# Date 2008-01-16 Time 02:57:34 PST -0800 (1200481054.32 s)
#phil __OFF__

Command line arguments: "../1049.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 21971
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1049

-------------------------------------------------------------------------------
  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, 47.3993, 85.9581, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 47.3993, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1358 1.99117
Completeness in resolution range: 0.954769
Completeness with d_max=infinity: 0.951846

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1358
                             d_min =   1.9912

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, 47.3993, 85.9581, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1358 1.99117
Completeness in resolution range: 0.954769
Completeness with d_max=infinity: 0.951846

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1362 -  4.2609 [2153/2181]  1941   212   9.8%
  bin  2:  4.2609 -  3.3946 [2060/2076]  1851   209  10.1%
  bin  3:  3.3946 -  2.9692 [2049/2068]  1844   205  10.0%
  bin  4:  2.9692 -  2.6994 [2033/2063]  1833   200   9.8%
  bin  5:  2.6994 -  2.5068 [2016/2035]  1816   200   9.9%
  bin  6:  2.5068 -  2.3596 [2005/2041]  1798   207  10.3%
  bin  7:  2.3596 -  2.2418 [1972/2005]  1775   197  10.0%
  bin  8:  2.2418 -  2.1445 [1997/2031]  1798   199  10.0%
  bin  9:  2.1445 -  2.0622 [1977/2005]  1780   197  10.0%
  bin 10:  2.0622 -  1.9912 [1327/2012]  1194   133  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1049/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:
        1.66 -     2.31: 5
        2.31 -     2.96: 1655
        2.96 -     3.61: 4487
        3.61 -     4.25: 9104
        4.25 -     4.90: 12776
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 207 " - " O   HOH Z 341 "  1.663 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z 206 " - " O   HOH Z 342 "  2.141 3.040 -x+1/2,-y+1,z+1/2
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " OG1 THR A 246 " - " O   HOH Z 201 "  2.232 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 28022 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_1049/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1049/model_refine_001.geo

CPU time processing inputs: 9.10


============================ 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 47.3993 85.95805 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4487   r_free= 0.4330   ksol= 0.00   Bsol= 0.00   scale= 0.807    |
|                                                                             |
| 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: 6.248538                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1362 -  4.7526 0.99   1390  155 0.3744 0.3520      6.5475      6.4833|
|  2:  4.7526 -  3.7918 0.99   1360  147 0.3483 0.3810      6.6968      6.7361|
|  3:  3.7918 -  3.3182 0.99   1316  151 0.3990 0.3616      6.5986      6.5782|
|  4:  3.3182 -  3.0175 0.99   1317  148 0.4293 0.3922      6.4802      6.3772|
|  5:  3.0175 -  2.8027 0.99   1310  141 0.4679 0.4741      6.3338      6.3811|
|  6:  2.8027 -  2.6383 0.99   1286  147 0.4817 0.4835      6.2498      6.2178|
|  7:  2.6383 -  2.5068 0.99   1306  137 0.4907 0.4602      6.2303      6.1862|
|  8:  2.5068 -  2.3981 0.98   1273  151 0.4941 0.4685      6.1505      6.1419|
|  9:  2.3981 -  2.3062 0.98   1279  143 0.4966 0.5034      6.1089      6.1262|
| 10:  2.3062 -  2.2268 0.98   1286  132 0.4959 0.4785      6.0929      6.0787|
| 11:  2.2268 -  2.1574 1.00   1279  147 0.5002 0.4581      6.0256      6.0312|
| 12:  2.1574 -  2.0959 0.97   1260  140 0.5118 0.5278      5.9745       6.012|
| 13:  2.0959 -  2.0409 0.98   1274  140 0.5226 0.4926      5.8797      5.8276|
| 14:  2.0409 -  1.9912 0.54    694   80 0.5171 0.4515      5.8497      5.7363|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1362 -  4.7526  1390   155  0.73  31.31   0.81     0.76      59498.36|
|  2:  4.7526 -  3.7918  1360   147  0.76  29.95   0.90     0.80      80451.01|
|  3:  3.7918 -  3.3182  1316   151  0.67  37.54   0.85     0.77      86051.76|
|  4:  3.3182 -  3.0175  1317   148  0.60  43.58   0.82     0.68      78498.06|
|  5:  3.0175 -  2.8027  1310   141  0.51  50.90   0.75     0.59      68074.68|
|  6:  2.8027 -  2.6383  1286   147  0.48  53.28   0.76     0.55      60310.52|
|  7:  2.6383 -  2.5068  1306   137  0.49  53.03   0.74     0.54      53790.07|
|  8:  2.5068 -  2.3981  1273   151  0.47  54.83   0.73     0.54      50288.67|
|  9:  2.3981 -  2.3062  1279   143  0.46  55.58   0.73     0.52      45713.72|
| 10:  2.3062 -  2.2268  1286   132  0.44  56.90   0.77     0.51      43888.09|
| 11:  2.2268 -  2.1574  1279   147  0.42  58.60   0.76     0.48      40390.49|
| 12:  2.1574 -  2.0959  1260   140  0.40  59.95   0.76     0.48      38997.01|
| 13:  2.0959 -  2.0409  1274   140  0.41  59.45   0.72     0.48      32230.17|
| 14:  2.0409 -  1.9912   694    80  0.50  52.68   0.73     0.54      23710.73|
|alpha:            min =        0.48 max =            0.80 mean =         0.59|
|beta:             min =    23710.73 max =        86051.76 mean =     55755.34|
|figures of merit: min =        0.00 max =            1.00 mean =         0.53|
|phase err.(work): min =        0.00 max =           89.98 mean =        49.48|
|phase err.(test): min =        0.00 max =           90.00 mean =        49.31|
|-----------------------------------------------------------------------------|

============================== 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 = 10.030339             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 76.682   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.749036              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.504   (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:       23 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      162 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      677 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1498 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2602 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3850 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5052 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6503 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7630 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.206 |
| 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 |       1.661 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.162)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.162)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4547   r_free= 0.4405   ksol= 0.00   Bsol= 0.00   scale= 0.777    |
|                                                                             |
| 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:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.250619                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4406   r_free= 0.4235   ksol= 0.30   Bsol= 20.00   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.26,9.22,7.42,0.00,0.00,0.00); trace/3= 8.30                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.244134                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.103524              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.728   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.738814              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.934   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4406      final r-factor (work) = 0.3375          |
| start r-factor (free) = 0.4235      final r-factor (free) = 0.3689          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 82.6707 = 9.10 * 0.50 * 6.2535 + 1.00 * 54.2063                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.9209 = 9.10 * 0.50 * 6.1050 + 1.00 * 0.1324                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3375      final r-factor (work) = 0.2847          |
| start r-factor (free) = 0.3689      final r-factor (free) = 0.3265          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.5248 = 0.74 * 1.00 * 6.1050 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.4266 = 0.74 * 1.00 * 5.9750 + 1.00 * 0.0121                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 15     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.162)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    65.06   10.52    None  None   None       |
|    all(noH): 2823   0      0.00    65.06   10.52    None  None   None       |
|    Sol.    : 438    0      0.00    65.06   25.99    None  None   None       |
|    Mac.    : 2385   0      0.00    55.23   7.67     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.507: 1356   |   5:    32.532 -  39.039:   89        |
|      1:     6.507 -  13.013:  718   |   6:    39.039 -  45.545:   59        |
|      2:    13.013 -  19.519:  297   |   7:    45.545 -  52.052:   25        |
|      3:    19.519 -  26.026:  169   |   8:    52.052 -  58.558:    5        |
|      4:    26.026 -  32.532:  102   |   9:    58.558 -  65.065:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2847 r_free = 0.3265             target_work(ml) = 5.930         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2843 r_free = 0.3265             target_work(ml) = 5.929         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2843   r_free= 0.3265   ksol= 0.30   Bsol= 20.00   scale= 1.068   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.26,9.22,7.42,0.00,0.00,0.00); trace/3= 8.30                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.929085                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2814   r_free= 0.3209   ksol= 0.33   Bsol= 50.00   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.22,5.84,4.98,0.00,0.00,0.00); trace/3= 5.35                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.929200                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.659178              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.349   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.463356              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.286  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2814      final r-factor (work) = 0.1926          |
| start r-factor (free) = 0.3209      final r-factor (free) = 0.2391          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.0535 = 4.66 * 0.50 * 5.9758 + 1.00 * 0.1324                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.5106 = 4.66 * 0.50 * 5.7696 + 1.00 * 0.0696                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1926      final r-factor (work) = 0.1740          |
| start r-factor (free) = 0.2391      final r-factor (free) = 0.2187          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.7020 = 0.46 * 1.00 * 5.7696 + 1.00 * 0.0286                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6408 = 0.46 * 1.00 * 5.5484 + 1.00 * 0.0700                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.162)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    70.42   11.53    None  None   None       |
|    all(noH): 2823   0      0.00    70.42   11.53    None  None   None       |
|    Sol.    : 438    0      1.01    70.42   32.97    None  None   None       |
|    Mac.    : 2385   0      0.00    68.97   7.60     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 -   7.043: 1502   |   5:    35.213 -  42.255:   87        |
|      1:     7.043 -  14.085:  664   |   6:    42.255 -  49.297:   88        |
|      2:    14.085 -  21.128:  195   |   7:    49.297 -  56.340:   48        |
|      3:    21.128 -  28.170:  108   |   8:    56.340 -  63.382:   15        |
|      4:    28.170 -  35.213:  107   |   9:    63.382 -  70.425:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1740 r_free = 0.2187             target_work(ml) = 5.510         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1739 r_free = 0.2188             target_work(ml) = 5.510         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1739   r_free= 0.2188   ksol= 0.33   Bsol= 50.00   scale= 1.033   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.22,5.84,4.98,0.00,0.00,0.00); trace/3= 5.35                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.509589                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1722   r_free= 0.2171   ksol= 0.34   Bsol= 59.89   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.44,3.89,4.01,0.00,0.00,0.00); trace/3= 3.78                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.509659                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.165759              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.433  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.957432              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 91.152   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1722      final r-factor (work) = 0.1336          |
| start r-factor (free) = 0.2171      final r-factor (free) = 0.1756          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8668 = 3.17 * 0.50 * 5.5575 + 1.00 * 0.0699                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6251 = 3.17 * 0.50 * 5.4047 + 1.00 * 0.0702                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1336      final r-factor (work) = 0.1250          |
| start r-factor (free) = 0.1756      final r-factor (free) = 0.1703          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.5983 = 1.96 * 1.00 * 5.4047 + 1.00 * 0.0190                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 10.2949 = 1.96 * 1.00 * 5.2516 + 1.00 * 0.0153                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.162)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.67   12.43    None  None   None       |
|    all(noH): 2823   0      0.00    86.67   12.43    None  None   None       |
|    Sol.    : 438    0      0.00    82.22   37.45    None  None   None       |
|    Mac.    : 2385   0      0.00    86.67   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 -   8.667: 1741   |   5:    43.334 -  52.000:   88        |
|      1:     8.667 -  17.334:  520   |   6:    52.000 -  60.667:   66        |
|      2:    17.334 -  26.000:  156   |   7:    60.667 -  69.334:   44        |
|      3:    26.000 -  34.667:  101   |   8:    69.334 -  78.001:    7        |
|      4:    34.667 -  43.334:   91   |   9:    78.001 -  86.667:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1250 r_free = 0.1703             target_work(ml) = 5.238         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1250 r_free = 0.1703             target_work(ml) = 5.238         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1250   r_free= 0.1703   ksol= 0.34   Bsol= 59.89   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.44,3.89,4.01,0.00,0.00,0.00); trace/3= 3.78                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.238191                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1253   r_free= 0.1709   ksol= 0.33   Bsol= 57.18   scale= 0.995   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.08,3.38,3.78,0.00,0.00,0.00); trace/3= 3.42                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.240332                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.719023              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 128.396  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.211934              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 131.886  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1253      final r-factor (work) = 0.1208          |
| start r-factor (free) = 0.1709      final r-factor (free) = 0.1672          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5854 = 1.72 * 0.50 * 5.2530 + 1.00 * 0.0705                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.5503 = 1.72 * 0.50 * 5.2262 + 1.00 * 0.0584                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1208      final r-factor (work) = 0.1215          |
| start r-factor (free) = 0.1672      final r-factor (free) = 0.1645          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1228 = 0.21 * 1.00 * 5.2262 + 1.00 * 0.0152                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1178 = 0.21 * 1.00 * 5.2196 + 1.00 * 0.0116                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 34     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.162)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.36   12.03    None  None   None       |
|    all(noH): 2823   0      0.00    85.36   12.03    None  None   None       |
|    Sol.    : 438    0      0.99    80.93   35.66    None  None   None       |
|    Mac.    : 2385   0      0.00    85.36   7.70     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.536: 1753   |   5:    42.681 -  51.217:   86        |
|      1:     8.536 -  17.072:  521   |   6:    51.217 -  59.753:   58        |
|      2:    17.072 -  25.609:  163   |   7:    59.753 -  68.290:   35        |
|      3:    25.609 -  34.145:  100   |   8:    68.290 -  76.826:    7        |
|      4:    34.145 -  42.681:   91   |   9:    76.826 -  85.362:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1215 r_free = 0.1645             target_work(ml) = 5.210         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1215 r_free = 0.1644             target_work(ml) = 5.209         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1215   r_free= 0.1644   ksol= 0.33   Bsol= 57.18   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.08,3.38,3.78,0.00,0.00,0.00); trace/3= 3.42                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.209201                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1215   r_free= 0.1643   ksol= 0.32   Bsol= 54.65   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.95,3.22,3.75,0.00,0.00,0.00); trace/3= 3.31                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.209121                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.560752              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 145.830  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.744929              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 146.138  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1215      final r-factor (work) = 0.1184          |
| start r-factor (free) = 0.1643      final r-factor (free) = 0.1615          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1311 = 1.56 * 0.50 * 5.2189 + 1.00 * 0.0584                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.1154 = 1.56 * 0.50 * 5.1977 + 1.00 * 0.0592                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1184      final r-factor (work) = 0.1171          |
| start r-factor (free) = 0.1615      final r-factor (free) = 0.1625          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8834 = 0.74 * 1.00 * 5.1977 + 1.00 * 0.0115                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8738 = 0.74 * 1.00 * 5.1826 + 1.00 * 0.0132                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.162)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.19   12.04    None  None   None       |
|    all(noH): 2823   0      0.00    89.19   12.04    None  None   None       |
|    Sol.    : 438    0      0.97    81.63   35.64    None  None   None       |
|    Mac.    : 2385   0      0.00    89.19   7.70     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.919: 1780   |   5:    44.593 -  53.512:   86        |
|      1:     8.919 -  17.837:  501   |   6:    53.512 -  62.430:   50        |
|      2:    17.837 -  26.756:  160   |   7:    62.430 -  71.349:   20        |
|      3:    26.756 -  35.675:  110   |   8:    71.349 -  80.268:    5        |
|      4:    35.675 -  44.593:  104   |   9:    80.268 -  89.186:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1171 r_free = 0.1625             target_work(ml) = 5.188         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1171 r_free = 0.1625             target_work(ml) = 5.188         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1171   r_free= 0.1625   ksol= 0.32   Bsol= 54.65   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.95,3.22,3.75,0.00,0.00,0.00); trace/3= 3.31                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.187808                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1362 -  4.7526 0.99   1390  155 0.1006 0.1296      5.3885      5.5202|
|  2:  4.7526 -  3.7918 0.99   1360  147 0.0881 0.1114      5.4521      5.6431|
|  3:  3.7918 -  3.3182 0.99   1316  151 0.1104 0.1555      5.5038      5.8714|
|  4:  3.3182 -  3.0175 0.99   1317  148 0.1242 0.1568      5.4844      5.6089|
|  5:  3.0175 -  2.8027 0.99   1310  141 0.1414 0.1903      5.3866      5.5933|
|  6:  2.8027 -  2.6383 0.99   1286  147 0.1303 0.1975      5.2685      5.5359|
|  7:  2.6383 -  2.5068 0.99   1306  137 0.1343 0.1703      5.2304      5.4109|
|  8:  2.5068 -  2.3981 0.98   1273  151 0.1249 0.1782      5.1174      5.3644|
|  9:  2.3981 -  2.3062 0.98   1279  143 0.1250 0.1887      5.0874      5.3472|
| 10:  2.3062 -  2.2268 0.98   1286  132 0.1191 0.1777      5.0051      5.2605|
| 11:  2.2268 -  2.1574 1.00   1279  147 0.1217 0.1811      4.9862      5.3162|
| 12:  2.1574 -  2.0959 0.97   1260  140 0.1135 0.1663      4.9041      5.1197|
| 13:  2.0959 -  2.0409 0.98   1274  140 0.1240 0.1811      4.8263      5.0989|
| 14:  2.0409 -  1.9912 0.54    694   80 0.1116 0.1744      4.7039      4.9428|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1362 -  4.7526  1390   155  0.94   8.72   0.97     0.95       6979.12|
|  2:  4.7526 -  3.7918  1360   147  0.95   7.86   1.00     0.99       8932.09|
|  3:  3.7918 -  3.3182  1316   151  0.93  11.79   1.02     1.01      10947.80|
|  4:  3.3182 -  3.0175  1317   148  0.91  14.27   1.00     0.98      11003.18|
|  5:  3.0175 -  2.8027  1310   141  0.89  17.31   0.99     0.96       9413.45|
|  6:  2.8027 -  2.6383  1286   147  0.89  16.93   0.98     0.95       7974.75|
|  7:  2.6383 -  2.5068  1306   137  0.90  16.56   0.98     0.95       6937.11|
|  8:  2.5068 -  2.3981  1273   151  0.90  16.12   0.98     0.96       5886.16|
|  9:  2.3981 -  2.3062  1279   143  0.90  16.33   1.00     0.96       5527.94|
| 10:  2.3062 -  2.2268  1286   132  0.90  16.28   0.98     0.95       4716.79|
| 11:  2.2268 -  2.1574  1279   147  0.90  16.74   0.99     0.95       4643.61|
| 12:  2.1574 -  2.0959  1260   140  0.91  15.38   0.99     0.98       4186.94|
| 13:  2.0959 -  2.0409  1274   140  0.89  17.42   0.99     0.97       3586.24|
| 14:  2.0409 -  1.9912   694    80  0.91  15.40   0.97     0.93       2719.46|
|alpha:            min =        0.93 max =            1.01 mean =         0.96|
|beta:             min =     2719.46 max =        11003.18 mean =      6845.95|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.96 mean =        14.70|
|phase err.(test): min =        0.00 max =           87.64 mean =        14.15|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1171   r_free= 0.1625   ksol= 0.32   Bsol= 55.87   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.35,-0.11,0.45,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.187843                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.99 - 15.14 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1171   r_free= 0.1625   ksol= 0.32   Bsol= 55.87   scale= 0.993   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.35,-0.11,0.45,-0.00,0.00,0.00); trace/3= 0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.187843                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1362 -  4.7526 0.99   1390  155 0.1004 0.1297      5.3874      5.5199|
|  2:  4.7526 -  3.7918 0.99   1360  147 0.0880 0.1113      5.4516       5.642|
|  3:  3.7918 -  3.3182 0.99   1316  151 0.1103 0.1555      5.5034      5.8715|
|  4:  3.3182 -  3.0175 0.99   1317  148 0.1243 0.1568      5.4847      5.6091|
|  5:  3.0175 -  2.8027 0.99   1310  141 0.1415 0.1905      5.3871      5.5937|
|  6:  2.8027 -  2.6383 0.99   1286  147 0.1304 0.1976       5.269      5.5363|
|  7:  2.6383 -  2.5068 0.99   1306  137 0.1343 0.1704      5.2308      5.4114|
|  8:  2.5068 -  2.3981 0.98   1273  151 0.1250 0.1783      5.1176      5.3646|
|  9:  2.3981 -  2.3062 0.98   1279  143 0.1250 0.1886      5.0876      5.3471|
| 10:  2.3062 -  2.2268 0.98   1286  132 0.1191 0.1778      5.0053       5.261|
| 11:  2.2268 -  2.1574 1.00   1279  147 0.1218 0.1811      4.9864      5.3161|
| 12:  2.1574 -  2.0959 0.97   1260  140 0.1135 0.1663      4.9042      5.1199|
| 13:  2.0959 -  2.0409 0.98   1274  140 0.1240 0.1812      4.8263       5.099|
| 14:  2.0409 -  1.9912 0.54    694   80 0.1116 0.1743      4.7039      4.9425|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1362 -  4.7526  1390   155  0.94   8.72   0.97     0.95       6979.37|
|  2:  4.7526 -  3.7918  1360   147  0.95   7.86   1.00     0.99       8926.38|
|  3:  3.7918 -  3.3182  1316   151  0.93  11.78   1.02     1.01      10938.64|
|  4:  3.3182 -  3.0175  1317   148  0.91  14.27   1.00     0.98      11007.49|
|  5:  3.0175 -  2.8027  1310   141  0.89  17.31   0.99     0.96       9422.14|
|  6:  2.8027 -  2.6383  1286   147  0.89  16.94   0.98     0.96       7983.24|
|  7:  2.6383 -  2.5068  1306   137  0.90  16.57   0.98     0.95       6942.44|
|  8:  2.5068 -  2.3981  1273   151  0.90  16.13   0.99     0.96       5888.94|
|  9:  2.3981 -  2.3062  1279   143  0.90  16.33   1.00     0.97       5530.44|
| 10:  2.3062 -  2.2268  1286   132  0.90  16.28   0.99     0.95       4718.04|
| 11:  2.2268 -  2.1574  1279   147  0.90  16.75   0.99     0.95       4645.67|
| 12:  2.1574 -  2.0959  1260   140  0.91  15.38   1.00     0.98       4188.07|
| 13:  2.0959 -  2.0409  1274   140  0.89  17.41   0.99     0.97       3586.55|
| 14:  2.0409 -  1.9912   694    80  0.91  15.40   0.97     0.93       2718.46|
|alpha:            min =        0.93 max =            1.01 mean =         0.97|
|beta:             min =     2718.46 max =        11007.49 mean =      6847.52|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.92 mean =        14.70|
|phase err.(test): min =        0.00 max =           87.64 mean =        14.15|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.162)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.35    92.53   15.38    None  None   None       |
|    all(noH): 2823   0      3.35    92.53   15.38    None  None   None       |
|    Sol.    : 438    0      4.31    84.98   38.99    None  None   None       |
|    Mac.    : 2385   0      3.35    92.53   11.05    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:     3.345 -  12.264: 1780   |   5:    47.938 -  56.857:   86        |
|      1:    12.264 -  21.183:  501   |   6:    56.857 -  65.776:   50        |
|      2:    21.183 -  30.101:  160   |   7:    65.776 -  74.694:   20        |
|      3:    30.101 -  39.020:  110   |   8:    74.694 -  83.613:    5        |
|      4:    39.020 -  47.938:  104   |   9:    83.613 -  92.531:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 329         
Filter by distance & map next to the model:
   mapped sites are within: 0.315 - 5.910
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 322 from: 329
   mapped sites are within: 0.701 - 5.910

peak=   10.277 closest distance to " CG2 VAL A 230 " =    1.414
peak=    8.034 closest distance to " CG2 VAL A 296 " =    1.198
peak=    6.146 closest distance to " O   HOH Z 111 " =    2.266
peak=    6.097 closest distance to " CG  LEU A   5 " =    1.221
peak=    5.973 closest distance to " CB  GLN A 223 " =    1.403
peak=    5.220 closest distance to " CG  LEU A 228 " =    1.215
peak=    5.220 closest distance to " CD2 LEU A   5 " =    1.158
peak=    5.203 closest distance to " CB  PRO A  54 " =    0.975
peak=    5.148 closest distance to " CG  PRO A  54 " =    1.298
peak=    4.973 closest distance to " CG  PRO A 198 " =    1.253
peak=    4.926 closest distance to " CB  SER A  63 " =    1.321
peak=    4.926 closest distance to " CD1AILE A 234 " =    1.052
peak=    4.797 closest distance to " O   HOH Z 232 " =    2.309
peak=    4.759 closest distance to " CB  VAL A 230 " =    1.216
peak=    4.751 closest distance to " CG  PRO A 213 " =    1.245
peak=    4.616 closest distance to " CB  GLN A 183 " =    1.306
peak=    4.586 closest distance to " CD2 LEU A 228 " =    1.251
peak=    4.566 closest distance to " CB  ASN A 148 " =    1.288
peak=    4.454 closest distance to " CB  ARG A 275 " =    0.885
peak=    4.385 closest distance to " O   HOH Z 247 " =    1.403
peak=    4.377 closest distance to " CB  GLU A 128 " =    1.095
peak=    4.375 closest distance to " C   PRO A 198 " =    1.558
peak=    4.369 closest distance to " O   HOH Z 369 " =    2.092
peak=    4.356 closest distance to " NE2 GLN A  11 " =    1.082
peak=    4.301 closest distance to " O   HOH Z 298 " =    1.777
peak=    4.284 closest distance to " CG  PRO A 243 " =    1.180
peak=    4.273 closest distance to " O   HOH Z 272 " =    1.911
peak=    4.262 closest distance to " CB  TRP A 266 " =    0.965
peak=    4.237 closest distance to " CA  TYR A  30 " =    0.962
peak=    4.225 closest distance to " O   HOH Z 316 " =    3.098
peak=    4.225 closest distance to " OD1 ASN A  69 " =    2.638
peak=    4.210 closest distance to " O   HOH Z 427 " =    3.149
peak=    4.196 closest distance to " O   HOH Z  54 " =    2.332
peak=    4.174 closest distance to " O   HOH Z 403 " =    1.719
peak=    4.117 closest distance to " O   HOH Z  63 " =    1.425
peak=    4.110 closest distance to " CB  VAL A 296 " =    1.053
peak=    4.097 closest distance to " O   HOH Z 184 " =    1.428
peak=    4.095 closest distance to " O   HOH Z 368 " =    2.238
peak=    4.094 closest distance to " O   HOH Z 423 " =    1.737
peak=    4.089 closest distance to " O   HOH Z 126 " =    1.996
peak=    4.085 closest distance to " CB  ARG A 190 " =    1.674
peak=    4.080 closest distance to " O   SER A  87 " =    2.305
peak=    4.059 closest distance to " CB  GLU A 152 " =    1.132
peak=    4.053 closest distance to " CB  SER A   3 " =    1.350
peak=    4.051 closest distance to " CG2 THR A 221 " =    1.034
peak=    4.046 closest distance to " CB  GLU A 277 " =    3.715
peak=    4.017 closest distance to " O   HOH Z  48 " =    1.544
peak=    4.014 closest distance to " CB  VAL A 265 " =    1.294
peak=    4.007 closest distance to " O   HOH Z 236 " =    1.842
peak=    4.007 closest distance to " O   HOH Z  88 " =    3.272
peak=    3.994 closest distance to " CB  ASP A 124 " =    0.709
peak=    3.993 closest distance to " O   HOH Z 303 " =    2.121
peak=    3.981 closest distance to " CB  LEU A 228 " =    1.227
peak=    3.972 closest distance to " CD  ARG A 159 " =    0.801
peak=    3.950 closest distance to " CA  ALA A  51 " =    1.038
peak=    3.950 closest distance to " CZ  PHE A 218 " =    1.062
peak=    3.944 closest distance to " CG1 ILE A  33 " =    1.302
peak=    3.943 closest distance to " O   HOH Z  78 " =    1.774
peak=    3.943 closest distance to " CZ  PHE A 192 " =    1.026
peak=    3.940 closest distance to " O   HOH Z  15 " =    2.100
peak=    3.921 closest distance to " CA  THR A 264 " =    0.701
peak=    3.915 closest distance to " O   HOH Z 234 " =    3.592
peak=    3.899 closest distance to " CA  ALA A  21 " =    1.273
peak=    3.896 closest distance to " CD  ARG A 269 " =    0.950
peak=    3.890 closest distance to " NH2 ARG A 156 " =    1.135
peak=    3.889 closest distance to " CB  LEU A 143 " =    1.184
peak=    3.881 closest distance to " OG  SER A  97 " =    2.978
peak=    3.880 closest distance to " CB BVAL A  41 " =    1.190
peak=    3.879 closest distance to " CG  ARG A  66 " =    2.755
peak=    3.878 closest distance to " O   HOH Z 425 " =    1.358
peak=    3.872 closest distance to " O   HOH Z  44 " =    2.094
peak=    3.870 closest distance to " O   HOH Z 102 " =    1.355
peak=    3.868 closest distance to " O   HOH Z 280 " =    2.913
peak=    3.862 closest distance to " O   HOH Z 263 " =    1.641
peak=    3.858 closest distance to " NH1AARG A 145 " =    1.106
peak=    3.858 closest distance to " O   HOH Z  61 " =    1.634
peak=    3.842 closest distance to " ND2 ASN A 249 " =    1.906
peak=    3.830 closest distance to " O   HOH Z 411 " =    3.665
peak=    3.803 closest distance to " O   MET A 105 " =    1.847
peak=    3.796 closest distance to " CD1 LEU A 300 " =    1.155
peak=    3.789 closest distance to " O   HOH Z 112 " =    1.631
peak=    3.783 closest distance to " O   HOH Z 134 " =    1.503
peak=    3.783 closest distance to " CA  LYS A 117 " =    1.262
peak=    3.783 closest distance to " O   ASP A 124 " =    1.125
peak=    3.776 closest distance to " CA  THR A 221 " =    0.916
peak=    3.776 closest distance to " CB  VAL A 202 " =    1.580
peak=    3.773 closest distance to " O   HOH Z  80 " =    1.779
peak=    3.770 closest distance to " O   HOH Z 126 " =    1.586
peak=    3.766 closest distance to " CB  SER A 216 " =    0.844
peak=    3.762 closest distance to " CG1 VAL A 153 " =    1.015
peak=    3.761 closest distance to " O   HOH Z 193 " =    2.174
peak=    3.760 closest distance to " CA  ALA A 295 " =    1.119
peak=    3.758 closest distance to " CB  ASN A  39 " =    0.883
peak=    3.757 closest distance to " O   HOH Z 203 " =    1.835
peak=    3.746 closest distance to " O   HOH Z 295 " =    1.491
peak=    3.742 closest distance to " CB  ASP A 140 " =    0.903
peak=    3.740 closest distance to " OD2 ASP A 286 " =    2.875
peak=    3.736 closest distance to " CG1BVAL A  72 " =    1.675
peak=    3.734 closest distance to " O   TRP A 274 " =    1.884
peak=    3.731 closest distance to " O   HOH Z  48 " =    1.734
peak=    3.731 closest distance to " CB  ARG A  79 " =    1.439
peak=    3.730 closest distance to " CB  TRP A 179 " =    1.428
peak=    3.721 closest distance to " CG  MET A 185 " =    1.233
peak=    3.721 closest distance to " CB  ALA A   9 " =    1.597
peak=    3.717 closest distance to " O   HOH Z 383 " =    2.133
peak=    3.715 closest distance to " CG BARG A 102 " =    1.867
peak=    3.708 closest distance to " CD ALYS A 290 " =    1.006
peak=    3.707 closest distance to " O   HOH Z 158 " =    3.022
peak=    3.704 closest distance to " CA  ARG A 195 " =    1.228
peak=    3.704 closest distance to " O   HOH Z  21 " =    1.698
peak=    3.702 closest distance to " CA  SER A  87 " =    0.968
peak=    3.697 closest distance to " O   HOH Z  43 " =    2.016
peak=    3.693 closest distance to " CD  LYS A 166 " =    1.320
peak=    3.690 closest distance to " CA  ASP A 191 " =    0.755
peak=    3.688 closest distance to " CB  SER A 212 " =    1.166
peak=    3.685 closest distance to " O   HOH Z 437 " =    1.991
peak=    3.679 closest distance to " O   HOH Z 163 " =    1.574
peak=    3.669 closest distance to " O   HOH Z  97 " =    2.073
peak=    3.669 closest distance to " CA  MET A  40 " =    1.177
peak=    3.666 closest distance to " ND2 ASN A 187 " =    1.504
peak=    3.660 closest distance to " CA  LEU A 282 " =    1.092
peak=    3.644 closest distance to " O   HOH Z 261 " =    1.826
peak=    3.642 closest distance to " O   HOH Z 128 " =    2.160
peak=    3.630 closest distance to " O   HOH Z 133 " =    2.305
peak=    3.628 closest distance to " CD1 LEU A  96 " =    0.702
peak=    3.619 closest distance to " ND1 HIS A  81 " =    1.652
peak=    3.617 closest distance to " O   HOH Z  20 " =    1.841
peak=    3.616 closest distance to " O   HOH Z 344 " =    2.954
peak=    3.613 closest distance to " O   HOH Z 346 " =    1.531
peak=    3.611 closest distance to " CD1 LEU A   5 " =    1.363
peak=    3.611 closest distance to " O   HOH Z 214 " =    2.182
peak=    3.596 closest distance to " O   HOH Z 227 " =    1.657
peak=    3.582 closest distance to " N   ASN A  39 " =    1.204
peak=    3.575 closest distance to " CA  ASP A 140 " =    1.250
peak=    3.573 closest distance to " CB  ALA A 291 " =    1.370
peak=    3.567 closest distance to " O   HOH Z 193 " =    1.866
peak=    3.565 closest distance to " CA  VAL A  41 " =    0.868
peak=    3.564 closest distance to " CB  MET A  47 " =    1.017
peak=    3.560 closest distance to " O   HOH Z  97 " =    2.660
peak=    3.560 closest distance to " O   ALA A 158 " =    1.406
peak=    3.558 closest distance to " O   HOH Z 329 " =    3.801
peak=    3.552 closest distance to " CG2 THR A 220 " =    0.961
peak=    3.548 closest distance to " NZ  LYS A 166 " =    3.132
peak=    3.535 closest distance to " CE1 TYR A 186 " =    1.299
peak=    3.524 closest distance to " CB  THR A 157 " =    1.207
peak=    3.520 closest distance to " O   HOH Z  68 " =    1.585
peak=    3.517 closest distance to " O   HOH Z 371 " =    3.246
peak=    3.515 closest distance to " CG  GLN A  88 " =    1.044
peak=    3.515 closest distance to " CB  PRO A 198 " =    1.031
peak=    3.514 closest distance to " O   GLN A 278 " =    1.339
peak=    3.508 closest distance to " N   VAL A 126 " =    1.441
peak=    3.502 closest distance to " CA  ARG A  36 " =    1.151
peak=    3.501 closest distance to " CB  ASN A 187 " =    1.097
peak=    3.495 closest distance to " CB  MET A  40 " =    0.793
peak=    3.494 closest distance to " CB  TRP A 150 " =    1.395
peak=    3.493 closest distance to " CB  GLU A  46 " =    1.015
peak=    3.490 closest distance to " NZ  LYS A 117 " =    3.215
peak=    3.488 closest distance to " O   HOH Z 402 " =    1.505
peak=    3.481 closest distance to " OG BSER A 164 " =    2.212
peak=    3.478 closest distance to " O   HOH Z 420 " =    2.156
peak=    3.473 closest distance to " CE  LYS A  76 " =    0.852
peak=    3.468 closest distance to " N   SER A 135 " =    1.421
peak=    3.441 closest distance to " O   HOH Z  49 " =    1.979
peak=    3.439 closest distance to " CG2 VAL A 257 " =    0.902
peak=    3.437 closest distance to " O   HOH Z 271 " =    2.475
peak=    3.434 closest distance to " O   HOH Z 193 " =    1.668
peak=    3.430 closest distance to " O   HOH Z 433 " =    1.457
peak=    3.429 closest distance to " CB  ALA A 248 " =    1.343
peak=    3.427 closest distance to " OD1 ASP A 231 " =    1.885
peak=    3.426 closest distance to " C   SER A  32 " =    1.057
peak=    3.424 closest distance to " O   HOH Z 172 " =    3.806
peak=    3.424 closest distance to " O   HOH Z 290 " =    1.073
peak=    3.423 closest distance to " O   HOH Z   4 " =    1.841
peak=    3.420 closest distance to " O   HOH Z 426 " =    1.477
peak=    3.417 closest distance to " CD1 ILE A 106 " =    0.977
peak=    3.417 closest distance to " OE1 GLN A  11 " =    1.824
peak=    3.415 closest distance to " O   HOH Z 197 " =    2.737
peak=    3.413 closest distance to " CG1 ILE A  49 " =    1.553
peak=    3.411 closest distance to " O   HOH Z 146 " =    2.370
peak=    3.405 closest distance to " CG  LEU A 167 " =    1.140
peak=    3.401 closest distance to " O   HOH Z 132 " =    2.637
peak=    3.401 closest distance to " O   HOH Z 142 " =    1.500
peak=    3.391 closest distance to " CB  ALA A 161 " =    0.917
peak=    3.390 closest distance to " CB  ASN A 142 " =    1.062
peak=    3.385 closest distance to " O   HOH Z  40 " =    2.682
peak=    3.385 closest distance to " O   HOH Z 180 " =    2.102
peak=    3.378 closest distance to " O   HOH Z 327 " =    2.496
peak=    3.372 closest distance to " CB  ARG A 139 " =    0.833
peak=    3.371 closest distance to " N   PHE A 130 " =    1.258
peak=    3.370 closest distance to " CA  ASN A 215 " =    1.243
peak=    3.370 closest distance to " O   HOH Z 171 " =    3.897
peak=    3.365 closest distance to " O   HOH Z 245 " =    1.341
peak=    3.365 closest distance to " CG AARG A 275 " =    1.199
peak=    3.351 closest distance to " CG  LEU A 281 " =    1.115
peak=    3.344 closest distance to " CA  LYS A 290 " =    1.286
peak=    3.344 closest distance to " NH1 ARG A  14 " =    0.991
peak=    3.340 closest distance to " O   HOH Z 155 " =    3.174
peak=    3.333 closest distance to " OG  SER A  22 " =    2.844
peak=    3.333 closest distance to " O   HOH Z 422 " =    2.682
peak=    3.332 closest distance to " CE1 HIS A 108 " =    1.164
peak=    3.330 closest distance to " CB  THR A  31 " =    1.703
peak=    3.328 closest distance to " OH  TYR A 214 " =    1.219
peak=    3.324 closest distance to " O   HOH Z 109 " =    2.527
peak=    3.323 closest distance to " OG1 THR A 294 " =    2.325
peak=    3.320 closest distance to " O   HOH Z 133 " =    1.762
peak=    3.319 closest distance to " O   HOH Z 368 " =    3.581
peak=    3.314 closest distance to " CB  HIS A 108 " =    0.814
peak=    3.308 closest distance to " CB  SER A 273 " =    0.858
peak=    3.308 closest distance to " O   HOH Z 313 " =    1.854
peak=    3.307 closest distance to " CD2 LEU A 255 " =    1.448
peak=    3.302 closest distance to " O   ALA A 165 " =    1.431
peak=    3.300 closest distance to " CA  ALA A 154 " =    1.112
peak=    3.299 closest distance to " CB  VAL A 268 " =    0.858
peak=    3.299 closest distance to " OD1 ASN A 217 " =    1.619
peak=    3.297 closest distance to " O   HOH Z 130 " =    2.166
peak=    3.295 closest distance to " CB  ASN A 110 " =    1.376
peak=    3.295 closest distance to " NH1 ARG A 269 " =    0.828
peak=    3.294 closest distance to " CA  ILE A 106 " =    0.812
peak=    3.294 closest distance to " O   HOH Z 281 " =    4.641
peak=    3.294 closest distance to " CB  SER A  62 " =    1.335
peak=    3.291 closest distance to " N   ASN A 127 " =    1.169
peak=    3.291 closest distance to " CB  ALA A 104 " =    0.779
peak=    3.289 closest distance to " O   HOH Z 104 " =    2.805
peak=    3.284 closest distance to " CB  LYS A 117 " =    1.161
peak=    3.283 closest distance to " O   HOH Z  19 " =    2.105
peak=    3.282 closest distance to " O   HOH Z  68 " =    2.052
peak=    3.282 closest distance to " CB  GLN A  89 " =    1.106
peak=    3.279 closest distance to " O   HOH Z 147 " =    1.682
peak=    3.279 closest distance to " O   HOH Z 345 " =    3.487
peak=    3.278 closest distance to " O   HOH Z 273 " =    2.752
peak=    3.276 closest distance to " CG  MET A 188 " =    0.907
peak=    3.274 closest distance to " CB  ALA A 242 " =    0.875
peak=    3.274 closest distance to " O   HOH Z 353 " =    2.777
peak=    3.274 closest distance to " O   HOH Z 355 " =    1.824
peak=    3.273 closest distance to " O   THR A  31 " =    1.552
peak=    3.270 closest distance to " O   HOH Z 145 " =    2.017
peak=    3.270 closest distance to " CG1 VAL A 174 " =    1.234
peak=    3.269 closest distance to " CA  ALA A 160 " =    0.902
peak=    3.267 closest distance to " CD2 LEU A 297 " =    0.839
peak=    3.265 closest distance to " O   HOH Z 425 " =    1.985
peak=    3.263 closest distance to " CG  GLN A  58 " =    2.792
peak=    3.262 closest distance to " CA  GLY A 211 " =    1.268
peak=    3.262 closest distance to " O   HOH Z 313 " =    1.750
peak=    3.262 closest distance to " O   HOH Z 365 " =    2.966
peak=    3.258 closest distance to " CZ  PHE A  38 " =    1.240
peak=    3.256 closest distance to " O   ALA A   1 " =    1.555
peak=    3.255 closest distance to " CA  ALA A 158 " =    1.174
peak=    3.246 closest distance to " O   HOH Z 116 " =    1.828
peak=    3.244 closest distance to " CD2 LEU A   5 " =    0.730
peak=    3.243 closest distance to " CG  GLU A  37 " =    0.810
peak=    3.242 closest distance to " O   HOH Z 387 " =    3.141
peak=    3.239 closest distance to " O   HOH Z 197 " =    1.842
peak=    3.239 closest distance to " CG2 ILE A 106 " =    0.929
peak=    3.237 closest distance to " O   HOH Z 213 " =    1.706
peak=    3.235 closest distance to " CA  GLU A 152 " =    0.872
peak=    3.234 closest distance to " CB  ALA A 248 " =    1.140
peak=    3.232 closest distance to " CB  TYR A 247 " =    0.994
peak=    3.231 closest distance to " NH1 ARG A  56 " =    1.050
peak=    3.231 closest distance to " CG2 VAL A 197 " =    1.106
peak=    3.227 closest distance to " CA  ALA A 299 " =    0.978
peak=    3.224 closest distance to " CG2 THR A  42 " =    0.892
peak=    3.224 closest distance to " CB  ILE A 120 " =    1.426
peak=    3.215 closest distance to " O   HOH Z 391 " =    2.996
peak=    3.213 closest distance to " NZ  LYS A  48 " =    1.391
peak=    3.211 closest distance to " O   HOH Z  57 " =    1.242
peak=    3.205 closest distance to " ND1 HIS A  86 " =    1.602
peak=    3.205 closest distance to " CG BARG A 275 " =    1.477
peak=    3.202 closest distance to " CB  GLN A  88 " =    1.263
peak=    3.201 closest distance to " CB  ARG A  79 " =    0.898
peak=    3.200 closest distance to " CB  LEU A 255 " =    0.869
peak=    3.198 closest distance to " NZ  LYS A  76 " =    1.546
peak=    3.196 closest distance to " O   HOH Z 332 " =    1.540
peak=    3.196 closest distance to " O   HOH Z 420 " =    5.910
peak=    3.195 closest distance to " OG  SER A 245 " =    1.627
peak=    3.195 closest distance to " CZ3 TRP A  92 " =    1.353
peak=    3.195 closest distance to " CD2 HIS A  81 " =    1.026
peak=    3.181 closest distance to " CG2 ILE A  20 " =    1.433
peak=    3.181 closest distance to " CG1 VAL A 296 " =    1.241
peak=    3.178 closest distance to " N   TYR A  15 " =    0.803
peak=    3.177 closest distance to " CB  ALA A 100 " =    1.330
peak=    3.176 closest distance to " CB  PRO A 243 " =    1.167
peak=    3.176 closest distance to " C   TYR A 214 " =    1.492
peak=    3.175 closest distance to " O   HOH Z 302 " =    1.938
peak=    3.174 closest distance to " C   GLY A  80 " =    1.115
peak=    3.173 closest distance to " CB  TYR A  30 " =    1.476
peak=    3.171 closest distance to " CB  ALA A 295 " =    1.328
peak=    3.167 closest distance to " O   HOH Z 394 " =    1.461
peak=    3.165 closest distance to " O   HOH Z 128 " =    2.117
peak=    3.164 closest distance to " O   HOH Z 145 " =    2.672
peak=    3.164 closest distance to " CE2 TYR A  30 " =    0.767
peak=    3.164 closest distance to " CA  MET A 105 " =    1.046
peak=    3.163 closest distance to " O   HOH Z 271 " =    1.929
peak=    3.161 closest distance to " CB  LYS A 193 " =    1.099
peak=    3.154 closest distance to " O   HOH Z 126 " =    1.802
peak=    3.151 closest distance to " O   HOH Z 248 " =    1.722
peak=    3.148 closest distance to " CD1 LEU A 222 " =    0.709
peak=    3.144 closest distance to " CZ3 TRP A 274 " =    4.668
peak=    3.140 closest distance to " O   HOH Z  10 " =    1.796
peak=    3.138 closest distance to " O   HOH Z 185 " =    2.311
peak=    3.137 closest distance to " CZ3 TRP A  85 " =    0.955
peak=    3.134 closest distance to " O   HOH Z 141 " =    1.641
peak=    3.126 closest distance to " CE2 TYR A 186 " =    0.917
peak=    3.126 closest distance to " CA  VAL A 126 " =    1.022
peak=    3.122 closest distance to " O   HOH Z 327 " =    1.790
peak=    3.113 closest distance to " O   HOH Z 435 " =    1.998
peak=    3.108 closest distance to " O   HOH Z 350 " =    1.580
peak=    3.105 closest distance to " CD1 ILE A  33 " =    1.613
peak=    3.105 closest distance to " CB  GLN A 278 " =    0.926
peak=    3.103 closest distance to " CA  ALA A 291 " =    0.953
peak=    3.103 closest distance to " N   GLN A 278 " =    1.014
peak=    3.098 closest distance to " CG2 VAL A 174 " =    1.267
peak=    3.097 closest distance to " O   HOH Z 293 " =    1.932
peak=    3.091 closest distance to " O   HOH Z 207 " =    2.167
peak=    3.089 closest distance to " O   HOH Z 299 " =    4.421
peak=    3.085 closest distance to " O   HOH Z  40 " =    1.523
peak=    3.083 closest distance to " CB  TYR A 116 " =    0.906
peak=    3.072 closest distance to " O   HOH Z 175 " =    3.586
peak=    3.070 closest distance to " CD1 ILE A 199 " =    0.823
peak=    3.069 closest distance to " CA  VAL A 112 " =    1.153
peak=    3.067 closest distance to " OG BSER A 212 " =    2.556
peak=    3.044 closest distance to " CB  ALA A  43 " =    0.901
peak=    3.043 closest distance to " O   HOH Z 128 " =    1.967

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 194         
Filter by distance & map next to the model:
   mapped sites are within: 0.801 - 5.518
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 193 from: 194
   mapped sites are within: 0.801 - 5.518

peak=   -5.124 closest distance to " CG2 VAL A 230 " =    0.870
peak=   -4.435 closest distance to " O   HOH Z 266 " =    4.882
peak=   -4.376 closest distance to " CD  ARG A 156 " =    2.029
peak=   -4.217 closest distance to " CE2 TYR A  30 " =    2.817
peak=   -4.162 closest distance to " CB  ALA A 161 " =    2.613
peak=   -4.105 closest distance to " O   HOH Z 290 " =    1.169
peak=   -4.096 closest distance to " CG  ASP A 231 " =    0.805
peak=   -4.051 closest distance to " O   HOH Z  52 " =    1.706
peak=   -4.046 closest distance to " CG1 VAL A 112 " =    2.647
peak=   -4.009 closest distance to " O   HOH Z 196 " =    2.403
peak=   -3.940 closest distance to " O   HOH Z 166 " =    1.886
peak=   -3.932 closest distance to " OG ASER A 134 " =    1.284
peak=   -3.904 closest distance to " O   SER A 271 " =    2.198
peak=   -3.901 closest distance to " CD  ARG A  14 " =    3.327
peak=   -3.873 closest distance to " NH2AARG A 275 " =    5.281
peak=   -3.861 closest distance to " NH2 ARG A  66 " =    1.736
peak=   -3.849 closest distance to " CD2 LEU A 167 " =    1.710
peak=   -3.841 closest distance to " O   HOH Z  17 " =    1.399
peak=   -3.834 closest distance to " N   ALA A 226 " =    2.163
peak=   -3.828 closest distance to " O   HOH Z 351 " =    1.534
peak=   -3.826 closest distance to " O   PRO A 163 " =    2.098
peak=   -3.802 closest distance to " CD  GLN A  58 " =    1.066
peak=   -3.795 closest distance to " OE1 GLN A 223 " =    2.092
peak=   -3.788 closest distance to " C   ALA A 158 " =    1.265
peak=   -3.763 closest distance to " CD2 LEU A 300 " =    2.776
peak=   -3.760 closest distance to " CD1 PHE A  59 " =    1.904
peak=   -3.758 closest distance to " O   HOH Z 231 " =    2.020
peak=   -3.751 closest distance to " CG1 VAL A 250 " =    2.763
peak=   -3.751 closest distance to " O   HOH Z  43 " =    1.616
peak=   -3.741 closest distance to " CA  ASP A 298 " =    1.066
peak=   -3.738 closest distance to " CZ3 TRP A 179 " =    1.184
peak=   -3.722 closest distance to " O   HOH Z 350 " =    1.817
peak=   -3.715 closest distance to " O   HOH Z 128 " =    2.522
peak=   -3.702 closest distance to " CG1 VAL A 265 " =    2.431
peak=   -3.693 closest distance to " CG2 VAL A 296 " =    1.452
peak=   -3.692 closest distance to " CG1 VAL A 112 " =    2.995
peak=   -3.683 closest distance to " O   HOH Z 103 " =    1.858
peak=   -3.682 closest distance to " CG2BVAL A  41 " =    2.655
peak=   -3.673 closest distance to " C   HIS A 108 " =    1.132
peak=   -3.673 closest distance to " CB  PRO A 243 " =    2.665
peak=   -3.668 closest distance to " O   HOH Z  11 " =    1.936
peak=   -3.661 closest distance to " OG  SER A  97 " =    2.233
peak=   -3.660 closest distance to " O   HOH Z 241 " =    1.122
peak=   -3.655 closest distance to " O   HOH Z 426 " =    1.637
peak=   -3.648 closest distance to " CG2 VAL A 112 " =    2.570
peak=   -3.638 closest distance to " O   ALA A 256 " =    1.674
peak=   -3.632 closest distance to " CD1 LEU A 228 " =    2.424
peak=   -3.627 closest distance to " O   HOH Z  10 " =    1.582
peak=   -3.624 closest distance to " CG  ARG A 269 " =    2.468
peak=   -3.605 closest distance to " O   HOH Z 118 " =    3.071
peak=   -3.601 closest distance to " CB  ALA A 248 " =    2.038
peak=   -3.597 closest distance to " O   HOH Z  13 " =    1.417
peak=   -3.597 closest distance to " O   HOH Z  19 " =    2.160
peak=   -3.593 closest distance to " O   HOH Z 292 " =    4.519
peak=   -3.591 closest distance to " O   HOH Z 184 " =    1.351
peak=   -3.586 closest distance to " CG  TRP A 266 " =    1.871
peak=   -3.577 closest distance to " N   ALA A  43 " =    2.601
peak=   -3.567 closest distance to " CD2 TYR A 293 " =    2.080
peak=   -3.551 closest distance to " ND2 ASN A  45 " =    1.276
peak=   -3.551 closest distance to " OG  SER A  87 " =    1.584
peak=   -3.527 closest distance to " CD1 LEU A 101 " =    2.744
peak=   -3.513 closest distance to " O   HOH Z 185 " =    2.387
peak=   -3.511 closest distance to " CA  GLY A 241 " =    3.083
peak=   -3.502 closest distance to " NE2 GLN A  88 " =    2.254
peak=   -3.499 closest distance to " CG  MET A 105 " =    0.940
peak=   -3.495 closest distance to " OD1 ASN A 148 " =    1.473
peak=   -3.493 closest distance to " CD  ARG A 139 " =    1.570
peak=   -3.490 closest distance to " O   PRO A 198 " =    1.239
peak=   -3.489 closest distance to " O   HOH Z 308 " =    1.719
peak=   -3.483 closest distance to " O   VAL A  67 " =    2.639
peak=   -3.478 closest distance to " O   HOH Z 165 " =    1.933
peak=   -3.477 closest distance to " O   HOH Z 311 " =    3.829
peak=   -3.468 closest distance to " OG  SER A  26 " =    1.356
peak=   -3.461 closest distance to " O   HOH Z 252 " =    4.101
peak=   -3.457 closest distance to " CB  SER A 134 " =    1.919
peak=   -3.456 closest distance to " O   HOH Z 283 " =    2.036
peak=   -3.455 closest distance to " CG  GLU A 277 " =    1.126
peak=   -3.454 closest distance to " O   HOH Z 231 " =    1.602
peak=   -3.454 closest distance to " CE BMET A  47 " =    2.109
peak=   -3.451 closest distance to " CG  ASP A  50 " =    2.393
peak=   -3.449 closest distance to " CG1 VAL A 296 " =    1.389
peak=   -3.447 closest distance to " CG  LEU A 101 " =    2.588
peak=   -3.445 closest distance to " CD  PRO A 213 " =    2.169
peak=   -3.442 closest distance to " OXT GLY A 302 " =    2.996
peak=   -3.442 closest distance to " O   HOH Z 407 " =    3.215
peak=   -3.439 closest distance to " O   HOH Z 353 " =    2.233
peak=   -3.434 closest distance to " O   HOH Z 111 " =    2.177
peak=   -3.430 closest distance to " CB  ALA A  43 " =    2.565
peak=   -3.430 closest distance to " CE3 TRP A 150 " =    2.218
peak=   -3.429 closest distance to " C   ASN A 285 " =    2.502
peak=   -3.428 closest distance to " CA  GLY A 241 " =    2.276
peak=   -3.418 closest distance to " O   HOH Z 389 " =    1.850
peak=   -3.417 closest distance to " CB  ALA A 291 " =    2.203
peak=   -3.414 closest distance to " CD1 LEU A  25 " =    2.505
peak=   -3.414 closest distance to " CD1 LEU A   5 " =    2.520
peak=   -3.411 closest distance to " CB  LEU A  83 " =    2.319
peak=   -3.408 closest distance to " O   HOH Z 431 " =    1.770
peak=   -3.407 closest distance to " O   HOH Z 423 " =    2.165
peak=   -3.405 closest distance to " O   HOH Z 166 " =    1.702
peak=   -3.401 closest distance to " CB  PRO A 163 " =    2.621
peak=   -3.400 closest distance to " NE2 GLN A 103 " =    1.822
peak=   -3.397 closest distance to " O   HOH Z 184 " =    1.574
peak=   -3.394 closest distance to " O   HOH Z 222 " =    1.532
peak=   -3.391 closest distance to " SD BMET A  47 " =    1.008
peak=   -3.391 closest distance to " CD  GLN A  88 " =    0.911
peak=   -3.385 closest distance to " O   HOH Z  38 " =    1.452
peak=   -3.383 closest distance to " O   GLY A 211 " =    1.432
peak=   -3.382 closest distance to " N   MET A 105 " =    2.685
peak=   -3.375 closest distance to " CA  GLY A 203 " =    2.355
peak=   -3.374 closest distance to " NH1 ARG A 195 " =    2.637
peak=   -3.374 closest distance to " N   GLN A  58 " =    1.849
peak=   -3.374 closest distance to " CA  ASN A 127 " =    1.024
peak=   -3.371 closest distance to " O   HOH Z 113 " =    2.065
peak=   -3.366 closest distance to " OG BSER A 134 " =    1.230
peak=   -3.365 closest distance to " OG  SER A  62 " =    1.709
peak=   -3.360 closest distance to " O   HOH Z  60 " =    1.938
peak=   -3.359 closest distance to " CB  ARG A  79 " =    2.618
peak=   -3.359 closest distance to " CB  PHE A 192 " =    1.798
peak=   -3.349 closest distance to " O   HOH Z 149 " =    2.201
peak=   -3.349 closest distance to " O   GLY A  17 " =    1.349
peak=   -3.347 closest distance to " CE  MET A 105 " =    2.164
peak=   -3.340 closest distance to " O   GLY A 203 " =    2.366
peak=   -3.333 closest distance to " N   THR A 235 " =    1.276
peak=   -3.332 closest distance to " CG  HIS A  86 " =    0.954
peak=   -3.331 closest distance to " CA  GLY A 133 " =    2.289
peak=   -3.327 closest distance to " CG  GLU A  53 " =    1.662
peak=   -3.327 closest distance to " N   THR A 157 " =    1.521
peak=   -3.325 closest distance to " NE2 GLN A  88 " =    0.943
peak=   -3.324 closest distance to " O   VAL A 189 " =    2.644
peak=   -3.322 closest distance to " N   SER A   3 " =    2.151
peak=   -3.319 closest distance to " CB  ALA A  10 " =    2.234
peak=   -3.319 closest distance to " O   HOH Z 234 " =    4.281
peak=   -3.316 closest distance to " O   HOH Z 177 " =    1.692
peak=   -3.314 closest distance to " OD1 ASN A 187 " =    1.564
peak=   -3.312 closest distance to " O   HOH Z 435 " =    2.676
peak=   -3.301 closest distance to " O   HOH Z 275 " =    1.503
peak=   -3.295 closest distance to " O   HOH Z 377 " =    2.013
peak=   -3.293 closest distance to " CB  ASN A  39 " =    2.157
peak=   -3.291 closest distance to " CD  GLN A 223 " =    1.326
peak=   -3.291 closest distance to " C   ASN A 187 " =    1.823
peak=   -3.287 closest distance to " C   SER A 206 " =    1.524
peak=   -3.285 closest distance to " CD  LYS A 289 " =    2.572
peak=   -3.284 closest distance to " OE1 GLN A  88 " =    1.012
peak=   -3.280 closest distance to " CE3 TRP A  70 " =    1.811
peak=   -3.275 closest distance to " NE  ARG A 259 " =    1.081
peak=   -3.268 closest distance to " ND2BASN A 224 " =    1.730
peak=   -3.267 closest distance to " NH2 ARG A  79 " =    2.006
peak=   -3.262 closest distance to " OD1 ASP A 191 " =    1.528
peak=   -3.259 closest distance to " NE2 GLN A 194 " =    1.871
peak=   -3.248 closest distance to " CD2 PHE A  61 " =    2.399
peak=   -3.235 closest distance to " O   GLY A  80 " =    2.318
peak=   -3.232 closest distance to " CG1 VAL A 197 " =    2.358
peak=   -3.232 closest distance to " NH2 ARG A 159 " =    2.344
peak=   -3.229 closest distance to " CD1 TRP A 179 " =    1.012
peak=   -3.225 closest distance to " O   HOH Z 295 " =    1.466
peak=   -3.223 closest distance to " ND2 ASN A  60 " =    1.769
peak=   -3.222 closest distance to " C   LEU A 143 " =    1.127
peak=   -3.221 closest distance to " O   HOH Z 189 " =    1.860
peak=   -3.221 closest distance to " O   HOH Z 102 " =    1.687
peak=   -3.214 closest distance to " CB  TYR A  15 " =    2.233
peak=   -3.209 closest distance to " O   LEU A 167 " =    1.519
peak=   -3.205 closest distance to " CD1 ILE A 151 " =    2.351
peak=   -3.198 closest distance to " O   ALA A   7 " =    1.540
peak=   -3.193 closest distance to " O   HOH Z 191 " =    5.518
peak=   -3.191 closest distance to " ND2 ASN A  60 " =    1.407
peak=   -3.180 closest distance to " CH2 TRP A 177 " =    2.137
peak=   -3.178 closest distance to " CG  LYS A 193 " =    2.409
peak=   -3.177 closest distance to " CZ  TYR A 169 " =    1.769
peak=   -3.173 closest distance to " C   MET A 188 " =    1.482
peak=   -3.161 closest distance to " O   ALA A 161 " =    1.603
peak=   -3.152 closest distance to " O   HOH Z 211 " =    1.632
peak=   -3.152 closest distance to " N   SER A 212 " =    1.926
peak=   -3.151 closest distance to " CG  GLU A   2 " =    1.793
peak=   -3.149 closest distance to " O   HOH Z 227 " =    1.241
peak=   -3.144 closest distance to " N   PHE A  59 " =    2.302
peak=   -3.142 closest distance to " O   HOH Z 285 " =    1.569
peak=   -3.139 closest distance to " O   HOH Z 151 " =    1.656
peak=   -3.132 closest distance to " O   HOH Z  60 " =    1.977
peak=   -3.130 closest distance to " CD  ARG A 259 " =    2.588
peak=   -3.105 closest distance to " O   ASP A 270 " =    1.626
peak=   -3.104 closest distance to " CB  TRP A  85 " =    2.450
peak=   -3.104 closest distance to " C   ASP A 270 " =    1.253
peak=   -3.103 closest distance to " O   HOH Z  37 " =    2.260
peak=   -3.098 closest distance to " CA  VAL A 197 " =    1.099
peak=   -3.097 closest distance to " O   HOH Z 313 " =    1.185
peak=   -3.094 closest distance to " C   THR A 279 " =    1.241
peak=   -3.084 closest distance to " OG  SER A 206 " =    1.762
peak=   -3.082 closest distance to " CD  PRO A 243 " =    1.998
peak=   -3.080 closest distance to " O   HOH Z 392 " =    1.797
peak=   -3.072 closest distance to " CD  GLN A  88 " =    0.801
peak=   -3.064 closest distance to " CB  ASP A 132 " =    2.299
peak=   -3.053 closest distance to " CA  SER A  62 " =    2.439
peak=   -3.019 closest distance to " CG2 VAL A 296 " =    1.879

================= 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    :  0.4487 0.4330   6.248538e+00   6.228875e+00
   1_bss:  0.4406 0.4235   6.244134e+00   6.220075e+00
   1_xyz:  0.3375 0.3689   6.062344e+00   6.122804e+00
   1_adp:  0.2847 0.3265   5.929920e+00   6.041674e+00
   1_occ:  0.2843 0.3265   5.929085e+00   6.042345e+00
   2_bss:  0.2814 0.3209   5.929200e+00   6.038413e+00
   2_xyz:  0.1926 0.2391   5.601398e+00   5.775668e+00
   2_adp:  0.1740 0.2187   5.509828e+00   5.696572e+00
   2_occ:  0.1739 0.2188   5.509589e+00   5.696750e+00
   3_bss:  0.1722 0.2171   5.509659e+00   5.696018e+00
   3_xyz:  0.1336 0.1756   5.281531e+00   5.497636e+00
   3_adp:  0.1250 0.1703   5.238352e+00   5.470632e+00
   3_occ:  0.1250 0.1703   5.238191e+00   5.470527e+00
   4_bss:  0.1253 0.1709   5.240332e+00   5.472088e+00
   4_xyz:  0.1208 0.1672   5.214915e+00   5.448686e+00
   4_adp:  0.1215 0.1645   5.209504e+00   5.431401e+00
   4_occ:  0.1215 0.1644   5.209201e+00   5.431232e+00
   5_bss:  0.1215 0.1643   5.209121e+00   5.431118e+00
   5_xyz:  0.1184 0.1615   5.188603e+00   5.414701e+00
   5_adp:  0.1171 0.1625   5.187783e+00   5.422134e+00
   5_occ:  0.1171 0.1625   5.187808e+00   5.422243e+00
   5_bss:  0.1171 0.1625   5.187843e+00   5.422287e+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:  0.300  20.000   8.264   9.223   7.422   0.000   0.000   0.000
   1_xyz:  0.300  20.000   8.264   9.223   7.422   0.000   0.000   0.000
   1_adp:  0.300  20.000   8.264   9.223   7.422   0.000   0.000   0.000
   1_occ:  0.300  20.000   8.264   9.223   7.422   0.000   0.000   0.000
   2_bss:  0.327  50.001   5.221   5.836   4.985   0.000   0.000   0.000
   2_xyz:  0.327  50.001   5.221   5.836   4.985   0.000   0.000   0.000
   2_adp:  0.327  50.001   5.221   5.836   4.985   0.000   0.000   0.000
   2_occ:  0.327  50.001   5.221   5.836   4.985   0.000   0.000   0.000
   3_bss:  0.335  59.888   3.443   3.887   4.008   0.000   0.000   0.000
   3_xyz:  0.335  59.888   3.443   3.887   4.008   0.000   0.000   0.000
   3_adp:  0.335  59.888   3.443   3.887   4.008   0.000   0.000   0.000
   3_occ:  0.335  59.888   3.443   3.887   4.008   0.000   0.000   0.000
   4_bss:  0.328  57.175   3.081   3.384   3.784   0.000   0.000   0.000
   4_xyz:  0.328  57.175   3.081   3.384   3.784   0.000   0.000   0.000
   4_adp:  0.328  57.175   3.081   3.384   3.784   0.000   0.000   0.000
   4_occ:  0.328  57.175   3.081   3.384   3.784   0.000   0.000   0.000
   5_bss:  0.325  54.649   2.949   3.221   3.753   0.000   0.000   0.000
   5_xyz:  0.325  54.649   2.949   3.221   3.753   0.000   0.000   0.000
   5_adp:  0.325  54.649   2.949   3.221   3.753   0.000   0.000   0.000
   5_occ:  0.325  54.649   2.949   3.221   3.753   0.000   0.000   0.000
   5_bss:  0.320  55.871  -0.347  -0.106   0.452  -0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  49.462 0.5286  0.5925    55755.278
   1_bss:  49.665 0.5239  0.7504    53884.206
   1_xyz:  41.147 0.6275  0.8772    38400.353
   1_adp:  34.644 0.7053  0.9713    29398.356
   1_occ:  34.675 0.7049  0.9703    29453.566
   2_bss:  34.409 0.7079  0.8784    29105.347
   2_xyz:  23.744 0.8241  0.9887    14775.677
   2_adp:  21.279 0.8494  1.0099    12360.614
   2_occ:  21.288 0.8493  1.0096    12371.773
   3_bss:  21.222 0.8501  0.9549    12339.607
   3_xyz:  16.341 0.8952  0.9800     7915.881
   3_adp:  15.709 0.9009  0.9807     7512.988
   3_occ:  15.707 0.9009  0.9806     7514.096
   4_bss:  15.749 0.9006  0.9673     7569.828
   4_xyz:  15.214 0.9054  0.9683     7176.965
   4_adp:  14.796 0.9090  0.9700     6977.344
   4_occ:  14.791 0.9091  0.9699     6976.850
   5_bss:  14.789 0.9091  0.9662     6973.617
   5_xyz:  14.463 0.9117  0.9674     6744.888
   5_adp:  14.644 0.9102  0.9641     6842.867
   5_occ:  14.647 0.9102  0.9641     6846.230
   5_bss:  14.650 0.9101  0.9653     6847.793
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.4206e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.4206e+01
   1_xyz:   1.643  0.013  0.106 17.839  0.007  4.112   1.3243e-01
   1_adp:   1.643  0.013  0.106 17.839  0.007  4.112   1.3243e-01
   1_occ:   1.643  0.013  0.106 17.839  0.007  4.112   1.3243e-01
   2_bss:   1.643  0.013  0.106 17.839  0.007  4.112   1.3243e-01
   2_xyz:   1.065  0.008  0.075 16.189  0.004  4.132   6.9648e-02
   2_adp:   1.065  0.008  0.075 16.189  0.004  4.132   6.9648e-02
   2_occ:   1.065  0.008  0.075 16.189  0.004  4.132   6.9648e-02
   3_bss:   1.065  0.008  0.075 16.189  0.004  4.132   6.9648e-02
   3_xyz:   1.085  0.008  0.084 15.895  0.004  4.133   7.0160e-02
   3_adp:   1.085  0.008  0.084 15.895  0.004  4.133   7.0160e-02
   3_occ:   1.085  0.008  0.084 15.895  0.004  4.133   7.0160e-02
   4_bss:   1.085  0.008  0.084 15.895  0.004  4.133   7.0160e-02
   4_xyz:   0.964  0.007  0.077 15.492  0.003  4.123   5.8380e-02
   4_adp:   0.964  0.007  0.077 15.492  0.003  4.123   5.8380e-02
   4_occ:   0.964  0.007  0.077 15.492  0.003  4.123   5.8380e-02
   5_bss:   0.964  0.007  0.077 15.492  0.003  4.123   5.8380e-02
   5_xyz:   0.985  0.007  0.078 15.302  0.003  4.125   5.9182e-02
   5_adp:   0.985  0.007  0.078 15.302  0.003  4.125   5.9182e-02
   5_occ:   0.985  0.007  0.078 15.302  0.003  4.125   5.9182e-02
   5_bss:   0.985  0.007  0.078 15.302  0.003  4.125   5.9182e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0285e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0285e+00
   1_xyz:  14.573  0.160  0.479 85.354  0.044  2.312   9.9726e-02
   1_adp:  14.573  0.160  0.479 85.354  0.044  2.312   9.9726e-02
   1_occ:  14.573  0.160  0.479 85.354  0.044  2.312   9.9726e-02
   2_bss:  14.573  0.160  0.479 85.354  0.044  2.312   9.9726e-02
   2_xyz:   6.946  0.073  0.254 88.366  0.032  2.228   5.1287e-02
   2_adp:   6.946  0.073  0.254 88.366  0.032  2.228   5.1287e-02
   2_occ:   6.946  0.073  0.254 88.366  0.032  2.228   5.1287e-02
   3_bss:   6.946  0.073  0.254 88.366  0.032  2.228   5.1287e-02
   3_xyz:   9.013  0.056  0.500 81.960  0.037  2.387   4.7284e-02
   3_adp:   9.013  0.056  0.500 81.960  0.037  2.387   4.7284e-02
   3_occ:   9.013  0.056  0.500 81.960  0.037  2.387   4.7284e-02
   4_bss:   9.013  0.056  0.500 81.960  0.037  2.387   4.7284e-02
   4_xyz:   7.652  0.039  0.460 83.602  0.039  2.393   3.5334e-02
   4_adp:   7.652  0.039  0.460 83.602  0.039  2.393   3.5334e-02
   4_occ:   7.652  0.039  0.460 83.602  0.039  2.393   3.5334e-02
   5_bss:   7.652  0.039  0.460 83.602  0.039  2.393   3.5334e-02
   5_xyz:   7.620  0.043  0.463 82.123  0.038  2.381   3.4605e-02
   5_adp:   7.620  0.043  0.463 82.123  0.038  2.381   3.4605e-02
   5_occ:   7.620  0.043  0.463 82.123  0.038  2.381   3.4605e-02
   5_bss:   7.620  0.043  0.463 82.123  0.038  2.381   3.4605e-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:  65.06   0.00  10.52  55.23   0.00   7.67  65.06   0.00  25.99
   1_occ:  65.06   0.00  10.52  55.23   0.00   7.67  65.06   0.00  25.99
   2_bss:  65.06   0.00  10.52  55.23   0.00   7.67  65.06   0.00  25.99
   2_xyz:  65.06   0.00  10.52  55.23   0.00   7.67  65.06   0.00  25.99
   2_adp:  70.42   0.00  11.53  68.97   0.00   7.60  70.42   1.01  32.97
   2_occ:  70.42   0.00  11.53  68.97   0.00   7.60  70.42   1.01  32.97
   3_bss:  70.42   0.00  11.53  68.97   0.00   7.60  70.42   1.01  32.97
   3_xyz:  70.42   0.00  11.53  68.97   0.00   7.60  70.42   1.01  32.97
   3_adp:  86.67   0.00  12.43  86.67   0.00   7.83  82.22   0.00  37.45
   3_occ:  86.67   0.00  12.43  86.67   0.00   7.83  82.22   0.00  37.45
   4_bss:  86.67   0.00  12.43  86.67   0.00   7.83  82.22   0.00  37.45
   4_xyz:  86.67   0.00  12.43  86.67   0.00   7.83  82.22   0.00  37.45
   4_adp:  85.36   0.00  12.03  85.36   0.00   7.70  80.93   0.99  35.66
   4_occ:  85.36   0.00  12.03  85.36   0.00   7.70  80.93   0.99  35.66
   5_bss:  85.36   0.00  12.03  85.36   0.00   7.70  80.93   0.99  35.66
   5_xyz:  85.36   0.00  12.03  85.36   0.00   7.70  80.93   0.99  35.66
   5_adp:  89.19   0.00  12.04  89.19   0.00   7.70  81.63   0.97  35.64
   5_occ:  89.19   0.00  12.04  89.19   0.00   7.70  81.63   0.97  35.64
   5_bss:  92.53   3.35  15.38  92.53   3.35  11.05  84.98   4.31  38.99
------------------------------------------------------------------------
 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:    1.204    0.026    0.412
   1_adp:    1.204    0.026    0.412
   1_occ:    1.204    0.026    0.412
   2_bss:    1.204    0.026    0.412
   2_xyz:    1.521    0.040    0.551
   2_adp:    1.521    0.040    0.551
   2_occ:    1.521    0.040    0.551
   3_bss:    1.521    0.040    0.551
   3_xyz:    1.490    0.038    0.599
   3_adp:    1.490    0.038    0.599
   3_occ:    1.490    0.038    0.599
   4_bss:    1.490    0.038    0.599
   4_xyz:    1.623    0.024    0.614
   4_adp:    1.623    0.024    0.614
   4_occ:    1.623    0.024    0.614
   5_bss:    1.623    0.024    0.614
   5_xyz:    1.685    0.020    0.628
   5_adp:    1.685    0.020    0.628
   5_occ:    1.685    0.020    0.628
   5_bss:    1.685    0.020    0.628
------------------------------------------------------------------------

CPU time actual refinement: 314.98


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1049/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_1049/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1049/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1049/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1049/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 314.83 
  Macro-tasks:
    bulk solvent and scale       = 40.73  
    individual site refinement   = 126.20 
    weights calculation          = 31.48  
    collect and process          = 6.51   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 205.04 
  Micro-tasks:
    mask                            = 1.72   
    f_calc                          = 94.68  
    alpha_beta                      = 8.43   
    target                          = 1.18   
    gradients_wrt_atomic_parameters = 104.97 
    fmodel                         = 6.95   
    r_factors                      = 0.18   
    phase_errors                   = 10.93  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 229.27 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.453 micro seconds
Total CPU time: 5.47 minutes
from_scatterers_fft:    640 calls, 94.20 s
gradients_fft:          584 calls, 92.00 s

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

# Date 2008-01-16 Time 03:03:01 PST -0800 (1200481381.36 s)
Start R-work = 0.4487, R-free = 0.4330 (no bulk solvent and anisotropic scale)
Final R-work = 0.1333, R-free = 0.1781 (no bulk solvent and anisotropic scale)

Start R-work = 0.4406, R-free = 0.4235
Final R-work = 0.1171, R-free = 0.1625