# Date 2008-01-16 Time 01:57:53 PST -0800 (1200477473.22 s)
#phil __OFF__

Command line arguments: "../636.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 23999
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 636

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 46.2261, 88.1178, 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: 3.28, per 1000 atoms: 1.16


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.2261, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0735 1.9729
Completeness in resolution range: 0.942141
Completeness with d_max=infinity: 0.93934

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0735
                             d_min =   1.9729

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 46.2261, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0735 1.9729
Completeness in resolution range: 0.942141
Completeness with d_max=infinity: 0.93934

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0740 -  4.2223 [2185/2210]  1965   220  10.1%
  bin  2:  4.2223 -  3.3636 [2094/2114]  1885   209  10.0%
  bin  3:  3.3636 -  2.9420 [2083/2102]  1878   205   9.8%
  bin  4:  2.9420 -  2.6746 [2034/2064]  1825   209  10.3%
  bin  5:  2.6746 -  2.4838 [2054/2073]  1853   201   9.8%
  bin  6:  2.4838 -  2.3380 [2020/2045]  1818   202  10.0%
  bin  7:  2.3380 -  2.2213 [2017/2045]  1812   205  10.2%
  bin  8:  2.2213 -  2.1248 [2018/2054]  1813   205  10.2%
  bin  9:  2.1248 -  2.0432 [2010/2052]  1816   194   9.7%
  bin 10:  2.0432 -  1.9729 [1074/2033]   965   109  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_636/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.68 -     2.32: 21
        2.32 -     2.97: 1720
        2.97 -     3.61: 4553
        3.61 -     4.26: 9171
        4.26 -     4.90: 12788
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.675 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.721 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.770 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " O   HOH Z  50 " - " O   HOH Z  95 "  1.952 3.040 -x+1,y+1/2,-z+1/2
  ... (remaining 28248 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_636/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_636/model_refine_001.geo

CPU time processing inputs: 9.14


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 46.22605 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.97 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4878   r_free= 0.4709   ksol= 0.00   Bsol= 0.00   scale= 0.786    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.289343                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0740 -  4.7096 0.99   1420  156 0.4076 0.3814      6.6223      6.5815|
|  2:  4.7096 -  3.7572 0.99   1369  155 0.4060 0.4063      6.7967      6.8023|
|  3:  3.7572 -  3.2879 0.99   1331  145 0.4399 0.3807      6.6773      6.6177|
|  4:  3.2879 -  2.9899 0.99   1336  150 0.4860 0.4637      6.5487      6.4931|
|  5:  2.9899 -  2.7770 0.99   1309  150 0.5205 0.4788      6.3646      6.3819|
|  6:  2.7770 -  2.6142 0.99   1324  143 0.5247 0.5393      6.2834      6.2109|
|  7:  2.6142 -  2.4838 0.99   1317  145 0.5265 0.5038      6.2386      6.2035|
|  8:  2.4838 -  2.3761 0.98   1292  146 0.5377 0.5076      6.1885      6.1774|
|  9:  2.3761 -  2.2850 0.98   1307  140 0.5246 0.5444      6.1238      6.1859|
| 10:  2.2850 -  2.2064 1.00   1282  149 0.5376 0.5169       6.104      6.0864|
| 11:  2.2064 -  2.1376 0.98   1306  145 0.5205 0.5270      6.0291      6.0487|
| 12:  2.1376 -  2.0767 0.98   1274  142 0.5338 0.5315      5.9631      5.9706|
| 13:  2.0767 -  2.0221 0.96   1265  139 0.5333 0.5054      5.8825      5.8033|
| 14:  2.0221 -  1.9729 0.38    498   54 0.5418 0.5101      5.8882      5.8317|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0740 -  4.7096  1420   156  0.71  33.81   0.79     0.75      70129.77|
|  2:  4.7096 -  3.7572  1369   155  0.72  33.61   0.86     0.80     100669.92|
|  3:  3.7572 -  3.2879  1331   145  0.61  42.67   0.84     0.74     108168.99|
|  4:  3.2879 -  2.9899  1336   150  0.52  49.98   0.77     0.62      97598.89|
|  5:  2.9899 -  2.7770  1309   150  0.41  58.93   0.74     0.50      81996.12|
|  6:  2.7770 -  2.6142  1324   143  0.37  62.31   0.70     0.43      74066.64|
|  7:  2.6142 -  2.4838  1317   145  0.31  67.10   0.73     0.36      71421.29|
|  8:  2.4838 -  2.3761  1292   146  0.29  68.08   0.71     0.35      64713.12|
|  9:  2.3761 -  2.2850  1307   140  0.29  68.30   0.72     0.35      59199.44|
| 10:  2.2850 -  2.2064  1282   149  0.31  66.63   0.73     0.37      50832.14|
| 11:  2.2064 -  2.1376  1306   145  0.29  68.08   0.75     0.37      49550.01|
| 12:  2.1376 -  2.0767  1274   142  0.29  68.47   0.74     0.37      44620.75|
| 13:  2.0767 -  2.0221  1265   139  0.28  69.25   0.72     0.36      39863.59|
| 14:  2.0221 -  1.9729   498    54  0.33  65.63   0.73     0.37      32047.46|
|alpha:            min =        0.35 max =            0.80 mean =         0.49|
|beta:             min =    32047.46 max =       108168.99 mean =     69502.07|
|figures of merit: min =        0.00 max =            1.00 mean =         0.42|
|phase err.(work): min =        0.00 max =           89.96 mean =        58.12|
|phase err.(test): min =        0.00 max =           89.88 mean =        58.41|
|-----------------------------------------------------------------------------|

============================== 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 = 15.431087             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 81.785   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.383014              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.462   (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:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       31 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      174 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      685 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1501 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2627 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3917 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5069 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6549 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7702 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.830 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.911 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.892)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.892)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4943   r_free= 0.4715   ksol= 0.00   Bsol= 0.00   scale= 0.756    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.291335                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4790   r_free= 0.4565   ksol= 0.34   Bsol= 0.26   scale= 1.004    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.99,9.34,11.53,0.00,0.00,0.00); trace/3= 9.29                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.74 A                  |
| x-ray target function (ml) for work reflections: 6.282732                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 12.246856             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.222   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.206102              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.255   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4790      final r-factor (work) = 0.3999          |
| start r-factor (free) = 0.4565      final r-factor (free) = 0.4220          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 92.3069 = 12.25 * 0.50 * 6.2836 + 1.00 * 53.8296                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 38.1232 = 12.25 * 0.50 * 6.2023 + 1.00 * 0.1440                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3999      final r-factor (work) = 0.3575          |
| start r-factor (free) = 0.4220      final r-factor (free) = 0.4141          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.4950 = 1.21 * 1.00 * 6.2023 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.4028 = 1.21 * 1.00 * 6.1234 + 1.00 * 0.0174                               |
|-----------------------------------------------------------------------------|
| number of iterations = 22      |    number of function evaluations = 23     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.892)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    82.78   14.23    None  None   None       |
|    all(noH): 2823   0      0.00    82.78   14.23    None  None   None       |
|    Sol.    : 438    0      0.00    82.78   25.34    None  None   None       |
|    Mac.    : 2385   0      0.00    59.69   12.19    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.278: 1066   |   5:    41.388 -  49.666:   61        |
|      1:     8.278 -  16.555:  826   |   6:    49.666 -  57.943:   33        |
|      2:    16.555 -  24.833:  482   |   7:    57.943 -  66.221:   11        |
|      3:    24.833 -  33.110:  223   |   8:    66.221 -  74.498:    1        |
|      4:    33.110 -  41.388:  119   |   9:    74.498 -  82.776:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3575 r_free = 0.4141             target_work(ml) = 6.111         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3570 r_free = 0.4139             target_work(ml) = 6.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3570   r_free= 0.4139   ksol= 0.34   Bsol= 0.26   scale= 1.133    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.99,9.34,11.53,0.00,0.00,0.00); trace/3= 9.29                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.110523                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3521   r_free= 0.4087   ksol= 0.34   Bsol= 33.91   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.20,4.73,6.90,0.00,0.00,0.00); trace/3= 4.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.55 A                  |
| x-ray target function (ml) for work reflections: 6.110595                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.711229              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 99.424   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.521508              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 133.194  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3521      final r-factor (work) = 0.2807          |
| start r-factor (free) = 0.4087      final r-factor (free) = 0.3418          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.6204 = 5.71 * 0.50 * 6.1200 + 1.00 * 0.1440                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.2431 = 5.71 * 0.50 * 6.0100 + 1.00 * 0.0809                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2807      final r-factor (work) = 0.2575          |
| start r-factor (free) = 0.3418      final r-factor (free) = 0.3232          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.1520 = 0.52 * 1.00 * 6.0100 + 1.00 * 0.0178                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.0844 = 0.52 * 1.00 * 5.8910 + 1.00 * 0.0121                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.892)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.92   13.56    None  None   None       |
|    all(noH): 2823   0      0.00    92.92   13.56    None  None   None       |
|    Sol.    : 438    0      0.00    92.92   31.52    None  None   None       |
|    Mac.    : 2385   0      0.00    65.83   10.26    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 -   9.292: 1340   |   5:    46.462 -  55.754:   49        |
|      1:     9.292 -  18.585:  830   |   6:    55.754 -  65.046:   23        |
|      2:    18.585 -  27.877:  304   |   7:    65.046 -  74.339:    5        |
|      3:    27.877 -  37.169:  172   |   8:    74.339 -  83.631:    3        |
|      4:    37.169 -  46.462:   96   |   9:    83.631 -  92.923:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2575 r_free = 0.3232             target_work(ml) = 5.866         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2573 r_free = 0.3231             target_work(ml) = 5.866         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2573   r_free= 0.3231   ksol= 0.34   Bsol= 33.91   scale= 1.058   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.20,4.73,6.90,0.00,0.00,0.00); trace/3= 4.94                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.865514                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2562   r_free= 0.3226   ksol= 0.34   Bsol= 51.86   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.99,2.74,4.76,0.00,0.00,0.00); trace/3= 3.16                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.39 A                  |
| x-ray target function (ml) for work reflections: 5.866749                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.892803              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 106.027  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.353030              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 120.734  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2562      final r-factor (work) = 0.1867          |
| start r-factor (free) = 0.3226      final r-factor (free) = 0.2385          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.5508 = 3.89 * 0.50 * 5.8929 + 1.00 * 0.0809                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 11.2471 = 3.89 * 0.50 * 5.7421 + 1.00 * 0.0706                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1867      final r-factor (work) = 0.1696          |
| start r-factor (free) = 0.2385      final r-factor (free) = 0.2206          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.0392 = 0.35 * 1.00 * 5.7421 + 1.00 * 0.0120                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9638 = 0.35 * 1.00 * 5.5332 + 1.00 * 0.0104                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.892)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.80   13.58    None  None   None       |
|    all(noH): 2823   0      0.00    90.80   13.58    None  None   None       |
|    Sol.    : 438    0      1.19    90.80   35.58    None  None   None       |
|    Mac.    : 2385   0      0.00    68.92   9.55     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 -   9.080: 1486   |   5:    45.401 -  54.481:   89        |
|      1:     9.080 -  18.161:  739   |   6:    54.481 -  63.562:   30        |
|      2:    18.161 -  27.241:  188   |   7:    63.562 -  72.642:    8        |
|      3:    27.241 -  36.321:  142   |   8:    72.642 -  81.722:    4        |
|      4:    36.321 -  45.401:  136   |   9:    81.722 -  90.802:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1696 r_free = 0.2206             target_work(ml) = 5.494         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1695 r_free = 0.2205             target_work(ml) = 5.494         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1695   r_free= 0.2205   ksol= 0.34   Bsol= 51.86   scale= 1.035   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.99,2.74,4.76,0.00,0.00,0.00); trace/3= 3.16                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.493615                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1686   r_free= 0.2190   ksol= 0.32   Bsol= 51.86   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.02,1.39,3.63,0.00,0.00,0.00); trace/3= 2.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.21 A                  |
| x-ray target function (ml) for work reflections: 5.492131                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.003322              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.880  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.301041              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.806  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1686      final r-factor (work) = 0.1362          |
| start r-factor (free) = 0.2190      final r-factor (free) = 0.1838          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.3885 = 3.00 * 0.50 * 5.5391 + 1.00 * 0.0706                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.1820 = 3.00 * 0.50 * 5.4052 + 1.00 * 0.0653                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1362      final r-factor (work) = 0.1290          |
| start r-factor (free) = 0.1838      final r-factor (free) = 0.1788          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.4478 = 2.30 * 1.00 * 5.4052 + 1.00 * 0.0103                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 12.1751 = 2.30 * 1.00 * 5.2849 + 1.00 * 0.0143                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.892)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.07   14.36    None  None   None       |
|    all(noH): 2823   0      0.00    92.07   14.36    None  None   None       |
|    Sol.    : 438    0      2.80    92.07   40.81    None  None   None       |
|    Mac.    : 2385   0      0.00    82.36   9.50     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 -   9.207: 1564   |   5:    46.033 -  55.240:  103        |
|      1:     9.207 -  18.413:  653   |   6:    55.240 -  64.446:   68        |
|      2:    18.413 -  27.620:  179   |   7:    64.446 -  73.653:   35        |
|      3:    27.620 -  36.826:  118   |   8:    73.653 -  82.859:   12        |
|      4:    36.826 -  46.033:   86   |   9:    82.859 -  92.066:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1290 r_free = 0.1788             target_work(ml) = 5.273         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1289 r_free = 0.1789             target_work(ml) = 5.273         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1289   r_free= 0.1789   ksol= 0.32   Bsol= 51.86   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.02,1.39,3.63,0.00,0.00,0.00); trace/3= 2.01                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.272557                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1292   r_free= 0.1790   ksol= 0.33   Bsol= 58.65   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.04,1.15,3.25,0.00,0.00,0.00); trace/3= 1.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.271873                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.350076              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 119.602  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.179724              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.480  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1292      final r-factor (work) = 0.1184          |
| start r-factor (free) = 0.1790      final r-factor (free) = 0.1683          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9181 = 3.35 * 0.50 * 5.2851 + 1.00 * 0.0653                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8439 = 3.35 * 0.50 * 5.2372 + 1.00 * 0.0714                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1184      final r-factor (work) = 0.1167          |
| start r-factor (free) = 0.1683      final r-factor (free) = 0.1667          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.4297 = 2.18 * 1.00 * 5.2372 + 1.00 * 0.0142                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.3428 = 2.18 * 1.00 * 5.1972 + 1.00 * 0.0144                              |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.892)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.80   14.17    None  None   None       |
|    all(noH): 2823   0      0.00    93.80   14.17    None  None   None       |
|    Sol.    : 438    0      2.42    93.80   40.48    None  None   None       |
|    Mac.    : 2385   0      0.00    86.43   9.34     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 -   9.380: 1615   |   5:    46.899 -  56.279:   93        |
|      1:     9.380 -  18.760:  625   |   6:    56.279 -  65.659:   62        |
|      2:    18.760 -  28.140:  178   |   7:    65.659 -  75.039:   35        |
|      3:    28.140 -  37.519:  114   |   8:    75.039 -  84.419:   12        |
|      4:    37.519 -  46.899:   81   |   9:    84.419 -  93.798:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1167 r_free = 0.1667             target_work(ml) = 5.191         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1166 r_free = 0.1667             target_work(ml) = 5.191         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1166   r_free= 0.1667   ksol= 0.33   Bsol= 58.65   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.04,1.15,3.25,0.00,0.00,0.00); trace/3= 1.81                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.191170                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0740 -  4.7096 0.99   1420  156 0.0945 0.1260      5.3618      5.5568|
|  2:  4.7096 -  3.7572 0.99   1369  155 0.0844 0.1178      5.4398      5.6556|
|  3:  3.7572 -  3.2879 0.99   1331  145 0.1113 0.1537      5.5119      5.8444|
|  4:  3.2879 -  2.9899 0.99   1336  150 0.1286 0.1859      5.4891      5.6863|
|  5:  2.9899 -  2.7770 0.99   1309  150 0.1370 0.1725      5.3677      5.5904|
|  6:  2.7770 -  2.6142 0.99   1324  143 0.1287 0.2182      5.2562       5.559|
|  7:  2.6142 -  2.4838 0.99   1317  145 0.1364 0.1647       5.232      5.3483|
|  8:  2.4838 -  2.3761 0.98   1292  146 0.1257 0.1765      5.1374      5.3793|
|  9:  2.3761 -  2.2850 0.98   1307  140 0.1290 0.1999      5.1043      5.4039|
| 10:  2.2850 -  2.2064 1.00   1282  149 0.1197 0.1796      5.0087      5.2623|
| 11:  2.2064 -  2.1376 0.98   1306  145 0.1208 0.1952       4.994      5.3409|
| 12:  2.1376 -  2.0767 0.98   1274  142 0.1241 0.1809      4.9461       5.223|
| 13:  2.0767 -  2.0221 0.96   1265  139 0.1100 0.1712      4.7925      5.0167|
| 14:  2.0221 -  1.9729 0.38    498   54 0.0919 0.1396       4.614       4.864|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0740 -  4.7096  1420   156  0.94   9.24   0.97     0.94       7208.42|
|  2:  4.7096 -  3.7572  1369   155  0.95   8.25   1.01     1.00       9460.67|
|  3:  3.7572 -  3.2879  1331   145  0.93  12.15   1.04     1.03      11217.61|
|  4:  3.2879 -  2.9899  1336   150  0.91  14.64   1.01     0.99      11147.86|
|  5:  2.9899 -  2.7770  1309   150  0.90  16.58   1.00     0.98       9136.61|
|  6:  2.7770 -  2.6142  1324   143  0.89  17.36   0.98     0.95       7864.91|
|  7:  2.6142 -  2.4838  1317   145  0.89  16.92   0.99     0.95       7034.41|
|  8:  2.4838 -  2.3761  1292   146  0.89  17.02   0.99     0.97       6262.67|
|  9:  2.3761 -  2.2850  1307   140  0.89  17.00   0.99     0.95       5779.74|
| 10:  2.2850 -  2.2064  1282   149  0.89  17.05   1.00     0.95       4974.86|
| 11:  2.2064 -  2.1376  1306   145  0.89  17.79   0.98     0.93       4950.71|
| 12:  2.1376 -  2.0767  1274   142  0.89  17.15   1.00     1.00       4572.84|
| 13:  2.0767 -  2.0221  1265   139  0.90  16.88   0.99     0.97       3518.36|
| 14:  2.0221 -  1.9729   498    54  0.93  12.67   0.97     0.95       2354.94|
|alpha:            min =        0.93 max =            1.03 mean =         0.97|
|beta:             min =     2354.94 max =        11217.61 mean =      7066.77|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.85 mean =        15.08|
|phase err.(test): min =        0.00 max =           89.86 mean =        14.50|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1165   r_free= 0.1666   ksol= 0.33   Bsol= 60.64   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.68,-0.70,1.38,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.191190                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.97 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1165   r_free= 0.1666   ksol= 0.33   Bsol= 60.64   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.68,-0.70,1.38,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.191190                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0740 -  4.7096 0.99   1420  156 0.0945 0.1261      5.3626      5.5583|
|  2:  4.7096 -  3.7572 0.99   1369  155 0.0844 0.1178      5.4406      5.6559|
|  3:  3.7572 -  3.2879 0.99   1331  145 0.1113 0.1539      5.5123      5.8454|
|  4:  3.2879 -  2.9899 0.99   1336  150 0.1286 0.1860      5.4892      5.6863|
|  5:  2.9899 -  2.7770 0.99   1309  150 0.1370 0.1723      5.3674      5.5897|
|  6:  2.7770 -  2.6142 0.99   1324  143 0.1286 0.2182       5.256      5.5593|
|  7:  2.6142 -  2.4838 0.99   1317  145 0.1364 0.1650      5.2322      5.3492|
|  8:  2.4838 -  2.3761 0.98   1292  146 0.1258 0.1764      5.1376      5.3786|
|  9:  2.3761 -  2.2850 0.98   1307  140 0.1289 0.1997      5.1043      5.4042|
| 10:  2.2850 -  2.2064 1.00   1282  149 0.1197 0.1797      5.0086      5.2623|
| 11:  2.2064 -  2.1376 0.98   1306  145 0.1208 0.1946      4.9937      5.3401|
| 12:  2.1376 -  2.0767 0.98   1274  142 0.1240 0.1808      4.9457      5.2229|
| 13:  2.0767 -  2.0221 0.96   1265  139 0.1100 0.1709      4.7917      5.0153|
| 14:  2.0221 -  1.9729 0.38    498   54 0.0920 0.1392      4.6134      4.8626|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0740 -  4.7096  1420   156  0.94   9.27   0.97     0.94       7223.26|
|  2:  4.7096 -  3.7572  1369   155  0.95   8.26   1.02     1.00       9477.29|
|  3:  3.7572 -  3.2879  1331   145  0.93  12.17   1.04     1.03      11232.79|
|  4:  3.2879 -  2.9899  1336   150  0.91  14.64   1.02     1.00      11150.21|
|  5:  2.9899 -  2.7770  1309   150  0.90  16.57   1.01     0.99       9133.90|
|  6:  2.7770 -  2.6142  1324   143  0.89  17.36   0.98     0.95       7861.39|
|  7:  2.6142 -  2.4838  1317   145  0.89  16.93   0.99     0.96       7036.88|
|  8:  2.4838 -  2.3761  1292   146  0.89  17.03   1.00     0.97       6266.61|
|  9:  2.3761 -  2.2850  1307   140  0.89  17.01   1.00     0.95       5785.04|
| 10:  2.2850 -  2.2064  1282   149  0.89  17.05   1.01     0.96       4972.26|
| 11:  2.2064 -  2.1376  1306   145  0.89  17.78   0.99     0.94       4945.66|
| 12:  2.1376 -  2.0767  1274   142  0.89  17.13   1.01     1.01       4568.45|
| 13:  2.0767 -  2.0221  1265   139  0.90  16.87   1.00     0.98       3510.98|
| 14:  2.0221 -  1.9729   498    54  0.93  12.64   0.98     0.96       2347.09|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     2347.09 max =        11232.79 mean =      7069.35|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.85 mean =        15.09|
|phase err.(test): min =        0.00 max =           89.86 mean =        14.50|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.892)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.99    95.79   16.16    None  None   None       |
|    all(noH): 2823   0      1.99    95.79   16.16    None  None   None       |
|    Sol.    : 438    0      4.41    95.79   42.47    None  None   None       |
|    Mac.    : 2385   0      1.99    88.42   11.33    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:     1.991 -  11.371: 1615   |   5:    48.890 -  58.270:   93        |
|      1:    11.371 -  20.750:  625   |   6:    58.270 -  67.650:   62        |
|      2:    20.750 -  30.130:  178   |   7:    67.650 -  77.029:   35        |
|      3:    30.130 -  39.510:  114   |   8:    77.029 -  86.409:   12        |
|      4:    39.510 -  48.890:   81   |   9:    86.409 -  95.789:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 317         
Filter by distance & map next to the model:
   mapped sites are within: 0.268 - 4.814
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 314 from: 317
   mapped sites are within: 0.714 - 4.814

peak=   10.446 closest distance to " CB  VAL A 230 " =    1.418
peak=    9.285 closest distance to " CB  VAL A 296 " =    1.554
peak=    7.267 closest distance to " O   HOH Z 130 " =    1.311
peak=    6.620 closest distance to " CD2 LEU A   5 " =    1.255
peak=    5.958 closest distance to " NE2 GLN A  11 " =    1.146
peak=    5.643 closest distance to " CG  LEU A 228 " =    1.124
peak=    5.462 closest distance to " CD1AILE A 234 " =    0.989
peak=    5.427 closest distance to " CG  PRO A  54 " =    1.363
peak=    5.401 closest distance to " O   HOH Z 142 " =    2.196
peak=    5.289 closest distance to " NH2 ARG A  56 " =    2.068
peak=    5.108 closest distance to " CG  LEU A   5 " =    1.144
peak=    4.998 closest distance to " O   HOH Z 232 " =    2.278
peak=    4.996 closest distance to " O   HOH Z  65 " =    1.149
peak=    4.807 closest distance to " O   HOH Z 427 " =    2.410
peak=    4.802 closest distance to " O   HOH Z   9 " =    2.353
peak=    4.702 closest distance to " CB  GLN A 223 " =    1.526
peak=    4.684 closest distance to " O   HOH Z   7 " =    1.318
peak=    4.641 closest distance to " CB  GLN A 183 " =    1.274
peak=    4.634 closest distance to " CB  ASN A 148 " =    1.411
peak=    4.607 closest distance to " O   HOH Z 425 " =    1.593
peak=    4.575 closest distance to " O   HOH Z 369 " =    2.183
peak=    4.531 closest distance to " O   HOH Z 287 " =    1.889
peak=    4.458 closest distance to " CB  PRO A  54 " =    1.039
peak=    4.380 closest distance to " O   HOH Z 427 " =    1.151
peak=    4.378 closest distance to " NH2AARG A 190 " =    1.851
peak=    4.368 closest distance to " CB  ASN A 142 " =    1.052
peak=    4.360 closest distance to " CG  LEU A 167 " =    1.264
peak=    4.293 closest distance to " O   HOH Z 423 " =    1.583
peak=    4.275 closest distance to " O   HOH Z  69 " =    0.949
peak=    4.270 closest distance to " O   HOH Z 362 " =    2.193
peak=    4.259 closest distance to " O   HOH Z  78 " =    1.625
peak=    4.199 closest distance to " O   HOH Z 359 " =    1.512
peak=    4.196 closest distance to " O   HOH Z 222 " =    1.216
peak=    4.172 closest distance to " O   HOH Z 417 " =    1.374
peak=    4.169 closest distance to " CB  VAL A 230 " =    1.224
peak=    4.161 closest distance to " CB  SER A  63 " =    1.229
peak=    4.160 closest distance to " CB  GLU A 277 " =    3.581
peak=    4.155 closest distance to " O   HOH Z 126 " =    2.119
peak=    4.142 closest distance to " O   SER A  87 " =    2.359
peak=    4.108 closest distance to " CB  VAL A 265 " =    1.312
peak=    4.074 closest distance to " O   HOH Z  59 " =    1.727
peak=    4.068 closest distance to " O   HOH Z 143 " =    1.407
peak=    4.064 closest distance to " O   HOH Z 346 " =    1.538
peak=    4.061 closest distance to " O   PRO A 198 " =    1.278
peak=    4.059 closest distance to " CH2 TRP A 266 " =    1.114
peak=    4.036 closest distance to " CG AARG A 275 " =    1.237
peak=    4.019 closest distance to " CB BVAL A  41 " =    1.174
peak=    4.008 closest distance to " O   HOH Z 248 " =    1.149
peak=    3.994 closest distance to " O   HOH Z 298 " =    1.655
peak=    3.993 closest distance to " O   HOH Z 272 " =    1.755
peak=    3.993 closest distance to " O   HOH Z 380 " =    1.925
peak=    3.976 closest distance to " CG  PRO A 213 " =    1.178
peak=    3.974 closest distance to " NH1AARG A 145 " =    1.206
peak=    3.958 closest distance to " O   HOH Z  30 " =    1.714
peak=    3.956 closest distance to " CG  PRO A 198 " =    1.261
peak=    3.948 closest distance to " CD2 LEU A 228 " =    1.257
peak=    3.942 closest distance to " CE  LYS A  76 " =    0.863
peak=    3.924 closest distance to " CD  ARG A 159 " =    0.738
peak=    3.922 closest distance to " NH2AARG A 145 " =    1.126
peak=    3.921 closest distance to " O   HOH Z 214 " =    2.466
peak=    3.916 closest distance to " CB  ARG A 275 " =    0.998
peak=    3.915 closest distance to " CB  TRP A 266 " =    1.111
peak=    3.898 closest distance to " O   HOH Z 303 " =    2.157
peak=    3.894 closest distance to " CB  VAL A 202 " =    1.675
peak=    3.882 closest distance to " CB  ARG A 190 " =    1.490
peak=    3.881 closest distance to " CB  SER A 216 " =    0.929
peak=    3.879 closest distance to " ND2 ASN A 187 " =    1.722
peak=    3.877 closest distance to " CD  ARG A  66 " =    2.734
peak=    3.875 closest distance to " O   HOH Z 422 " =    2.610
peak=    3.864 closest distance to " CG  ARG A 138 " =    1.229
peak=    3.863 closest distance to " CD  ARG A 269 " =    1.017
peak=    3.845 closest distance to " O   HOH Z  68 " =    2.209
peak=    3.842 closest distance to " O   HOH Z 371 " =    2.820
peak=    3.837 closest distance to " O   HOH Z 419 " =    2.082
peak=    3.837 closest distance to " O   PRO A 198 " =    1.561
peak=    3.832 closest distance to " O   HOH Z  88 " =    3.350
peak=    3.828 closest distance to " CB  ASN A  39 " =    1.059
peak=    3.818 closest distance to " CZ  PHE A 218 " =    1.101
peak=    3.816 closest distance to " O   HOH Z 234 " =    3.611
peak=    3.816 closest distance to " CA  LYS A 117 " =    1.224
peak=    3.802 closest distance to " CG  LYS A  76 " =    1.775
peak=    3.800 closest distance to " O   HOH Z 258 " =    1.863
peak=    3.798 closest distance to " O   HOH Z   2 " =    1.627
peak=    3.790 closest distance to " CB  ASP A 124 " =    0.849
peak=    3.787 closest distance to " CB  LYS A 117 " =    1.220
peak=    3.783 closest distance to " CA  ASN A 127 " =    1.114
peak=    3.779 closest distance to " CG2 THR A 221 " =    1.148
peak=    3.777 closest distance to " O   HOH Z 437 " =    1.849
peak=    3.763 closest distance to " OG ASER A 258 " =    3.043
peak=    3.758 closest distance to " O   HOH Z 365 " =    3.032
peak=    3.755 closest distance to " CB  GLN A  88 " =    1.310
peak=    3.751 closest distance to " CB  ARG A  79 " =    1.404
peak=    3.742 closest distance to " CG  GLN A  58 " =    0.941
peak=    3.734 closest distance to " CD2 TRP A 179 " =    1.274
peak=    3.723 closest distance to " O   HOH Z 258 " =    1.083
peak=    3.722 closest distance to " O  BHOH Z 338 " =    2.453
peak=    3.711 closest distance to " O   HOH Z 126 " =    1.554
peak=    3.704 closest distance to " CA  VAL A 125 " =    1.128
peak=    3.702 closest distance to " O   HOH Z 218 " =    1.588
peak=    3.700 closest distance to " CA  ALA A 160 " =    0.950
peak=    3.698 closest distance to " O   HOH Z 406 " =    1.526
peak=    3.698 closest distance to " O   HOH Z 180 " =    2.120
peak=    3.697 closest distance to " CG  PRO A 243 " =    1.115
peak=    3.693 closest distance to " O   HOH Z   1 " =    1.754
peak=    3.692 closest distance to " CE3 TRP A 150 " =    1.154
peak=    3.680 closest distance to " CB  SER A   3 " =    1.459
peak=    3.665 closest distance to " O   HOH Z 133 " =    2.908
peak=    3.656 closest distance to " O   HOH Z 265 " =    1.766
peak=    3.654 closest distance to " O   HOH Z 203 " =    1.808
peak=    3.646 closest distance to " O   HOH Z  61 " =    1.662
peak=    3.645 closest distance to " O   HOH Z   3 " =    2.086
peak=    3.644 closest distance to " O   HOH Z  80 " =    1.501
peak=    3.644 closest distance to " O   HOH Z 411 " =    3.518
peak=    3.642 closest distance to " O   HOH Z 127 " =    1.106
peak=    3.640 closest distance to " O   HOH Z  76 " =    1.109
peak=    3.638 closest distance to " CA  TYR A  30 " =    0.978
peak=    3.631 closest distance to " CG2 ILE A  20 " =    1.639
peak=    3.624 closest distance to " CD1 ILE A  33 " =    1.828
peak=    3.616 closest distance to " CA  SER A  87 " =    1.027
peak=    3.616 closest distance to " NZ  LYS A 117 " =    3.024
peak=    3.610 closest distance to " O   HOH Z 368 " =    3.517
peak=    3.603 closest distance to " O   HOH Z 403 " =    1.564
peak=    3.596 closest distance to " CB  ASP A 140 " =    1.031
peak=    3.584 closest distance to " O   HOH Z  63 " =    1.285
peak=    3.571 closest distance to " O   HOH Z 153 " =    3.698
peak=    3.568 closest distance to " CA  MET A 105 " =    0.928
peak=    3.563 closest distance to " O   HOH Z 193 " =    1.598
peak=    3.562 closest distance to " OD1 ASN A  69 " =    2.540
peak=    3.558 closest distance to " ND1 HIS A  86 " =    1.781
peak=    3.555 closest distance to " CA  ALA A  51 " =    1.051
peak=    3.554 closest distance to " O   HOH Z 290 " =    1.056
peak=    3.547 closest distance to " CG2 ILE A 234 " =    0.944
peak=    3.546 closest distance to " CG2 VAL A 257 " =    0.880
peak=    3.537 closest distance to " CA  ALA A 291 " =    0.816
peak=    3.532 closest distance to " O   HOH Z 368 " =    2.094
peak=    3.529 closest distance to " O   HOH Z  10 " =    1.718
peak=    3.528 closest distance to " CB  ASN A 215 " =    1.234
peak=    3.526 closest distance to " O   HOH Z 329 " =    4.112
peak=    3.524 closest distance to " CB  SER A  26 " =    1.658
peak=    3.522 closest distance to " O   HOH Z 286 " =    2.248
peak=    3.517 closest distance to " O   HOH Z 211 " =    0.936
peak=    3.516 closest distance to " CB  GLU A 128 " =    1.057
peak=    3.516 closest distance to " O   HOH Z  61 " =    1.647
peak=    3.511 closest distance to " O   HOH Z 195 " =    1.314
peak=    3.510 closest distance to " N   ALA A 256 " =    1.024
peak=    3.509 closest distance to " O   HOH Z 389 " =    1.295
peak=    3.509 closest distance to " O   HOH Z 280 " =    2.950
peak=    3.502 closest distance to " CA  ARG A 195 " =    1.180
peak=    3.498 closest distance to " O   HOH Z 236 " =    1.509
peak=    3.493 closest distance to " CB  ALA A 114 " =    1.375
peak=    3.491 closest distance to " CB  ARG A  79 " =    0.918
peak=    3.490 closest distance to " O   HOH Z 145 " =    1.651
peak=    3.489 closest distance to " OG  SER A  62 " =    2.703
peak=    3.483 closest distance to " O   HOH Z 184 " =    1.414
peak=    3.477 closest distance to " O   HOH Z  40 " =    2.267
peak=    3.475 closest distance to " CB  TYR A 169 " =    0.780
peak=    3.471 closest distance to " O   HOH Z  69 " =    2.043
peak=    3.471 closest distance to " O   HOH Z 405 " =    1.449
peak=    3.469 closest distance to " O   HOH Z 193 " =    1.694
peak=    3.469 closest distance to " O   HOH Z 357 " =    2.135
peak=    3.464 closest distance to " O   HOH Z 325 " =    2.219
peak=    3.461 closest distance to " CG BARG A 102 " =    1.869
peak=    3.457 closest distance to " CA  PHE A 283 " =    1.246
peak=    3.456 closest distance to " O   HOH Z 128 " =    1.892
peak=    3.454 closest distance to " OE2 GLU A   2 " =    2.033
peak=    3.451 closest distance to " OG BSER A 164 " =    2.298
peak=    3.450 closest distance to " O   HOH Z 193 " =    1.476
peak=    3.449 closest distance to " CB  ALA A  43 " =    0.824
peak=    3.448 closest distance to " ND2 ASN A 249 " =    0.855
peak=    3.448 closest distance to " O   HOH Z 128 " =    2.177
peak=    3.446 closest distance to " NE2 HIS A 207 " =    1.198
peak=    3.444 closest distance to " N   PHE A 130 " =    1.313
peak=    3.440 closest distance to " CB  GLN A  89 " =    1.278
peak=    3.431 closest distance to " CB  ARG A 138 " =    0.863
peak=    3.427 closest distance to " O   HOH Z  97 " =    2.077
peak=    3.426 closest distance to " O   HOH Z 251 " =    1.567
peak=    3.421 closest distance to " CB  THR A 157 " =    1.136
peak=    3.418 closest distance to " CB  GLU A 152 " =    1.155
peak=    3.416 closest distance to " O   HOH Z 323 " =    1.649
peak=    3.415 closest distance to " O   HOH Z 145 " =    1.985
peak=    3.409 closest distance to " O   HOH Z 188 " =    2.989
peak=    3.408 closest distance to " CA  ILE A 234 " =    1.093
peak=    3.407 closest distance to " O   HOH Z 421 " =    2.164
peak=    3.407 closest distance to " CB  TRP A 179 " =    1.456
peak=    3.405 closest distance to " O   HOH Z 112 " =    0.912
peak=    3.405 closest distance to " O   HOH Z  88 " =    2.968
peak=    3.405 closest distance to " NE2 GLN A  73 " =    1.367
peak=    3.404 closest distance to " O   CYS A 168 " =    1.229
peak=    3.402 closest distance to " O   HOH Z  20 " =    1.527
peak=    3.401 closest distance to " N   SER A 135 " =    1.363
peak=    3.398 closest distance to " O   HOH Z 158 " =    3.101
peak=    3.391 closest distance to " CB  SER A 212 " =    1.266
peak=    3.379 closest distance to " CZ3 TRP A 177 " =    1.067
peak=    3.377 closest distance to " CB  ASN A 110 " =    1.114
peak=    3.375 closest distance to " OG  SER A  62 " =    2.982
peak=    3.371 closest distance to " N   ASN A 127 " =    1.337
peak=    3.367 closest distance to " CE  LYS A  48 " =    1.145
peak=    3.366 closest distance to " O   HOH Z 261 " =    1.610
peak=    3.365 closest distance to " CB  SER A 276 " =    1.101
peak=    3.362 closest distance to " CA  ALA A 158 " =    1.268
peak=    3.362 closest distance to " O   HOH Z 189 " =    2.999
peak=    3.348 closest distance to " O   HOH Z 394 " =    3.582
peak=    3.348 closest distance to " N   GLY A 133 " =    3.831
peak=    3.344 closest distance to " CG1BVAL A  72 " =    1.389
peak=    3.344 closest distance to " O   HOH Z 303 " =    2.733
peak=    3.340 closest distance to " O   HOH Z 216 " =    3.471
peak=    3.339 closest distance to " CE1 TYR A 186 " =    1.278
peak=    3.336 closest distance to " CB  THR A  52 " =    0.986
peak=    3.330 closest distance to " CD  LYS A 166 " =    1.368
peak=    3.330 closest distance to " O   HOH Z 343 " =    3.193
peak=    3.329 closest distance to " CA  ARG A 102 " =    1.121
peak=    3.328 closest distance to " OE2 GLU A  53 " =    1.990
peak=    3.325 closest distance to " O   PHE A 192 " =    1.362
peak=    3.322 closest distance to " CA  GLY A 267 " =    1.179
peak=    3.322 closest distance to " CD1 LEU A 300 " =    1.033
peak=    3.318 closest distance to " CB  GLU A  46 " =    0.938
peak=    3.318 closest distance to " CB  MET A  40 " =    0.805
peak=    3.316 closest distance to " CB  ALA A 248 " =    1.060
peak=    3.312 closest distance to " O   HOH Z 222 " =    2.158
peak=    3.312 closest distance to " N   SER A 271 " =    1.016
peak=    3.310 closest distance to " CG2 ILE A 120 " =    1.400
peak=    3.310 closest distance to " O   HOH Z  43 " =    1.791
peak=    3.308 closest distance to " ND2BASN A 224 " =    0.817
peak=    3.307 closest distance to " O   HOH Z   1 " =    1.748
peak=    3.304 closest distance to " CD  ARG A  24 " =    1.026
peak=    3.304 closest distance to " CB  SER A  97 " =    1.028
peak=    3.300 closest distance to " O   HOH Z 273 " =    3.024
peak=    3.299 closest distance to " O   HOH Z 299 " =    4.279
peak=    3.298 closest distance to " CA  ASN A 215 " =    1.112
peak=    3.297 closest distance to " CG1 ILE A 151 " =    1.135
peak=    3.295 closest distance to " CD1 LEU A 281 " =    1.025
peak=    3.291 closest distance to " NZ  LYS A  48 " =    1.302
peak=    3.290 closest distance to " OG BSER A  99 " =    2.162
peak=    3.289 closest distance to " CB  TRP A 150 " =    1.198
peak=    3.284 closest distance to " CB  HIS A 108 " =    0.800
peak=    3.284 closest distance to " O   HOH Z 425 " =    2.175
peak=    3.277 closest distance to " CA  LYS A 290 " =    1.272
peak=    3.274 closest distance to " O   HOH Z 305 " =    3.480
peak=    3.274 closest distance to " CZ  PHE A  38 " =    1.191
peak=    3.271 closest distance to " O   HOH Z  53 " =    2.381
peak=    3.267 closest distance to " O   HOH Z 392 " =    1.157
peak=    3.264 closest distance to " O   HOH Z 196 " =    1.359
peak=    3.254 closest distance to " OG BSER A 212 " =    2.813
peak=    3.250 closest distance to " O   HOH Z 148 " =    2.321
peak=    3.248 closest distance to " CZ3 TRP A  92 " =    1.211
peak=    3.244 closest distance to " C   ALA A 299 " =    0.963
peak=    3.234 closest distance to " O   HOH Z  44 " =    1.725
peak=    3.233 closest distance to " CE3 TRP A 274 " =    1.237
peak=    3.228 closest distance to " O   HOH Z 146 " =    1.435
peak=    3.226 closest distance to " CB  PRO A  90 " =    1.152
peak=    3.223 closest distance to " CB  LEU A 237 " =    0.859
peak=    3.215 closest distance to " O   TYR A 116 " =    1.245
peak=    3.208 closest distance to " CB  LEU A 143 " =    1.143
peak=    3.201 closest distance to " CG  GLN A  88 " =    1.098
peak=    3.200 closest distance to " CG2 ILE A 239 " =    0.714
peak=    3.199 closest distance to " O   HOH Z 122 " =    1.900
peak=    3.198 closest distance to " CA  ASN A 217 " =    1.202
peak=    3.198 closest distance to " O   HOH Z  85 " =    2.115
peak=    3.197 closest distance to " CA  ALA A 129 " =    1.302
peak=    3.197 closest distance to " CA  THR A 221 " =    1.024
peak=    3.194 closest distance to " O   HOH Z 281 " =    2.296
peak=    3.192 closest distance to " CB  SER A  62 " =    1.003
peak=    3.191 closest distance to " O   HOH Z 373 " =    1.481
peak=    3.191 closest distance to " CB  SER A 210 " =    0.755
peak=    3.190 closest distance to " O   HOH Z 285 " =    2.120
peak=    3.189 closest distance to " O   HOH Z  39 " =    0.952
peak=    3.189 closest distance to " CE AMET A  47 " =    1.423
peak=    3.187 closest distance to " CB  ALA A   1 " =    4.814
peak=    3.184 closest distance to " N   ASP A 162 " =    1.076
peak=    3.181 closest distance to " CA  ALA A  21 " =    1.254
peak=    3.179 closest distance to " O   HOH Z 361 " =    1.325
peak=    3.179 closest distance to " CG  GLN A  89 " =    1.522
peak=    3.178 closest distance to " O   HOH Z 272 " =    2.336
peak=    3.171 closest distance to " O   HOH Z 119 " =    1.810
peak=    3.171 closest distance to " CB  ASP A 171 " =    1.155
peak=    3.167 closest distance to " CA  ARG A  36 " =    1.004
peak=    3.167 closest distance to " O   HOH Z  49 " =    0.840
peak=    3.163 closest distance to " OE1 GLN A 240 " =    1.506
peak=    3.163 closest distance to " CG2BVAL A 121 " =    0.801
peak=    3.160 closest distance to " CB  LEU A 300 " =    0.893
peak=    3.159 closest distance to " O   HOH Z 109 " =    2.514
peak=    3.158 closest distance to " CA  LEU A 101 " =    1.471
peak=    3.157 closest distance to " CB  ASN A 187 " =    1.089
peak=    3.153 closest distance to " CB  THR A  31 " =    1.571
peak=    3.153 closest distance to " O   HOH Z 227 " =    1.817
peak=    3.144 closest distance to " NH2BARG A 145 " =    2.029
peak=    3.143 closest distance to " O   HOH Z   4 " =    1.361
peak=    3.137 closest distance to " O   HOH Z 294 " =    1.482
peak=    3.134 closest distance to " CB  PHE A 204 " =    1.051
peak=    3.134 closest distance to " O   ASP A 124 " =    1.157
peak=    3.130 closest distance to " O   THR A 294 " =    1.071
peak=    3.120 closest distance to " NE  ARG A  56 " =    3.562
peak=    3.119 closest distance to " O   MET A 105 " =    1.870
peak=    3.117 closest distance to " CE ALYS A 290 " =    1.210
peak=    3.109 closest distance to " O   HOH Z 389 " =    3.094
peak=    3.107 closest distance to " O   GLY A  57 " =    2.479
peak=    3.105 closest distance to " O   THR A 182 " =    1.447
peak=    3.102 closest distance to " O   THR A 220 " =    1.400
peak=    3.099 closest distance to " O   HOH Z 116 " =    1.031
peak=    3.091 closest distance to " CB  LEU A  83 " =    0.721
peak=    3.091 closest distance to " O   ASN A 209 " =    1.337
peak=    3.088 closest distance to " O   ASP A 200 " =    1.706
peak=    3.087 closest distance to " O   HOH Z 172 " =    2.900
peak=    3.079 closest distance to " CA  ARG A 159 " =    1.143
peak=    3.070 closest distance to " O   HOH Z  71 " =    1.173
peak=    3.060 closest distance to " CG  MET A 185 " =    1.284
peak=    3.059 closest distance to " O   HOH Z  88 " =    3.429
peak=    3.058 closest distance to " O   HOH Z 344 " =    2.898
peak=    3.053 closest distance to " O   HOH Z  55 " =    2.034
peak=    3.051 closest distance to " CD2 PHE A  59 " =    1.307
peak=    3.042 closest distance to " O   HOH Z 424 " =    2.646
peak=    3.039 closest distance to " O   HOH Z 193 " =    1.064
peak=    3.015 closest distance to " O   HOH Z 176 " =    2.124
peak=    3.006 closest distance to " O   HOH Z  85 " =    1.027

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 228         
Filter by distance & map next to the model:
   mapped sites are within: 0.773 - 5.548
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 228 from: 228
   mapped sites are within: 0.773 - 5.548

peak=   -4.566 closest distance to " OG BSER A 134 " =    1.317
peak=   -4.539 closest distance to " CD  ARG A 156 " =    2.039
peak=   -4.450 closest distance to " CD  ARG A  14 " =    3.189
peak=   -4.392 closest distance to " CB  PRO A 243 " =    2.703
peak=   -4.166 closest distance to " CG2 VAL A 230 " =    0.832
peak=   -4.157 closest distance to " O   HOH Z 131 " =    4.075
peak=   -4.143 closest distance to " O   HOH Z 211 " =    0.864
peak=   -4.082 closest distance to " CZ2 TRP A  92 " =    2.855
peak=   -4.073 closest distance to " CG2 VAL A 202 " =    2.711
peak=   -4.063 closest distance to " O   VAL A  67 " =    2.522
peak=   -4.016 closest distance to " O   PRO A 198 " =    1.209
peak=   -4.013 closest distance to " O   HOH Z 231 " =    2.015
peak=   -3.922 closest distance to " O   HOH Z 411 " =    5.403
peak=   -3.907 closest distance to " C   HIS A 108 " =    1.294
peak=   -3.906 closest distance to " OG  SER A  97 " =    2.222
peak=   -3.900 closest distance to " O   HOH Z 185 " =    2.142
peak=   -3.851 closest distance to " CB  VAL A 230 " =    1.144
peak=   -3.839 closest distance to " O   HOH Z  69 " =    1.815
peak=   -3.831 closest distance to " CG  GLN A 223 " =    2.370
peak=   -3.829 closest distance to " O   HOH Z 359 " =    3.208
peak=   -3.807 closest distance to " O   PRO A 163 " =    2.006
peak=   -3.807 closest distance to " CB  ALA A  43 " =    2.614
peak=   -3.794 closest distance to " O   HOH Z 377 " =    2.111
peak=   -3.763 closest distance to " O   HOH Z  52 " =    1.378
peak=   -3.759 closest distance to " CE2 TYR A  30 " =    2.644
peak=   -3.759 closest distance to " O   HOH Z  43 " =    1.808
peak=   -3.754 closest distance to " CA  ASP A  27 " =    2.437
peak=   -3.753 closest distance to " O   HOH Z 231 " =    0.908
peak=   -3.736 closest distance to " O   HOH Z 111 " =    1.590
peak=   -3.734 closest distance to " O   HOH Z 147 " =    2.057
peak=   -3.697 closest distance to " O   HOH Z 389 " =    1.521
peak=   -3.692 closest distance to " ND2 ASN A 187 " =    1.504
peak=   -3.688 closest distance to " CD  GLN A  58 " =    1.056
peak=   -3.683 closest distance to " CE BMET A  47 " =    1.196
peak=   -3.680 closest distance to " CD2 LEU A 237 " =    2.775
peak=   -3.676 closest distance to " O   HOH Z 191 " =    5.548
peak=   -3.669 closest distance to " CD1 LEU A 101 " =    2.329
peak=   -3.657 closest distance to " CD1 LEU A 255 " =    2.894
peak=   -3.654 closest distance to " CD2 LEU A   5 " =    1.007
peak=   -3.653 closest distance to " CG2 VAL A 296 " =    2.037
peak=   -3.649 closest distance to " O   HOH Z  73 " =    2.337
peak=   -3.645 closest distance to " O   SER A  22 " =    2.445
peak=   -3.640 closest distance to " CA  ASP A 298 " =    1.052
peak=   -3.626 closest distance to " N   THR A 157 " =    1.514
peak=   -3.624 closest distance to " O   HOH Z 394 " =    1.561
peak=   -3.623 closest distance to " CB  ALA A   7 " =    2.097
peak=   -3.618 closest distance to " CD2 TYR A 293 " =    1.888
peak=   -3.614 closest distance to " O   HOH Z 429 " =    1.935
peak=   -3.612 closest distance to " CB  ALA A 161 " =    2.488
peak=   -3.611 closest distance to " N   ALA A 226 " =    2.033
peak=   -3.600 closest distance to " O   SER A 135 " =    1.500
peak=   -3.591 closest distance to " OG  SER A  87 " =    1.373
peak=   -3.586 closest distance to " CB  ASP A 132 " =    2.395
peak=   -3.581 closest distance to " CZ2 TRP A 274 " =    0.908
peak=   -3.578 closest distance to " CG2 THR A 178 " =    2.325
peak=   -3.577 closest distance to " O   HOH Z 357 " =    2.082
peak=   -3.567 closest distance to " CE2 PHE A 218 " =    2.487
peak=   -3.565 closest distance to " CB  PRO A 163 " =    2.267
peak=   -3.565 closest distance to " O   HOH Z 193 " =    1.183
peak=   -3.562 closest distance to " N   ALA A  43 " =    2.695
peak=   -3.545 closest distance to " NH2 ARG A  79 " =    2.071
peak=   -3.541 closest distance to " ND2 ASN A 249 " =    2.175
peak=   -3.540 closest distance to " OG  SER A  62 " =    4.346
peak=   -3.536 closest distance to " CA  GLY A 241 " =    2.336
peak=   -3.528 closest distance to " CG1 VAL A 250 " =    2.669
peak=   -3.507 closest distance to " OE2 GLU A 152 " =    1.262
peak=   -3.504 closest distance to " O   HOH Z  51 " =    0.773
peak=   -3.502 closest distance to " O   HOH Z 292 " =    1.655
peak=   -3.497 closest distance to " CA  GLY A  98 " =    1.918
peak=   -3.490 closest distance to " O   HOH Z 351 " =    1.615
peak=   -3.487 closest distance to " O   HOH Z  39 " =    1.037
peak=   -3.483 closest distance to " O   PRO A 243 " =    2.483
peak=   -3.479 closest distance to " O   GLY A  17 " =    1.187
peak=   -3.471 closest distance to " C   MET A 188 " =    1.442
peak=   -3.469 closest distance to " O   ILE A  49 " =    1.653
peak=   -3.456 closest distance to " OH  TYR A 172 " =    1.766
peak=   -3.451 closest distance to " O   HOH Z 352 " =    1.429
peak=   -3.442 closest distance to " OE1 GLU A 277 " =    2.207
peak=   -3.437 closest distance to " O   HOH Z 208 " =    2.241
peak=   -3.431 closest distance to " O   PHE A 218 " =    1.468
peak=   -3.430 closest distance to " ND2 ASN A  45 " =    2.219
peak=   -3.428 closest distance to " O   HOH Z 134 " =    4.237
peak=   -3.427 closest distance to " CB  PHE A 192 " =    1.926
peak=   -3.421 closest distance to " O   HOH Z 313 " =    1.582
peak=   -3.420 closest distance to " O   HOH Z 389 " =    2.243
peak=   -3.417 closest distance to " O   ALA A  84 " =    1.707
peak=   -3.410 closest distance to " C   GLN A 205 " =    1.949
peak=   -3.409 closest distance to " O   HOH Z 103 " =    1.653
peak=   -3.404 closest distance to " CG2 ILE A  20 " =    2.868
peak=   -3.403 closest distance to " CD1 ILE A 199 " =    2.509
peak=   -3.396 closest distance to " CZ3 TRP A 179 " =    1.251
peak=   -3.395 closest distance to " CD2 HIS A 207 " =    2.227
peak=   -3.394 closest distance to " O   HOH Z 108 " =    1.537
peak=   -3.390 closest distance to " CG1 VAL A 112 " =    3.100
peak=   -3.390 closest distance to " O   HOH Z 198 " =    1.964
peak=   -3.382 closest distance to " O   GLU A 152 " =    1.485
peak=   -3.380 closest distance to " CB  TRP A  85 " =    2.556
peak=   -3.368 closest distance to " O   HOH Z 275 " =    1.783
peak=   -3.358 closest distance to " C   ARG A 269 " =    1.411
peak=   -3.357 closest distance to " CG  TRP A 266 " =    1.925
peak=   -3.355 closest distance to " CB  ALA A 291 " =    2.184
peak=   -3.352 closest distance to " O   ASP A  27 " =    1.814
peak=   -3.344 closest distance to " O   HOH Z  11 " =    1.749
peak=   -3.342 closest distance to " O   HOH Z 238 " =    1.011
peak=   -3.342 closest distance to " CE2 TRP A  70 " =    2.401
peak=   -3.336 closest distance to " ND2 ASN A  45 " =    1.288
peak=   -3.335 closest distance to " CB  ALA A 114 " =    2.401
peak=   -3.331 closest distance to " O   HOH Z 117 " =    1.921
peak=   -3.328 closest distance to " NE2 GLN A  11 " =    1.868
peak=   -3.326 closest distance to " CB  GLN A  55 " =    1.239
peak=   -3.326 closest distance to " O   ALA A  10 " =    1.818
peak=   -3.319 closest distance to " CG2 ILE A 151 " =    2.502
peak=   -3.315 closest distance to " O   HOH Z 318 " =    1.961
peak=   -3.315 closest distance to " O   ARG A 145 " =    1.421
peak=   -3.313 closest distance to " CZ  PHE A  38 " =    2.482
peak=   -3.309 closest distance to " CA  ASN A 127 " =    1.103
peak=   -3.307 closest distance to " O   HOH Z 276 " =    1.487
peak=   -3.305 closest distance to " O   MET A  40 " =    2.855
peak=   -3.305 closest distance to " CZ  TYR A 186 " =    2.367
peak=   -3.304 closest distance to " O   HOH Z 384 " =    2.281
peak=   -3.302 closest distance to " O   HOH Z 115 " =    2.009
peak=   -3.302 closest distance to " CD  LYS A 289 " =    2.323
peak=   -3.301 closest distance to " N   VAL A 232 " =    2.027
peak=   -3.298 closest distance to " CE3 TRP A 150 " =    2.281
peak=   -3.298 closest distance to " N   ASP A 171 " =    2.627
peak=   -3.296 closest distance to " CB  ALA A 129 " =    2.448
peak=   -3.295 closest distance to " O   HOH Z  20 " =    1.412
peak=   -3.294 closest distance to " O   SER A 271 " =    2.082
peak=   -3.294 closest distance to " OXT GLY A 302 " =    3.272
peak=   -3.293 closest distance to " CB  ALA A 131 " =    2.025
peak=   -3.289 closest distance to " O   SER A 276 " =    1.583
peak=   -3.280 closest distance to " O   HOH Z 295 " =    1.655
peak=   -3.277 closest distance to " O   HOH Z 427 " =    1.740
peak=   -3.273 closest distance to " O   HOH Z 183 " =    1.522
peak=   -3.268 closest distance to " CB  VAL A 189 " =    2.315
peak=   -3.266 closest distance to " O   HOH Z 166 " =    2.119
peak=   -3.262 closest distance to " ND2 ASN A 173 " =    1.750
peak=   -3.261 closest distance to " O   HOH Z  60 " =    1.896
peak=   -3.257 closest distance to " O   HOH Z 236 " =    1.362
peak=   -3.253 closest distance to " O   HOH Z 364 " =    2.664
peak=   -3.253 closest distance to " O   HOH Z 368 " =    2.238
peak=   -3.252 closest distance to " O   HOH Z 165 " =    2.129
peak=   -3.252 closest distance to " O   HOH Z 285 " =    2.131
peak=   -3.246 closest distance to " O   HOH Z 368 " =    1.638
peak=   -3.246 closest distance to " O   HOH Z 412 " =    4.269
peak=   -3.246 closest distance to " O   HOH Z 426 " =    1.682
peak=   -3.234 closest distance to " NH2AARG A 275 " =    5.249
peak=   -3.234 closest distance to " O   HOH Z  64 " =    1.346
peak=   -3.234 closest distance to " OG  SER A  28 " =    2.118
peak=   -3.229 closest distance to " CA  GLY A 203 " =    2.462
peak=   -3.229 closest distance to " O   HOH Z 140 " =    1.365
peak=   -3.228 closest distance to " ND2 ASN A  69 " =    1.728
peak=   -3.228 closest distance to " O   HOH Z  24 " =    1.284
peak=   -3.223 closest distance to " CB  TYR A  15 " =    2.225
peak=   -3.223 closest distance to " CG  PHE A 283 " =    2.655
peak=   -3.222 closest distance to " OG ASER A 134 " =    1.252
peak=   -3.222 closest distance to " O   HOH Z 102 " =    1.508
peak=   -3.221 closest distance to " CD1 LEU A 297 " =    2.173
peak=   -3.220 closest distance to " CG2 VAL A 296 " =    1.237
peak=   -3.219 closest distance to " OG  SER A 141 " =    1.935
peak=   -3.213 closest distance to " O   VAL A 189 " =    2.595
peak=   -3.209 closest distance to " O   HOH Z 374 " =    1.835
peak=   -3.202 closest distance to " ND2 ASN A  60 " =    1.475
peak=   -3.199 closest distance to " O   HOH Z 111 " =    4.520
peak=   -3.198 closest distance to " O   HOH Z 348 " =    1.797
peak=   -3.197 closest distance to " CA  GLY A 133 " =    1.920
peak=   -3.193 closest distance to " O   HOH Z 253 " =    3.808
peak=   -3.191 closest distance to " N   VAL A  72 " =    1.712
peak=   -3.191 closest distance to " O   HOH Z 162 " =    2.531
peak=   -3.186 closest distance to " O   HOH Z 350 " =    1.673
peak=   -3.185 closest distance to " CD2 LEU A 297 " =    2.053
peak=   -3.185 closest distance to " CG  GLU A 277 " =    1.313
peak=   -3.184 closest distance to " O   HOH Z 281 " =    2.608
peak=   -3.179 closest distance to " CD  GLN A 278 " =    2.125
peak=   -3.177 closest distance to " CB  ALA A 227 " =    2.437
peak=   -3.177 closest distance to " O   HOH Z 290 " =    1.213
peak=   -3.176 closest distance to " CB  PRO A  90 " =    1.766
peak=   -3.176 closest distance to " NH2 ARG A 219 " =    1.792
peak=   -3.170 closest distance to " CG1 VAL A 112 " =    2.549
peak=   -3.169 closest distance to " CD  LYS A 166 " =    2.405
peak=   -3.169 closest distance to " CG2 VAL A 189 " =    1.873
peak=   -3.167 closest distance to " O   ALA A 292 " =    2.015
peak=   -3.166 closest distance to " O   LYS A 289 " =    3.019
peak=   -3.164 closest distance to " O   HOH Z  68 " =    1.323
peak=   -3.161 closest distance to " O   HOH Z 189 " =    2.388
peak=   -3.161 closest distance to " NE2 GLN A 278 " =    1.906
peak=   -3.157 closest distance to " CG2 THR A 178 " =    2.253
peak=   -3.155 closest distance to " CB  ASN A  39 " =    2.212
peak=   -3.152 closest distance to " OH  TYR A 247 " =    1.743
peak=   -3.148 closest distance to " O   HOH Z 346 " =    1.687
peak=   -3.145 closest distance to " O   HOH Z 216 " =    1.463
peak=   -3.144 closest distance to " CB  ASP A 171 " =    2.238
peak=   -3.138 closest distance to " CA  GLY A 241 " =    3.076
peak=   -3.137 closest distance to " CZ  TYR A 169 " =    1.749
peak=   -3.136 closest distance to " O   HOH Z  65 " =    1.479
peak=   -3.135 closest distance to " CD2 PHE A 225 " =    1.120
peak=   -3.133 closest distance to " O   HOH Z 252 " =    3.904
peak=   -3.133 closest distance to " CG  GLN A  88 " =    0.793
peak=   -3.130 closest distance to " O   HOH Z 353 " =    1.797
peak=   -3.129 closest distance to " O   GLN A 144 " =    1.439
peak=   -3.127 closest distance to " C   ASN A 285 " =    2.183
peak=   -3.126 closest distance to " CG1 VAL A 125 " =    2.085
peak=   -3.122 closest distance to " CB  SER A 210 " =    1.096
peak=   -3.118 closest distance to " O   HOH Z 144 " =    1.002
peak=   -3.117 closest distance to " O   HOH Z 357 " =    1.807
peak=   -3.116 closest distance to " CE  LYS A  76 " =    2.749
peak=   -3.113 closest distance to " OD1 ASP A 191 " =    1.834
peak=   -3.112 closest distance to " O   HOH Z 166 " =    1.423
peak=   -3.110 closest distance to " O   HOH Z 201 " =    1.878
peak=   -3.102 closest distance to " NE2 GLN A 240 " =    1.633
peak=   -3.097 closest distance to " O   HOH Z 407 " =    2.968
peak=   -3.095 closest distance to " O   HOH Z 158 " =    1.949
peak=   -3.094 closest distance to " SG BCYS A 201 " =    2.186
peak=   -3.086 closest distance to " O   TRP A  70 " =    1.471
peak=   -3.085 closest distance to " CB  PRO A  54 " =    2.486
peak=   -3.075 closest distance to " CB  PHE A 130 " =    1.250
peak=   -3.070 closest distance to " O   HOH Z 371 " =    1.507
peak=   -3.069 closest distance to " O   HOH Z 232 " =    2.102
peak=   -3.065 closest distance to " CA  HIS A 207 " =    1.212
peak=   -3.064 closest distance to " CA  GLY A 133 " =    2.298
peak=   -3.062 closest distance to " N   ALA A 244 " =    1.332
peak=   -3.062 closest distance to " OG  SER A 245 " =    1.463
peak=   -3.050 closest distance to " OE1 GLN A  88 " =    1.189
peak=   -3.046 closest distance to " O   HOH Z 139 " =    5.076
peak=   -3.044 closest distance to " O   TYR A 186 " =    1.727
peak=   -3.037 closest distance to " O   HOH Z 116 " =    2.031
peak=   -3.036 closest distance to " OD1 ASP A 171 " =    1.660
peak=   -3.034 closest distance to " O   GLN A 240 " =    2.539

================= 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    :  0.4878 0.4709   6.289343e+00   6.268918e+00
   1_bss:  0.4790 0.4565   6.282732e+00   6.261464e+00
   1_xyz:  0.3999 0.4220   6.179539e+00   6.204420e+00
   1_adp:  0.3575 0.4141   6.111036e+00   6.192245e+00
   1_occ:  0.3570 0.4139   6.110523e+00   6.192916e+00
   2_bss:  0.3521 0.4087   6.110595e+00   6.190564e+00
   2_xyz:  0.2807 0.3418   5.923076e+00   6.059656e+00
   2_adp:  0.2575 0.3232   5.865503e+00   6.013833e+00
   2_occ:  0.2573 0.3231   5.865514e+00   6.014154e+00
   3_bss:  0.2562 0.3226   5.866749e+00   6.015405e+00
   3_xyz:  0.1867 0.2385   5.582956e+00   5.776134e+00
   3_adp:  0.1696 0.2206   5.494423e+00   5.697572e+00
   3_occ:  0.1695 0.2205   5.493615e+00   5.697110e+00
   4_bss:  0.1686 0.2190   5.492131e+00   5.695922e+00
   4_xyz:  0.1362 0.1838   5.312634e+00   5.533955e+00
   4_adp:  0.1290 0.1788   5.272564e+00   5.505087e+00
   4_occ:  0.1289 0.1789   5.272557e+00   5.505240e+00
   5_bss:  0.1292 0.1790   5.271873e+00   5.503728e+00
   5_xyz:  0.1184 0.1683   5.202944e+00   5.449693e+00
   5_adp:  0.1167 0.1667   5.191492e+00   5.439406e+00
   5_occ:  0.1166 0.1667   5.191170e+00   5.438968e+00
   5_bss:  0.1165 0.1666   5.191190e+00   5.438983e+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:  0.337   0.255   6.993   9.344  11.529   0.000   0.000   0.000
   1_xyz:  0.337   0.255   6.993   9.344  11.529   0.000   0.000   0.000
   1_adp:  0.337   0.255   6.993   9.344  11.529   0.000   0.000   0.000
   1_occ:  0.337   0.255   6.993   9.344  11.529   0.000   0.000   0.000
   2_bss:  0.338  33.911   3.198   4.729   6.900   0.000   0.000   0.000
   2_xyz:  0.338  33.911   3.198   4.729   6.900   0.000   0.000   0.000
   2_adp:  0.338  33.911   3.198   4.729   6.900   0.000   0.000   0.000
   2_occ:  0.338  33.911   3.198   4.729   6.900   0.000   0.000   0.000
   3_bss:  0.336  51.859   1.986   2.743   4.760   0.000   0.000   0.000
   3_xyz:  0.336  51.859   1.986   2.743   4.760   0.000   0.000   0.000
   3_adp:  0.336  51.859   1.986   2.743   4.760   0.000   0.000   0.000
   3_occ:  0.336  51.859   1.986   2.743   4.760   0.000   0.000   0.000
   4_bss:  0.324  51.859   1.018   1.388   3.628   0.000   0.000   0.000
   4_xyz:  0.324  51.859   1.018   1.388   3.628   0.000   0.000   0.000
   4_adp:  0.324  51.859   1.018   1.388   3.628   0.000   0.000   0.000
   4_occ:  0.324  51.859   1.018   1.388   3.628   0.000   0.000   0.000
   5_bss:  0.326  58.647   1.043   1.152   3.246   0.000   0.000   0.000
   5_xyz:  0.326  58.647   1.043   1.152   3.246   0.000   0.000   0.000
   5_adp:  0.326  58.647   1.043   1.152   3.246   0.000   0.000   0.000
   5_occ:  0.326  58.647   1.043   1.152   3.246   0.000   0.000   0.000
   5_bss:  0.326  60.638  -0.680  -0.705   1.385   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  58.148 0.4169  0.4898    69505.307
   1_bss:  57.812 0.4200  0.6425    67603.960
   1_xyz:  48.847 0.5331  0.7962    51525.907
   1_adp:  46.569 0.5616  0.9056    49143.181
   1_occ:  46.699 0.5600  0.9019    49312.119
   2_bss:  46.198 0.5661  0.7886    48544.862
   2_xyz:  36.687 0.6801  0.9218    31447.842
   2_adp:  33.347 0.7197  0.9505    27473.226
   2_occ:  33.389 0.7192  0.9492    27482.029
   3_bss:  33.337 0.7199  0.8925    27544.408
   3_xyz:  23.609 0.8253  0.9926    14754.404
   3_adp:  21.171 0.8504  1.0074    12442.592
   3_occ:  21.155 0.8505  1.0074    12417.005
   4_bss:  21.091 0.8510  0.9669    12352.829
   4_xyz:  17.227 0.8874  0.9811     8697.011
   4_adp:  16.603 0.8931  0.9733     8202.777
   4_occ:  16.606 0.8930  0.9732     8201.518
   5_bss:  16.564 0.8934  0.9665     8177.164
   5_xyz:  15.327 0.9039  0.9746     7226.627
   5_adp:  15.033 0.9066  0.9694     7076.138
   5_occ:  15.025 0.9067  0.9694     7067.243
   5_bss:  15.028 0.9067  0.9756     7069.820
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3830e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3830e+01
   1_xyz:   1.722  0.013  0.107 18.307  0.006  4.108   1.4403e-01
   1_adp:   1.722  0.013  0.107 18.307  0.006  4.108   1.4403e-01
   1_occ:   1.722  0.013  0.107 18.307  0.006  4.108   1.4403e-01
   2_bss:   1.722  0.013  0.107 18.307  0.006  4.108   1.4403e-01
   2_xyz:   1.163  0.008  0.081 16.198  0.005  4.124   8.0892e-02
   2_adp:   1.163  0.008  0.081 16.198  0.005  4.124   8.0892e-02
   2_occ:   1.163  0.008  0.081 16.198  0.005  4.124   8.0892e-02
   3_bss:   1.163  0.008  0.081 16.198  0.005  4.124   8.0892e-02
   3_xyz:   1.097  0.007  0.081 16.049  0.004  4.118   7.0592e-02
   3_adp:   1.097  0.007  0.081 16.049  0.004  4.118   7.0592e-02
   3_occ:   1.097  0.007  0.081 16.049  0.004  4.118   7.0592e-02
   4_bss:   1.097  0.007  0.081 16.049  0.004  4.118   7.0592e-02
   4_xyz:   1.025  0.008  0.076 15.846  0.004  4.127   6.5254e-02
   4_adp:   1.025  0.008  0.076 15.846  0.004  4.127   6.5254e-02
   4_occ:   1.025  0.008  0.076 15.846  0.004  4.127   6.5254e-02
   5_bss:   1.025  0.008  0.076 15.846  0.004  4.127   6.5254e-02
   5_xyz:   1.076  0.009  0.081 15.649  0.004  4.114   7.1446e-02
   5_adp:   1.076  0.009  0.081 15.649  0.004  4.114   7.1446e-02
   5_occ:   1.076  0.009  0.081 15.649  0.004  4.114   7.1446e-02
   5_bss:   1.076  0.009  0.081 15.649  0.004  4.114   7.1446e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9777e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9777e+00
   1_xyz:  13.711  0.186  0.417 84.961  0.033  2.112   1.0120e-01
   1_adp:  13.711  0.186  0.417 84.961  0.033  2.112   1.0120e-01
   1_occ:  13.711  0.186  0.417 84.961  0.033  2.112   1.0120e-01
   2_bss:  13.711  0.186  0.417 84.961  0.033  2.112   1.0120e-01
   2_xyz:   8.243  0.079  0.289 87.045  0.037  2.304   4.7838e-02
   2_adp:   8.243  0.079  0.289 87.045  0.037  2.304   4.7838e-02
   2_occ:   8.243  0.079  0.289 87.045  0.037  2.304   4.7838e-02
   3_bss:   8.243  0.079  0.289 87.045  0.037  2.304   4.7838e-02
   3_xyz:   8.273  0.048  0.368 87.553  0.033  2.249   5.1810e-02
   3_adp:   8.273  0.048  0.368 87.553  0.033  2.249   5.1810e-02
   3_occ:   8.273  0.048  0.368 87.553  0.033  2.249   5.1810e-02
   4_bss:   8.273  0.048  0.368 87.553  0.033  2.249   5.1810e-02
   4_xyz:   8.927  0.058  0.289 80.466  0.039  2.324   5.6847e-02
   4_adp:   8.927  0.058  0.289 80.466  0.039  2.324   5.6847e-02
   4_occ:   8.927  0.058  0.289 80.466  0.039  2.324   5.6847e-02
   5_bss:   8.927  0.058  0.289 80.466  0.039  2.324   5.6847e-02
   5_xyz:   6.869  0.056  0.343 83.507  0.043  2.336   5.4087e-02
   5_adp:   6.869  0.056  0.343 83.507  0.043  2.336   5.4087e-02
   5_occ:   6.869  0.056  0.343 83.507  0.043  2.336   5.4087e-02
   5_bss:   6.869  0.056  0.343 83.507  0.043  2.336   5.4087e-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:  82.78   0.00  14.23  59.69   0.00  12.19  82.78   0.00  25.34
   1_occ:  82.78   0.00  14.23  59.69   0.00  12.19  82.78   0.00  25.34
   2_bss:  82.78   0.00  14.23  59.69   0.00  12.19  82.78   0.00  25.34
   2_xyz:  82.78   0.00  14.23  59.69   0.00  12.19  82.78   0.00  25.34
   2_adp:  92.92   0.00  13.56  65.83   0.00  10.26  92.92   0.00  31.52
   2_occ:  92.92   0.00  13.56  65.83   0.00  10.26  92.92   0.00  31.52
   3_bss:  92.92   0.00  13.56  65.83   0.00  10.26  92.92   0.00  31.52
   3_xyz:  92.92   0.00  13.56  65.83   0.00  10.26  92.92   0.00  31.52
   3_adp:  90.80   0.00  13.58  68.92   0.00   9.55  90.80   1.19  35.58
   3_occ:  90.80   0.00  13.58  68.92   0.00   9.55  90.80   1.19  35.58
   4_bss:  90.80   0.00  13.58  68.92   0.00   9.55  90.80   1.19  35.58
   4_xyz:  90.80   0.00  13.58  68.92   0.00   9.55  90.80   1.19  35.58
   4_adp:  92.07   0.00  14.36  82.36   0.00   9.50  92.07   2.80  40.81
   4_occ:  92.07   0.00  14.36  82.36   0.00   9.50  92.07   2.80  40.81
   5_bss:  92.07   0.00  14.36  82.36   0.00   9.50  92.07   2.80  40.81
   5_xyz:  92.07   0.00  14.36  82.36   0.00   9.50  92.07   2.80  40.81
   5_adp:  93.80   0.00  14.17  86.43   0.00   9.34  93.80   2.42  40.48
   5_occ:  93.80   0.00  14.17  86.43   0.00   9.34  93.80   2.42  40.48
   5_bss:  95.79   1.99  16.16  88.42   1.99  11.33  95.79   4.41  42.47
------------------------------------------------------------------------
 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:    1.296    0.023    0.411
   1_adp:    1.296    0.023    0.411
   1_occ:    1.296    0.023    0.411
   2_bss:    1.296    0.023    0.411
   2_xyz:    1.787    0.038    0.558
   2_adp:    1.787    0.038    0.558
   2_occ:    1.787    0.038    0.558
   3_bss:    1.787    0.038    0.558
   3_xyz:    1.588    0.057    0.680
   3_adp:    1.588    0.057    0.680
   3_occ:    1.588    0.057    0.680
   4_bss:    1.588    0.057    0.680
   4_xyz:    1.691    0.056    0.729
   4_adp:    1.691    0.056    0.729
   4_occ:    1.691    0.056    0.729
   5_bss:    1.691    0.056    0.729
   5_xyz:    1.783    0.024    0.747
   5_adp:    1.783    0.024    0.747
   5_occ:    1.783    0.024    0.747
   5_bss:    1.783    0.024    0.747
------------------------------------------------------------------------

CPU time actual refinement: 346.61


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_636/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_636/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_636/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_636/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_636/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 346.46 
  Macro-tasks:
    bulk solvent and scale       = 41.88  
    individual site refinement   = 150.31 
    weights calculation          = 31.87  
    collect and process          = 6.60   
    model show statistics        = 0.13   
    TOTAL for macro-tasks        = 230.79 
  Micro-tasks:
    mask                            = 2.36   
    f_calc                          = 106.76 
    alpha_beta                      = 8.32   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 119.23 
    fmodel                         = 7.75   
    r_factors                      = 0.20   
    phase_errors                   = 10.43  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 256.49 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.784 micro seconds
Total CPU time: 6.00 minutes
from_scatterers_fft:    655 calls, 106.39 s
gradients_fft:          600 calls, 104.98 s

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

# Date 2008-01-16 Time 02:03:53 PST -0800 (1200477833.95 s)
Start R-work = 0.4878, R-free = 0.4709 (no bulk solvent and anisotropic scale)
Final R-work = 0.1339, R-free = 0.1825 (no bulk solvent and anisotropic scale)

Start R-work = 0.4790, R-free = 0.4565
Final R-work = 0.1165, R-free = 0.1666