# Date 2008-01-16 Time 02:51:40 PST -0800 (1200480700.17 s)
#phil __OFF__

Command line arguments: "../1006.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 13286
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1006

-------------------------------------------------------------------------------
  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: (71.3037, 46.4607, 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: 3.27, per 1000 atoms: 1.16


================================== 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: (71.3037, 46.4607, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1569 1.98276
Completeness in resolution range: 0.956354
Completeness with d_max=infinity: 0.953514

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1569
                             d_min =   1.9828

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: (71.3037, 46.4607, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1569 1.98276
Completeness in resolution range: 0.956354
Completeness with d_max=infinity: 0.953514

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1573 -  4.2434 [2147/2173]  1934   213   9.9%
  bin  2:  4.2434 -  3.3804 [2067/2087]  1858   209  10.1%
  bin  3:  3.3804 -  2.9567 [2044/2063]  1842   202   9.9%
  bin  4:  2.9567 -  2.6880 [2025/2055]  1820   205  10.1%
  bin  5:  2.6880 -  2.4963 [2012/2031]  1817   195   9.7%
  bin  6:  2.4963 -  2.3496 [1993/2018]  1783   210  10.5%
  bin  7:  2.3496 -  2.2324 [2000/2028]  1803   197   9.8%
  bin  8:  2.2324 -  2.1355 [1972/2008]  1777   195   9.9%
  bin  9:  2.1355 -  2.0535 [1963/2005]  1764   199  10.1%
  bin 10:  2.0535 -  1.9828 [1366/2015]  1232   134   9.8%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1006/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 18
        2.42 -     3.04: 2184
        3.04 -     3.66: 4685
        3.66 -     4.28: 9036
        4.28 -     4.90: 12295
  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
  " O   HOH Z 201 " - " O   HOH Z 349 "  2.230 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 208 " - " O   HOH Z 342 "  2.257 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 107 " - " O   HOH Z 340 "  2.304 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28213 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_1006/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1006/model_refine_001.geo

CPU time processing inputs: 9.16


============================ 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 = 71.30375 46.4607 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: 1.98 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4492   r_free= 0.4361   ksol= 0.00   Bsol= 0.00   scale= 0.811    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.61 A                  |
| x-ray target function (ml) for work reflections: 6.247320                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1573 -  4.7332 0.99   1395  157 0.3798 0.3665      6.5516      6.5233|
|  2:  4.7332 -  3.7760 0.99   1345  148 0.3473 0.3613      6.7056      6.6719|
|  3:  3.7760 -  3.3044 0.99   1326  144 0.3878 0.3576      6.5799      6.6029|
|  4:  3.3044 -  3.0048 0.99   1312  153 0.4271 0.3887      6.4835      6.4117|
|  5:  3.0048 -  2.7909 0.99   1298  143 0.4814 0.4686      6.3407      6.3646|
|  6:  2.7909 -  2.6272 0.99   1304  140 0.4690 0.4867      6.2449      6.1869|
|  7:  2.6272 -  2.4963 0.99   1291  139 0.5066 0.4866      6.2367       6.222|
|  8:  2.4963 -  2.3880 0.98   1259  147 0.5039 0.4357      6.1539      6.1298|
|  9:  2.3880 -  2.2964 0.98   1274  148 0.4735 0.4979      6.0896      6.1378|
| 10:  2.2964 -  2.2174 1.00   1296  140 0.5127 0.4497      6.1002      6.0611|
| 11:  2.2174 -  2.1483 0.98   1291  136 0.5044 0.4743      6.0262      5.9885|
| 12:  2.1483 -  2.0870 0.98   1247  145 0.4987 0.5608      5.9625      6.0239|
| 13:  2.0870 -  2.0322 0.99   1282  137 0.5248 0.5025      5.8781      5.8022|
| 14:  2.0322 -  1.9828 0.55    710   82 0.5283 0.4935      5.8629      5.7819|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1573 -  4.7332  1395   157  0.72  32.66   0.80     0.76      65178.68|
|  2:  4.7332 -  3.7760  1345   148  0.77  29.46   0.90     0.82      81161.69|
|  3:  3.7760 -  3.3044  1326   144  0.69  36.54   0.87     0.79      84579.58|
|  4:  3.3044 -  3.0048  1312   153  0.63  41.82   0.82     0.71      76225.93|
|  5:  3.0048 -  2.7909  1298   143  0.52  50.29   0.75     0.61      67048.72|
|  6:  2.7909 -  2.6272  1304   140  0.48  53.59   0.75     0.54      61807.32|
|  7:  2.6272 -  2.4963  1291   139  0.44  56.60   0.75     0.50      58224.20|
|  8:  2.4963 -  2.3880  1259   147  0.43  57.85   0.74     0.50      53353.41|
|  9:  2.3880 -  2.2964  1274   148  0.47  54.81   0.74     0.51      45649.44|
| 10:  2.2964 -  2.2174  1296   140  0.45  55.82   0.77     0.52      41204.04|
| 11:  2.2174 -  2.1483  1291   136  0.42  58.20   0.77     0.50      40901.93|
| 12:  2.1483 -  2.0870  1247   145  0.38  61.77   0.77     0.46      40804.91|
| 13:  2.0870 -  2.0322  1282   137  0.36  63.35   0.73     0.45      35386.81|
| 14:  2.0322 -  1.9828   710    82  0.47  54.89   0.72     0.50      24443.62|
|alpha:            min =        0.45 max =            0.82 mean =         0.59|
|beta:             min =    24443.62 max =        84579.58 mean =     56731.70|
|figures of merit: min =        0.00 max =            1.00 mean =         0.52|
|phase err.(work): min =        0.00 max =           90.00 mean =        50.15|
|phase err.(test): min =        0.00 max =           90.00 mean =        50.20|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.533760              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.516   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.814682              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.479   (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:      169 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      681 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1500 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2633 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3926 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5040 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6557 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7693 |
|-----------------------------------------------------------------------------|
|-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 |       53.869 |
| 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 |       1.689 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.972)------------------------------------------|
|    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 = 11.972)------------------------------------------|
|    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: 1.98 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4562   r_free= 0.4420   ksol= 0.00   Bsol= 0.00   scale= 0.780    |
|                                                                             |
| 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:   0.62 A                  |
| x-ray target function (ml) for work reflections: 6.250791                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4415   r_free= 0.4243   ksol= 0.34   Bsol= 16.43   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.71,8.88,7.71,0.00,0.00,0.00); trace/3= 8.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.241493                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.659868              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.392   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.794968              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.668   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4415      final r-factor (work) = 0.3419          |
| start r-factor (free) = 0.4243      final r-factor (free) = 0.3601          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 80.9397 = 8.66 * 0.50 * 6.2520 + 1.00 * 53.8688                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 26.6132 = 8.66 * 0.50 * 6.1176 + 1.00 * 0.1243                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3419      final r-factor (work) = 0.2843          |
| start r-factor (free) = 0.3601      final r-factor (free) = 0.3268          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8781 = 0.79 * 1.00 * 6.1176 + 1.00 * 0.0148                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7619 = 0.79 * 1.00 * 5.9734 + 1.00 * 0.0132                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.972)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    68.85   11.45    None  None   None       |
|    all(noH): 2823   0      0.00    68.85   11.45    None  None   None       |
|    Sol.    : 438    0      0.00    68.85   27.67    None  None   None       |
|    Mac.    : 2385   0      0.00    65.52   8.47     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.885: 1279   |   5:    34.427 -  41.312:   74        |
|      1:     6.885 -  13.771:  745   |   6:    41.312 -  48.197:   48        |
|      2:    13.771 -  20.656:  344   |   7:    48.197 -  55.082:   24        |
|      3:    20.656 -  27.541:  173   |   8:    55.082 -  61.968:   12        |
|      4:    27.541 -  34.427:  117   |   9:    61.968 -  68.853:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2843 r_free = 0.3268             target_work(ml) = 5.932         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2840 r_free = 0.3269             target_work(ml) = 5.932         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2840   r_free= 0.3269   ksol= 0.34   Bsol= 16.43   scale= 1.094   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.71,8.88,7.71,0.00,0.00,0.00); trace/3= 8.44                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.37 A                  |
| x-ray target function (ml) for work reflections: 5.931548                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2794   r_free= 0.3214   ksol= 0.35   Bsol= 45.90   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.18,4.79,4.52,0.00,0.00,0.00); trace/3= 4.83                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.929077                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.976966              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 95.349   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.401421              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.829  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2794      final r-factor (work) = 0.2017          |
| start r-factor (free) = 0.3214      final r-factor (free) = 0.2503          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.0179 = 2.98 * 0.50 * 5.9752 + 1.00 * 0.1239                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6676 = 2.98 * 0.50 * 5.7819 + 1.00 * 0.0614                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2017      final r-factor (work) = 0.1853          |
| start r-factor (free) = 0.2503      final r-factor (free) = 0.2365          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3341 = 0.40 * 1.00 * 5.7819 + 1.00 * 0.0131                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2605 = 0.40 * 1.00 * 5.6025 + 1.00 * 0.0115                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.972)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    70.97   11.55    None  None   None       |
|    all(noH): 2823   0      0.00    70.97   11.55    None  None   None       |
|    Sol.    : 438    0      0.00    70.97   31.57    None  None   None       |
|    Mac.    : 2385   0      0.00    66.33   7.87     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 -   7.097: 1457   |   5:    35.486 -  42.583:  108        |
|      1:     7.097 -  14.194:  669   |   6:    42.583 -  49.680:   57        |
|      2:    14.194 -  21.292:  225   |   7:    49.680 -  56.778:   26        |
|      3:    21.292 -  28.389:  131   |   8:    56.778 -  63.875:   12        |
|      4:    28.389 -  35.486:  133   |   9:    63.875 -  70.972:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1853 r_free = 0.2365             target_work(ml) = 5.576         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1852 r_free = 0.2367             target_work(ml) = 5.576         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1852   r_free= 0.2367   ksol= 0.35   Bsol= 45.90   scale= 1.031   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.18,4.79,4.52,0.00,0.00,0.00); trace/3= 4.83                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.575882                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1843   r_free= 0.2350   ksol= 0.34   Bsol= 45.90   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.65,3.17,4.09,0.00,0.00,0.00); trace/3= 3.64                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.574988                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.712720              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.978  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.405381              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 142.628  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1843      final r-factor (work) = 0.1403          |
| start r-factor (free) = 0.2350      final r-factor (free) = 0.1871          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.6650 = 2.71 * 0.50 * 5.6059 + 1.00 * 0.0614                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.4626 = 2.71 * 0.50 * 5.4571 + 1.00 * 0.0608                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1403      final r-factor (work) = 0.1303          |
| start r-factor (free) = 0.1871      final r-factor (free) = 0.1779          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.6807 = 1.41 * 1.00 * 5.4571 + 1.00 * 0.0114                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.4635 = 1.41 * 1.00 * 5.3007 + 1.00 * 0.0140                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.972)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.53   12.38    None  None   None       |
|    all(noH): 2823   0      0.00    77.53   12.38    None  None   None       |
|    Sol.    : 438    0      0.42    77.53   36.34    None  None   None       |
|    Mac.    : 2385   0      0.00    75.47   7.98     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 -   7.753: 1569   |   5:    38.767 -  46.520:   87        |
|      1:     7.753 -  15.507:  613   |   6:    46.520 -  54.273:   86        |
|      2:    15.507 -  23.260:  183   |   7:    54.273 -  62.027:   49        |
|      3:    23.260 -  31.013:  111   |   8:    62.027 -  69.780:   16        |
|      4:    31.013 -  38.767:  100   |   9:    69.780 -  77.533:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1303 r_free = 0.1779             target_work(ml) = 5.275         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1302 r_free = 0.1778             target_work(ml) = 5.274         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1302   r_free= 0.1778   ksol= 0.34   Bsol= 45.90   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.65,3.17,4.09,0.00,0.00,0.00); trace/3= 3.64                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.274464                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1303   r_free= 0.1773   ksol= 0.32   Bsol= 45.90   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.15,2.71,3.92,0.00,0.00,0.00); trace/3= 3.26                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.273530                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.617032              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 127.885  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.288039              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.751  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1303      final r-factor (work) = 0.1226          |
| start r-factor (free) = 0.1773      final r-factor (free) = 0.1700          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3469 = 1.62 * 0.50 * 5.3012 + 1.00 * 0.0608                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2974 = 1.62 * 0.50 * 5.2490 + 1.00 * 0.0535                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1226      final r-factor (work) = 0.1217          |
| start r-factor (free) = 0.1700      final r-factor (free) = 0.1662          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5259 = 0.29 * 1.00 * 5.2490 + 1.00 * 0.0139                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5169 = 0.29 * 1.00 * 5.2258 + 1.00 * 0.0117                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.972)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.43   12.12    None  None   None       |
|    all(noH): 2823   0      0.00    77.43   12.12    None  None   None       |
|    Sol.    : 438    0      1.35    77.43   35.45    None  None   None       |
|    Mac.    : 2385   0      0.00    75.97   7.83     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 -   7.743: 1617   |   5:    38.717 -  46.461:   81        |
|      1:     7.743 -  15.487:  590   |   6:    46.461 -  54.204:   88        |
|      2:    15.487 -  23.230:  172   |   7:    54.204 -  61.947:   37        |
|      3:    23.230 -  30.974:  108   |   8:    61.947 -  69.691:   16        |
|      4:    30.974 -  38.717:  105   |   9:    69.691 -  77.434:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1217 r_free = 0.1662             target_work(ml) = 5.212         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1217 r_free = 0.1661             target_work(ml) = 5.212         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1217   r_free= 0.1661   ksol= 0.32   Bsol= 45.90   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.15,2.71,3.92,0.00,0.00,0.00); trace/3= 3.26                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.212187                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1217   r_free= 0.1660   ksol= 0.32   Bsol= 45.90   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.00,2.60,3.90,0.00,0.00,0.00); trace/3= 3.17                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.212075                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.664062              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 144.296  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.545476              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 149.429  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1217      final r-factor (work) = 0.1174          |
| start r-factor (free) = 0.1660      final r-factor (free) = 0.1619          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.4011 = 1.66 * 0.50 * 5.2253 + 1.00 * 0.0535                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3805 = 1.66 * 0.50 * 5.1952 + 1.00 * 0.0580                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1174      final r-factor (work) = 0.1165          |
| start r-factor (free) = 0.1619      final r-factor (free) = 0.1617          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8455 = 0.55 * 1.00 * 5.1952 + 1.00 * 0.0116                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8382 = 0.55 * 1.00 * 5.1806 + 1.00 * 0.0123                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.972)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.34   12.03    None  None   None       |
|    all(noH): 2823   0      0.00    78.34   12.03    None  None   None       |
|    Sol.    : 438    0      1.19    78.34   35.09    None  None   None       |
|    Mac.    : 2385   0      0.00    77.94   7.79     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 -   7.834: 1633   |   5:    39.169 -  47.003:   85        |
|      1:     7.834 -  15.668:  577   |   6:    47.003 -  54.837:   79        |
|      2:    15.668 -  23.502:  174   |   7:    54.837 -  62.671:   34        |
|      3:    23.502 -  31.336:  117   |   8:    62.671 -  70.505:   15        |
|      4:    31.336 -  39.169:  100   |   9:    70.505 -  78.339:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1165 r_free = 0.1617             target_work(ml) = 5.181         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1165 r_free = 0.1617             target_work(ml) = 5.181         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1165   r_free= 0.1617   ksol= 0.32   Bsol= 45.90   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.00,2.60,3.90,0.00,0.00,0.00); trace/3= 3.17                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.180630                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1573 -  4.7332 0.99   1395  157 0.1009 0.1319      5.3964      5.5514|
|  2:  4.7332 -  3.7760 0.99   1345  148 0.0891 0.1142      5.4587      5.6274|
|  3:  3.7760 -  3.3044 0.99   1326  144 0.1094 0.1500      5.4979      5.8503|
|  4:  3.3044 -  3.0048 0.99   1312  153 0.1233 0.1735      5.4786      5.6532|
|  5:  3.0048 -  2.7909 0.99   1298  143 0.1417 0.1778      5.3709      5.5825|
|  6:  2.7909 -  2.6272 0.99   1304  140 0.1251 0.1925      5.2327      5.5091|
|  7:  2.6272 -  2.4963 0.99   1291  139 0.1335 0.1628      5.2161       5.353|
|  8:  2.4963 -  2.3880 0.98   1259  147 0.1242 0.1824      5.1033      5.3829|
|  9:  2.3880 -  2.2964 0.98   1274  148 0.1244 0.1903       5.088        5.38|
| 10:  2.2964 -  2.2174 1.00   1296  140 0.1191 0.1639      4.9967      5.1832|
| 11:  2.2174 -  2.1483 0.98   1291  136 0.1186 0.1911      4.9898      5.3183|
| 12:  2.1483 -  2.0870 0.98   1247  145 0.1141 0.1722      4.9057      5.1915|
| 13:  2.0870 -  2.0322 0.99   1282  137 0.1224 0.1764       4.825      5.0829|
| 14:  2.0322 -  1.9828 0.55    710   82 0.1088 0.1633      4.6898      4.9025|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1573 -  4.7332  1395   157  0.94   9.23   0.98     0.95       7407.09|
|  2:  4.7332 -  3.7760  1345   148  0.95   8.14   1.01     1.00       9241.01|
|  3:  3.7760 -  3.3044  1326   144  0.93  11.61   1.02     1.02      10752.44|
|  4:  3.3044 -  3.0048  1312   153  0.92  14.14   1.01     0.98      10912.30|
|  5:  3.0048 -  2.7909  1298   143  0.89  16.75   0.99     0.97       9003.46|
|  6:  2.7909 -  2.6272  1304   140  0.90  16.34   0.98     0.96       7438.12|
|  7:  2.6272 -  2.4963  1291   139  0.90  16.19   0.99     0.96       6682.48|
|  8:  2.4963 -  2.3880  1259   147  0.90  16.14   0.98     0.96       5579.64|
|  9:  2.3880 -  2.2964  1274   148  0.90  16.35   1.00     0.97       5570.15|
| 10:  2.2964 -  2.2174  1296   140  0.90  16.29   1.00     0.96       4655.48|
| 11:  2.2174 -  2.1483  1291   136  0.90  16.59   0.99     0.95       4714.78|
| 12:  2.1483 -  2.0870  1247   145  0.91  15.70   1.01     1.01       4231.08|
| 13:  2.0870 -  2.0322  1282   137  0.89  16.94   1.00     0.97       3538.95|
| 14:  2.0322 -  1.9828   710    82  0.91  15.06   0.98     0.95       2686.63|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2686.63 max =        10912.30 mean =      6767.54|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.99 mean =        14.60|
|phase err.(test): min =        0.00 max =           88.35 mean =        14.03|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1165   r_free= 0.1617   ksol= 0.32   Bsol= 49.88   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.18,-0.56,0.74,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.180453                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.16 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1165   r_free= 0.1617   ksol= 0.32   Bsol= 49.88   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.18,-0.56,0.74,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.180453                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1573 -  4.7332 0.99   1395  157 0.1009 0.1317      5.3949       5.551|
|  2:  4.7332 -  3.7760 0.99   1345  148 0.0892 0.1144      5.4597      5.6287|
|  3:  3.7760 -  3.3044 0.99   1326  144 0.1094 0.1501      5.4984      5.8506|
|  4:  3.3044 -  3.0048 0.99   1312  153 0.1232 0.1734      5.4783      5.6527|
|  5:  3.0048 -  2.7909 0.99   1298  143 0.1416 0.1778      5.3704      5.5821|
|  6:  2.7909 -  2.6272 0.99   1304  140 0.1250 0.1924      5.2322      5.5085|
|  7:  2.6272 -  2.4963 0.99   1291  139 0.1335 0.1628      5.2157      5.3527|
|  8:  2.4963 -  2.3880 0.98   1259  147 0.1242 0.1823      5.1031      5.3825|
|  9:  2.3880 -  2.2964 0.98   1274  148 0.1244 0.1903      5.0879        5.38|
| 10:  2.2964 -  2.2174 1.00   1296  140 0.1191 0.1638      4.9966      5.1829|
| 11:  2.2174 -  2.1483 0.98   1291  136 0.1186 0.1911      4.9897      5.3185|
| 12:  2.1483 -  2.0870 0.98   1247  145 0.1141 0.1721      4.9057      5.1915|
| 13:  2.0870 -  2.0322 0.99   1282  137 0.1224 0.1764      4.8249      5.0829|
| 14:  2.0322 -  1.9828 0.55    710   82 0.1088 0.1633      4.6899      4.9024|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.1573 -  4.7332  1395   157  0.94   9.21   0.98     0.95       7380.21|
|  2:  4.7332 -  3.7760  1345   148  0.95   8.14   1.01     1.00       9241.89|
|  3:  3.7760 -  3.3044  1326   144  0.93  11.63   1.03     1.02      10766.98|
|  4:  3.3044 -  3.0048  1312   153  0.92  14.14   1.01     0.99      10909.71|
|  5:  3.0048 -  2.7909  1298   143  0.89  16.75   0.99     0.97       8994.61|
|  6:  2.7909 -  2.6272  1304   140  0.90  16.33   0.99     0.96       7430.74|
|  7:  2.6272 -  2.4963  1291   139  0.90  16.19   0.99     0.96       6675.53|
|  8:  2.4963 -  2.3880  1259   147  0.90  16.14   0.98     0.96       5576.92|
|  9:  2.3880 -  2.2964  1274   148  0.90  16.35   1.00     0.97       5567.63|
| 10:  2.2964 -  2.2174  1296   140  0.90  16.29   1.00     0.96       4654.34|
| 11:  2.2174 -  2.1483  1291   136  0.90  16.59   1.00     0.95       4713.84|
| 12:  2.1483 -  2.0870  1247   145  0.91  15.70   1.01     1.01       4230.66|
| 13:  2.0870 -  2.0322  1282   137  0.89  16.94   1.00     0.98       3538.35|
| 14:  2.0322 -  1.9828   710    82  0.91  15.06   0.98     0.95       2686.47|
|alpha:            min =        0.95 max =            1.02 mean =         0.97|
|beta:             min =     2686.47 max =        10909.71 mean =      6764.06|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.60|
|phase err.(test): min =        0.00 max =           88.38 mean =        14.02|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.972)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.21    81.55   15.24    None  None   None       |
|    all(noH): 2823   0      3.21    81.55   15.24    None  None   None       |
|    Sol.    : 438    0      4.40    81.55   38.31    None  None   None       |
|    Mac.    : 2385   0      3.21    81.15   11.01    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     3.213 -  11.047: 1633   |   5:    42.382 -  50.216:   85        |
|      1:    11.047 -  18.881:  577   |   6:    50.216 -  58.050:   79        |
|      2:    18.881 -  26.715:  174   |   7:    58.050 -  65.884:   34        |
|      3:    26.715 -  34.549:  117   |   8:    65.884 -  73.718:   15        |
|      4:    34.549 -  42.382:  100   |   9:    73.718 -  81.552:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 316         
Filter by distance & map next to the model:
   mapped sites are within: 0.358 - 4.692
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 311 from: 316
   mapped sites are within: 0.711 - 4.692

peak=   10.988 closest distance to " CB  VAL A 230 " =    1.472
peak=    8.312 closest distance to " CG2 VAL A 296 " =    1.215
peak=    7.776 closest distance to " CG  ARG A 138 " =    1.181
peak=    6.599 closest distance to " CD2 LEU A   5 " =    1.226
peak=    6.103 closest distance to " CD1AILE A 234 " =    1.118
peak=    6.093 closest distance to " NH2 ARG A  56 " =    2.175
peak=    5.778 closest distance to " CG  LEU A   5 " =    1.241
peak=    5.581 closest distance to " CG  PRO A  54 " =    1.354
peak=    5.562 closest distance to " NH1 ARG A 138 " =    0.988
peak=    5.509 closest distance to " NE2 GLN A  11 " =    1.162
peak=    5.452 closest distance to " CB  GLN A 223 " =    1.409
peak=    5.258 closest distance to " CG  LEU A 228 " =    1.184
peak=    5.236 closest distance to " O   HOH Z 144 " =    1.994
peak=    5.226 closest distance to " O   HOH Z 232 " =    2.298
peak=    5.151 closest distance to " CB  GLN A 183 " =    1.225
peak=    4.958 closest distance to " CB  PRO A  54 " =    1.020
peak=    4.910 closest distance to " CG  PRO A 198 " =    1.227
peak=    4.714 closest distance to " CB  ASN A 148 " =    1.354
peak=    4.692 closest distance to " O   HOH Z 427 " =    2.835
peak=    4.639 closest distance to " O   HOH Z 369 " =    2.019
peak=    4.624 closest distance to " O   HOH Z 425 " =    1.508
peak=    4.619 closest distance to " CG  PRO A 213 " =    1.241
peak=    4.594 closest distance to " CD2 LEU A 228 " =    1.174
peak=    4.567 closest distance to " O   PRO A 198 " =    1.615
peak=    4.556 closest distance to " O   HOH Z 298 " =    1.854
peak=    4.535 closest distance to " CD  ARG A 138 " =    1.136
peak=    4.531 closest distance to " CB  SER A  63 " =    1.312
peak=    4.494 closest distance to " O   HOH Z 316 " =    3.032
peak=    4.483 closest distance to " CB  TRP A 266 " =    0.999
peak=    4.443 closest distance to " O   HOH Z 126 " =    1.992
peak=    4.421 closest distance to " CB  VAL A 230 " =    1.207
peak=    4.392 closest distance to " CB  ASP A 124 " =    0.731
peak=    4.336 closest distance to " CG  PRO A 243 " =    1.161
peak=    4.334 closest distance to " ND2 ASN A 187 " =    1.517
peak=    4.326 closest distance to " O   HOH Z  55 " =    2.354
peak=    4.302 closest distance to " O   HOH Z 272 " =    1.851
peak=    4.262 closest distance to " CB  SER A   3 " =    1.400
peak=    4.247 closest distance to " O   HOH Z 236 " =    2.073
peak=    4.226 closest distance to " CB  GLU A 152 " =    1.324
peak=    4.222 closest distance to " O   HOH Z 411 " =    3.546
peak=    4.201 closest distance to " O   HOH Z   7 " =    1.237
peak=    4.190 closest distance to " NH1AARG A 145 " =    1.094
peak=    4.190 closest distance to " CB  ARG A 275 " =    0.921
peak=    4.160 closest distance to " CG  LEU A 167 " =    1.198
peak=    4.082 closest distance to " CB  SER A 216 " =    0.881
peak=    4.075 closest distance to " CB  ASN A  39 " =    0.933
peak=    4.069 closest distance to " O   HOH Z  78 " =    1.768
peak=    4.060 closest distance to " O   HOH Z 368 " =    2.084
peak=    4.058 closest distance to " CB  VAL A 296 " =    1.132
peak=    4.054 closest distance to " CB  VAL A 265 " =    1.303
peak=    4.031 closest distance to " O   HOH Z 303 " =    2.262
peak=    4.022 closest distance to " CB  TYR A 169 " =    0.711
peak=    4.006 closest distance to " CD  ARG A 159 " =    0.759
peak=    3.985 closest distance to " O   HOH Z  78 " =    2.175
peak=    3.982 closest distance to " O   HOH Z  88 " =    3.231
peak=    3.964 closest distance to " OD2 ASP A 286 " =    2.806
peak=    3.963 closest distance to " O   HOH Z 234 " =    3.776
peak=    3.941 closest distance to " O   HOH Z   2 " =    1.657
peak=    3.937 closest distance to " CD  ARG A  66 " =    2.331
peak=    3.922 closest distance to " CB  LEU A 143 " =    1.170
peak=    3.915 closest distance to " O   HOH Z 193 " =    1.716
peak=    3.913 closest distance to " CB  LEU A 228 " =    1.203
peak=    3.902 closest distance to " O   HOH Z 346 " =    1.591
peak=    3.888 closest distance to " CG  GLN A  88 " =    1.087
peak=    3.866 closest distance to " CB  GLU A 128 " =    1.074
peak=    3.860 closest distance to " O   SER A  87 " =    2.334
peak=    3.857 closest distance to " CA  TYR A  30 " =    0.973
peak=    3.853 closest distance to " O   HOH Z 193 " =    1.814
peak=    3.842 closest distance to " CZ  PHE A 218 " =    1.075
peak=    3.832 closest distance to " O   HOH Z 437 " =    1.853
peak=    3.828 closest distance to " O   HOH Z 158 " =    2.984
peak=    3.811 closest distance to " O   HOH Z   1 " =    1.923
peak=    3.809 closest distance to " CG2 THR A 221 " =    1.065
peak=    3.795 closest distance to " CB  SER A 212 " =    1.263
peak=    3.791 closest distance to " OD1 ASN A  69 " =    2.702
peak=    3.775 closest distance to " CA  ALA A  21 " =    1.175
peak=    3.775 closest distance to " O   HOH Z  44 " =    2.317
peak=    3.761 closest distance to " CG1 ILE A  33 " =    1.307
peak=    3.756 closest distance to " CB  MET A  40 " =    0.848
peak=    3.753 closest distance to " CD1 LEU A 300 " =    1.180
peak=    3.750 closest distance to " O   HOH Z 261 " =    2.085
peak=    3.731 closest distance to " O   HOH Z 313 " =    1.827
peak=    3.728 closest distance to " CE  LYS A  76 " =    0.893
peak=    3.722 closest distance to " CA  SER A  87 " =    0.942
peak=    3.720 closest distance to " CB  ARG A  79 " =    1.488
peak=    3.715 closest distance to " ND2 ASN A 249 " =    1.963
peak=    3.713 closest distance to " O   HOH Z 184 " =    1.453
peak=    3.713 closest distance to " N   PHE A 130 " =    1.246
peak=    3.710 closest distance to " CB  TRP A 179 " =    1.414
peak=    3.709 closest distance to " CB  VAL A 202 " =    1.591
peak=    3.701 closest distance to " CG BARG A 102 " =    1.870
peak=    3.700 closest distance to " O   HOH Z 435 " =    2.059
peak=    3.696 closest distance to " O   HOH Z  30 " =    1.538
peak=    3.696 closest distance to " CB  ASN A 142 " =    0.927
peak=    3.694 closest distance to " CB  THR A  82 " =    1.297
peak=    3.689 closest distance to " O   HOH Z 352 " =    1.793
peak=    3.683 closest distance to " CA  ALA A  51 " =    1.012
peak=    3.679 closest distance to " CB  ASP A 140 " =    0.926
peak=    3.673 closest distance to " O   HOH Z 410 " =    1.366
peak=    3.671 closest distance to " CA  THR A 264 " =    0.753
peak=    3.645 closest distance to " O   HOH Z 403 " =    1.658
peak=    3.644 closest distance to " O   HOH Z 180 " =    2.106
peak=    3.642 closest distance to " CA  ILE A 234 " =    0.940
peak=    3.641 closest distance to " NZ  LYS A 117 " =    3.197
peak=    3.639 closest distance to " CG2 VAL A 257 " =    0.910
peak=    3.635 closest distance to " O   HOH Z  61 " =    1.607
peak=    3.632 closest distance to " O   HOH Z 222 " =    2.347
peak=    3.629 closest distance to " CD BLYS A 290 " =    1.010
peak=    3.629 closest distance to " O   HOH Z 214 " =    2.030
peak=    3.625 closest distance to " NH1 ARG A  56 " =    0.930
peak=    3.623 closest distance to " O   HOH Z   9 " =    1.966
peak=    3.620 closest distance to " O   HOH Z 193 " =    1.908
peak=    3.616 closest distance to " CA  ASN A 215 " =    1.195
peak=    3.614 closest distance to " ND1 HIS A  86 " =    1.680
peak=    3.614 closest distance to " O   MET A 105 " =    1.727
peak=    3.610 closest distance to " O   HOH Z   9 " =    1.170
peak=    3.609 closest distance to " O   HOH Z 263 " =    1.595
peak=    3.597 closest distance to " CA  LEU A 282 " =    1.092
peak=    3.596 closest distance to " CB  ASN A 187 " =    1.089
peak=    3.595 closest distance to " O   HOH Z 130 " =    2.085
peak=    3.591 closest distance to " CB  HIS A 108 " =    0.855
peak=    3.588 closest distance to " CB BVAL A  41 " =    1.253
peak=    3.587 closest distance to " CB  GLU A 277 " =    3.602
peak=    3.580 closest distance to " CD1 ILE A  33 " =    1.680
peak=    3.576 closest distance to " O   HOH Z 280 " =    2.987
peak=    3.569 closest distance to " CA  LYS A 117 " =    1.174
peak=    3.561 closest distance to " O   HOH Z 273 " =    2.751
peak=    3.556 closest distance to " O   HOH Z 344 " =    2.947
peak=    3.554 closest distance to " O   HOH Z 423 " =    1.529
peak=    3.550 closest distance to " O   HOH Z 282 " =    1.867
peak=    3.542 closest distance to " CG1BVAL A  72 " =    1.589
peak=    3.537 closest distance to " CB  LYS A 117 " =    1.221
peak=    3.530 closest distance to " CB  ALA A 104 " =    0.779
peak=    3.529 closest distance to " OG  SER A  97 " =    2.970
peak=    3.528 closest distance to " CA  ALA A 299 " =    0.990
peak=    3.526 closest distance to " CA  ARG A 195 " =    1.261
peak=    3.523 closest distance to " CA  LYS A 290 " =    1.321
peak=    3.513 closest distance to " O   HOH Z 353 " =    2.664
peak=    3.510 closest distance to " O   HOH Z 135 " =    2.014
peak=    3.503 closest distance to " O   HOH Z 128 " =    2.070
peak=    3.501 closest distance to " CD2 LEU A 255 " =    1.641
peak=    3.498 closest distance to " CB  VAL A 250 " =    1.051
peak=    3.497 closest distance to " O   HOH Z 290 " =    1.124
peak=    3.496 closest distance to " O   ALA A 158 " =    1.410
peak=    3.496 closest distance to " O   HOH Z   3 " =    1.870
peak=    3.488 closest distance to " O   HOH Z 183 " =    1.323
peak=    3.488 closest distance to " O   HOH Z 132 " =    2.566
peak=    3.482 closest distance to " CA  ALA A 158 " =    1.151
peak=    3.476 closest distance to " O   HOH Z 112 " =    1.450
peak=    3.473 closest distance to " CG1 ILE A 151 " =    1.177
peak=    3.472 closest distance to " CG1 VAL A 153 " =    0.952
peak=    3.468 closest distance to " O   HOH Z 409 " =    2.877
peak=    3.466 closest distance to " CD  ARG A 269 " =    0.985
peak=    3.465 closest distance to " O   HOH Z 147 " =    1.679
peak=    3.464 closest distance to " CG  ARG A 159 " =    1.006
peak=    3.464 closest distance to " CB  SER A 210 " =    0.827
peak=    3.463 closest distance to " CA  ALA A 154 " =    1.071
peak=    3.461 closest distance to " CZ  PHE A 192 " =    0.955
peak=    3.460 closest distance to " CB  ASN A 110 " =    1.170
peak=    3.452 closest distance to " CB  THR A 157 " =    1.114
peak=    3.452 closest distance to " O   HOH Z 368 " =    3.584
peak=    3.452 closest distance to " CD  LYS A 166 " =    1.359
peak=    3.450 closest distance to " O   HOH Z  97 " =    2.006
peak=    3.448 closest distance to " O   HOH Z 126 " =    1.639
peak=    3.448 closest distance to " CG  MET A 185 " =    1.194
peak=    3.438 closest distance to " O   HOH Z  40 " =    2.051
peak=    3.438 closest distance to " O   HOH Z 185 " =    1.835
peak=    3.436 closest distance to " OG  SER A  62 " =    2.913
peak=    3.435 closest distance to " CG1 ILE A  49 " =    1.512
peak=    3.431 closest distance to " CE1 TYR A 186 " =    1.371
peak=    3.431 closest distance to " CB  ARG A 190 " =    1.662
peak=    3.427 closest distance to " CB  GLU A 236 " =    1.219
peak=    3.426 closest distance to " O   HOH Z 313 " =    1.673
peak=    3.423 closest distance to " O   HOH Z 109 " =    2.517
peak=    3.423 closest distance to " CB  GLN A  88 " =    1.286
peak=    3.414 closest distance to " O   HOH Z 371 " =    2.972
peak=    3.408 closest distance to " CA  GLY A 267 " =    0.982
peak=    3.408 closest distance to " O   HOH Z 305 " =    3.437
peak=    3.403 closest distance to " CB  MET A  47 " =    0.981
peak=    3.397 closest distance to " O   HOH Z 422 " =    2.647
peak=    3.396 closest distance to " O   HOH Z  59 " =    1.868
peak=    3.395 closest distance to " O   HOH Z 133 " =    1.733
peak=    3.387 closest distance to " NZ ALYS A 290 " =    1.052
peak=    3.386 closest distance to " CA  ARG A  36 " =    1.129
peak=    3.386 closest distance to " CB  LEU A 237 " =    0.858
peak=    3.385 closest distance to " CA  THR A 221 " =    0.902
peak=    3.380 closest distance to " O   HOH Z  63 " =    1.318
peak=    3.372 closest distance to " N   SER A 135 " =    1.260
peak=    3.371 closest distance to " CE3 TRP A 150 " =    0.950
peak=    3.368 closest distance to " O   TYR A 116 " =    1.228
peak=    3.363 closest distance to " N   ALA A 256 " =    1.081
peak=    3.361 closest distance to " CA  TYR A 116 " =    1.473
peak=    3.361 closest distance to " OG  SER A 206 " =    1.157
peak=    3.355 closest distance to " CG1 VAL A 174 " =    1.102
peak=    3.354 closest distance to " O   HOH Z 271 " =    2.057
peak=    3.354 closest distance to " N   SER A 271 " =    0.992
peak=    3.351 closest distance to " CB  TYR A  30 " =    1.534
peak=    3.350 closest distance to " O   HOH Z  10 " =    1.769
peak=    3.348 closest distance to " CA  ALA A 291 " =    0.918
peak=    3.346 closest distance to " O   HOH Z 145 " =    3.607
peak=    3.345 closest distance to " CB  TRP A 150 " =    1.371
peak=    3.345 closest distance to " CD1 LEU A 228 " =    1.956
peak=    3.343 closest distance to " OE2 GLU A   2 " =    1.729
peak=    3.341 closest distance to " O   HOH Z   1 " =    1.881
peak=    3.341 closest distance to " O   HOH Z 126 " =    1.533
peak=    3.334 closest distance to " N   SER A  12 " =    1.626
peak=    3.333 closest distance to " O   HOH Z 423 " =    2.624
peak=    3.332 closest distance to " O   HOH Z 302 " =    1.796
peak=    3.332 closest distance to " CB  ALA A   9 " =    1.586
peak=    3.329 closest distance to " CA  MET A  40 " =    1.060
peak=    3.329 closest distance to " O   HOH Z 419 " =    1.842
peak=    3.325 closest distance to " CD  ARG A  14 " =    1.255
peak=    3.324 closest distance to " N   VAL A 126 " =    1.277
peak=    3.320 closest distance to " O   HOH Z  61 " =    1.539
peak=    3.319 closest distance to " NH1 ARG A  14 " =    0.896
peak=    3.316 closest distance to " CA  ALA A 295 " =    1.104
peak=    3.303 closest distance to " OG  SER A  62 " =    3.064
peak=    3.302 closest distance to " O   HOH Z 371 " =    1.666
peak=    3.299 closest distance to " NE AARG A 275 " =    1.337
peak=    3.292 closest distance to " O   HOH Z 303 " =    1.821
peak=    3.288 closest distance to " CZ3 TRP A  92 " =    1.316
peak=    3.287 closest distance to " O   HOH Z 366 " =    2.906
peak=    3.287 closest distance to " CB  GLN A  89 " =    1.186
peak=    3.286 closest distance to " CB  ALA A 248 " =    1.352
peak=    3.285 closest distance to " CB  GLN A 103 " =    1.005
peak=    3.284 closest distance to " O   HOH Z  58 " =    1.629
peak=    3.280 closest distance to " CD  GLN A 240 " =    1.652
peak=    3.274 closest distance to " CZ3 TRP A 123 " =    1.496
peak=    3.268 closest distance to " CA  ARG A 102 " =    1.156
peak=    3.267 closest distance to " O   HOH Z  68 " =    2.019
peak=    3.261 closest distance to " CB  ALA A   1 " =    4.692
peak=    3.260 closest distance to " CB  SER A 273 " =    0.894
peak=    3.257 closest distance to " CG2 ILE A 106 " =    1.019
peak=    3.253 closest distance to " CB  GLU A  46 " =    1.051
peak=    3.253 closest distance to " O   HOH Z 248 " =    1.689
peak=    3.253 closest distance to " O   HOH Z 334 " =    1.618
peak=    3.244 closest distance to " CD2 TYR A 186 " =    1.087
peak=    3.243 closest distance to " CB  ALA A 291 " =    1.361
peak=    3.239 closest distance to " NH2BARG A 190 " =    1.586
peak=    3.238 closest distance to " OG BSER A 164 " =    2.267
peak=    3.238 closest distance to " O   HOH Z 329 " =    3.872
peak=    3.236 closest distance to " O   HOH Z 392 " =    1.286
peak=    3.235 closest distance to " CA  ILE A 106 " =    0.807
peak=    3.231 closest distance to " O   HOH Z 359 " =    3.923
peak=    3.230 closest distance to " O   HOH Z 345 " =    3.514
peak=    3.229 closest distance to " O   HOH Z 148 " =    2.299
peak=    3.227 closest distance to " O   HOH Z 148 " =    3.481
peak=    3.225 closest distance to " O   HOH Z 425 " =    2.074
peak=    3.221 closest distance to " O   HOH Z 407 " =    2.192
peak=    3.221 closest distance to " CD2 TRP A 179 " =    1.346
peak=    3.218 closest distance to " O   HOH Z 108 " =    2.648
peak=    3.218 closest distance to " ND1 HIS A  81 " =    1.703
peak=    3.215 closest distance to " O   HOH Z  88 " =    2.808
peak=    3.214 closest distance to " CA  LEU A 101 " =    1.612
peak=    3.211 closest distance to " O   HOH Z 116 " =    1.729
peak=    3.211 closest distance to " CB  ILE A 120 " =    1.391
peak=    3.210 closest distance to " ND2 ASN A 249 " =    0.870
peak=    3.208 closest distance to " O   HOH Z 303 " =    3.062
peak=    3.207 closest distance to " CB  VAL A 268 " =    0.865
peak=    3.206 closest distance to " O   HOH Z 124 " =    1.909
peak=    3.205 closest distance to " N   ASN A 127 " =    1.275
peak=    3.204 closest distance to " O   HOH Z 197 " =    3.294
peak=    3.202 closest distance to " NH2BARG A 145 " =    2.005
peak=    3.199 closest distance to " O   HOH Z  21 " =    1.669
peak=    3.197 closest distance to " O   HOH Z 172 " =    3.334
peak=    3.195 closest distance to " O   HOH Z 189 " =    3.121
peak=    3.190 closest distance to " O   HOH Z 332 " =    1.585
peak=    3.190 closest distance to " CB  LEU A 255 " =    0.773
peak=    3.188 closest distance to " ND2 ASN A 110 " =    1.677
peak=    3.185 closest distance to " O   HOH Z 392 " =    1.919
peak=    3.184 closest distance to " N   SER A 146 " =    1.665
peak=    3.183 closest distance to " O   HOH Z 175 " =    2.105
peak=    3.180 closest distance to " O   HOH Z 340 " =    2.181
peak=    3.179 closest distance to " C   GLN A  88 " =    1.552
peak=    3.178 closest distance to " CA  TYR A 186 " =    1.559
peak=    3.178 closest distance to " N   TYR A  15 " =    0.829
peak=    3.175 closest distance to " O   HOH Z 216 " =    2.821
peak=    3.172 closest distance to " O   HOH Z 173 " =    1.728
peak=    3.166 closest distance to " OD1BASN A 224 " =    2.366
peak=    3.158 closest distance to " CD1 ILE A 106 " =    0.830
peak=    3.156 closest distance to " O   HOH Z 285 " =    2.867
peak=    3.154 closest distance to " OE2 GLU A  53 " =    2.097
peak=    3.153 closest distance to " O   HOH Z 380 " =    1.620
peak=    3.145 closest distance to " CA  MET A 105 " =    0.948
peak=    3.142 closest distance to " CD  ARG A 195 " =    3.429
peak=    3.141 closest distance to " CG2 ILE A  20 " =    1.546
peak=    3.140 closest distance to " O   HOH Z 110 " =    1.566
peak=    3.131 closest distance to " CG BARG A 275 " =    1.497
peak=    3.130 closest distance to " O   HOH Z   4 " =    1.684
peak=    3.130 closest distance to " CA  VAL A  41 " =    0.853
peak=    3.130 closest distance to " CD1 LEU A  96 " =    0.775
peak=    3.125 closest distance to " O   TRP A 274 " =    1.768
peak=    3.123 closest distance to " NZ  LYS A  48 " =    1.429
peak=    3.121 closest distance to " CB  PRO A 243 " =    1.360
peak=    3.119 closest distance to " CB  SER A  62 " =    1.147
peak=    3.118 closest distance to " O   HOH Z 273 " =    1.618
peak=    3.116 closest distance to " NE2 HIS A 207 " =    1.338
peak=    3.115 closest distance to " O   HOH Z 327 " =    1.924
peak=    3.115 closest distance to " O   HOH Z  85 " =    2.021
peak=    3.113 closest distance to " CG  MET A 113 " =    1.560
peak=    3.111 closest distance to " CB  ARG A 139 " =    0.965
peak=    3.105 closest distance to " O   PRO A  90 " =    1.460
peak=    3.104 closest distance to " O   HOH Z 303 " =    2.549
peak=    3.102 closest distance to " CA  ASN A 127 " =    1.112
peak=    3.096 closest distance to " O  BHOH Z 338 " =    2.484
peak=    3.089 closest distance to " O   HOH Z 294 " =    1.519
peak=    3.088 closest distance to " CG2 ILE A 109 " =    0.780
peak=    3.080 closest distance to " CG  GLN A  89 " =    1.485
peak=    3.076 closest distance to " CB  ALA A 227 " =    0.962
peak=    3.074 closest distance to " OG  SER A  22 " =    2.939
peak=    3.065 closest distance to " O   ASN A 209 " =    1.514

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 210         
Filter by distance & map next to the model:
   mapped sites are within: 0.601 - 5.403
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 208 from: 210
   mapped sites are within: 0.778 - 5.403

peak=   -5.069 closest distance to " CG2 VAL A 230 " =    0.810
peak=   -4.569 closest distance to " CD  ARG A 138 " =    1.135
peak=   -4.412 closest distance to " CD  ARG A 156 " =    2.019
peak=   -4.403 closest distance to " CG  ARG A 138 " =    0.880
peak=   -4.203 closest distance to " O   HOH Z 231 " =    1.688
peak=   -4.160 closest distance to " O   HOH Z 266 " =    5.218
peak=   -4.151 closest distance to " CD  ARG A  14 " =    3.206
peak=   -4.099 closest distance to " O   HOH Z 290 " =    1.186
peak=   -4.087 closest distance to " OG BSER A 134 " =    1.286
peak=   -4.036 closest distance to " CB  PRO A 243 " =    2.639
peak=   -4.005 closest distance to " CD  GLN A 223 " =    2.138
peak=   -3.954 closest distance to " CB  PRO A 163 " =    2.515
peak=   -3.932 closest distance to " CE2 TYR A  30 " =    2.890
peak=   -3.912 closest distance to " CG2 VAL A 296 " =    1.412
peak=   -3.869 closest distance to " O   HOH Z 351 " =    1.466
peak=   -3.862 closest distance to " O   HOH Z  52 " =    1.604
peak=   -3.856 closest distance to " OE1 GLN A  88 " =    1.043
peak=   -3.852 closest distance to " O   VAL A  67 " =    2.574
peak=   -3.843 closest distance to " N   THR A 157 " =    1.425
peak=   -3.821 closest distance to " O   HOH Z 435 " =    2.805
peak=   -3.820 closest distance to " O   HOH Z 377 " =    1.751
peak=   -3.805 closest distance to " CA  ASP A  27 " =    2.426
peak=   -3.799 closest distance to " O   HOH Z 389 " =    1.951
peak=   -3.790 closest distance to " CB  ALA A  43 " =    2.555
peak=   -3.766 closest distance to " O   PRO A 198 " =    1.191
peak=   -3.762 closest distance to " O   GLY A 203 " =    2.450
peak=   -3.758 closest distance to " N   ALA A  43 " =    2.448
peak=   -3.748 closest distance to " CG1 VAL A 112 " =    3.069
peak=   -3.747 closest distance to " O   HOH Z 394 " =    1.506
peak=   -3.731 closest distance to " CZ3 TRP A 179 " =    1.157
peak=   -3.726 closest distance to " CG1 VAL A 296 " =    1.385
peak=   -3.723 closest distance to " CD2 LEU A   5 " =    1.014
peak=   -3.722 closest distance to " O   HOH Z  60 " =    2.294
peak=   -3.696 closest distance to " CA  GLY A 241 " =    2.293
peak=   -3.693 closest distance to " CG  TRP A 266 " =    1.758
peak=   -3.682 closest distance to " O   HOH Z  43 " =    1.706
peak=   -3.672 closest distance to " OG  SER A  87 " =    1.422
peak=   -3.668 closest distance to " CB  ALA A 161 " =    2.659
peak=   -3.668 closest distance to " O   PRO A 163 " =    2.018
peak=   -3.655 closest distance to " O   HOH Z 211 " =    1.479
peak=   -3.643 closest distance to " CD1 TYR A 247 " =    2.815
peak=   -3.624 closest distance to " O   HOH Z 281 " =    2.701
peak=   -3.617 closest distance to " CB  PHE A 192 " =    1.759
peak=   -3.614 closest distance to " CB  ALA A 248 " =    2.509
peak=   -3.614 closest distance to " CE2 PHE A 218 " =    2.566
peak=   -3.612 closest distance to " O   HOH Z  44 " =    2.248
peak=   -3.605 closest distance to " C   ALA A 158 " =    1.350
peak=   -3.586 closest distance to " ND2 ASN A  45 " =    1.201
peak=   -3.582 closest distance to " CG  MET A 105 " =    0.970
peak=   -3.574 closest distance to " CD1 LEU A 228 " =    2.351
peak=   -3.565 closest distance to " CB  VAL A 230 " =    1.128
peak=   -3.564 closest distance to " NH2AARG A 275 " =    5.403
peak=   -3.563 closest distance to " O   HOH Z 359 " =    1.672
peak=   -3.555 closest distance to " O   HOH Z 185 " =    2.212
peak=   -3.555 closest distance to " C   HIS A 108 " =    1.211
peak=   -3.553 closest distance to " O   HOH Z 166 " =    2.192
peak=   -3.540 closest distance to " CG1 VAL A 112 " =    2.650
peak=   -3.536 closest distance to " O   HOH Z 166 " =    2.059
peak=   -3.531 closest distance to " OG  SER A  97 " =    2.210
peak=   -3.527 closest distance to " CG  ASP A 231 " =    0.778
peak=   -3.521 closest distance to " NH2 ARG A  79 " =    1.947
peak=   -3.516 closest distance to " O   HOH Z 359 " =    3.333
peak=   -3.513 closest distance to " O   HOH Z 241 " =    1.292
peak=   -3.511 closest distance to " CD1 LEU A 101 " =    2.333
peak=   -3.510 closest distance to " O   HOH Z 350 " =    1.764
peak=   -3.507 closest distance to " O   SER A 271 " =    2.266
peak=   -3.496 closest distance to " O   VAL A 189 " =    2.573
peak=   -3.495 closest distance to " OD1 ASN A 187 " =    1.472
peak=   -3.493 closest distance to " CG1 VAL A 197 " =    2.400
peak=   -3.493 closest distance to " C   MET A 188 " =    1.538
peak=   -3.490 closest distance to " O   GLY A 211 " =    1.282
peak=   -3.489 closest distance to " C   ASN A 285 " =    2.431
peak=   -3.485 closest distance to " O   HOH Z 231 " =    1.287
peak=   -3.482 closest distance to " O   GLY A  17 " =    1.344
peak=   -3.477 closest distance to " O   GLY A  80 " =    2.454
peak=   -3.477 closest distance to " CG2 ILE A  49 " =    2.812
peak=   -3.475 closest distance to " CE BMET A  47 " =    1.634
peak=   -3.472 closest distance to " CG  PHE A 283 " =    2.709
peak=   -3.470 closest distance to " O   ILE A  49 " =    1.794
peak=   -3.458 closest distance to " C   LEU A 222 " =    0.786
peak=   -3.455 closest distance to " OG ASER A 134 " =    1.263
peak=   -3.453 closest distance to " CD2 PHE A  61 " =    1.861
peak=   -3.447 closest distance to " CD  ARG A 139 " =    1.687
peak=   -3.441 closest distance to " O   HOH Z  38 " =    1.633
peak=   -3.434 closest distance to " O   HOH Z 407 " =    3.168
peak=   -3.427 closest distance to " CD  GLN A  58 " =    0.942
peak=   -3.422 closest distance to " CG2 THR A   4 " =    2.011
peak=   -3.418 closest distance to " CG  PRO A 163 " =    2.465
peak=   -3.418 closest distance to " CB  ALA A 248 " =    2.045
peak=   -3.417 closest distance to " O   HOH Z 102 " =    1.637
peak=   -3.413 closest distance to " O   ARG A 145 " =    1.520
peak=   -3.409 closest distance to " OG  SER A 206 " =    1.642
peak=   -3.407 closest distance to " O   HOH Z 198 " =    2.268
peak=   -3.406 closest distance to " O   HOH Z 295 " =    1.554
peak=   -3.402 closest distance to " CE  MET A 105 " =    2.343
peak=   -3.397 closest distance to " O   HOH Z 275 " =    1.508
peak=   -3.393 closest distance to " O   SER A  22 " =    2.236
peak=   -3.392 closest distance to " O   HOH Z 166 " =    1.382
peak=   -3.382 closest distance to " O   HOH Z 111 " =    2.245
peak=   -3.373 closest distance to " O   TRP A  70 " =    1.446
peak=   -3.373 closest distance to " O   HOH Z 368 " =    1.628
peak=   -3.362 closest distance to " CD  LYS A 289 " =    2.472
peak=   -3.359 closest distance to " CZ2 TRP A 274 " =    0.937
peak=   -3.359 closest distance to " CZ  PHE A  38 " =    2.641
peak=   -3.354 closest distance to " CG1 VAL A 265 " =    2.449
peak=   -3.344 closest distance to " O   HOH Z   9 " =    1.559
peak=   -3.344 closest distance to " O   HOH Z  51 " =    1.144
peak=   -3.340 closest distance to " CB  ALA A   9 " =    2.606
peak=   -3.340 closest distance to " CZ  PHE A 192 " =    2.825
peak=   -3.336 closest distance to " N   ALA A 226 " =    2.135
peak=   -3.335 closest distance to " O   HOH Z 128 " =    2.480
peak=   -3.323 closest distance to " CB  ASN A  39 " =    2.228
peak=   -3.319 closest distance to " CD1 PHE A  59 " =    1.915
peak=   -3.316 closest distance to " O   HOH Z 388 " =    2.159
peak=   -3.312 closest distance to " NH2BARG A 275 " =    1.723
peak=   -3.311 closest distance to " CD1 LEU A 101 " =    2.539
peak=   -3.309 closest distance to " CB  TRP A  85 " =    2.475
peak=   -3.309 closest distance to " O   HOH Z 309 " =    2.350
peak=   -3.308 closest distance to " O   PRO A 198 " =    1.406
peak=   -3.305 closest distance to " O   HOH Z   2 " =    1.899
peak=   -3.302 closest distance to " N   GLN A  58 " =    1.944
peak=   -3.302 closest distance to " OH  TYR A 214 " =    1.112
peak=   -3.302 closest distance to " O   HOH Z 114 " =    3.132
peak=   -3.300 closest distance to " CD1 ILE A 199 " =    2.594
peak=   -3.296 closest distance to " CA  SER A 135 " =    1.393
peak=   -3.295 closest distance to " O   HOH Z 437 " =    1.771
peak=   -3.295 closest distance to " CB  ALA A 291 " =    2.144
peak=   -3.295 closest distance to " N   ALA A 248 " =    1.578
peak=   -3.294 closest distance to " O   HOH Z 103 " =    1.895
peak=   -3.293 closest distance to " OG BSER A 134 " =    1.799
peak=   -3.292 closest distance to " O   SER A 135 " =    1.442
peak=   -3.292 closest distance to " CB  ALA A 291 " =    2.263
peak=   -3.289 closest distance to " CE1 TYR A 169 " =    2.506
peak=   -3.289 closest distance to " CD  PRO A 213 " =    2.121
peak=   -3.288 closest distance to " SG BCYS A 201 " =    2.185
peak=   -3.287 closest distance to " CA  ASN A 127 " =    1.125
peak=   -3.287 closest distance to " CD2 LEU A 167 " =    1.861
peak=   -3.277 closest distance to " CD2 LEU A 237 " =    2.709
peak=   -3.276 closest distance to " O   HOH Z 111 " =    1.088
peak=   -3.270 closest distance to " CD  PRO A 243 " =    2.068
peak=   -3.265 closest distance to " CB  TYR A  15 " =    2.152
peak=   -3.262 closest distance to " CA  GLY A 203 " =    2.381
peak=   -3.260 closest distance to " O   HOH Z 140 " =    1.363
peak=   -3.258 closest distance to " O   HOH Z 147 " =    2.012
peak=   -3.257 closest distance to " OD1 ASN A 148 " =    1.399
peak=   -3.255 closest distance to " O   HOH Z 427 " =    1.660
peak=   -3.253 closest distance to " O   HOH Z  13 " =    1.647
peak=   -3.253 closest distance to " O   HOH Z 298 " =    1.191
peak=   -3.250 closest distance to " CE3 TRP A 150 " =    2.200
peak=   -3.247 closest distance to " O   HOH Z 292 " =    1.693
peak=   -3.243 closest distance to " CA  GLY A  98 " =    1.981
peak=   -3.243 closest distance to " O   HOH Z 380 " =    1.215
peak=   -3.243 closest distance to " CB  PHE A 130 " =    1.277
peak=   -3.236 closest distance to " CD2 LEU A 300 " =    2.754
peak=   -3.235 closest distance to " NH2 ARG A  66 " =    2.353
peak=   -3.235 closest distance to " OXT GLY A 302 " =    3.144
peak=   -3.234 closest distance to " CG2 VAL A 202 " =    2.681
peak=   -3.232 closest distance to " CB  ASP A 132 " =    2.340
peak=   -3.227 closest distance to " CD  GLN A 223 " =    1.637
peak=   -3.227 closest distance to " N   SER A 212 " =    1.956
peak=   -3.219 closest distance to " OG1 THR A 178 " =    1.300
peak=   -3.208 closest distance to " O   HOH Z  90 " =    2.898
peak=   -3.205 closest distance to " O   HOH Z 193 " =    1.993
peak=   -3.204 closest distance to " O   GLN A 240 " =    2.466
peak=   -3.204 closest distance to " CB  ALA A 227 " =    2.402
peak=   -3.201 closest distance to " O   HOH Z 191 " =    5.364
peak=   -3.196 closest distance to " CG  GLN A 278 " =    2.330
peak=   -3.192 closest distance to " O   HOH Z 113 " =    2.519
peak=   -3.190 closest distance to " O   HOH Z 417 " =    2.752
peak=   -3.182 closest distance to " C   ASP A 231 " =    2.523
peak=   -3.180 closest distance to " O   VAL A  67 " =    2.562
peak=   -3.175 closest distance to " O   HOH Z  73 " =    2.181
peak=   -3.171 closest distance to " CA  GLY A 241 " =    3.076
peak=   -3.171 closest distance to " NZ  LYS A 119 " =    3.398
peak=   -3.169 closest distance to " CG  GLN A  88 " =    0.874
peak=   -3.166 closest distance to " N   ASP A 270 " =    1.485
peak=   -3.166 closest distance to " O   HOH Z 417 " =    2.714
peak=   -3.160 closest distance to " O   HOH Z 377 " =    0.971
peak=   -3.160 closest distance to " O   HOH Z 313 " =    1.502
peak=   -3.158 closest distance to " O   HOH Z 353 " =    2.024
peak=   -3.153 closest distance to " N   SER A 276 " =    1.312
peak=   -3.149 closest distance to " O   TYR A  30 " =    2.753
peak=   -3.148 closest distance to " O   HOH Z 198 " =    1.633
peak=   -3.144 closest distance to " O   HOH Z 410 " =    2.110
peak=   -3.139 closest distance to " O   HOH Z 357 " =    1.847
peak=   -3.131 closest distance to " O   HOH Z  65 " =    1.189
peak=   -3.126 closest distance to " CZ  TYR A 169 " =    1.568
peak=   -3.124 closest distance to " N   LYS A 166 " =    1.942
peak=   -3.121 closest distance to " CG  GLU A 277 " =    1.234
peak=   -3.120 closest distance to " CB  ALA A 114 " =    2.435
peak=   -3.120 closest distance to " C   ASN A 187 " =    1.695
peak=   -3.118 closest distance to " O   HOH Z 390 " =    2.413
peak=   -3.115 closest distance to " CD2 HIS A 207 " =    2.454
peak=   -3.115 closest distance to " O   MET A  40 " =    2.807
peak=   -3.113 closest distance to " O   HOH Z 423 " =    1.227
peak=   -3.098 closest distance to " CE  LYS A  76 " =    2.651
peak=   -3.097 closest distance to " O   ALA A 180 " =    1.311
peak=   -3.089 closest distance to " ND2 ASN A  60 " =    1.712
peak=   -3.085 closest distance to " O   HOH Z 106 " =    2.006
peak=   -3.079 closest distance to " N   ASN A  60 " =    1.236
peak=   -3.075 closest distance to " O   HOH Z  52 " =    1.353
peak=   -3.063 closest distance to " CD1 LEU A 297 " =    2.554
peak=   -3.061 closest distance to " O   HOH Z 184 " =    1.861
peak=   -3.027 closest distance to " OD2 ASP A  50 " =    2.227
peak=   -3.018 closest distance to " N   ALA A 248 " =    2.455
peak=   -3.018 closest distance to " CG1 VAL A 296 " =    1.305
peak=   -3.015 closest distance to " CD2 TYR A 293 " =    2.005
peak=   -3.012 closest distance to " CE BMET A  47 " =    1.162

================= 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    :  0.4492 0.4361   6.247320e+00   6.227410e+00
   1_bss:  0.4415 0.4243   6.241493e+00   6.218107e+00
   1_xyz:  0.3419 0.3601   6.069808e+00   6.109959e+00
   1_adp:  0.2843 0.3268   5.932229e+00   6.035556e+00
   1_occ:  0.2840 0.3269   5.931548e+00   6.036702e+00
   2_bss:  0.2794 0.3214   5.929077e+00   6.032495e+00
   2_xyz:  0.2017 0.2503   5.645874e+00   5.809995e+00
   2_adp:  0.1853 0.2365   5.575825e+00   5.754853e+00
   2_occ:  0.1852 0.2367   5.575882e+00   5.755320e+00
   3_bss:  0.1843 0.2350   5.574988e+00   5.752694e+00
   3_xyz:  0.1403 0.1871   5.333923e+00   5.548970e+00
   3_adp:  0.1303 0.1779   5.274760e+00   5.499843e+00
   3_occ:  0.1302 0.1778   5.274464e+00   5.499507e+00
   4_bss:  0.1303 0.1773   5.273530e+00   5.497777e+00
   4_xyz:  0.1226 0.1700   5.226726e+00   5.457917e+00
   4_adp:  0.1217 0.1662   5.212499e+00   5.436855e+00
   4_occ:  0.1217 0.1661   5.212187e+00   5.436342e+00
   5_bss:  0.1217 0.1660   5.212075e+00   5.436190e+00
   5_xyz:  0.1174 0.1619   5.184563e+00   5.417248e+00
   5_adp:  0.1165 0.1617   5.180971e+00   5.418117e+00
   5_occ:  0.1165 0.1617   5.180630e+00   5.417586e+00
   5_bss:  0.1165 0.1617   5.180453e+00   5.417489e+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:  0.340  16.427   8.715   8.885   7.714   0.000   0.000   0.000
   1_xyz:  0.340  16.427   8.715   8.885   7.714   0.000   0.000   0.000
   1_adp:  0.340  16.427   8.715   8.885   7.714   0.000   0.000   0.000
   1_occ:  0.340  16.427   8.715   8.885   7.714   0.000   0.000   0.000
   2_bss:  0.346  45.901   5.178   4.793   4.517   0.000   0.000   0.000
   2_xyz:  0.346  45.901   5.178   4.793   4.517   0.000   0.000   0.000
   2_adp:  0.346  45.901   5.178   4.793   4.517   0.000   0.000   0.000
   2_occ:  0.346  45.901   5.178   4.793   4.517   0.000   0.000   0.000
   3_bss:  0.337  45.901   3.650   3.168   4.095   0.000   0.000   0.000
   3_xyz:  0.337  45.901   3.650   3.168   4.095   0.000   0.000   0.000
   3_adp:  0.337  45.901   3.650   3.168   4.095   0.000   0.000   0.000
   3_occ:  0.337  45.901   3.650   3.168   4.095   0.000   0.000   0.000
   4_bss:  0.323  45.901   3.153   2.714   3.915   0.000   0.000   0.000
   4_xyz:  0.323  45.901   3.153   2.714   3.915   0.000   0.000   0.000
   4_adp:  0.323  45.901   3.153   2.714   3.915   0.000   0.000   0.000
   4_occ:  0.323  45.901   3.153   2.714   3.915   0.000   0.000   0.000
   5_bss:  0.323  45.901   3.000   2.603   3.900   0.000   0.000   0.000
   5_xyz:  0.323  45.901   3.000   2.603   3.900   0.000   0.000   0.000
   5_adp:  0.323  45.901   3.000   2.603   3.900   0.000   0.000   0.000
   5_occ:  0.323  45.901   3.000   2.603   3.900   0.000   0.000   0.000
   5_bss:  0.319  49.882  -0.180  -0.559   0.739   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  50.153 0.5195  0.5901    56730.838
   1_bss:  50.787 0.5094  0.7406    55098.080
   1_xyz:  40.076 0.6410  0.9078    37258.818
   1_adp:  34.074 0.7126  1.0112    29570.973
   1_occ:  34.156 0.7116  1.0092    29639.930
   2_bss:  33.819 0.7154  0.8922    29160.521
   2_xyz:  24.719 0.8143  0.9777    16041.384
   2_adp:  22.776 0.8349  0.9900    14163.301
   2_occ:  22.797 0.8346  0.9896    14175.749
   3_bss:  22.705 0.8356  0.9489    14084.662
   3_xyz:  17.578 0.8841  0.9851     8905.810
   3_adp:  16.463 0.8943  0.9893     8075.961
   3_occ:  16.459 0.8943  0.9892     8069.971
   4_bss:  16.416 0.8947  0.9753     8023.565
   4_xyz:  15.483 0.9029  0.9767     7338.886
   4_adp:  14.948 0.9076  0.9766     7054.166
   4_occ:  14.941 0.9077  0.9766     7042.175
   5_bss:  14.938 0.9077  0.9733     7039.121
   5_xyz:  14.565 0.9107  0.9751     6768.209
   5_adp:  14.552 0.9108  0.9726     6774.740
   5_occ:  14.543 0.9109  0.9726     6767.782
   5_bss:  14.539 0.9109  0.9741     6764.302
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.3869e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.3869e+01
   1_xyz:   1.563  0.012  0.102 18.054  0.006  4.122   1.2426e-01
   1_adp:   1.563  0.012  0.102 18.054  0.006  4.122   1.2426e-01
   1_occ:   1.563  0.012  0.102 18.054  0.006  4.122   1.2426e-01
   2_bss:   1.563  0.012  0.102 18.054  0.006  4.122   1.2426e-01
   2_xyz:   0.988  0.007  0.069 16.023  0.004  4.120   6.1396e-02
   2_adp:   0.988  0.007  0.069 16.023  0.004  4.120   6.1396e-02
   2_occ:   0.988  0.007  0.069 16.023  0.004  4.120   6.1396e-02
   3_bss:   0.988  0.007  0.069 16.023  0.004  4.120   6.1396e-02
   3_xyz:   0.999  0.007  0.079 15.664  0.003  4.130   6.0799e-02
   3_adp:   0.999  0.007  0.079 15.664  0.003  4.130   6.0799e-02
   3_occ:   0.999  0.007  0.079 15.664  0.003  4.130   6.0799e-02
   4_bss:   0.999  0.007  0.079 15.664  0.003  4.130   6.0799e-02
   4_xyz:   0.903  0.006  0.072 15.476  0.003  4.113   5.3458e-02
   4_adp:   0.903  0.006  0.072 15.476  0.003  4.113   5.3458e-02
   4_occ:   0.903  0.006  0.072 15.476  0.003  4.113   5.3458e-02
   5_bss:   0.903  0.006  0.072 15.476  0.003  4.113   5.3458e-02
   5_xyz:   0.971  0.006  0.077 15.439  0.003  4.115   5.7974e-02
   5_adp:   0.971  0.006  0.077 15.439  0.003  4.115   5.7974e-02
   5_occ:   0.971  0.006  0.077 15.439  0.003  4.115   5.7974e-02
   5_bss:   0.971  0.006  0.077 15.439  0.003  4.115   5.7974e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9845e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9845e+00
   1_xyz:  12.615  0.156  0.413 87.217  0.036  2.250   9.2598e-02
   1_adp:  12.615  0.156  0.413 87.217  0.036  2.250   9.2598e-02
   1_occ:  12.615  0.156  0.413 87.217  0.036  2.250   9.2598e-02
   2_bss:  12.615  0.156  0.413 87.217  0.036  2.250   9.2598e-02
   2_xyz:   6.484  0.061  0.261 89.551  0.047  2.409   4.2450e-02
   2_adp:   6.484  0.061  0.261 89.551  0.047  2.409   4.2450e-02
   2_occ:   6.484  0.061  0.261 89.551  0.047  2.409   4.2450e-02
   3_bss:   6.484  0.061  0.261 89.551  0.047  2.409   4.2450e-02
   3_xyz:   8.064  0.063  0.453 82.022  0.025  2.340   3.9592e-02
   3_adp:   8.064  0.063  0.453 82.022  0.025  2.340   3.9592e-02
   3_occ:   8.064  0.063  0.453 82.022  0.025  2.340   3.9592e-02
   4_bss:   8.064  0.063  0.453 82.022  0.025  2.340   3.9592e-02
   4_xyz:   7.703  0.049  0.369 83.304  0.039  2.387   3.0103e-02
   4_adp:   7.703  0.049  0.369 83.304  0.039  2.387   3.0103e-02
   4_occ:   7.703  0.049  0.369 83.304  0.039  2.387   3.0103e-02
   5_bss:   7.703  0.049  0.369 83.304  0.039  2.387   3.0103e-02
   5_xyz:   7.903  0.058  0.440 84.168  0.034  2.360   3.3101e-02
   5_adp:   7.903  0.058  0.440 84.168  0.034  2.360   3.3101e-02
   5_occ:   7.903  0.058  0.440 84.168  0.034  2.360   3.3101e-02
   5_bss:   7.903  0.058  0.440 84.168  0.034  2.360   3.3101e-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:  68.85   0.00  11.45  65.52   0.00   8.47  68.85   0.00  27.67
   1_occ:  68.85   0.00  11.45  65.52   0.00   8.47  68.85   0.00  27.67
   2_bss:  68.85   0.00  11.45  65.52   0.00   8.47  68.85   0.00  27.67
   2_xyz:  68.85   0.00  11.45  65.52   0.00   8.47  68.85   0.00  27.67
   2_adp:  70.97   0.00  11.55  66.33   0.00   7.87  70.97   0.00  31.57
   2_occ:  70.97   0.00  11.55  66.33   0.00   7.87  70.97   0.00  31.57
   3_bss:  70.97   0.00  11.55  66.33   0.00   7.87  70.97   0.00  31.57
   3_xyz:  70.97   0.00  11.55  66.33   0.00   7.87  70.97   0.00  31.57
   3_adp:  77.53   0.00  12.38  75.47   0.00   7.98  77.53   0.42  36.34
   3_occ:  77.53   0.00  12.38  75.47   0.00   7.98  77.53   0.42  36.34
   4_bss:  77.53   0.00  12.38  75.47   0.00   7.98  77.53   0.42  36.34
   4_xyz:  77.53   0.00  12.38  75.47   0.00   7.98  77.53   0.42  36.34
   4_adp:  77.43   0.00  12.12  75.97   0.00   7.83  77.43   1.35  35.45
   4_occ:  77.43   0.00  12.12  75.97   0.00   7.83  77.43   1.35  35.45
   5_bss:  77.43   0.00  12.12  75.97   0.00   7.83  77.43   1.35  35.45
   5_xyz:  77.43   0.00  12.12  75.97   0.00   7.83  77.43   1.35  35.45
   5_adp:  78.34   0.00  12.03  77.94   0.00   7.79  78.34   1.19  35.09
   5_occ:  78.34   0.00  12.03  77.94   0.00   7.79  78.34   1.19  35.09
   5_bss:  81.55   3.21  15.24  81.15   3.21  11.01  81.55   4.40  38.31
------------------------------------------------------------------------
 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:    1.191    0.022    0.404
   1_adp:    1.191    0.022    0.404
   1_occ:    1.191    0.022    0.404
   2_bss:    1.191    0.022    0.404
   2_xyz:    1.456    0.028    0.511
   2_adp:    1.456    0.028    0.511
   2_occ:    1.456    0.028    0.511
   3_bss:    1.456    0.028    0.511
   3_xyz:    1.484    0.036    0.573
   3_adp:    1.484    0.036    0.573
   3_occ:    1.484    0.036    0.573
   4_bss:    1.484    0.036    0.573
   4_xyz:    1.743    0.025    0.596
   4_adp:    1.743    0.025    0.596
   4_occ:    1.743    0.025    0.596
   5_bss:    1.743    0.025    0.596
   5_xyz:    1.793    0.023    0.607
   5_adp:    1.793    0.023    0.607
   5_occ:    1.793    0.023    0.607
   5_bss:    1.793    0.023    0.607
------------------------------------------------------------------------

CPU time actual refinement: 325.25


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1006/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_1006/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1006/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1006/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1006/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 325.10 
  Macro-tasks:
    bulk solvent and scale       = 39.20  
    individual site refinement   = 131.39 
    weights calculation          = 31.99  
    collect and process          = 6.62   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 209.32 
  Micro-tasks:
    mask                            = 1.78   
    f_calc                          = 99.95  
    alpha_beta                      = 8.68   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 109.97 
    fmodel                         = 7.17   
    r_factors                      = 0.30   
    phase_errors                   = 10.88  
    foms                           = 0.31   
    TOTAL for micro-tasks          = 240.23 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.586 micro seconds
Total CPU time: 5.65 minutes
from_scatterers_fft:    650 calls, 99.52 s
gradients_fft:          594 calls, 96.67 s

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

# Date 2008-01-16 Time 02:57:18 PST -0800 (1200481038.35 s)
Start R-work = 0.4492, R-free = 0.4361 (no bulk solvent and anisotropic scale)
Final R-work = 0.1336, R-free = 0.1783 (no bulk solvent and anisotropic scale)

Start R-work = 0.4415, R-free = 0.4243
Final R-work = 0.1165, R-free = 0.1617