# Date 2008-01-16 Time 02:08:56 PST -0800 (1200478136.17 s)
#phil __OFF__

Command line arguments: "../712.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 = 22754
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 712

-------------------------------------------------------------------------------
  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, 47.8686, 87.6859, 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: 3.24, 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, 47.8686, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.054 2.00068
Completeness in resolution range: 0.954537
Completeness with d_max=infinity: 0.951569

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0540
                             d_min =   2.0007

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, 47.8686, 87.6859, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.054 2.00068
Completeness in resolution range: 0.954537
Completeness with d_max=infinity: 0.951569

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0544 -  4.2804 [2164/2192]  1947   217  10.0%
  bin  2:  4.2804 -  3.4105 [2058/2077]  1854   204   9.9%
  bin  3:  3.4105 -  2.9832 [2050/2070]  1845   205  10.0%
  bin  4:  2.9832 -  2.7122 [2021/2046]  1820   201   9.9%
  bin  5:  2.7122 -  2.5187 [2014/2033]  1805   209  10.4%
  bin  6:  2.5187 -  2.3708 [1996/2042]  1801   195   9.8%
  bin  7:  2.3708 -  2.2525 [1997/2030]  1801   196   9.8%
  bin  8:  2.2525 -  2.1547 [1988/2024]  1784   204  10.3%
  bin  9:  2.1547 -  2.0720 [1958/1987]  1759   199  10.2%
  bin 10:  2.0720 -  2.0007 [1343/2021]  1214   129   9.6%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_712/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.15 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 19
        2.42 -     3.04: 2151
        3.04 -     3.66: 4601
        3.66 -     4.28: 8827
        4.28 -     4.90: 12270
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.846 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 207 " - " O   HOH Z 341 "  2.015 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 343 " - " O   HOH Z 277 "  2.111 3.040 -x+1/2,-y+1,z-1/2
  " O   HOH Z 277 " - " O   HOH Z 343 "  2.111 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 27863 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_712/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_712/model_refine_001.geo

CPU time processing inputs: 9.00


============================ 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 47.8686 87.68585 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4943   r_free= 0.4808   ksol= 0.00   Bsol= 0.00   scale= 0.772    |
|                                                                             |
| 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:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.292642                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.7738 0.99   1400  157 0.3974 0.3947      6.6025      6.5935|
|  2:  4.7738 -  3.8094 0.99   1346  151 0.4208 0.4620      6.8236      6.9311|
|  3:  3.8094 -  3.3338 0.99   1325  147 0.4656 0.4210      6.7128      6.6508|
|  4:  3.3338 -  3.0317 0.99   1308  136 0.4843 0.4448      6.5468      6.4706|
|  5:  3.0317 -  2.8159 0.99   1306  150 0.5283 0.4973      6.3905      6.4123|
|  6:  2.8159 -  2.6508 0.98   1297  143 0.5232 0.5305      6.2866      6.2066|
|  7:  2.6508 -  2.5187 0.99   1289  152 0.5133 0.4568      6.2479      6.1319|
|  8:  2.5187 -  2.4095 0.98   1309  136 0.5271 0.4639      6.1929      6.1758|
|  9:  2.4095 -  2.3171 0.98   1277  146 0.5381 0.6058      6.1151      6.1919|
| 10:  2.3171 -  2.2374 0.97   1260  138 0.5698 0.5050      6.1284      6.1397|
| 11:  2.2374 -  2.1677 0.99   1285  147 0.5251 0.5295      6.0265      6.0473|
| 12:  2.1677 -  2.1059 0.98   1282  139 0.5398 0.5479      5.9756      6.0144|
| 13:  2.1059 -  2.0506 0.97   1248  136 0.5496 0.5089      5.8969      5.8244|
| 14:  2.0506 -  2.0007 0.54    698   81 0.5503 0.5355      5.8721      5.7796|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0544 -  4.7738  1400   157  0.68  36.23   0.79     0.69      77119.80|
|  2:  4.7738 -  3.8094  1346   151  0.68  37.18   0.86     0.72     115088.43|
|  3:  3.8094 -  3.3338  1325   147  0.57  46.00   0.79     0.67     121091.75|
|  4:  3.3338 -  3.0317  1308   136  0.49  52.45   0.78     0.57     103039.04|
|  5:  3.0317 -  2.8159  1306   150  0.42  58.27   0.72     0.49      81486.49|
|  6:  2.8159 -  2.6508  1297   143  0.41  59.16   0.70     0.47      69265.44|
|  7:  2.6508 -  2.5187  1289   152  0.40  60.05   0.73     0.45      63053.94|
|  8:  2.5187 -  2.4095  1309   136  0.38  61.82   0.72     0.43      59025.54|
|  9:  2.4095 -  2.3171  1277   146  0.31  67.09   0.69     0.37      58472.73|
| 10:  2.3171 -  2.2374  1260   138  0.28  68.82   0.71     0.34      53811.02|
| 11:  2.2374 -  2.1677  1285   147  0.28  69.19   0.72     0.34      50358.10|
| 12:  2.1677 -  2.1059  1282   139  0.28  68.90   0.75     0.36      45488.99|
| 13:  2.1059 -  2.0506  1248   136  0.26  70.71   0.69     0.32      39566.06|
| 14:  2.0506 -  2.0007   698    81  0.22  73.32   0.71     0.23      30973.19|
|alpha:            min =        0.23 max =            0.72 mean =         0.47|
|beta:             min =    30973.19 max =       121091.75 mean =     70867.52|
|figures of merit: min =        0.00 max =            1.00 mean =         0.41|
|phase err.(work): min =        0.00 max =           89.97 mean =        58.45|
|phase err.(test): min =        0.00 max =           89.95 mean =        58.72|
|-----------------------------------------------------------------------------|

============================== 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 = 15.443269             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.476   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.568737              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.249   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       28 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      163 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      671 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1476 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2571 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3851 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     4984 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6465 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7624 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.464 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.092    4.900  1.196 |       1.737 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.267)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.267)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5001   r_free= 0.4811   ksol= 0.00   Bsol= 0.00   scale= 0.744    |
|                                                                             |
| 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:   0.80 A                  |
| x-ray target function (ml) for work reflections: 6.294212                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4875   r_free= 0.4727   ksol= 0.30   Bsol= 20.00   scale= 0.968   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.84,11.06,9.47,0.00,0.00,0.00); trace/3= 8.79                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.79 A                  |
| x-ray target function (ml) for work reflections: 6.286102                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 13.972794             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.551   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.395428              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.556   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4875      final r-factor (work) = 0.4118          |
| start r-factor (free) = 0.4727      final r-factor (free) = 0.4241          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 98.4260 = 13.97 * 0.50 * 6.2925 + 1.00 * 54.4640                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 43.5803 = 13.97 * 0.50 * 6.2175 + 1.00 * 0.1426                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4118      final r-factor (work) = 0.3671          |
| start r-factor (free) = 0.4241      final r-factor (free) = 0.4146          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.6908 = 1.40 * 1.00 * 6.2175 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 8.5920 = 1.40 * 1.00 * 6.1413 + 1.00 * 0.0223                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.267)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    113.18  15.07    None  None   None       |
|    all(noH): 2823   0      0.00    113.18  15.07    None  None   None       |
|    Sol.    : 438    0      0.00    113.18  28.07    None  None   None       |
|    Mac.    : 2385   0      0.00    87.23   12.68    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  11.318: 1415   |   5:    56.588 -  67.906:   27        |
|      1:    11.318 -  22.635:  787   |   6:    67.906 -  79.224:   13        |
|      2:    22.635 -  33.953:  353   |   7:    79.224 -  90.541:    3        |
|      3:    33.953 -  45.271:  157   |   8:    90.541 - 101.859:    2        |
|      4:    45.271 -  56.588:   64   |   9:   101.859 - 113.177:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3671 r_free = 0.4146             target_work(ml) = 6.127         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3663 r_free = 0.4140             target_work(ml) = 6.126         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3663   r_free= 0.4140   ksol= 0.30   Bsol= 20.00   scale= 1.094   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.84,11.06,9.47,0.00,0.00,0.00); trace/3= 8.79                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.57 A                  |
| x-ray target function (ml) for work reflections: 6.125996                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3640   r_free= 0.4087   ksol= 0.32   Bsol= 50.00   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.63,7.01,5.74,0.00,0.00,0.00); trace/3= 5.12                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.127886                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.640326              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.071  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.478123              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 123.369  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3640      final r-factor (work) = 0.2871          |
| start r-factor (free) = 0.4087      final r-factor (free) = 0.3482          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.7192 = 9.64 * 0.50 * 6.1361 + 1.00 * 0.1421                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.0966 = 9.64 * 0.50 * 6.0165 + 1.00 * 0.0962                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2871      final r-factor (work) = 0.2680          |
| start r-factor (free) = 0.3482      final r-factor (free) = 0.3268          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8992 = 0.48 * 1.00 * 6.0165 + 1.00 * 0.0226                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8429 = 0.48 * 1.00 * 5.9150 + 1.00 * 0.0148                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.267)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    108.46  13.58    None  None   None       |
|    all(noH): 2823   0      0.00    108.46  13.58    None  None   None       |
|    Sol.    : 438    0      0.00    108.46  30.62    None  None   None       |
|    Mac.    : 2385   0      0.00    77.86   10.46    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.846: 1585   |   5:    54.232 -  65.078:   28        |
|      1:    10.846 -  21.693:  710   |   6:    65.078 -  75.924:    9        |
|      2:    21.693 -  32.539:  278   |   7:    75.924 -  86.771:    3        |
|      3:    32.539 -  43.385:  139   |   8:    86.771 -  97.617:    3        |
|      4:    43.385 -  54.232:   67   |   9:    97.617 - 108.463:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2680 r_free = 0.3268             target_work(ml) = 5.894         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        6 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2678 r_free = 0.3270             target_work(ml) = 5.894         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2678   r_free= 0.3270   ksol= 0.32   Bsol= 50.00   scale= 1.036   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.63,7.01,5.74,0.00,0.00,0.00); trace/3= 5.12                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.41 A                  |
| x-ray target function (ml) for work reflections: 5.893769                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2667   r_free= 0.3262   ksol= 0.31   Bsol= 50.00   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.81,4.44,3.74,0.00,0.00,0.00); trace/3= 3.33                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.894456                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.576633              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 107.436  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.287141              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 113.831  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2667      final r-factor (work) = 0.2139          |
| start r-factor (free) = 0.3262      final r-factor (free) = 0.2542          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.6763 = 3.58 * 0.50 * 5.9162 + 1.00 * 0.0962                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.4540 = 3.58 * 0.50 * 5.8093 + 1.00 * 0.0651                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2139      final r-factor (work) = 0.2010          |
| start r-factor (free) = 0.2542      final r-factor (free) = 0.2400          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6806 = 0.29 * 1.00 * 5.8093 + 1.00 * 0.0125                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.6347 = 0.29 * 1.00 * 5.6581 + 1.00 * 0.0100                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.267)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    103.22  13.51    None  None   None       |
|    all(noH): 2823   0      0.00    103.22  13.51    None  None   None       |
|    Sol.    : 438    0      1.00    103.22  33.75    None  None   None       |
|    Mac.    : 2385   0      0.00    67.76   9.79     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.322: 1645   |   5:    51.610 -  61.932:   54        |
|      1:    10.322 -  20.644:  624   |   6:    61.932 -  72.255:   12        |
|      2:    20.644 -  30.966:  238   |   7:    72.255 -  82.577:    3        |
|      3:    30.966 -  41.288:  147   |   8:    82.577 -  92.899:    2        |
|      4:    41.288 -  51.610:   97   |   9:    92.899 - 103.221:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2010 r_free = 0.2400             target_work(ml) = 5.640         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       13 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2008 r_free = 0.2403             target_work(ml) = 5.640         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2008   r_free= 0.2403   ksol= 0.31   Bsol= 50.00   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.81,4.44,3.74,0.00,0.00,0.00); trace/3= 3.33                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.640448                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2005   r_free= 0.2394   ksol= 0.33   Bsol= 64.83   scale= 0.987   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.07,2.97,3.02,0.00,0.00,0.00); trace/3= 2.35                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.27 A                  |
| x-ray target function (ml) for work reflections: 5.639203                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.309431              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.201  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.358306              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 155.029  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2005      final r-factor (work) = 0.1468          |
| start r-factor (free) = 0.2394      final r-factor (free) = 0.1878          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.0889 = 5.31 * 0.50 * 5.6592 + 1.00 * 0.0653                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.6904 = 5.31 * 0.50 * 5.4999 + 1.00 * 0.0897                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1468      final r-factor (work) = 0.1354          |
| start r-factor (free) = 0.1878      final r-factor (free) = 0.1801          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9806 = 0.36 * 1.00 * 5.4999 + 1.00 * 0.0099                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9171 = 0.36 * 1.00 * 5.3196 + 1.00 * 0.0111                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.267)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    98.27   13.56    None  None   None       |
|    all(noH): 2823   0      0.00    98.27   13.56    None  None   None       |
|    Sol.    : 438    0      1.14    98.27   36.59    None  None   None       |
|    Mac.    : 2385   0      0.00    71.29   9.33     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 -   9.827: 1656   |   5:    49.136 -  58.963:   85        |
|      1:     9.827 -  19.655:  631   |   6:    58.963 -  68.791:   25        |
|      2:    19.655 -  29.482:  162   |   7:    68.791 -  78.618:    9        |
|      3:    29.482 -  39.309:  131   |   8:    78.618 -  88.445:    2        |
|      4:    39.309 -  49.136:  121   |   9:    88.445 -  98.272:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1354 r_free = 0.1801             target_work(ml) = 5.299         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1352 r_free = 0.1802             target_work(ml) = 5.298         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1352   r_free= 0.1802   ksol= 0.33   Bsol= 64.83   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.07,2.97,3.02,0.00,0.00,0.00); trace/3= 2.35                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.298096                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1353   r_free= 0.1806   ksol= 0.33   Bsol= 64.83   scale= 0.989   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.93,2.19,2.85,0.00,0.00,0.00); trace/3= 1.99                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.299106                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.088041              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 125.005  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.634753              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 147.344  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1353      final r-factor (work) = 0.1217          |
| start r-factor (free) = 0.1806      final r-factor (free) = 0.1666          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.9648 = 4.09 * 0.50 * 5.3204 + 1.00 * 0.0897                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 10.8335 = 4.09 * 0.50 * 5.2554 + 1.00 * 0.0913                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1217      final r-factor (work) = 0.1187          |
| start r-factor (free) = 0.1666      final r-factor (free) = 0.1663          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3468 = 0.63 * 1.00 * 5.2554 + 1.00 * 0.0109                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.3187 = 0.63 * 1.00 * 5.2042 + 1.00 * 0.0153                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.267)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.41   13.57    None  None   None       |
|    all(noH): 2823   0      0.00    93.41   13.57    None  None   None       |
|    Sol.    : 438    0      1.15    93.41   37.72    None  None   None       |
|    Mac.    : 2385   0      0.00    77.34   9.13     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 -   9.341: 1627   |   5:    46.707 -  56.049:   95        |
|      1:     9.341 -  18.683:  640   |   6:    56.049 -  65.390:   51        |
|      2:    18.683 -  28.024:  157   |   7:    65.390 -  74.731:   18        |
|      3:    28.024 -  37.366:  119   |   8:    74.731 -  84.073:    6        |
|      4:    37.366 -  46.707:  109   |   9:    84.073 -  93.414:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1187 r_free = 0.1663             target_work(ml) = 5.202         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1186 r_free = 0.1664             target_work(ml) = 5.202         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1186   r_free= 0.1664   ksol= 0.33   Bsol= 64.83   scale= 0.988   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.93,2.19,2.85,0.00,0.00,0.00); trace/3= 1.99                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.201776                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.7738 0.99   1400  157 0.1020 0.1364       5.424        5.58|
|  2:  4.7738 -  3.8094 0.99   1346  151 0.0864 0.1093      5.4505      5.6423|
|  3:  3.8094 -  3.3338 0.99   1325  147 0.1122 0.1541      5.5096      5.8736|
|  4:  3.3338 -  3.0317 0.99   1308  136 0.1261 0.1625      5.4778      5.6225|
|  5:  3.0317 -  2.8159 0.99   1306  150 0.1441 0.1727      5.3981      5.5426|
|  6:  2.8159 -  2.6508 0.98   1297  143 0.1358 0.2240      5.2874      5.6018|
|  7:  2.6508 -  2.5187 0.99   1289  152 0.1344 0.1710      5.2348      5.3859|
|  8:  2.5187 -  2.4095 0.98   1309  136 0.1240 0.1823      5.1552      5.4288|
|  9:  2.4095 -  2.3171 0.98   1277  146 0.1267 0.2023      5.0953      5.4164|
| 10:  2.3171 -  2.2374 0.97   1260  138 0.1255 0.1692      5.0607      5.2376|
| 11:  2.2374 -  2.1677 0.99   1285  147 0.1225 0.2042      4.9979      5.3295|
| 12:  2.1677 -  2.1059 0.98   1282  139 0.1156 0.1814      4.8975      5.2244|
| 13:  2.1059 -  2.0506 0.97   1248  136 0.1148 0.1795      4.8139       5.051|
| 14:  2.0506 -  2.0007 0.54    698   81 0.1149 0.1730      4.7521      4.9646|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0544 -  4.7738  1400   157  0.94   9.79   0.97     0.94       8131.91|
|  2:  4.7738 -  3.8094  1346   151  0.95   8.37   1.00     0.98       9407.89|
|  3:  3.8094 -  3.3338  1325   147  0.93  11.50   1.02     1.01      10728.78|
|  4:  3.3338 -  3.0317  1308   136  0.92  13.81   1.00     0.98      10544.37|
|  5:  3.0317 -  2.8159  1306   150  0.89  17.20   0.99     0.97       9385.73|
|  6:  2.8159 -  2.6508  1297   143  0.88  17.88   0.97     0.94       8219.72|
|  7:  2.6508 -  2.5187  1289   152  0.89  16.86   0.98     0.95       7126.88|
|  8:  2.5187 -  2.4095  1309   136  0.90  16.74   0.98     0.95       6473.52|
|  9:  2.4095 -  2.3171  1277   146  0.89  17.67   0.99     0.94       5836.88|
| 10:  2.3171 -  2.2374  1260   138  0.88  18.01   0.98     0.94       5498.32|
| 11:  2.2374 -  2.1677  1285   147  0.89  17.55   0.98     0.93       4965.83|
| 12:  2.1677 -  2.1059  1282   139  0.90  16.24   1.00     0.98       4186.15|
| 13:  2.1059 -  2.0506  1248   136  0.90  16.84   0.98     0.96       3588.93|
| 14:  2.0506 -  2.0007   698    81  0.90  16.42   0.94     0.90       3021.16|
|alpha:            min =        0.90 max =            1.01 mean =         0.96|
|beta:             min =     3021.16 max =        10728.78 mean =      7110.13|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.92 mean =        15.24|
|phase err.(test): min =        0.00 max =           89.89 mean =        14.53|
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1185   r_free= 0.1662   ksol= 0.32   Bsol= 63.54   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.94,0.04,0.90,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.201509                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 2.00 - 15.05 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1185   r_free= 0.1662   ksol= 0.32   Bsol= 63.54   scale= 0.992   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.94,0.04,0.90,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.201509                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0544 -  4.7738 0.99   1400  157 0.1017 0.1363      5.4202       5.578|
|  2:  4.7738 -  3.8094 0.99   1346  151 0.0863 0.1092      5.4496      5.6414|
|  3:  3.8094 -  3.3338 0.99   1325  147 0.1123 0.1539      5.5099      5.8747|
|  4:  3.3338 -  3.0317 0.99   1308  136 0.1261 0.1626      5.4781      5.6227|
|  5:  3.0317 -  2.8159 0.99   1306  150 0.1443 0.1727      5.3987      5.5428|
|  6:  2.8159 -  2.6508 0.98   1297  143 0.1357 0.2237      5.2871      5.6011|
|  7:  2.6508 -  2.5187 0.99   1289  152 0.1345 0.1714       5.235      5.3869|
|  8:  2.5187 -  2.4095 0.98   1309  136 0.1241 0.1822      5.1557      5.4291|
|  9:  2.4095 -  2.3171 0.98   1277  146 0.1266 0.2021      5.0957      5.4166|
| 10:  2.3171 -  2.2374 0.97   1260  138 0.1255 0.1697       5.061      5.2395|
| 11:  2.2374 -  2.1677 0.99   1285  147 0.1225 0.2040      4.9977      5.3283|
| 12:  2.1677 -  2.1059 0.98   1282  139 0.1156 0.1812      4.8973       5.225|
| 13:  2.1059 -  2.0506 0.97   1248  136 0.1149 0.1786      4.8135      5.0496|
| 14:  2.0506 -  2.0007 0.54    698   81 0.1148 0.1723      4.7516      4.9625|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0544 -  4.7738  1400   157  0.94   9.75   0.97     0.94       8068.51|
|  2:  4.7738 -  3.8094  1346   151  0.95   8.34   1.00     0.99       9374.61|
|  3:  3.8094 -  3.3338  1325   147  0.93  11.50   1.02     1.01      10733.37|
|  4:  3.3338 -  3.0317  1308   136  0.92  13.82   1.00     0.98      10550.39|
|  5:  3.0317 -  2.8159  1306   150  0.89  17.20   1.00     0.97       9391.59|
|  6:  2.8159 -  2.6508  1297   143  0.88  17.87   0.97     0.94       8215.38|
|  7:  2.6508 -  2.5187  1289   152  0.89  16.86   0.98     0.95       7129.81|
|  8:  2.5187 -  2.4095  1309   136  0.90  16.75   0.99     0.95       6481.50|
|  9:  2.4095 -  2.3171  1277   146  0.89  17.69   1.00     0.95       5847.72|
| 10:  2.3171 -  2.2374  1260   138  0.88  18.02   0.99     0.95       5503.67|
| 11:  2.2374 -  2.1677  1285   147  0.89  17.55   0.98     0.93       4966.85|
| 12:  2.1677 -  2.1059  1282   139  0.90  16.24   1.00     0.99       4184.76|
| 13:  2.1059 -  2.0506  1248   136  0.90  16.83   0.99     0.97       3582.70|
| 14:  2.0506 -  2.0007   698    81  0.90  16.38   0.95     0.91       3011.20|
|alpha:            min =        0.91 max =            1.01 mean =         0.96|
|beta:             min =     3011.20 max =        10733.37 mean =      7104.57|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.89 mean =        15.23|
|phase err.(test): min =        0.00 max =           89.93 mean =        14.52|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.267)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.15    95.56   15.71    None  None   None       |
|    all(noH): 2823   0      2.15    95.56   15.71    None  None   None       |
|    Sol.    : 438    0      3.29    95.56   39.86    None  None   None       |
|    Mac.    : 2385   0      2.15    79.49   11.28    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.146 -  11.487: 1627   |   5:    48.853 -  58.194:   95        |
|      1:    11.487 -  20.828:  640   |   6:    58.194 -  67.536:   51        |
|      2:    20.828 -  30.170:  157   |   7:    67.536 -  76.877:   18        |
|      3:    30.170 -  39.511:  119   |   8:    76.877 -  86.218:    6        |
|      4:    39.511 -  48.853:  109   |   9:    86.218 -  95.560:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 326         
Filter by distance & map next to the model:
   mapped sites are within: 0.488 - 5.287
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 319 from: 326
   mapped sites are within: 0.734 - 5.287

peak=    9.402 closest distance to " CG2 VAL A 230 " =    1.345
peak=    6.226 closest distance to " O   HOH Z 210 " =    1.427
peak=    6.097 closest distance to " NH2 ARG A  56 " =    2.299
peak=    5.952 closest distance to " CG  LEU A   5 " =    1.220
peak=    5.467 closest distance to " CD1AILE A 234 " =    1.139
peak=    5.416 closest distance to " CB  VAL A 296 " =    1.145
peak=    5.223 closest distance to " CB  GLN A 223 " =    1.421
peak=    5.091 closest distance to " CB  SER A  63 " =    1.203
peak=    5.016 closest distance to " CG  LEU A 228 " =    1.188
peak=    4.893 closest distance to " CB  VAL A 230 " =    1.243
peak=    4.780 closest distance to " CG1 VAL A 296 " =    1.176
peak=    4.621 closest distance to " O   HOH Z 232 " =    2.360
peak=    4.573 closest distance to " O   PRO A 198 " =    1.527
peak=    4.560 closest distance to " O   HOH Z 403 " =    1.853
peak=    4.558 closest distance to " CB  GLN A 183 " =    1.294
peak=    4.548 closest distance to " O   HOH Z 433 " =    1.625
peak=    4.538 closest distance to " CG  PRO A  54 " =    1.271
peak=    4.523 closest distance to " O   HOH Z 120 " =    1.153
peak=    4.502 closest distance to " O   HOH Z  49 " =    1.295
peak=    4.481 closest distance to " O   HOH Z 412 " =    3.622
peak=    4.443 closest distance to " O   HOH Z 130 " =    2.448
peak=    4.441 closest distance to " CA  TYR A  30 " =    0.942
peak=    4.429 closest distance to " NE2 GLN A  11 " =    1.114
peak=    4.421 closest distance to " CA  ALA A  51 " =    1.017
peak=    4.355 closest distance to " CB  ARG A 275 " =    0.909
peak=    4.317 closest distance to " O   HOH Z 154 " =    1.643
peak=    4.303 closest distance to " O   HOH Z 248 " =    1.569
peak=    4.303 closest distance to " CZ  PHE A 218 " =    1.276
peak=    4.290 closest distance to " O   HOH Z 128 " =    1.524
peak=    4.278 closest distance to " O   ALA A 165 " =    1.328
peak=    4.270 closest distance to " O   SER A  87 " =    2.321
peak=    4.263 closest distance to " O   HOH Z  63 " =    2.333
peak=    4.262 closest distance to " O   HOH Z 130 " =    1.165
peak=    4.250 closest distance to " CB  ARG A 190 " =    1.724
peak=    4.250 closest distance to " O   HOH Z 234 " =    3.689
peak=    4.243 closest distance to " CB  PRO A  54 " =    0.886
peak=    4.234 closest distance to " O   HOH Z  48 " =    1.839
peak=    4.208 closest distance to " CG  PRO A 280 " =    0.806
peak=    4.196 closest distance to " O   HOH Z  44 " =    2.053
peak=    4.174 closest distance to " OG BSER A 164 " =    2.062
peak=    4.153 closest distance to " O   HOH Z 261 " =    2.315
peak=    4.151 closest distance to " O   HOH Z 402 " =    1.556
peak=    4.125 closest distance to " CB BVAL A  41 " =    1.001
peak=    4.090 closest distance to " O   HOH Z 359 " =    1.652
peak=    4.084 closest distance to " O   HOH Z  43 " =    2.038
peak=    4.083 closest distance to " CG  PRO A 198 " =    1.231
peak=    4.083 closest distance to " O   HOH Z 142 " =    1.641
peak=    4.074 closest distance to " O   HOH Z  40 " =    2.024
peak=    4.073 closest distance to " O   HOH Z 425 " =    1.576
peak=    4.066 closest distance to " CB  GLU A 277 " =    3.743
peak=    4.058 closest distance to " O   HOH Z 102 " =    1.382
peak=    4.055 closest distance to " O   HOH Z 265 " =    2.026
peak=    4.039 closest distance to " CB  GLU A 128 " =    1.152
peak=    4.018 closest distance to " CD  LYS A 166 " =    1.425
peak=    4.009 closest distance to " O   HOH Z 431 " =    1.250
peak=    4.001 closest distance to " O   HOH Z 126 " =    1.646
peak=    3.985 closest distance to " O   HOH Z 346 " =    1.520
peak=    3.980 closest distance to " CB  VAL A 202 " =    1.470
peak=    3.966 closest distance to " CD2 LEU A   5 " =    1.101
peak=    3.959 closest distance to " CA  ILE A 106 " =    0.764
peak=    3.951 closest distance to " CA  ALA A 295 " =    1.011
peak=    3.950 closest distance to " CG2 VAL A 296 " =    0.969
peak=    3.943 closest distance to " O   ASP A 124 " =    1.336
peak=    3.922 closest distance to " O   HOH Z 251 " =    1.520
peak=    3.911 closest distance to " CA  TYR A 116 " =    1.354
peak=    3.901 closest distance to " CD2 TRP A 179 " =    1.295
peak=    3.896 closest distance to " CB  ARG A  79 " =    1.460
peak=    3.885 closest distance to " O   HOH Z 303 " =    2.312
peak=    3.879 closest distance to " O   HOH Z 146 " =    1.699
peak=    3.870 closest distance to " CG2 ILE A 234 " =    1.083
peak=    3.865 closest distance to " O   HOH Z 280 " =    2.826
peak=    3.857 closest distance to " O   HOH Z 214 " =    1.458
peak=    3.842 closest distance to " CZ3 TRP A  85 " =    0.936
peak=    3.835 closest distance to " O   HOH Z  61 " =    1.528
peak=    3.835 closest distance to " O   HOH Z 369 " =    2.051
peak=    3.817 closest distance to " O   HOH Z 423 " =    1.687
peak=    3.812 closest distance to " O   HOH Z 417 " =    2.994
peak=    3.809 closest distance to " OD1 ASN A  69 " =    2.402
peak=    3.808 closest distance to " CB  ASN A 148 " =    1.391
peak=    3.805 closest distance to " O   HOH Z 126 " =    1.980
peak=    3.805 closest distance to " O   HOH Z 365 " =    2.312
peak=    3.802 closest distance to " CE1 TYR A 186 " =    1.259
peak=    3.799 closest distance to " CB  GLU A 152 " =    1.108
peak=    3.795 closest distance to " CB  TRP A 179 " =    1.431
peak=    3.792 closest distance to " O   HOH Z 258 " =    2.212
peak=    3.787 closest distance to " O   HOH Z 422 " =    2.532
peak=    3.780 closest distance to " CB  ALA A   9 " =    1.706
peak=    3.780 closest distance to " O   HOH Z 214 " =    3.115
peak=    3.774 closest distance to " CB  GLU A  46 " =    0.959
peak=    3.773 closest distance to " O   HOH Z 393 " =    3.589
peak=    3.750 closest distance to " O   HOH Z 134 " =    1.757
peak=    3.735 closest distance to " O   HOH Z 316 " =    3.140
peak=    3.734 closest distance to " CD1 LEU A  96 " =    0.767
peak=    3.730 closest distance to " CG  PRO A 213 " =    1.183
peak=    3.729 closest distance to " CG1 ILE A  33 " =    1.163
peak=    3.725 closest distance to " CD2 LEU A 228 " =    1.230
peak=    3.720 closest distance to " CG  MET A 185 " =    1.218
peak=    3.710 closest distance to " CG2 THR A 221 " =    1.128
peak=    3.708 closest distance to " O   HOH Z 124 " =    1.179
peak=    3.708 closest distance to " CB  TRP A 266 " =    1.084
peak=    3.691 closest distance to " CA  ALA A 160 " =    0.969
peak=    3.690 closest distance to " O   HOH Z 245 " =    1.334
peak=    3.685 closest distance to " O   HOH Z  80 " =    1.967
peak=    3.683 closest distance to " OG BSER A 134 " =    2.850
peak=    3.678 closest distance to " CB  ASN A 142 " =    1.173
peak=    3.676 closest distance to " O   PRO A 213 " =    1.462
peak=    3.670 closest distance to " CB  ASP A 140 " =    0.999
peak=    3.669 closest distance to " O   HOH Z 193 " =    1.831
peak=    3.668 closest distance to " CD  PRO A  54 " =    1.017
peak=    3.662 closest distance to " O   HOH Z 287 " =    1.882
peak=    3.662 closest distance to " NE2 GLN A  77 " =    3.311
peak=    3.658 closest distance to " CB  THR A  52 " =    0.863
peak=    3.656 closest distance to " CE  LYS A  76 " =    0.823
peak=    3.645 closest distance to " NH2 ARG A 156 " =    1.098
peak=    3.645 closest distance to " CG1 VAL A 153 " =    1.052
peak=    3.642 closest distance to " NH1AARG A 145 " =    1.300
peak=    3.635 closest distance to " CA  ARG A 195 " =    1.198
peak=    3.633 closest distance to " CB  ALA A 248 " =    1.058
peak=    3.632 closest distance to " O   ASN A  74 " =    2.038
peak=    3.631 closest distance to " O   HOH Z 394 " =    1.540
peak=    3.622 closest distance to " O   HOH Z 238 " =    0.988
peak=    3.619 closest distance to " O   HOH Z 368 " =    3.535
peak=    3.614 closest distance to " CG  PRO A 243 " =    1.135
peak=    3.608 closest distance to " O   HOH Z 285 " =    2.546
peak=    3.603 closest distance to " O   HOH Z  78 " =    1.632
peak=    3.602 closest distance to " CB  GLN A  88 " =    1.193
peak=    3.601 closest distance to " OE1 GLN A  55 " =    1.452
peak=    3.593 closest distance to " O   HOH Z  56 " =    1.747
peak=    3.591 closest distance to " CB  SER A  26 " =    1.747
peak=    3.587 closest distance to " O   HOH Z  48 " =    1.659
peak=    3.583 closest distance to " O   HOH Z 298 " =    1.842
peak=    3.582 closest distance to " CG AARG A 275 " =    1.215
peak=    3.569 closest distance to " CB  ALA A 100 " =    1.353
peak=    3.568 closest distance to " O   HOH Z  19 " =    1.780
peak=    3.568 closest distance to " O   HOH Z 154 " =    2.326
peak=    3.561 closest distance to " O   HOH Z 435 " =    1.985
peak=    3.556 closest distance to " CB  SER A   3 " =    1.341
peak=    3.556 closest distance to " O   HOH Z 383 " =    2.042
peak=    3.556 closest distance to " CA  SER A  12 " =    1.400
peak=    3.553 closest distance to " OD2 ASP A 298 " =    3.649
peak=    3.548 closest distance to " O   HOH Z 406 " =    1.532
peak=    3.544 closest distance to " O   HOH Z 189 " =    2.917
peak=    3.542 closest distance to " O   HOH Z 291 " =    1.531
peak=    3.541 closest distance to " O   ASP A 200 " =    1.693
peak=    3.536 closest distance to " O  BHOH Z  74 " =    1.410
peak=    3.530 closest distance to " O  BHOH Z 338 " =    2.335
peak=    3.528 closest distance to " O   HOH Z 247 " =    1.464
peak=    3.527 closest distance to " C   ASN A 209 " =    1.181
peak=    3.524 closest distance to " O   HOH Z 345 " =    1.651
peak=    3.512 closest distance to " O   HOH Z 357 " =    2.214
peak=    3.511 closest distance to " O   HOH Z  67 " =    1.994
peak=    3.510 closest distance to " CB  ARG A  79 " =    0.935
peak=    3.510 closest distance to " CG1 ILE A  49 " =    1.620
peak=    3.509 closest distance to " O   HOH Z 427 " =    3.005
peak=    3.507 closest distance to " CZ  PHE A  38 " =    1.200
peak=    3.503 closest distance to " O   HOH Z 174 " =    2.223
peak=    3.498 closest distance to " O   HOH Z 299 " =    4.456
peak=    3.485 closest distance to " CA  ALA A  21 " =    1.247
peak=    3.484 closest distance to " CD2 TYR A 186 " =    0.985
peak=    3.482 closest distance to " CB  GLN A  89 " =    1.191
peak=    3.475 closest distance to " O   HOH Z 193 " =    1.599
peak=    3.472 closest distance to " CB  GLN A 103 " =    0.980
peak=    3.469 closest distance to " CD  LYS A 119 " =    1.888
peak=    3.469 closest distance to " CD1 LEU A 300 " =    1.143
peak=    3.456 closest distance to " CG2 VAL A 197 " =    1.153
peak=    3.455 closest distance to " CA  LEU A 282 " =    1.130
peak=    3.454 closest distance to " OD1 ASN A 217 " =    1.800
peak=    3.452 closest distance to " CE1 HIS A 108 " =    1.066
peak=    3.442 closest distance to " O   HOH Z 420 " =    5.287
peak=    3.442 closest distance to " CD  ARG A 159 " =    0.811
peak=    3.429 closest distance to " CA  ASP A 191 " =    1.038
peak=    3.427 closest distance to " O   HOH Z 418 " =    1.333
peak=    3.420 closest distance to " O   HOH Z 435 " =    2.948
peak=    3.419 closest distance to " O   HOH Z 130 " =    2.215
peak=    3.411 closest distance to " O   HOH Z 185 " =    1.658
peak=    3.407 closest distance to " CB  ASN A  39 " =    0.790
peak=    3.406 closest distance to " CA  ARG A  36 " =    1.040
peak=    3.406 closest distance to " O   HOH Z  21 " =    1.791
peak=    3.398 closest distance to " CZ  PHE A 192 " =    1.104
peak=    3.398 closest distance to " O   HOH Z 365 " =    2.713
peak=    3.396 closest distance to " CA  SER A  87 " =    0.933
peak=    3.395 closest distance to " CG2 ILE A 120 " =    1.152
peak=    3.394 closest distance to " O   HOH Z 414 " =    1.687
peak=    3.390 closest distance to " CA  ASP A 162 " =    1.041
peak=    3.384 closest distance to " O   HOH Z 133 " =    2.478
peak=    3.384 closest distance to " OG1 THR A 294 " =    2.378
peak=    3.382 closest distance to " O   HOH Z  83 " =    1.545
peak=    3.379 closest distance to " N   ASN A  39 " =    1.232
peak=    3.377 closest distance to " OG  SER A 276 " =    1.361
peak=    3.375 closest distance to " O   HOH Z 196 " =    1.099
peak=    3.374 closest distance to " CB  SER A  28 " =    1.054
peak=    3.372 closest distance to " CB  VAL A 265 " =    1.292
peak=    3.371 closest distance to " O   ALA A 158 " =    1.282
peak=    3.365 closest distance to " O   HOH Z 355 " =    1.814
peak=    3.362 closest distance to " O   HOH Z 271 " =    2.684
peak=    3.357 closest distance to " O   HOH Z 272 " =    1.895
peak=    3.357 closest distance to " ND2 ASN A 187 " =    1.463
peak=    3.356 closest distance to " CB  ASN A 285 " =    0.905
peak=    3.356 closest distance to " CZ3 TRP A 266 " =    1.112
peak=    3.355 closest distance to " OE1 GLU A   2 " =    1.755
peak=    3.352 closest distance to " O   HOH Z 147 " =    1.745
peak=    3.348 closest distance to " CA  GLN A  88 " =    1.341
peak=    3.347 closest distance to " O   HOH Z 423 " =    3.066
peak=    3.345 closest distance to " CG ALYS A 290 " =    1.079
peak=    3.342 closest distance to " O   TRP A 274 " =    1.836
peak=    3.339 closest distance to " O   HOH Z 203 " =    1.769
peak=    3.339 closest distance to " CE  LYS A 119 " =    1.084
peak=    3.339 closest distance to " CB  ASN A 110 " =    1.205
peak=    3.336 closest distance to " CA  VAL A  41 " =    0.846
peak=    3.336 closest distance to " CG  GLU A  37 " =    0.914
peak=    3.334 closest distance to " O   HOH Z 199 " =    1.563
peak=    3.325 closest distance to " CB  PHE A 283 " =    0.734
peak=    3.319 closest distance to " O   HOH Z 158 " =    3.198
peak=    3.319 closest distance to " CA  GLY A 267 " =    0.880
peak=    3.319 closest distance to " CB  ALA A 295 " =    1.446
peak=    3.316 closest distance to " CG  GLN A  77 " =    0.928
peak=    3.316 closest distance to " OD1 ASN A  45 " =    1.468
peak=    3.316 closest distance to " O   HOH Z 163 " =    1.533
peak=    3.315 closest distance to " OG  SER A 135 " =    1.346
peak=    3.315 closest distance to " CD  ARG A 195 " =    0.947
peak=    3.309 closest distance to " CA  GLY A 211 " =    1.337
peak=    3.304 closest distance to " O   HOH Z 336 " =    1.826
peak=    3.303 closest distance to " N   SER A 164 " =    0.912
peak=    3.302 closest distance to " CB  SER A  62 " =    0.872
peak=    3.299 closest distance to " CG2 ILE A  20 " =    1.454
peak=    3.297 closest distance to " O   HOH Z 371 " =    3.065
peak=    3.294 closest distance to " CD ALYS A 290 " =    1.048
peak=    3.291 closest distance to " N   CYS A 260 " =    0.827
peak=    3.289 closest distance to " OH  TYR A 116 " =    1.233
peak=    3.289 closest distance to " CA  LYS A 117 " =    1.287
peak=    3.287 closest distance to " O   HOH Z 353 " =    2.674
peak=    3.286 closest distance to " OG  SER A 245 " =    1.530
peak=    3.285 closest distance to " O   HOH Z 313 " =    1.810
peak=    3.285 closest distance to " CD2 LEU A 297 " =    0.780
peak=    3.281 closest distance to " CB  PHE A 204 " =    0.887
peak=    3.279 closest distance to " CA  ALA A 158 " =    1.321
peak=    3.278 closest distance to " CG  GLN A  11 " =    1.311
peak=    3.266 closest distance to " CD1 LEU A 228 " =    1.633
peak=    3.263 closest distance to " CG  ARG A 138 " =    1.319
peak=    3.261 closest distance to " O   HOH Z 126 " =    1.765
peak=    3.258 closest distance to " O   HOH Z 419 " =    1.902
peak=    3.257 closest distance to " NH2 ARG A  79 " =    1.290
peak=    3.253 closest distance to " CG2BVAL A  72 " =    1.848
peak=    3.250 closest distance to " O   HOH Z  54 " =    1.573
peak=    3.250 closest distance to " CA  THR A 246 " =    0.966
peak=    3.249 closest distance to " CB  PHE A 204 " =    0.963
peak=    3.247 closest distance to " O   HOH Z 112 " =    1.774
peak=    3.247 closest distance to " O   HOH Z 421 " =    1.855
peak=    3.242 closest distance to " O   HOH Z 438 " =    3.079
peak=    3.237 closest distance to " CB  ALA A 291 " =    1.209
peak=    3.233 closest distance to " NH2AARG A 275 " =    3.069
peak=    3.230 closest distance to " O   HOH Z 327 " =    1.543
peak=    3.228 closest distance to " O   HOH Z 313 " =    1.678
peak=    3.228 closest distance to " C   ILE A 106 " =    1.885
peak=    3.225 closest distance to " O   HOH Z 145 " =    2.168
peak=    3.222 closest distance to " CB  ASN A 215 " =    1.248
peak=    3.220 closest distance to " CA  ALA A 100 " =    0.976
peak=    3.220 closest distance to " O   HOH Z 299 " =    2.473
peak=    3.219 closest distance to " O   HOH Z 109 " =    2.288
peak=    3.216 closest distance to " CA  GLU A 152 " =    0.948
peak=    3.215 closest distance to " CD  ARG A 269 " =    1.121
peak=    3.211 closest distance to " O   HOH Z  46 " =    1.322
peak=    3.211 closest distance to " CD  ARG A  66 " =    2.489
peak=    3.209 closest distance to " O   HOH Z 227 " =    1.643
peak=    3.209 closest distance to " NH1 ARG A  14 " =    0.986
peak=    3.207 closest distance to " O   HOH Z 117 " =    2.021
peak=    3.203 closest distance to " CA  SER A  32 " =    1.727
peak=    3.199 closest distance to " O   HOH Z 427 " =    3.142
peak=    3.197 closest distance to " CD1 LEU A 101 " =    1.122
peak=    3.197 closest distance to " CB  TYR A 247 " =    0.994
peak=    3.195 closest distance to " OE1 GLN A  11 " =    1.936
peak=    3.194 closest distance to " ND2 ASN A 249 " =    1.979
peak=    3.193 closest distance to " O   HOH Z 411 " =    1.702
peak=    3.192 closest distance to " O   GLY A  91 " =    1.259
peak=    3.192 closest distance to " CG  GLN A  58 " =    2.882
peak=    3.191 closest distance to " CB  LEU A   5 " =    1.290
peak=    3.185 closest distance to " O   HOH Z 130 " =    2.349
peak=    3.174 closest distance to " CD1 ILE A 199 " =    1.138
peak=    3.173 closest distance to " CB  ARG A 219 " =    1.528
peak=    3.172 closest distance to " O   HOH Z   9 " =    2.307
peak=    3.167 closest distance to " CA  THR A 264 " =    0.771
peak=    3.165 closest distance to " N   GLU A  44 " =    2.208
peak=    3.157 closest distance to " O   HOH Z 125 " =    4.041
peak=    3.156 closest distance to " O   GLN A  88 " =    1.617
peak=    3.154 closest distance to " N   PHE A 130 " =    1.208
peak=    3.151 closest distance to " CG2 THR A 220 " =    0.769
peak=    3.149 closest distance to " N   ASP A 162 " =    1.374
peak=    3.149 closest distance to " CB  ALA A 248 " =    1.415
peak=    3.147 closest distance to " O   HOH Z 176 " =    1.569
peak=    3.144 closest distance to " CB  MET A 105 " =    1.271
peak=    3.142 closest distance to " CB  ALA A  43 " =    0.854
peak=    3.142 closest distance to " CA  ARG A 139 " =    1.316
peak=    3.141 closest distance to " CA  ASP A 140 " =    1.264
peak=    3.137 closest distance to " O   HOH Z  90 " =    3.519
peak=    3.134 closest distance to " O   HOH Z 294 " =    1.533
peak=    3.129 closest distance to " O   HOH Z 421 " =    2.540
peak=    3.129 closest distance to " CB  PRO A  90 " =    1.200
peak=    3.124 closest distance to " O   HOH Z 191 " =    4.166
peak=    3.121 closest distance to " CB  ALA A   1 " =    5.077
peak=    3.121 closest distance to " O   HOH Z 301 " =    1.841
peak=    3.120 closest distance to " CB  LEU A 228 " =    1.347
peak=    3.115 closest distance to " OG1 THR A 279 " =    1.782
peak=    3.108 closest distance to " CZ3 TRP A  92 " =    1.252
peak=    3.105 closest distance to " O   HOH Z 393 " =    3.496
peak=    3.101 closest distance to " CB  SER A 273 " =    0.857
peak=    3.091 closest distance to " CB  TYR A  30 " =    1.088
peak=    3.090 closest distance to " O   HOH Z 150 " =    1.840
peak=    3.085 closest distance to " N   TYR A 247 " =    1.280
peak=    3.081 closest distance to " OG1 THR A 294 " =    1.600
peak=    3.079 closest distance to " O   HOH Z 156 " =    2.513
peak=    3.077 closest distance to " CB  SER A  97 " =    1.130
peak=    3.074 closest distance to " ND2 ASN A 249 " =    0.885
peak=    3.065 closest distance to " CG  ARG A 219 " =    1.161
peak=    3.059 closest distance to " O   HOH Z 420 " =    1.851
peak=    3.059 closest distance to " O   HOH Z 344 " =    3.064
peak=    3.058 closest distance to " O   HOH Z 357 " =    2.597
peak=    3.041 closest distance to " O   HOH Z 188 " =    2.492
peak=    3.026 closest distance to " O   HOH Z 368 " =    1.811
peak=    3.012 closest distance to " CB  LYS A 117 " =    1.107

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 208         
Filter by distance & map next to the model:
   mapped sites are within: 0.732 - 5.521
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 208 from: 208
   mapped sites are within: 0.732 - 5.521

peak=   -5.357 closest distance to " CG2 VAL A 230 " =    0.839
peak=   -4.791 closest distance to " CD  GLN A  58 " =    0.975
peak=   -4.647 closest distance to " O   HOH Z 166 " =    1.510
peak=   -4.375 closest distance to " CB  PRO A 243 " =    2.775
peak=   -4.363 closest distance to " O   HOH Z 411 " =    5.521
peak=   -4.336 closest distance to " CG1 VAL A 250 " =    2.689
peak=   -4.333 closest distance to " CD  ARG A  14 " =    3.352
peak=   -4.243 closest distance to " O   VAL A  67 " =    2.818
peak=   -4.109 closest distance to " CD1 PHE A  59 " =    2.059
peak=   -4.087 closest distance to " CA  ASP A 298 " =    1.053
peak=   -4.078 closest distance to " OG  SER A  97 " =    2.385
peak=   -4.034 closest distance to " CD  ARG A 156 " =    2.141
peak=   -4.000 closest distance to " CD1 LEU A 101 " =    2.466
peak=   -4.000 closest distance to " O   HOH Z 231 " =    2.185
peak=   -3.981 closest distance to " CH2 TRP A 179 " =    1.232
peak=   -3.953 closest distance to " OXT GLY A 302 " =    2.820
peak=   -3.948 closest distance to " CG1 VAL A 296 " =    1.068
peak=   -3.936 closest distance to " O   HOH Z  10 " =    1.622
peak=   -3.927 closest distance to " O   HOH Z  13 " =    1.731
peak=   -3.922 closest distance to " CG2 ILE A  49 " =    2.818
peak=   -3.895 closest distance to " CG  ARG A 269 " =    2.311
peak=   -3.879 closest distance to " O   PRO A 198 " =    1.278
peak=   -3.856 closest distance to " OD1 ASN A 249 " =    2.489
peak=   -3.840 closest distance to " O   HOH Z  37 " =    1.874
peak=   -3.836 closest distance to " CB  ALA A 248 " =    2.172
peak=   -3.809 closest distance to " O   HOH Z 196 " =    2.585
peak=   -3.809 closest distance to " CA  SER A 276 " =    1.534
peak=   -3.801 closest distance to " O   HOH Z 351 " =    1.550
peak=   -3.782 closest distance to " CG1 VAL A 112 " =    2.665
peak=   -3.775 closest distance to " CB  PHE A 208 " =    2.402
peak=   -3.773 closest distance to " O   SER A 271 " =    2.136
peak=   -3.766 closest distance to " O   PRO A 163 " =    2.205
peak=   -3.761 closest distance to " C   HIS A 108 " =    1.234
peak=   -3.748 closest distance to " O   HOH Z 264 " =    1.728
peak=   -3.741 closest distance to " CE3 TRP A 150 " =    2.425
peak=   -3.716 closest distance to " O   HOH Z 136 " =    2.510
peak=   -3.713 closest distance to " O   HOH Z 283 " =    2.233
peak=   -3.693 closest distance to " O   HOH Z 407 " =    3.051
peak=   -3.680 closest distance to " O   HOH Z 177 " =    1.845
peak=   -3.678 closest distance to " OD1 ASN A 148 " =    1.501
peak=   -3.675 closest distance to " CZ  TYR A 169 " =    1.801
peak=   -3.657 closest distance to " O   VAL A  67 " =    2.872
peak=   -3.656 closest distance to " ND2 ASN A  45 " =    2.240
peak=   -3.654 closest distance to " O   HOH Z 150 " =    1.347
peak=   -3.649 closest distance to " O   HOH Z 394 " =    1.680
peak=   -3.646 closest distance to " ND2BASN A 224 " =    1.880
peak=   -3.645 closest distance to " O   HOH Z 166 " =    1.536
peak=   -3.636 closest distance to " O   HOH Z 426 " =    1.699
peak=   -3.635 closest distance to " CD2 TYR A 293 " =    1.961
peak=   -3.633 closest distance to " O   HOH Z 210 " =    0.732
peak=   -3.630 closest distance to " O   HOH Z 290 " =    1.166
peak=   -3.612 closest distance to " CB  ALA A 161 " =    2.609
peak=   -3.604 closest distance to " CD2 LEU A 300 " =    2.727
peak=   -3.594 closest distance to " O   HOH Z 193 " =    1.410
peak=   -3.588 closest distance to " OE1 GLN A 223 " =    2.268
peak=   -3.555 closest distance to " O   HOH Z 171 " =    2.296
peak=   -3.544 closest distance to " CE2 PHE A  61 " =    2.559
peak=   -3.526 closest distance to " NH2 ARG A  79 " =    2.109
peak=   -3.522 closest distance to " CG  GLU A 277 " =    1.130
peak=   -3.522 closest distance to " CE2 TYR A  30 " =    2.696
peak=   -3.505 closest distance to " CB  PHE A 192 " =    2.084
peak=   -3.504 closest distance to " O   HOH Z 301 " =    2.534
peak=   -3.503 closest distance to " O   HOH Z 374 " =    1.999
peak=   -3.502 closest distance to " CD  GLN A 223 " =    1.290
peak=   -3.493 closest distance to " CD  ARG A 139 " =    1.610
peak=   -3.492 closest distance to " O   HOH Z  92 " =    1.632
peak=   -3.487 closest distance to " ND2 ASN A  45 " =    1.206
peak=   -3.487 closest distance to " O   HOH Z 285 " =    1.666
peak=   -3.486 closest distance to " O   HOH Z 252 " =    3.534
peak=   -3.483 closest distance to " CG2 ILE A 263 " =    2.355
peak=   -3.479 closest distance to " CG2 VAL A 189 " =    2.108
peak=   -3.473 closest distance to " CB  PRO A 163 " =    2.531
peak=   -3.472 closest distance to " N   ALA A 226 " =    2.064
peak=   -3.471 closest distance to " OG BSER A 134 " =    1.340
peak=   -3.471 closest distance to " O   HOH Z 200 " =    1.300
peak=   -3.470 closest distance to " CG  ASP A 231 " =    0.841
peak=   -3.467 closest distance to " C   LEU A 143 " =    1.112
peak=   -3.467 closest distance to " CG  GLU A  53 " =    1.619
peak=   -3.464 closest distance to " CA  GLY A 203 " =    2.430
peak=   -3.463 closest distance to " O   HOH Z  56 " =    2.136
peak=   -3.462 closest distance to " O   HOH Z 234 " =    4.412
peak=   -3.461 closest distance to " OD2 ASP A 171 " =    2.277
peak=   -3.458 closest distance to " O   ALA A  34 " =    2.546
peak=   -3.458 closest distance to " O   GLY A  17 " =    1.156
peak=   -3.454 closest distance to " O   HOH Z 174 " =    2.033
peak=   -3.449 closest distance to " OG BSER A 210 " =    1.358
peak=   -3.447 closest distance to " O   HOH Z 120 " =    0.771
peak=   -3.443 closest distance to " OD2 ASP A 298 " =    0.884
peak=   -3.443 closest distance to " O   HOH Z 185 " =    2.496
peak=   -3.440 closest distance to " O   HOH Z 431 " =    2.466
peak=   -3.436 closest distance to " OE1 GLN A  88 " =    0.852
peak=   -3.435 closest distance to " O   SER A 276 " =    1.613
peak=   -3.429 closest distance to " O   ARG A  24 " =    2.159
peak=   -3.429 closest distance to " O   HOH Z 109 " =    3.615
peak=   -3.425 closest distance to " CA  GLY A 133 " =    2.368
peak=   -3.424 closest distance to " N   ALA A 242 " =    1.944
peak=   -3.422 closest distance to " CG  ASP A  50 " =    2.229
peak=   -3.420 closest distance to " CB  ALA A  10 " =    2.211
peak=   -3.416 closest distance to " CG2 THR A 182 " =    2.400
peak=   -3.415 closest distance to " O   VAL A 189 " =    2.630
peak=   -3.413 closest distance to " O   HOH Z 216 " =    1.239
peak=   -3.413 closest distance to " O   GLY A  75 " =    2.053
peak=   -3.413 closest distance to " CB  VAL A 230 " =    1.035
peak=   -3.401 closest distance to " N   SER A   3 " =    2.355
peak=   -3.395 closest distance to " O   HOH Z  78 " =    1.781
peak=   -3.394 closest distance to " CB  ALA A 291 " =    2.187
peak=   -3.389 closest distance to " CG1 VAL A 112 " =    2.659
peak=   -3.386 closest distance to " O   HOH Z 154 " =    1.400
peak=   -3.384 closest distance to " O   HOH Z 165 " =    1.903
peak=   -3.380 closest distance to " CG  MET A 105 " =    0.920
peak=   -3.375 closest distance to " OG1 THR A  82 " =    1.414
peak=   -3.374 closest distance to " CA  SER A  62 " =    2.530
peak=   -3.370 closest distance to " C   ALA A 158 " =    1.337
peak=   -3.362 closest distance to " CG  LEU A  83 " =    2.030
peak=   -3.362 closest distance to " CD1 ILE A 151 " =    2.389
peak=   -3.361 closest distance to " ND2 ASN A 187 " =    1.643
peak=   -3.358 closest distance to " O   HOH Z 377 " =    2.078
peak=   -3.354 closest distance to " OH  TYR A 247 " =    2.010
peak=   -3.349 closest distance to " O   HOH Z 340 " =    1.643
peak=   -3.347 closest distance to " CG2 THR A   4 " =    1.869
peak=   -3.343 closest distance to " CD  GLN A 223 " =    0.975
peak=   -3.342 closest distance to " CD2 LEU A 167 " =    1.785
peak=   -3.332 closest distance to " CG2 VAL A 112 " =    2.473
peak=   -3.331 closest distance to " O   SER A 210 " =    1.753
peak=   -3.331 closest distance to " O   HOH Z 131 " =    4.077
peak=   -3.330 closest distance to " O   HOH Z 231 " =    2.231
peak=   -3.330 closest distance to " CB  SER A 210 " =    1.126
peak=   -3.329 closest distance to " O   HOH Z  60 " =    2.253
peak=   -3.326 closest distance to " CA  TYR A  68 " =    3.090
peak=   -3.310 closest distance to " O   HOH Z  19 " =    2.398
peak=   -3.308 closest distance to " CD1 LEU A  25 " =    2.477
peak=   -3.295 closest distance to " CB  ASP A 132 " =    2.305
peak=   -3.292 closest distance to " CA  LYS A 166 " =    2.189
peak=   -3.291 closest distance to " NH2 ARG A  36 " =    2.450
peak=   -3.290 closest distance to " O   ALA A   1 " =    1.776
peak=   -3.289 closest distance to " O   HOH Z 275 " =    1.495
peak=   -3.286 closest distance to " C   LYS A  76 " =    1.649
peak=   -3.284 closest distance to " C   SER A 206 " =    1.474
peak=   -3.279 closest distance to " OE2 GLU A 277 " =    2.910
peak=   -3.277 closest distance to " O   HOH Z 236 " =    1.734
peak=   -3.273 closest distance to " O   HOH Z 396 " =    2.024
peak=   -3.264 closest distance to " O   PHE A 218 " =    1.476
peak=   -3.263 closest distance to " O   HOH Z 384 " =    1.949
peak=   -3.262 closest distance to " NE  ARG A  66 " =    4.433
peak=   -3.262 closest distance to " O   HOH Z 156 " =    3.590
peak=   -3.261 closest distance to " O   HOH Z 120 " =    2.168
peak=   -3.261 closest distance to " O   HOH Z  90 " =    3.531
peak=   -3.260 closest distance to " O   HOH Z  52 " =    1.919
peak=   -3.260 closest distance to " O   HOH Z   6 " =    1.827
peak=   -3.257 closest distance to " O   HOH Z 113 " =    2.416
peak=   -3.257 closest distance to " O   GLY A  80 " =    2.705
peak=   -3.256 closest distance to " O   HOH Z 259 " =    1.727
peak=   -3.254 closest distance to " CA  ASN A 110 " =    1.100
peak=   -3.254 closest distance to " OG BSER A 134 " =    1.931
peak=   -3.253 closest distance to " CG1 VAL A  78 " =    2.477
peak=   -3.249 closest distance to " CE3 TRP A 274 " =    2.550
peak=   -3.246 closest distance to " CB  ALA A  43 " =    2.535
peak=   -3.244 closest distance to " O   SER A  95 " =    1.876
peak=   -3.244 closest distance to " CZ  ARG A  79 " =    1.769
peak=   -3.244 closest distance to " CG1BVAL A  72 " =    5.453
peak=   -3.233 closest distance to " OD1 ASN A 173 " =    1.447
peak=   -3.231 closest distance to " CD1 ILE A 109 " =    2.642
peak=   -3.227 closest distance to " CD1 TYR A 247 " =    2.397
peak=   -3.226 closest distance to " NH2 ARG A  66 " =    1.609
peak=   -3.226 closest distance to " CA  VAL A 197 " =    0.976
peak=   -3.218 closest distance to " O   HOH Z 397 " =    1.135
peak=   -3.217 closest distance to " CB  TRP A  85 " =    2.612
peak=   -3.217 closest distance to " CD  GLN A  88 " =    0.838
peak=   -3.215 closest distance to " O   HOH Z 395 " =    1.391
peak=   -3.214 closest distance to " O   ASP A 107 " =    1.881
peak=   -3.204 closest distance to " O   HOH Z 435 " =    2.374
peak=   -3.204 closest distance to " CA  GLY A 241 " =    3.281
peak=   -3.201 closest distance to " C   THR A 279 " =    1.151
peak=   -3.199 closest distance to " CD2 PHE A 225 " =    1.202
peak=   -3.196 closest distance to " O   HOH Z 109 " =    1.227
peak=   -3.196 closest distance to " CE1 TYR A 247 " =    2.628
peak=   -3.191 closest distance to " N   LYS A 289 " =    1.636
peak=   -3.188 closest distance to " CG  GLN A  11 " =    1.494
peak=   -3.186 closest distance to " O   HOH Z 126 " =    1.953
peak=   -3.186 closest distance to " O   HOH Z  40 " =    2.560
peak=   -3.180 closest distance to " O   HOH Z 177 " =    1.400
peak=   -3.179 closest distance to " C   VAL A 265 " =    0.912
peak=   -3.179 closest distance to " CD2 PHE A  61 " =    2.078
peak=   -3.176 closest distance to " O   HOH Z  77 " =    1.953
peak=   -3.173 closest distance to " O   HOH Z 378 " =    1.515
peak=   -3.170 closest distance to " O   HOH Z  44 " =    2.137
peak=   -3.169 closest distance to " O   ALA A  10 " =    1.666
peak=   -3.167 closest distance to " O   ASN A 187 " =    1.680
peak=   -3.163 closest distance to " CG1 VAL A 112 " =    2.758
peak=   -3.158 closest distance to " O   GLN A  77 " =    1.986
peak=   -3.156 closest distance to " CD1 ILE A 263 " =    2.055
peak=   -3.148 closest distance to " O   HOH Z 110 " =    1.515
peak=   -3.142 closest distance to " C   MET A 188 " =    1.545
peak=   -3.141 closest distance to " CG  LEU A   5 " =    1.584
peak=   -3.138 closest distance to " O   HOH Z  70 " =    2.172
peak=   -3.137 closest distance to " CA  ASN A 127 " =    1.137
peak=   -3.127 closest distance to " CG  TRP A 266 " =    1.757
peak=   -3.124 closest distance to " O   HOH Z 353 " =    2.276
peak=   -3.117 closest distance to " O   HOH Z 423 " =    2.311
peak=   -3.103 closest distance to " O   HOH Z 377 " =    1.418
peak=   -3.097 closest distance to " O   HOH Z 139 " =    3.419
peak=   -3.096 closest distance to " N   ALA A  43 " =    2.648
peak=   -3.089 closest distance to " O   HOH Z 313 " =    1.279
peak=   -3.069 closest distance to " O   THR A  18 " =    1.495
peak=   -3.064 closest distance to " CB  ASN A  45 " =    2.097
peak=   -3.062 closest distance to " CB  ASP A 132 " =    2.401
peak=   -3.061 closest distance to " CD1 LEU A 167 " =    2.046
peak=   -3.059 closest distance to " O   HOH Z 265 " =    1.899

================= 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    :  0.4943 0.4808   6.292642e+00   6.277340e+00
   1_bss:  0.4875 0.4727   6.286102e+00   6.272976e+00
   1_xyz:  0.4118 0.4241   6.200328e+00   6.211684e+00
   1_adp:  0.3671 0.4146   6.126841e+00   6.193918e+00
   1_occ:  0.3663 0.4140   6.125996e+00   6.194508e+00
   2_bss:  0.3640 0.4087   6.127886e+00   6.194785e+00
   2_xyz:  0.2871 0.3482   5.941640e+00   6.078737e+00
   2_adp:  0.2680 0.3268   5.894314e+00   6.034104e+00
   2_occ:  0.2678 0.3270   5.893769e+00   6.034675e+00
   3_bss:  0.2667 0.3262   5.894456e+00   6.034630e+00
   3_xyz:  0.2139 0.2542   5.688552e+00   5.837829e+00
   3_adp:  0.2010 0.2400   5.640369e+00   5.793149e+00
   3_occ:  0.2008 0.2403   5.640448e+00   5.794308e+00
   4_bss:  0.2005 0.2394   5.639203e+00   5.792459e+00
   4_xyz:  0.1468 0.1878   5.360178e+00   5.559032e+00
   4_adp:  0.1354 0.1801   5.298758e+00   5.515867e+00
   4_occ:  0.1352 0.1802   5.298096e+00   5.515469e+00
   5_bss:  0.1353 0.1806   5.299106e+00   5.515498e+00
   5_xyz:  0.1217 0.1666   5.216592e+00   5.446765e+00
   5_adp:  0.1187 0.1663   5.201534e+00   5.439843e+00
   5_occ:  0.1186 0.1664   5.201776e+00   5.440453e+00
   5_bss:  0.1185 0.1662   5.201509e+00   5.440289e+00
------------------------------------------------------------------------
 stage     k_sol   b_sol     b11     b22     b33     b12     b13     b23
   0    :  0.000   0.000   0.000   0.000   0.000   0.000   0.000   0.000
   1_bss:  0.300  20.000   5.837  11.057   9.468   0.000   0.000   0.000
   1_xyz:  0.300  20.000   5.837  11.057   9.468   0.000   0.000   0.000
   1_adp:  0.300  20.000   5.837  11.057   9.468   0.000   0.000   0.000
   1_occ:  0.300  20.000   5.837  11.057   9.468   0.000   0.000   0.000
   2_bss:  0.318  50.001   2.626   7.008   5.739   0.000   0.000   0.000
   2_xyz:  0.318  50.001   2.626   7.008   5.739   0.000   0.000   0.000
   2_adp:  0.318  50.001   2.626   7.008   5.739   0.000   0.000   0.000
   2_occ:  0.318  50.001   2.626   7.008   5.739   0.000   0.000   0.000
   3_bss:  0.306  50.001   1.815   4.439   3.735   0.000   0.000   0.000
   3_xyz:  0.306  50.001   1.815   4.439   3.735   0.000   0.000   0.000
   3_adp:  0.306  50.001   1.815   4.439   3.735   0.000   0.000   0.000
   3_occ:  0.306  50.001   1.815   4.439   3.735   0.000   0.000   0.000
   4_bss:  0.327  64.829   1.070   2.970   3.019   0.000   0.000   0.000
   4_xyz:  0.327  64.829   1.070   2.970   3.019   0.000   0.000   0.000
   4_adp:  0.327  64.829   1.070   2.970   3.019   0.000   0.000   0.000
   4_occ:  0.327  64.829   1.070   2.970   3.019   0.000   0.000   0.000
   5_bss:  0.333  64.829   0.934   2.187   2.850   0.000   0.000   0.000
   5_xyz:  0.333  64.829   0.934   2.187   2.850   0.000   0.000   0.000
   5_adp:  0.333  64.829   0.934   2.187   2.850   0.000   0.000   0.000
   5_occ:  0.333  64.829   0.934   2.187   2.850   0.000   0.000   0.000
   5_bss:  0.325  63.543  -0.941   0.045   0.896   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  58.480 0.4135  0.4719    70856.717
   1_bss:  58.362 0.4140  0.6105    70142.683
   1_xyz:  48.932 0.5328  0.7658    52197.302
   1_adp:  46.165 0.5676  0.8752    48653.049
   1_occ:  46.166 0.5676  0.8744    48703.039
   2_bss:  45.912 0.5708  0.7777    48514.725
   2_xyz:  37.936 0.6664  0.8994    33910.203
   2_adp:  35.113 0.7001  0.9172    29967.948
   2_occ:  35.122 0.7000  0.9164    29961.735
   3_bss:  34.977 0.7018  0.8638    29884.670
   3_xyz:  25.804 0.8033  0.9533    17319.237
   3_adp:  24.011 0.8226  0.9660    15542.290
   3_occ:  24.041 0.8223  0.9655    15575.895
   4_bss:  23.942 0.8233  0.9340    15441.463
   4_xyz:  17.888 0.8812  0.9721     9069.873
   4_adp:  16.860 0.8907  0.9701     8376.726
   4_occ:  16.847 0.8908  0.9702     8375.677
   5_bss:  16.862 0.8908  0.9580     8410.656
   5_xyz:  15.335 0.9041  0.9635     7222.194
   5_adp:  15.158 0.9057  0.9562     7102.430
   5_occ:  15.169 0.9056  0.9561     7109.224
   5_bss:  15.163 0.9056  0.9615     7103.658
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.092   5.4464e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.092   5.4464e+01
   1_xyz:   1.695  0.013  0.107 18.118  0.007  4.125   1.4256e-01
   1_adp:   1.695  0.013  0.107 18.118  0.007  4.125   1.4256e-01
   1_occ:   1.695  0.013  0.107 18.118  0.007  4.125   1.4256e-01
   2_bss:   1.695  0.013  0.107 18.118  0.007  4.125   1.4256e-01
   2_xyz:   1.328  0.010  0.086 16.327  0.005  4.111   9.6229e-02
   2_adp:   1.328  0.010  0.086 16.327  0.005  4.111   9.6229e-02
   2_occ:   1.328  0.010  0.086 16.327  0.005  4.111   9.6229e-02
   3_bss:   1.328  0.010  0.086 16.327  0.005  4.111   9.6229e-02
   3_xyz:   1.059  0.007  0.074 15.649  0.004  4.132   6.5105e-02
   3_adp:   1.059  0.007  0.074 15.649  0.004  4.132   6.5105e-02
   3_occ:   1.059  0.007  0.074 15.649  0.004  4.132   6.5105e-02
   4_bss:   1.059  0.007  0.074 15.649  0.004  4.132   6.5105e-02
   4_xyz:   1.227  0.011  0.091 15.728  0.004  4.115   8.9720e-02
   4_adp:   1.227  0.011  0.091 15.728  0.004  4.115   8.9720e-02
   4_occ:   1.227  0.011  0.091 15.728  0.004  4.115   8.9720e-02
   5_bss:   1.227  0.011  0.091 15.728  0.004  4.115   8.9720e-02
   5_xyz:   1.232  0.012  0.097 15.792  0.004  4.125   9.1255e-02
   5_adp:   1.232  0.012  0.097 15.792  0.004  4.125   9.1255e-02
   5_occ:   1.232  0.012  0.097 15.792  0.004  4.125   9.1255e-02
   5_bss:   1.232  0.012  0.097 15.792  0.004  4.125   9.1255e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0612e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0612e+00
   1_xyz:  15.325  0.162  0.465 89.090  0.047  2.262   1.0438e-01
   1_adp:  15.325  0.162  0.465 89.090  0.047  2.262   1.0438e-01
   1_occ:  15.325  0.162  0.465 89.090  0.047  2.262   1.0438e-01
   2_bss:  15.325  0.162  0.465 89.090  0.047  2.262   1.0438e-01
   2_xyz:   9.320  0.090  0.324 84.748  0.022  2.060   6.4797e-02
   2_adp:   9.320  0.090  0.324 84.748  0.022  2.060   6.4797e-02
   2_occ:   9.320  0.090  0.324 84.748  0.022  2.060   6.4797e-02
   3_bss:   9.320  0.090  0.324 84.748  0.022  2.060   6.4797e-02
   3_xyz:   7.462  0.058  0.269 87.964  0.051  2.175   6.0485e-02
   3_adp:   7.462  0.058  0.269 87.964  0.051  2.175   6.0485e-02
   3_occ:   7.462  0.058  0.269 87.964  0.051  2.175   6.0485e-02
   4_bss:   7.462  0.058  0.269 87.964  0.051  2.175   6.0485e-02
   4_xyz:   8.948  0.071  0.438 82.984  0.032  2.102   6.6020e-02
   4_adp:   8.948  0.071  0.438 82.984  0.032  2.102   6.6020e-02
   4_occ:   8.948  0.071  0.438 82.984  0.032  2.102   6.6020e-02
   5_bss:   8.948  0.071  0.438 82.984  0.032  2.102   6.6020e-02
   5_xyz:   8.614  0.053  0.582 82.565  0.034  2.251   6.5385e-02
   5_adp:   8.614  0.053  0.582 82.565  0.034  2.251   6.5385e-02
   5_occ:   8.614  0.053  0.582 82.565  0.034  2.251   6.5385e-02
   5_bss:   8.614  0.053  0.582 82.565  0.034  2.251   6.5385e-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: 113.18   0.00  15.07  87.23   0.00  12.68 113.18   0.00  28.07
   1_occ: 113.18   0.00  15.07  87.23   0.00  12.68 113.18   0.00  28.07
   2_bss: 113.18   0.00  15.07  87.23   0.00  12.68 113.18   0.00  28.07
   2_xyz: 113.18   0.00  15.07  87.23   0.00  12.68 113.18   0.00  28.07
   2_adp: 108.46   0.00  13.58  77.86   0.00  10.46 108.46   0.00  30.62
   2_occ: 108.46   0.00  13.58  77.86   0.00  10.46 108.46   0.00  30.62
   3_bss: 108.46   0.00  13.58  77.86   0.00  10.46 108.46   0.00  30.62
   3_xyz: 108.46   0.00  13.58  77.86   0.00  10.46 108.46   0.00  30.62
   3_adp: 103.22   0.00  13.51  67.76   0.00   9.79 103.22   1.00  33.75
   3_occ: 103.22   0.00  13.51  67.76   0.00   9.79 103.22   1.00  33.75
   4_bss: 103.22   0.00  13.51  67.76   0.00   9.79 103.22   1.00  33.75
   4_xyz: 103.22   0.00  13.51  67.76   0.00   9.79 103.22   1.00  33.75
   4_adp:  98.27   0.00  13.56  71.29   0.00   9.33  98.27   1.14  36.59
   4_occ:  98.27   0.00  13.56  71.29   0.00   9.33  98.27   1.14  36.59
   5_bss:  98.27   0.00  13.56  71.29   0.00   9.33  98.27   1.14  36.59
   5_xyz:  98.27   0.00  13.56  71.29   0.00   9.33  98.27   1.14  36.59
   5_adp:  93.41   0.00  13.57  77.34   0.00   9.13  93.41   1.15  37.72
   5_occ:  93.41   0.00  13.57  77.34   0.00   9.13  93.41   1.15  37.72
   5_bss:  95.56   2.15  15.71  79.49   2.15  11.28  95.56   3.29  39.86
------------------------------------------------------------------------
 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:    1.216    0.027    0.409
   1_adp:    1.216    0.027    0.409
   1_occ:    1.216    0.027    0.409
   2_bss:    1.216    0.027    0.409
   2_xyz:    1.736    0.068    0.597
   2_adp:    1.736    0.068    0.597
   2_occ:    1.736    0.068    0.597
   3_bss:    1.736    0.068    0.597
   3_xyz:    1.813    0.055    0.673
   3_adp:    1.813    0.055    0.673
   3_occ:    1.813    0.055    0.673
   4_bss:    1.813    0.055    0.673
   4_xyz:    1.893    0.028    0.785
   4_adp:    1.893    0.028    0.785
   4_occ:    1.893    0.028    0.785
   5_bss:    1.893    0.028    0.785
   5_xyz:    1.878    0.068    0.812
   5_adp:    1.878    0.068    0.812
   5_occ:    1.878    0.068    0.812
   5_bss:    1.878    0.068    0.812
------------------------------------------------------------------------

CPU time actual refinement: 334.41


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_712/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_712/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_712/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_712/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_712/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 334.25 
  Macro-tasks:
    bulk solvent and scale       = 41.38  
    individual site refinement   = 135.78 
    weights calculation          = 32.04  
    collect and process          = 6.38   
    model show statistics        = 0.14   
    TOTAL for macro-tasks        = 215.72 
  Micro-tasks:
    mask                            = 2.35   
    f_calc                          = 102.97 
    alpha_beta                      = 8.20   
    target                          = 1.12   
    gradients_wrt_atomic_parameters = 113.54 
    fmodel                         = 7.14   
    r_factors                      = 0.24   
    phase_errors                   = 10.49  
    foms                           = 0.22   
    TOTAL for micro-tasks          = 246.27 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.692 micro seconds
Total CPU time: 5.79 minutes
from_scatterers_fft:    658 calls, 102.68 s
gradients_fft:          602 calls, 100.17 s

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

# Date 2008-01-16 Time 02:14:43 PST -0800 (1200478483.80 s)
Start R-work = 0.4943, R-free = 0.4808 (no bulk solvent and anisotropic scale)
Final R-work = 0.1353, R-free = 0.1810 (no bulk solvent and anisotropic scale)

Start R-work = 0.4875, R-free = 0.4727
Final R-work = 0.1185, R-free = 0.1662