# Date 2008-01-16 Time 02:52:00 PST -0800 (1200480720.67 s)
#phil __OFF__

Command line arguments: "../1008.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = sunbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 2486
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 1008

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (71.3037, 46.4607, 87.2539, 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: 3.32, per 1000 atoms: 1.18


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 46.4607, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1984 1.98322
Completeness in resolution range: 0.948207
Completeness with d_max=infinity: 0.945415

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1984
                             d_min =   1.9832

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (71.3037, 46.4607, 87.2539, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1984 1.98322
Completeness in resolution range: 0.948207
Completeness with d_max=infinity: 0.945415

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1989 -  4.2446 [2172/2198]  1953   219  10.1%
  bin  2:  4.2446 -  3.3813 [2087/2107]  1880   207   9.9%
  bin  3:  3.3813 -  2.9574 [2064/2083]  1857   207  10.0%
  bin  4:  2.9574 -  2.6887 [2042/2072]  1836   206  10.1%
  bin  5:  2.6887 -  2.4968 [2013/2032]  1820   193   9.6%
  bin  6:  2.4968 -  2.3502 [2020/2045]  1809   211  10.4%
  bin  7:  2.3502 -  2.2329 [2010/2038]  1809   201  10.0%
  bin  8:  2.2329 -  2.1360 [1999/2035]  1801   198   9.9%
  bin  9:  2.1360 -  2.0539 [1989/2031]  1795   194   9.8%
  bin 10:  2.0539 -  1.9832 [1193/2018]  1070   123  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1008/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 17
        2.42 -     3.04: 2171
        3.04 -     3.66: 4671
        3.66 -     4.28: 8964
        4.28 -     4.90: 12276
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 201 " - " O   HOH Z 349 "  2.290 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 324 " - " O   HOH Z 374 "  2.305 3.040 -x,y-1/2,-z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.305 3.040 x,y+1,z
  ... (remaining 28094 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_1008/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1008/model_refine_001.geo

CPU time processing inputs: 9.50


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 71.30375 46.4607 87.2539 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4629   r_free= 0.4463   ksol= 0.00   Bsol= 0.00   scale= 0.800    |
|                                                                             |
| 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:   0.64 A                  |
| x-ray target function (ml) for work reflections: 6.261760                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1989 -  4.7347 0.99   1408  157 0.3865 0.3598      6.5748      6.5173|
|  2:  4.7347 -  3.7770 0.99   1351  151 0.3627 0.3786      6.7292      6.7394|
|  3:  3.7770 -  3.3052 0.99   1340  144 0.4038 0.3679      6.6079      6.5795|
|  4:  3.3052 -  3.0056 0.99   1327  152 0.4504 0.4080      6.5039      6.4428|
|  5:  3.0056 -  2.7915 0.99   1320  147 0.4928 0.4614      6.3517      6.3565|
|  6:  2.7915 -  2.6279 0.99   1302  142 0.4835 0.4990      6.2517      6.1899|
|  7:  2.6279 -  2.4968 0.99   1298  139 0.5239 0.5124      6.2476      6.2244|
|  8:  2.4968 -  2.3886 0.98   1287  147 0.5134 0.4520      6.1597      6.1642|
|  9:  2.3886 -  2.2970 0.98   1276  150 0.4989 0.5151      6.1024      6.1627|
| 10:  2.2970 -  2.2179 1.00   1315  147 0.5252 0.4682       6.101      6.0525|
| 11:  2.2179 -  2.1488 0.98   1291  134 0.5119 0.4891      6.0318      6.0116|
| 12:  2.1488 -  2.0875 0.98   1262  144 0.5226 0.5414      5.9569      6.0143|
| 13:  2.0875 -  2.0327 0.99   1293  136 0.5202 0.5064       5.872      5.7779|
| 14:  2.0327 -  1.9832 0.43    560   69 0.5357 0.4801      5.8815      5.7937|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1989 -  4.7347  1408   157  0.72  32.66   0.79     0.76      65341.72|
|  2:  4.7347 -  3.7770  1351   151  0.75  30.53   0.89     0.81      86220.75|
|  3:  3.7770 -  3.3052  1340   144  0.67  38.13   0.86     0.77      91419.66|
|  4:  3.3052 -  3.0056  1327   152  0.59  44.29   0.80     0.68      81717.34|
|  5:  3.0056 -  2.7915  1320   147  0.51  51.35   0.74     0.60      69783.43|
|  6:  2.7915 -  2.6279  1302   142  0.47  54.17   0.74     0.53      62044.94|
|  7:  2.6279 -  2.4968  1298   139  0.42  58.34   0.74     0.48      60076.00|
|  8:  2.4968 -  2.3886  1287   147  0.38  61.37   0.73     0.44      56488.36|
|  9:  2.3886 -  2.2970  1276   150  0.39  60.36   0.73     0.45      51616.15|
| 10:  2.2970 -  2.2179  1315   147  0.39  60.57   0.75     0.46      46271.87|
| 11:  2.2179 -  2.1488  1291   134  0.39  60.72   0.77     0.47      43677.68|
| 12:  2.1488 -  2.0875  1262   144  0.37  62.23   0.75     0.46      40424.92|
| 13:  2.0875 -  2.0327  1293   136  0.37  62.27   0.71     0.46      34545.26|
| 14:  2.0327 -  1.9832   560    69  0.44  56.82   0.72     0.47      26594.59|
|alpha:            min =        0.44 max =            0.81 mean =         0.57|
|beta:             min =    26594.59 max =        91419.66 mean =     59936.26|
|figures of merit: min =        0.00 max =            1.00 mean =         0.50|
|phase err.(work): min =        0.00 max =           89.98 mean =        51.96|
|phase err.(test): min =        0.00 max =           89.99 mean =        51.96|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.384030             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.288   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.911862              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.169   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      169 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      682 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1485 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2617 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3903 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5027 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6531 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7657 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       54.063 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.691 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.073)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 12.073)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4694   r_free= 0.4532   ksol= 0.00   Bsol= 0.00   scale= 0.770    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.63 A                  |
| x-ray target function (ml) for work reflections: 6.264496                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4551   r_free= 0.4357   ksol= 0.34   Bsol= 20.00   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.35,8.38,9.04,0.00,0.00,0.00); trace/3= 8.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.65 A                  |
| x-ray target function (ml) for work reflections: 6.255831                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.409684              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.742   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.876024              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 76.849   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4551      final r-factor (work) = 0.3572          |
| start r-factor (free) = 0.4357      final r-factor (free) = 0.3714          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 83.5261 = 9.41 * 0.50 * 6.2622 + 1.00 * 54.0633                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 29.0331 = 9.41 * 0.50 * 6.1430 + 1.00 * 0.1312                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3572      final r-factor (work) = 0.3043          |
| start r-factor (free) = 0.3714      final r-factor (free) = 0.3512          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.3959 = 0.88 * 1.00 * 6.1430 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.2843 = 0.88 * 1.00 * 6.0159 + 1.00 * 0.0142                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.073)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.40   12.14    None  None   None       |
|    all(noH): 2823   0      0.00    79.40   12.14    None  None   None       |
|    Sol.    : 438    0      0.00    79.40   28.15    None  None   None       |
|    Mac.    : 2385   0      0.00    63.28   9.20     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.940: 1328   |   5:    39.700 -  47.640:   65        |
|      1:     7.940 -  15.880:  749   |   6:    47.640 -  55.580:   34        |
|      2:    15.880 -  23.820:  368   |   7:    55.580 -  63.520:   19        |
|      3:    23.820 -  31.760:  169   |   8:    63.520 -  71.460:    6        |
|      4:    31.760 -  39.700:   84   |   9:    71.460 -  79.400:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3043 r_free = 0.3512             target_work(ml) = 5.985         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3039 r_free = 0.3515             target_work(ml) = 5.985         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3039   r_free= 0.3515   ksol= 0.34   Bsol= 20.00   scale= 1.098   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.35,8.38,9.04,0.00,0.00,0.00); trace/3= 8.59                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.42 A                  |
| x-ray target function (ml) for work reflections: 5.984503                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2999   r_free= 0.3466   ksol= 0.35   Bsol= 50.00   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.00,4.49,5.67,0.00,0.00,0.00); trace/3= 5.05                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.44 A                  |
| x-ray target function (ml) for work reflections: 5.983572                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.226044              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.493   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.392995              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 137.027  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2999      final r-factor (work) = 0.2032          |
| start r-factor (free) = 0.3466      final r-factor (free) = 0.2533          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.8476 = 5.23 * 0.50 * 6.0146 + 1.00 * 0.1312                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.2976 = 5.23 * 0.50 * 5.8272 + 1.00 * 0.0710                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2032      final r-factor (work) = 0.1820          |
| start r-factor (free) = 0.2533      final r-factor (free) = 0.2317          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3045 = 0.39 * 1.00 * 5.8272 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2100 = 0.39 * 1.00 * 5.5947 + 1.00 * 0.0114                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 32     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.073)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    80.00   12.00    None  None   None       |
|    all(noH): 2823   0      0.00    80.00   12.00    None  None   None       |
|    Sol.    : 438    0      0.00    80.00   32.76    None  None   None       |
|    Mac.    : 2385   0      0.00    64.61   8.18     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 -   8.000: 1529   |   5:    39.998 -  47.997:   88        |
|      1:     8.000 -  15.999:  662   |   6:    47.997 -  55.997:   38        |
|      2:    15.999 -  23.999:  212   |   7:    55.997 -  63.996:   24        |
|      3:    23.999 -  31.998:  113   |   8:    63.996 -  71.996:    2        |
|      4:    31.998 -  39.998:  153   |   9:    71.996 -  79.995:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1820 r_free = 0.2317             target_work(ml) = 5.552         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1819 r_free = 0.2317             target_work(ml) = 5.551         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1819   r_free= 0.2317   ksol= 0.35   Bsol= 50.00   scale= 1.043   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.00,4.49,5.67,0.00,0.00,0.00); trace/3= 5.05                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.551177                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1803   r_free= 0.2295   ksol= 0.33   Bsol= 50.00   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.15,2.71,4.19,0.00,0.00,0.00); trace/3= 3.35                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.551251                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.011466              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.012  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 3.330726              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.703  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1803      final r-factor (work) = 0.1451          |
| start r-factor (free) = 0.2295      final r-factor (free) = 0.1905          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.7087 = 2.01 * 0.50 * 5.6051 + 1.00 * 0.0714                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.5451 = 2.01 * 0.50 * 5.4576 + 1.00 * 0.0563                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1451      final r-factor (work) = 0.1363          |
| start r-factor (free) = 0.1905      final r-factor (free) = 0.1867          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 18.1889 = 3.33 * 1.00 * 5.4576 + 1.00 * 0.0113                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 17.7748 = 3.33 * 1.00 * 5.3314 + 1.00 * 0.0172                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.073)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.96   13.32    None  None   None       |
|    all(noH): 2823   0      0.00    91.96   13.32    None  None   None       |
|    Sol.    : 438    0      0.51    91.96   39.26    None  None   None       |
|    Mac.    : 2385   0      0.00    80.05   8.55     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 -   9.196: 1673   |   5:    45.978 -  55.174:   92        |
|      1:     9.196 -  18.391:  580   |   6:    55.174 -  64.370:   64        |
|      2:    18.391 -  27.587:  155   |   7:    64.370 -  73.565:   30        |
|      3:    27.587 -  36.783:  119   |   8:    73.565 -  82.761:   14        |
|      4:    36.783 -  45.978:   91   |   9:    82.761 -  91.957:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1363 r_free = 0.1867             target_work(ml) = 5.323         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1363 r_free = 0.1869             target_work(ml) = 5.323         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1363   r_free= 0.1869   ksol= 0.33   Bsol= 50.00   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.15,2.71,4.19,0.00,0.00,0.00); trace/3= 3.35                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.323158                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1362   r_free= 0.1866   ksol= 0.33   Bsol= 60.69   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.77,2.39,3.98,0.00,0.00,0.00); trace/3= 3.05                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.322545                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.528676              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 123.223  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.212461              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 96.963   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1362      final r-factor (work) = 0.1198          |
| start r-factor (free) = 0.1866      final r-factor (free) = 0.1718          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.4620 = 3.53 * 0.50 * 5.3310 + 1.00 * 0.0563                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 9.3742 = 3.53 * 0.50 * 5.2703 + 1.00 * 0.0755                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1198      final r-factor (work) = 0.1192          |
| start r-factor (free) = 0.1718      final r-factor (free) = 0.1655          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1361 = 0.21 * 1.00 * 5.2703 + 1.00 * 0.0163                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1237 = 0.21 * 1.00 * 5.2252 + 1.00 * 0.0135                               |
|-----------------------------------------------------------------------------|
| number of iterations = 14      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.073)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    83.95   12.58    None  None   None       |
|    all(noH): 2823   0      0.00    83.95   12.58    None  None   None       |
|    Sol.    : 438    0      1.66    83.95   36.23    None  None   None       |
|    Mac.    : 2385   0      0.00    78.26   8.24     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 -   8.396: 1651   |   5:    41.977 -  50.373:   83        |
|      1:     8.396 -  16.791:  605   |   6:    50.373 -  58.768:   65        |
|      2:    16.791 -  25.186:  155   |   7:    58.768 -  67.164:   33        |
|      3:    25.186 -  33.582:  118   |   8:    67.164 -  75.559:   16        |
|      4:    33.582 -  41.977:   90   |   9:    75.559 -  83.955:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1192 r_free = 0.1655             target_work(ml) = 5.201         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1190 r_free = 0.1653             target_work(ml) = 5.200         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1190   r_free= 0.1653   ksol= 0.33   Bsol= 60.69   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.77,2.39,3.98,0.00,0.00,0.00); trace/3= 3.05                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.200471                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1190   r_free= 0.1652   ksol= 0.33   Bsol= 60.69   scale= 0.999   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.59,2.25,3.86,0.00,0.00,0.00); trace/3= 2.90                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.200419                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.942997              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 149.833  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.216780              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 101.495  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1190      final r-factor (work) = 0.1188          |
| start r-factor (free) = 0.1652      final r-factor (free) = 0.1637          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1510 = 1.94 * 0.50 * 5.2244 + 1.00 * 0.0755                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1141 = 1.94 * 0.50 * 5.2008 + 1.00 * 0.0615                               |
|-----------------------------------------------------------------------------|
| number of iterations = 24      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1188      final r-factor (work) = 0.1191          |
| start r-factor (free) = 0.1637      final r-factor (free) = 0.1635          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1420 = 0.22 * 1.00 * 5.2008 + 1.00 * 0.0146                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1449 = 0.22 * 1.00 * 5.1985 + 1.00 * 0.0180                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.073)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.45   12.09    None  None   None       |
|    all(noH): 2823   0      0.00    77.45   12.09    None  None   None       |
|    Sol.    : 438    0      2.02    77.45   34.02    None  None   None       |
|    Mac.    : 2385   0      0.00    77.37   8.07     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.745: 1554   |   5:    38.725 -  46.470:   78        |
|      1:     7.745 -  15.490:  663   |   6:    46.470 -  54.215:   79        |
|      2:    15.490 -  23.235:  171   |   7:    54.215 -  61.960:   21        |
|      3:    23.235 -  30.980:  119   |   8:    61.960 -  69.705:   17        |
|      4:    30.980 -  38.725:  113   |   9:    69.705 -  77.450:    8        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1191 r_free = 0.1635             target_work(ml) = 5.198         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1190 r_free = 0.1634             target_work(ml) = 5.198         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1190   r_free= 0.1634   ksol= 0.33   Bsol= 60.69   scale= 0.996   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.59,2.25,3.86,0.00,0.00,0.00); trace/3= 2.90                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.197726                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1989 -  4.7347 0.99   1408  157 0.1041 0.1369      5.4199      5.5859|
|  2:  4.7347 -  3.7770 0.99   1351  151 0.0915 0.1186       5.484      5.6645|
|  3:  3.7770 -  3.3052 0.99   1340  144 0.1118 0.1534      5.5197      5.8477|
|  4:  3.3052 -  3.0056 0.99   1327  152 0.1274 0.1730        5.49      5.6527|
|  5:  3.0056 -  2.7915 0.99   1320  147 0.1440 0.1748      5.3815      5.5906|
|  6:  2.7915 -  2.6279 0.99   1302  142 0.1283 0.2085      5.2355      5.5312|
|  7:  2.6279 -  2.4968 0.99   1298  139 0.1353 0.1602      5.2243      5.3455|
|  8:  2.4968 -  2.3886 0.98   1287  147 0.1253 0.1734      5.1216      5.3599|
|  9:  2.3886 -  2.2970 0.98   1276  150 0.1299 0.1909      5.1086      5.3765|
| 10:  2.2970 -  2.2179 1.00   1315  147 0.1228 0.1733      5.0026      5.2081|
| 11:  2.2179 -  2.1488 0.98   1291  134 0.1201 0.1948      4.9918       5.348|
| 12:  2.1488 -  2.0875 0.98   1262  144 0.1185 0.1767      4.8993      5.1952|
| 13:  2.0875 -  2.0327 0.99   1293  136 0.1239 0.1699      4.8332      5.0316|
| 14:  2.0327 -  1.9832 0.43    560   69 0.1088 0.1526      4.7279      4.8934|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1989 -  4.7347  1408   157  0.94   9.48   0.98     0.95       7652.69|
|  2:  4.7347 -  3.7770  1351   151  0.95   8.29   1.00     0.99       9630.39|
|  3:  3.7770 -  3.3052  1340   144  0.93  11.89   1.02     1.01      11300.00|
|  4:  3.3052 -  3.0056  1327   152  0.91  14.42   1.00     0.98      11052.18|
|  5:  3.0056 -  2.7915  1320   147  0.89  16.80   0.99     0.98       9066.73|
|  6:  2.7915 -  2.6279  1302   142  0.90  16.51   0.98     0.96       7344.03|
|  7:  2.6279 -  2.4968  1298   139  0.90  16.19   0.99     0.95       6632.85|
|  8:  2.4968 -  2.3886  1287   147  0.90  16.26   0.99     0.97       5832.36|
|  9:  2.3886 -  2.2970  1276   150  0.90  16.68   1.00     0.96       5713.00|
| 10:  2.2970 -  2.2179  1315   147  0.90  16.48   1.00     0.97       4677.05|
| 11:  2.2179 -  2.1488  1291   134  0.90  16.18   0.99     0.94       4604.17|
| 12:  2.1488 -  2.0875  1262   144  0.90  16.16   1.01     1.01       4149.41|
| 13:  2.0875 -  2.0327  1293   136  0.89  17.39   1.00     0.97       3636.84|
| 14:  2.0327 -  1.9832   560    69  0.91  14.97   0.99     0.96       2890.43|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2890.43 max =        11300.00 mean =      6930.31|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.95 mean =        14.77|
|phase err.(test): min =        0.00 max =           89.32 mean =        14.17|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1190   r_free= 0.1633   ksol= 0.32   Bsol= 55.06   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.33,-0.65,0.98,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.197654                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.20 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1190   r_free= 0.1633   ksol= 0.32   Bsol= 55.06   scale= 0.994   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.33,-0.65,0.98,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.197654                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1989 -  4.7347 0.99   1408  157 0.1035 0.1364      5.4148       5.581|
|  2:  4.7347 -  3.7770 0.99   1351  151 0.0909 0.1180      5.4785      5.6589|
|  3:  3.7770 -  3.3052 0.99   1340  144 0.1116 0.1531      5.5174      5.8461|
|  4:  3.3052 -  3.0056 0.99   1327  152 0.1275 0.1734      5.4909      5.6543|
|  5:  3.0056 -  2.7915 0.99   1320  147 0.1443 0.1751      5.3837      5.5933|
|  6:  2.7915 -  2.6279 0.99   1302  142 0.1287 0.2089      5.2379      5.5333|
|  7:  2.6279 -  2.4968 0.99   1298  139 0.1355 0.1602      5.2259      5.3466|
|  8:  2.4968 -  2.3886 0.98   1287  147 0.1256 0.1736      5.1229      5.3611|
|  9:  2.3886 -  2.2970 0.98   1276  150 0.1299 0.1908      5.1097      5.3764|
| 10:  2.2970 -  2.2179 1.00   1315  147 0.1231 0.1737      5.0039      5.2099|
| 11:  2.2179 -  2.1488 0.98   1291  134 0.1202 0.1948      4.9925      5.3478|
| 12:  2.1488 -  2.0875 0.98   1262  144 0.1185 0.1770      4.8998      5.1962|
| 13:  2.0875 -  2.0327 0.99   1293  136 0.1240 0.1699      4.8338       5.032|
| 14:  2.0327 -  1.9832 0.43    560   69 0.1087 0.1529      4.7283      4.8944|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1989 -  4.7347  1408   157  0.94   9.42   0.98     0.95       7575.55|
|  2:  4.7347 -  3.7770  1351   151  0.95   8.24   1.00     0.99       9547.90|
|  3:  3.7770 -  3.3052  1340   144  0.93  11.82   1.01     1.01      11227.24|
|  4:  3.3052 -  3.0056  1327   152  0.91  14.43   1.00     0.98      11059.08|
|  5:  3.0056 -  2.7915  1320   147  0.89  16.84   0.99     0.97       9102.22|
|  6:  2.7915 -  2.6279  1302   142  0.90  16.56   0.98     0.95       7380.40|
|  7:  2.6279 -  2.4968  1298   139  0.90  16.22   0.98     0.95       6660.07|
|  8:  2.4968 -  2.3886  1287   147  0.90  16.28   0.99     0.96       5847.34|
|  9:  2.3886 -  2.2970  1276   150  0.90  16.70   1.00     0.96       5725.51|
| 10:  2.2970 -  2.2179  1315   147  0.89  16.50   1.00     0.96       4687.56|
| 11:  2.2179 -  2.1488  1291   134  0.90  16.20   0.99     0.94       4614.84|
| 12:  2.1488 -  2.0875  1262   144  0.90  16.17   1.00     1.00       4155.97|
| 13:  2.0875 -  2.0327  1293   136  0.89  17.40   0.99     0.97       3641.91|
| 14:  2.0327 -  1.9832   560    69  0.91  14.98   0.98     0.96       2895.01|
|alpha:            min =        0.94 max =            1.01 mean =         0.97|
|beta:             min =     2895.01 max =        11227.24 mean =      6924.71|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.84 mean =        14.77|
|phase err.(test): min =        0.00 max =           89.47 mean =        14.17|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 12.073)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.81    80.26   14.90    None  None   None       |
|    all(noH): 2823   0      2.81    80.26   14.90    None  None   None       |
|    Sol.    : 438    0      4.83    80.26   36.83    None  None   None       |
|    Mac.    : 2385   0      2.81    80.18   10.88    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.808 -  10.553: 1554   |   5:    41.533 -  49.278:   78        |
|      1:    10.553 -  18.298:  663   |   6:    49.278 -  57.023:   79        |
|      2:    18.298 -  26.043:  171   |   7:    57.023 -  64.768:   21        |
|      3:    26.043 -  33.788:  119   |   8:    64.768 -  72.513:   17        |
|      4:    33.788 -  41.533:  113   |   9:    72.513 -  80.258:    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)= 330         
Filter by distance & map next to the model:
   mapped sites are within: 0.340 - 4.811
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 325 from: 330
   mapped sites are within: 0.750 - 4.811

peak=   10.889 closest distance to " CB  VAL A 230 " =    1.493
peak=    7.355 closest distance to " CG2 VAL A 296 " =    1.169
peak=    6.202 closest distance to " CD2 LEU A   5 " =    1.275
peak=    5.868 closest distance to " NH1 ARG A 138 " =    1.056
peak=    5.696 closest distance to " O   HOH Z 111 " =    2.045
peak=    5.661 closest distance to " CG  ARG A 138 " =    1.056
peak=    5.636 closest distance to " CG  LEU A   5 " =    1.243
peak=    5.560 closest distance to " CG  PRO A  54 " =    1.422
peak=    5.449 closest distance to " O   HOH Z 232 " =    2.275
peak=    5.353 closest distance to " CB  GLN A 223 " =    1.431
peak=    5.307 closest distance to " NE2 GLN A  11 " =    1.154
peak=    5.305 closest distance to " O   HOH Z 142 " =    2.085
peak=    5.071 closest distance to " CG  LEU A 228 " =    1.186
peak=    4.893 closest distance to " CG  PRO A 198 " =    1.315
peak=    4.879 closest distance to " CB  PRO A  54 " =    1.065
peak=    4.798 closest distance to " O   HOH Z 265 " =    2.311
peak=    4.750 closest distance to " CB  GLN A 183 " =    1.175
peak=    4.633 closest distance to " CD  ARG A 138 " =    1.174
peak=    4.607 closest distance to " CB  ASP A 124 " =    0.775
peak=    4.582 closest distance to " CB  ASN A 148 " =    1.346
peak=    4.576 closest distance to " ND2 ASN A 187 " =    1.546
peak=    4.564 closest distance to " O   HOH Z 236 " =    2.108
peak=    4.557 closest distance to " O   HOH Z   9 " =    1.556
peak=    4.517 closest distance to " CB  TRP A 266 " =    0.975
peak=    4.472 closest distance to " CB  SER A  63 " =    1.253
peak=    4.467 closest distance to " O   HOH Z 427 " =    2.849
peak=    4.463 closest distance to " O   HOH Z 369 " =    2.044
peak=    4.445 closest distance to " O   PRO A 198 " =    1.588
peak=    4.430 closest distance to " O   HOH Z 425 " =    1.519
peak=    4.423 closest distance to " O   HOH Z 272 " =    1.838
peak=    4.412 closest distance to " CD1AILE A 234 " =    1.082
peak=    4.409 closest distance to " O   HOH Z 298 " =    1.905
peak=    4.377 closest distance to " CG  LEU A 167 " =    1.213
peak=    4.363 closest distance to " CG  PRO A 243 " =    1.186
peak=    4.348 closest distance to " CB  VAL A 230 " =    1.233
peak=    4.345 closest distance to " CB  ARG A 275 " =    0.906
peak=    4.339 closest distance to " CZ  PHE A 218 " =    1.079
peak=    4.330 closest distance to " CG  PRO A 213 " =    1.273
peak=    4.282 closest distance to " O   HOH Z 126 " =    1.992
peak=    4.252 closest distance to " CB  GLU A 152 " =    1.170
peak=    4.250 closest distance to " CA  VAL A 296 " =    1.118
peak=    4.244 closest distance to " CB  ASN A  39 " =    0.909
peak=    4.224 closest distance to " CD2 LEU A 228 " =    1.195
peak=    4.191 closest distance to " O   HOH Z   7 " =    1.322
peak=    4.177 closest distance to " O   HOH Z 303 " =    2.213
peak=    4.158 closest distance to " CB  ASN A 142 " =    0.952
peak=    4.153 closest distance to " O   HOH Z 316 " =    3.034
peak=    4.127 closest distance to " CA  SER A  87 " =    0.903
peak=    4.096 closest distance to " CD  ARG A 159 " =    0.750
peak=    4.080 closest distance to " CB  SER A   3 " =    1.395
peak=    4.079 closest distance to " O   HOH Z  44 " =    2.229
peak=    4.073 closest distance to " CB  SER A 210 " =    0.789
peak=    4.053 closest distance to " O   HOH Z 234 " =    3.834
peak=    4.044 closest distance to " O   HOH Z 368 " =    2.040
peak=    4.033 closest distance to " CB  VAL A 265 " =    1.312
peak=    3.993 closest distance to " ND2 ASN A 249 " =    1.977
peak=    3.990 closest distance to " CB  SER A 216 " =    0.857
peak=    3.974 closest distance to " CB  LEU A 228 " =    1.172
peak=    3.955 closest distance to " O   HOH Z  88 " =    3.093
peak=    3.934 closest distance to " O   HOH Z 346 " =    1.604
peak=    3.927 closest distance to " CD  ARG A  66 " =    2.196
peak=    3.918 closest distance to " O   SER A  87 " =    2.334
peak=    3.910 closest distance to " NH1AARG A 145 " =    1.210
peak=    3.899 closest distance to " CB  ARG A  79 " =    1.500
peak=    3.874 closest distance to " CB  ASN A 187 " =    1.047
peak=    3.868 closest distance to " CD  LYS A 166 " =    1.305
peak=    3.860 closest distance to " CG  GLN A  88 " =    1.036
peak=    3.859 closest distance to " O   HOH Z 261 " =    2.114
peak=    3.848 closest distance to " O   HOH Z 411 " =    3.431
peak=    3.830 closest distance to " NH2AARG A 190 " =    1.813
peak=    3.820 closest distance to " O   HOH Z  78 " =    1.579
peak=    3.817 closest distance to " O   HOH Z 158 " =    3.161
peak=    3.810 closest distance to " N   PHE A 130 " =    1.247
peak=    3.807 closest distance to " CB  GLU A 128 " =    1.003
peak=    3.798 closest distance to " CA  PRO A  54 " =    1.352
peak=    3.797 closest distance to " CA  ALA A  51 " =    1.000
peak=    3.783 closest distance to " O   HOH Z   1 " =    1.932
peak=    3.764 closest distance to " CB  LEU A 143 " =    1.190
peak=    3.737 closest distance to " CG BARG A 102 " =    1.891
peak=    3.732 closest distance to " CA  TYR A  30 " =    0.988
peak=    3.728 closest distance to " CG1 ILE A 151 " =    1.230
peak=    3.717 closest distance to " O   HOH Z 214 " =    2.069
peak=    3.716 closest distance to " O   HOH Z 193 " =    1.721
peak=    3.711 closest distance to " CB AVAL A  41 " =    1.099
peak=    3.709 closest distance to " CB  SER A 212 " =    1.311
peak=    3.708 closest distance to " O   HOH Z  30 " =    1.643
peak=    3.697 closest distance to " CB  GLN A  88 " =    1.257
peak=    3.683 closest distance to " CB  ALA A 104 " =    0.757
peak=    3.683 closest distance to " CG2 THR A 221 " =    1.008
peak=    3.682 closest distance to " CB  ASN A 110 " =    1.113
peak=    3.680 closest distance to " CA  THR A 264 " =    0.771
peak=    3.678 closest distance to " CD1 LEU A 300 " =    1.125
peak=    3.673 closest distance to " CB  ILE A 120 " =    1.304
peak=    3.663 closest distance to " O   HOH Z 368 " =    3.590
peak=    3.657 closest distance to " O   HOH Z   2 " =    1.639
peak=    3.656 closest distance to " O   HOH Z 184 " =    1.530
peak=    3.654 closest distance to " CB  ARG A 190 " =    1.611
peak=    3.648 closest distance to " O   HOH Z 130 " =    2.086
peak=    3.646 closest distance to " O   HOH Z 263 " =    1.632
peak=    3.645 closest distance to " O   HOH Z 437 " =    1.825
peak=    3.640 closest distance to " O   HOH Z 193 " =    1.909
peak=    3.634 closest distance to " O   HOH Z 410 " =    1.426
peak=    3.627 closest distance to " O   HOH Z 353 " =    2.572
peak=    3.612 closest distance to " CG1 VAL A 153 " =    0.924
peak=    3.611 closest distance to " ND1 HIS A  86 " =    1.705
peak=    3.609 closest distance to " O   HOH Z  10 " =    1.817
peak=    3.603 closest distance to " CA  ARG A 195 " =    1.194
peak=    3.599 closest distance to " CG2 VAL A 257 " =    0.932
peak=    3.593 closest distance to " OD2 ASP A 286 " =    2.873
peak=    3.587 closest distance to " O   TYR A 116 " =    1.252
peak=    3.586 closest distance to " CA  ASN A 215 " =    1.161
peak=    3.583 closest distance to " OG  SER A  97 " =    2.997
peak=    3.577 closest distance to " CA  ALA A  21 " =    1.187
peak=    3.572 closest distance to " CB  GLU A  46 " =    0.963
peak=    3.561 closest distance to " CB  ALA A   9 " =    1.595
peak=    3.560 closest distance to " CG1 ILE A  49 " =    1.532
peak=    3.539 closest distance to " O   HOH Z 423 " =    1.611
peak=    3.535 closest distance to " CB  VAL A 202 " =    1.550
peak=    3.534 closest distance to " O   HOH Z  61 " =    1.587
peak=    3.534 closest distance to " O   HOH Z 273 " =    2.777
peak=    3.529 closest distance to " CB  ASP A 140 " =    0.891
peak=    3.528 closest distance to " CE  LYS A  76 " =    0.881
peak=    3.528 closest distance to " O   HOH Z   3 " =    1.940
peak=    3.523 closest distance to " CB  GLN A 103 " =    1.075
peak=    3.520 closest distance to " OD1 ASN A  69 " =    2.599
peak=    3.515 closest distance to " C   ALA A 299 " =    0.988
peak=    3.514 closest distance to " O   HOH Z 294 " =    1.532
peak=    3.511 closest distance to " O   HOH Z 222 " =    2.206
peak=    3.511 closest distance to " CD2 TYR A 186 " =    1.112
peak=    3.511 closest distance to " O   HOH Z   1 " =    1.931
peak=    3.510 closest distance to " CD BLYS A 290 " =    1.049
peak=    3.507 closest distance to " O   HOH Z 132 " =    2.641
peak=    3.506 closest distance to " NH1 ARG A  14 " =    0.916
peak=    3.506 closest distance to " CD1 ILE A  33 " =    1.792
peak=    3.502 closest distance to " O   HOH Z 126 " =    1.457
peak=    3.502 closest distance to " O   HOH Z 435 " =    1.996
peak=    3.502 closest distance to " CB  SER A 273 " =    0.950
peak=    3.500 closest distance to " CB  MET A  40 " =    0.853
peak=    3.493 closest distance to " O   HOH Z  21 " =    1.762
peak=    3.492 closest distance to " CB  VAL A 250 " =    1.100
peak=    3.478 closest distance to " CA  ALA A 295 " =    1.082
peak=    3.478 closest distance to " CB  GLU A 277 " =    3.618
peak=    3.477 closest distance to " O   HOH Z 280 " =    3.098
peak=    3.470 closest distance to " O   HOH Z 180 " =    2.118
peak=    3.468 closest distance to " O   HOH Z 156 " =    2.865
peak=    3.465 closest distance to " O   HOH Z 171 " =    4.139
peak=    3.465 closest distance to " CB  HIS A 108 " =    0.804
peak=    3.463 closest distance to " CG1BVAL A  72 " =    1.646
peak=    3.461 closest distance to " CB  THR A  82 " =    1.360
peak=    3.461 closest distance to " O   PHE A 192 " =    1.374
peak=    3.460 closest distance to " O   HOH Z 185 " =    1.871
peak=    3.457 closest distance to " NE2 HIS A 207 " =    1.161
peak=    3.450 closest distance to " CD  ARG A 269 " =    0.968
peak=    3.449 closest distance to " CA  TYR A 116 " =    1.452
peak=    3.445 closest distance to " CA  THR A 221 " =    0.873
peak=    3.445 closest distance to " CE1 TYR A 186 " =    1.331
peak=    3.444 closest distance to " O   HOH Z 147 " =    1.729
peak=    3.443 closest distance to " O   HOH Z 222 " =    1.323
peak=    3.442 closest distance to " N   SER A 135 " =    1.337
peak=    3.433 closest distance to " O   HOH Z 406 " =    1.547
peak=    3.432 closest distance to " O   ASN A 209 " =    1.433
peak=    3.432 closest distance to " OE2 GLU A   2 " =    1.859
peak=    3.431 closest distance to " O   HOH Z 291 " =    1.628
peak=    3.424 closest distance to " CB  THR A 157 " =    1.135
peak=    3.419 closest distance to " CA  ALA A 154 " =    1.090
peak=    3.419 closest distance to " CA  ARG A  36 " =    1.167
peak=    3.418 closest distance to " CG1 VAL A 296 " =    1.265
peak=    3.416 closest distance to " CA  ILE A 234 " =    0.947
peak=    3.411 closest distance to " CD  GLN A 240 " =    1.620
peak=    3.408 closest distance to " O   HOH Z 403 " =    1.622
peak=    3.407 closest distance to " N   SER A 271 " =    0.991
peak=    3.402 closest distance to " O   HOH Z 290 " =    1.248
peak=    3.398 closest distance to " CZ  PHE A 192 " =    0.969
peak=    3.396 closest distance to " CB  TRP A 150 " =    1.420
peak=    3.395 closest distance to " NE AARG A 275 " =    1.408
peak=    3.393 closest distance to " O   HOH Z 183 " =    1.387
peak=    3.391 closest distance to " CD1 LEU A   5 " =    1.392
peak=    3.386 closest distance to " O   HOH Z 193 " =    1.964
peak=    3.383 closest distance to " O   HOH Z 248 " =    1.670
peak=    3.381 closest distance to " CB  MET A  47 " =    1.017
peak=    3.380 closest distance to " O   HOH Z 264 " =    1.564
peak=    3.380 closest distance to " O   HOH Z  61 " =    1.583
peak=    3.379 closest distance to " O   HOH Z 126 " =    1.649
peak=    3.369 closest distance to " CB  LYS A 117 " =    1.251
peak=    3.369 closest distance to " O   HOH Z 128 " =    2.114
peak=    3.364 closest distance to " O   HOH Z 148 " =    3.523
peak=    3.364 closest distance to " CA  MET A  40 " =    1.116
peak=    3.362 closest distance to " CA  LYS A 117 " =    1.163
peak=    3.361 closest distance to " CE3 TRP A  85 " =    1.226
peak=    3.358 closest distance to " C   GLN A  88 " =    1.489
peak=    3.355 closest distance to " O   HOH Z 424 " =    2.631
peak=    3.355 closest distance to " CA  ILE A 106 " =    0.767
peak=    3.347 closest distance to " CG  MET A 185 " =    1.154
peak=    3.344 closest distance to " CB  GLN A  89 " =    1.124
peak=    3.344 closest distance to " CA  ASP A 162 " =    0.909
peak=    3.343 closest distance to " O   HOH Z 302 " =    1.819
peak=    3.342 closest distance to " O   HOH Z 285 " =    2.564
peak=    3.341 closest distance to " CB  PRO A 243 " =    1.400
peak=    3.340 closest distance to " NZ  LYS A 117 " =    3.227
peak=    3.337 closest distance to " CD2 TRP A 179 " =    1.293
peak=    3.337 closest distance to " O   HOH Z 175 " =    3.625
peak=    3.336 closest distance to " NH2AARG A 145 " =    1.169
peak=    3.336 closest distance to " O   HOH Z  57 " =    1.201
peak=    3.336 closest distance to " CB  ASN A 173 " =    1.004
peak=    3.335 closest distance to " O   HOH Z 422 " =    2.724
peak=    3.331 closest distance to " O   HOH Z 172 " =    3.055
peak=    3.331 closest distance to " CB  LEU A 237 " =    0.837
peak=    3.327 closest distance to " CB  TRP A 179 " =    1.509
peak=    3.326 closest distance to " O   MET A 105 " =    1.674
peak=    3.324 closest distance to " NH2BARG A 190 " =    1.514
peak=    3.322 closest distance to " CB  ALA A 114 " =    1.119
peak=    3.318 closest distance to " CA  ALA A 291 " =    0.925
peak=    3.314 closest distance to " CA  LEU A 282 " =    1.069
peak=    3.313 closest distance to " O   HOH Z 166 " =    3.776
peak=    3.312 closest distance to " O   HOH Z 419 " =    1.824
peak=    3.310 closest distance to " CZ3 TRP A 266 " =    1.057
peak=    3.309 closest distance to " N   ASN A 127 " =    1.260
peak=    3.305 closest distance to " O   HOH Z 409 " =    2.806
peak=    3.301 closest distance to " O   PRO A  90 " =    1.626
peak=    3.300 closest distance to " O   HOH Z 148 " =    2.259
peak=    3.300 closest distance to " O   HOH Z 109 " =    2.541
peak=    3.300 closest distance to " O   HOH Z 313 " =    1.605
peak=    3.299 closest distance to " CG1 ILE A  33 " =    1.336
peak=    3.294 closest distance to " ND2 ASN A 249 " =    0.894
peak=    3.294 closest distance to " O   HOH Z 392 " =    1.313
peak=    3.292 closest distance to " OG  SER A 135 " =    1.255
peak=    3.291 closest distance to " CB  ALA A 248 " =    1.097
peak=    3.291 closest distance to " O   HOH Z 197 " =    3.320
peak=    3.285 closest distance to " CA  TYR A 186 " =    1.551
peak=    3.284 closest distance to " OG  SER A  62 " =    2.891
peak=    3.282 closest distance to " CB  ALA A 291 " =    1.289
peak=    3.278 closest distance to " CA  ASN A 284 " =    0.847
peak=    3.278 closest distance to " O   ALA A 158 " =    1.404
peak=    3.276 closest distance to " O   HOH Z 344 " =    2.994
peak=    3.274 closest distance to " CZ3 TRP A  92 " =    1.395
peak=    3.273 closest distance to " OG  SER A  62 " =    3.067
peak=    3.273 closest distance to " O   HOH Z  59 " =    1.994
peak=    3.272 closest distance to " CZ  PHE A  38 " =    1.162
peak=    3.269 closest distance to " CB  ALA A   1 " =    4.811
peak=    3.268 closest distance to " OG BSER A 212 " =    2.794
peak=    3.263 closest distance to " CG  MET A 185 " =    0.979
peak=    3.262 closest distance to " OG  SER A 206 " =    1.169
peak=    3.261 closest distance to " CB  LEU A  83 " =    0.785
peak=    3.256 closest distance to " N   ALA A 256 " =    1.094
peak=    3.254 closest distance to " CA  ALA A 158 " =    1.188
peak=    3.253 closest distance to " ND1 HIS A  81 " =    1.806
peak=    3.248 closest distance to " O   HOH Z 303 " =    3.038
peak=    3.244 closest distance to " O   HOH Z 215 " =    2.955
peak=    3.242 closest distance to " CB  ALA A 242 " =    0.810
peak=    3.240 closest distance to " O   HOH Z 305 " =    3.449
peak=    3.239 closest distance to " CE3 TRP A 150 " =    0.968
peak=    3.233 closest distance to " CG BARG A 275 " =    1.486
peak=    3.231 closest distance to " O   HOH Z 329 " =    3.023
peak=    3.228 closest distance to " O   HOH Z 260 " =    1.470
peak=    3.228 closest distance to " O   HOH Z 238 " =    3.641
peak=    3.227 closest distance to " CA  TYR A  30 " =    1.079
peak=    3.223 closest distance to " O   HOH Z 332 " =    1.534
peak=    3.222 closest distance to " CD1 ILE A 106 " =    0.857
peak=    3.218 closest distance to " N   SER A  12 " =    1.604
peak=    3.212 closest distance to " CG  ARG A 159 " =    1.013
peak=    3.209 closest distance to " CA  ASN A 127 " =    1.095
peak=    3.207 closest distance to " O   HOH Z 110 " =    1.571
peak=    3.207 closest distance to " O   HOH Z 380 " =    1.748
peak=    3.206 closest distance to " CA  ASN A 217 " =    1.357
peak=    3.201 closest distance to " OG BSER A 164 " =    2.314
peak=    3.199 closest distance to " O   HOH Z 153 " =    3.819
peak=    3.195 closest distance to " N   TYR A  15 " =    0.798
peak=    3.191 closest distance to " CD1 LEU A 228 " =    2.013
peak=    3.190 closest distance to " CB  SER A  62 " =    1.137
peak=    3.189 closest distance to " O   HOH Z 162 " =    3.944
peak=    3.188 closest distance to " CA  GLY A 267 " =    1.000
peak=    3.183 closest distance to " CG2 ILE A 106 " =    0.906
peak=    3.181 closest distance to " O   HOH Z  40 " =    1.942
peak=    3.179 closest distance to " CG2 ILE A 120 " =    1.215
peak=    3.179 closest distance to " CG2 ILE A 151 " =    0.787
peak=    3.178 closest distance to " CB  GLU A 236 " =    1.125
peak=    3.168 closest distance to " O   PHE A  61 " =    1.442
peak=    3.165 closest distance to " O   LEU A 228 " =    1.930
peak=    3.163 closest distance to " O   HOH Z 154 " =    1.778
peak=    3.163 closest distance to " CG2 ILE A  20 " =    1.537
peak=    3.159 closest distance to " O   HOH Z  63 " =    1.249
peak=    3.158 closest distance to " O   HOH Z 352 " =    1.767
peak=    3.149 closest distance to " NZ ALYS A 290 " =    0.995
peak=    3.149 closest distance to " CA  GLU A 152 " =    0.899
peak=    3.146 closest distance to " CG  GLU A  37 " =    0.825
peak=    3.137 closest distance to " CD2 LEU A 255 " =    1.744
peak=    3.136 closest distance to " CB  ASN A 224 " =    0.985
peak=    3.136 closest distance to " O   HOH Z 392 " =    1.961
peak=    3.134 closest distance to " O   HOH Z 133 " =    1.808
peak=    3.131 closest distance to " O   HOH Z  43 " =    1.921
peak=    3.131 closest distance to " CE3 TRP A 274 " =    2.430
peak=    3.130 closest distance to " CB  ALA A 160 " =    1.272
peak=    3.130 closest distance to " OH  TYR A 214 " =    1.247
peak=    3.127 closest distance to " O   HOH Z 303 " =    2.575
peak=    3.126 closest distance to " CB  VAL A 268 " =    0.823
peak=    3.125 closest distance to " O   HOH Z  58 " =    1.604
peak=    3.123 closest distance to " O   HOH Z 188 " =    1.965
peak=    3.121 closest distance to " CG  MET A 113 " =    1.447
peak=    3.116 closest distance to " CA  LYS A 290 " =    1.319
peak=    3.113 closest distance to " O   HOH Z 213 " =    2.222
peak=    3.112 closest distance to " CB  SER A  26 " =    1.690
peak=    3.112 closest distance to " O   HOH Z  78 " =    2.236
peak=    3.111 closest distance to " CG1 VAL A 174 " =    1.036
peak=    3.109 closest distance to " CB  TYR A 116 " =    0.975
peak=    3.106 closest distance to " O   PRO A 198 " =    1.306
peak=    3.104 closest distance to " O   HOH Z   4 " =    1.654
peak=    3.102 closest distance to " CB  ARG A 138 " =    1.394
peak=    3.098 closest distance to " O   HOH Z 105 " =    1.554
peak=    3.096 closest distance to " N   ARG A 156 " =    1.351
peak=    3.096 closest distance to " CD1 LEU A 281 " =    1.098
peak=    3.093 closest distance to " OE2 GLU A  53 " =    2.088
peak=    3.093 closest distance to " O   HOH Z 173 " =    1.748
peak=    3.092 closest distance to " NZ  LYS A  48 " =    1.428
peak=    3.092 closest distance to " O   HOH Z 345 " =    3.502
peak=    3.091 closest distance to " CD1 LEU A 261 " =    1.214
peak=    3.085 closest distance to " NH2BARG A 145 " =    1.953
peak=    3.081 closest distance to " O   HOH Z 371 " =    2.897
peak=    3.080 closest distance to " CB  ALA A 227 " =    0.936
peak=    3.068 closest distance to " O   HOH Z 383 " =    2.260
peak=    3.053 closest distance to " CB  ALA A  43 " =    0.966
peak=    3.034 closest distance to " CG  ARG A 269 " =    1.798
peak=    3.027 closest distance to " O   HOH Z 271 " =    2.094
peak=    3.010 closest distance to " CB  PHE A 204 " =    0.762
peak=    3.009 closest distance to " O   GLN A 278 " =    1.548
peak=    3.003 closest distance to " O   HOH Z 175 " =    2.174

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 202         
Filter by distance & map next to the model:
   mapped sites are within: 0.557 - 5.558
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 196 from: 202
   mapped sites are within: 0.748 - 5.558

peak=   -5.586 closest distance to " CG2 VAL A 230 " =    0.752
peak=   -4.489 closest distance to " O   HOH Z 290 " =    1.126
peak=   -4.310 closest distance to " O   HOH Z 231 " =    0.849
peak=   -4.268 closest distance to " O   HOH Z 211 " =    1.203
peak=   -4.242 closest distance to " CD  ARG A  14 " =    3.180
peak=   -4.200 closest distance to " CB  PRO A 243 " =    2.609
peak=   -4.160 closest distance to " O   HOH Z 231 " =    1.714
peak=   -4.141 closest distance to " O   PRO A 198 " =    1.191
peak=   -4.096 closest distance to " CD  ARG A 156 " =    2.087
peak=   -4.089 closest distance to " O   HOH Z 351 " =    1.417
peak=   -4.086 closest distance to " CG  ARG A 138 " =    0.958
peak=   -4.075 closest distance to " CG1 VAL A 112 " =    2.650
peak=   -4.014 closest distance to " CD  ARG A 138 " =    1.199
peak=   -3.984 closest distance to " CA  GLY A 241 " =    2.367
peak=   -3.983 closest distance to " O   VAL A  67 " =    2.592
peak=   -3.975 closest distance to " O   GLY A 203 " =    2.469
peak=   -3.961 closest distance to " CG2 VAL A 296 " =    1.042
peak=   -3.929 closest distance to " CB  ALA A 248 " =    2.507
peak=   -3.908 closest distance to " O   HOH Z 394 " =    1.486
peak=   -3.890 closest distance to " OE1 GLN A  88 " =    1.019
peak=   -3.875 closest distance to " O   HOH Z 435 " =    2.855
peak=   -3.853 closest distance to " CD  GLN A 223 " =    2.187
peak=   -3.848 closest distance to " O   HOH Z  52 " =    1.555
peak=   -3.837 closest distance to " N   THR A 157 " =    1.478
peak=   -3.823 closest distance to " CB  PRO A 163 " =    2.460
peak=   -3.816 closest distance to " OG BSER A 134 " =    1.433
peak=   -3.806 closest distance to " O   HOH Z 389 " =    2.093
peak=   -3.801 closest distance to " CG1 VAL A 296 " =    1.324
peak=   -3.791 closest distance to " CD2 LEU A   5 " =    0.980
peak=   -3.776 closest distance to " CB  VAL A 230 " =    1.108
peak=   -3.773 closest distance to " CG2 VAL A 202 " =    2.736
peak=   -3.754 closest distance to " O   HOH Z 411 " =    5.349
peak=   -3.746 closest distance to " N   ALA A  43 " =    2.425
peak=   -3.730 closest distance to " CD  GLN A  58 " =    0.868
peak=   -3.726 closest distance to " OG  SER A  97 " =    2.298
peak=   -3.720 closest distance to " O   HOH Z  51 " =    0.997
peak=   -3.712 closest distance to " CB  ALA A  43 " =    2.574
peak=   -3.711 closest distance to " CZ3 TRP A 179 " =    1.169
peak=   -3.705 closest distance to " O   HOH Z 359 " =    3.182
peak=   -3.696 closest distance to " O   TYR A 247 " =    2.834
peak=   -3.694 closest distance to " CA  ASP A  27 " =    2.421
peak=   -3.691 closest distance to " CZ2 TRP A  92 " =    2.864
peak=   -3.677 closest distance to " O   HOH Z 185 " =    2.219
peak=   -3.673 closest distance to " CE2 TYR A  30 " =    2.791
peak=   -3.649 closest distance to " C   LEU A 222 " =    0.826
peak=   -3.641 closest distance to " CG1 VAL A 112 " =    2.933
peak=   -3.638 closest distance to " CB  TRP A  85 " =    2.619
peak=   -3.631 closest distance to " O   HOH Z  44 " =    2.283
peak=   -3.628 closest distance to " CD1 LEU A 228 " =    2.406
peak=   -3.625 closest distance to " CG  TRP A 266 " =    1.818
peak=   -3.623 closest distance to " O   HOH Z 429 " =    2.061
peak=   -3.609 closest distance to " OG  SER A  87 " =    1.411
peak=   -3.608 closest distance to " CA  GLY A 241 " =    3.092
peak=   -3.607 closest distance to " CB  PHE A 192 " =    1.770
peak=   -3.605 closest distance to " CB  ALA A 161 " =    2.608
peak=   -3.597 closest distance to " O   HOH Z 359 " =    1.604
peak=   -3.585 closest distance to " NH2AARG A 275 " =    5.419
peak=   -3.581 closest distance to " CG  MET A 105 " =    0.999
peak=   -3.580 closest distance to " O   GLY A  17 " =    1.366
peak=   -3.570 closest distance to " C   ALA A 158 " =    1.478
peak=   -3.567 closest distance to " O   VAL A 189 " =    2.523
peak=   -3.564 closest distance to " O   HOH Z 295 " =    1.524
peak=   -3.548 closest distance to " CE3 TRP A 150 " =    2.259
peak=   -3.541 closest distance to " CD1 LEU A 101 " =    2.377
peak=   -3.537 closest distance to " O   HOH Z 166 " =    2.290
peak=   -3.533 closest distance to " NH2 ARG A  79 " =    1.977
peak=   -3.529 closest distance to " ND2 ASN A  45 " =    1.232
peak=   -3.517 closest distance to " O   HOH Z 377 " =    1.729
peak=   -3.507 closest distance to " CZ2 TRP A 274 " =    0.918
peak=   -3.501 closest distance to " O   HOH Z 241 " =    1.255
peak=   -3.499 closest distance to " O   PRO A 163 " =    1.968
peak=   -3.489 closest distance to " O   HOH Z 140 " =    1.318
peak=   -3.488 closest distance to " O   HOH Z 275 " =    1.820
peak=   -3.483 closest distance to " C   MET A 188 " =    1.556
peak=   -3.479 closest distance to " CD  GLU A 277 " =    1.130
peak=   -3.475 closest distance to " SG BCYS A 201 " =    2.278
peak=   -3.474 closest distance to " O   HOH Z 281 " =    2.632
peak=   -3.474 closest distance to " O   HOH Z  73 " =    2.092
peak=   -3.470 closest distance to " CG1 VAL A 265 " =    2.440
peak=   -3.460 closest distance to " CG  ASP A 231 " =    0.748
peak=   -3.454 closest distance to " OH  TYR A 172 " =    1.772
peak=   -3.447 closest distance to " C   ASN A 285 " =    2.416
peak=   -3.437 closest distance to " CA  SER A 135 " =    1.373
peak=   -3.437 closest distance to " O   HOH Z 100 " =    1.169
peak=   -3.433 closest distance to " O   ARG A 145 " =    1.520
peak=   -3.426 closest distance to " CD2 LEU A 237 " =    2.744
peak=   -3.426 closest distance to " CE BMET A  47 " =    1.574
peak=   -3.418 closest distance to " CE2 PHE A 218 " =    2.500
peak=   -3.406 closest distance to " CG1 VAL A 197 " =    2.448
peak=   -3.393 closest distance to " C   GLU A 236 " =    0.900
peak=   -3.391 closest distance to " O   HOH Z  43 " =    1.699
peak=   -3.386 closest distance to " CD1 ILE A 199 " =    2.633
peak=   -3.386 closest distance to " N   ALA A 226 " =    2.144
peak=   -3.386 closest distance to " O   HOH Z 166 " =    2.025
peak=   -3.384 closest distance to " CD  GLN A  88 " =    0.848
peak=   -3.383 closest distance to " O   HOH Z 103 " =    1.876
peak=   -3.381 closest distance to " C   HIS A 108 " =    1.156
peak=   -3.380 closest distance to " O   GLY A  80 " =    2.496
peak=   -3.379 closest distance to " O   HOH Z  60 " =    2.410
peak=   -3.377 closest distance to " ND2 ASN A  60 " =    1.604
peak=   -3.376 closest distance to " O   ILE A  49 " =    1.726
peak=   -3.375 closest distance to " CZ  PHE A 192 " =    2.798
peak=   -3.375 closest distance to " CG1 VAL A 112 " =    2.738
peak=   -3.358 closest distance to " CD1 LEU A 101 " =    2.858
peak=   -3.356 closest distance to " CD1 ILE A  33 " =    2.517
peak=   -3.349 closest distance to " O   GLY A 211 " =    1.278
peak=   -3.348 closest distance to " O   HOH Z 128 " =    2.641
peak=   -3.343 closest distance to " CA  GLY A  98 " =    1.978
peak=   -3.340 closest distance to " O   HOH Z  65 " =    1.157
peak=   -3.333 closest distance to " O   HOH Z 417 " =    3.047
peak=   -3.330 closest distance to " O   HOH Z 313 " =    1.320
peak=   -3.313 closest distance to " O   SER A  22 " =    2.222
peak=   -3.313 closest distance to " CB  VAL A 296 " =    1.056
peak=   -3.308 closest distance to " O   SER A 271 " =    2.279
peak=   -3.306 closest distance to " O   HOH Z   9 " =    1.659
peak=   -3.306 closest distance to " O   HOH Z 136 " =    0.936
peak=   -3.301 closest distance to " CD2 PHE A  61 " =    1.845
peak=   -3.301 closest distance to " O   HOH Z 437 " =    1.736
peak=   -3.295 closest distance to " O   VAL A  67 " =    2.769
peak=   -3.295 closest distance to " CG  PRO A 163 " =    2.559
peak=   -3.288 closest distance to " NE2 GLN A  88 " =    0.976
peak=   -3.287 closest distance to " CD  PRO A 213 " =    2.041
peak=   -3.287 closest distance to " ND2 ASN A  45 " =    1.881
peak=   -3.287 closest distance to " O   HOH Z  38 " =    1.550
peak=   -3.284 closest distance to " CD2 TYR A 293 " =    1.916
peak=   -3.279 closest distance to " O   HOH Z 118 " =    1.270
peak=   -3.268 closest distance to " O   HOH Z 345 " =    2.126
peak=   -3.267 closest distance to " N   SER A   3 " =    2.032
peak=   -3.265 closest distance to " CZ  PHE A 130 " =    1.038
peak=   -3.261 closest distance to " O   HOH Z 108 " =    1.447
peak=   -3.253 closest distance to " OG  SER A 206 " =    1.760
peak=   -3.250 closest distance to " O   HOH Z  11 " =    1.933
peak=   -3.250 closest distance to " O   HOH Z 111 " =    1.939
peak=   -3.250 closest distance to " CG  PHE A 283 " =    2.757
peak=   -3.245 closest distance to " CA  GLY A 203 " =    2.484
peak=   -3.242 closest distance to " CB  PHE A 130 " =    1.300
peak=   -3.241 closest distance to " CB  ASP A 132 " =    2.353
peak=   -3.239 closest distance to " CZ  PHE A  38 " =    2.652
peak=   -3.235 closest distance to " O   HOH Z 177 " =    1.858
peak=   -3.233 closest distance to " O   HOH Z 350 " =    1.751
peak=   -3.232 closest distance to " OG  SER A  63 " =    1.115
peak=   -3.228 closest distance to " O   HOH Z 166 " =    1.436
peak=   -3.226 closest distance to " O   ASP A  27 " =    1.944
peak=   -3.222 closest distance to " N   ASP A 270 " =    1.561
peak=   -3.218 closest distance to " O   HOH Z 198 " =    2.239
peak=   -3.216 closest distance to " O   HOH Z 198 " =    0.986
peak=   -3.215 closest distance to " C   PHE A  59 " =    1.204
peak=   -3.215 closest distance to " ND2BASN A 224 " =    1.513
peak=   -3.212 closest distance to " OG BSER A 134 " =    1.842
peak=   -3.209 closest distance to " O   TRP A  70 " =    1.423
peak=   -3.198 closest distance to " C   LEU A 143 " =    1.150
peak=   -3.196 closest distance to " CD1 TYR A 169 " =    2.562
peak=   -3.191 closest distance to " O   HOH Z 390 " =    2.355
peak=   -3.185 closest distance to " CA  VAL A 296 " =    1.068
peak=   -3.185 closest distance to " N   SER A 212 " =    1.904
peak=   -3.183 closest distance to " O   HOH Z 353 " =    2.046
peak=   -3.181 closest distance to " O   HOH Z 412 " =    4.420
peak=   -3.180 closest distance to " CD2 HIS A 207 " =    2.407
peak=   -3.180 closest distance to " CD  PRO A 243 " =    2.031
peak=   -3.178 closest distance to " NE2 GLN A 278 " =    2.037
peak=   -3.169 closest distance to " O   HOH Z 309 " =    2.304
peak=   -3.168 closest distance to " O   HOH Z 357 " =    1.901
peak=   -3.165 closest distance to " O   HOH Z  52 " =    1.762
peak=   -3.164 closest distance to " O   HOH Z 389 " =    1.392
peak=   -3.164 closest distance to " O   HOH Z 368 " =    1.555
peak=   -3.164 closest distance to " CB  ALA A 114 " =    2.468
peak=   -3.160 closest distance to " O   HOH Z 112 " =    1.349
peak=   -3.151 closest distance to " NH2 ARG A  79 " =    1.558
peak=   -3.141 closest distance to " O   HOH Z 275 " =    1.444
peak=   -3.140 closest distance to " CB  TYR A  15 " =    2.181
peak=   -3.139 closest distance to " N   ALA A 248 " =    1.600
peak=   -3.138 closest distance to " O   HOH Z 407 " =    3.158
peak=   -3.138 closest distance to " O   PRO A 198 " =    1.348
peak=   -3.138 closest distance to " O   HOH Z 251 " =    4.888
peak=   -3.137 closest distance to " CD  ARG A 139 " =    1.751
peak=   -3.134 closest distance to " CB  ALA A   9 " =    2.606
peak=   -3.133 closest distance to " O   HOH Z 102 " =    1.531
peak=   -3.132 closest distance to " CG  GLU A 152 " =    0.785
peak=   -3.122 closest distance to " CD1 LEU A 297 " =    2.530
peak=   -3.120 closest distance to " O   HOH Z 111 " =    4.497
peak=   -3.113 closest distance to " N   ASP A 191 " =    1.127
peak=   -3.112 closest distance to " C   LYS A  76 " =    1.346
peak=   -3.106 closest distance to " CE  LYS A  76 " =    2.653
peak=   -3.102 closest distance to " O   SER A  62 " =    2.368
peak=   -3.102 closest distance to " O   HOH Z 216 " =    1.464
peak=   -3.100 closest distance to " N   LYS A 166 " =    1.959
peak=   -3.097 closest distance to " O   HOH Z 292 " =    1.661
peak=   -3.097 closest distance to " O   HOH Z  63 " =    1.846
peak=   -3.088 closest distance to " OH  TYR A 247 " =    1.874
peak=   -3.087 closest distance to " O   HOH Z  51 " =    1.250
peak=   -3.081 closest distance to " N   ALA A 248 " =    2.446
peak=   -3.054 closest distance to " O   HOH Z 406 " =    2.154
peak=   -3.049 closest distance to " O   HOH Z 336 " =    5.558
peak=   -3.044 closest distance to " N   SER A 276 " =    1.321
peak=   -3.037 closest distance to " CE  MET A 105 " =    2.358
peak=   -3.030 closest distance to " OD1 ASP A 171 " =    1.650

================= 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    :  0.4629 0.4463   6.261760e+00   6.239719e+00
   1_bss:  0.4551 0.4357   6.255831e+00   6.231717e+00
   1_xyz:  0.3572 0.3714   6.101483e+00   6.131849e+00
   1_adp:  0.3043 0.3512   5.985257e+00   6.082506e+00
   1_occ:  0.3039 0.3515   5.984503e+00   6.082752e+00
   2_bss:  0.2999 0.3466   5.983572e+00   6.079383e+00
   2_xyz:  0.2032 0.2533   5.652659e+00   5.817034e+00
   2_adp:  0.1820 0.2317   5.551607e+00   5.732483e+00
   2_occ:  0.1819 0.2317   5.551177e+00   5.732526e+00
   3_bss:  0.1803 0.2295   5.551251e+00   5.731151e+00
   3_xyz:  0.1451 0.1905   5.360604e+00   5.566045e+00
   3_adp:  0.1363 0.1867   5.323034e+00   5.546336e+00
   3_occ:  0.1363 0.1869   5.323158e+00   5.546752e+00
   4_bss:  0.1362 0.1866   5.322545e+00   5.546372e+00
   4_xyz:  0.1198 0.1718   5.223715e+00   5.469616e+00
   4_adp:  0.1192 0.1655   5.201194e+00   5.431479e+00
   4_occ:  0.1190 0.1653   5.200471e+00   5.430607e+00
   5_bss:  0.1190 0.1652   5.200419e+00   5.430529e+00
   5_xyz:  0.1188 0.1637   5.197363e+00   5.425264e+00
   5_adp:  0.1191 0.1635   5.198203e+00   5.427075e+00
   5_occ:  0.1190 0.1634   5.197726e+00   5.426512e+00
   5_bss:  0.1190 0.1633   5.197654e+00   5.426464e+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:  0.339  20.001   8.346   8.378   9.035   0.000   0.000   0.000
   1_xyz:  0.339  20.001   8.346   8.378   9.035   0.000   0.000   0.000
   1_adp:  0.339  20.001   8.346   8.378   9.035   0.000   0.000   0.000
   1_occ:  0.339  20.001   8.346   8.378   9.035   0.000   0.000   0.000
   2_bss:  0.346  50.000   5.005   4.489   5.667   0.000   0.000   0.000
   2_xyz:  0.346  50.000   5.005   4.489   5.667   0.000   0.000   0.000
   2_adp:  0.346  50.000   5.005   4.489   5.667   0.000   0.000   0.000
   2_occ:  0.346  50.000   5.005   4.489   5.667   0.000   0.000   0.000
   3_bss:  0.326  50.000   3.151   2.710   4.192   0.000   0.000   0.000
   3_xyz:  0.326  50.000   3.151   2.710   4.192   0.000   0.000   0.000
   3_adp:  0.326  50.000   3.151   2.710   4.192   0.000   0.000   0.000
   3_occ:  0.326  50.000   3.151   2.710   4.192   0.000   0.000   0.000
   4_bss:  0.330  60.693   2.765   2.393   3.978   0.000   0.000   0.000
   4_xyz:  0.330  60.693   2.765   2.393   3.978   0.000   0.000   0.000
   4_adp:  0.330  60.693   2.765   2.393   3.978   0.000   0.000   0.000
   4_occ:  0.330  60.693   2.765   2.393   3.978   0.000   0.000   0.000
   5_bss:  0.332  60.693   2.594   2.246   3.865   0.000   0.000   0.000
   5_xyz:  0.332  60.693   2.594   2.246   3.865   0.000   0.000   0.000
   5_adp:  0.332  60.693   2.594   2.246   3.865   0.000   0.000   0.000
   5_occ:  0.332  60.693   2.594   2.246   3.865   0.000   0.000   0.000
   5_bss:  0.322  55.061  -0.331  -0.649   0.980   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  51.960 0.4966  0.5683    59932.319
   1_bss:  52.204 0.4922  0.7267    58542.028
   1_xyz:  42.114 0.6163  0.8796    40151.249
   1_adp:  37.356 0.6739  0.9785    34004.100
   1_occ:  37.395 0.6733  0.9770    34020.896
   2_bss:  37.092 0.6768  0.8670    33547.368
   2_xyz:  25.279 0.8080  0.9925    16351.268
   2_adp:  22.371 0.8387  1.0104    13514.986
   2_occ:  22.367 0.8387  1.0101    13489.838
   3_bss:  22.302 0.8394  0.9508    13449.035
   3_xyz:  17.937 0.8810  0.9797     9255.640
   3_adp:  17.475 0.8855  0.9792     8928.109
   3_occ:  17.486 0.8854  0.9790     8933.432
   4_bss:  17.483 0.8854  0.9680     8932.221
   4_xyz:  15.863 0.8992  0.9757     7544.438
   4_adp:  14.962 0.9072  0.9797     7043.941
   4_occ:  14.956 0.9072  0.9795     7028.908
   5_bss:  14.954 0.9073  0.9746     7026.962
   5_xyz:  14.738 0.9094  0.9741     6918.944
   5_adp:  14.716 0.9097  0.9720     6937.048
   5_occ:  14.708 0.9097  0.9720     6930.016
   5_bss:  14.711 0.9097  0.9686     6924.428
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.4063e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.4063e+01
   1_xyz:   1.621  0.013  0.105 18.146  0.006  4.111   1.3120e-01
   1_adp:   1.621  0.013  0.105 18.146  0.006  4.111   1.3120e-01
   1_occ:   1.621  0.013  0.105 18.146  0.006  4.111   1.3120e-01
   2_bss:   1.621  0.013  0.105 18.146  0.006  4.111   1.3120e-01
   2_xyz:   1.068  0.008  0.079 16.295  0.005  4.129   7.0990e-02
   2_adp:   1.068  0.008  0.079 16.295  0.005  4.129   7.0990e-02
   2_occ:   1.068  0.008  0.079 16.295  0.005  4.129   7.0990e-02
   3_bss:   1.068  0.008  0.079 16.295  0.005  4.129   7.0990e-02
   3_xyz:   0.942  0.006  0.074 15.675  0.003  4.119   5.6289e-02
   3_adp:   0.942  0.006  0.074 15.675  0.003  4.119   5.6289e-02
   3_occ:   0.942  0.006  0.074 15.675  0.003  4.119   5.6289e-02
   4_bss:   0.942  0.006  0.074 15.675  0.003  4.119   5.6289e-02
   4_xyz:   1.118  0.010  0.088 15.822  0.004  4.128   7.5493e-02
   4_adp:   1.118  0.010  0.088 15.822  0.004  4.128   7.5493e-02
   4_occ:   1.118  0.010  0.088 15.822  0.004  4.128   7.5493e-02
   5_bss:   1.118  0.010  0.088 15.822  0.004  4.128   7.5493e-02
   5_xyz:   0.989  0.007  0.078 15.556  0.003  4.112   6.1463e-02
   5_adp:   0.989  0.007  0.078 15.556  0.003  4.112   6.1463e-02
   5_occ:   0.989  0.007  0.078 15.556  0.003  4.112   6.1463e-02
   5_bss:   0.989  0.007  0.078 15.556  0.003  4.112   6.1463e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   7.0097e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   7.0097e+00
   1_xyz:  13.315  0.162  0.402 85.856  0.033  2.254   9.6793e-02
   1_adp:  13.315  0.162  0.402 85.856  0.033  2.254   9.6793e-02
   1_occ:  13.315  0.162  0.402 85.856  0.033  2.254   9.6793e-02
   2_bss:  13.315  0.162  0.402 85.856  0.033  2.254   9.6793e-02
   2_xyz:   7.536  0.056  0.275 86.940  0.048  2.294   5.2029e-02
   2_adp:   7.536  0.056  0.275 86.940  0.048  2.294   5.2029e-02
   2_occ:   7.536  0.056  0.275 86.940  0.048  2.294   5.2029e-02
   3_bss:   7.536  0.056  0.275 86.940  0.048  2.294   5.2029e-02
   3_xyz:   7.674  0.049  0.373 84.183  0.026  2.366   3.2827e-02
   3_adp:   7.674  0.049  0.373 84.183  0.026  2.366   3.2827e-02
   3_occ:   7.674  0.049  0.373 84.183  0.026  2.366   3.2827e-02
   4_bss:   7.674  0.049  0.373 84.183  0.026  2.366   3.2827e-02
   4_xyz:   9.315  0.070  0.533 82.558  0.041  2.309   5.1029e-02
   4_adp:   9.315  0.070  0.533 82.558  0.041  2.309   5.1029e-02
   4_occ:   9.315  0.070  0.533 82.558  0.041  2.309   5.1029e-02
   5_bss:   9.315  0.070  0.533 82.558  0.041  2.309   5.1029e-02
   5_xyz:   8.359  0.050  0.446 83.194  0.037  2.363   3.9000e-02
   5_adp:   8.359  0.050  0.446 83.194  0.037  2.363   3.9000e-02
   5_occ:   8.359  0.050  0.446 83.194  0.037  2.363   3.9000e-02
   5_bss:   8.359  0.050  0.446 83.194  0.037  2.363   3.9000e-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:  79.40   0.00  12.14  63.28   0.00   9.20  79.40   0.00  28.15
   1_occ:  79.40   0.00  12.14  63.28   0.00   9.20  79.40   0.00  28.15
   2_bss:  79.40   0.00  12.14  63.28   0.00   9.20  79.40   0.00  28.15
   2_xyz:  79.40   0.00  12.14  63.28   0.00   9.20  79.40   0.00  28.15
   2_adp:  80.00   0.00  12.00  64.61   0.00   8.18  80.00   0.00  32.76
   2_occ:  80.00   0.00  12.00  64.61   0.00   8.18  80.00   0.00  32.76
   3_bss:  80.00   0.00  12.00  64.61   0.00   8.18  80.00   0.00  32.76
   3_xyz:  80.00   0.00  12.00  64.61   0.00   8.18  80.00   0.00  32.76
   3_adp:  91.96   0.00  13.32  80.05   0.00   8.55  91.96   0.51  39.26
   3_occ:  91.96   0.00  13.32  80.05   0.00   8.55  91.96   0.51  39.26
   4_bss:  91.96   0.00  13.32  80.05   0.00   8.55  91.96   0.51  39.26
   4_xyz:  91.96   0.00  13.32  80.05   0.00   8.55  91.96   0.51  39.26
   4_adp:  83.95   0.00  12.58  78.26   0.00   8.24  83.95   1.66  36.23
   4_occ:  83.95   0.00  12.58  78.26   0.00   8.24  83.95   1.66  36.23
   5_bss:  83.95   0.00  12.58  78.26   0.00   8.24  83.95   1.66  36.23
   5_xyz:  83.95   0.00  12.58  78.26   0.00   8.24  83.95   1.66  36.23
   5_adp:  77.45   0.00  12.09  77.37   0.00   8.07  77.45   2.02  34.02
   5_occ:  77.45   0.00  12.09  77.37   0.00   8.07  77.45   2.02  34.02
   5_bss:  80.26   2.81  14.90  80.18   2.81  10.88  80.26   4.83  36.83
------------------------------------------------------------------------
 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:    1.221    0.009    0.406
   1_adp:    1.221    0.009    0.406
   1_occ:    1.221    0.009    0.406
   2_bss:    1.221    0.009    0.406
   2_xyz:    1.371    0.043    0.555
   2_adp:    1.371    0.043    0.555
   2_occ:    1.371    0.043    0.555
   3_bss:    1.371    0.043    0.555
   3_xyz:    1.483    0.054    0.592
   3_adp:    1.483    0.054    0.592
   3_occ:    1.483    0.054    0.592
   4_bss:    1.483    0.054    0.592
   4_xyz:    1.647    0.018    0.627
   4_adp:    1.647    0.018    0.627
   4_occ:    1.647    0.018    0.627
   5_bss:    1.647    0.018    0.627
   5_xyz:    1.734    0.016    0.634
   5_adp:    1.734    0.016    0.634
   5_occ:    1.734    0.016    0.634
   5_bss:    1.734    0.016    0.634
------------------------------------------------------------------------

CPU time actual refinement: 326.65


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1008/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_1008/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1008/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1008/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_1008/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 326.50 
  Macro-tasks:
    bulk solvent and scale       = 40.75  
    individual site refinement   = 129.95 
    weights calculation          = 32.21  
    collect and process          = 6.57   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 209.60 
  Micro-tasks:
    mask                            = 1.78   
    f_calc                          = 99.61  
    alpha_beta                      = 8.50   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 109.51 
    fmodel                         = 7.16   
    r_factors                      = 0.22   
    phase_errors                   = 10.51  
    foms                           = 0.29   
    TOTAL for micro-tasks          = 238.77 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.630 micro seconds
Total CPU time: 5.67 minutes
from_scatterers_fft:    653 calls, 99.23 s
gradients_fft:          597 calls, 96.28 s

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

# Date 2008-01-16 Time 02:57:39 PST -0800 (1200481059.57 s)
Start R-work = 0.4629, R-free = 0.4463 (no bulk solvent and anisotropic scale)
Final R-work = 0.1360, R-free = 0.1805 (no bulk solvent and anisotropic scale)

Start R-work = 0.4551, R-free = 0.4357
Final R-work = 0.1190, R-free = 0.1633