# Date 2008-01-16 Time 01:56:59 PST -0800 (1200477419.21 s)
#phil __OFF__

Command line arguments: "../625.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = firebird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 11362
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 625

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 45.9914, 88.1178, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.24, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 45.9914, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0735 1.96324
Completeness in resolution range: 0.933743
Completeness with d_max=infinity: 0.930992

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0735
                             d_min =   1.9632

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 45.9914, 88.1178, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0735 1.96324
Completeness in resolution range: 0.933743
Completeness with d_max=infinity: 0.930992

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0740 -  4.2020 [2203/2228]  1981   222  10.1%
  bin  2:  4.2020 -  3.3473 [2124/2144]  1916   208   9.8%
  bin  3:  3.3473 -  2.9277 [2085/2104]  1875   210  10.1%
  bin  4:  2.9277 -  2.6616 [2067/2097]  1854   213  10.3%
  bin  5:  2.6616 -  2.4717 [2066/2085]  1867   199   9.6%
  bin  6:  2.4717 -  2.3265 [2050/2075]  1843   207  10.1%
  bin  7:  2.3265 -  2.2104 [2015/2043]  1810   205  10.2%
  bin  8:  2.2104 -  2.1144 [2040/2076]  1831   209  10.2%
  bin  9:  2.1144 -  2.0333 [2027/2076]  1837   190   9.4%
  bin 10:  2.0333 -  1.9632 [ 912/2051]   816    96  10.5%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_625/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:
        1.64 -     2.29: 28
        2.29 -     2.94: 1626
        2.94 -     3.60: 4529
        3.60 -     4.25: 9220
        4.25 -     4.90: 12908
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OE1 GLN A  55 " - " O   HOH Z 403 "  1.640 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z  42 " - " O   HOH Z 183 "  1.764 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  41 " - " O   HOH Z 182 "  1.765 3.040 -x+1,y+1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.883 3.040 x,y+1,z
  ... (remaining 28306 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_625/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_625/model_refine_001.geo

CPU time processing inputs: 9.05


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 45.9914 88.1178 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5015   r_free= 0.4894   ksol= 0.00   Bsol= 0.00   scale= 0.776    |
|                                                                             |
| 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:   0.86 A                  |
| x-ray target function (ml) for work reflections: 6.303275                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0740 -  4.6872 0.99   1429  157 0.4263 0.4024      6.6521      6.6359|
|  2:  4.6872 -  3.7391 0.99   1381  157 0.4348 0.4209      6.8492      6.8199|
|  3:  3.7391 -  3.2720 0.99   1353  149 0.4605 0.4017      6.6984      6.6502|
|  4:  3.2720 -  2.9753 0.99   1340  151 0.5025 0.4785      6.5609      6.5048|
|  5:  2.9753 -  2.7635 0.99   1332  145 0.5402 0.5268      6.3736      6.4134|
|  6:  2.7635 -  2.6014 0.99   1327  147 0.5372 0.5478      6.2855       6.213|
|  7:  2.6014 -  2.4717 0.99   1331  146 0.5275 0.5057      6.2488      6.2059|
|  8:  2.4717 -  2.3645 0.98   1320  152 0.5545 0.5185      6.1883       6.182|
|  9:  2.3645 -  2.2738 0.98   1285  141 0.5329 0.5619      6.1294      6.1911|
| 10:  2.2738 -  2.1956 1.00   1330  147 0.5291 0.5500      6.0878      6.1193|
| 11:  2.1956 -  2.1272 0.98   1311  146 0.5206 0.5236      6.0422      6.0127|
| 12:  2.1272 -  2.0665 0.98   1291  137 0.5385 0.5724      5.9474      5.9813|
| 13:  2.0665 -  2.0122 0.92   1229  141 0.5563 0.5272      5.8894      5.8089|
| 14:  2.0122 -  1.9632 0.29    371   43 0.5471 0.5117      5.8781      5.8479|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0740 -  4.6872  1429   157  0.68  36.36   0.78     0.73      79941.86|
|  2:  4.6872 -  3.7391  1381   157  0.69  36.29   0.85     0.77     114780.50|
|  3:  3.7391 -  3.2720  1353   149  0.57  46.43   0.83     0.71     122874.41|
|  4:  3.2720 -  2.9753  1340   151  0.47  54.60   0.76     0.57     111302.65|
|  5:  2.9753 -  2.7635  1332   145  0.34  64.26   0.71     0.42      91478.94|
|  6:  2.7635 -  2.6014  1327   147  0.30  67.68   0.70     0.36      81295.43|
|  7:  2.6014 -  2.4717  1331   146  0.23  72.42   0.73     0.28      75914.09|
|  8:  2.4717 -  2.3645  1320   152  0.23  73.12   0.71     0.28      69043.54|
|  9:  2.3645 -  2.2738  1285   141  0.20  75.44   0.72     0.24      64350.47|
| 10:  2.2738 -  2.1956  1330   147  0.22  73.99   0.73     0.26      56073.24|
| 11:  2.1956 -  2.1272  1311   146  0.19  75.51   0.76     0.25      54557.65|
| 12:  2.1272 -  2.0665  1291   137  0.22  73.83   0.74     0.29      47813.31|
| 13:  2.0665 -  2.0122  1229   141  0.23  73.02   0.70     0.31      42049.06|
| 14:  2.0122 -  1.9632   371    43  0.30  67.42   0.73     0.34      32324.72|
|alpha:            min =        0.24 max =            0.77 mean =         0.42|
|beta:             min =    32324.72 max =       122874.41 mean =     77381.86|
|figures of merit: min =        0.00 max =            1.00 mean =         0.35|
|phase err.(work): min =        0.00 max =           89.99 mean =        63.00|
|phase err.(test): min =        0.00 max =           89.95 mean =        63.28|
|-----------------------------------------------------------------------------|

============================== 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 = 20.766401             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.633   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.878936              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.002   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       37 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      174 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      692 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1511 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2644 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3925 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5079 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6550 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7737 |
|-----------------------------------------------------------------------------|
|-Geometry statistics: start--------------------------------------------------|
|      Type |    Count |    Deviation from ideal |     Targets | Target (sum) |
|           |          |    rmsd      max    min |             |              |
|      bond |     2439 |   0.414    1.400  0.000 |     454.651 |              |
|     angle |     3299 |  24.226   74.492  0.009 |     193.752 |              |
| chirality |      348 |   2.119    6.404  0.009 |     112.240 |       53.700 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.089    4.900  1.196 |       2.091 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.812)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      10.00   10.00   10.00    None  None   None       |
|    all(noH): 2823   0      10.00   10.00   10.00    None  None   None       |
|    Sol.    : 438    0      10.00   10.00   10.00    None  None   None       |
|    Mac.    : 2385   0      10.00   10.00   10.00    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:    10.000 -  10.000: 2823   |   5:    10.000 -  10.000:    0        |
|      1:    10.000 -  10.000:    0   |   6:    10.000 -  10.000:    0        |
|      2:    10.000 -  10.000:    0   |   7:    10.000 -  10.000:    0        |
|      3:    10.000 -  10.000:    0   |   8:    10.000 -  10.000:    0        |
|      4:    10.000 -  10.000:    0   |   9:    10.000 -  10.000:    0        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

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

Randomizing
|-ADP statistics (Wilson B = 11.812)------------------------------------------|
|    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: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5068   r_free= 0.4909   ksol= 0.00   Bsol= 0.00   scale= 0.747    |
|                                                                             |
| 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:   0.83 A                  |
| x-ray target function (ml) for work reflections: 6.304097                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4931   r_free= 0.4767   ksol= 0.33   Bsol= 0.00   scale= 0.982    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.61,9.21,10.94,0.00,0.00,0.00); trace/3= 8.92                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.82 A                  |
| x-ray target function (ml) for work reflections: 6.298096                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.943731             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.634   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.543256              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.141   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4931      final r-factor (work) = 0.4242          |
| start r-factor (free) = 0.4767      final r-factor (free) = 0.4499          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 103.8897 = 15.94 * 0.50 * 6.2958 + 1.00 * 53.7003                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 49.8650 = 15.94 * 0.50 * 6.2356 + 1.00 * 0.1554                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4242      final r-factor (work) = 0.3869          |
| start r-factor (free) = 0.4499      final r-factor (free) = 0.4491          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.6376 = 1.54 * 1.00 * 6.2356 + 1.00 * 0.0144                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 9.5559 = 1.54 * 1.00 * 6.1793 + 1.00 * 0.0196                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.812)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.42   16.05    None  None   None       |
|    all(noH): 2823   0      0.00    85.42   16.05    None  None   None       |
|    Sol.    : 438    0      0.00    85.42   24.74    None  None   None       |
|    Mac.    : 2385   0      0.00    74.10   14.46    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.542:  916   |   5:    42.710 -  51.252:   77        |
|      1:     8.542 -  17.084:  821   |   6:    51.252 -  59.793:   34        |
|      2:    17.084 -  25.626:  570   |   7:    59.793 -  68.335:   11        |
|      3:    25.626 -  34.168:  260   |   8:    68.335 -  76.877:    8        |
|      4:    34.168 -  42.710:  123   |   9:    76.877 -  85.419:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3869 r_free = 0.4491             target_work(ml) = 6.172         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3867 r_free = 0.4495             target_work(ml) = 6.172         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3867   r_free= 0.4495   ksol= 0.33   Bsol= 0.00   scale= 1.137    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.61,9.21,10.94,0.00,0.00,0.00); trace/3= 8.92                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.171928                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3831   r_free= 0.4446   ksol= 0.34   Bsol= 35.00   scale= 1.035   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.12,5.05,6.47,0.00,0.00,0.00); trace/3= 4.88                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.173091                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.954288              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 101.459  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.665518              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 144.800  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3831      final r-factor (work) = 0.3201          |
| start r-factor (free) = 0.4446      final r-factor (free) = 0.3910          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.8939 = 9.95 * 0.50 * 6.1759 + 1.00 * 0.1554                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.4602 = 9.95 * 0.50 * 6.1013 + 1.00 * 0.0930                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3201      final r-factor (work) = 0.2988          |
| start r-factor (free) = 0.3910      final r-factor (free) = 0.3778          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0806 = 0.67 * 1.00 * 6.1013 + 1.00 * 0.0201                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.0123 = 0.67 * 1.00 * 6.0104 + 1.00 * 0.0122                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.812)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    87.12   15.10    None  None   None       |
|    all(noH): 2823   0      0.00    87.12   15.10    None  None   None       |
|    Sol.    : 438    0      0.00    87.12   30.36    None  None   None       |
|    Mac.    : 2385   0      0.00    66.62   12.30    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 -   8.712: 1053   |   5:    43.558 -  52.270:   57        |
|      1:     8.712 -  17.423:  854   |   6:    52.270 -  60.982:   20        |
|      2:    17.423 -  26.135:  484   |   7:    60.982 -  69.693:   16        |
|      3:    26.135 -  34.847:  203   |   8:    69.693 -  78.405:    3        |
|      4:    34.847 -  43.558:  132   |   9:    78.405 -  87.116:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2988 r_free = 0.3778             target_work(ml) = 5.995         |
| occupancies: max = 1.00  min = 0.09   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2985 r_free = 0.3779             target_work(ml) = 5.995         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2985   r_free= 0.3779   ksol= 0.34   Bsol= 35.00   scale= 1.075   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.12,5.05,6.47,0.00,0.00,0.00); trace/3= 4.88                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 5.995151                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2968   r_free= 0.3762   ksol= 0.35   Bsol= 59.59   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.48,2.44,3.96,0.00,0.00,0.00); trace/3= 2.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.49 A                  |
| x-ray target function (ml) for work reflections: 5.996845                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.282558              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 105.912  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.721834              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 157.362  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2968      final r-factor (work) = 0.2187          |
| start r-factor (free) = 0.3762      final r-factor (free) = 0.2833          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.9942 = 9.28 * 0.50 * 6.0116 + 1.00 * 0.0928                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.4399 = 9.28 * 0.50 * 5.8916 + 1.00 * 0.0955                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2187      final r-factor (work) = 0.1905          |
| start r-factor (free) = 0.2833      final r-factor (free) = 0.2552          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2649 = 0.72 * 1.00 * 5.8916 + 1.00 * 0.0122                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.1026 = 0.72 * 1.00 * 5.6651 + 1.00 * 0.0133                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.812)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.68   15.29    None  None   None       |
|    all(noH): 2823   0      0.00    90.68   15.29    None  None   None       |
|    Sol.    : 438    0      0.54    90.68   38.69    None  None   None       |
|    Mac.    : 2385   0      0.00    77.03   10.99    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 -   9.068: 1281   |   5:    45.342 -  54.410:  102        |
|      1:     9.068 -  18.137:  819   |   6:    54.410 -  63.478:   51        |
|      2:    18.137 -  27.205:  250   |   7:    63.478 -  72.547:   18        |
|      3:    27.205 -  36.273:  156   |   8:    72.547 -  81.615:    6        |
|      4:    36.273 -  45.342:  138   |   9:    81.615 -  90.684:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1905 r_free = 0.2552             target_work(ml) = 5.613         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        8 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1903 r_free = 0.2545             target_work(ml) = 5.612         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1903   r_free= 0.2545   ksol= 0.35   Bsol= 59.59   scale= 1.046   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.48,2.44,3.96,0.00,0.00,0.00); trace/3= 2.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.611542                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1894   r_free= 0.2534   ksol= 0.33   Bsol= 58.22   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.47,0.74,2.62,0.00,0.00,0.00); trace/3= 1.27                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.609586                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.404363              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.427  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.261091              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 134.337  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1894      final r-factor (work) = 0.1502          |
| start r-factor (free) = 0.2534      final r-factor (free) = 0.2044          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.5825 = 4.40 * 0.50 * 5.6703 + 1.00 * 0.0955                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 12.2276 = 4.40 * 0.50 * 5.5206 + 1.00 * 0.0703                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1502      final r-factor (work) = 0.1397          |
| start r-factor (free) = 0.2044      final r-factor (free) = 0.1935          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.9750 = 1.26 * 1.00 * 5.5206 + 1.00 * 0.0131                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.7907 = 1.26 * 1.00 * 5.3738 + 1.00 * 0.0139                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.812)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.88   15.38    None  None   None       |
|    all(noH): 2823   0      0.00    92.88   15.38    None  None   None       |
|    Sol.    : 438    0      3.55    92.88   42.35    None  None   None       |
|    Mac.    : 2385   0      0.00    81.79   10.43    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 -   9.288: 1430   |   5:    46.440 -  55.727:  101        |
|      1:     9.288 -  18.576:  746   |   6:    55.727 -  65.015:   80        |
|      2:    18.576 -  27.864:  197   |   7:    65.015 -  74.303:   34        |
|      3:    27.864 -  37.152:  124   |   8:    74.303 -  83.591:   12        |
|      4:    37.152 -  46.440:   95   |   9:    83.591 -  92.879:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1397 r_free = 0.1935             target_work(ml) = 5.345         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1395 r_free = 0.1931             target_work(ml) = 5.344         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1395   r_free= 0.1931   ksol= 0.33   Bsol= 58.22   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.47,0.74,2.62,0.00,0.00,0.00); trace/3= 1.27                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.343642                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1400   r_free= 0.1932   ksol= 0.33   Bsol= 58.22   scale= 1.007   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.39,0.37,2.46,0.00,0.00,0.00); trace/3= 1.07                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.342453                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 2.534560              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 126.072  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.326665              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.877  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1400      final r-factor (work) = 0.1285          |
| start r-factor (free) = 0.1932      final r-factor (free) = 0.1785          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.8806 = 2.53 * 0.50 * 5.3739 + 1.00 * 0.0703                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 6.7916 = 2.53 * 0.50 * 5.3119 + 1.00 * 0.0599                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1285      final r-factor (work) = 0.1253          |
| start r-factor (free) = 0.1785      final r-factor (free) = 0.1752          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 7.0609 = 1.33 * 1.00 * 5.3119 + 1.00 * 0.0138                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 6.9995 = 1.33 * 1.00 * 5.2594 + 1.00 * 0.0220                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.812)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    97.40   15.29    None  None   None       |
|    all(noH): 2823   0      0.00    97.40   15.29    None  None   None       |
|    Sol.    : 438    0      3.26    97.40   43.01    None  None   None       |
|    Mac.    : 2385   0      0.00    93.53   10.20    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 -   9.740: 1561   |   5:    48.698 -  58.438:   81        |
|      1:     9.740 -  19.479:  668   |   6:    58.438 -  68.177:   67        |
|      2:    19.479 -  29.219:  180   |   7:    68.177 -  77.917:   32        |
|      3:    29.219 -  38.959:  117   |   8:    77.917 -  87.657:   18        |
|      4:    38.959 -  48.698:   90   |   9:    87.657 -  97.396:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1253 r_free = 0.1752             target_work(ml) = 5.249         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1252 r_free = 0.1752             target_work(ml) = 5.249         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        9 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1252   r_free= 0.1752   ksol= 0.33   Bsol= 58.22   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.39,0.37,2.46,0.00,0.00,0.00); trace/3= 1.07                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.248558                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0740 -  4.6872 0.99   1429  157 0.0992 0.1293      5.4038      5.6063|
|  2:  4.6872 -  3.7391 0.99   1381  157 0.0894 0.1223      5.4829      5.6953|
|  3:  3.7391 -  3.2720 0.99   1353  149 0.1175 0.1601      5.5552      5.8749|
|  4:  3.2720 -  2.9753 0.99   1340  151 0.1409 0.1895      5.5564      5.7208|
|  5:  2.9753 -  2.7635 0.99   1332  145 0.1499 0.1935      5.4312      5.6575|
|  6:  2.7635 -  2.6014 0.99   1327  147 0.1396 0.2190      5.3111      5.6052|
|  7:  2.6014 -  2.4717 0.99   1331  146 0.1420 0.1802      5.2672       5.408|
|  8:  2.4717 -  2.3645 0.98   1320  152 0.1378 0.1874      5.1897      5.4302|
|  9:  2.3645 -  2.2738 0.98   1285  141 0.1364 0.2078      5.1522       5.412|
| 10:  2.2738 -  2.1956 1.00   1330  147 0.1290 0.1886      5.0605      5.3278|
| 11:  2.1956 -  2.1272 0.98   1311  146 0.1303 0.2129      5.0589      5.4267|
| 12:  2.1272 -  2.0665 0.98   1291  137 0.1337 0.2001      5.0028      5.2562|
| 13:  2.0665 -  2.0122 0.92   1229  141 0.1179 0.1662      4.8415      5.0167|
| 14:  2.0122 -  1.9632 0.29    371   43 0.1044 0.1777      4.6928      4.9964|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0740 -  4.6872  1429   157  0.94   9.70   0.97     0.94       7685.67|
|  2:  4.6872 -  3.7391  1381   157  0.95   8.70   1.02     1.01      10111.89|
|  3:  3.7391 -  3.2720  1353   149  0.92  13.12   1.04     1.04      12387.62|
|  4:  3.2720 -  2.9753  1340   151  0.90  16.15   1.02     1.00      12745.24|
|  5:  2.9753 -  2.7635  1332   145  0.89  17.82   1.00     0.98      10306.86|
|  6:  2.7635 -  2.6014  1327   147  0.88  18.54   0.98     0.95       8691.15|
|  7:  2.6014 -  2.4717  1331   146  0.88  17.98   1.00     0.96       7768.37|
|  8:  2.4717 -  2.3645  1320   152  0.88  18.23   1.00     0.96       6841.76|
|  9:  2.3645 -  2.2738  1285   141  0.88  18.19   0.99     0.94       6354.85|
| 10:  2.2738 -  2.1956  1330   147  0.88  18.13   1.00     0.96       5582.98|
| 11:  2.1956 -  2.1272  1311   146  0.88  19.03   0.98     0.92       5547.74|
| 12:  2.1272 -  2.0665  1291   137  0.88  18.59   1.00     0.99       5179.39|
| 13:  2.0665 -  2.0122  1229   141  0.88  18.56   0.99     0.96       3945.11|
| 14:  2.0122 -  1.9632   371    43  0.93  13.13   0.99     0.96       2638.69|
|alpha:            min =        0.92 max =            1.04 mean =         0.97|
|beta:             min =     2638.69 max =        12745.24 mean =      7872.81|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.98 mean =        16.21|
|phase err.(test): min =        0.00 max =           89.63 mean =        15.52|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1251   r_free= 0.1751   ksol= 0.33   Bsol= 59.41   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.64,-0.75,1.40,0.00,0.00,0.00); trace/3= -0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.248606                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.07 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1251   r_free= 0.1751   ksol= 0.33   Bsol= 59.41   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.64,-0.75,1.40,0.00,0.00,0.00); trace/3= -0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.248606                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0740 -  4.6872 0.99   1429  157 0.0992 0.1293      5.4044      5.6072|
|  2:  4.6872 -  3.7391 0.99   1381  157 0.0894 0.1223      5.4833      5.6953|
|  3:  3.7391 -  3.2720 0.99   1353  149 0.1175 0.1602      5.5553      5.8752|
|  4:  3.2720 -  2.9753 0.99   1340  151 0.1409 0.1895      5.5564      5.7207|
|  5:  2.9753 -  2.7635 0.99   1332  145 0.1499 0.1935      5.4311      5.6572|
|  6:  2.7635 -  2.6014 0.99   1327  147 0.1396 0.2190       5.311      5.6052|
|  7:  2.6014 -  2.4717 0.99   1331  146 0.1420 0.1804      5.2673      5.4084|
|  8:  2.4717 -  2.3645 0.98   1320  152 0.1378 0.1874      5.1899      5.4301|
|  9:  2.3645 -  2.2738 0.98   1285  141 0.1364 0.2076      5.1524      5.4118|
| 10:  2.2738 -  2.1956 1.00   1330  147 0.1290 0.1887      5.0606      5.3282|
| 11:  2.1956 -  2.1272 0.98   1311  146 0.1303 0.2128      5.0589      5.4269|
| 12:  2.1272 -  2.0665 0.98   1291  137 0.1337 0.2001      5.0027      5.2559|
| 13:  2.0665 -  2.0122 0.92   1229  141 0.1179 0.1659       4.841      5.0157|
| 14:  2.0122 -  1.9632 0.29    371   43 0.1044 0.1775      4.6923      4.9953|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|R-free likelihood based estimates for figures of merit, absolute phase error,|
|and distribution parameters alpha and beta (Acta Cryst. (1995). A51, 880-887)|
|                                                                             |
| Bin     Resolution      No. Refl.   FOM  Phase Scale    Alpha        Beta   |
|  #        range        work  test        error factor                       |
|  1: 15.0740 -  4.6872  1429   157  0.94   9.70   0.97     0.94       7694.60|
|  2:  4.6872 -  3.7391  1381   157  0.95   8.70   1.02     1.01      10120.32|
|  3:  3.7391 -  3.2720  1353   149  0.92  13.12   1.04     1.04      12395.51|
|  4:  3.2720 -  2.9753  1340   151  0.90  16.15   1.03     1.00      12745.55|
|  5:  2.9753 -  2.7635  1332   145  0.89  17.82   1.00     0.98      10304.52|
|  6:  2.7635 -  2.6014  1327   147  0.88  18.54   0.99     0.95       8688.10|
|  7:  2.6014 -  2.4717  1331   146  0.88  17.98   1.00     0.96       7768.86|
|  8:  2.4717 -  2.3645  1320   152  0.88  18.24   1.00     0.97       6843.91|
|  9:  2.3645 -  2.2738  1285   141  0.88  18.19   0.99     0.94       6358.91|
| 10:  2.2738 -  2.1956  1330   147  0.88  18.14   1.01     0.97       5584.89|
| 11:  2.1956 -  2.1272  1311   146  0.88  19.04   0.99     0.92       5549.51|
| 12:  2.1272 -  2.0665  1291   137  0.88  18.59   1.00     1.00       5177.76|
| 13:  2.0665 -  2.0122  1229   141  0.88  18.55   1.00     0.97       3940.08|
| 14:  2.0122 -  1.9632   371    43  0.93  13.10   0.99     0.97       2632.70|
|alpha:            min =        0.92 max =            1.04 mean =         0.97|
|beta:             min =     2632.70 max =        12745.55 mean =      7874.59|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.98 mean =        16.21|
|phase err.(test): min =        0.00 max =           89.63 mean =        15.52|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.812)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.19    98.59   16.48    None  None   None       |
|    all(noH): 2823   0      1.19    98.59   16.48    None  None   None       |
|    Sol.    : 438    0      4.45    98.59   44.20    None  None   None       |
|    Mac.    : 2385   0      1.19    94.72   11.39    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.189 -  10.929: 1561   |   5:    49.888 -  59.627:   81        |
|      1:    10.929 -  20.669:  668   |   6:    59.627 -  69.367:   67        |
|      2:    20.669 -  30.408:  180   |   7:    69.367 -  79.106:   32        |
|      3:    30.408 -  40.148:  117   |   8:    79.106 -  88.846:   18        |
|      4:    40.148 -  49.888:   90   |   9:    88.846 -  98.586:    9        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 333         
Filter by distance & map next to the model:
   mapped sites are within: 0.307 - 4.407
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 328 from: 333
   mapped sites are within: 0.729 - 4.407

peak=    9.740 closest distance to " CB  VAL A 230 " =    1.452
peak=    8.654 closest distance to " CB  VAL A 296 " =    1.558
peak=    8.178 closest distance to " O   HOH Z 130 " =    1.721
peak=    6.836 closest distance to " CD2 LEU A   5 " =    1.316
peak=    6.013 closest distance to " CD1AILE A 234 " =    1.007
peak=    5.932 closest distance to " O   HOH Z 222 " =    1.466
peak=    5.657 closest distance to " O   HOH Z  65 " =    1.600
peak=    5.656 closest distance to " CG  PRO A  54 " =    1.510
peak=    5.513 closest distance to " O   HOH Z   7 " =    1.859
peak=    5.427 closest distance to " NE2 GLN A  11 " =    1.177
peak=    5.248 closest distance to " O   HOH Z 127 " =    1.215
peak=    5.205 closest distance to " CG  LEU A 228 " =    1.163
peak=    4.955 closest distance to " NH2 ARG A  56 " =    2.161
peak=    4.952 closest distance to " O   HOH Z 425 " =    1.789
peak=    4.950 closest distance to " O   HOH Z 287 " =    1.998
peak=    4.950 closest distance to " O   HOH Z 143 " =    2.129
peak=    4.888 closest distance to " O   HOH Z 385 " =    1.125
peak=    4.855 closest distance to " O   HOH Z  69 " =    1.314
peak=    4.809 closest distance to " O   HOH Z 427 " =    2.152
peak=    4.798 closest distance to " O   HOH Z 232 " =    2.247
peak=    4.742 closest distance to " O   HOH Z 417 " =    1.988
peak=    4.727 closest distance to " CG  PRO A 280 " =    1.014
peak=    4.707 closest distance to " O   HOH Z 389 " =    1.631
peak=    4.617 closest distance to " CG  LEU A   5 " =    1.190
peak=    4.607 closest distance to " CB  PRO A  54 " =    1.170
peak=    4.513 closest distance to " O   HOH Z  24 " =    2.037
peak=    4.512 closest distance to " O   HOH Z   9 " =    2.601
peak=    4.499 closest distance to " CB  VAL A 230 " =    1.225
peak=    4.490 closest distance to " O   HOH Z 423 " =    1.855
peak=    4.472 closest distance to " O   HOH Z 369 " =    2.225
peak=    4.402 closest distance to " O   HOH Z  66 " =    1.105
peak=    4.396 closest distance to " CG  PRO A 198 " =    1.325
peak=    4.393 closest distance to " O   HOH Z 427 " =    1.180
peak=    4.388 closest distance to " O   HOH Z 258 " =    1.121
peak=    4.375 closest distance to " O   HOH Z  63 " =    1.553
peak=    4.357 closest distance to " CB  SER A  63 " =    1.295
peak=    4.355 closest distance to " O   HOH Z 418 " =    0.993
peak=    4.323 closest distance to " O   PRO A 198 " =    1.320
peak=    4.311 closest distance to " NH2AARG A 145 " =    1.126
peak=    4.292 closest distance to " CB  GLN A 223 " =    1.587
peak=    4.267 closest distance to " CB  ASN A 148 " =    1.482
peak=    4.253 closest distance to " CH2 TRP A 266 " =    1.178
peak=    4.247 closest distance to " O   HOH Z  59 " =    1.806
peak=    4.208 closest distance to " CG  GLN A  58 " =    1.064
peak=    4.201 closest distance to " O   HOH Z 126 " =    2.055
peak=    4.200 closest distance to " CB  SER A 216 " =    1.018
peak=    4.194 closest distance to " O   HOH Z 415 " =    1.019
peak=    4.183 closest distance to " CB  GLN A 183 " =    1.251
peak=    4.146 closest distance to " O   HOH Z 392 " =    1.199
peak=    4.123 closest distance to " O   HOH Z  49 " =    1.055
peak=    4.099 closest distance to " O   HOH Z 359 " =    1.501
peak=    4.095 closest distance to " O   HOH Z 124 " =    1.358
peak=    4.090 closest distance to " O   HOH Z  78 " =    1.722
peak=    4.090 closest distance to " O   HOH Z 316 " =    3.035
peak=    4.083 closest distance to " CB  ASN A 142 " =    0.985
peak=    4.054 closest distance to " CB  SER A   3 " =    1.489
peak=    4.037 closest distance to " CG  LEU A 167 " =    1.289
peak=    4.036 closest distance to " O   HOH Z 298 " =    1.726
peak=    4.033 closest distance to " CG2 ILE A 234 " =    0.918
peak=    4.027 closest distance to " O   HOH Z 112 " =    1.128
peak=    4.026 closest distance to " O   HOH Z 225 " =    1.636
peak=    4.011 closest distance to " O   HOH Z 380 " =    2.059
peak=    4.011 closest distance to " CB  ASN A  39 " =    0.947
peak=    4.010 closest distance to " O   HOH Z 362 " =    1.663
peak=    4.005 closest distance to " NH1AARG A 145 " =    1.167
peak=    4.000 closest distance to " ND2BASN A 224 " =    0.876
peak=    4.000 closest distance to " CB  GLU A 277 " =    3.594
peak=    3.983 closest distance to " O   HOH Z 272 " =    1.807
peak=    3.969 closest distance to " CB  ASP A 124 " =    0.848
peak=    3.949 closest distance to " NH2AARG A 190 " =    1.785
peak=    3.947 closest distance to " CD2 LEU A 228 " =    1.326
peak=    3.942 closest distance to " CE3 TRP A 150 " =    1.130
peak=    3.931 closest distance to " O   HOH Z 375 " =    1.043
peak=    3.927 closest distance to " O   HOH Z 361 " =    1.300
peak=    3.926 closest distance to " CA  ALA A 160 " =    0.984
peak=    3.908 closest distance to " O   HOH Z 153 " =    3.665
peak=    3.901 closest distance to " CA  ASN A 127 " =    1.144
peak=    3.881 closest distance to " O   HOH Z 303 " =    2.168
peak=    3.875 closest distance to " CB  ARG A 275 " =    1.041
peak=    3.873 closest distance to " O   HOH Z  88 " =    3.449
peak=    3.870 closest distance to " CG  PRO A 243 " =    1.082
peak=    3.869 closest distance to " O   HOH Z 214 " =    2.608
peak=    3.859 closest distance to " O   HOH Z  39 " =    1.297
peak=    3.859 closest distance to " O   HOH Z 211 " =    1.102
peak=    3.843 closest distance to " CD  LYS A  76 " =    1.886
peak=    3.834 closest distance to " O   HOH Z 424 " =    1.046
peak=    3.823 closest distance to " CB  LYS A 117 " =    1.199
peak=    3.817 closest distance to " CG2 ILE A  20 " =    1.683
peak=    3.817 closest distance to " O   HOH Z 258 " =    2.055
peak=    3.809 closest distance to " O   HOH Z 368 " =    3.389
peak=    3.808 closest distance to " O   HOH Z 414 " =    1.209
peak=    3.806 closest distance to " CG  PRO A 213 " =    1.237
peak=    3.797 closest distance to " O   HOH Z  91 " =    2.484
peak=    3.790 closest distance to " O   HOH Z 422 " =    2.549
peak=    3.784 closest distance to " CB  VAL A 202 " =    1.644
peak=    3.782 closest distance to " O   HOH Z 245 " =    1.137
peak=    3.780 closest distance to " O   HOH Z 411 " =    3.194
peak=    3.780 closest distance to " O   HOH Z 139 " =    1.114
peak=    3.776 closest distance to " CD  ARG A  66 " =    2.466
peak=    3.775 closest distance to " O   HOH Z   2 " =    1.744
peak=    3.764 closest distance to " O   HOH Z 419 " =    2.002
peak=    3.764 closest distance to " O   HOH Z 438 " =    2.189
peak=    3.763 closest distance to " CB  SER A 276 " =    1.169
peak=    3.750 closest distance to " CG  ARG A 138 " =    1.275
peak=    3.750 closest distance to " CD  ARG A 159 " =    0.729
peak=    3.746 closest distance to " NZ  LYS A 117 " =    2.993
peak=    3.741 closest distance to " O   HOH Z 425 " =    2.112
peak=    3.732 closest distance to " O   HOH Z 143 " =    1.475
peak=    3.729 closest distance to " CG2 THR A 221 " =    1.327
peak=    3.729 closest distance to " CE3 TRP A 274 " =    1.268
peak=    3.698 closest distance to " CB  TRP A 266 " =    1.091
peak=    3.696 closest distance to " CA  ILE A 234 " =    1.074
peak=    3.694 closest distance to " O   HOH Z  61 " =    1.677
peak=    3.694 closest distance to " CA  ALA A  51 " =    1.062
peak=    3.688 closest distance to " O   HOH Z  80 " =    1.486
peak=    3.682 closest distance to " CB  ALA A  43 " =    0.825
peak=    3.669 closest distance to " CB  TRP A 179 " =    1.493
peak=    3.662 closest distance to " O   HOH Z 373 " =    1.527
peak=    3.662 closest distance to " O   HOH Z 145 " =    2.484
peak=    3.659 closest distance to " CA  PHE A 283 " =    1.239
peak=    3.656 closest distance to " CB  ARG A 190 " =    1.736
peak=    3.655 closest distance to " O   HOH Z  76 " =    1.111
peak=    3.654 closest distance to " O   HOH Z 371 " =    2.933
peak=    3.654 closest distance to " CE  LYS A  76 " =    0.888
peak=    3.650 closest distance to " ND1 HIS A  86 " =    1.827
peak=    3.650 closest distance to " CG AARG A 275 " =    1.274
peak=    3.648 closest distance to " CG2 VAL A 257 " =    0.805
peak=    3.647 closest distance to " O   HOH Z  26 " =    1.405
peak=    3.643 closest distance to " O   HOH Z 329 " =    4.110
peak=    3.639 closest distance to " O   HOH Z 193 " =    1.685
peak=    3.635 closest distance to " O   HOH Z  51 " =    1.900
peak=    3.633 closest distance to " O   TYR A 116 " =    1.245
peak=    3.633 closest distance to " O   HOH Z 352 " =    1.829
peak=    3.620 closest distance to " CB  SER A 212 " =    1.458
peak=    3.617 closest distance to " OG BSER A 212 " =    2.782
peak=    3.609 closest distance to " O   HOH Z 350 " =    1.525
peak=    3.604 closest distance to " CD  ARG A 269 " =    1.038
peak=    3.604 closest distance to " ND2 ASN A 249 " =    0.868
peak=    3.596 closest distance to " O   HOH Z 218 " =    1.747
peak=    3.590 closest distance to " CB  LEU A 237 " =    0.904
peak=    3.588 closest distance to " O   HOH Z 331 " =    1.012
peak=    3.587 closest distance to " O   HOH Z 123 " =    1.002
peak=    3.587 closest distance to " O   HOH Z 132 " =    2.913
peak=    3.586 closest distance to " N   SER A 271 " =    1.021
peak=    3.580 closest distance to " CB  SER A 210 " =    0.943
peak=    3.580 closest distance to " O   HOH Z 425 " =    2.067
peak=    3.579 closest distance to " CB  ASN A 215 " =    1.235
peak=    3.565 closest distance to " CA  TYR A  30 " =    1.022
peak=    3.564 closest distance to " O   HOH Z   1 " =    1.834
peak=    3.558 closest distance to " O   HOH Z 353 " =    1.744
peak=    3.558 closest distance to " O   HOH Z 365 " =    3.101
peak=    3.553 closest distance to " CE AMET A  47 " =    1.387
peak=    3.549 closest distance to " O   HOH Z 403 " =    1.426
peak=    3.546 closest distance to " CD1 LEU A 281 " =    1.023
peak=    3.539 closest distance to " CB  HIS A 108 " =    0.835
peak=    3.536 closest distance to " O   HOH Z 357 " =    2.206
peak=    3.533 closest distance to " CB  VAL A 265 " =    1.297
peak=    3.533 closest distance to " CD  GLN A  77 " =    1.238
peak=    3.524 closest distance to " CD1 ILE A  33 " =    1.845
peak=    3.522 closest distance to " O   HOH Z 146 " =    1.563
peak=    3.521 closest distance to " CG BARG A 102 " =    1.941
peak=    3.521 closest distance to " CA  ARG A 195 " =    1.243
peak=    3.515 closest distance to " N   GLN A 278 " =    1.474
peak=    3.505 closest distance to " O   MET A 105 " =    1.794
peak=    3.504 closest distance to " NH1 ARG A  14 " =    1.066
peak=    3.497 closest distance to " NE2 GLN A  73 " =    1.384
peak=    3.496 closest distance to " O   HOH Z 346 " =    1.569
peak=    3.493 closest distance to " O   HOH Z  10 " =    1.693
peak=    3.491 closest distance to " O   HOH Z 195 " =    1.451
peak=    3.490 closest distance to " O   HOH Z 421 " =    2.158
peak=    3.489 closest distance to " CB  ARG A 138 " =    0.877
peak=    3.479 closest distance to " O   HOH Z  97 " =    1.975
peak=    3.477 closest distance to " N   TYR A  15 " =    1.107
peak=    3.468 closest distance to " CG  GLN A  11 " =    2.240
peak=    3.466 closest distance to " CB BVAL A  41 " =    1.147
peak=    3.463 closest distance to " CA  GLY A 267 " =    1.253
peak=    3.462 closest distance to " N   ARG A 156 " =    1.262
peak=    3.452 closest distance to " O   HOH Z 327 " =    1.626
peak=    3.451 closest distance to " O   HOH Z 378 " =    0.985
peak=    3.450 closest distance to " CA  MET A 105 " =    0.873
peak=    3.449 closest distance to " O   HOH Z  68 " =    2.240
peak=    3.446 closest distance to " CA  ALA A 129 " =    1.281
peak=    3.441 closest distance to " CA  SER A  87 " =    1.052
peak=    3.433 closest distance to " OG  SER A  62 " =    3.009
peak=    3.429 closest distance to " O   HOH Z 236 " =    1.595
peak=    3.427 closest distance to " O   HOH Z  58 " =    1.873
peak=    3.425 closest distance to " CB  MET A  47 " =    1.177
peak=    3.424 closest distance to " CB  GLN A  88 " =    1.327
peak=    3.424 closest distance to " CB  TYR A 169 " =    0.735
peak=    3.423 closest distance to " OG  SER A  62 " =    2.657
peak=    3.423 closest distance to " CB  GLU A 128 " =    1.096
peak=    3.422 closest distance to " O   HOH Z 109 " =    2.448
peak=    3.418 closest distance to " N   ASN A 127 " =    1.374
peak=    3.417 closest distance to " CB  PHE A 204 " =    1.094
peak=    3.408 closest distance to " CD2 TRP A 179 " =    1.345
peak=    3.405 closest distance to " OG BSER A 164 " =    2.245
peak=    3.403 closest distance to " O   HOH Z 158 " =    1.020
peak=    3.400 closest distance to " N   PHE A 130 " =    1.238
peak=    3.394 closest distance to " O   ILE A  20 " =    2.065
peak=    3.390 closest distance to " NZ  LYS A 117 " =    1.175
peak=    3.389 closest distance to " O   HOH Z 290 " =    0.974
peak=    3.389 closest distance to " CB  SER A 273 " =    0.888
peak=    3.382 closest distance to " N   SER A 135 " =    1.366
peak=    3.371 closest distance to " O   HOH Z 162 " =    1.127
peak=    3.370 closest distance to " O   HOH Z  44 " =    1.907
peak=    3.369 closest distance to " CA  ARG A 159 " =    1.263
peak=    3.368 closest distance to " CG1 ILE A 151 " =    1.123
peak=    3.366 closest distance to " O   HOH Z 193 " =    1.479
peak=    3.363 closest distance to " CG  GLN A  89 " =    1.552
peak=    3.362 closest distance to " CB  PRO A  90 " =    1.086
peak=    3.362 closest distance to " O   HOH Z  30 " =    1.366
peak=    3.359 closest distance to " CE  LYS A 119 " =    1.110
peak=    3.357 closest distance to " O   HOH Z 216 " =    3.856
peak=    3.349 closest distance to " O   HOH Z 410 " =    1.512
peak=    3.348 closest distance to " O   HOH Z 251 " =    1.679
peak=    3.346 closest distance to " CB  ALA A 114 " =    0.846
peak=    3.345 closest distance to " CE1 HIS A  81 " =    1.655
peak=    3.342 closest distance to " CA  THR A 221 " =    0.955
peak=    3.341 closest distance to " O   HOH Z  20 " =    1.602
peak=    3.337 closest distance to " O   HOH Z 260 " =    2.424
peak=    3.337 closest distance to " CG2BVAL A 121 " =    0.814
peak=    3.336 closest distance to " NE  ARG A 138 " =    1.158
peak=    3.333 closest distance to " O   HOH Z  61 " =    1.669
peak=    3.332 closest distance to " N   SER A  97 " =    0.809
peak=    3.331 closest distance to " O   HOH Z  32 " =    2.217
peak=    3.328 closest distance to " O  BHOH Z  74 " =    1.257
peak=    3.324 closest distance to " CD1 LEU A 300 " =    1.031
peak=    3.324 closest distance to " C   ASN A 209 " =    1.568
peak=    3.323 closest distance to " CA  VAL A 125 " =    1.091
peak=    3.321 closest distance to " CZ  PHE A 218 " =    1.110
peak=    3.320 closest distance to " O   HOH Z 356 " =    1.302
peak=    3.318 closest distance to " N   CYS A 260 " =    0.903
peak=    3.313 closest distance to " O   HOH Z  92 " =    1.232
peak=    3.311 closest distance to " OE2 GLU A  53 " =    1.854
peak=    3.310 closest distance to " O   HOH Z 424 " =    2.610
peak=    3.308 closest distance to " O   HOH Z  78 " =    2.171
peak=    3.307 closest distance to " O   THR A 220 " =    1.362
peak=    3.300 closest distance to " O   HOH Z 422 " =    1.086
peak=    3.299 closest distance to " O   HOH Z 116 " =    1.068
peak=    3.298 closest distance to " O   HOH Z 184 " =    1.385
peak=    3.297 closest distance to " CB  ARG A  79 " =    0.897
peak=    3.296 closest distance to " C   ASP A 132 " =    3.904
peak=    3.287 closest distance to " O   CYS A 168 " =    1.367
peak=    3.284 closest distance to " O   HOH Z 189 " =    3.352
peak=    3.284 closest distance to " CB  TRP A 274 " =    1.147
peak=    3.283 closest distance to " O   HOH Z 389 " =    2.675
peak=    3.283 closest distance to " O   HOH Z 368 " =    4.198
peak=    3.282 closest distance to " O   HOH Z 343 " =    2.867
peak=    3.272 closest distance to " NH2BARG A 190 " =    1.305
peak=    3.269 closest distance to " O   HOH Z  69 " =    1.650
peak=    3.266 closest distance to " O  BHOH Z 338 " =    2.444
peak=    3.263 closest distance to " N   ALA A 256 " =    1.007
peak=    3.257 closest distance to " O   HOH Z 328 " =    1.629
peak=    3.251 closest distance to " O   HOH Z 392 " =    1.439
peak=    3.250 closest distance to " NE2 HIS A 207 " =    1.086
peak=    3.249 closest distance to " O   HOH Z 438 " =    2.347
peak=    3.242 closest distance to " O   HOH Z   6 " =    1.620
peak=    3.241 closest distance to " NH1BARG A 145 " =    1.342
peak=    3.236 closest distance to " O   HOH Z 423 " =    1.541
peak=    3.236 closest distance to " CB  LEU A 228 " =    1.340
peak=    3.234 closest distance to " O   HOH Z 218 " =    1.685
peak=    3.233 closest distance to " O   HOH Z 180 " =    2.223
peak=    3.233 closest distance to " O   THR A 182 " =    1.521
peak=    3.227 closest distance to " CB  MET A  40 " =    0.806
peak=    3.223 closest distance to " O   HOH Z 434 " =    1.541
peak=    3.218 closest distance to " O   HOH Z 150 " =    1.159
peak=    3.215 closest distance to " O   HOH Z 222 " =    2.157
peak=    3.215 closest distance to " CA  ASN A 215 " =    1.046
peak=    3.213 closest distance to " O   HOH Z  88 " =    3.140
peak=    3.208 closest distance to " C   GLN A  73 " =    1.072
peak=    3.207 closest distance to " O   HOH Z 379 " =    1.352
peak=    3.207 closest distance to " NZ  LYS A  48 " =    1.275
peak=    3.206 closest distance to " CB  ARG A 156 " =    1.107
peak=    3.205 closest distance to " CB  LEU A 143 " =    1.083
peak=    3.204 closest distance to " N   GLU A   2 " =    1.484
peak=    3.201 closest distance to " OG  SER A 135 " =    1.272
peak=    3.201 closest distance to " CA  LEU A 282 " =    1.258
peak=    3.200 closest distance to " NE2 GLN A  58 " =    4.407
peak=    3.198 closest distance to " CA  ARG A 156 " =    0.960
peak=    3.194 closest distance to " O   HOH Z 293 " =    1.615
peak=    3.194 closest distance to " O   HOH Z 325 " =    1.996
peak=    3.193 closest distance to " CZ  PHE A  38 " =    1.257
peak=    3.192 closest distance to " O   HOH Z 148 " =    2.327
peak=    3.186 closest distance to " CG2 VAL A 197 " =    1.156
peak=    3.186 closest distance to " CB  ILE A 234 " =    1.236
peak=    3.184 closest distance to " CA  ILE A 106 " =    0.749
peak=    3.183 closest distance to " N   ASP A 162 " =    1.123
peak=    3.181 closest distance to " CB  TRP A 150 " =    0.910
peak=    3.173 closest distance to " CG2 VAL A 232 " =    1.189
peak=    3.171 closest distance to " CG2 ILE A 120 " =    1.248
peak=    3.168 closest distance to " CB  ALA A  10 " =    0.904
peak=    3.160 closest distance to " O   HOH Z  88 " =    2.840
peak=    3.152 closest distance to " CB  SER A  26 " =    1.677
peak=    3.151 closest distance to " CA  ARG A 102 " =    1.163
peak=    3.150 closest distance to " CA  ALA A 158 " =    1.163
peak=    3.148 closest distance to " OE2 GLU A   2 " =    2.019
peak=    3.142 closest distance to " OE2 GLU A  44 " =    1.132
peak=    3.142 closest distance to " CE1 HIS A 115 " =    3.930
peak=    3.141 closest distance to " O   HOH Z 172 " =    2.273
peak=    3.139 closest distance to " O   HOH Z 383 " =    1.983
peak=    3.139 closest distance to " CG  ARG A 159 " =    0.840
peak=    3.138 closest distance to " O   HOH Z 193 " =    1.188
peak=    3.133 closest distance to " CB  ASP A 107 " =    1.120
peak=    3.129 closest distance to " O   HOH Z 303 " =    2.071
peak=    3.124 closest distance to " O   HOH Z  71 " =    1.241
peak=    3.118 closest distance to " O   HOH Z 193 " =    1.605
peak=    3.118 closest distance to " OG ASER A 212 " =    1.884
peak=    3.117 closest distance to " O   HOH Z 272 " =    2.335
peak=    3.111 closest distance to " O   HOH Z 394 " =    3.420
peak=    3.110 closest distance to " O   HOH Z  40 " =    1.980
peak=    3.109 closest distance to " CB  GLU A 152 " =    1.306
peak=    3.109 closest distance to " O   HOH Z 281 " =    2.012
peak=    3.109 closest distance to " O   HOH Z 158 " =    2.745
peak=    3.106 closest distance to " O   HOH Z 188 " =    3.014
peak=    3.105 closest distance to " CA  ALA A 291 " =    0.854
peak=    3.103 closest distance to " CA  LYS A 117 " =    1.229
peak=    3.099 closest distance to " CA  GLY A 136 " =    1.041
peak=    3.096 closest distance to " O   HOH Z 323 " =    1.721
peak=    3.095 closest distance to " CB  LEU A 300 " =    0.957
peak=    3.095 closest distance to " CB  THR A  31 " =    1.578
peak=    3.087 closest distance to " CB  ALA A 248 " =    1.042
peak=    3.081 closest distance to " CA  TYR A  30 " =    1.098
peak=    3.075 closest distance to " O   PHE A 192 " =    1.403
peak=    3.063 closest distance to " O   HOH Z  46 " =    1.075
peak=    3.062 closest distance to " O   HOH Z   1 " =    1.810
peak=    3.051 closest distance to " CD  LYS A 166 " =    1.388
peak=    3.048 closest distance to " CZ3 TRP A  92 " =    1.196
peak=    3.046 closest distance to " CA  ASP A 149 " =    1.291

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 207         
Filter by distance & map next to the model:
   mapped sites are within: 0.678 - 5.646
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 206 from: 207
   mapped sites are within: 0.730 - 5.646

peak=   -4.658 closest distance to " O   HOH Z 131 " =    4.009
peak=   -4.375 closest distance to " CB  VAL A 230 " =    1.137
peak=   -4.356 closest distance to " CD  ARG A  14 " =    3.089
peak=   -4.340 closest distance to " O   PRO A 198 " =    1.206
peak=   -4.323 closest distance to " CG2 VAL A 230 " =    0.730
peak=   -4.218 closest distance to " O   HOH Z 415 " =    1.030
peak=   -4.158 closest distance to " O   HOH Z  69 " =    1.734
peak=   -4.143 closest distance to " OG BSER A 134 " =    1.551
peak=   -4.117 closest distance to " CG  ARG A 219 " =    2.394
peak=   -4.063 closest distance to " N   THR A 157 " =    1.494
peak=   -4.056 closest distance to " CA  ASP A  27 " =    2.417
peak=   -4.004 closest distance to " OE1 GLU A 277 " =    2.198
peak=   -3.953 closest distance to " CB  GLN A  55 " =    1.166
peak=   -3.934 closest distance to " O   HOH Z 211 " =    0.768
peak=   -3.929 closest distance to " CB  PRO A 243 " =    2.665
peak=   -3.928 closest distance to " O   SER A 135 " =    1.459
peak=   -3.919 closest distance to " O   HOH Z 389 " =    1.276
peak=   -3.914 closest distance to " O   HOH Z 100 " =    0.962
peak=   -3.889 closest distance to " CB  ALA A  43 " =    2.557
peak=   -3.850 closest distance to " O   HOH Z  39 " =    0.919
peak=   -3.843 closest distance to " O   HOH Z 266 " =    5.159
peak=   -3.840 closest distance to " O   VAL A  67 " =    2.517
peak=   -3.840 closest distance to " O   SER A  22 " =    2.582
peak=   -3.829 closest distance to " CD  ARG A 156 " =    1.928
peak=   -3.805 closest distance to " CZ2 TRP A  92 " =    2.877
peak=   -3.784 closest distance to " CD1 LEU A 255 " =    2.929
peak=   -3.752 closest distance to " O   HOH Z 147 " =    2.038
peak=   -3.744 closest distance to " NE2 GLN A  55 " =    1.138
peak=   -3.727 closest distance to " O   HOH Z 359 " =    3.304
peak=   -3.725 closest distance to " ND2 ASN A 187 " =    1.500
peak=   -3.722 closest distance to " O   HOH Z 276 " =    1.260
peak=   -3.710 closest distance to " OG  SER A 245 " =    1.446
peak=   -3.710 closest distance to " O   HOH Z 292 " =    1.658
peak=   -3.704 closest distance to " CD2 LEU A 237 " =    2.681
peak=   -3.702 closest distance to " CB  ALA A 291 " =    2.249
peak=   -3.695 closest distance to " O   HOH Z 111 " =    1.714
peak=   -3.678 closest distance to " N   PRO A 163 " =    1.464
peak=   -3.678 closest distance to " OG  SER A  87 " =    1.450
peak=   -3.675 closest distance to " CD2 TYR A 293 " =    1.827
peak=   -3.671 closest distance to " O   HOH Z 185 " =    2.040
peak=   -3.671 closest distance to " ND2 ASN A 249 " =    2.149
peak=   -3.667 closest distance to " CD  LYS A 166 " =    2.506
peak=   -3.666 closest distance to " CZ  PHE A  38 " =    2.428
peak=   -3.661 closest distance to " CA  GLY A  98 " =    1.885
peak=   -3.651 closest distance to " O   HOH Z 407 " =    2.852
peak=   -3.643 closest distance to " O   PRO A 243 " =    2.553
peak=   -3.631 closest distance to " O   HOH Z  60 " =    1.774
peak=   -3.630 closest distance to " CE2 TYR A  30 " =    2.612
peak=   -3.627 closest distance to " CE BMET A  47 " =    1.211
peak=   -3.621 closest distance to " CG2AVAL A  41 " =    2.855
peak=   -3.620 closest distance to " C   HIS A 108 " =    1.236
peak=   -3.610 closest distance to " CB  ALA A   9 " =    2.411
peak=   -3.610 closest distance to " O   HOH Z 133 " =    1.342
peak=   -3.609 closest distance to " O   HOH Z 368 " =    2.358
peak=   -3.607 closest distance to " CA  ASN A 127 " =    1.254
peak=   -3.600 closest distance to " OG  SER A  97 " =    2.190
peak=   -3.588 closest distance to " O   HOH Z  52 " =    0.914
peak=   -3.585 closest distance to " C   MET A 188 " =    1.491
peak=   -3.580 closest distance to " O   HOH Z 238 " =    0.898
peak=   -3.580 closest distance to " CA  GLY A 241 " =    2.299
peak=   -3.579 closest distance to " O   HOH Z 163 " =    1.914
peak=   -3.566 closest distance to " CG2 VAL A 202 " =    2.757
peak=   -3.566 closest distance to " CD2 TYR A 116 " =    2.273
peak=   -3.566 closest distance to " CB  ALA A 248 " =    2.129
peak=   -3.566 closest distance to " O   HOH Z 359 " =    1.659
peak=   -3.557 closest distance to " CE2 PHE A 218 " =    2.535
peak=   -3.556 closest distance to " N   ALA A  43 " =    2.648
peak=   -3.549 closest distance to " O   HOH Z 134 " =    4.231
peak=   -3.539 closest distance to " OE2 GLU A 152 " =    1.222
peak=   -3.530 closest distance to " O   PRO A 163 " =    1.960
peak=   -3.521 closest distance to " O   HOH Z 275 " =    1.733
peak=   -3.510 closest distance to " CA  HIS A 207 " =    1.196
peak=   -3.501 closest distance to " O   SER A 141 " =    1.833
peak=   -3.499 closest distance to " O   HOH Z 368 " =    1.687
peak=   -3.498 closest distance to " CB  ASP A 132 " =    2.384
peak=   -3.498 closest distance to " O   HOH Z 385 " =    1.421
peak=   -3.493 closest distance to " C   ARG A 269 " =    1.333
peak=   -3.492 closest distance to " C   ILE A 239 " =    2.083
peak=   -3.471 closest distance to " O   HOH Z  11 " =    1.704
peak=   -3.466 closest distance to " CD2 LEU A   5 " =    0.970
peak=   -3.463 closest distance to " CB  ALA A 114 " =    2.483
peak=   -3.462 closest distance to " CA  GLY A 203 " =    2.452
peak=   -3.461 closest distance to " O   HOH Z 298 " =    2.911
peak=   -3.458 closest distance to " O   HOH Z 374 " =    1.758
peak=   -3.457 closest distance to " CB  TRP A  85 " =    2.426
peak=   -3.455 closest distance to " CB  TYR A  68 " =    1.278
peak=   -3.449 closest distance to " CZ2 TRP A 274 " =    0.918
peak=   -3.445 closest distance to " O   HOH Z 231 " =    2.002
peak=   -3.437 closest distance to " OG  SER A  62 " =    4.239
peak=   -3.436 closest distance to " CD1 LEU A 101 " =    2.272
peak=   -3.435 closest distance to " O   ALA A  10 " =    1.683
peak=   -3.435 closest distance to " CD  LYS A 289 " =    2.283
peak=   -3.432 closest distance to " ND2 ASN A 285 " =    2.063
peak=   -3.426 closest distance to " O   HOH Z  24 " =    1.118
peak=   -3.422 closest distance to " O   HOH Z  64 " =    1.277
peak=   -3.417 closest distance to " CB  PHE A 130 " =    1.217
peak=   -3.410 closest distance to " O   HOH Z 313 " =    1.547
peak=   -3.409 closest distance to " OD2 ASP A  27 " =    1.674
peak=   -3.407 closest distance to " CB  ALA A   7 " =    2.062
peak=   -3.407 closest distance to " OH  TYR A 172 " =    1.807
peak=   -3.405 closest distance to " ND2 ASN A  45 " =    2.281
peak=   -3.399 closest distance to " CD  PRO A 213 " =    2.107
peak=   -3.395 closest distance to " O   HOH Z 198 " =    1.882
peak=   -3.393 closest distance to " O   ALA A  84 " =    1.741
peak=   -3.391 closest distance to " O   HOH Z 193 " =    1.111
peak=   -3.388 closest distance to " CG  LEU A 281 " =    1.853
peak=   -3.386 closest distance to " O   HOH Z 351 " =    1.545
peak=   -3.376 closest distance to " C   VAL A 265 " =    0.894
peak=   -3.372 closest distance to " O   HOH Z 339 " =    1.720
peak=   -3.371 closest distance to " O   HOH Z 105 " =    1.970
peak=   -3.369 closest distance to " O   HOH Z 100 " =    1.090
peak=   -3.367 closest distance to " O   ILE A  49 " =    1.651
peak=   -3.362 closest distance to " CG  TRP A 266 " =    1.835
peak=   -3.350 closest distance to " ND2 ASN A  45 " =    1.275
peak=   -3.350 closest distance to " NH2AARG A 275 " =    5.268
peak=   -3.347 closest distance to " O   HOH Z  83 " =    1.455
peak=   -3.338 closest distance to " O   HOH Z 140 " =    1.216
peak=   -3.331 closest distance to " O   HOH Z  73 " =    2.373
peak=   -3.319 closest distance to " N   ASP A 171 " =    2.641
peak=   -3.309 closest distance to " O   HOH Z 404 " =    1.370
peak=   -3.308 closest distance to " CG2 ILE A  20 " =    2.764
peak=   -3.302 closest distance to " CG  MET A 105 " =    0.956
peak=   -3.295 closest distance to " O   HOH Z 435 " =    2.305
peak=   -3.295 closest distance to " CG2 VAL A 296 " =    2.103
peak=   -3.293 closest distance to " CG2 THR A  52 " =    2.873
peak=   -3.292 closest distance to " O   HOH Z 426 " =    1.670
peak=   -3.290 closest distance to " NE2 GLN A 223 " =    1.513
peak=   -3.288 closest distance to " O   GLU A 152 " =    1.597
peak=   -3.288 closest distance to " O   HOH Z 295 " =    1.845
peak=   -3.287 closest distance to " O   HOH Z 350 " =    1.697
peak=   -3.286 closest distance to " CB  ALA A 129 " =    2.419
peak=   -3.284 closest distance to " CG1 VAL A 125 " =    2.344
peak=   -3.283 closest distance to " OG  SER A 273 " =    2.432
peak=   -3.280 closest distance to " O   HOH Z 174 " =    2.999
peak=   -3.280 closest distance to " C   ALA A 158 " =    1.340
peak=   -3.279 closest distance to " N   LEU A 282 " =    2.102
peak=   -3.279 closest distance to " CZ2 TRP A  70 " =    2.427
peak=   -3.275 closest distance to " O   HOH Z 318 " =    2.023
peak=   -3.274 closest distance to " O   HOH Z 368 " =    1.458
peak=   -3.268 closest distance to " O   HOH Z  52 " =    2.034
peak=   -3.265 closest distance to " O   HOH Z  43 " =    1.935
peak=   -3.255 closest distance to " C   GLU A   2 " =    1.874
peak=   -3.255 closest distance to " O   HOH Z 427 " =    1.804
peak=   -3.250 closest distance to " O   HOH Z  65 " =    1.305
peak=   -3.250 closest distance to " O   HOH Z 364 " =    2.345
peak=   -3.243 closest distance to " CG2 VAL A 189 " =    1.948
peak=   -3.238 closest distance to " O   HOH Z 377 " =    1.147
peak=   -3.233 closest distance to " C   GLN A 205 " =    2.053
peak=   -3.230 closest distance to " NH2 ARG A 219 " =    1.707
peak=   -3.225 closest distance to " CB  PRO A  54 " =    2.429
peak=   -3.219 closest distance to " O   HOH Z 255 " =    2.567
peak=   -3.219 closest distance to " O   HOH Z 165 " =    2.194
peak=   -3.218 closest distance to " O   ASP A  27 " =    1.961
peak=   -3.218 closest distance to " O   HOH Z 166 " =    1.654
peak=   -3.214 closest distance to " NH2 ARG A  79 " =    2.168
peak=   -3.213 closest distance to " CD2 PHE A 130 " =    2.915
peak=   -3.213 closest distance to " O   ALA A   1 " =    1.727
peak=   -3.209 closest distance to " CG2 THR A 178 " =    2.262
peak=   -3.207 closest distance to " CB  ASN A  39 " =    2.115
peak=   -3.206 closest distance to " OH  TYR A 247 " =    1.650
peak=   -3.204 closest distance to " CG2 ILE A 151 " =    2.540
peak=   -3.204 closest distance to " O   HOH Z 286 " =    1.732
peak=   -3.203 closest distance to " CD2 PHE A  61 " =    2.041
peak=   -3.200 closest distance to " CB  ALA A 227 " =    2.398
peak=   -3.198 closest distance to " CA  GLY A 133 " =    1.956
peak=   -3.195 closest distance to " O   HOH Z  32 " =    2.139
peak=   -3.194 closest distance to " N   GLN A 223 " =    2.038
peak=   -3.193 closest distance to " O   HOH Z 331 " =    1.062
peak=   -3.191 closest distance to " O   ASP A 191 " =    1.915
peak=   -3.187 closest distance to " O   HOH Z 292 " =    1.451
peak=   -3.184 closest distance to " O   ALA A  51 " =    1.266
peak=   -3.178 closest distance to " CB  ALA A 131 " =    1.940
peak=   -3.176 closest distance to " CG1 VAL A 250 " =    2.725
peak=   -3.172 closest distance to " O   HOH Z 139 " =    5.175
peak=   -3.166 closest distance to " O   HOH Z  52 " =    1.841
peak=   -3.165 closest distance to " CZ  TYR A 169 " =    1.754
peak=   -3.163 closest distance to " N   VAL A 232 " =    2.104
peak=   -3.159 closest distance to " O   HOH Z 117 " =    2.063
peak=   -3.156 closest distance to " CG  GLN A 278 " =    2.109
peak=   -3.155 closest distance to " O   ASN A 187 " =    1.449
peak=   -3.153 closest distance to " CG  GLN A  58 " =    1.214
peak=   -3.152 closest distance to " O   HOH Z 389 " =    2.421
peak=   -3.149 closest distance to " O   HOH Z 278 " =    1.208
peak=   -3.145 closest distance to " ND2 ASN A  69 " =    1.708
peak=   -3.144 closest distance to " O   ARG A  79 " =    2.605
peak=   -3.143 closest distance to " CB  ALA A 291 " =    1.780
peak=   -3.131 closest distance to " CD2 HIS A 207 " =    2.206
peak=   -3.129 closest distance to " CB  PRO A 213 " =    2.215
peak=   -3.126 closest distance to " OE1 GLN A  88 " =    1.106
peak=   -3.124 closest distance to " CE1 TYR A 247 " =    2.652
peak=   -3.117 closest distance to " O   HOH Z 256 " =    1.402
peak=   -3.105 closest distance to " O   ALA A   1 " =    1.522
peak=   -3.101 closest distance to " CD2 LEU A  25 " =    2.257
peak=   -3.099 closest distance to " CA  GLY A  57 " =    2.108
peak=   -3.092 closest distance to " CG  GLN A  88 " =    0.776
peak=   -3.084 closest distance to " O   HOH Z 191 " =    5.646
peak=   -3.079 closest distance to " O   HOH Z 371 " =    1.261
peak=   -3.076 closest distance to " O   LYS A 289 " =    2.961
peak=   -3.075 closest distance to " CG  PRO A 163 " =    2.572
peak=   -3.067 closest distance to " O   HOH Z 412 " =    3.997
peak=   -3.067 closest distance to " CG  ARG A 259 " =    2.414
peak=   -3.064 closest distance to " CZ3 TRP A 179 " =    1.292
peak=   -3.062 closest distance to " O   HOH Z 111 " =    4.676
peak=   -3.042 closest distance to " CG1 VAL A 112 " =    2.587
peak=   -3.030 closest distance to " O   HOH Z 414 " =    1.546
peak=   -3.028 closest distance to " O   TRP A  70 " =    1.416

================= 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    :  0.5015 0.4894   6.303275e+00   6.286354e+00
   1_bss:  0.4931 0.4767   6.298096e+00   6.279135e+00
   1_xyz:  0.4242 0.4499   6.219525e+00   6.245748e+00
   1_adp:  0.3869 0.4491   6.172068e+00   6.243664e+00
   1_occ:  0.3867 0.4495   6.171928e+00   6.243823e+00
   2_bss:  0.3831 0.4446   6.173091e+00   6.242882e+00
   2_xyz:  0.3201 0.3910   6.032417e+00   6.155704e+00
   2_adp:  0.2988 0.3778   5.995401e+00   6.130977e+00
   2_occ:  0.2985 0.3779   5.995151e+00   6.131332e+00
   3_bss:  0.2968 0.3762   5.996845e+00   6.131986e+00
   3_xyz:  0.2187 0.2833   5.727665e+00   5.910276e+00
   3_adp:  0.1905 0.2552   5.613241e+00   5.823427e+00
   3_occ:  0.1903 0.2545   5.611542e+00   5.822104e+00
   4_bss:  0.1894 0.2534   5.609586e+00   5.820309e+00
   4_xyz:  0.1502 0.2044   5.404064e+00   5.636213e+00
   4_adp:  0.1397 0.1935   5.344834e+00   5.581561e+00
   4_occ:  0.1395 0.1931   5.343642e+00   5.580316e+00
   5_bss:  0.1400 0.1932   5.342453e+00   5.578531e+00
   5_xyz:  0.1285 0.1785   5.269341e+00   5.510221e+00
   5_adp:  0.1253 0.1752   5.248712e+00   5.489484e+00
   5_occ:  0.1252 0.1752   5.248558e+00   5.489362e+00
   5_bss:  0.1251 0.1751   5.248606e+00   5.489377e+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:  0.332   0.000   6.605   9.206  10.943   0.000   0.000   0.000
   1_xyz:  0.332   0.000   6.605   9.206  10.943   0.000   0.000   0.000
   1_adp:  0.332   0.000   6.605   9.206  10.943   0.000   0.000   0.000
   1_occ:  0.332   0.000   6.605   9.206  10.943   0.000   0.000   0.000
   2_bss:  0.344  34.996   3.116   5.047   6.473   0.000   0.000   0.000
   2_xyz:  0.344  34.996   3.116   5.047   6.473   0.000   0.000   0.000
   2_adp:  0.344  34.996   3.116   5.047   6.473   0.000   0.000   0.000
   2_occ:  0.344  34.996   3.116   5.047   6.473   0.000   0.000   0.000
   3_bss:  0.349  59.587   1.477   2.435   3.964   0.000   0.000   0.000
   3_xyz:  0.349  59.587   1.477   2.435   3.964   0.000   0.000   0.000
   3_adp:  0.349  59.587   1.477   2.435   3.964   0.000   0.000   0.000
   3_occ:  0.349  59.587   1.477   2.435   3.964   0.000   0.000   0.000
   4_bss:  0.330  58.219   0.469   0.736   2.616   0.000   0.000   0.000
   4_xyz:  0.330  58.219   0.469   0.736   2.616   0.000   0.000   0.000
   4_adp:  0.330  58.219   0.469   0.736   2.616   0.000   0.000   0.000
   4_occ:  0.330  58.219   0.469   0.736   2.616   0.000   0.000   0.000
   5_bss:  0.326  58.219   0.385   0.365   2.463   0.000   0.000   0.000
   5_xyz:  0.326  58.219   0.385   0.365   2.463   0.000   0.000   0.000
   5_adp:  0.326  58.219   0.385   0.365   2.463   0.000   0.000   0.000
   5_occ:  0.326  58.219   0.385   0.365   2.463   0.000   0.000   0.000
   5_bss:  0.326  59.409  -0.644  -0.751   1.396   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  63.032 0.3534  0.4227    77383.857
   1_bss:  61.678 0.3704  0.5703    75240.685
   1_xyz:  54.729 0.4589  0.6908    62290.509
   1_adp:  53.832 0.4700  0.7848    61559.804
   1_occ:  53.985 0.4681  0.7807    61807.264
   2_bss:  53.520 0.4739  0.6949    61048.064
   2_xyz:  43.575 0.5978  0.8677    43282.638
   2_adp:  41.222 0.6269  0.8987    39984.092
   2_occ:  41.258 0.6265  0.8975    39982.159
   3_bss:  41.122 0.6283  0.8319    39963.309
   3_xyz:  28.957 0.7680  0.9803    20965.839
   3_adp:  25.366 0.8072  0.9996    17003.513
   3_occ:  25.310 0.8077  0.9996    16899.910
   4_bss:  25.217 0.8085  0.9535    16795.374
   4_xyz:  19.945 0.8616  0.9793    10808.001
   4_adp:  18.526 0.8754  0.9733     9718.033
   4_occ:  18.487 0.8758  0.9733     9679.951
   5_bss:  18.435 0.8761  0.9665     9617.408
   5_xyz:  16.681 0.8921  0.9759     8177.159
   5_adp:  16.137 0.8973  0.9695     7882.519
   5_occ:  16.136 0.8973  0.9693     7872.498
   5_bss:  16.138 0.8972  0.9734     7874.280
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.089   5.3700e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.089   5.3700e+01
   1_xyz:   1.782  0.014  0.110 18.644  0.006  4.106   1.5538e-01
   1_adp:   1.782  0.014  0.110 18.644  0.006  4.106   1.5538e-01
   1_occ:   1.782  0.014  0.110 18.644  0.006  4.106   1.5538e-01
   2_bss:   1.782  0.014  0.110 18.644  0.006  4.106   1.5538e-01
   2_xyz:   1.204  0.008  0.083 16.801  0.005  4.124   9.2985e-02
   2_adp:   1.204  0.008  0.083 16.801  0.005  4.124   9.2985e-02
   2_occ:   1.204  0.008  0.083 16.801  0.005  4.124   9.2985e-02
   3_bss:   1.204  0.008  0.083 16.801  0.005  4.124   9.2985e-02
   3_xyz:   1.275  0.010  0.095 16.349  0.005  4.128   9.5468e-02
   3_adp:   1.275  0.010  0.095 16.349  0.005  4.128   9.5468e-02
   3_occ:   1.275  0.010  0.095 16.349  0.005  4.128   9.5468e-02
   4_bss:   1.275  0.010  0.095 16.349  0.005  4.128   9.5468e-02
   4_xyz:   1.074  0.008  0.078 15.845  0.004  4.111   7.0340e-02
   4_adp:   1.074  0.008  0.078 15.845  0.004  4.111   7.0340e-02
   4_occ:   1.074  0.008  0.078 15.845  0.004  4.111   7.0340e-02
   5_bss:   1.074  0.008  0.078 15.845  0.004  4.111   7.0340e-02
   5_xyz:   0.974  0.007  0.074 15.321  0.004  4.118   5.9929e-02
   5_adp:   0.974  0.007  0.074 15.321  0.004  4.118   5.9929e-02
   5_occ:   0.974  0.007  0.074 15.321  0.004  4.118   5.9929e-02
   5_bss:   0.974  0.007  0.074 15.321  0.004  4.118   5.9929e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9596e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9596e+00
   1_xyz:  13.966  0.194  0.433 84.853  0.035  2.072   1.0531e-01
   1_adp:  13.966  0.194  0.433 84.853  0.035  2.072   1.0531e-01
   1_occ:  13.966  0.194  0.433 84.853  0.035  2.072   1.0531e-01
   2_bss:  13.966  0.194  0.433 84.853  0.035  2.072   1.0531e-01
   2_xyz:   6.804  0.072  0.297 88.188  0.037  2.023   6.3397e-02
   2_adp:   6.804  0.072  0.297 88.188  0.037  2.023   6.3397e-02
   2_occ:   6.804  0.072  0.297 88.188  0.037  2.023   6.3397e-02
   3_bss:   6.804  0.072  0.297 88.188  0.037  2.023   6.3397e-02
   3_xyz:   8.903  0.060  0.393 89.564  0.035  2.154   7.9232e-02
   3_adp:   8.903  0.060  0.393 89.564  0.035  2.154   7.9232e-02
   3_occ:   8.903  0.060  0.393 89.564  0.035  2.154   7.9232e-02
   4_bss:   8.903  0.060  0.393 89.564  0.035  2.154   7.9232e-02
   4_xyz:   9.289  0.056  0.301 83.313  0.036  2.280   5.0801e-02
   4_adp:   9.289  0.056  0.301 83.313  0.036  2.280   5.0801e-02
   4_occ:   9.289  0.056  0.301 83.313  0.036  2.280   5.0801e-02
   5_bss:   9.289  0.056  0.301 83.313  0.036  2.280   5.0801e-02
   5_xyz:   6.922  0.048  0.272 81.294  0.036  2.358   4.5249e-02
   5_adp:   6.922  0.048  0.272 81.294  0.036  2.358   4.5249e-02
   5_occ:   6.922  0.048  0.272 81.294  0.036  2.358   4.5249e-02
   5_bss:   6.922  0.048  0.272 81.294  0.036  2.358   4.5249e-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:  85.42   0.00  16.05  74.10   0.00  14.46  85.42   0.00  24.74
   1_occ:  85.42   0.00  16.05  74.10   0.00  14.46  85.42   0.00  24.74
   2_bss:  85.42   0.00  16.05  74.10   0.00  14.46  85.42   0.00  24.74
   2_xyz:  85.42   0.00  16.05  74.10   0.00  14.46  85.42   0.00  24.74
   2_adp:  87.12   0.00  15.10  66.62   0.00  12.30  87.12   0.00  30.36
   2_occ:  87.12   0.00  15.10  66.62   0.00  12.30  87.12   0.00  30.36
   3_bss:  87.12   0.00  15.10  66.62   0.00  12.30  87.12   0.00  30.36
   3_xyz:  87.12   0.00  15.10  66.62   0.00  12.30  87.12   0.00  30.36
   3_adp:  90.68   0.00  15.29  77.03   0.00  10.99  90.68   0.54  38.69
   3_occ:  90.68   0.00  15.29  77.03   0.00  10.99  90.68   0.54  38.69
   4_bss:  90.68   0.00  15.29  77.03   0.00  10.99  90.68   0.54  38.69
   4_xyz:  90.68   0.00  15.29  77.03   0.00  10.99  90.68   0.54  38.69
   4_adp:  92.88   0.00  15.38  81.79   0.00  10.43  92.88   3.55  42.35
   4_occ:  92.88   0.00  15.38  81.79   0.00  10.43  92.88   3.55  42.35
   5_bss:  92.88   0.00  15.38  81.79   0.00  10.43  92.88   3.55  42.35
   5_xyz:  92.88   0.00  15.38  81.79   0.00  10.43  92.88   3.55  42.35
   5_adp:  97.40   0.00  15.29  93.53   0.00  10.20  97.40   3.26  43.01
   5_occ:  97.40   0.00  15.29  93.53   0.00  10.20  97.40   3.26  43.01
   5_bss:  98.59   1.19  16.48  94.72   1.19  11.39  98.59   4.45  44.20
------------------------------------------------------------------------
 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:    1.312    0.032    0.415
   1_adp:    1.312    0.032    0.415
   1_occ:    1.312    0.032    0.415
   2_bss:    1.312    0.032    0.415
   2_xyz:    1.829    0.049    0.585
   2_adp:    1.829    0.049    0.585
   2_occ:    1.829    0.049    0.585
   3_bss:    1.829    0.049    0.585
   3_xyz:    1.702    0.040    0.757
   3_adp:    1.702    0.040    0.757
   3_occ:    1.702    0.040    0.757
   4_bss:    1.702    0.040    0.757
   4_xyz:    1.742    0.054    0.816
   4_adp:    1.742    0.054    0.816
   4_occ:    1.742    0.054    0.816
   5_bss:    1.742    0.054    0.816
   5_xyz:    1.821    0.052    0.840
   5_adp:    1.821    0.052    0.840
   5_occ:    1.821    0.052    0.840
   5_bss:    1.821    0.052    0.840
------------------------------------------------------------------------

CPU time actual refinement: 320.23


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_625/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_625/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_625/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_625/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_625/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 320.08 
  Macro-tasks:
    bulk solvent and scale       = 41.21  
    individual site refinement   = 128.87 
    weights calculation          = 31.66  
    collect and process          = 6.36   
    model show statistics        = 0.11   
    TOTAL for macro-tasks        = 208.21 
  Micro-tasks:
    mask                            = 2.31   
    f_calc                          = 97.97  
    alpha_beta                      = 8.38   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 106.67 
    fmodel                         = 6.78   
    r_factors                      = 0.26   
    phase_errors                   = 10.19  
    foms                           = 0.26   
    TOTAL for micro-tasks          = 233.97 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 4.581 micro seconds
Total CPU time: 5.56 minutes
from_scatterers_fft:    619 calls, 97.65 s
gradients_fft:          563 calls, 94.19 s

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

# Date 2008-01-16 Time 02:02:31 PST -0800 (1200477751.38 s)
Start R-work = 0.5015, R-free = 0.4894 (no bulk solvent and anisotropic scale)
Final R-work = 0.1416, R-free = 0.1906 (no bulk solvent and anisotropic scale)

Start R-work = 0.4931, R-free = 0.4767
Final R-work = 0.1251, R-free = 0.1751