# Date 2008-01-16 Time 02:33:45 PST -0800 (1200479625.36 s)
#phil __OFF__

Command line arguments: "../885.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 9881
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 885

-------------------------------------------------------------------------------
  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: (70.9525, 46.4607, 86.39, 90, 90, 90)
  Space group: P 21 21 21 (No. 19)

/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb
  Monomer Library directory:
    "/net/rosie/scratch3/phzwart/CCTBX/Sources/mon_lib"
  Total number of atoms: 2823
  Number of models: 1
  Model: 0
    Number of conformers: 2
    Conformer: "A"
      Number of atoms: 2769
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
        Number of residues, atoms: 436, 436
          Classifications: {'water': 436}
          Link IDs: {None: 435}
    Conformer: "B"
      Number of atoms: 2771
      Common with "A": 2717
      Number of chains: 2
        Number of residues, atoms: 302, 2333
          Classifications: {'peptide': 302}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'CIS': 1, 'TRANS': 293}
          bond proxies already assigned to first conformer: 2332
        Number of residues, atoms: 438, 438
          Classifications: {'water': 438}
          Link IDs: {None: 437}
  Time building chain proxies: 3.26, per 1000 atoms: 1.15


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

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

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

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:FOBS,SIGMA
Observation type: xray.amplitude
Type of data: double, size=19589
Type of sigmas: double, size=19589
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.9525, 46.4607, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1028 1.98276
Completeness in resolution range: 0.961518
Completeness with d_max=infinity: 0.9586

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.1028
                             d_min =   1.9828

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: (70.9525, 46.4607, 86.39, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.1028 1.98276
Completeness in resolution range: 0.961518
Completeness with d_max=infinity: 0.9586

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.1032 -  4.2431 [2137/2162]  1924   213  10.0%
  bin  2:  4.2431 -  3.3803 [2050/2070]  1845   205  10.0%
  bin  3:  3.3803 -  2.9566 [2041/2060]  1836   205  10.0%
  bin  4:  2.9566 -  2.6880 [2007/2037]  1808   199   9.9%
  bin  5:  2.6880 -  2.4962 [2010/2029]  1813   197   9.8%
  bin  6:  2.4962 -  2.3496 [1982/2007]  1776   206  10.4%
  bin  7:  2.3496 -  2.2324 [1973/2001]  1775   198  10.0%
  bin  8:  2.2324 -  2.1355 [1972/2008]  1777   195   9.9%
  bin  9:  2.1355 -  2.0535 [1974/2016]  1779   195   9.9%
  bin 10:  2.0535 -  1.9828 [1443/1983]  1297   146  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_885/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.13 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.81 -     2.42: 17
        2.42 -     3.04: 2187
        3.04 -     3.66: 4688
        3.66 -     4.28: 9068
        4.28 -     4.90: 12292
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " CZ BARG A 275 " - " O  BHOH Z 338 "  2.218 3.270
  " O   HOH Z 201 " - " O   HOH Z 349 "  2.274 3.040 -x+1/2,-y+1,z+1/2
  " OG1 THR A  29 " - " O   HOH Z 245 "  2.305 3.040 x,y+1,z
  " O   HOH Z 280 " - " O   HOH Z 438 "  2.318 3.040 -x,y-1/2,-z+1/2
  ... (remaining 28247 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_885/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_885/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 = 70.9525 46.4607 86.39 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.98 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4395   r_free= 0.4256   ksol= 0.00   Bsol= 0.00   scale= 0.819    |
|                                                                             |
| 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:   0.58 A                  |
| x-ray target function (ml) for work reflections: 6.234516                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1032 -  4.7328 0.99   1390  155 0.3733 0.3601      6.5375      6.4993|
|  2:  4.7328 -  3.7759 0.99   1337  150 0.3331 0.3368      6.6737      6.6397|
|  3:  3.7759 -  3.3043 0.99   1316  141 0.3719 0.3445      6.5532      6.5758|
|  4:  3.3043 -  3.0048 0.99   1305  152 0.4173 0.3762      6.4721      6.3837|
|  5:  3.0048 -  2.7908 0.99   1294  143 0.4654 0.4499      6.3218      6.3436|
|  6:  2.7908 -  2.6272 0.99   1298  138 0.4650 0.4926      6.2414       6.161|
|  7:  2.6272 -  2.4962 0.99   1286  140 0.4935 0.4688      6.2177      6.2283|
|  8:  2.4962 -  2.3880 0.98   1269  148 0.4943 0.4387      6.1546      6.1326|
|  9:  2.3880 -  2.2964 0.98   1256  145 0.4669 0.4880      6.0807       6.108|
| 10:  2.2964 -  2.2174 1.00   1294  138 0.5030 0.4566      6.0961      6.0465|
| 11:  2.2174 -  2.1483 0.98   1268  138 0.5009 0.4732      6.0174      6.0007|
| 12:  2.1483 -  2.0870 0.98   1248  142 0.4930 0.5184      5.9728      6.0053|
| 13:  2.0870 -  2.0322 0.99   1282  139 0.5111 0.4979      5.8709      5.8237|
| 14:  2.0322 -  1.9828 0.62    787   90 0.5218 0.5122       5.858      5.7749|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1032 -  4.7328  1390   155  0.73  31.93   0.81     0.77      62098.08|
|  2:  4.7328 -  3.7759  1337   150  0.78  28.19   0.91     0.83      74928.54|
|  3:  3.7759 -  3.3043  1316   141  0.71  34.70   0.88     0.81      77106.72|
|  4:  3.3043 -  3.0048  1305   152  0.65  39.48   0.83     0.73      69418.47|
|  5:  3.0048 -  2.7908  1294   143  0.55  48.07   0.76     0.63      62333.75|
|  6:  2.7908 -  2.6272  1298   138  0.51  51.22   0.75     0.56      57506.42|
|  7:  2.6272 -  2.4962  1286   140  0.47  54.52   0.76     0.53      55417.12|
|  8:  2.4962 -  2.3880  1269   148  0.46  55.19   0.75     0.53      50661.88|
|  9:  2.3880 -  2.2964  1256   145  0.49  52.68   0.75     0.55      43983.82|
| 10:  2.2964 -  2.2174  1294   138  0.48  53.58   0.78     0.56      38916.75|
| 11:  2.2174 -  2.1483  1268   138  0.46  55.44   0.77     0.54      38509.97|
| 12:  2.1483 -  2.0870  1248   142  0.42  58.67   0.79     0.51      38801.65|
| 13:  2.0870 -  2.0322  1282   139  0.38  61.71   0.74     0.47      34307.49|
| 14:  2.0322 -  1.9828   787    90  0.45  56.24   0.73     0.47      25042.29|
|alpha:            min =        0.47 max =            0.83 mean =         0.61|
|beta:             min =    25042.29 max =        77106.72 mean =     53089.42|
|figures of merit: min =        0.00 max =            1.00 mean =         0.54|
|phase err.(work): min =        0.00 max =           89.96 mean =        48.24|
|phase err.(test): min =        0.00 max =           89.97 mean =        48.38|
|-----------------------------------------------------------------------------|

============================== 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 = 8.348355              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 75.532   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.730329              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.223   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        2 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       21 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      169 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      684 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1499 |
| 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:     3921 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5068 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6566 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7694 |
|-----------------------------------------------------------------------------|
|-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 |       53.800 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.090    4.900  1.196 |       1.693 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.921)------------------------------------------|
|    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 = 11.921)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4469   r_free= 0.4317   ksol= 0.00   Bsol= 0.00   scale= 0.787    |
|                                                                             |
| 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:   0.59 A                  |
| x-ray target function (ml) for work reflections: 6.239618                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4311   r_free= 0.4122   ksol= 0.35   Bsol= 13.39   scale= 1.020   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.99,9.12,7.86,0.00,0.00,0.00); trace/3= 8.32                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.60 A                  |
| x-ray target function (ml) for work reflections: 6.229144                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.723826              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 77.397   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.718560              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 77.073   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4311      final r-factor (work) = 0.3259          |
| start r-factor (free) = 0.4122      final r-factor (free) = 0.3458          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 77.9082 = 7.72 * 0.50 * 6.2426 + 1.00 * 53.7996                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 23.6403 = 7.72 * 0.50 * 6.0903 + 1.00 * 0.1200                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3259      final r-factor (work) = 0.2646          |
| start r-factor (free) = 0.3458      final r-factor (free) = 0.3058          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.3910 = 0.72 * 1.00 * 6.0903 + 1.00 * 0.0147                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.2704 = 0.72 * 1.00 * 5.9253 + 1.00 * 0.0127                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.921)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    66.27   11.08    None  None   None       |
|    all(noH): 2823   0      0.00    66.27   11.08    None  None   None       |
|    Sol.    : 438    0      0.00    66.27   27.38    None  None   None       |
|    Mac.    : 2385   0      0.00    62.21   8.08     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.627: 1284   |   5:    33.134 -  39.761:   87        |
|      1:     6.627 -  13.254:  753   |   6:    39.761 -  46.388:   52        |
|      2:    13.254 -  19.881:  308   |   7:    46.388 -  53.015:   22        |
|      3:    19.881 -  26.508:  173   |   8:    53.015 -  59.642:   11        |
|      4:    26.508 -  33.134:  129   |   9:    59.642 -  66.269:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2646 r_free = 0.3058             target_work(ml) = 5.871         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2642 r_free = 0.3058             target_work(ml) = 5.870         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2642   r_free= 0.3058   ksol= 0.35   Bsol= 13.39   scale= 1.095   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.99,9.12,7.86,0.00,0.00,0.00); trace/3= 8.32                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.32 A                  |
| x-ray target function (ml) for work reflections: 5.870203                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2591   r_free= 0.2987   ksol= 0.35   Bsol= 44.01   scale= 1.003   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.54,4.85,4.92,0.00,0.00,0.00); trace/3= 4.77                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.35 A                  |
| x-ray target function (ml) for work reflections: 5.865807                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.138676              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 94.649   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.343954              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 122.587  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2591      final r-factor (work) = 0.1680          |
| start r-factor (free) = 0.2987      final r-factor (free) = 0.2131          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.3552 = 5.14 * 0.50 * 5.9298 + 1.00 * 0.1197                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 14.6528 = 5.14 * 0.50 * 5.6750 + 1.00 * 0.0718                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1680      final r-factor (work) = 0.1482          |
| start r-factor (free) = 0.2131      final r-factor (free) = 0.1946          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.9645 = 0.34 * 1.00 * 5.6750 + 1.00 * 0.0126                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8746 = 0.34 * 1.00 * 5.4192 + 1.00 * 0.0106                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.921)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    67.89   11.41    None  None   None       |
|    all(noH): 2823   0      0.00    67.89   11.41    None  None   None       |
|    Sol.    : 438    0      0.00    67.66   32.52    None  None   None       |
|    Mac.    : 2385   0      0.00    67.89   7.53     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   6.789: 1475   |   5:    33.944 -  40.733:  103        |
|      1:     6.789 -  13.578:  664   |   6:    40.733 -  47.522:   81        |
|      2:    13.578 -  20.367:  208   |   7:    47.522 -  54.311:   52        |
|      3:    20.367 -  27.155:  113   |   8:    54.311 -  61.100:   17        |
|      4:    27.155 -  33.944:  104   |   9:    61.100 -  67.889:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1482 r_free = 0.1946             target_work(ml) = 5.373         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1481 r_free = 0.1945             target_work(ml) = 5.372         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1481   r_free= 0.1945   ksol= 0.35   Bsol= 44.01   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.54,4.85,4.92,0.00,0.00,0.00); trace/3= 4.77                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.371921                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1475   r_free= 0.1925   ksol= 0.33   Bsol= 44.01   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.35,3.21,4.25,0.00,0.00,0.00); trace/3= 3.60                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.370599                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.831517              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 109.226  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.670350              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 139.886  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1475      final r-factor (work) = 0.1276          |
| start r-factor (free) = 0.1925      final r-factor (free) = 0.1711          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0419 = 1.83 * 0.50 * 5.4273 + 1.00 * 0.0718                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9164 = 1.83 * 0.50 * 5.3065 + 1.00 * 0.0569                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1276      final r-factor (work) = 0.1233          |
| start r-factor (free) = 0.1711      final r-factor (free) = 0.1675          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5678 = 0.67 * 1.00 * 5.3065 + 1.00 * 0.0106                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.5185 = 0.67 * 1.00 * 5.2297 + 1.00 * 0.0127                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.921)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.59   11.94    None  None   None       |
|    all(noH): 2823   0      0.00    76.59   11.94    None  None   None       |
|    Sol.    : 438    0      0.73    74.80   35.12    None  None   None       |
|    Mac.    : 2385   0      0.00    76.59   7.68     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.659: 1622   |   5:    38.293 -  45.951:   84        |
|      1:     7.659 -  15.317:  578   |   6:    45.951 -  53.610:   79        |
|      2:    15.317 -  22.976:  181   |   7:    53.610 -  61.268:   43        |
|      3:    22.976 -  30.634:  103   |   8:    61.268 -  68.927:   15        |
|      4:    30.634 -  38.293:  107   |   9:    68.927 -  76.585:   11        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1233 r_free = 0.1675             target_work(ml) = 5.219         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1232 r_free = 0.1675             target_work(ml) = 5.218         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1232   r_free= 0.1675   ksol= 0.33   Bsol= 44.01   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.35,3.21,4.25,0.00,0.00,0.00); trace/3= 3.60                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.218491                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1232   r_free= 0.1674   ksol= 0.32   Bsol= 44.01   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.13,2.94,4.17,0.00,0.00,0.00); trace/3= 3.42                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.217752                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.387143              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 112.266  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.214433              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 143.431  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1232      final r-factor (work) = 0.1122          |
| start r-factor (free) = 0.1674      final r-factor (free) = 0.1594          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.9127 = 3.39 * 0.50 * 5.2291 + 1.00 * 0.0569                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8435 = 3.39 * 0.50 * 5.1771 + 1.00 * 0.0758                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1122      final r-factor (work) = 0.1119          |
| start r-factor (free) = 0.1594      final r-factor (free) = 0.1576          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1227 = 0.21 * 1.00 * 5.1771 + 1.00 * 0.0126                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.1159 = 0.21 * 1.00 * 5.1541 + 1.00 * 0.0107                               |
|-----------------------------------------------------------------------------|
| number of iterations = 16      |    number of function evaluations = 18     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.921)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    76.66   11.67    None  None   None       |
|    all(noH): 2823   0      0.00    76.66   11.67    None  None   None       |
|    Sol.    : 438    0      1.45    72.62   34.20    None  None   None       |
|    Mac.    : 2385   0      0.00    76.66   7.54     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.667: 1673   |   5:    38.332 -  45.999:   82        |
|      1:     7.667 -  15.333:  564   |   6:    45.999 -  53.665:   74        |
|      2:    15.333 -  22.999:  155   |   7:    53.665 -  61.332:   37        |
|      3:    22.999 -  30.666:  111   |   8:    61.332 -  68.998:   13        |
|      4:    30.666 -  38.332:  104   |   9:    68.998 -  76.665:   10        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1119 r_free = 0.1576             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1118 r_free = 0.1574             target_work(ml) = 5.145         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1118   r_free= 0.1574   ksol= 0.32   Bsol= 44.01   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.13,2.94,4.17,0.00,0.00,0.00); trace/3= 3.42                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.144609                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1119   r_free= 0.1571   ksol= 0.32   Bsol= 44.01   scale= 1.002   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.07,2.84,4.17,0.00,0.00,0.00); trace/3= 3.36                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.144608                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.477185              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 141.268  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.263560              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 151.638  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1119      final r-factor (work) = 0.1150          |
| start r-factor (free) = 0.1571      final r-factor (free) = 0.1573          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8822 = 1.48 * 0.50 * 5.1536 + 1.00 * 0.0758                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 3.8639 = 1.48 * 0.50 * 5.1588 + 1.00 * 0.0536                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1150      final r-factor (work) = 0.1146          |
| start r-factor (free) = 0.1573      final r-factor (free) = 0.1574          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3703 = 0.26 * 1.00 * 5.1588 + 1.00 * 0.0107                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.3736 = 0.26 * 1.00 * 5.1589 + 1.00 * 0.0140                               |
|-----------------------------------------------------------------------------|
| number of iterations = 13      |    number of function evaluations = 16     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.921)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    77.00   11.56    None  None   None       |
|    all(noH): 2823   0      0.00    77.00   11.56    None  None   None       |
|    Sol.    : 438    0      1.49    70.98   33.68    None  None   None       |
|    Mac.    : 2385   0      0.00    77.00   7.50     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.700: 1663   |   5:    38.500 -  46.201:   85        |
|      1:     7.700 -  15.400:  583   |   6:    46.201 -  53.901:   70        |
|      2:    15.400 -  23.100:  147   |   7:    53.901 -  61.601:   31        |
|      3:    23.100 -  30.800:  114   |   8:    61.601 -  69.301:   15        |
|      4:    30.800 -  38.500:  108   |   9:    69.301 -  77.001:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1146 r_free = 0.1574             target_work(ml) = 5.160         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1146 r_free = 0.1574             target_work(ml) = 5.160         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1146   r_free= 0.1574   ksol= 0.32   Bsol= 44.01   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.07,2.84,4.17,0.00,0.00,0.00); trace/3= 3.36                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.159735                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1032 -  4.7328 0.99   1390  155 0.1006 0.1259      5.3922      5.5078|
|  2:  4.7328 -  3.7759 0.99   1337  150 0.0889 0.1162      5.4574      5.6339|
|  3:  3.7759 -  3.3043 0.99   1316  141 0.1080 0.1498      5.4859      5.8581|
|  4:  3.3043 -  3.0048 0.99   1305  152 0.1220 0.1663      5.4633      5.6043|
|  5:  3.0048 -  2.7908 0.99   1294  143 0.1381 0.1726      5.3533      5.5553|
|  6:  2.7908 -  2.6272 0.99   1298  138 0.1213 0.1866      5.2027      5.4676|
|  7:  2.6272 -  2.4962 0.99   1286  140 0.1320 0.1546       5.192      5.3399|
|  8:  2.4962 -  2.3880 0.98   1269  148 0.1185 0.1733      5.0747      5.3582|
|  9:  2.3880 -  2.2964 0.98   1256  145 0.1213 0.1881      5.0656      5.3295|
| 10:  2.2964 -  2.2174 1.00   1294  138 0.1166 0.1645      4.9701      5.2165|
| 11:  2.2174 -  2.1483 0.98   1268  138 0.1178 0.1774      4.9622       5.275|
| 12:  2.1483 -  2.0870 0.98   1248  142 0.1137 0.1679      4.8868      5.1617|
| 13:  2.0870 -  2.0322 0.99   1282  139 0.1188 0.1754      4.8068       5.077|
| 14:  2.0322 -  1.9828 0.62    787   90 0.1062 0.1640       4.678      4.8762|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1032 -  4.7328  1390   155  0.94   9.04   0.98     0.95       6977.45|
|  2:  4.7328 -  3.7759  1337   150  0.95   7.88   1.01     1.00       8970.37|
|  3:  3.7759 -  3.3043  1316   141  0.93  11.31   1.02     1.01      10426.49|
|  4:  3.3043 -  3.0048  1305   152  0.92  13.76   1.01     0.98      10425.65|
|  5:  3.0048 -  2.7908  1294   143  0.90  16.12   0.99     0.97       8557.34|
|  6:  2.7908 -  2.6272  1298   138  0.90  15.84   0.98     0.96       6935.93|
|  7:  2.6272 -  2.4962  1286   140  0.91  15.54   0.99     0.96       6196.13|
|  8:  2.4962 -  2.3880  1269   148  0.91  15.17   0.99     0.97       5272.34|
|  9:  2.3880 -  2.2964  1256   145  0.91  15.72   1.01     0.98       5251.26|
| 10:  2.2964 -  2.2174  1294   138  0.90  15.57   1.00     0.97       4369.54|
| 11:  2.2174 -  2.1483  1268   138  0.90  16.18   1.00     0.95       4373.53|
| 12:  2.1483 -  2.0870  1248   142  0.91  14.98   1.01     1.01       3952.85|
| 13:  2.0870 -  2.0322  1282   139  0.90  16.60   1.00     0.99       3415.85|
| 14:  2.0322 -  1.9828   787    90  0.92  14.17   0.98     0.95       2572.70|
|alpha:            min =        0.95 max =            1.01 mean =         0.98|
|beta:             min =     2572.70 max =        10426.49 mean =      6403.07|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.88 mean =        14.07|
|phase err.(test): min =        0.00 max =           89.22 mean =        13.60|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1146   r_free= 0.1573   ksol= 0.32   Bsol= 47.48   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.29,-0.52,0.81,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.159776                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.98 - 15.10 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1146   r_free= 0.1573   ksol= 0.32   Bsol= 47.48   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.29,-0.52,0.81,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.159776                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.1032 -  4.7328 0.99   1390  155 0.1006 0.1259      5.3929      5.5083|
|  2:  4.7328 -  3.7759 0.99   1337  150 0.0889 0.1162      5.4573      5.6336|
|  3:  3.7759 -  3.3043 0.99   1316  141 0.1080 0.1497      5.4858      5.8581|
|  4:  3.3043 -  3.0048 0.99   1305  152 0.1220 0.1663      5.4633      5.6044|
|  5:  3.0048 -  2.7908 0.99   1294  143 0.1381 0.1726      5.3533      5.5554|
|  6:  2.7908 -  2.6272 0.99   1298  138 0.1213 0.1866      5.2027      5.4676|
|  7:  2.6272 -  2.4962 0.99   1286  140 0.1320 0.1546       5.192      5.3399|
|  8:  2.4962 -  2.3880 0.98   1269  148 0.1185 0.1733      5.0747      5.3582|
|  9:  2.3880 -  2.2964 0.98   1256  145 0.1213 0.1881      5.0656      5.3295|
| 10:  2.2964 -  2.2174 1.00   1294  138 0.1166 0.1645      4.9701      5.2165|
| 11:  2.2174 -  2.1483 0.98   1268  138 0.1178 0.1774      4.9622       5.275|
| 12:  2.1483 -  2.0870 0.98   1248  142 0.1137 0.1679      4.8868      5.1617|
| 13:  2.0870 -  2.0322 0.99   1282  139 0.1188 0.1754      4.8068       5.077|
| 14:  2.0322 -  1.9828 0.62    787   90 0.1062 0.1640       4.678      4.8762|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.1032 -  4.7328  1390   155  0.94   9.04   0.98     0.95       6989.15|
|  2:  4.7328 -  3.7759  1337   150  0.95   7.88   1.01     1.00       8973.62|
|  3:  3.7759 -  3.3043  1316   141  0.93  11.31   1.02     1.01      10423.45|
|  4:  3.3043 -  3.0048  1305   152  0.92  13.76   1.01     0.98      10425.58|
|  5:  3.0048 -  2.7908  1294   143  0.90  16.12   0.99     0.97       8557.77|
|  6:  2.7908 -  2.6272  1298   138  0.90  15.84   0.98     0.96       6936.35|
|  7:  2.6272 -  2.4962  1286   140  0.91  15.54   0.99     0.96       6196.38|
|  8:  2.4962 -  2.3880  1269   148  0.91  15.17   0.99     0.97       5272.46|
|  9:  2.3880 -  2.2964  1256   145  0.91  15.72   1.01     0.98       5251.31|
| 10:  2.2964 -  2.2174  1294   138  0.90  15.57   1.00     0.97       4369.55|
| 11:  2.2174 -  2.1483  1268   138  0.90  16.18   1.00     0.95       4373.53|
| 12:  2.1483 -  2.0870  1248   142  0.91  14.98   1.01     1.01       3952.84|
| 13:  2.0870 -  2.0322  1282   139  0.90  16.60   1.00     0.99       3415.83|
| 14:  2.0322 -  1.9828   787    90  0.92  14.17   0.98     0.95       2572.69|
|alpha:            min =        0.95 max =            1.01 mean =         0.98|
|beta:             min =     2572.69 max =        10425.58 mean =      6404.09|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.78 mean =        14.08|
|phase err.(test): min =        0.00 max =           89.35 mean =        13.60|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.921)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      3.36    80.36   14.92    None  None   None       |
|    all(noH): 2823   0      3.36    80.36   14.92    None  None   None       |
|    Sol.    : 438    0      4.85    74.34   37.04    None  None   None       |
|    Mac.    : 2385   0      3.36    80.36   10.86    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:     3.360 -  11.060: 1663   |   5:    41.860 -  49.560:   85        |
|      1:    11.060 -  18.760:  583   |   6:    49.560 -  57.260:   70        |
|      2:    18.760 -  26.460:  147   |   7:    57.260 -  64.960:   31        |
|      3:    26.460 -  34.160:  114   |   8:    64.960 -  72.660:   15        |
|      4:    34.160 -  41.860:  108   |   9:    72.660 -  80.360:    7        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 308         
Filter by distance & map next to the model:
   mapped sites are within: 0.372 - 4.745
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 304 from: 308
   mapped sites are within: 0.731 - 4.745

peak=   11.149 closest distance to " CB  VAL A 230 " =    1.472
peak=    7.198 closest distance to " CG2 VAL A 296 " =    1.096
peak=    6.288 closest distance to " CD2 LEU A   5 " =    1.279
peak=    6.040 closest distance to " CG  LEU A   5 " =    1.238
peak=    5.865 closest distance to " NH2 ARG A  56 " =    2.166
peak=    5.720 closest distance to " CG  PRO A  54 " =    1.378
peak=    5.677 closest distance to " NE2 GLN A  11 " =    1.183
peak=    5.393 closest distance to " O   HOH Z 142 " =    1.946
peak=    5.295 closest distance to " CB  GLN A 223 " =    1.449
peak=    5.127 closest distance to " CG  LEU A 228 " =    1.178
peak=    5.070 closest distance to " CB  VAL A 296 " =    1.115
peak=    5.049 closest distance to " CB  PRO A  54 " =    1.040
peak=    4.986 closest distance to " O   HOH Z 232 " =    2.315
peak=    4.907 closest distance to " CB  SER A  63 " =    1.335
peak=    4.906 closest distance to " CG  PRO A 213 " =    1.236
peak=    4.832 closest distance to " CB  GLN A 183 " =    1.190
peak=    4.726 closest distance to " CG  PRO A 198 " =    1.259
peak=    4.704 closest distance to " C   PRO A 198 " =    1.537
peak=    4.698 closest distance to " CB  ASN A 148 " =    1.341
peak=    4.683 closest distance to " O   HOH Z 126 " =    1.920
peak=    4.657 closest distance to " O   HOH Z 369 " =    2.026
peak=    4.657 closest distance to " CB  VAL A 230 " =    1.181
peak=    4.618 closest distance to " O   HOH Z 427 " =    2.845
peak=    4.546 closest distance to " CG  PRO A 243 " =    1.155
peak=    4.514 closest distance to " O   HOH Z 209 " =    2.312
peak=    4.512 closest distance to " CD2 LEU A 228 " =    1.159
peak=    4.509 closest distance to " CB  SER A   3 " =    1.383
peak=    4.478 closest distance to " O   HOH Z 272 " =    1.874
peak=    4.467 closest distance to " O   HOH Z 316 " =    3.049
peak=    4.425 closest distance to " ND2 ASN A 187 " =    1.547
peak=    4.408 closest distance to " CB  ARG A 275 " =    0.867
peak=    4.395 closest distance to " O   HOH Z 425 " =    1.449
peak=    4.361 closest distance to " O   HOH Z 236 " =    1.991
peak=    4.360 closest distance to " O   HOH Z 298 " =    1.770
peak=    4.312 closest distance to " CB  GLU A 152 " =    1.237
peak=    4.293 closest distance to " CB  TRP A 266 " =    0.979
peak=    4.276 closest distance to " CB  SER A 216 " =    0.817
peak=    4.180 closest distance to " O   HOH Z  78 " =    1.713
peak=    4.173 closest distance to " CB  ASN A  39 " =    0.902
peak=    4.158 closest distance to " CB  GLU A 128 " =    0.982
peak=    4.147 closest distance to " CB  VAL A 265 " =    1.323
peak=    4.122 closest distance to " O   HOH Z 346 " =    1.624
peak=    4.117 closest distance to " OD1 ASN A  69 " =    2.589
peak=    4.102 closest distance to " O   HOH Z   7 " =    1.182
peak=    4.092 closest distance to " O   HOH Z  55 " =    2.434
peak=    4.077 closest distance to " CB  ARG A  79 " =    1.452
peak=    4.077 closest distance to " O   HOH Z  68 " =    2.145
peak=    4.072 closest distance to " O   HOH Z  61 " =    1.633
peak=    4.071 closest distance to " CZ  PHE A 218 " =    1.063
peak=    4.069 closest distance to " N   PHE A 130 " =    1.230
peak=    4.059 closest distance to " CG  LEU A 167 " =    1.190
peak=    4.054 closest distance to " O   HOH Z 234 " =    3.733
peak=    4.048 closest distance to " CA  ALA A  51 " =    1.004
peak=    4.006 closest distance to " CG2 VAL A 257 " =    0.914
peak=    3.978 closest distance to " O   HOH Z 368 " =    2.007
peak=    3.959 closest distance to " CA  THR A 264 " =    0.748
peak=    3.957 closest distance to " CD  ARG A  66 " =    2.503
peak=    3.951 closest distance to " CB  ASN A 142 " =    0.994
peak=    3.945 closest distance to " CD  ARG A 159 " =    0.731
peak=    3.936 closest distance to " O   SER A  87 " =    2.342
peak=    3.923 closest distance to " O   HOH Z  43 " =    1.845
peak=    3.922 closest distance to " O   HOH Z 193 " =    1.588
peak=    3.904 closest distance to " O   HOH Z  30 " =    1.511
peak=    3.904 closest distance to " O   HOH Z 193 " =    1.856
peak=    3.890 closest distance to " O   HOH Z 126 " =    1.567
peak=    3.881 closest distance to " CA  TYR A  30 " =    0.972
peak=    3.880 closest distance to " CB  LEU A 143 " =    1.150
peak=    3.879 closest distance to " O   HOH Z   9 " =    1.260
peak=    3.874 closest distance to " O   HOH Z 303 " =    2.189
peak=    3.865 closest distance to " NH1AARG A 145 " =    1.129
peak=    3.865 closest distance to " CA  ASN A 215 " =    1.128
peak=    3.857 closest distance to " NH2AARG A 190 " =    1.803
peak=    3.852 closest distance to " CA  SER A  87 " =    0.919
peak=    3.850 closest distance to " CB  SER A 212 " =    1.194
peak=    3.847 closest distance to " CB  ASN A 187 " =    1.089
peak=    3.844 closest distance to " OG  SER A  97 " =    2.947
peak=    3.841 closest distance to " O   HOH Z 261 " =    2.131
peak=    3.832 closest distance to " O   HOH Z 403 " =    1.679
peak=    3.810 closest distance to " O   HOH Z 203 " =    1.797
peak=    3.803 closest distance to " O   HOH Z 411 " =    3.692
peak=    3.784 closest distance to " CB  TRP A 179 " =    1.431
peak=    3.781 closest distance to " ND2 ASN A 249 " =    1.937
peak=    3.773 closest distance to " CB  VAL A 202 " =    1.559
peak=    3.772 closest distance to " O   HOH Z 263 " =    1.613
peak=    3.770 closest distance to " O   HOH Z  88 " =    3.268
peak=    3.765 closest distance to " O   HOH Z 158 " =    3.162
peak=    3.752 closest distance to " CB  ALA A 291 " =    1.313
peak=    3.740 closest distance to " OD2 ASP A 286 " =    2.837
peak=    3.737 closest distance to " CG1 VAL A 153 " =    0.958
peak=    3.724 closest distance to " O   HOH Z 437 " =    1.872
peak=    3.702 closest distance to " O   HOH Z   9 " =    2.053
peak=    3.702 closest distance to " CB  LEU A 228 " =    1.239
peak=    3.690 closest distance to " CD BLYS A 290 " =    1.110
peak=    3.685 closest distance to " CB  ASP A 140 " =    0.847
peak=    3.678 closest distance to " CG2 THR A 221 " =    1.057
peak=    3.671 closest distance to " CG1BVAL A  72 " =    1.606
peak=    3.658 closest distance to " CB  SER A 210 " =    0.750
peak=    3.642 closest distance to " O   HOH Z 368 " =    3.578
peak=    3.638 closest distance to " ND1 HIS A  86 " =    1.733
peak=    3.627 closest distance to " O   HOH Z 273 " =    2.723
peak=    3.624 closest distance to " O   HOH Z 353 " =    2.566
peak=    3.622 closest distance to " CB  MET A  40 " =    0.825
peak=    3.615 closest distance to " CB  THR A 157 " =    1.145
peak=    3.614 closest distance to " CZ  PHE A 192 " =    0.901
peak=    3.606 closest distance to " CB BVAL A  41 " =    1.208
peak=    3.602 closest distance to " CB  HIS A 108 " =    0.831
peak=    3.600 closest distance to " O   HOH Z 280 " =    2.993
peak=    3.594 closest distance to " O   HOH Z 419 " =    1.888
peak=    3.587 closest distance to " O   HOH Z   2 " =    1.648
peak=    3.579 closest distance to " CA  LEU A 282 " =    1.073
peak=    3.577 closest distance to " NZ  LYS A 117 " =    3.133
peak=    3.569 closest distance to " O   HOH Z 180 " =    2.128
peak=    3.563 closest distance to " CG1 VAL A 296 " =    1.222
peak=    3.556 closest distance to " CB  GLU A 277 " =    3.555
peak=    3.544 closest distance to " CE  LYS A  76 " =    0.869
peak=    3.543 closest distance to " CD1 LEU A 300 " =    1.151
peak=    3.542 closest distance to " C   ALA A 299 " =    0.962
peak=    3.525 closest distance to " CD1 ILE A  33 " =    1.697
peak=    3.523 closest distance to " O   HOH Z  97 " =    2.023
peak=    3.519 closest distance to " O   HOH Z 148 " =    3.428
peak=    3.516 closest distance to " O   HOH Z 409 " =    2.928
peak=    3.515 closest distance to " O   TYR A 116 " =    1.290
peak=    3.513 closest distance to " O   HOH Z  10 " =    1.741
peak=    3.511 closest distance to " O   HOH Z 248 " =    1.649
peak=    3.510 closest distance to " N   ASN A  39 " =    1.105
peak=    3.506 closest distance to " O   HOH Z 305 " =    3.525
peak=    3.506 closest distance to " O   HOH Z  21 " =    1.718
peak=    3.502 closest distance to " O   HOH Z 132 " =    2.560
peak=    3.499 closest distance to " O   HOH Z 435 " =    2.013
peak=    3.498 closest distance to " CB  ALA A   9 " =    1.539
peak=    3.496 closest distance to " CD  ARG A 269 " =    1.045
peak=    3.483 closest distance to " CB  THR A  82 " =    1.310
peak=    3.482 closest distance to " O   HOH Z 291 " =    1.631
peak=    3.479 closest distance to " O   HOH Z 344 " =    2.955
peak=    3.478 closest distance to " N   SER A 135 " =    1.301
peak=    3.474 closest distance to " O   HOH Z   1 " =    1.828
peak=    3.473 closest distance to " O   HOH Z 286 " =    2.370
peak=    3.473 closest distance to " CB  ALA A 104 " =    0.735
peak=    3.472 closest distance to " O   HOH Z 214 " =    1.988
peak=    3.465 closest distance to " NH2 ARG A 156 " =    1.098
peak=    3.465 closest distance to " CG1 ILE A  33 " =    1.324
peak=    3.461 closest distance to " CB  ARG A 190 " =    1.620
peak=    3.457 closest distance to " CA  LYS A 117 " =    1.213
peak=    3.454 closest distance to " CG  GLN A  88 " =    1.083
peak=    3.452 closest distance to " O   HOH Z 145 " =    1.773
peak=    3.448 closest distance to " CB  VAL A 250 " =    1.119
peak=    3.444 closest distance to " OG  SER A 206 " =    1.205
peak=    3.438 closest distance to " O   HOH Z 147 " =    1.700
peak=    3.438 closest distance to " CE1 TYR A 186 " =    1.373
peak=    3.433 closest distance to " OG BSER A 164 " =    2.243
peak=    3.432 closest distance to " O   HOH Z 128 " =    2.052
peak=    3.430 closest distance to " O   HOH Z 423 " =    1.477
peak=    3.430 closest distance to " O   HOH Z 366 " =    2.849
peak=    3.427 closest distance to " CB  ASN A 224 " =    0.976
peak=    3.426 closest distance to " O   HOH Z 290 " =    1.145
peak=    3.425 closest distance to " O   HOH Z 410 " =    1.415
peak=    3.422 closest distance to " NE2 HIS A 207 " =    1.290
peak=    3.421 closest distance to " CD  LYS A 166 " =    1.328
peak=    3.414 closest distance to " CA  ASP A 162 " =    1.003
peak=    3.413 closest distance to " O   HOH Z 345 " =    3.500
peak=    3.412 closest distance to " CA  LYS A 290 " =    1.233
peak=    3.404 closest distance to " CD2 TRP A 179 " =    1.341
peak=    3.402 closest distance to " CG BARG A 102 " =    1.846
peak=    3.402 closest distance to " N   ARG A 156 " =    1.287
peak=    3.397 closest distance to " CB  SER A 273 " =    0.917
peak=    3.393 closest distance to " O   HOH Z 184 " =    1.269
peak=    3.392 closest distance to " CA  ARG A 102 " =    1.176
peak=    3.392 closest distance to " NH2BARG A 190 " =    1.634
peak=    3.392 closest distance to " CA  ALA A  21 " =    1.149
peak=    3.390 closest distance to " CB  GLN A  88 " =    1.236
peak=    3.390 closest distance to " O   HOH Z   1 " =    1.805
peak=    3.382 closest distance to " O   HOH Z 227 " =    1.665
peak=    3.381 closest distance to " N   GLN A 278 " =    1.102
peak=    3.379 closest distance to " CA  ARG A 195 " =    1.170
peak=    3.377 closest distance to " CG  MET A 185 " =    1.214
peak=    3.374 closest distance to " CA  TYR A 116 " =    1.439
peak=    3.374 closest distance to " CA  ILE A 234 " =    0.915
peak=    3.371 closest distance to " O   MET A 105 " =    1.701
peak=    3.371 closest distance to " O   HOH Z 371 " =    2.849
peak=    3.370 closest distance to " CB  MET A  47 " =    1.040
peak=    3.370 closest distance to " CA  PHE A 283 " =    1.137
peak=    3.369 closest distance to " O   HOH Z 197 " =    3.266
peak=    3.366 closest distance to " OE2 GLU A  53 " =    2.034
peak=    3.365 closest distance to " CB  ILE A 120 " =    1.300
peak=    3.364 closest distance to " NH2BARG A 145 " =    1.934
peak=    3.363 closest distance to " O   HOH Z 359 " =    3.974
peak=    3.358 closest distance to " N   VAL A 126 " =    1.331
peak=    3.357 closest distance to " O   HOH Z  63 " =    1.305
peak=    3.352 closest distance to " CB  GLU A  46 " =    1.023
peak=    3.352 closest distance to " CA  ALA A 295 " =    1.055
peak=    3.351 closest distance to " O   HOH Z 135 " =    1.918
peak=    3.348 closest distance to " O   HOH Z  61 " =    1.600
peak=    3.348 closest distance to " O   HOH Z  59 " =    1.845
peak=    3.346 closest distance to " O   HOH Z 133 " =    1.646
peak=    3.345 closest distance to " O   HOH Z 193 " =    1.912
peak=    3.339 closest distance to " CB  ALA A  34 " =    0.808
peak=    3.337 closest distance to " O   HOH Z 128 " =    1.885
peak=    3.336 closest distance to " OG  SER A  62 " =    2.875
peak=    3.336 closest distance to " CG2 ILE A  20 " =    1.573
peak=    3.334 closest distance to " CA  ALA A 158 " =    1.165
peak=    3.334 closest distance to " CG  GLN A 278 " =    1.356
peak=    3.330 closest distance to " O   HOH Z 145 " =    3.604
peak=    3.326 closest distance to " O   HOH Z 380 " =    1.644
peak=    3.319 closest distance to " O   HOH Z 313 " =    1.665
peak=    3.319 closest distance to " CA  VAL A  41 " =    0.799
peak=    3.317 closest distance to " O   HOH Z 285 " =    2.762
peak=    3.314 closest distance to " O   HOH Z 392 " =    1.312
peak=    3.306 closest distance to " CA  ILE A 106 " =    0.762
peak=    3.305 closest distance to " CA  THR A 221 " =    0.891
peak=    3.303 closest distance to " O   HOH Z 417 " =    2.067
peak=    3.302 closest distance to " CA  ALA A 154 " =    1.018
peak=    3.301 closest distance to " O   HOH Z 250 " =    1.367
peak=    3.300 closest distance to " CD2 LEU A 255 " =    1.598
peak=    3.298 closest distance to " NH1 ARG A  14 " =    0.924
peak=    3.295 closest distance to " CG1 ILE A  49 " =    1.394
peak=    3.294 closest distance to " O   HOH Z 371 " =    1.691
peak=    3.293 closest distance to " CD1 LEU A   5 " =    1.432
peak=    3.291 closest distance to " O   HOH Z 350 " =    1.610
peak=    3.288 closest distance to " O   HOH Z 294 " =    1.562
peak=    3.287 closest distance to " O   HOH Z  58 " =    1.560
peak=    3.286 closest distance to " CG  ARG A 159 " =    0.945
peak=    3.286 closest distance to " CG BARG A 275 " =    1.459
peak=    3.285 closest distance to " O   HOH Z   3 " =    1.929
peak=    3.284 closest distance to " CG1 ILE A 151 " =    1.083
peak=    3.284 closest distance to " NZ  LYS A  76 " =    1.387
peak=    3.282 closest distance to " O   HOH Z 172 " =    3.132
peak=    3.277 closest distance to " NH1 ARG A 138 " =    1.181
peak=    3.274 closest distance to " CB  LYS A 117 " =    1.230
peak=    3.268 closest distance to " CB  ALA A 137 " =    1.062
peak=    3.267 closest distance to " CA  TYR A  30 " =    1.079
peak=    3.265 closest distance to " CD  PRO A 243 " =    1.394
peak=    3.263 closest distance to " CB  ARG A 139 " =    0.962
peak=    3.262 closest distance to " ND2 ASN A 110 " =    1.777
peak=    3.261 closest distance to " OD1BASN A 224 " =    2.346
peak=    3.259 closest distance to " O   HOH Z  88 " =    2.738
peak=    3.259 closest distance to " O   HOH Z 126 " =    1.466
peak=    3.256 closest distance to " N   SER A 146 " =    1.717
peak=    3.253 closest distance to " CG  MET A 185 " =    0.990
peak=    3.244 closest distance to " CA  GLY A 267 " =    0.960
peak=    3.235 closest distance to " CA  ARG A  36 " =    1.115
peak=    3.232 closest distance to " O   HOH Z 175 " =    2.143
peak=    3.230 closest distance to " CA  MET A 105 " =    0.939
peak=    3.230 closest distance to " O   TRP A 274 " =    1.832
peak=    3.229 closest distance to " CB  ALA A 242 " =    0.785
peak=    3.225 closest distance to " CB  ASN A 110 " =    1.115
peak=    3.225 closest distance to " O   HOH Z 271 " =    2.077
peak=    3.223 closest distance to " ND1 HIS A  81 " =    1.764
peak=    3.221 closest distance to " CB  ALA A 248 " =    1.378
peak=    3.215 closest distance to " NE AARG A 275 " =    1.279
peak=    3.215 closest distance to " O   HOH Z  40 " =    1.964
peak=    3.214 closest distance to " CA  ALA A 291 " =    0.903
peak=    3.209 closest distance to " CB  ALA A 114 " =    1.175
peak=    3.208 closest distance to " O   HOH Z 109 " =    2.538
peak=    3.203 closest distance to " O   HOH Z 303 " =    1.829
peak=    3.201 closest distance to " CD1 LEU A 228 " =    2.043
peak=    3.200 closest distance to " O   HOH Z 383 " =    1.824
peak=    3.198 closest distance to " CB  SER A  62 " =    1.217
peak=    3.197 closest distance to " CZ  PHE A  38 " =    1.160
peak=    3.192 closest distance to " O   HOH Z 329 " =    3.869
peak=    3.190 closest distance to " CB  TRP A 150 " =    1.469
peak=    3.186 closest distance to " O   HOH Z 148 " =    2.088
peak=    3.182 closest distance to " CZ3 TRP A 123 " =    1.293
peak=    3.180 closest distance to " CB  SER A 245 " =    3.224
peak=    3.180 closest distance to " O   HOH Z 329 " =    2.859
peak=    3.179 closest distance to " N   SER A  12 " =    1.585
peak=    3.176 closest distance to " N   SER A 271 " =    0.977
peak=    3.175 closest distance to " O   HOH Z 128 " =    2.197
peak=    3.175 closest distance to " O   ALA A 292 " =    1.729
peak=    3.174 closest distance to " N   ALA A 256 " =    1.140
peak=    3.171 closest distance to " O   HOH Z 423 " =    2.704
peak=    3.165 closest distance to " O   HOH Z 422 " =    2.655
peak=    3.162 closest distance to " O   HOH Z  93 " =    2.649
peak=    3.162 closest distance to " CB  ALA A   1 " =    4.745
peak=    3.161 closest distance to " O   HOH Z 406 " =    1.706
peak=    3.158 closest distance to " ND2 ASN A 249 " =    0.861
peak=    3.158 closest distance to " O   HOH Z 425 " =    1.920
peak=    3.151 closest distance to " N   ASN A 127 " =    1.235
peak=    3.147 closest distance to " O   HOH Z 173 " =    1.642
peak=    3.145 closest distance to " CD1 ILE A 106 " =    0.912
peak=    3.145 closest distance to " CD2 TYR A 186 " =    1.002
peak=    3.140 closest distance to " CG  LEU A 281 " =    1.111
peak=    3.139 closest distance to " NZ  LYS A  48 " =    1.334
peak=    3.139 closest distance to " OE2 GLU A   2 " =    1.742
peak=    3.130 closest distance to " O   GLN A 278 " =    1.532
peak=    3.117 closest distance to " CB  VAL A 268 " =    0.846
peak=    3.117 closest distance to " O   HOH Z 216 " =    2.781
peak=    3.116 closest distance to " CG1 VAL A 174 " =    1.042
peak=    3.109 closest distance to " CB  ASN A 215 " =    1.122
peak=    3.109 closest distance to " O   HOH Z 227 " =    2.059
peak=    3.107 closest distance to " O   ALA A 158 " =    1.412
peak=    3.107 closest distance to " CB  ILE A  20 " =    1.438
peak=    3.100 closest distance to " O  BHOH Z 338 " =    2.512
peak=    3.097 closest distance to " CD1AILE A 234 " =    0.933
peak=    3.097 closest distance to " O   ASN A 209 " =    1.307
peak=    3.097 closest distance to " OG  SER A  62 " =    2.970
peak=    3.095 closest distance to " O   HOH Z 357 " =    1.958
peak=    3.088 closest distance to " O   HOH Z 201 " =    3.158
peak=    3.082 closest distance to " CG  ARG A 138 " =    1.311
peak=    3.078 closest distance to " O   HOH Z 213 " =    2.485
peak=    3.073 closest distance to " O   HOH Z 116 " =    1.687
peak=    3.071 closest distance to " CD1 LEU A  96 " =    0.768
peak=    3.060 closest distance to " O   HOH Z 302 " =    1.831
peak=    3.037 closest distance to " O   HOH Z 124 " =    2.181
peak=    3.036 closest distance to " O   HOH Z 238 " =    3.679

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 206         
Filter by distance & map next to the model:
   mapped sites are within: 0.571 - 5.286
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 204 from: 206
   mapped sites are within: 0.731 - 5.286

peak=   -5.327 closest distance to " CG2 VAL A 230 " =    0.731
peak=   -4.530 closest distance to " CB  PRO A 243 " =    2.633
peak=   -4.395 closest distance to " CD  ARG A 156 " =    2.006
peak=   -4.279 closest distance to " O   HOH Z 290 " =    1.134
peak=   -4.275 closest distance to " O   HOH Z 231 " =    1.705
peak=   -4.244 closest distance to " CD  ARG A  14 " =    3.218
peak=   -4.089 closest distance to " O   HOH Z 351 " =    1.469
peak=   -3.987 closest distance to " O   HOH Z 266 " =    5.152
peak=   -3.982 closest distance to " CB  ALA A 161 " =    2.613
peak=   -3.980 closest distance to " CZ3 TRP A 179 " =    1.205
peak=   -3.951 closest distance to " OG BSER A 134 " =    1.258
peak=   -3.937 closest distance to " CG  GLN A 223 " =    1.922
peak=   -3.908 closest distance to " CB  ALA A 248 " =    2.057
peak=   -3.891 closest distance to " O   PRO A 198 " =    1.156
peak=   -3.862 closest distance to " CG1 VAL A 296 " =    1.353
peak=   -3.850 closest distance to " O   HOH Z 435 " =    2.884
peak=   -3.836 closest distance to " C   ALA A 158 " =    1.428
peak=   -3.831 closest distance to " O   VAL A  67 " =    2.601
peak=   -3.821 closest distance to " CD  GLN A  58 " =    0.983
peak=   -3.796 closest distance to " CG2 VAL A 296 " =    1.286
peak=   -3.793 closest distance to " CG  ASP A 231 " =    0.733
peak=   -3.786 closest distance to " CE2 TYR A  30 " =    2.718
peak=   -3.770 closest distance to " N   ALA A  43 " =    2.444
peak=   -3.768 closest distance to " CA  GLY A 241 " =    2.319
peak=   -3.763 closest distance to " N   THR A 157 " =    1.435
peak=   -3.743 closest distance to " OG  SER A  87 " =    1.413
peak=   -3.738 closest distance to " CB  PRO A 163 " =    2.571
peak=   -3.736 closest distance to " C   HIS A 108 " =    1.220
peak=   -3.735 closest distance to " O   HOH Z 211 " =    1.521
peak=   -3.715 closest distance to " CD1 LEU A 228 " =    2.295
peak=   -3.706 closest distance to " CB  VAL A 296 " =    1.176
peak=   -3.692 closest distance to " CB  ALA A  43 " =    2.520
peak=   -3.692 closest distance to " O   HOH Z 185 " =    2.253
peak=   -3.692 closest distance to " O   GLY A  80 " =    2.479
peak=   -3.689 closest distance to " O   GLY A 203 " =    2.403
peak=   -3.682 closest distance to " ND2 ASN A  45 " =    1.458
peak=   -3.675 closest distance to " CG1 VAL A 112 " =    2.968
peak=   -3.670 closest distance to " NH2 ARG A  79 " =    1.940
peak=   -3.646 closest distance to " O   PRO A 163 " =    2.010
peak=   -3.645 closest distance to " O   HOH Z 394 " =    1.503
peak=   -3.639 closest distance to " O   HOH Z  11 " =    1.907
peak=   -3.634 closest distance to " CB  PHE A 192 " =    1.888
peak=   -3.631 closest distance to " CD1 LEU A 101 " =    2.820
peak=   -3.631 closest distance to " O   HOH Z 389 " =    2.017
peak=   -3.626 closest distance to " O   TYR A 247 " =    2.832
peak=   -3.620 closest distance to " CG  MET A 105 " =    0.937
peak=   -3.619 closest distance to " O   HOH Z 140 " =    1.410
peak=   -3.612 closest distance to " CG1 VAL A 112 " =    2.634
peak=   -3.611 closest distance to " N   GLN A  58 " =    1.991
peak=   -3.595 closest distance to " O   HOH Z  60 " =    2.349
peak=   -3.584 closest distance to " O   VAL A 189 " =    2.597
peak=   -3.577 closest distance to " O   ALA A 161 " =    1.592
peak=   -3.568 closest distance to " C   LEU A 222 " =    0.848
peak=   -3.557 closest distance to " O   HOH Z 166 " =    2.282
peak=   -3.556 closest distance to " O   HOH Z 231 " =    1.334
peak=   -3.552 closest distance to " NH2AARG A 275 " =    5.286
peak=   -3.552 closest distance to " CG  TRP A 266 " =    1.827
peak=   -3.547 closest distance to " O   HOH Z  44 " =    2.255
peak=   -3.539 closest distance to " CD1 LEU A 101 " =    2.410
peak=   -3.532 closest distance to " CD2 LEU A   5 " =    1.028
peak=   -3.522 closest distance to " CB  ALA A 244 " =    2.084
peak=   -3.512 closest distance to " O   VAL A  67 " =    2.667
peak=   -3.506 closest distance to " O   HOH Z  52 " =    1.308
peak=   -3.498 closest distance to " CA  GLY A 203 " =    2.391
peak=   -3.494 closest distance to " CG  LEU A 101 " =    2.494
peak=   -3.480 closest distance to " C   ASP A 231 " =    2.646
peak=   -3.478 closest distance to " CD  LYS A 289 " =    2.516
peak=   -3.475 closest distance to " O   HOH Z 372 " =    2.431
peak=   -3.472 closest distance to " N   ALA A 226 " =    2.152
peak=   -3.470 closest distance to " O   ARG A 145 " =    1.525
peak=   -3.463 closest distance to " O   HOH Z 114 " =    3.010
peak=   -3.462 closest distance to " O   HOH Z 377 " =    0.782
peak=   -3.461 closest distance to " CB  ALA A 248 " =    2.464
peak=   -3.456 closest distance to " OG BSER A 134 " =    1.744
peak=   -3.450 closest distance to " N   PHE A  59 " =    2.309
peak=   -3.450 closest distance to " CA  GLY A 241 " =    3.079
peak=   -3.447 closest distance to " CA  ASP A  27 " =    2.428
peak=   -3.434 closest distance to " CD1 PHE A  59 " =    1.939
peak=   -3.430 closest distance to " CB  ALA A 291 " =    2.221
peak=   -3.429 closest distance to " OG  SER A  97 " =    2.273
peak=   -3.423 closest distance to " CG  PHE A 283 " =    2.678
peak=   -3.420 closest distance to " CB  VAL A 230 " =    1.086
peak=   -3.417 closest distance to " OXT GLY A 302 " =    3.000
peak=   -3.412 closest distance to " OD1 ASN A 187 " =    1.647
peak=   -3.410 closest distance to " O   HOH Z 377 " =    1.976
peak=   -3.408 closest distance to " CE  MET A 105 " =    2.342
peak=   -3.404 closest distance to " O   GLY A 196 " =    1.164
peak=   -3.401 closest distance to " C   MET A 188 " =    1.438
peak=   -3.401 closest distance to " ND2 ASN A 187 " =    1.651
peak=   -3.397 closest distance to " CG1 VAL A 197 " =    2.280
peak=   -3.394 closest distance to " O   GLY A  17 " =    1.339
peak=   -3.389 closest distance to " O   MET A  40 " =    2.750
peak=   -3.382 closest distance to " OE1 GLN A  88 " =    1.148
peak=   -3.377 closest distance to " O   HOH Z  38 " =    1.709
peak=   -3.366 closest distance to " OG  SER A  63 " =    1.128
peak=   -3.365 closest distance to " O   HOH Z 407 " =    3.129
peak=   -3.361 closest distance to " O   GLY A 211 " =    1.254
peak=   -3.351 closest distance to " O   HOH Z 426 " =    1.710
peak=   -3.346 closest distance to " O   GLY A 229 " =    1.856
peak=   -3.345 closest distance to " CG2 ILE A 263 " =    2.401
peak=   -3.343 closest distance to " CB  ALA A 291 " =    2.247
peak=   -3.343 closest distance to " N   SER A 212 " =    1.857
peak=   -3.342 closest distance to " CE2 PHE A 218 " =    2.491
peak=   -3.328 closest distance to " CA  GLY A  98 " =    1.930
peak=   -3.324 closest distance to " O   HOH Z 390 " =    2.401
peak=   -3.324 closest distance to " O   HOH Z  51 " =    1.157
peak=   -3.323 closest distance to " O   HOH Z 417 " =    2.871
peak=   -3.323 closest distance to " O   HOH Z 359 " =    1.608
peak=   -3.321 closest distance to " ND2 ASN A 249 " =    2.400
peak=   -3.316 closest distance to " CB  TRP A  85 " =    2.476
peak=   -3.315 closest distance to " ND2 ASN A  60 " =    1.777
peak=   -3.315 closest distance to " CD  ARG A 139 " =    1.651
peak=   -3.312 closest distance to " CD  PRO A 243 " =    2.098
peak=   -3.312 closest distance to " O   HOH Z 241 " =    1.308
peak=   -3.310 closest distance to " CA  VAL A 296 " =    1.039
peak=   -3.310 closest distance to " CB  TYR A  15 " =    2.144
peak=   -3.308 closest distance to " O   SER A  22 " =    2.217
peak=   -3.304 closest distance to " O   HOH Z 359 " =    3.353
peak=   -3.299 closest distance to " CD1 TYR A 169 " =    2.513
peak=   -3.297 closest distance to " CD2 TYR A 247 " =    2.396
peak=   -3.294 closest distance to " N   SER A   3 " =    1.909
peak=   -3.292 closest distance to " O   HOH Z 388 " =    2.153
peak=   -3.291 closest distance to " C   ASN A 187 " =    1.756
peak=   -3.287 closest distance to " CZ  PHE A 192 " =    2.809
peak=   -3.286 closest distance to " OH  TYR A 172 " =    1.792
peak=   -3.277 closest distance to " O   PRO A 198 " =    1.336
peak=   -3.276 closest distance to " O   HOH Z 102 " =    1.650
peak=   -3.274 closest distance to " CG1 VAL A 250 " =    2.780
peak=   -3.274 closest distance to " O   HOH Z 275 " =    1.490
peak=   -3.273 closest distance to " O   HOH Z 103 " =    1.808
peak=   -3.263 closest distance to " OXT GLY A 302 " =    3.492
peak=   -3.262 closest distance to " CD2 LEU A 300 " =    2.813
peak=   -3.261 closest distance to " O   HOH Z   9 " =    1.564
peak=   -3.261 closest distance to " O   HOH Z 350 " =    1.885
peak=   -3.254 closest distance to " O   SER A 135 " =    1.428
peak=   -3.250 closest distance to " C   ASN A 285 " =    2.463
peak=   -3.250 closest distance to " CD  GLN A 223 " =    1.224
peak=   -3.249 closest distance to " CE BMET A  47 " =    1.641
peak=   -3.248 closest distance to " SG  CYS A 254 " =    2.820
peak=   -3.245 closest distance to " CD2 TYR A 293 " =    2.030
peak=   -3.245 closest distance to " OD1 ASN A 148 " =    1.423
peak=   -3.245 closest distance to " CZ  PHE A  59 " =    1.448
peak=   -3.240 closest distance to " O   HOH Z  73 " =    2.205
peak=   -3.231 closest distance to " O   HOH Z 198 " =    1.490
peak=   -3.227 closest distance to " O   HOH Z  63 " =    1.631
peak=   -3.227 closest distance to " CB  ASP A 132 " =    2.318
peak=   -3.222 closest distance to " O   HOH Z 281 " =    2.735
peak=   -3.219 closest distance to " O   HOH Z 368 " =    1.568
peak=   -3.213 closest distance to " N   ALA A 248 " =    1.613
peak=   -3.199 closest distance to " C   VAL A 265 " =    0.851
peak=   -3.198 closest distance to " CD1 LEU A 297 " =    2.549
peak=   -3.195 closest distance to " NH2BARG A 275 " =    1.715
peak=   -3.193 closest distance to " O   HOH Z 346 " =    1.793
peak=   -3.190 closest distance to " CD2 HIS A 207 " =    2.450
peak=   -3.188 closest distance to " CZ  TYR A 169 " =    1.552
peak=   -3.181 closest distance to " O   HOH Z 210 " =    0.926
peak=   -3.181 closest distance to " CD2 LEU A 300 " =    3.027
peak=   -3.177 closest distance to " O   HOH Z 176 " =    0.863
peak=   -3.177 closest distance to " O   LYS A 289 " =    3.068
peak=   -3.176 closest distance to " O   HOH Z 222 " =    1.519
peak=   -3.173 closest distance to " CB  ALA A   9 " =    2.574
peak=   -3.171 closest distance to " O   HOH Z 281 " =    3.096
peak=   -3.170 closest distance to " O   HOH Z  43 " =    1.793
peak=   -3.169 closest distance to " OG  SER A 206 " =    1.735
peak=   -3.166 closest distance to " O   HOH Z 166 " =    1.468
peak=   -3.163 closest distance to " O   HOH Z 295 " =    1.526
peak=   -3.159 closest distance to " N   THR A  52 " =    1.790
peak=   -3.158 closest distance to " O   HOH Z 423 " =    1.205
peak=   -3.152 closest distance to " CB  ASN A  69 " =    1.276
peak=   -3.152 closest distance to " NE2 GLN A 278 " =    2.032
peak=   -3.151 closest distance to " CG  GLU A 277 " =    1.241
peak=   -3.150 closest distance to " CD  PRO A 213 " =    2.109
peak=   -3.144 closest distance to " O   VAL A 121 " =    1.179
peak=   -3.144 closest distance to " CD  GLN A  88 " =    0.873
peak=   -3.144 closest distance to " CG  GLU A 152 " =    1.248
peak=   -3.139 closest distance to " O   HOH Z 313 " =    1.572
peak=   -3.135 closest distance to " OD2 ASP A  50 " =    2.289
peak=   -3.133 closest distance to " N   ASP A 270 " =    1.481
peak=   -3.132 closest distance to " CE  LYS A  76 " =    2.734
peak=   -3.123 closest distance to " O   HOH Z 423 " =    2.077
peak=   -3.117 closest distance to " N   SER A 276 " =    1.310
peak=   -3.117 closest distance to " O   ALA A  51 " =    1.439
peak=   -3.112 closest distance to " O   HOH Z 111 " =    2.190
peak=   -3.111 closest distance to " ND2BASN A 224 " =    1.583
peak=   -3.108 closest distance to " O   HOH Z  13 " =    1.651
peak=   -3.103 closest distance to " CB  CYS A 254 " =    2.178
peak=   -3.096 closest distance to " SG BCYS A 201 " =    2.266
peak=   -3.096 closest distance to " O   HOH Z 134 " =    3.556
peak=   -3.094 closest distance to " O   HOH Z 389 " =    1.479
peak=   -3.092 closest distance to " CA  ALA A 248 " =    2.562
peak=   -3.092 closest distance to " CE3 TRP A 150 " =    2.131
peak=   -3.090 closest distance to " CG  PRO A 163 " =    2.495
peak=   -3.090 closest distance to " CB  ALA A 114 " =    2.512
peak=   -3.090 closest distance to " O   HOH Z 175 " =    4.188
peak=   -3.087 closest distance to " O   ARG A  24 " =    1.975
peak=   -3.076 closest distance to " O   HOH Z 377 " =    1.171
peak=   -3.073 closest distance to " O   HOH Z 357 " =    1.879
peak=   -3.071 closest distance to " C   VAL A 174 " =    1.820
peak=   -3.043 closest distance to " O   HOH Z 412 " =    4.319
peak=   -3.036 closest distance to " N   ALA A 248 " =    1.880
peak=   -3.023 closest distance to " CD1 ILE A 199 " =    2.592
peak=   -3.017 closest distance to " O   HOH Z 313 " =    1.105
peak=   -3.008 closest distance to " O   HOH Z 353 " =    1.999
peak=   -3.005 closest distance to " OG  SER A   3 " =    1.242

================= 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    :  0.4395 0.4256   6.234516e+00   6.211300e+00
   1_bss:  0.4311 0.4122   6.229144e+00   6.201715e+00
   1_xyz:  0.3259 0.3458   6.036001e+00   6.079247e+00
   1_adp:  0.2646 0.3058   5.871211e+00   5.978901e+00
   1_occ:  0.2642 0.3058   5.870203e+00   5.980237e+00
   2_bss:  0.2591 0.2987   5.865807e+00   5.973594e+00
   2_xyz:  0.1680 0.2131   5.481319e+00   5.667031e+00
   2_adp:  0.1482 0.1946   5.372572e+00   5.577309e+00
   2_occ:  0.1481 0.1945   5.371921e+00   5.576721e+00
   3_bss:  0.1475 0.1925   5.370599e+00   5.574170e+00
   3_xyz:  0.1276 0.1711   5.246090e+00   5.464598e+00
   3_adp:  0.1233 0.1675   5.218723e+00   5.442436e+00
   3_occ:  0.1232 0.1675   5.218491e+00   5.442163e+00
   4_bss:  0.1232 0.1674   5.217752e+00   5.441591e+00
   4_xyz:  0.1122 0.1594   5.153671e+00   5.402488e+00
   4_adp:  0.1119 0.1576   5.145215e+00   5.389405e+00
   4_occ:  0.1118 0.1574   5.144609e+00   5.388615e+00
   5_bss:  0.1119 0.1571   5.144608e+00   5.387082e+00
   5_xyz:  0.1150 0.1573   5.160755e+00   5.391036e+00
   5_adp:  0.1146 0.1574   5.159848e+00   5.392896e+00
   5_occ:  0.1146 0.1574   5.159735e+00   5.392717e+00
   5_bss:  0.1146 0.1573   5.159776e+00   5.392741e+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:  0.351  13.388   7.991   9.117   7.859   0.000   0.000   0.000
   1_xyz:  0.351  13.388   7.991   9.117   7.859   0.000   0.000   0.000
   1_adp:  0.351  13.388   7.991   9.117   7.859   0.000   0.000   0.000
   1_occ:  0.351  13.388   7.991   9.117   7.859   0.000   0.000   0.000
   2_bss:  0.345  44.011   4.544   4.847   4.921   0.000   0.000   0.000
   2_xyz:  0.345  44.011   4.544   4.847   4.921   0.000   0.000   0.000
   2_adp:  0.345  44.011   4.544   4.847   4.921   0.000   0.000   0.000
   2_occ:  0.345  44.011   4.544   4.847   4.921   0.000   0.000   0.000
   3_bss:  0.331  44.011   3.347   3.209   4.248   0.000   0.000   0.000
   3_xyz:  0.331  44.011   3.347   3.209   4.248   0.000   0.000   0.000
   3_adp:  0.331  44.011   3.347   3.209   4.248   0.000   0.000   0.000
   3_occ:  0.331  44.011   3.347   3.209   4.248   0.000   0.000   0.000
   4_bss:  0.320  44.011   3.131   2.942   4.173   0.000   0.000   0.000
   4_xyz:  0.320  44.011   3.131   2.942   4.173   0.000   0.000   0.000
   4_adp:  0.320  44.011   3.131   2.942   4.173   0.000   0.000   0.000
   4_occ:  0.320  44.011   3.131   2.942   4.173   0.000   0.000   0.000
   5_bss:  0.320  44.011   3.066   2.838   4.174   0.000   0.000   0.000
   5_xyz:  0.320  44.011   3.066   2.838   4.174   0.000   0.000   0.000
   5_adp:  0.320  44.011   3.066   2.838   4.174   0.000   0.000   0.000
   5_occ:  0.320  44.011   3.066   2.838   4.174   0.000   0.000   0.000
   5_bss:  0.322  47.484  -0.293  -0.521   0.815   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  48.254 0.5433  0.6130    53088.747
   1_bss:  48.582 0.5371  0.7737    51271.962
   1_xyz:  37.775 0.6684  0.9364    33668.929
   1_adp:  30.794 0.7501  1.0394    24900.099
   1_occ:  30.852 0.7494  1.0374    24930.313
   2_bss:  30.433 0.7538  0.9185    24307.724
   2_xyz:  20.525 0.8562  1.0021    11350.573
   2_adp:  18.119 0.8796  1.0157     9467.602
   2_occ:  18.099 0.8798  1.0156     9449.738
   3_bss:  18.024 0.8804  0.9732     9379.277
   3_xyz:  15.591 0.9018  0.9841     7423.143
   3_adp:  15.117 0.9060  0.9848     7142.672
   3_occ:  15.111 0.9060  0.9846     7136.555
   4_bss:  15.096 0.9062  0.9780     7120.896
   4_xyz:  14.329 0.9122  0.9807     6545.311
   4_adp:  13.991 0.9152  0.9806     6378.301
   4_occ:  13.977 0.9153  0.9806     6364.597
   5_bss:  13.982 0.9152  0.9782     6347.609
   5_xyz:  13.994 0.9153  0.9773     6376.092
   5_adp:  14.031 0.9150  0.9760     6407.676
   5_occ:  14.028 0.9150  0.9759     6403.195
   5_bss:  14.028 0.9150  0.9759     6404.222
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.090   5.3800e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.090   5.3800e+01
   1_xyz:   1.524  0.012  0.101 18.094  0.006  4.122   1.1996e-01
   1_adp:   1.524  0.012  0.101 18.094  0.006  4.122   1.1996e-01
   1_occ:   1.524  0.012  0.101 18.094  0.006  4.122   1.1996e-01
   2_bss:   1.524  0.012  0.101 18.094  0.006  4.122   1.1996e-01
   2_xyz:   1.090  0.008  0.081 16.282  0.005  4.122   7.1784e-02
   2_adp:   1.090  0.008  0.081 16.282  0.005  4.122   7.1784e-02
   2_occ:   1.090  0.008  0.081 16.282  0.005  4.122   7.1784e-02
   3_bss:   1.090  0.008  0.081 16.282  0.005  4.122   7.1784e-02
   3_xyz:   0.938  0.006  0.074 15.791  0.003  4.126   5.6897e-02
   3_adp:   0.938  0.006  0.074 15.791  0.003  4.126   5.6897e-02
   3_occ:   0.938  0.006  0.074 15.791  0.003  4.126   5.6897e-02
   4_bss:   0.938  0.006  0.074 15.791  0.003  4.126   5.6897e-02
   4_xyz:   1.113  0.009  0.091 15.850  0.004  4.112   7.5786e-02
   4_adp:   1.113  0.009  0.091 15.850  0.004  4.112   7.5786e-02
   4_occ:   1.113  0.009  0.091 15.850  0.004  4.112   7.5786e-02
   5_bss:   1.113  0.009  0.091 15.850  0.004  4.112   7.5786e-02
   5_xyz:   0.908  0.006  0.074 15.372  0.003  4.112   5.3641e-02
   5_adp:   0.908  0.006  0.074 15.372  0.003  4.112   5.3641e-02
   5_occ:   0.908  0.006  0.074 15.372  0.003  4.112   5.3641e-02
   5_bss:   0.908  0.006  0.074 15.372  0.003  4.112   5.3641e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9755e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9755e+00
   1_xyz:  12.887  0.147  0.413 88.601  0.033  2.254   8.8522e-02
   1_adp:  12.887  0.147  0.413 88.601  0.033  2.254   8.8522e-02
   1_occ:  12.887  0.147  0.413 88.601  0.033  2.254   8.8522e-02
   2_bss:  12.887  0.147  0.413 88.601  0.033  2.254   8.8522e-02
   2_xyz:   7.325  0.075  0.348 83.622  0.043  2.307   6.0562e-02
   2_adp:   7.325  0.075  0.348 83.622  0.043  2.307   6.0562e-02
   2_occ:   7.325  0.075  0.348 83.622  0.043  2.307   6.0562e-02
   3_bss:   7.325  0.075  0.348 83.622  0.043  2.307   6.0562e-02
   3_xyz:   7.376  0.053  0.414 82.836  0.031  2.339   5.9786e-02
   3_adp:   7.376  0.053  0.414 82.836  0.031  2.339   5.9786e-02
   3_occ:   7.376  0.053  0.414 82.836  0.031  2.339   5.9786e-02
   4_bss:   7.376  0.053  0.414 82.836  0.031  2.339   5.9786e-02
   4_xyz:   7.491  0.053  0.663 83.466  0.041  2.278   6.4943e-02
   4_adp:   7.491  0.053  0.663 83.466  0.041  2.278   6.4943e-02
   4_occ:   7.491  0.053  0.663 83.466  0.041  2.278   6.4943e-02
   5_bss:   7.491  0.053  0.663 83.466  0.041  2.278   6.4943e-02
   5_xyz:   7.420  0.040  0.461 83.875  0.036  2.365   2.9335e-02
   5_adp:   7.420  0.040  0.461 83.875  0.036  2.365   2.9335e-02
   5_occ:   7.420  0.040  0.461 83.875  0.036  2.365   2.9335e-02
   5_bss:   7.420  0.040  0.461 83.875  0.036  2.365   2.9335e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  66.27   0.00  11.08  62.21   0.00   8.08  66.27   0.00  27.38
   1_occ:  66.27   0.00  11.08  62.21   0.00   8.08  66.27   0.00  27.38
   2_bss:  66.27   0.00  11.08  62.21   0.00   8.08  66.27   0.00  27.38
   2_xyz:  66.27   0.00  11.08  62.21   0.00   8.08  66.27   0.00  27.38
   2_adp:  67.89   0.00  11.41  67.89   0.00   7.53  67.66   0.00  32.52
   2_occ:  67.89   0.00  11.41  67.89   0.00   7.53  67.66   0.00  32.52
   3_bss:  67.89   0.00  11.41  67.89   0.00   7.53  67.66   0.00  32.52
   3_xyz:  67.89   0.00  11.41  67.89   0.00   7.53  67.66   0.00  32.52
   3_adp:  76.59   0.00  11.94  76.59   0.00   7.68  74.80   0.73  35.12
   3_occ:  76.59   0.00  11.94  76.59   0.00   7.68  74.80   0.73  35.12
   4_bss:  76.59   0.00  11.94  76.59   0.00   7.68  74.80   0.73  35.12
   4_xyz:  76.59   0.00  11.94  76.59   0.00   7.68  74.80   0.73  35.12
   4_adp:  76.66   0.00  11.67  76.66   0.00   7.54  72.62   1.45  34.20
   4_occ:  76.66   0.00  11.67  76.66   0.00   7.54  72.62   1.45  34.20
   5_bss:  76.66   0.00  11.67  76.66   0.00   7.54  72.62   1.45  34.20
   5_xyz:  76.66   0.00  11.67  76.66   0.00   7.54  72.62   1.45  34.20
   5_adp:  77.00   0.00  11.56  77.00   0.00   7.50  70.98   1.49  33.68
   5_occ:  77.00   0.00  11.56  77.00   0.00   7.50  70.98   1.49  33.68
   5_bss:  80.36   3.36  14.92  80.36   3.36  10.86  74.34   4.85  37.04
------------------------------------------------------------------------
 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:    1.180    0.022    0.402
   1_adp:    1.180    0.022    0.402
   1_occ:    1.180    0.022    0.402
   2_bss:    1.180    0.022    0.402
   2_xyz:    1.281    0.034    0.524
   2_adp:    1.281    0.034    0.524
   2_occ:    1.281    0.034    0.524
   3_bss:    1.281    0.034    0.524
   3_xyz:    1.516    0.042    0.551
   3_adp:    1.516    0.042    0.551
   3_occ:    1.516    0.042    0.551
   4_bss:    1.516    0.042    0.551
   4_xyz:    1.668    0.031    0.576
   4_adp:    1.668    0.031    0.576
   4_occ:    1.668    0.031    0.576
   5_bss:    1.668    0.031    0.576
   5_xyz:    1.702    0.039    0.580
   5_adp:    1.702    0.039    0.580
   5_occ:    1.702    0.039    0.580
   5_bss:    1.702    0.039    0.580
------------------------------------------------------------------------

CPU time actual refinement: 313.37


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_885/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_885/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_885/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_885/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_885/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 313.21 
  Macro-tasks:
    bulk solvent and scale       = 39.00  
    individual site refinement   = 123.23 
    weights calculation          = 31.05  
    collect and process          = 6.46   
    model show statistics        = 0.09   
    TOTAL for macro-tasks        = 199.83 
  Micro-tasks:
    mask                            = 1.74   
    f_calc                          = 95.52  
    alpha_beta                      = 8.13   
    target                          = 1.17   
    gradients_wrt_atomic_parameters = 105.25 
    fmodel                         = 6.64   
    r_factors                      = 0.22   
    phase_errors                   = 10.90  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 229.82 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.457 micro seconds
Total CPU time: 5.44 minutes
from_scatterers_fft:    645 calls, 95.19 s
gradients_fft:          589 calls, 92.26 s

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

# Date 2008-01-16 Time 02:39:10 PST -0800 (1200479950.61 s)
Start R-work = 0.4395, R-free = 0.4256 (no bulk solvent and anisotropic scale)
Final R-work = 0.1319, R-free = 0.1748 (no bulk solvent and anisotropic scale)

Start R-work = 0.4311, R-free = 0.4122
Final R-work = 0.1146, R-free = 0.1573