512 closest distance to " N   GLN A  58 " =    1.884
peak=   -3.510 closest distance to " CB  PRO A 280 " =    2.137
peak=   -3.506 closest distance to " O   HOH Z 166 " =    1.591
peak=   -3.499 closest distance to " C   ALA A 158 " =    1.273
peak=   -3.497 closest distance to " O   HOH Z  52 " =    1.464
peak=   -3.490 closest distance to " CG2 ILE A 263 " =    2.297
peak=   -3.485 closest distance to " O   HOH Z 211 " =    1.595
peak=   -3.485 closest distance to " CG  PHE A 283 " =    2.687
peak=   -3.479 closest distance to " CG1 VAL A 296 " =    1.346
peak=   -3.477 closest distance to " NE2 GLN A  88 " =    1.884
peak=   -3.474 closest distance to " O   MET A  40 " =    2.681
peak=   -3.470 closest distance to " OD1 ASN A 148 " =    1.467
peak=   -3.468 closest distance to " N   ASP A 171 " =    2.285
peak=   -3.466 closest distance to " N   THR A 235 " =    1.320
peak=   -3.453 closest distance to " CE3 TRP A 150 " =    2.035
peak=   -3.448 closest distance to " O   HOH Z 295 " =    1.582
peak=   -3.442 closest distance to " NE2 GLN A 278 " =    1.964
peak=   -3.441 closest distance to " O   HOH Z 198 " =    2.103
peak=   -3.436 closest distance to " OG  SER A  62 " =    1.634
peak=   -3.431 closest distance to " CB  ASP A 132 " =    2.363
peak=   -3.429 closest distance to " OG  SER A  97 " =    2.224
peak=   -3.428 closest distance to " N   ALA A 248 " =    1.652
peak=   -3.423 closest distance to " O   HOH Z 417 " =    2.830
peak=   -3.421 closest distance to " NZ  LYS A 119 " =    3.502
peak=   -3.410 closest distance to " CD2 LEU A 300 " =    2.854
peak=   -3.407 closest distance to " C   LEU A 222 " =    0.771
peak=   -3.404 closest distance to " CD2 LEU A 300 " =    2.857
peak=   -3.404 closest distance to " O   LYS A 117 " =    1.685
peak=   -3.402 closest distance to " O   SER A  22 " =    2.324
peak=   -3.401 closest distance to " O   HOH Z 103 " =    1.726
peak=   -3.401 closest distance to " CG1 VAL A 250 " =    2.744
peak=   -3.400 closest distance to " N   GLN A  77 " =    1.597
peak=   -3.388 closest distance to " O   HOH Z  13 " =    1.576
peak=   -3.384 closest distance to " CG1 VAL A 197 " =    2.274
peak=   -3.380 closest distance to " CD1 LEU A 228 " =    2.159
peak=   -3.380 closest distance to " O   HOH Z  43 " =    1.740
peak=   -3.378 closest distance to " CA  ASP A 298 " =    1.072
peak=   -3.376 closest distance to " N   SER A 276 " =    1.300
peak=   -3.371 closest distance to " N   PHE A  59 " =    2.171
peak=   -3.365 closest distance to " CB  VAL A 230 " =    1.046
peak=   -3.364 closest distance to " O   HOH Z 281 " =    2.716
peak=   -3.363 closest distance to " CG  ARG A 269 " =    2.333
peak=   -3.363 closest distance to " C   PHE A  59 " =    1.364
peak=   -3.362 closest distance to " O   HOH Z 102 " =    1.569
peak=   -3.362 closest distance to " CA  GLY A 203 " =    2.425
peak=   -3.361 closest distance to " O   HOH Z  60 " =    1.983
peak=   -3.359 closest distance to " CZ  PHE A 192 " =    2.865
peak=   -3.358 closest distance to " CA  GLY A 241 " =    2.285
peak=   -3.356 closest distance to " O   ALA A  51 " =    1.340
peak=   -3.354 closest distance to " ND2 ASN A  60 " =    1.454
peak=   -3.347 closest distance to " CB  ASN A  39 " =    2.244
peak=   -3.344 closest distance to " CD1 LEU A 101 " =    2.325
peak=   -3.339 closest distance to " O   ALA A  10 " =    1.728
peak=   -3.330 closest distance to " CB  ASP A 171 " =    2.208
peak=   -3.329 closest distance to " O   GLY A 196 " =    1.152
peak=   -3.327 closest distance to " CG1 VAL A 230 " =    1.905
peak=   -3.325 closest distance to " C   ASP A 231 " =    2.617
peak=   -3.325 closest distance to " CD1 LEU A 101 " =    2.866
peak=   -3.322 closest distance to " ND2 ASN A 249 " =    2.417
peak=   -3.322 closest distance to " OG  SER A  87 " =    1.374
peak=   -3.322 closest distance to " O   SER A  95 " =    1.590
peak=   -3.320 closest distance to " O   ALA A 161 " =    1.621
peak=   -3.318 closest distance to " C   LEU A 143 " =    1.078
peak=   -3.317 closest distance to " CD1 ILE A 199 " =    2.474
peak=   -3.309 closest distance to " O   HOH Z  73 " =    2.165
peak=   -3.307 closest distance to " CZ  TYR A 169 " =    1.647
peak=   -3.305 closest distance to " O   HOH Z 359 " =    3.257
peak=   -3.303 closest distance to " C   ASN A 187 " =    1.844
peak=   -3.295 closest distance to " CD  PRO A 213 " =    2.160
peak=   -3.291 closest distance to " CA  GLY A  98 " =    1.887
peak=   -3.288 closest distance to " O   HOH Z 313 " =    1.121
peak=   -3.286 closest distance to " O   HOH Z 423 " =    2.072
peak=   -3.286 closest distance to " NE2 GLN A 194 " =    1.742
peak=   -3.283 closest distance to " OG  SER A 206 " =    1.694
peak=   -3.277 closest distance to " OXT GLY A 302 " =    3.563
peak=   -3.269 closest distance to " O   HOH Z 350 " =    1.765
peak=   -3.268 closest distance to " CG  GLN A 278 " =    2.122
peak=   -3.260 closest distance to " CB  VAL A 296 " =    1.104
peak=   -3.260 closest distance to " O   HOH Z 191 " =    5.490
peak=   -3.259 closest distance to " O   HOH Z 417 " =    2.615
peak=   -3.259 closest distance to " CG  LEU A 228 " =    1.052
peak=   -3.258 closest distance to " CB  TYR A  15 " =    2.175
peak=   -3.256 closest distance to " C   GLY A  17 " =    1.280
peak=   -3.255 closest distance to " O   HOH Z 139 " =    3.055
peak=   -3.254 closest distance to " CD1 LEU A 297 " =    2.474
peak=   -3.247 closest distance to " CB  ASN A 252 " =    1.799
peak=   -3.246 closest distance to " O   PRO A 198 " =    1.341
peak=   -3.238 closest distance to " O   HOH Z 371 " =    2.026
peak=   -3.235 closest distance to " O   HOH Z 313 " =    1.630
peak=   -3.233 closest distance to " O   HOH Z 426 " =    1.711
peak=   -3.228 closest distance to " O   PHE A 218 " =    1.665
peak=   -3.223 closest distance to " O   HOH Z 140 " =    1.613
peak=   -3.218 closest distance to " OG BSER A 134 " =    1.689
peak=   -3.212 closest distance to " O   HOH Z 256 " =    1.307
peak=   -3.201 closest distance to " CD2 LEU A   5 " =    1.175
peak=   -3.198 closest distance to " CD2 LEU A 237 " =    2.813
peak=   -3.198 closest distance to " O   HOH Z  10 " =    1.435
peak=   -3.196 closest distance to " NH2BARG A 275 " =    1.710
peak=   -3.193 closest distance to " O   HOH Z 311 " =    3.806
peak=   -3.192 closest distance to " CB  ASN A  69 " =    1.175
peak=   -3.190 closest distance to " CB  GLN A  11 " =    1.916
peak=   -3.190 closest distance to " O   HOH Z 175 " =    4.338
peak=   -3.187 closest distance to " CA  GLY A 133 " =    2.299
peak=   -3.186 closest distance to " NH2 ARG A  79 " =    1.562
peak=   -3.185 closest distance to " O   HOH Z 123 " =    2.415
peak=   -3.177 closest distance to " O   HOH Z  47 " =    1.643
peak=   -3.173 closest distance to " C   VAL A 174 " =    1.756
peak=   -3.173 closest distance to " O   HOH Z 353 " =    2.011
peak=   -3.172 closest distance to " NH1 ARG A  36 " =    1.957
peak=   -3.168 closest distance to " O   TRP A  70 " =    1.486
peak=   -3.166 closest distance to " N   HIS A 115 " =    2.105
peak=   -3.159 closest distance to " O   HOH Z 252 " =    4.160
peak=   -3.159 closest distance to " O   HOH Z 149 " =    2.240
peak=   -3.159 closest distance to " NH2 ARG A 159 " =    2.324
peak=   -3.141 closest distance to " O   HOH Z 369 " =    2.292
peak=   -3.140 closest distance to " OD2 ASP A 191 " =    1.387
peak=   -3.132 closest distance to " O   GLN A 240 " =    2.359
peak=   -3.129 closest distance to " CE1 HIS A  81 " =    1.422
peak=   -3.126 closest distance to " CA  PRO A 243 " =    2.235
peak=   -3.124 closest distance to " O   HOH Z 189 " =    1.890
peak=   -3.124 closest distance to " OG1 THR A 178 " =    1.276
peak=   -3.118 closest distance to " O   HOH Z 310 " =    1.815
peak=   -3.116 closest distance to " CD2 TYR A 293 " =    2.162
peak=   -3.110 closest distance to " O   HOH Z 134 " =    3.597
peak=   -3.104 closest distance to " CA  GLY A 133 " =    1.959
peak=   -3.103 closest distance to " CG  ASP A  50 " =    2.455
peak=   -3.097 closest distance to " OD1 ASP A 200 " =    1.465
peak=   -3.097 closest distance to " ND2 ASN A 252 " =    1.913
peak=   -3.092 closest distance to " N   ALA A 248 " =    2.349
peak=   -3.091 closest distance to " CG  PRO A 163 " =    2.537
peak=   -3.088 closest distance to " CA  ASP A  27 " =    2.403
peak=   -3.078 closest distance to " OE2 GLU A 152 " =    1.218
peak=   -3.072 closest distance to " CG  GLU A 277 " =    1.207
peak=   -3.050 closest distance to " CD2 TYR A 247 " =    2.346
peak=   -3.043 closest distance to " O   HOH Z 234 " =    4.072
peak=   -3.037 closest distance to " O   VAL A 125 " =    2.337
peak=   -3.036 closest distance to " CG2 VAL A 230 " =    2.642
peak=   -3.029 closest distance to " CE BMET A  47 " =    1.264
peak=   -3.024 closest distance to " CG  LEU A 101 " =    2.339

================= 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    :  0.4095 0.3950   6.192961e+00   6.163123e+00
   1_bss:  0.4011 0.3849   6.188786e+00   6.147127e+00
   1_xyz:  0.2857 0.3060   5.927347e+00   5.975138e+00
   1_adp:  0.2081 0.2368   5.635072e+00   5.760535e+00
   1_occ:  0.2075 0.2366   5.633432e+00   5.760897e+00
   2_bss:  0.2011 0.2292   5.628033e+00   5.751408e+00
   2_xyz:  0.1392 0.1755   5.300635e+00   5.489915e+00
   2_adp:  0.1273 0.1657   5.227222e+00   5.431831e+00
   2_occ:  0.1272 0.1655   5.226440e+00   5.431037e+00
   3_bss:  0.1270 0.1651   5.226610e+00   5.430960e+00
   3_xyz:  0.1164 0.1571   5.163873e+00   5.392386e+00
   3_adp:  0.1125 0.1562   5.145263e+00   5.386700e+00
   3_occ:  0.1124 0.1562   5.145175e+00   5.386675e+00
   4_bss:  0.1124 0.1561   5.144097e+00   5.385802e+00
   4_xyz:  0.1120 0.1571   5.145245e+00   5.389845e+00
   4_adp:  0.1123 0.1558   5.143072e+00   5.383900e+00
   4_occ:  0.1122 0.1558   5.142733e+00   5.383740e+00
   5_bss:  0.1122 0.1558   5.142740e+00   5.383739e+00
   5_xyz:  0.1097 0.1551   5.130580e+00   5.380330e+00
   5_adp:  0.1092 0.1557   5.131139e+00   5.383691e+00
   5_occ:  0.1092 0.1557   5.131269e+00   5.383899e+00
   5_bss:  0.1092 0.1557   5.131282e+00   5.383916e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.359  20.001   7.337   8.543   8.205   0.000   0.000   0.000
   1_xyz:  0.359  20.001   7.337   8.543   8.205   0.000   0.000   0.000
   1_adp:  0.359  20.001   7.337   8.543   8.205   0.000   0.000   0.000
   1_occ:  0.359  20.001   7.337   8.543   8.205   0.000   0.000   0.000
   2_bss:  0.342  36.681   4.127   4.614   5.397   0.000   0.000   0.000
   2_xyz:  0.342  36.681   4.127   4.614   5.397   0.000   0.000   0.000
   2_adp:  0.342  36.681   4.127   4.614   5.397   0.000   0.000   0.000
   2_occ:  0.342  36.681   4.127   4.614   5.397   0.000   0.000   0.000
   3_bss:  0.327  36.681   3.455   3.750   4.826   0.000   0.000   0.000
   3_xyz:  0.327  36.681   3.455   3.750   4.826   0.000   0.000   0.000
   3_adp:  0.327  36.681   3.455   3.750   4.826   0.000   0.000   0.000
   3_occ:  0.327  36.681   3.455   3.750   4.826   0.000   0.000   0.000
   4_bss:  0.323  41.960   3.524   3.754   4.907   0.000   0.000   0.000
   4_xyz:  0.323  41.960   3.524   3.754   4.907   0.000   0.000   0.000
   4_adp:  0.323  41.960   3.524   3.754   4.907   0.000   0.000   0.000
   4_occ:  0.323  41.960   3.524   3.754   4.907   0.000   0.000   0.000
   5_bss:  0.323  41.960   3.532   3.763   4.935   0.000   0.000   0.000
   5_xyz:  0.323  41.960   3.532   3.763   4.935   0.000   0.000   0.000
   5_adp:  0.323  41.960   3.532   3.763   4.935   0.000   0.000   0.000
   5_occ:  0.323  41.960   3.532   3.763   4.935   0.000   0.000   0.000
   5_bss:  0.323  46.092  -0.536  -0.327   0.864  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  42.895 0.6101  0.6719    44530.172
   1_bss:  42.928 0.6072  0.8497    42074.805
   1_xyz:  32.082 0.7341  0.9970    24973.224
   1_adp:  22.509 0.8386  1.0811    14099.959
   1_occ:  22.531 0.8383  1.0802    14079.654
   2_bss:  22.192 0.8414  0.9593    13641.779
   2_xyz:  16.227 0.8961  0.9975     7763.284
   2_adp:  14.860 0.9080  1.0052     6942.305
   2_occ:  14.848 0.9081  1.0052     6926.349
   3_bss:  14.848 0.9080  0.9788     6930.393
   3_xyz:  13.989 0.9152  0.9806     6368.852
   3_adp:  13.886 0.9161  0.9774     6283.854
   3_occ:  13.887 0.9161  0.9773     6281.527
   4_bss:  13.863 0.9163  0.9794     6267.138
   4_xyz:  13.915 0.9160  0.9788     6342.724
   4_adp:  13.773 0.9172  0.9782     6263.639
   4_occ:  13.772 0.9172  0.9781     6262.153
   5_bss:  13.772 0.9172  0.9786     6262.051
   5_xyz:  13.687 0.9178  0.9792     6225.642
   5_adp:  13.757 0.9173  0.9767     6251.488
   5_occ:  13.762 0.9173  0.9766     6253.040
   5_bss:  13.762 0.9173  0.9786     6253.377
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.3688e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.3688e+01
   1_xyz:   1.413  0.010  0.097 17.858  0.005  4.120   1.0556e-01
   1_adp:   1.413  0.010  0.097 17.858  0.005  4.120   1.0556e-01
   1_occ:   1.413  0.010  0.097 17.858  0.005  4.120   1.0556e-01
   2_bss:   1.413  0.010  0.097 17.858  0.005  4.120   1.0556e-01
   2_xyz:   1.015  0.007  0.080 16.373  0.004  4.121   6.5025e-02
   2_adp:   1.015  0.007  0.080 16.373  0.004  4.121   6.5025e-02
   2_occ:   1.015  0.007  0.080 16.373  0.004  4.121   6.5025e-02
   3_bss:   1.015  0.007  0.080 16.373  0.004  4.121   6.5025e-02
   3_xyz:   0.988  0.007  0.082 15.965  0.004  4.118   6.1692e-02
   3_adp:   0.988  0.007  0.082 15.965  0.004  4.118   6.1692e-02
   3_occ:   0.988  0.007  0.082 15.965  0.004  4.118   6.1692e-02
   4_bss:   0.988  0.007  0.082 15.965  0.004  4.118   6.1692e-02
   4_xyz:   0.925  0.006  0.076 15.687  0.003  4.119   5.5657e-02
   4_adp:   0.925  0.006  0.076 15.687  0.003  4.119   5.5657e-02
   4_occ:   0.925  0.006  0.076 15.687  0.003  4.119   5.5657e-02
   5_bss:   0.925  0.006  0.076 15.687  0.003  4.119   5.5657e-02
   5_xyz:   0.990  0.007  0.081 15.721  0.004  4.120   6.1471e-02
   5_adp:   0.990  0.007  0.081 15.721  0.004  4.120   6.1471e-02
   5_occ:   0.990  0.007  0.081 15.721  0.004  4.120   6.1471e-02
   5_bss:   0.990  0.007  0.081 15.721  0.004  4.120   6.1471e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9612e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9612e+00
   1_xyz:  11.079  0.124  0.440 88.164  0.031  2.264   7.6677e-02
   1_adp:  11.079  0.124  0.440 88.164  0.031  2.264   7.6677e-02
   1_occ:  11.079  0.124  0.440 88.164  0.031  2.264   7.6677e-02
   2_bss:  11.079  0.124  0.440 88.164  0.031  2.264   7.6677e-02
   2_xyz:   8.173  0.048  0.474 84.228  0.033  2.245   4.9773e-02
   2_adp:   8.173  0.048  0.474 84.228  0.033  2.245   4.9773e-02
   2_occ:   8.173  0.048  0.474 84.228  0.033  2.245   4.9773e-02
   3_bss:   8.173  0.048  0.474 84.228  0.033  2.245   4.9773e-02
   3_xyz:   6.358  0.041  0.553 83.460  0.035  2.309   4.0350e-02
   3_adp:   6.358  0.041  0.553 83.460  0.035  2.309   4.0350e-02
   3_occ:   6.358  0.041  0.553 83.460  0.035  2.309   4.0350e-02
   4_bss:   6.358  0.041  0.553 83.460  0.035  2.309   4.0350e-02
   4_xyz:   6.596  0.039  0.481 83.220  0.035  2.380   3.5539e-02
   4_adp:   6.596  0.039  0.481 83.220  0.035  2.380   3.5539e-02
   4_occ:   6.596  0.039  0.481 83.220  0.035  2.380   3.5539e-02
   5_bss:   6.596  0.039  0.481 83.220  0.035  2.380   3.5539e-02
   5_xyz:   6.442  0.042  0.549 83.150  0.036  2.298   4.2100e-02
   5_adp:   6.442  0.042  0.549 83.150  0.036  2.298   4.2100e-02
   5_occ:   6.442  0.042  0.549 83.150  0.036  2.298   4.2100e-02
   5_bss:   6.442  0.042  0.549 83.150  0.036  2.298   4.2100e-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:  50.57   0.00   9.73  42.10   0.00   6.67  50.57   0.00  26.40
   1_occ:  50.57   0.00   9.73  42.10   0.00   6.67  50.57   0.00  26.40
   2_bss:  50.57   0.00   9.73  42.10   0.00   6.67  50.57   0.00  26.40
   2_xyz:  50.57   0.00   9.73  42.10   0.00   6.67  50.57   0.00  26.40
   2_adp:  51.69   0.00  10.19  48.48   0.00   6.64  51.69   0.00  29.56
   2_occ:  51.69   0.00  10.19  48.48   0.00   6.64  51.69   0.00  29.56
   3_bss:  51.69   0.00  10.19  48.48   0.00   6.64  51.69   0.00  29.56
   3_xyz:  51.69   0.00  10.19  48.48   0.00   6.64  51.69   0.00  29.56
   3_adp:  71.68   0.00  11.09  71.68   0.00   6.94  71.40   0.00  33.71
   3_occ:  71.68   0.00  11.09  71.68   0.00   6.94  71.40   0.00  33.71
   4_bss:  71.68   0.00  11.09  71.68   0.00   6.94  71.40   0.00  33.71
   4_xyz:  71.68   0.00  11.09  71.68   0.00   6.94  71.40   0.00  33.71
   4_adp:  76.12   0.00  10.83  76.12   0.00   6.85  68.58   0.34  32.52
   4_occ:  76.12   0.00  10.83  76.12   0.00   6.85  68.58   0.34  32.52
   5_bss:  76.12   0.00  10.83  76.12   0.00   6.85  68.58   0.34  32.52
   5_xyz:  76.12   0.00  10.83  76.12   0.00   6.85  68.58   0.34  32.52
   5_adp:  80.63   0.00  10.89  80.63   0.00   6.84  70.98   0.15  32.97
   5_occ:  80.63   0.00  10.89  80.63   0.00   6.84  70.98   0.15  32.97
   5_bss:  84.76   4.13  15.02  84.76   4.13  10.97  75.11   4.28  37.10
------------------------------------------------------------------------
 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:    1.150    0.013    0.395
   1_adp:    1.150    0.013    0.395
   1_occ:    1.150    0.013    0.395
   2_bss:    1.150    0.013    0.395
   2_xyz:    1.285    0.027    0.470
   2_adp:    1.285    0.027    0.470
   2_occ:    1.285    0.027    0.470
   3_bss:    1.285    0.027    0.470
   3_xyz:    1.376    0.036    0.489
   3_adp:    1.376    0.036    0.489
   3_occ:    1.376    0.036    0.489
   4_bss:    1.376    0.036    0.489
   4_xyz:    1.428    0.052    0.495
   4_adp:    1.428    0.052    0.495
   4_occ:    1.428    0.052    0.495
   5_bss:    1.428    0.052    0.495
   5_xyz:    1.484    0.036    0.501
   5_adp:    1.484    0.036    0.501
   5_occ:    1.484    0.036    0.501
   5_bss:    1.484    0.036    0.501
------------------------------------------------------------------------

CPU time actual refinement: 277.23


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_654/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_654/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_654/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_654/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_654/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 277.10 
  Macro-tasks:
    bulk solvent and scale       = 34.90  
    individual site refinement   = 116.14 
    weights calculation          = 27.63  
    collect and process          = 5.51   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 184.29 
  Micro-tasks:
    mask                            = 0.97   
    f_calc                          = 83.64  
    alpha_beta                      = 7.08   
    target                          = 1.00   
    gradients_wrt_atomic_parameters = 94.23  
    fmodel                         = 6.07   
    r_factors                      = 0.18   
    phase_errors                   = 9.06   
    foms                           = 0.27   
    TOTAL for micro-tasks          = 202.50 
NUMBER OF MASK CALCS=  3
Time per interpreted Python bytecode instruction: 3.836 micro seconds
Total CPU time: 4.81 minutes
from_scatterers_fft:    665 calls, 83.22 s
gradients_fft:          609 calls, 82.08 s

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

# Date 2008-01-16 Time 02:06:47 PST -0800 (1200478007.22 s)
Start R-work = 0.4095, R-free = 0.3950 (no bulk solvent and anisotropic scale)
Final R-work = 0.1271, R-free = 0.1721 (no bulk solvent and anisotropic scale)

Start R-work = 0.4011, R-free = 0.3849
Final R-work = 0.1092, R-free = 0.1557