# Date 2008-01-16 Time 01:57:53 PST -0800 (1200477473.26 s)
#phil __OFF__

Command line arguments: "../638.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 14120
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 638

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 46.4607, 84.2302, 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: (70.25, 46.4607, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8895 1.95116
Completeness in resolution range: 0.949171
Completeness with d_max=infinity: 0.946329

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8895
                             d_min =   1.9512

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.4607, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8895 1.95116
Completeness in resolution range: 0.949171
Completeness with d_max=infinity: 0.946329

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8899 -  4.1757 [2168/2197]  1954   214   9.9%
  bin  2:  4.1757 -  3.3265 [2075/2091]  1865   210  10.1%
  bin  3:  3.3265 -  2.9096 [2047/2066]  1841   206  10.1%
  bin  4:  2.9096 -  2.6452 [2047/2077]  1849   198   9.7%
  bin  5:  2.6452 -  2.4565 [2038/2057]  1834   204  10.0%
  bin  6:  2.4565 -  2.3122 [2014/2050]  1806   208  10.3%
  bin  7:  2.3122 -  2.1968 [1988/2021]  1787   201  10.1%
  bin  8:  2.1968 -  2.1014 [2004/2038]  1808   196   9.8%
  bin  9:  2.1014 -  2.0207 [1982/2010]  1781   201  10.1%
  bin 10:  2.0207 -  1.9512 [1226/2031]  1105   121   9.9%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_638/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.71 -     2.35: 34
        2.35 -     2.99: 1915
        2.99 -     3.63: 4702
        3.63 -     4.26: 9264
        4.26 -     4.90: 12878
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.715 3.040 -x+1/2,-y+1,z+1/2
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.722 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z 110 " - " O   HOH Z 355 "  1.773 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.786 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28788 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_638/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_638/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 = 70.25 46.4607 84.23025 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: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4808   r_free= 0.4736   ksol= 0.00   Bsol= 0.00   scale= 0.802    |
|                                                                             |
| 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:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.281527                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8899 -  4.6576 0.99   1403  157 0.4013 0.4103      6.5936      6.6478|
|  2:  4.6576 -  3.7158 0.99   1359  145 0.4065 0.3922       6.798      6.7619|
|  3:  3.7158 -  3.2517 0.99   1321  154 0.4445 0.4086      6.6801      6.7574|
|  4:  3.2517 -  2.9569 0.99   1332  147 0.4564 0.4508      6.5296      6.4927|
|  5:  2.9569 -  2.7464 0.99   1313  143 0.5087 0.4984      6.3722      6.3374|
|  6:  2.7464 -  2.5853 0.99   1299  145 0.4997 0.5472      6.2712      6.2771|
|  7:  2.5853 -  2.4565 0.99   1316  141 0.5157 0.4651      6.2535       6.197|
|  8:  2.4565 -  2.3500 0.98   1274  151 0.5352 0.5298       6.165      6.1858|
|  9:  2.3500 -  2.2598 0.98   1301  149 0.5134 0.5109      6.1231      6.1099|
| 10:  2.2598 -  2.1821 0.98   1279  133 0.5440 0.5281      6.1063      6.1234|
| 11:  2.1821 -  2.1141 1.00   1278  141 0.5223 0.5062      6.0464      6.0204|
| 12:  2.1141 -  2.0538 0.97   1266  139 0.5094 0.5238      5.9574      6.0055|
| 13:  2.0538 -  1.9998 0.98   1286  143 0.5475 0.5089      5.8813      5.8094|
| 14:  1.9998 -  1.9512 0.46    603   71 0.5537 0.5740      5.8483      5.8063|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8899 -  4.6576  1403   157  0.66  37.67   0.80     0.71      81943.25|
|  2:  4.6576 -  3.7158  1359   145  0.68  36.75   0.87     0.77     114902.41|
|  3:  3.7158 -  3.2517  1321   154  0.58  45.26   0.84     0.73     121311.85|
|  4:  3.2517 -  2.9569  1332   147  0.51  50.80   0.82     0.63     105335.23|
|  5:  2.9569 -  2.7464  1313   143  0.41  59.07   0.75     0.51      85326.96|
|  6:  2.7464 -  2.5853  1299   145  0.39  60.59   0.73     0.46      72452.10|
|  7:  2.5853 -  2.4565  1316   141  0.37  62.20   0.75     0.42      65139.80|
|  8:  2.4565 -  2.3500  1274   151  0.36  63.17   0.72     0.44      59369.08|
|  9:  2.3500 -  2.2598  1301   149  0.36  62.93   0.75     0.43      54067.57|
| 10:  2.2598 -  2.1821  1279   133  0.34  64.22   0.76     0.43      50019.35|
| 11:  2.1821 -  2.1141  1278   141  0.33  65.31   0.78     0.41      46512.62|
| 12:  2.1141 -  2.0538  1266   139  0.31  67.22   0.76     0.39      44383.75|
| 13:  2.0538 -  1.9998  1286   143  0.26  70.84   0.74     0.34      38893.01|
| 14:  1.9998 -  1.9512   603    71  0.24  72.32   0.72     0.28      32877.65|
|alpha:            min =        0.28 max =            0.77 mean =         0.51|
|beta:             min =    32877.65 max =       121311.85 mean =     71411.19|
|figures of merit: min =        0.00 max =            1.00 mean =         0.42|
|phase err.(work): min =        0.00 max =           89.99 mean =        57.64|
|phase err.(test): min =        0.00 max =           89.97 mean =        57.92|
|-----------------------------------------------------------------------------|

============================== 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 = 13.514161             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.264   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.411913              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.935   (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:        6 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       24 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      186 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      715 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1539 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2699 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3992 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5153 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6648 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7860 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.002 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.088    4.900  1.196 |       2.072 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.501)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.501)------------------------------------------|
|    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: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4872   r_free= 0.4793   ksol= 0.00   Bsol= 0.00   scale= 0.770    |
|                                                                             |
| 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:   0.76 A                  |
| x-ray target function (ml) for work reflections: 6.283912                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4726   r_free= 0.4638   ksol= 0.39   Bsol= 20.00   scale= 0.974   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.56,7.55,8.67,0.00,0.00,0.00); trace/3= 7.26                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.75 A                  |
| x-ray target function (ml) for work reflections: 6.277168                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 11.016947             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.509   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.215545              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.094   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4726      final r-factor (work) = 0.4015          |
| start r-factor (free) = 0.4638      final r-factor (free) = 0.4182          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 87.5826 = 11.02 * 0.50 * 6.2777 + 1.00 * 53.0021                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 34.3113 = 11.02 * 0.50 * 6.2049 + 1.00 * 0.1316                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4015      final r-factor (work) = 0.3582          |
| start r-factor (free) = 0.4182      final r-factor (free) = 0.4084          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.5567 = 1.22 * 1.00 * 6.2049 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.4654 = 1.22 * 1.00 * 6.1278 + 1.00 * 0.0169                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.501)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    66.01   13.05    None  None   None       |
|    all(noH): 2823   0      0.00    66.01   13.05    None  None   None       |
|    Sol.    : 438    0      0.00    66.01   24.37    None  None   None       |
|    Mac.    : 2385   0      0.00    59.09   10.97    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.601:  935   |   5:    33.005 -  39.606:   98        |
|      1:     6.601 -  13.202:  776   |   6:    39.606 -  46.207:   41        |
|      2:    13.202 -  19.803:  476   |   7:    46.207 -  52.808:   19        |
|      3:    19.803 -  26.404:  280   |   8:    52.808 -  59.409:    8        |
|      4:    26.404 -  33.005:  188   |   9:    59.409 -  66.010:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3582 r_free = 0.4084             target_work(ml) = 6.118         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3578 r_free = 0.4088             target_work(ml) = 6.118         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3578   r_free= 0.4088   ksol= 0.39   Bsol= 20.00   scale= 1.083   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.56,7.55,8.67,0.00,0.00,0.00); trace/3= 7.26                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.117507                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3558   r_free= 0.4063   ksol= 0.35   Bsol= 28.45   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.95,3.98,6.10,0.00,0.00,0.00); trace/3= 4.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.56 A                  |
| x-ray target function (ml) for work reflections: 6.117750                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.658219              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 98.288   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.520250              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.968  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3558      final r-factor (work) = 0.2813          |
| start r-factor (free) = 0.4063      final r-factor (free) = 0.3390          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.4575 = 5.66 * 0.50 * 6.1241 + 1.00 * 0.1316                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.1032 = 5.66 * 0.50 * 6.0187 + 1.00 * 0.0755                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2813      final r-factor (work) = 0.2621          |
| start r-factor (free) = 0.3390      final r-factor (free) = 0.3214          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.2267 = 0.52 * 1.00 * 6.0187 + 1.00 * 0.0954                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0832 = 0.52 * 1.00 * 5.9053 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.501)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    69.82   13.22    None  None   None       |
|    all(noH): 2823   0      0.00    69.82   13.22    None  None   None       |
|    Sol.    : 438    0      0.00    69.82   29.72    None  None   None       |
|    Mac.    : 2385   0      0.00    66.95   10.19    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 -   6.982: 1065   |   5:    34.910 -  41.891:  108        |
|      1:     6.982 -  13.964:  803   |   6:    41.891 -  48.873:   48        |
|      2:    13.964 -  20.946:  378   |   7:    48.873 -  55.855:   21        |
|      3:    20.946 -  27.928:  217   |   8:    55.855 -  62.837:    5        |
|      4:    27.928 -  34.910:  173   |   9:    62.837 -  69.819:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2621 r_free = 0.3214             target_work(ml) = 5.885         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2619 r_free = 0.3219             target_work(ml) = 5.885         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2619   r_free= 0.3219   ksol= 0.35   Bsol= 28.45   scale= 1.054   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.95,3.98,6.10,0.00,0.00,0.00); trace/3= 4.34                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.884889                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2611   r_free= 0.3200   ksol= 0.35   Bsol= 28.45   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.72,2.25,4.10,0.00,0.00,0.00); trace/3= 2.69                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.884227                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.159854              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.028  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 4.582653              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.745  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2611      final r-factor (work) = 0.1849          |
| start r-factor (free) = 0.3200      final r-factor (free) = 0.2403          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 18.2663 = 6.16 * 0.50 * 5.9062 + 1.00 * 0.0755                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.7879 = 6.16 * 0.50 * 5.7505 + 1.00 * 0.0768                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1849      final r-factor (work) = 0.1592          |
| start r-factor (free) = 0.2403      final r-factor (free) = 0.2195          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 26.3635 = 4.58 * 1.00 * 5.7505 + 1.00 * 0.0110                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 25.3012 = 4.58 * 1.00 * 5.5177 + 1.00 * 0.0154                              |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.501)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.07   14.32    None  None   None       |
|    all(noH): 2823   0      0.00    85.07   14.32    None  None   None       |
|    Sol.    : 438    0      2.12    83.34   39.63    None  None   None       |
|    Mac.    : 2385   0      0.00    85.07   9.67     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 -   8.508: 1462   |   5:    42.537 -  51.045:   96        |
|      1:     8.508 -  17.015:  680   |   6:    51.045 -  59.552:   85        |
|      2:    17.015 -  25.523:  199   |   7:    59.552 -  68.060:   43        |
|      3:    25.523 -  34.030:  130   |   8:    68.060 -  76.567:   17        |
|      4:    34.030 -  42.537:  102   |   9:    76.567 -  85.075:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1592 r_free = 0.2195             target_work(ml) = 5.465         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1590 r_free = 0.2193             target_work(ml) = 5.464         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1590   r_free= 0.2193   ksol= 0.35   Bsol= 28.45   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.72,2.25,4.10,0.00,0.00,0.00); trace/3= 2.69                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.464278                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1586   r_free= 0.2160   ksol= 0.32   Bsol= 35.68   scale= 1.014   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.56,1.63,2.63,0.00,0.00,0.00); trace/3= 1.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.452582                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.254679              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.323  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.215218              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 112.413  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1586      final r-factor (work) = 0.1303          |
| start r-factor (free) = 0.2160      final r-factor (free) = 0.1817          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.8181 = 4.25 * 0.50 * 5.5192 + 1.00 * 0.0768                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.5128 = 4.25 * 0.50 * 5.3802 + 1.00 * 0.0674                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1303      final r-factor (work) = 0.1242          |
| start r-factor (free) = 0.1817      final r-factor (free) = 0.1683          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1731 = 0.22 * 1.00 * 5.3802 + 1.00 * 0.0152                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1423 = 0.22 * 1.00 * 5.2629 + 1.00 * 0.0096                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.501)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    84.91   13.40    None  None   None       |
|    all(noH): 2823   0      0.00    84.91   13.40    None  None   None       |
|    Sol.    : 438    0      2.64    83.51   36.56    None  None   None       |
|    Mac.    : 2385   0      0.00    84.91   9.14     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 -   8.491: 1547   |   5:    42.457 -  50.948:   93        |
|      1:     8.491 -  16.983:  675   |   6:    50.948 -  59.439:   58        |
|      2:    16.983 -  25.474:  175   |   7:    59.439 -  67.931:   27        |
|      3:    25.474 -  33.965:  118   |   8:    67.931 -  76.422:   12        |
|      4:    33.965 -  42.457:  112   |   9:    76.422 -  84.913:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1242 r_free = 0.1683             target_work(ml) = 5.221         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1240 r_free = 0.1676             target_work(ml) = 5.218         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1240   r_free= 0.1676   ksol= 0.32   Bsol= 35.68   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.56,1.63,2.63,0.00,0.00,0.00); trace/3= 1.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.218485                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1242   r_free= 0.1680   ksol= 0.32   Bsol= 36.07   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.40,1.48,2.17,0.00,0.00,0.00); trace/3= 1.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.219919                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.541583              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 125.129  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.895954              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.211  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1242      final r-factor (work) = 0.1158          |
| start r-factor (free) = 0.1680      final r-factor (free) = 0.1606          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7547 = 2.54 * 0.50 * 5.2623 + 1.00 * 0.0674                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.6617 = 2.54 * 0.50 * 5.1919 + 1.00 * 0.0639                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1158      final r-factor (work) = 0.1132          |
| start r-factor (free) = 0.1606      final r-factor (free) = 0.1614          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6613 = 0.90 * 1.00 * 5.1919 + 1.00 * 0.0096                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.6307 = 0.90 * 1.00 * 5.1559 + 1.00 * 0.0113                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.501)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.33   13.48    None  None   None       |
|    all(noH): 2823   0      0.00    95.33   13.48    None  None   None       |
|    Sol.    : 438    0      2.80    86.49   37.38    None  None   None       |
|    Mac.    : 2385   0      0.00    95.33   9.09     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.533: 1710   |   5:    47.664 -  57.197:   81        |
|      1:     9.533 -  19.066:  582   |   6:    57.197 -  66.730:   38        |
|      2:    19.066 -  28.598:  149   |   7:    66.730 -  76.263:   21        |
|      3:    28.598 -  38.131:  125   |   8:    76.263 -  85.795:    8        |
|      4:    38.131 -  47.664:  106   |   9:    85.795 -  95.328:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1132 r_free = 0.1614             target_work(ml) = 5.157         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1132 r_free = 0.1613             target_work(ml) = 5.156         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1132   r_free= 0.1613   ksol= 0.32   Bsol= 36.07   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.40,1.48,2.17,0.00,0.00,0.00); trace/3= 1.68                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.156015                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8899 -  4.6576 0.99   1403  157 0.0997 0.1234       5.381      5.5212|
|  2:  4.6576 -  3.7158 0.99   1359  145 0.0867 0.1229      5.4388      5.6808|
|  3:  3.7158 -  3.2517 0.99   1321  154 0.1105 0.1535      5.4984      5.8244|
|  4:  3.2517 -  2.9569 0.99   1332  147 0.1236 0.1627      5.4677      5.6278|
|  5:  2.9569 -  2.7464 0.99   1313  143 0.1323 0.1696      5.3262      5.4861|
|  6:  2.7464 -  2.5853 0.99   1299  145 0.1239 0.1876      5.2183      5.5054|
|  7:  2.5853 -  2.4565 0.99   1316  141 0.1270 0.1679      5.1832       5.384|
|  8:  2.4565 -  2.3500 0.98   1274  151 0.1166 0.1712      5.0609      5.3166|
|  9:  2.3500 -  2.2598 0.98   1301  149 0.1116 0.1902      5.0219      5.3305|
| 10:  2.2598 -  2.1821 0.98   1279  133 0.1120 0.1703      4.9655      5.1977|
| 11:  2.1821 -  2.1141 1.00   1278  141 0.1156 0.1832      4.9532      5.3004|
| 12:  2.1141 -  2.0538 0.97   1266  139 0.1100 0.1668      4.8811      5.1239|
| 13:  2.0538 -  1.9998 0.98   1286  143 0.1183 0.1832      4.7975      5.0448|
| 14:  1.9998 -  1.9512 0.46    603   71 0.1014 0.1676      4.6585      4.9319|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8899 -  4.6576  1403   157  0.95   8.45   0.98     0.96       6686.52|
|  2:  4.6576 -  3.7158  1359   145  0.95   7.79   1.03     1.02       8797.69|
|  3:  3.7158 -  3.2517  1321   154  0.93  11.83   1.04     1.03      10721.05|
|  4:  3.2517 -  2.9569  1332   147  0.92  13.86   1.02     1.00      10515.44|
|  5:  2.9569 -  2.7464  1313   143  0.89  16.43   1.00     0.96       8359.92|
|  6:  2.7464 -  2.5853  1299   145  0.90  16.23   0.99     0.97       7282.91|
|  7:  2.5853 -  2.4565  1316   141  0.90  15.79   0.99     0.96       6455.05|
|  8:  2.4565 -  2.3500  1274   151  0.90  15.88   0.99     0.96       5340.63|
|  9:  2.3500 -  2.2598  1301   149  0.91  15.39   1.02     1.01       5115.62|
| 10:  2.2598 -  2.1821  1279   133  0.90  15.93   1.01     0.97       4517.99|
| 11:  2.1821 -  2.1141  1278   141  0.90  16.40   1.01     0.98       4502.84|
| 12:  2.1141 -  2.0538  1266   139  0.91  15.49   1.02     1.01       4111.17|
| 13:  2.0538 -  1.9998  1286   143  0.89  16.85   1.02     1.00       3395.93|
| 14:  1.9998 -  1.9512   603    71  0.91  15.05   1.00     0.98       2616.28|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2616.28 max =        10721.05 mean =      6499.17|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.95 mean =        14.29|
|phase err.(test): min =        0.00 max =           88.87 mean =        13.78|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1131   r_free= 0.1613   ksol= 0.32   Bsol= 38.86   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.28,-0.21,0.49,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.155908                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.89 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1131   r_free= 0.1613   ksol= 0.32   Bsol= 38.86   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.28,-0.21,0.49,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.155908                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8899 -  4.6576 0.99   1403  157 0.0997 0.1235      5.3807      5.5217|
|  2:  4.6576 -  3.7158 0.99   1359  145 0.0869 0.1231      5.4398      5.6823|
|  3:  3.7158 -  3.2517 0.99   1321  154 0.1105 0.1535       5.499       5.825|
|  4:  3.2517 -  2.9569 0.99   1332  147 0.1236 0.1626      5.4677      5.6275|
|  5:  2.9569 -  2.7464 0.99   1313  143 0.1323 0.1695       5.326      5.4852|
|  6:  2.7464 -  2.5853 0.99   1299  145 0.1238 0.1875      5.2179      5.5051|
|  7:  2.5853 -  2.4565 0.99   1316  141 0.1270 0.1679      5.1828      5.3838|
|  8:  2.4565 -  2.3500 0.98   1274  151 0.1166 0.1711      5.0605      5.3159|
|  9:  2.3500 -  2.2598 0.98   1301  149 0.1116 0.1903      5.0217      5.3307|
| 10:  2.2598 -  2.1821 0.98   1279  133 0.1120 0.1702      4.9652      5.1971|
| 11:  2.1821 -  2.1141 1.00   1278  141 0.1156 0.1833       4.953      5.3006|
| 12:  2.1141 -  2.0538 0.97   1266  139 0.1100 0.1668      4.8809      5.1238|
| 13:  2.0538 -  1.9998 0.98   1286  143 0.1183 0.1831      4.7972      5.0444|
| 14:  1.9998 -  1.9512 0.46    603   71 0.1014 0.1676      4.6582      4.9317|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 14.8899 -  4.6576  1403   157  0.95   8.46   0.98     0.96       6687.61|
|  2:  4.6576 -  3.7158  1359   145  0.95   7.80   1.03     1.02       8811.27|
|  3:  3.7158 -  3.2517  1321   154  0.93  11.84   1.04     1.03      10739.91|
|  4:  3.2517 -  2.9569  1332   147  0.92  13.86   1.02     1.00      10516.09|
|  5:  2.9569 -  2.7464  1313   143  0.89  16.43   1.00     0.96       8353.92|
|  6:  2.7464 -  2.5853  1299   145  0.90  16.22   0.99     0.97       7277.15|
|  7:  2.5853 -  2.4565  1316   141  0.90  15.79   0.99     0.96       6448.23|
|  8:  2.4565 -  2.3500  1274   151  0.90  15.88   0.99     0.96       5336.05|
|  9:  2.3500 -  2.2598  1301   149  0.91  15.38   1.02     1.01       5112.28|
| 10:  2.2598 -  2.1821  1279   133  0.90  15.93   1.01     0.97       4516.29|
| 11:  2.1821 -  2.1141  1278   141  0.90  16.40   1.01     0.98       4501.04|
| 12:  2.1141 -  2.0538  1266   139  0.91  15.48   1.02     1.01       4109.36|
| 13:  2.0538 -  1.9998  1286   143  0.89  16.84   1.02     1.00       3393.79|
| 14:  1.9998 -  1.9512   603    71  0.91  15.04   1.00     0.98       2614.41|
|alpha:            min =        0.96 max =            1.03 mean =         0.99|
|beta:             min =     2614.41 max =        10739.91 mean =      6499.20|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.29|
|phase err.(test): min =        0.00 max =           88.89 mean =        13.77|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.501)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.68    97.01   15.16    None  None   None       |
|    all(noH): 2823   0      1.68    97.01   15.16    None  None   None       |
|    Sol.    : 438    0      4.48    88.17   39.06    None  None   None       |
|    Mac.    : 2385   0      1.68    97.01   10.77    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:     1.681 -  11.213: 1710   |   5:    49.345 -  58.877:   81        |
|      1:    11.213 -  20.746:  582   |   6:    58.877 -  68.410:   38        |
|      2:    20.746 -  30.279:  149   |   7:    68.410 -  77.943:   21        |
|      3:    30.279 -  39.812:  125   |   8:    77.943 -  87.476:    8        |
|      4:    39.812 -  49.345:  106   |   9:    87.476 -  97.009:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 324         
Filter by distance & map next to the model:
   mapped sites are within: 0.407 - 5.730
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 322 from: 324
   mapped sites are within: 0.763 - 5.730

peak=   10.888 closest distance to " CB  VAL A 230 " =    1.426
peak=    8.639 closest distance to " CG2 VAL A 296 " =    1.275
peak=    6.274 closest distance to " O   HOH Z 278 " =    1.761
peak=    6.002 closest distance to " NE2 GLN A  11 " =    1.194
peak=    5.937 closest distance to " CG  LEU A   5 " =    1.181
peak=    5.600 closest distance to " NH2 ARG A  56 " =    2.080
peak=    5.579 closest distance to " CD1AILE A 234 " =    1.008
peak=    5.375 closest distance to " CD2 LEU A   5 " =    1.160
peak=    5.328 closest distance to " O   HOH Z 132 " =    1.473
peak=    5.244 closest distance to " O   HOH Z 124 " =    1.562
peak=    5.241 closest distance to " CG  PRO A  54 " =    1.186
peak=    5.171 closest distance to " O   HOH Z 202 " =    1.467
peak=    5.106 closest distance to " CG  LEU A 228 " =    1.200
peak=    5.072 closest distance to " O   HOH Z 142 " =    1.841
peak=    4.975 closest distance to " O   HOH Z 427 " =    2.724
peak=    4.941 closest distance to " O   HOH Z 126 " =    1.921
peak=    4.910 closest distance to " O   HOH Z 193 " =    1.742
peak=    4.902 closest distance to " CG  PRO A 213 " =    1.214
peak=    4.881 closest distance to " O   HOH Z 260 " =    1.368
peak=    4.858 closest distance to " O   HOH Z 236 " =    1.474
peak=    4.851 closest distance to " CB  VAL A 230 " =    1.133
peak=    4.788 closest distance to " CB  SER A  63 " =    1.303
peak=    4.778 closest distance to " O   HOH Z 263 " =    1.445
peak=    4.733 closest distance to " O   HOH Z 143 " =    1.249
peak=    4.727 closest distance to " O   HOH Z 373 " =    2.200
peak=    4.673 closest distance to " CB  GLN A 223 " =    1.459
peak=    4.654 closest distance to " CB  GLN A 183 " =    1.320
peak=    4.649 closest distance to " CA  GLY A 241 " =    3.759
peak=    4.627 closest distance to " O   HOH Z 232 " =    2.223
peak=    4.621 closest distance to " O   HOH Z 203 " =    1.677
peak=    4.598 closest distance to " CB  VAL A 296 " =    1.069
peak=    4.543 closest distance to " CB  SER A   3 " =    1.387
peak=    4.531 closest distance to " O   HOH Z 108 " =    1.457
peak=    4.517 closest distance to " CB  ARG A 275 " =    0.885
peak=    4.494 closest distance to " O   PRO A 198 " =    1.535
peak=    4.462 closest distance to " CB  ASN A 148 " =    1.365
peak=    4.452 closest distance to " CB  PRO A  54 " =    0.924
peak=    4.412 closest distance to " CG  PRO A 198 " =    1.318
peak=    4.325 closest distance to " O   SER A  87 " =    2.312
peak=    4.312 closest distance to " O   HOH Z 214 " =    1.190
peak=    4.294 closest distance to " O   HOH Z 133 " =    1.525
peak=    4.269 closest distance to " O   HOH Z 371 " =    3.102
peak=    4.248 closest distance to " CB  TYR A 169 " =    0.968
peak=    4.239 closest distance to " CD2 LEU A 228 " =    1.246
peak=    4.216 closest distance to " O   HOH Z 117 " =    2.051
peak=    4.190 closest distance to " O   HOH Z 196 " =    3.248
peak=    4.188 closest distance to " NZ  LYS A 117 " =    3.126
peak=    4.154 closest distance to " O   HOH Z 280 " =    2.943
peak=    4.153 closest distance to " O   HOH Z 134 " =    1.349
peak=    4.151 closest distance to " OD1 ASN A  69 " =    2.569
peak=    4.150 closest distance to " O   HOH Z 316 " =    2.884
peak=    4.147 closest distance to " CG2 VAL A 257 " =    0.862
peak=    4.123 closest distance to " O   HOH Z   9 " =    2.281
peak=    4.121 closest distance to " O   HOH Z 205 " =    0.984
peak=    4.116 closest distance to " O   HOH Z 272 " =    1.866
peak=    4.106 closest distance to " CA  TYR A  30 " =    1.011
peak=    4.102 closest distance to " CB  GLU A 152 " =    1.216
peak=    4.079 closest distance to " CB  VAL A 265 " =    1.219
peak=    4.060 closest distance to " CB  TRP A 179 " =    1.298
peak=    4.042 closest distance to " O   HOH Z  61 " =    1.654
peak=    4.039 closest distance to " CG1BVAL A  72 " =    1.387
peak=    4.036 closest distance to " O   HOH Z  78 " =    1.771
peak=    4.008 closest distance to " CG  LEU A 167 " =    1.163
peak=    4.005 closest distance to " OD2 ASP A 286 " =    2.618
peak=    4.004 closest distance to " O   HOH Z 303 " =    2.123
peak=    3.982 closest distance to " CB  ARG A  79 " =    1.324
peak=    3.970 closest distance to " O   HOH Z 344 " =    1.224
peak=    3.966 closest distance to " O   HOH Z 326 " =    1.445
peak=    3.945 closest distance to " CB  LEU A 228 " =    1.341
peak=    3.909 closest distance to " O   HOH Z 192 " =    1.344
peak=    3.905 closest distance to " O   HOH Z  59 " =    1.690
peak=    3.902 closest distance to " O   HOH Z 357 " =    1.807
peak=    3.894 closest distance to " O   HOH Z  97 " =    1.190
peak=    3.892 closest distance to " O   HOH Z 209 " =    2.386
peak=    3.873 closest distance to " O   HOH Z 368 " =    1.996
peak=    3.867 closest distance to " OE1 GLU A   2 " =    2.117
peak=    3.862 closest distance to " CB  GLN A  88 " =    1.276
peak=    3.856 closest distance to " CB  ARG A 139 " =    1.064
peak=    3.824 closest distance to " O   HOH Z  10 " =    1.733
peak=    3.820 closest distance to " O   HOH Z 189 " =    2.557
peak=    3.812 closest distance to " O   HOH Z 193 " =    1.832
peak=    3.807 closest distance to " O   HOH Z 234 " =    3.636
peak=    3.804 closest distance to " C   ALA A 299 " =    0.944
peak=    3.801 closest distance to " CA  VAL A  41 " =    0.929
peak=    3.800 closest distance to " CB  GLU A 128 " =    1.130
peak=    3.794 closest distance to " O   HOH Z 227 " =    1.720
peak=    3.783 closest distance to " CG  GLN A  88 " =    1.028
peak=    3.778 closest distance to " O   HOH Z 346 " =    1.478
peak=    3.776 closest distance to " O   HOH Z 345 " =    3.233
peak=    3.774 closest distance to " O   HOH Z  59 " =    2.083
peak=    3.767 closest distance to " CB  GLU A 277 " =    3.471
peak=    3.756 closest distance to " O   HOH Z  93 " =    2.340
peak=    3.739 closest distance to " O   HOH Z 425 " =    1.349
peak=    3.737 closest distance to " CB  VAL A 202 " =    1.634
peak=    3.737 closest distance to " O   HOH Z 145 " =    1.418
peak=    3.724 closest distance to " O   HOH Z 298 " =    1.752
peak=    3.697 closest distance to " CB  SER A 216 " =    0.879
peak=    3.697 closest distance to " CA  ASN A 215 " =    1.173
peak=    3.684 closest distance to " CB  SER A 273 " =    0.899
peak=    3.682 closest distance to " O   HOH Z  68 " =    1.727
peak=    3.676 closest distance to " O   HOH Z 284 " =    1.497
peak=    3.674 closest distance to " O   HOH Z 287 " =    1.757
peak=    3.671 closest distance to " O   HOH Z 209 " =    2.289
peak=    3.669 closest distance to " O   HOH Z 148 " =    1.514
peak=    3.668 closest distance to " CZ AARG A 102 " =    1.807
peak=    3.656 closest distance to " O   HOH Z 158 " =    2.943
peak=    3.653 closest distance to " O   HOH Z  48 " =    1.485
peak=    3.650 closest distance to " O   HOH Z  54 " =    1.583
peak=    3.649 closest distance to " CA  VAL A 126 " =    1.105
peak=    3.640 closest distance to " CB  ASN A 148 " =    1.824
peak=    3.639 closest distance to " O   HOH Z 272 " =    2.342
peak=    3.637 closest distance to " O   HOH Z 322 " =    2.143
peak=    3.629 closest distance to " O   HOH Z 250 " =    1.352
peak=    3.626 closest distance to " C   LYS A 290 " =    1.293
peak=    3.625 closest distance to " O   HOH Z 193 " =    1.533
peak=    3.625 closest distance to " N   PHE A 130 " =    1.379
peak=    3.624 closest distance to " CG  ARG A  66 " =    2.823
peak=    3.621 closest distance to " O   HOH Z 374 " =    2.430
peak=    3.602 closest distance to " CB BVAL A  41 " =    1.130
peak=    3.602 closest distance to " O   HOH Z  43 " =    2.031
peak=    3.601 closest distance to " O   HOH Z 112 " =    1.575
peak=    3.601 closest distance to " O   HOH Z  61 " =    1.576
peak=    3.600 closest distance to " CG2 THR A 221 " =    1.123
peak=    3.595 closest distance to " CG  MET A 188 " =    1.255
peak=    3.595 closest distance to " CG1 ILE A  33 " =    1.328
peak=    3.590 closest distance to " CB  ALA A 291 " =    1.445
peak=    3.584 closest distance to " CB  LEU A 255 " =    0.852
peak=    3.573 closest distance to " O   HOH Z  44 " =    1.839
peak=    3.559 closest distance to " O   HOH Z 380 " =    1.630
peak=    3.556 closest distance to " O   HOH Z  48 " =    1.411
peak=    3.551 closest distance to " CA  THR A 264 " =    0.763
peak=    3.548 closest distance to " OG BSER A 164 " =    2.252
peak=    3.546 closest distance to " CD BLYS A 290 " =    1.213
peak=    3.546 closest distance to " O   HOH Z 194 " =    2.259
peak=    3.545 closest distance to " O   HOH Z  89 " =    2.141
peak=    3.545 closest distance to " O   HOH Z 136 " =    1.042
peak=    3.544 closest distance to " O   HOH Z 281 " =    4.570
peak=    3.543 closest distance to " N   ARG A 156 " =    1.252
peak=    3.543 closest distance to " CG  GLU A 277 " =    2.156
peak=    3.543 closest distance to " CE1 TYR A 186 " =    1.252
peak=    3.541 closest distance to " NH1 ARG A  14 " =    1.044
peak=    3.540 closest distance to " O   HOH Z  37 " =    1.235
peak=    3.538 closest distance to " O   HOH Z 344 " =    2.808
peak=    3.532 closest distance to " O   HOH Z 425 " =    2.063
peak=    3.531 closest distance to " O   HOH Z 403 " =    1.365
peak=    3.525 closest distance to " O   HOH Z 180 " =    2.185
peak=    3.523 closest distance to " O   HOH Z 261 " =    1.972
peak=    3.523 closest distance to " O   HOH Z 128 " =    1.915
peak=    3.519 closest distance to " O   HOH Z 411 " =    1.770
peak=    3.519 closest distance to " O   HOH Z  63 " =    1.083
peak=    3.518 closest distance to " O   HOH Z 369 " =    2.149
peak=    3.500 closest distance to " CG1BVAL A 121 " =    1.101
peak=    3.499 closest distance to " O   HOH Z  11 " =    1.575
peak=    3.498 closest distance to " O   HOH Z  85 " =    1.266
peak=    3.484 closest distance to " O   HOH Z   7 " =    1.376
peak=    3.484 closest distance to " O   HOH Z 276 " =    1.317
peak=    3.483 closest distance to " O   HOH Z 389 " =    2.976
peak=    3.481 closest distance to " NH2 ARG A 156 " =    1.066
peak=    3.474 closest distance to " O   HOH Z 247 " =    1.164
peak=    3.472 closest distance to " CB  ARG A 102 " =    0.775
peak=    3.470 closest distance to " O   HOH Z 108 " =    1.724
peak=    3.465 closest distance to " CA  ALA A 154 " =    1.097
peak=    3.462 closest distance to " O   MET A 105 " =    1.743
peak=    3.456 closest distance to " CG2 ILE A 120 " =    1.304
peak=    3.452 closest distance to " O   HOH Z 303 " =    1.718
peak=    3.446 closest distance to " CG  PRO A 243 " =    1.237
peak=    3.446 closest distance to " O   HOH Z  88 " =    3.102
peak=    3.439 closest distance to " CA  THR A 221 " =    0.911
peak=    3.437 closest distance to " NZ  LYS A  76 " =    1.294
peak=    3.436 closest distance to " CG  ASN A  60 " =    1.041
peak=    3.433 closest distance to " CD1 LEU A 300 " =    1.223
peak=    3.431 closest distance to " O   HOH Z 271 " =    1.796
peak=    3.429 closest distance to " O   HOH Z 426 " =    1.469
peak=    3.424 closest distance to " O   HOH Z 130 " =    2.179
peak=    3.416 closest distance to " CB  THR A 157 " =    1.015
peak=    3.411 closest distance to " OG  SER A  62 " =    3.172
peak=    3.402 closest distance to " N   TRP A 177 " =    1.690
peak=    3.397 closest distance to " CD2 LEU A 255 " =    1.362
peak=    3.396 closest distance to " N   SER A 135 " =    1.394
peak=    3.391 closest distance to " O   HOH Z 280 " =    2.431
peak=    3.386 closest distance to " CA  ASN A  74 " =    1.271
peak=    3.386 closest distance to " CA  ALA A 248 " =    1.203
peak=    3.386 closest distance to " O   GLY A  57 " =    2.436
peak=    3.384 closest distance to " CA  ALA A  51 " =    1.025
peak=    3.381 closest distance to " CA  ALA A  21 " =    1.105
peak=    3.373 closest distance to " O   HOH Z  80 " =    1.638
peak=    3.373 closest distance to " O   GLN A  58 " =    1.472
peak=    3.370 closest distance to " CD1 LEU A 228 " =    1.624
peak=    3.367 closest distance to " NH2 ARG A 219 " =    1.820
peak=    3.367 closest distance to " O   HOH Z  68 " =    2.123
peak=    3.358 closest distance to " O   HOH Z 423 " =    1.855
peak=    3.358 closest distance to " O   HOH Z 118 " =    1.501
peak=    3.355 closest distance to " CE  LYS A  76 " =    0.915
peak=    3.355 closest distance to " O   HOH Z 438 " =    2.400
peak=    3.355 closest distance to " O   HOH Z 248 " =    1.745
peak=    3.354 closest distance to " O   HOH Z  71 " =    3.020
peak=    3.351 closest distance to " O   HOH Z 132 " =    2.587
peak=    3.342 closest distance to " O   HOH Z 366 " =    3.259
peak=    3.341 closest distance to " O   HOH Z 419 " =    1.657
peak=    3.333 closest distance to " CG  ARG A 138 " =    1.078
peak=    3.332 closest distance to " O   HOH Z 422 " =    2.502
peak=    3.326 closest distance to " OE1 GLN A  11 " =    1.800
peak=    3.320 closest distance to " CD  PRO A 243 " =    1.668
peak=    3.320 closest distance to " ND2 ASN A 187 " =    1.721
peak=    3.315 closest distance to " O   HOH Z 327 " =    1.677
peak=    3.308 closest distance to " OD1 ASP A 286 " =    1.551
peak=    3.306 closest distance to " CA  LEU A 101 " =    1.385
peak=    3.305 closest distance to " NH2BARG A 190 " =    1.552
peak=    3.302 closest distance to " O   HOH Z 389 " =    1.633
peak=    3.300 closest distance to " O   HOH Z 123 " =    1.026
peak=    3.298 closest distance to " CA  PHE A 283 " =    1.481
peak=    3.294 closest distance to " CB  ASN A 142 " =    0.975
peak=    3.294 closest distance to " CZ2 TRP A 274 " =    1.766
peak=    3.293 closest distance to " O   HOH Z 128 " =    2.218
peak=    3.292 closest distance to " CA  ALA A 295 " =    1.027
peak=    3.290 closest distance to " CG AARG A 275 " =    1.023
peak=    3.281 closest distance to " O   HOH Z   1 " =    1.686
peak=    3.279 closest distance to " O   HOH Z 285 " =    1.701
peak=    3.275 closest distance to " CB  ALA A   9 " =    1.510
peak=    3.273 closest distance to " O   HOH Z   1 " =    1.586
peak=    3.272 closest distance to " O   HOH Z 367 " =    3.624
peak=    3.271 closest distance to " O   HOH Z 265 " =    2.157
peak=    3.269 closest distance to " O   SER A  26 " =    1.532
peak=    3.264 closest distance to " O   HOH Z 280 " =    1.555
peak=    3.263 closest distance to " O   HOH Z  59 " =    2.046
peak=    3.262 closest distance to " O   HOH Z 222 " =    2.383
peak=    3.261 closest distance to " NE2 GLN A  58 " =    5.568
peak=    3.259 closest distance to " O   HOH Z 151 " =    1.694
peak=    3.256 closest distance to " O   HOH Z 283 " =    1.560
peak=    3.255 closest distance to " O   HOH Z 148 " =    3.160
peak=    3.250 closest distance to " O   HOH Z 152 " =    2.821
peak=    3.248 closest distance to " O   ALA A 165 " =    1.246
peak=    3.248 closest distance to " CG1 VAL A 153 " =    0.865
peak=    3.246 closest distance to " CD  LYS A 119 " =    1.363
peak=    3.245 closest distance to " O   HOH Z 172 " =    5.730
peak=    3.245 closest distance to " CD  ARG A 138 " =    0.978
peak=    3.243 closest distance to " O   HOH Z 332 " =    1.563
peak=    3.241 closest distance to " O   HOH Z 116 " =    1.580
peak=    3.238 closest distance to " O   HOH Z 245 " =    1.310
peak=    3.237 closest distance to " O   HOH Z  40 " =    2.023
peak=    3.237 closest distance to " CG  MET A 185 " =    1.119
peak=    3.234 closest distance to " O   HOH Z 279 " =    2.202
peak=    3.233 closest distance to " O   HOH Z  58 " =    1.532
peak=    3.233 closest distance to " O   HOH Z 153 " =    3.653
peak=    3.220 closest distance to " O   HOH Z 217 " =    1.249
peak=    3.217 closest distance to " O   HOH Z 213 " =    1.652
peak=    3.215 closest distance to " CB  ALA A 295 " =    1.426
peak=    3.211 closest distance to " CB  ALA A 114 " =    1.497
peak=    3.208 closest distance to " O   ALA A 158 " =    1.334
peak=    3.207 closest distance to " O   HOH Z 255 " =    1.731
peak=    3.206 closest distance to " O   HOH Z 213 " =    1.908
peak=    3.200 closest distance to " CE AMET A  47 " =    1.366
peak=    3.198 closest distance to " OE2 GLU A  53 " =    1.961
peak=    3.195 closest distance to " CG  GLN A  77 " =    2.283
peak=    3.194 closest distance to " O   HOH Z  15 " =    1.472
peak=    3.194 closest distance to " CD2 HIS A  81 " =    1.065
peak=    3.192 closest distance to " O   HOH Z 214 " =    1.989
peak=    3.191 closest distance to " ND1 HIS A  86 " =    1.723
peak=    3.190 closest distance to " O   HOH Z 199 " =    0.897
peak=    3.188 closest distance to " O   HOH Z 263 " =    1.894
peak=    3.185 closest distance to " O   HOH Z 388 " =    1.772
peak=    3.185 closest distance to " CG2 ILE A  20 " =    1.674
peak=    3.185 closest distance to " O   HOH Z 356 " =    1.241
peak=    3.185 closest distance to " CB  TYR A  30 " =    1.565
peak=    3.184 closest distance to " OD1 ASP A 231 " =    1.814
peak=    3.182 closest distance to " CG  GLN A  89 " =    1.459
peak=    3.181 closest distance to " O   HOH Z 328 " =    1.796
peak=    3.174 closest distance to " CB  ALA A 180 " =    1.242
peak=    3.173 closest distance to " CB  VAL A 268 " =    0.809
peak=    3.171 closest distance to " O   HOH Z 423 " =    2.614
peak=    3.170 closest distance to " CB  ARG A 190 " =    1.785
peak=    3.169 closest distance to " CD  ARG A 269 " =    1.041
peak=    3.169 closest distance to " CA  ARG A 275 " =    1.884
peak=    3.166 closest distance to " CB  SER A  26 " =    1.560
peak=    3.164 closest distance to " O   HOH Z 259 " =    2.061
peak=    3.164 closest distance to " CA  LYS A 117 " =    1.202
peak=    3.163 closest distance to " CA  GLY A 136 " =    1.188
peak=    3.163 closest distance to " O   HOH Z 172 " =    3.566
peak=    3.161 closest distance to " NE AARG A 275 " =    1.345
peak=    3.160 closest distance to " O   HOH Z 313 " =    1.799
peak=    3.155 closest distance to " O   HOH Z  50 " =    1.549
peak=    3.153 closest distance to " CG  LYS A 166 " =    1.469
peak=    3.149 closest distance to " O   HOH Z 355 " =    1.747
peak=    3.149 closest distance to " CH2 TRP A 274 " =    2.342
peak=    3.149 closest distance to " OG ASER A 134 " =    1.360
peak=    3.148 closest distance to " OG  SER A  62 " =    2.849
peak=    3.147 closest distance to " OG  SER A  22 " =    2.889
peak=    3.144 closest distance to " NH1BARG A 145 " =    1.351
peak=    3.140 closest distance to " O   HOH Z 244 " =    1.630
peak=    3.137 closest distance to " O   HOH Z 383 " =    2.098
peak=    3.134 closest distance to " O   HOH Z  49 " =    2.224
peak=    3.134 closest distance to " O   HOH Z 359 " =    3.677
peak=    3.134 closest distance to " NZ  LYS A  48 " =    2.009
peak=    3.134 closest distance to " O   HOH Z 430 " =    1.637
peak=    3.132 closest distance to " OD1BASN A 224 " =    2.174
peak=    3.128 closest distance to " O   HOH Z 406 " =    1.651
peak=    3.125 closest distance to " O   HOH Z 273 " =    2.876
peak=    3.125 closest distance to " O   HOH Z   2 " =    1.589
peak=    3.124 closest distance to " O   HOH Z 222 " =    2.365
peak=    3.118 closest distance to " CB  TRP A 266 " =    1.067
peak=    3.116 closest distance to " CB  ASN A 215 " =    0.941
peak=    3.109 closest distance to " NZ  LYS A 117 " =    1.109
peak=    3.108 closest distance to " O   HOH Z 389 " =    1.169
peak=    3.107 closest distance to " O   HOH Z 145 " =    3.244
peak=    3.106 closest distance to " O   HOH Z 409 " =    3.493
peak=    3.106 closest distance to " SD  MET A 185 " =    1.453
peak=    3.105 closest distance to " CA  SER A  87 " =    0.965
peak=    3.083 closest distance to " CB  ILE A  20 " =    1.516
peak=    3.080 closest distance to " O   HOH Z  21 " =    1.696
peak=    3.075 closest distance to " O   HOH Z 189 " =    2.684
peak=    3.074 closest distance to " O   HOH Z  89 " =    2.261
peak=    3.073 closest distance to " CB  LEU A 237 " =    0.926
peak=    3.069 closest distance to " CG  LEU A 281 " =    0.928
peak=    3.068 closest distance to " O   HOH Z 409 " =    3.393
peak=    3.067 closest distance to " O   HOH Z 106 " =    2.334
peak=    3.062 closest distance to " O   HOH Z  89 " =    1.632
peak=    3.061 closest distance to " CA  ARG A 195 " =    1.211
peak=    3.053 closest distance to " CB  ARG A 138 " =    0.921
peak=    3.053 closest distance to " O   HOH Z 329 " =    3.382
peak=    3.051 closest distance to " CB  THR A  31 " =    1.628
peak=    3.037 closest distance to " O   HOH Z 417 " =    2.023
peak=    3.008 closest distance to " N   ASN A  39 " =    0.995

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 193         
Filter by distance & map next to the model:
   mapped sites are within: 0.702 - 5.325
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 192 from: 193
   mapped sites are within: 0.702 - 5.325

peak=   -4.616 closest distance to " CG2 VAL A 230 " =    0.807
peak=   -4.508 closest distance to " SG  CYS A 254 " =    3.187
peak=   -4.485 closest distance to " CD  ARG A 156 " =    1.974
peak=   -4.446 closest distance to " CG2 THR A   4 " =    1.912
peak=   -4.377 closest distance to " O   HOH Z 231 " =    1.640
peak=   -4.322 closest distance to " O   PRO A 198 " =    1.322
peak=   -4.168 closest distance to " CB  PRO A 243 " =    2.587
peak=   -4.164 closest distance to " O   HOH Z  43 " =    1.959
peak=   -4.105 closest distance to " N   HIS A 115 " =    1.957
peak=   -4.094 closest distance to " CG2 VAL A 296 " =    1.460
peak=   -4.088 closest distance to " O   HOH Z 388 " =    2.030
peak=   -4.049 closest distance to " O   PRO A 163 " =    2.000
peak=   -4.013 closest distance to " O   ILE A 109 " =    2.570
peak=   -4.012 closest distance to " O   HOH Z 198 " =    2.384
peak=   -3.978 closest distance to " N   GLN A  58 " =    1.782
peak=   -3.948 closest distance to " O   HOH Z 377 " =    2.159
peak=   -3.945 closest distance to " CB  PRO A 163 " =    2.677
peak=   -3.936 closest distance to " OG ASER A 134 " =    1.165
peak=   -3.931 closest distance to " O   VAL A  67 " =    2.759
peak=   -3.929 closest distance to " CE2 TYR A  30 " =    2.838
peak=   -3.925 closest distance to " CD1 LEU A 101 " =    2.356
peak=   -3.915 closest distance to " O   ALA A 161 " =    1.540
peak=   -3.907 closest distance to " O   PRO A 198 " =    1.306
peak=   -3.892 closest distance to " O   HOH Z 166 " =    1.398
peak=   -3.891 closest distance to " O   HOH Z 339 " =    1.722
peak=   -3.874 closest distance to " O   HOH Z  98 " =    1.682
peak=   -3.866 closest distance to " CA  TYR A  68 " =    2.708
peak=   -3.860 closest distance to " NH2 ARG A  79 " =    1.825
peak=   -3.839 closest distance to " CD1 LEU A 255 " =    2.838
peak=   -3.836 closest distance to " OG BSER A 134 " =    1.249
peak=   -3.826 closest distance to " N   SER A 276 " =    1.244
peak=   -3.823 closest distance to " O   HOH Z 102 " =    1.765
peak=   -3.811 closest distance to " CG  LYS A 193 " =    2.215
peak=   -3.772 closest distance to " CB  TYR A  15 " =    2.116
peak=   -3.769 closest distance to " CZ  PHE A  59 " =    1.555
peak=   -3.753 closest distance to " CB  ASP A 132 " =    2.229
peak=   -3.751 closest distance to " O   HOH Z 266 " =    4.424
peak=   -3.731 closest distance to " O   ALA A  51 " =    1.377
peak=   -3.725 closest distance to " CA  GLY A 133 " =    1.929
peak=   -3.718 closest distance to " O   HOH Z 426 " =    2.252
peak=   -3.714 closest distance to " CB  ALA A  51 " =    1.754
peak=   -3.682 closest distance to " C   ASP A 231 " =    2.552
peak=   -3.682 closest distance to " C   HIS A 108 " =    1.139
peak=   -3.676 closest distance to " O   HOH Z 290 " =    1.092
peak=   -3.667 closest distance to " CD  LYS A 289 " =    2.565
peak=   -3.665 closest distance to " CG  GLN A 223 " =    1.930
peak=   -3.652 closest distance to " CB  ALA A 100 " =    2.472
peak=   -3.649 closest distance to " OG BSER A 134 " =    1.611
peak=   -3.641 closest distance to " O   HOH Z 410 " =    2.006
peak=   -3.638 closest distance to " CG  PHE A 283 " =    2.654
peak=   -3.633 closest distance to " O   HOH Z 389 " =    1.754
peak=   -3.631 closest distance to " C   ASN A 187 " =    1.832
peak=   -3.627 closest distance to " CG  LEU A 228 " =    1.008
peak=   -3.626 closest distance to " CA  GLY A  35 " =    2.013
peak=   -3.615 closest distance to " O   HOH Z 385 " =    1.769
peak=   -3.600 closest distance to " CB  ALA A 248 " =    1.907
peak=   -3.599 closest distance to " O   HOH Z 103 " =    1.675
peak=   -3.569 closest distance to " CB  ALA A 244 " =    2.037
peak=   -3.569 closest distance to " OXT GLY A 302 " =    2.815
peak=   -3.565 closest distance to " CB  ASN A  39 " =    2.021
peak=   -3.561 closest distance to " O   SER A 135 " =    1.536
peak=   -3.557 closest distance to " N   ALA A 248 " =    1.639
peak=   -3.556 closest distance to " O   HOH Z 423 " =    1.168
peak=   -3.552 closest distance to " O   HOH Z 111 " =    4.603
peak=   -3.549 closest distance to " O   HOH Z  63 " =    0.864
peak=   -3.547 closest distance to " CD1 LEU A 228 " =    2.123
peak=   -3.547 closest distance to " O   HOH Z 436 " =    1.470
peak=   -3.547 closest distance to " CG  ASP A 231 " =    0.759
peak=   -3.539 closest distance to " NH2AARG A 275 " =    5.270
peak=   -3.528 closest distance to " O   HOH Z  93 " =    1.615
peak=   -3.517 closest distance to " O   ASN A 187 " =    1.462
peak=   -3.509 closest distance to " OH  TYR A 214 " =    1.337
peak=   -3.509 closest distance to " CD  GLN A  88 " =    0.874
peak=   -3.505 closest distance to " C   PHE A 155 " =    0.702
peak=   -3.497 closest distance to " O   HOH Z 351 " =    1.418
peak=   -3.488 closest distance to " O   HOH Z 426 " =    1.573
peak=   -3.482 closest distance to " O   HOH Z 143 " =    0.988
peak=   -3.481 closest distance to " CB  ASP A  27 " =    2.491
peak=   -3.479 closest distance to " O   HOH Z 175 " =    4.322
peak=   -3.475 closest distance to " CE2 PHE A 218 " =    2.502
peak=   -3.466 closest distance to " O   HOH Z  44 " =    2.140
peak=   -3.453 closest distance to " O   HOH Z 148 " =    1.796
peak=   -3.446 closest distance to " ND2 ASN A  60 " =    1.375
peak=   -3.446 closest distance to " O   HOH Z 191 " =    5.325
peak=   -3.442 closest distance to " OE1 GLN A  73 " =    2.253
peak=   -3.440 closest distance to " N   THR A 157 " =    1.505
peak=   -3.439 closest distance to " O   HOH Z  13 " =    1.444
peak=   -3.438 closest distance to " O   HOH Z  60 " =    2.467
peak=   -3.432 closest distance to " CD1 PHE A  59 " =    1.924
peak=   -3.421 closest distance to " CE3 TRP A 274 " =    2.366
peak=   -3.416 closest distance to " CG  PRO A 163 " =    2.688
peak=   -3.415 closest distance to " O   HOH Z 137 " =    1.489
peak=   -3.404 closest distance to " O   HOH Z 364 " =    2.568
peak=   -3.403 closest distance to " C   ASN A 285 " =    2.309
peak=   -3.400 closest distance to " CE  MET A 105 " =    1.938
peak=   -3.391 closest distance to " OD1 ASN A 187 " =    1.609
peak=   -3.385 closest distance to " O   HOH Z 385 " =    1.981
peak=   -3.382 closest distance to " OG  SER A  87 " =    1.307
peak=   -3.378 closest distance to " CA  ASP A 298 " =    1.049
peak=   -3.378 closest distance to " N   GLN A  77 " =    1.598
peak=   -3.377 closest distance to " CG1 VAL A 112 " =    2.819
peak=   -3.370 closest distance to " ND2 ASN A  45 " =    0.986
peak=   -3.365 closest distance to " O   ALA A 158 " =    1.046
peak=   -3.364 closest distance to " O   HOH Z 184 " =    1.023
peak=   -3.364 closest distance to " OD1 ASN A 249 " =    1.295
peak=   -3.363 closest distance to " O   HOH Z  11 " =    1.944
peak=   -3.353 closest distance to " C   LEU A 143 " =    1.213
peak=   -3.352 closest distance to " OG  SER A  87 " =    1.655
peak=   -3.349 closest distance to " OD2 ASP A 270 " =    1.347
peak=   -3.349 closest distance to " CG  TRP A 266 " =    1.585
peak=   -3.348 closest distance to " O   HOH Z 205 " =    1.453
peak=   -3.344 closest distance to " O   HOH Z  97 " =    0.845
peak=   -3.344 closest distance to " O   TRP A  70 " =    1.522
peak=   -3.337 closest distance to " OD1 ASP A 191 " =    1.606
peak=   -3.336 closest distance to " O   TYR A  30 " =    2.853
peak=   -3.334 closest distance to " O   HOH Z 350 " =    2.018
peak=   -3.328 closest distance to " OG  SER A 206 " =    1.808
peak=   -3.323 closest distance to " O   HOH Z 411 " =    3.679
peak=   -3.323 closest distance to " CD  GLU A 152 " =    2.525
peak=   -3.310 closest distance to " O   HOH Z 417 " =    2.644
peak=   -3.305 closest distance to " CG  MET A 105 " =    0.889
peak=   -3.304 closest distance to " ND2 ASN A 249 " =    2.055
peak=   -3.301 closest distance to " O   HOH Z 165 " =    2.196
peak=   -3.290 closest distance to " O   HOH Z 423 " =    2.120
peak=   -3.290 closest distance to " O   SER A  22 " =    2.344
peak=   -3.289 closest distance to " CG2 VAL A 112 " =    2.546
peak=   -3.287 closest distance to " O   HOH Z 393 " =    3.670
peak=   -3.287 closest distance to " OH  TYR A 169 " =    1.072
peak=   -3.286 closest distance to " C   ALA A 158 " =    1.253
peak=   -3.276 closest distance to " N   ALA A   9 " =    1.478
peak=   -3.273 closest distance to " CD1 ILE A 239 " =    2.399
peak=   -3.272 closest distance to " O   HOH Z 298 " =    1.356
peak=   -3.272 closest distance to " O   HOH Z 205 " =    0.911
peak=   -3.271 closest distance to " OD1 ASP A 200 " =    1.191
peak=   -3.270 closest distance to " O   HOH Z 407 " =    3.067
peak=   -3.266 closest distance to " OG1 THR A  82 " =    1.395
peak=   -3.264 closest distance to " O   HOH Z 189 " =    1.779
peak=   -3.264 closest distance to " O   HOH Z 365 " =    1.286
peak=   -3.258 closest distance to " CB  ALA A  43 " =    2.324
peak=   -3.252 closest distance to " CD  ARG A 139 " =    1.682
peak=   -3.243 closest distance to " OG  SER A 245 " =    1.103
peak=   -3.241 closest distance to " CG1 VAL A 197 " =    2.287
peak=   -3.237 closest distance to " OD1 ASP A 191 " =    1.368
peak=   -3.237 closest distance to " O   TRP A  92 " =    1.810
peak=   -3.233 closest distance to " O   GLU A  44 " =    1.721
peak=   -3.227 closest distance to " CE  LYS A  76 " =    2.941
peak=   -3.226 closest distance to " O   ASP A 191 " =    1.661
peak=   -3.226 closest distance to " O   GLY A  57 " =    1.327
peak=   -3.226 closest distance to " N   ALA A 114 " =    2.315
peak=   -3.225 closest distance to " CA  ALA A 227 " =    2.364
peak=   -3.223 closest distance to " CA  ASN A 127 " =    1.145
peak=   -3.222 closest distance to " ND2 ASN A  39 " =    1.417
peak=   -3.222 closest distance to " O   HOH Z  90 " =    2.747
peak=   -3.222 closest distance to " O   HOH Z 313 " =    1.698
peak=   -3.219 closest distance to " C   LEU A 282 " =    1.692
peak=   -3.213 closest distance to " O   HOH Z 228 " =    1.458
peak=   -3.211 closest distance to " CE2 TRP A 179 " =    1.346
peak=   -3.210 closest distance to " ND2 ASN A 209 " =    1.842
peak=   -3.200 closest distance to " O   HOH Z 234 " =    4.093
peak=   -3.190 closest distance to " O   ALA A   8 " =    1.698
peak=   -3.189 closest distance to " CZ  TYR A 169 " =    1.682
peak=   -3.184 closest distance to " O   GLY A 118 " =    1.419
peak=   -3.183 closest distance to " O   HOH Z 198 " =    1.602
peak=   -3.176 closest distance to " O   HOH Z 427 " =    1.493
peak=   -3.166 closest distance to " O   HOH Z 438 " =    1.073
peak=   -3.165 closest distance to " O   HOH Z 311 " =    3.561
peak=   -3.165 closest distance to " N   GLN A  58 " =    1.296
peak=   -3.164 closest distance to " NE2 GLN A  88 " =    2.310
peak=   -3.160 closest distance to " O   HOH Z 100 " =    1.205
peak=   -3.158 closest distance to " O   VAL A 197 " =    1.243
peak=   -3.145 closest distance to " O   MET A  40 " =    2.669
peak=   -3.144 closest distance to " CD2 TYR A 293 " =    2.066
peak=   -3.143 closest distance to " O   HOH Z 158 " =    2.090
peak=   -3.141 closest distance to " NH2 ARG A 138 " =    1.292
peak=   -3.139 closest distance to " O   HOH Z 222 " =    3.151
peak=   -3.138 closest distance to " CD2 LEU A 237 " =    2.643
peak=   -3.137 closest distance to " O   SER A 146 " =    0.874
peak=   -3.137 closest distance to " O   HOH Z 134 " =    2.632
peak=   -3.134 closest distance to " O   HOH Z  68 " =    1.916
peak=   -3.129 closest distance to " O   HOH Z 137 " =    1.456
peak=   -3.126 closest distance to " CG  ASN A 217 " =    2.335
peak=   -3.121 closest distance to " O   HOH Z 211 " =    1.514
peak=   -3.120 closest distance to " NH2 ARG A  66 " =    2.891
peak=   -3.108 closest distance to " CG  ASP A  50 " =    2.170
peak=   -3.101 closest distance to " OE1 GLN A  77 " =    1.656
peak=   -3.097 closest distance to " O   LYS A 289 " =    3.056
peak=   -3.077 closest distance to " CG  GLU A 277 " =    1.210
peak=   -3.062 closest distance to " OG ASER A 216 " =    1.072
peak=   -3.057 closest distance to " CZ2 TRP A  92 " =    2.766
peak=   -3.051 closest distance to " O   ARG A 145 " =    1.462
peak=   -3.046 closest distance to " O   ARG A  56 " =    1.359
peak=   -3.025 closest distance to " CB  TYR A 172 " =    2.175

================= 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    :  0.4808 0.4736   6.281527e+00   6.276115e+00
   1_bss:  0.4726 0.4638   6.277168e+00   6.267635e+00
   1_xyz:  0.4015 0.4182   6.184243e+00   6.211582e+00
   1_adp:  0.3582 0.4084   6.117995e+00   6.195791e+00
   1_occ:  0.3578 0.4088   6.117507e+00   6.195980e+00
   2_bss:  0.3558 0.4063   6.117750e+00   6.194170e+00
   2_xyz:  0.2813 0.3390   5.933281e+00   6.071790e+00
   2_adp:  0.2621 0.3214   5.884952e+00   6.035272e+00
   2_occ:  0.2619 0.3219   5.884889e+00   6.035783e+00
   3_bss:  0.2611 0.3200   5.884227e+00   6.033749e+00
   3_xyz:  0.1849 0.2403   5.584485e+00   5.778847e+00
   3_adp:  0.1592 0.2195   5.465197e+00   5.693979e+00
   3_occ:  0.1590 0.2193   5.464278e+00   5.692949e+00
   4_bss:  0.1586 0.2160   5.452582e+00   5.680622e+00
   4_xyz:  0.1303 0.1817   5.278524e+00   5.520918e+00
   4_adp:  0.1242 0.1683   5.220830e+00   5.446645e+00
   4_occ:  0.1240 0.1676   5.218485e+00   5.443697e+00
   5_bss:  0.1242 0.1680   5.219919e+00   5.446037e+00
   5_xyz:  0.1158 0.1606   5.166420e+00   5.399854e+00
   5_adp:  0.1132 0.1614   5.156640e+00   5.399580e+00
   5_occ:  0.1132 0.1613   5.156015e+00   5.398782e+00
   5_bss:  0.1131 0.1613   5.155908e+00   5.398740e+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:  0.388  20.001   5.557   7.548   8.671   0.000   0.000   0.000
   1_xyz:  0.388  20.001   5.557   7.548   8.671   0.000   0.000   0.000
   1_adp:  0.388  20.001   5.557   7.548   8.671   0.000   0.000   0.000
   1_occ:  0.388  20.001   5.557   7.548   8.671   0.000   0.000   0.000
   2_bss:  0.348  28.449   2.955   3.979   6.098   0.000   0.000   0.000
   2_xyz:  0.348  28.449   2.955   3.979   6.098   0.000   0.000   0.000
   2_adp:  0.348  28.449   2.955   3.979   6.098   0.000   0.000   0.000
   2_occ:  0.348  28.449   2.955   3.979   6.098   0.000   0.000   0.000
   3_bss:  0.348  28.449   1.717   2.247   4.102   0.000   0.000   0.000
   3_xyz:  0.348  28.449   1.717   2.247   4.102   0.000   0.000   0.000
   3_adp:  0.348  28.449   1.717   2.247   4.102   0.000   0.000   0.000
   3_occ:  0.348  28.449   1.717   2.247   4.102   0.000   0.000   0.000
   4_bss:  0.322  35.685   1.560   1.627   2.634   0.000   0.000   0.000
   4_xyz:  0.322  35.685   1.560   1.627   2.634   0.000   0.000   0.000
   4_adp:  0.322  35.685   1.560   1.627   2.634   0.000   0.000   0.000
   4_occ:  0.322  35.685   1.560   1.627   2.634   0.000   0.000   0.000
   5_bss:  0.321  36.068   1.396   1.475   2.170   0.000   0.000   0.000
   5_xyz:  0.321  36.068   1.396   1.475   2.170   0.000   0.000   0.000
   5_adp:  0.321  36.068   1.396   1.475   2.170   0.000   0.000   0.000
   5_occ:  0.321  36.068   1.396   1.475   2.170   0.000   0.000   0.000
   5_bss:  0.321  38.856  -0.285  -0.205   0.490   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  57.664 0.4242  0.5080    71410.512
   1_bss:  57.975 0.4179  0.6089    68052.426
   1_xyz:  48.405 0.5394  0.7745    52206.991
   1_adp:  46.284 0.5662  0.8632    49699.078
   1_occ:  46.411 0.5646  0.8601    49799.570
   2_bss:  46.150 0.5676  0.7805    49365.826
   2_xyz:  36.777 0.6796  0.9159    31870.179
   2_adp:  34.209 0.7099  0.9524    28711.446
   2_occ:  34.235 0.7096  0.9517    28753.260
   3_bss:  34.029 0.7119  0.8992    28471.697
   3_xyz:  24.147 0.8202  0.9903    15191.706
   3_adp:  21.419 0.8481  1.0000    12606.987
   3_occ:  21.392 0.8484  1.0000    12564.978
   4_bss:  20.977 0.8520  0.9755    12044.974
   4_xyz:  17.090 0.8879  0.9922     8314.243
   4_adp:  15.307 0.9039  0.9963     7181.624
   4_occ:  15.246 0.9044  0.9965     7133.803
   5_bss:  15.281 0.9042  0.9866     7209.646
   5_xyz:  14.288 0.9126  0.9906     6521.142
   5_adp:  14.252 0.9131  0.9864     6510.819
   5_occ:  14.238 0.9132  0.9863     6499.131
   5_bss:  14.236 0.9132  0.9864     6499.169
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.3002e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.3002e+01
   1_xyz:   1.609  0.012  0.103 18.298  0.006  4.107   1.3162e-01
   1_adp:   1.609  0.012  0.103 18.298  0.006  4.107   1.3162e-01
   1_occ:   1.609  0.012  0.103 18.298  0.006  4.107   1.3162e-01
   2_bss:   1.609  0.012  0.103 18.298  0.006  4.107   1.3162e-01
   2_xyz:   1.107  0.007  0.076 16.092  0.004  4.107   7.5476e-02
   2_adp:   1.107  0.007  0.076 16.092  0.004  4.107   7.5476e-02
   2_occ:   1.107  0.007  0.076 16.092  0.004  4.107   7.5476e-02
   3_bss:   1.107  0.007  0.076 16.092  0.004  4.107   7.5476e-02
   3_xyz:   1.154  0.008  0.084 16.057  0.004  4.119   7.6780e-02
   3_adp:   1.154  0.008  0.084 16.057  0.004  4.119   7.6780e-02
   3_occ:   1.154  0.008  0.084 16.057  0.004  4.119   7.6780e-02
   4_bss:   1.154  0.008  0.084 16.057  0.004  4.119   7.6780e-02
   4_xyz:   1.074  0.007  0.078 15.697  0.004  4.106   6.7385e-02
   4_adp:   1.074  0.007  0.078 15.697  0.004  4.106   6.7385e-02
   4_occ:   1.074  0.007  0.078 15.697  0.004  4.106   6.7385e-02
   5_bss:   1.074  0.007  0.078 15.697  0.004  4.106   6.7385e-02
   5_xyz:   1.033  0.007  0.079 15.618  0.004  4.107   6.3870e-02
   5_adp:   1.033  0.007  0.079 15.618  0.004  4.107   6.3870e-02
   5_occ:   1.033  0.007  0.079 15.618  0.004  4.107   6.3870e-02
   5_bss:   1.033  0.007  0.079 15.618  0.004  4.107   6.3870e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.8692e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.8692e+00
   1_xyz:  12.683  0.159  0.410 84.576  0.049  2.187   8.9483e-02
   1_adp:  12.683  0.159  0.410 84.576  0.049  2.187   8.9483e-02
   1_occ:  12.683  0.159  0.410 84.576  0.049  2.187   8.9483e-02
   2_bss:  12.683  0.159  0.410 84.576  0.049  2.187   8.9483e-02
   2_xyz:   6.964  0.070  0.303 78.939  0.030  2.276   4.5999e-02
   2_adp:   6.964  0.070  0.303 78.939  0.030  2.276   4.5999e-02
   2_occ:   6.964  0.070  0.303 78.939  0.030  2.276   4.5999e-02
   3_bss:   6.964  0.070  0.303 78.939  0.030  2.276   4.5999e-02
   3_xyz:   7.069  0.061  0.444 87.885  0.029  2.279   7.5650e-02
   3_adp:   7.069  0.061  0.444 87.885  0.029  2.279   7.5650e-02
   3_occ:   7.069  0.061  0.444 87.885  0.029  2.279   7.5650e-02
   4_bss:   7.069  0.061  0.444 87.885  0.029  2.279   7.5650e-02
   4_xyz:   6.930  0.041  0.453 81.727  0.030  2.295   5.7673e-02
   4_adp:   6.930  0.041  0.453 81.727  0.030  2.295   5.7673e-02
   4_occ:   6.930  0.041  0.453 81.727  0.030  2.295   5.7673e-02
   5_bss:   6.930  0.041  0.453 81.727  0.030  2.295   5.7673e-02
   5_xyz:   6.574  0.039  0.548 84.987  0.028  2.242   6.2478e-02
   5_adp:   6.574  0.039  0.548 84.987  0.028  2.242   6.2478e-02
   5_occ:   6.574  0.039  0.548 84.987  0.028  2.242   6.2478e-02
   5_bss:   6.574  0.039  0.548 84.987  0.028  2.242   6.2478e-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:  66.01   0.00  13.05  59.09   0.00  10.97  66.01   0.00  24.37
   1_occ:  66.01   0.00  13.05  59.09   0.00  10.97  66.01   0.00  24.37
   2_bss:  66.01   0.00  13.05  59.09   0.00  10.97  66.01   0.00  24.37
   2_xyz:  66.01   0.00  13.05  59.09   0.00  10.97  66.01   0.00  24.37
   2_adp:  69.82   0.00  13.22  66.95   0.00  10.19  69.82   0.00  29.72
   2_occ:  69.82   0.00  13.22  66.95   0.00  10.19  69.82   0.00  29.72
   3_bss:  69.82   0.00  13.22  66.95   0.00  10.19  69.82   0.00  29.72
   3_xyz:  69.82   0.00  13.22  66.95   0.00  10.19  69.82   0.00  29.72
   3_adp:  85.07   0.00  14.32  85.07   0.00   9.67  83.34   2.12  39.63
   3_occ:  85.07   0.00  14.32  85.07   0.00   9.67  83.34   2.12  39.63
   4_bss:  85.07   0.00  14.32  85.07   0.00   9.67  83.34   2.12  39.63
   4_xyz:  85.07   0.00  14.32  85.07   0.00   9.67  83.34   2.12  39.63
   4_adp:  84.91   0.00  13.40  84.91   0.00   9.14  83.51   2.64  36.56
   4_occ:  84.91   0.00  13.40  84.91   0.00   9.14  83.51   2.64  36.56
   5_bss:  84.91   0.00  13.40  84.91   0.00   9.14  83.51   2.64  36.56
   5_xyz:  84.91   0.00  13.40  84.91   0.00   9.14  83.51   2.64  36.56
   5_adp:  95.33   0.00  13.48  95.33   0.00   9.09  86.49   2.80  37.38
   5_occ:  95.33   0.00  13.48  95.33   0.00   9.09  86.49   2.80  37.38
   5_bss:  97.01   1.68  15.16  97.01   1.68  10.77  88.17   4.48  39.06
------------------------------------------------------------------------
 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:    1.224    0.013    0.402
   1_adp:    1.224    0.013    0.402
   1_occ:    1.224    0.013    0.402
   2_bss:    1.224    0.013    0.402
   2_xyz:    1.645    0.047    0.549
   2_adp:    1.645    0.047    0.549
   2_occ:    1.645    0.047    0.549
   3_bss:    1.645    0.047    0.549
   3_xyz:    1.536    0.056    0.687
   3_adp:    1.536    0.056    0.687
   3_occ:    1.536    0.056    0.687
   4_bss:    1.536    0.056    0.687
   4_xyz:    1.744    0.033    0.729
   4_adp:    1.744    0.033    0.729
   4_occ:    1.744    0.033    0.729
   5_bss:    1.744    0.033    0.729
   5_xyz:    1.842    0.044    0.745
   5_adp:    1.842    0.044    0.745
   5_occ:    1.842    0.044    0.745
   5_bss:    1.842    0.044    0.745
------------------------------------------------------------------------

CPU time actual refinement: 357.05


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_638/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_638/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_638/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_638/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_638/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 356.90 
  Macro-tasks:
    bulk solvent and scale       = 41.57  
    individual site refinement   = 159.03 
    weights calculation          = 31.61  
    collect and process          = 6.39   
    model show statistics        = 0.10   
    TOTAL for macro-tasks        = 238.70 
  Micro-tasks:
    mask                            = 2.44   
    f_calc                          = 113.49 
    alpha_beta                      = 8.22   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 125.10 
    fmodel                         = 7.32   
    r_factors                      = 0.23   
    phase_errors                   = 10.29  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 268.47 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.917 micro seconds
Total CPU time: 6.18 minutes
from_scatterers_fft:    657 calls, 113.23 s
gradients_fft:          601 calls, 111.11 s

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

# Date 2008-01-16 Time 02:04:03 PST -0800 (1200477843.30 s)
Start R-work = 0.4808, R-free = 0.4736 (no bulk solvent and anisotropic scale)
Final R-work = 0.1300, R-free = 0.1780 (no bulk solvent and anisotropic scale)

Start R-work = 0.4726, R-free = 0.4638
Final R-work = 0.1131, R-free = 0.1613