# Date 2008-01-16 Time 02:38:14 PST -0800 (1200479894.21 s)
#phil __OFF__

Command line arguments: "../914.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 5337
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 914

-------------------------------------------------------------------------------
  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, 47.1647, 84.6622, 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, 47.1647, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0179 1.96131
Completeness in resolution range: 0.935482
Completeness with d_max=infinity: 0.932676

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  15.0179
                             d_min =   1.9613

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, 47.1647, 84.6622, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 15.0179 1.96131
Completeness in resolution range: 0.935482
Completeness with d_max=infinity: 0.932676

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 15.0183 -  4.1977 [2202/2231]  1984   218   9.9%
  bin  2:  4.1977 -  3.3439 [2097/2120]  1888   209  10.0%
  bin  3:  3.3439 -  2.9248 [2089/2111]  1873   216  10.3%
  bin  4:  2.9248 -  2.6590 [2068/2087]  1873   195   9.4%
  bin  5:  2.6590 -  2.4693 [2058/2087]  1842   216  10.5%
  bin  6:  2.4693 -  2.3242 [2029/2071]  1833   196   9.7%
  bin  7:  2.3242 -  2.2082 [2029/2065]  1826   203  10.0%
  bin  8:  2.2082 -  2.1124 [2017/2054]  1816   201  10.0%
  bin  9:  2.1124 -  2.0312 [2027/2059]  1821   206  10.2%
  bin 10:  2.0312 -  1.9613 [ 973/2055]   874    99  10.2%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_914/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:
        1.70 -     2.34: 26
        2.34 -     2.98: 1824
        2.98 -     3.62: 4594
        3.62 -     4.26: 9157
        4.26 -     4.90: 12785
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z 100 " - " O   HOH Z 352 "  1.704 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 113 " - " O   HOH Z 350 "  1.727 3.040 -x+1/2,-y+1,z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  " NH2 ARG A 259 " - " O   HOH Z   3 "  1.992 3.120 -x,y-1/2,-z+1/2
  " O   HOH Z  17 " - " O   HOH Z 333 "  2.059 3.040 -x,y+1/2,-z+1/2
  ... (remaining 28381 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_914/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_914/model_refine_001.geo

CPU time processing inputs: 9.12


============================ 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 47.16465 84.6622 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4591   r_free= 0.4561   ksol= 0.00   Bsol= 0.00   scale= 0.808    |
|                                                                             |
| 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:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.259453                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.6823 0.99   1423  159 0.3784 0.3711      6.5611      6.5456|
|  2:  4.6823 -  3.7353 0.99   1375  146 0.3663 0.3684      6.7243       6.732|
|  3:  3.7353 -  3.2687 0.99   1350  158 0.4155 0.3876       6.625      6.6667|
|  4:  3.2687 -  2.9723 0.99   1344  148 0.4313 0.4412       6.475      6.4728|
|  5:  2.9723 -  2.7607 0.99   1310  147 0.4875 0.5005      6.3464      6.3602|
|  6:  2.7607 -  2.5988 0.98   1332  146 0.4782 0.5138      6.2464      6.2152|
|  7:  2.5988 -  2.4693 0.99   1326  150 0.5003 0.4358      6.2502      6.1208|
|  8:  2.4693 -  2.3622 0.99   1290  143 0.5200 0.5226      6.1491      6.2035|
|  9:  2.3622 -  2.2716 0.98   1326  148 0.5057 0.5048      6.1126      6.0866|
| 10:  2.2716 -  2.1934 0.98   1301  148 0.5118 0.5243      6.0809      6.1082|
| 11:  2.1934 -  2.1251 0.98   1303  137 0.5130 0.5000       6.021      6.0217|
| 12:  2.1251 -  2.0645 0.99   1295  144 0.5167 0.5668       5.949      5.9866|
| 13:  2.0645 -  2.0102 0.94   1253  146 0.5344 0.4877      5.8748      5.8305|
| 14:  2.0102 -  1.9613 0.30    402   39 0.5387 0.6205      5.8324      5.7961|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0183 -  4.6823  1423   159  0.72  32.22   0.81     0.75      63211.36|
|  2:  4.6823 -  3.7353  1375   146  0.72  33.04   0.90     0.79      92171.82|
|  3:  3.7353 -  3.2687  1350   158  0.63  41.71   0.84     0.75     102449.56|
|  4:  3.2687 -  2.9723  1344   148  0.54  48.88   0.83     0.64      93924.08|
|  5:  2.9723 -  2.7607  1310   147  0.44  56.48   0.75     0.54      79619.37|
|  6:  2.7607 -  2.5988  1332   146  0.44  56.67   0.75     0.52      65538.31|
|  7:  2.5988 -  2.4693  1326   150  0.46  55.09   0.75     0.52      56637.25|
|  8:  2.4693 -  2.3622  1290   143  0.44  56.58   0.72     0.53      51412.57|
|  9:  2.3622 -  2.2716  1326   148  0.42  58.42   0.75     0.50      48589.11|
| 10:  2.2716 -  2.1934  1301   148  0.38  61.57   0.76     0.45      47949.75|
| 11:  2.1934 -  2.1251  1303   137  0.33  65.39   0.78     0.40      45721.32|
| 12:  2.1251 -  2.0645  1295   144  0.28  69.43   0.75     0.35      45137.72|
| 13:  2.0645 -  2.0102  1253   146  0.26  70.78   0.73     0.33      39146.48|
| 14:  2.0102 -  1.9613   402    39  0.29  68.75   0.70     0.34      32247.05|
|alpha:            min =        0.33 max =            0.79 mean =         0.54|
|beta:             min =    32247.05 max =       102449.56 mean =     63590.61|
|figures of merit: min =        0.00 max =            1.00 mean =         0.47|
|phase err.(work): min =        0.00 max =           89.99 mean =        54.33|
|phase err.(test): min =        0.00 max =           90.00 mean =        54.49|
|-----------------------------------------------------------------------------|

============================== 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 = 12.193996             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.099   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.991469              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.414   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-Geometry statistics: start--------------------------------------------------|
|            Histogram of deviations from ideal values for                    |
| Bonds                | Angles                   |  Nonbonded contacts       |
| 0.000 - 0.140:   597 |   0.009 -   7.457:   713 |  1.196 -  1.566:        3 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       25 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      167 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      705 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1506 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2649 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     3941 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5048 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6601 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7747 |
|-----------------------------------------------------------------------------|
|-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 |       53.622 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.091    4.900  1.196 |       1.819 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.860)------------------------------------------|
|    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 = 11.860)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4655   r_free= 0.4620   ksol= 0.00   Bsol= 0.00   scale= 0.777    |
|                                                                             |
| 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:   0.70 A                  |
| x-ray target function (ml) for work reflections: 6.262587                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4506   r_free= 0.4441   ksol= 0.34   Bsol= 12.33   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.66,8.16,9.32,0.00,0.00,0.00); trace/3= 8.38                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.71 A                  |
| x-ray target function (ml) for work reflections: 6.258245                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.035255             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 80.545   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.949862              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 79.428   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4506      final r-factor (work) = 0.3612          |
| start r-factor (free) = 0.4441      final r-factor (free) = 0.3955          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 85.0362 = 10.04 * 0.50 * 6.2608 + 1.00 * 53.6218                            |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.9914 = 10.04 * 0.50 * 6.1497 + 1.00 * 0.1345                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3612      final r-factor (work) = 0.3133          |
| start r-factor (free) = 0.3955      final r-factor (free) = 0.3698          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.8557 = 0.95 * 1.00 * 6.1497 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7534 = 0.95 * 1.00 * 6.0429 + 1.00 * 0.0135                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.860)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.33   11.85    None  None   None       |
|    all(noH): 2823   0      0.00    78.33   11.85    None  None   None       |
|    Sol.    : 438    0      0.00    78.33   26.79    None  None   None       |
|    Mac.    : 2385   0      0.00    68.29   9.11     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 -   7.834: 1343   |   5:    39.167 -  47.001:   64        |
|      1:     7.834 -  15.667:  753   |   6:    47.001 -  54.834:   20        |
|      2:    15.667 -  23.500:  326   |   7:    54.834 -  62.668:   14        |
|      3:    23.500 -  31.334:  193   |   8:    62.668 -  70.501:    5        |
|      4:    31.334 -  39.167:  104   |   9:    70.501 -  78.335:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3133 r_free = 0.3698             target_work(ml) = 6.017         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3129 r_free = 0.3700             target_work(ml) = 6.017         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3129   r_free= 0.3700   ksol= 0.34   Bsol= 12.33   scale= 1.095   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (7.66,8.16,9.32,0.00,0.00,0.00); trace/3= 8.38                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.016571                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3091   r_free= 0.3650   ksol= 0.33   Bsol= 50.00   scale= 1.004   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.06,4.36,6.07,0.00,0.00,0.00); trace/3= 4.83                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.47 A                  |
| x-ray target function (ml) for work reflections: 6.015226                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 7.301708              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.476   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.495193              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 130.298  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3091      final r-factor (work) = 0.2125          |
| start r-factor (free) = 0.3650      final r-factor (free) = 0.2743          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 22.1909 = 7.30 * 0.50 * 6.0414 + 1.00 * 0.1345                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 21.5224 = 7.30 * 0.50 * 5.8742 + 1.00 * 0.0766                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2125      final r-factor (work) = 0.1896          |
| start r-factor (free) = 0.2743      final r-factor (free) = 0.2464          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.9225 = 0.50 * 1.00 * 5.8742 + 1.00 * 0.0136                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.8103 = 0.50 * 1.00 * 5.6521 + 1.00 * 0.0115                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.860)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.41   12.27    None  None   None       |
|    all(noH): 2823   0      0.00    78.41   12.27    None  None   None       |
|    Sol.    : 438    0      1.68    78.41   32.47    None  None   None       |
|    Mac.    : 2385   0      0.00    69.86   8.56     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 -   7.841: 1469   |   5:    39.206 -  47.047:  103        |
|      1:     7.841 -  15.682:  703   |   6:    47.047 -  54.888:   54        |
|      2:    15.682 -  23.524:  204   |   7:    54.888 -  62.729:   12        |
|      3:    23.524 -  31.365:  129   |   8:    62.729 -  70.571:    5        |
|      4:    31.365 -  39.206:  143   |   9:    70.571 -  78.412:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1896 r_free = 0.2464             target_work(ml) = 5.598         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1894 r_free = 0.2465             target_work(ml) = 5.597         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1894   r_free= 0.2465   ksol= 0.33   Bsol= 50.00   scale= 1.048   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.06,4.36,6.07,0.00,0.00,0.00); trace/3= 4.83                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.23 A                  |
| x-ray target function (ml) for work reflections: 5.597031                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1869   r_free= 0.2437   ksol= 0.33   Bsol= 46.14   scale= 0.997   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.48,2.69,3.47,0.00,0.00,0.00); trace/3= 2.88                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.24 A                  |
| x-ray target function (ml) for work reflections: 5.594170                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.729223              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 103.437  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.888293              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 120.298  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1869      final r-factor (work) = 0.1394          |
| start r-factor (free) = 0.2437      final r-factor (free) = 0.1857          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.4680 = 4.73 * 0.50 * 5.6633 + 1.00 * 0.0766                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.0367 = 4.73 * 0.50 * 5.4834 + 1.00 * 0.0706                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1394      final r-factor (work) = 0.1277          |
| start r-factor (free) = 0.1857      final r-factor (free) = 0.1743          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.8822 = 0.89 * 1.00 * 5.4834 + 1.00 * 0.0113                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 4.7097 = 0.89 * 1.00 * 5.2879 + 1.00 * 0.0125                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.860)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    86.10   12.94    None  None   None       |
|    all(noH): 2823   0      0.00    86.10   12.94    None  None   None       |
|    Sol.    : 438    0      1.75    77.73   37.06    None  None   None       |
|    Mac.    : 2385   0      0.00    86.10   8.51     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.610: 1616   |   5:    43.048 -  51.658:  104        |
|      1:     8.610 -  17.219:  631   |   6:    51.658 -  60.267:   65        |
|      2:    17.219 -  25.829:  155   |   7:    60.267 -  68.877:   28        |
|      3:    25.829 -  34.439:  101   |   8:    68.877 -  77.487:   10        |
|      4:    34.439 -  43.048:  109   |   9:    77.487 -  86.096:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1277 r_free = 0.1743             target_work(ml) = 5.256         |
| occupancies: max = 1.00  min = 0.02   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1275 r_free = 0.1741             target_work(ml) = 5.255         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1275   r_free= 0.1741   ksol= 0.33   Bsol= 46.14   scale= 1.013   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.48,2.69,3.47,0.00,0.00,0.00); trace/3= 2.88                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.255164                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1278   r_free= 0.1744   ksol= 0.32   Bsol= 45.44   scale= 1.000   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.18,2.37,2.80,0.00,0.00,0.00); trace/3= 2.45                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.16 A                  |
| x-ray target function (ml) for work reflections: 5.256535                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.617806              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 121.242  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.465776              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.911  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1278      final r-factor (work) = 0.1222          |
| start r-factor (free) = 0.1744      final r-factor (free) = 0.1669          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.3496 = 1.62 * 0.50 * 5.2899 + 1.00 * 0.0706                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.2947 = 1.62 * 0.50 * 5.2423 + 1.00 * 0.0542                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1222      final r-factor (work) = 0.1207          |
| start r-factor (free) = 0.1669      final r-factor (free) = 0.1653          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4541 = 0.47 * 1.00 * 5.2423 + 1.00 * 0.0124                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.4426 = 0.47 * 1.00 * 5.2190 + 1.00 * 0.0117                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.860)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    90.76   12.80    None  None   None       |
|    all(noH): 2823   0      0.00    90.76   12.80    None  None   None       |
|    Sol.    : 438    0      1.63    76.78   36.35    None  None   None       |
|    Mac.    : 2385   0      0.00    90.76   8.48     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.076: 1694   |   5:    45.381 -  54.457:   84        |
|      1:     9.076 -  18.152:  583   |   6:    54.457 -  63.533:   46        |
|      2:    18.152 -  27.228:  155   |   7:    63.533 -  72.609:   19        |
|      3:    27.228 -  36.304:  111   |   8:    72.609 -  81.685:    8        |
|      4:    36.304 -  45.381:  120   |   9:    81.685 -  90.761:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1207 r_free = 0.1653             target_work(ml) = 5.214         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1206 r_free = 0.1652             target_work(ml) = 5.213         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1206   r_free= 0.1652   ksol= 0.32   Bsol= 45.44   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.18,2.37,2.80,0.00,0.00,0.00); trace/3= 2.45                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.213308                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1206   r_free= 0.1652   ksol= 0.32   Bsol= 45.44   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.18,2.37,2.80,0.00,0.00,0.00); trace/3= 2.45                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.213308                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.022349              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 143.955  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.359490              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 158.898  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1206      final r-factor (work) = 0.1122          |
| start r-factor (free) = 0.1652      final r-factor (free) = 0.1596          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9407 = 3.02 * 0.50 * 5.2188 + 1.00 * 0.0542                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 7.9023 = 3.02 * 0.50 * 5.1821 + 1.00 * 0.0712                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1122      final r-factor (work) = 0.1119          |
| start r-factor (free) = 0.1596      final r-factor (free) = 0.1585          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8745 = 0.36 * 1.00 * 5.1821 + 1.00 * 0.0116                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.8659 = 0.36 * 1.00 * 5.1602 + 1.00 * 0.0109                               |
|-----------------------------------------------------------------------------|
| number of iterations = 17      |    number of function evaluations = 22     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.860)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.42   12.58    None  None   None       |
|    all(noH): 2823   0      0.00    91.42   12.58    None  None   None       |
|    Sol.    : 438    0      1.58    75.43   35.60    None  None   None       |
|    Mac.    : 2385   0      0.00    91.42   8.35     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.142: 1729   |   5:    45.711 -  54.854:   74        |
|      1:     9.142 -  18.285:  567   |   6:    54.854 -  63.996:   48        |
|      2:    18.285 -  27.427:  145   |   7:    63.996 -  73.138:   12        |
|      3:    27.427 -  36.569:  123   |   8:    73.138 -  82.280:    7        |
|      4:    36.569 -  45.711:  115   |   9:    82.280 -  91.423:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1119 r_free = 0.1585             target_work(ml) = 5.158         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1119 r_free = 0.1584             target_work(ml) = 5.158         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1119   r_free= 0.1584   ksol= 0.32   Bsol= 45.44   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.18,2.37,2.80,0.00,0.00,0.00); trace/3= 2.45                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.157523                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.6823 0.99   1423  159 0.0956 0.1298       5.363      5.5504|
|  2:  4.6823 -  3.7353 0.99   1375  146 0.0854 0.1126      5.4251      5.6417|
|  3:  3.7353 -  3.2687 0.99   1350  158 0.1047 0.1601       5.466      5.8742|
|  4:  3.2687 -  2.9723 0.99   1344  148 0.1223 0.1481      5.4523      5.5729|
|  5:  2.9723 -  2.7607 0.99   1310  147 0.1310 0.1702      5.3252       5.503|
|  6:  2.7607 -  2.5988 0.98   1332  146 0.1268 0.1843      5.2275      5.4778|
|  7:  2.5988 -  2.4693 0.99   1326  150 0.1239 0.1741       5.177      5.4098|
|  8:  2.4693 -  2.3622 0.99   1290  143 0.1173 0.1658      5.0663      5.2976|
|  9:  2.3622 -  2.2716 0.98   1326  148 0.1184 0.1884      5.0394      5.3158|
| 10:  2.2716 -  2.1934 0.98   1301  148 0.1150 0.1706      4.9923      5.2472|
| 11:  2.1934 -  2.1251 0.98   1303  137 0.1137 0.1757      4.9361      5.2948|
| 12:  2.1251 -  2.0645 0.99   1295  144 0.1114 0.1779      4.8767      5.0959|
| 13:  2.0645 -  2.0102 0.94   1253  146 0.1178 0.1744      4.7837      5.0233|
| 14:  2.0102 -  1.9613 0.30    402   39 0.1073 0.1648      4.6552       4.866|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0183 -  4.6823  1423   159  0.94   8.79   0.98     0.96       7099.66|
|  2:  4.6823 -  3.7353  1375   146  0.95   8.13   1.01     1.00       8905.04|
|  3:  3.7353 -  3.2687  1350   158  0.93  11.61   1.03     1.02      10510.60|
|  4:  3.2687 -  2.9723  1344   148  0.92  14.09   1.01     0.99      10456.59|
|  5:  2.9723 -  2.7607  1310   147  0.90  16.38   0.99     0.96       8430.98|
|  6:  2.7607 -  2.5988  1332   146  0.90  16.55   0.99     0.96       7305.59|
|  7:  2.5988 -  2.4693  1326   150  0.91  15.51   0.99     0.96       6381.43|
|  8:  2.4693 -  2.3622  1290   143  0.90  16.18   0.99     0.96       5520.99|
|  9:  2.3622 -  2.2716  1326   148  0.90  16.24   1.00     0.97       5183.81|
| 10:  2.2716 -  2.1934  1301   148  0.90  16.00   1.00     0.97       4813.59|
| 11:  2.1934 -  2.1251  1303   137  0.89  16.77   1.00     0.96       4459.24|
| 12:  2.1251 -  2.0645  1295   144  0.91  15.71   1.01     1.00       4043.98|
| 13:  2.0645 -  2.0102  1253   146  0.90  16.39   1.00     0.99       3298.40|
| 14:  2.0102 -  1.9613   402    39  0.90  16.03   0.99     0.97       2598.87|
|alpha:            min =        0.96 max =            1.02 mean =         0.98|
|beta:             min =     2598.87 max =        10510.60 mean =      6597.33|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        14.45|
|phase err.(test): min =        0.00 max =           88.48 mean =        13.91|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1119   r_free= 0.1584   ksol= 0.32   Bsol= 47.89   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.27,-0.08,0.35,0.00,0.00,0.00); trace/3= -0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.157523                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 15.02 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1119   r_free= 0.1584   ksol= 0.32   Bsol= 47.89   scale= 1.001   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.27,-0.08,0.35,0.00,0.00,0.00); trace/3= -0.00                           |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.157523                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 15.0183 -  4.6823 0.99   1423  159 0.0956 0.1298       5.363      5.5504|
|  2:  4.6823 -  3.7353 0.99   1375  146 0.0854 0.1126      5.4251      5.6417|
|  3:  3.7353 -  3.2687 0.99   1350  158 0.1047 0.1601       5.466      5.8742|
|  4:  3.2687 -  2.9723 0.99   1344  148 0.1223 0.1481      5.4523      5.5729|
|  5:  2.9723 -  2.7607 0.99   1310  147 0.1310 0.1702      5.3252       5.503|
|  6:  2.7607 -  2.5988 0.98   1332  146 0.1268 0.1843      5.2275      5.4778|
|  7:  2.5988 -  2.4693 0.99   1326  150 0.1239 0.1741       5.177      5.4098|
|  8:  2.4693 -  2.3622 0.99   1290  143 0.1173 0.1658      5.0663      5.2976|
|  9:  2.3622 -  2.2716 0.98   1326  148 0.1184 0.1884      5.0394      5.3158|
| 10:  2.2716 -  2.1934 0.98   1301  148 0.1150 0.1706      4.9923      5.2472|
| 11:  2.1934 -  2.1251 0.98   1303  137 0.1137 0.1757      4.9361      5.2948|
| 12:  2.1251 -  2.0645 0.99   1295  144 0.1114 0.1779      4.8767      5.0959|
| 13:  2.0645 -  2.0102 0.94   1253  146 0.1178 0.1744      4.7837      5.0233|
| 14:  2.0102 -  1.9613 0.30    402   39 0.1073 0.1648      4.6552       4.866|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 15.0183 -  4.6823  1423   159  0.94   8.79   0.98     0.96       7099.66|
|  2:  4.6823 -  3.7353  1375   146  0.95   8.13   1.01     1.00       8905.04|
|  3:  3.7353 -  3.2687  1350   158  0.93  11.61   1.03     1.02      10510.60|
|  4:  3.2687 -  2.9723  1344   148  0.92  14.09   1.01     0.99      10456.59|
|  5:  2.9723 -  2.7607  1310   147  0.90  16.38   0.99     0.96       8430.98|
|  6:  2.7607 -  2.5988  1332   146  0.90  16.55   0.99     0.96       7305.59|
|  7:  2.5988 -  2.4693  1326   150  0.91  15.51   0.99     0.96       6381.43|
|  8:  2.4693 -  2.3622  1290   143  0.90  16.18   0.99     0.96       5520.99|
|  9:  2.3622 -  2.2716  1326   148  0.90  16.24   1.00     0.97       5183.81|
| 10:  2.2716 -  2.1934  1301   148  0.90  16.00   1.00     0.97       4813.59|
| 11:  2.1934 -  2.1251  1303   137  0.89  16.77   1.00     0.96       4459.24|
| 12:  2.1251 -  2.0645  1295   144  0.91  15.71   1.01     1.00       4043.98|
| 13:  2.0645 -  2.0102  1253   146  0.90  16.39   1.00     0.99       3298.40|
| 14:  2.0102 -  1.9613   402    39  0.90  16.03   0.99     0.97       2598.87|
|alpha:            min =        0.96 max =            1.02 mean =         0.98|
|beta:             min =     2598.87 max =        10510.60 mean =      6597.33|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        14.45|
|phase err.(test): min =        0.00 max =           88.48 mean =        13.91|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.860)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.45    93.87   15.03    None  None   None       |
|    all(noH): 2823   0      2.45    93.87   15.03    None  None   None       |
|    Sol.    : 438    0      4.03    77.88   38.04    None  None   None       |
|    Mac.    : 2385   0      2.45    93.87   10.80    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.448 -  11.591: 1729   |   5:    48.160 -  57.302:   74        |
|      1:    11.591 -  20.733:  567   |   6:    57.302 -  66.444:   48        |
|      2:    20.733 -  29.875:  145   |   7:    66.444 -  75.586:   12        |
|      3:    29.875 -  39.017:  123   |   8:    75.586 -  84.729:    7        |
|      4:    39.017 -  48.160:  115   |   9:    84.729 -  93.871:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 344         
Filter by distance & map next to the model:
   mapped sites are within: 0.390 - 5.798
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 341 from: 344
   mapped sites are within: 0.725 - 5.798

peak=   10.382 closest distance to " CG2 VAL A 230 " =    1.450
peak=    7.027 closest distance to " CG2 VAL A 296 " =    1.125
peak=    6.517 closest distance to " NH2 ARG A  56 " =    2.202
peak=    6.124 closest distance to " CG  LEU A   5 " =    1.256
peak=    5.456 closest distance to " CD2 LEU A   5 " =    1.194
peak=    5.319 closest distance to " O   HOH Z 278 " =    1.075
peak=    5.242 closest distance to " CG  LEU A 228 " =    1.228
peak=    5.188 closest distance to " CB  GLN A 223 " =    1.447
peak=    5.158 closest distance to " CB  GLN A 183 " =    1.274
peak=    5.088 closest distance to " CB  SER A  63 " =    1.285
peak=    5.043 closest distance to " NE2 GLN A  11 " =    1.157
peak=    4.973 closest distance to " CB  VAL A 296 " =    1.092
peak=    4.970 closest distance to " CG  PRO A  54 " =    1.193
peak=    4.809 closest distance to " CB  PRO A  54 " =    0.837
peak=    4.656 closest distance to " O   HOH Z 247 " =    1.310
peak=    4.635 closest distance to " O   HOH Z 193 " =    1.888
peak=    4.600 closest distance to " OD1 ASN A  69 " =    2.617
peak=    4.589 closest distance to " O   HOH Z  48 " =    1.678
peak=    4.579 closest distance to " O   HOH Z 368 " =    2.169
peak=    4.540 closest distance to " CB  VAL A 230 " =    1.231
peak=    4.510 closest distance to " O   HOH Z 126 " =    1.935
peak=    4.508 closest distance to " C   PRO A 198 " =    1.528
peak=    4.507 closest distance to " O   HOH Z 132 " =    1.026
peak=    4.498 closest distance to " CB  GLU A 152 " =    1.179
peak=    4.490 closest distance to " CG  PRO A 213 " =    1.206
peak=    4.479 closest distance to " CD2 LEU A 228 " =    1.217
peak=    4.458 closest distance to " CB  SER A   3 " =    1.390
peak=    4.437 closest distance to " CD1AILE A 234 " =    0.988
peak=    4.420 closest distance to " O   HOH Z 316 " =    2.863
peak=    4.343 closest distance to " CB  TYR A 169 " =    0.911
peak=    4.337 closest distance to " CB  GLU A 128 " =    1.091
peak=    4.331 closest distance to " O   HOH Z 108 " =    1.330
peak=    4.302 closest distance to " O   HOH Z 371 " =    3.262
peak=    4.298 closest distance to " O   HOH Z 280 " =    3.049
peak=    4.289 closest distance to " O   HOH Z 124 " =    1.403
peak=    4.287 closest distance to " O   HOH Z 232 " =    2.261
peak=    4.279 closest distance to " O   HOH Z  78 " =    1.989
peak=    4.247 closest distance to " O   HOH Z 427 " =    2.980
peak=    4.229 closest distance to " O   HOH Z 298 " =    1.878
peak=    4.218 closest distance to " CB  ASN A 148 " =    1.430
peak=    4.214 closest distance to " O   HOH Z 128 " =    2.080
peak=    4.213 closest distance to " O   SER A  87 " =    2.236
peak=    4.197 closest distance to " CA  ALA A  21 " =    1.189
peak=    4.193 closest distance to " O   HOH Z  97 " =    1.927
peak=    4.176 closest distance to " CB  ARG A 275 " =    0.846
peak=    4.153 closest distance to " CG1BVAL A  72 " =    1.602
peak=    4.146 closest distance to " O   HOH Z 236 " =    1.839
peak=    4.146 closest distance to " O   HOH Z 263 " =    1.555
peak=    4.129 closest distance to " O   HOH Z  80 " =    1.698
peak=    4.127 closest distance to " CB  GLU A 277 " =    3.586
peak=    4.121 closest distance to " O   HOH Z 423 " =    1.858
peak=    4.086 closest distance to " O   HOH Z 369 " =    2.010
peak=    4.081 closest distance to " CG  PRO A 198 " =    1.371
peak=    4.080 closest distance to " O   HOH Z 144 " =    1.605
peak=    4.079 closest distance to " O   HOH Z  20 " =    1.886
peak=    4.074 closest distance to " O   HOH Z 389 " =    1.918
peak=    4.048 closest distance to " O   HOH Z 126 " =    1.572
peak=    4.037 closest distance to " CB  VAL A 202 " =    1.586
peak=    4.024 closest distance to " O   HOH Z 303 " =    2.093
peak=    4.023 closest distance to " O   HOH Z 411 " =    3.729
peak=    4.021 closest distance to " O   HOH Z  93 " =    2.667
peak=    3.994 closest distance to " O   HOH Z 234 " =    3.753
peak=    3.981 closest distance to " CB  VAL A 265 " =    1.232
peak=    3.978 closest distance to " O   HOH Z  37 " =    1.218
peak=    3.976 closest distance to " O   HOH Z 272 " =    1.899
peak=    3.973 closest distance to " OD2 ASP A 286 " =    2.840
peak=    3.961 closest distance to " O   HOH Z 295 " =    1.558
peak=    3.955 closest distance to " O   HOH Z 133 " =    2.267
peak=    3.948 closest distance to " O   HOH Z 403 " =    1.717
peak=    3.946 closest distance to " O   HOH Z  55 " =    2.429
peak=    3.937 closest distance to " O   TRP A 274 " =    1.860
peak=    3.936 closest distance to " CB  ARG A  79 " =    1.424
peak=    3.934 closest distance to " O   HOH Z 112 " =    1.520
peak=    3.930 closest distance to " O   HOH Z  88 " =    3.171
peak=    3.926 closest distance to " O   HOH Z  11 " =    1.214
peak=    3.923 closest distance to " O   HOH Z 344 " =    2.859
peak=    3.912 closest distance to " O   HOH Z  15 " =    2.337
peak=    3.900 closest distance to " O   HOH Z 193 " =    2.035
peak=    3.890 closest distance to " CA  TYR A  30 " =    0.963
peak=    3.887 closest distance to " O   HOH Z  68 " =    1.695
peak=    3.883 closest distance to " O   HOH Z  54 " =    1.564
peak=    3.875 closest distance to " OG BSER A 164 " =    2.161
peak=    3.867 closest distance to " CA  THR A 221 " =    0.898
peak=    3.866 closest distance to " CG  ARG A  66 " =    2.768
peak=    3.865 closest distance to " CG2 THR A 221 " =    1.038
peak=    3.857 closest distance to " O   HOH Z 203 " =    1.613
peak=    3.853 closest distance to " O   HOH Z 108 " =    2.005
peak=    3.838 closest distance to " CD1 LEU A 300 " =    1.165
peak=    3.836 closest distance to " CB  TRP A 266 " =    0.970
peak=    3.832 closest distance to " NH2 ARG A 156 " =    1.168
peak=    3.824 closest distance to " O   HOH Z  61 " =    1.583
peak=    3.813 closest distance to " CG1 ILE A  33 " =    1.291
peak=    3.808 closest distance to " O   HOH Z 346 " =    1.539
peak=    3.801 closest distance to " O   HOH Z  63 " =    2.045
peak=    3.800 closest distance to " CB  TRP A 179 " =    1.402
peak=    3.799 closest distance to " O   HOH Z 260 " =    1.157
peak=    3.781 closest distance to " O   HOH Z 133 " =    1.695
peak=    3.781 closest distance to " O   HOH Z 426 " =    1.485
peak=    3.771 closest distance to " CA  ALA A  51 " =    1.006
peak=    3.770 closest distance to " O   MET A 105 " =    1.821
peak=    3.750 closest distance to " CG  ARG A 138 " =    1.093
peak=    3.743 closest distance to " O   HOH Z 134 " =    1.444
peak=    3.723 closest distance to " CB  LEU A 228 " =    1.345
peak=    3.719 closest distance to " O   HOH Z  21 " =    1.744
peak=    3.705 closest distance to " O   ALA A 158 " =    1.330
peak=    3.701 closest distance to " O   HOH Z 425 " =    1.357
peak=    3.689 closest distance to " O   HOH Z  49 " =    2.515
peak=    3.668 closest distance to " CG  PRO A 243 " =    1.193
peak=    3.659 closest distance to " O   HOH Z 180 " =    2.142
peak=    3.638 closest distance to " CA  VAL A  41 " =    0.892
peak=    3.631 closest distance to " CB  ARG A 139 " =    0.934
peak=    3.630 closest distance to " O   HOH Z 214 " =    2.084
peak=    3.627 closest distance to " CA  LYS A 117 " =    1.263
peak=    3.614 closest distance to " O   HOH Z 345 " =    3.280
peak=    3.599 closest distance to " O   HOH Z  44 " =    2.304
peak=    3.595 closest distance to " O   HOH Z 116 " =    1.734
peak=    3.591 closest distance to " O   HOH Z 197 " =    2.755
peak=    3.587 closest distance to " O   HOH Z 313 " =    1.781
peak=    3.582 closest distance to " O   HOH Z 271 " =    1.906
peak=    3.580 closest distance to " CD  ARG A 269 " =    0.910
peak=    3.579 closest distance to " O   ALA A   1 " =    1.497
peak=    3.579 closest distance to " CB  GLN A  88 " =    1.221
peak=    3.576 closest distance to " CG  PRO A 280 " =    0.725
peak=    3.572 closest distance to " O   HOH Z 329 " =    3.772
peak=    3.566 closest distance to " O   HOH Z 130 " =    2.251
peak=    3.565 closest distance to " O   HOH Z  48 " =    1.614
peak=    3.563 closest distance to " CB  ALA A 248 " =    0.984
peak=    3.561 closest distance to " OG  SER A  22 " =    2.824
peak=    3.558 closest distance to " O   HOH Z 374 " =    3.050
peak=    3.557 closest distance to " O   HOH Z 411 " =    1.863
peak=    3.555 closest distance to " O   HOH Z 420 " =    2.112
peak=    3.551 closest distance to " CA  VAL A 126 " =    1.022
peak=    3.547 closest distance to " CB  ASN A 148 " =    1.939
peak=    3.545 closest distance to " CA  ASN A 215 " =    1.184
peak=    3.545 closest distance to " ND2 ASN A 187 " =    1.614
peak=    3.541 closest distance to " O   HOH Z 189 " =    2.645
peak=    3.540 closest distance to " NZ  LYS A 117 " =    3.281
peak=    3.533 closest distance to " CB  LEU A 143 " =    1.176
peak=    3.528 closest distance to " CD BLYS A 290 " =    1.090
peak=    3.528 closest distance to " CB  SER A 216 " =    0.793
peak=    3.518 closest distance to " NE2 GLN A  58 " =    5.798
peak=    3.516 closest distance to " O   HOH Z 355 " =    1.839
peak=    3.516 closest distance to " CA  ALA A 295 " =    1.054
peak=    3.514 closest distance to " O   HOH Z 171 " =    2.474
peak=    3.511 closest distance to " CG BARG A 102 " =    1.890
peak=    3.506 closest distance to " CA  LEU A 282 " =    1.051
peak=    3.504 closest distance to " CA  ASP A 191 " =    0.784
peak=    3.502 closest distance to " CB  ASP A 140 " =    0.820
peak=    3.502 closest distance to " O   HOH Z 273 " =    2.515
peak=    3.499 closest distance to " O   HOH Z 422 " =    2.627
peak=    3.496 closest distance to " O   HOH Z 158 " =    2.958
peak=    3.496 closest distance to " O   HOH Z 281 " =    4.349
peak=    3.495 closest distance to " OE1 GLN A  11 " =    1.733
peak=    3.487 closest distance to " CB  ASN A 187 " =    1.091
peak=    3.485 closest distance to " O   HOH Z  61 " =    1.629
peak=    3.485 closest distance to " O   HOH Z  63 " =    1.270
peak=    3.485 closest distance to " O   HOH Z  59 " =    2.364
peak=    3.484 closest distance to " O   HOH Z 250 " =    1.379
peak=    3.483 closest distance to " CB  ALA A 291 " =    1.393
peak=    3.481 closest distance to " O   HOH Z 126 " =    1.789
peak=    3.480 closest distance to " O   THR A  31 " =    1.523
peak=    3.480 closest distance to " O   HOH Z 215 " =    1.611
peak=    3.479 closest distance to " O   HOH Z  63 " =    1.061
peak=    3.478 closest distance to " O   HOH Z 135 " =    1.843
peak=    3.474 closest distance to " CD  LYS A 166 " =    1.346
peak=    3.474 closest distance to " CG  GLN A  88 " =    1.036
peak=    3.468 closest distance to " O   HOH Z 374 " =    2.502
peak=    3.466 closest distance to " OE1 GLU A   2 " =    2.188
peak=    3.461 closest distance to " O   HOH Z 261 " =    2.065
peak=    3.458 closest distance to " CA  ALA A 158 " =    1.112
peak=    3.454 closest distance to " CA  ASN A  74 " =    1.146
peak=    3.452 closest distance to " CB  ALA A 248 " =    1.415
peak=    3.450 closest distance to " O   HOH Z 383 " =    2.093
peak=    3.449 closest distance to " O   HOH Z 276 " =    1.294
peak=    3.445 closest distance to " CB  ASN A  39 " =    0.839
peak=    3.439 closest distance to " O   HOH Z 172 " =    4.007
peak=    3.439 closest distance to " O   HOH Z 132 " =    2.893
peak=    3.437 closest distance to " N   ASN A 127 " =    1.375
peak=    3.437 closest distance to " CG2 VAL A 174 " =    1.333
peak=    3.436 closest distance to " O   HOH Z 236 " =    1.658
peak=    3.435 closest distance to " O   HOH Z 227 " =    1.715
peak=    3.431 closest distance to " CA  THR A 264 " =    0.820
peak=    3.425 closest distance to " ND1 HIS A  81 " =    1.571
peak=    3.423 closest distance to " O   HOH Z 427 " =    3.184
peak=    3.421 closest distance to " CD  ARG A 159 " =    0.812
peak=    3.420 closest distance to " CA  ASP A 140 " =    1.182
peak=    3.414 closest distance to " N   ASN A  39 " =    1.217
peak=    3.411 closest distance to " O   HOH Z  30 " =    1.176
peak=    3.410 closest distance to " O   HOH Z  40 " =    1.418
peak=    3.410 closest distance to " NH2 ARG A  79 " =    1.346
peak=    3.404 closest distance to " CD  LYS A 119 " =    1.894
peak=    3.401 closest distance to " NH1 ARG A  56 " =    1.037
peak=    3.400 closest distance to " O   HOH Z 332 " =    1.550
peak=    3.396 closest distance to " OD1 ASN A 217 " =    1.723
peak=    3.394 closest distance to " N   ARG A 156 " =    1.324
peak=    3.387 closest distance to " CB  ALA A   9 " =    1.521
peak=    3.384 closest distance to " CA  GLY A 211 " =    1.191
peak=    3.383 closest distance to " O   HOH Z 279 " =    2.214
peak=    3.382 closest distance to " O   HOH Z 425 " =    2.084
peak=    3.380 closest distance to " CD1 ILE A 106 " =    1.152
peak=    3.375 closest distance to " CG AARG A 275 " =    1.093
peak=    3.373 closest distance to " CB  TYR A 169 " =    0.863
peak=    3.371 closest distance to " CG  MET A 188 " =    1.353
peak=    3.370 closest distance to " O   HOH Z 175 " =    3.498
peak=    3.367 closest distance to " O   HOH Z 163 " =    1.474
peak=    3.360 closest distance to " ND1 HIS A  86 " =    1.695
peak=    3.360 closest distance to " O   HOH Z 128 " =    1.904
peak=    3.358 closest distance to " CD2 LEU A 255 " =    1.220
peak=    3.355 closest distance to " CA  MET A  40 " =    1.068
peak=    3.352 closest distance to " CG2 ILE A 120 " =    1.264
peak=    3.349 closest distance to " CB  LEU A 255 " =    0.825
peak=    3.347 closest distance to " CG  MET A 185 " =    1.248
peak=    3.345 closest distance to " C   LYS A 290 " =    1.315
peak=    3.343 closest distance to " CA  SER A  87 " =    0.875
peak=    3.342 closest distance to " O   HOH Z 171 " =    3.789
peak=    3.341 closest distance to " CB  THR A  82 " =    1.340
peak=    3.340 closest distance to " NH1AARG A 145 " =    0.954
peak=    3.329 closest distance to " O   HOH Z 118 " =    1.452
peak=    3.324 closest distance to " O   HOH Z 419 " =    1.652
peak=    3.320 closest distance to " O   HOH Z 209 " =    2.332
peak=    3.319 closest distance to " O   HOH Z 409 " =    3.509
peak=    3.315 closest distance to " O   HOH Z 128 " =    2.118
peak=    3.313 closest distance to " CD2 TRP A 179 " =    1.375
peak=    3.313 closest distance to " CG1 VAL A 153 " =    0.977
peak=    3.312 closest distance to " O   HOH Z 245 " =    1.357
peak=    3.309 closest distance to " O   HOH Z 367 " =    3.402
peak=    3.307 closest distance to " CG2 THR A 220 " =    0.995
peak=    3.307 closest distance to " NE2 GLN A  58 " =    4.177
peak=    3.306 closest distance to " O   HOH Z 261 " =    1.841
peak=    3.305 closest distance to " CB BVAL A  41 " =    1.168
peak=    3.302 closest distance to " CA  GLY A 267 " =    0.985
peak=    3.302 closest distance to " CD2 HIS A  81 " =    1.138
peak=    3.301 closest distance to " O   HOH Z 388 " =    1.845
peak=    3.301 closest distance to " O   HOH Z 280 " =    1.639
peak=    3.298 closest distance to " NH2BARG A 102 " =    0.890
peak=    3.292 closest distance to " O   HOH Z  43 " =    2.145
peak=    3.290 closest distance to " CE1 TYR A 186 " =    1.247
peak=    3.287 closest distance to " CB  GLU A  46 " =    1.049
peak=    3.287 closest distance to " CB  SER A 141 " =    1.022
peak=    3.284 closest distance to " CB  ARG A 190 " =    1.738
peak=    3.283 closest distance to " OD1 ASP A 231 " =    1.865
peak=    3.283 closest distance to " O   HOH Z 423 " =    3.141
peak=    3.278 closest distance to " C   ALA A 299 " =    0.977
peak=    3.270 closest distance to " O   HOH Z 357 " =    1.964
peak=    3.269 closest distance to " CB  ALA A 295 " =    1.333
peak=    3.268 closest distance to " O   HOH Z  10 " =    1.842
peak=    3.268 closest distance to " O   HOH Z 334 " =    1.464
peak=    3.265 closest distance to " O   HOH Z 128 " =    1.809
peak=    3.263 closest distance to " CA  ILE A 106 " =    0.831
peak=    3.263 closest distance to " NH2BARG A 145 " =    2.150
peak=    3.261 closest distance to " CB  TYR A  30 " =    1.448
peak=    3.261 closest distance to " CA  ALA A 291 " =    0.941
peak=    3.260 closest distance to " CD1 ILE A  33 " =    1.626
peak=    3.259 closest distance to " CD2 TYR A 186 " =    1.012
peak=    3.258 closest distance to " O   HOH Z  19 " =    2.224
peak=    3.256 closest distance to " OG1 THR A 294 " =    2.326
peak=    3.253 closest distance to " CB  ALA A 161 " =    0.900
peak=    3.252 closest distance to " O   HOH Z 406 " =    1.580
peak=    3.247 closest distance to " CB  ALA A 100 " =    1.266
peak=    3.246 closest distance to " O   HOH Z 147 " =    1.631
peak=    3.245 closest distance to " O   GLN A  58 " =    1.636
peak=    3.245 closest distance to " O   HOH Z 437 " =    2.175
peak=    3.241 closest distance to " CB  THR A  31 " =    1.613
peak=    3.239 closest distance to " CB  LYS A 117 " =    1.126
peak=    3.237 closest distance to " NH2 ARG A 219 " =    1.832
peak=    3.236 closest distance to " O   HOH Z  85 " =    1.294
peak=    3.235 closest distance to " O   HOH Z 365 " =    2.733
peak=    3.232 closest distance to " O   HOH Z 175 " =    2.191
peak=    3.231 closest distance to " O   HOH Z 280 " =    2.255
peak=    3.225 closest distance to " CB  SER A  62 " =    1.280
peak=    3.224 closest distance to " O   ALA A 165 " =    1.348
peak=    3.221 closest distance to " CA  ASN A 176 " =    1.151
peak=    3.221 closest distance to " CA  ARG A  36 " =    1.102
peak=    3.218 closest distance to " CG2AVAL A 121 " =    2.258
peak=    3.217 closest distance to " O   HOH Z 248 " =    1.817
peak=    3.215 closest distance to " CG  MET A 185 " =    1.051
peak=    3.214 closest distance to " O   HOH Z 207 " =    2.181
peak=    3.212 closest distance to " O   ASP A 124 " =    1.121
peak=    3.210 closest distance to " CB  ASN A 142 " =    1.068
peak=    3.209 closest distance to " CG  GLU A 277 " =    2.182
peak=    3.208 closest distance to " C   SER A  32 " =    1.015
peak=    3.208 closest distance to " CZ  PHE A 192 " =    1.034
peak=    3.207 closest distance to " O   HOH Z 345 " =    1.680
peak=    3.197 closest distance to " O   HOH Z 151 " =    1.743
peak=    3.193 closest distance to " O   HOH Z   4 " =    1.823
peak=    3.190 closest distance to " CB  GLN A  89 " =    1.025
peak=    3.190 closest distance to " O   HOH Z  44 " =    1.711
peak=    3.189 closest distance to " CB  MET A  40 " =    0.862
peak=    3.183 closest distance to " O   HOH Z 366 " =    3.026
peak=    3.180 closest distance to " O   HOH Z 337 " =    3.681
peak=    3.180 closest distance to " O   HOH Z 438 " =    2.115
peak=    3.179 closest distance to " CG  GLN A  55 " =    2.222
peak=    3.177 closest distance to " NZ  LYS A  48 " =    1.343
peak=    3.175 closest distance to " O   HOH Z 248 " =    1.646
peak=    3.174 closest distance to " O   HOH Z  71 " =    2.074
peak=    3.173 closest distance to " O   HOH Z 211 " =    2.477
peak=    3.171 closest distance to " CA  ALA A 154 " =    1.106
peak=    3.169 closest distance to " O   HOH Z 394 " =    1.722
peak=    3.168 closest distance to " CG  LEU A 167 " =    1.179
peak=    3.167 closest distance to " NH1 ARG A  14 " =    1.026
peak=    3.166 closest distance to " CB  ASN A 110 " =    1.295
peak=    3.163 closest distance to " O   HOH Z 151 " =    1.741
peak=    3.163 closest distance to " CG1 VAL A 174 " =    1.215
peak=    3.160 closest distance to " CZ2 TRP A 274 " =    1.835
peak=    3.159 closest distance to " CB  GLU A 152 " =    1.370
peak=    3.158 closest distance to " CZ2 TRP A 179 " =    1.670
peak=    3.155 closest distance to " CG1 ILE A  49 " =    1.501
peak=    3.149 closest distance to " N   SER A 135 " =    1.403
peak=    3.148 closest distance to " CB  THR A 157 " =    1.033
peak=    3.144 closest distance to " O   HOH Z 281 " =    3.780
peak=    3.143 closest distance to " NZ  LYS A  76 " =    1.270
peak=    3.142 closest distance to " O   HOH Z 184 " =    1.266
peak=    3.140 closest distance to " O   HOH Z 282 " =    2.046
peak=    3.138 closest distance to " CA  GLN A 194 " =    1.229
peak=    3.137 closest distance to " O   HOH Z 155 " =    2.830
peak=    3.137 closest distance to " CA  LEU A 101 " =    1.564
peak=    3.131 closest distance to " OD1 ASP A 286 " =    1.601
peak=    3.130 closest distance to " CZ  PHE A 218 " =    1.051
peak=    3.129 closest distance to " O   HOH Z  63 " =    1.781
peak=    3.125 closest distance to " OG1 THR A 279 " =    1.805
peak=    3.125 closest distance to " O   HOH Z 193 " =    1.534
peak=    3.123 closest distance to " O   HOH Z 286 " =    2.484
peak=    3.123 closest distance to " OG  SER A 206 " =    1.263
peak=    3.121 closest distance to " O   HOH Z 244 " =    1.622
peak=    3.119 closest distance to " CB  LYS A 193 " =    1.194
peak=    3.118 closest distance to " O   HOH Z 155 " =    1.528
peak=    3.117 closest distance to " CG2 ILE A  20 " =    1.524
peak=    3.114 closest distance to " C   TYR A 214 " =    1.542
peak=    3.107 closest distance to " CB  SER A 212 " =    1.174
peak=    3.102 closest distance to " O   HOH Z 109 " =    2.741
peak=    3.100 closest distance to " CA  ALA A 233 " =    1.478
peak=    3.098 closest distance to " O   HOH Z 420 " =    5.658
peak=    3.097 closest distance to " O   HOH Z   9 " =    1.642
peak=    3.072 closest distance to " CB  ILE A 120 " =    1.526
peak=    3.070 closest distance to " O   HOH Z 197 " =    1.963
peak=    3.068 closest distance to " CD1 LEU A 101 " =    1.166
peak=    3.050 closest distance to " O   HOH Z 213 " =    1.681
peak=    3.041 closest distance to " OG  SER A  97 " =    2.548
peak=    3.021 closest distance to " CD  ARG A 219 " =    1.027
peak=    3.010 closest distance to " CA  ARG A  56 " =    1.841
peak=    2.999 closest distance to " O   HOH Z 424 " =    2.471

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 198         
Filter by distance & map next to the model:
   mapped sites are within: 0.613 - 5.210
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 196 from: 198
   mapped sites are within: 0.773 - 5.210

peak=   -5.441 closest distance to " CG2 VAL A 230 " =    0.836
peak=   -4.582 closest distance to " CD  ARG A 156 " =    1.953
peak=   -4.510 closest distance to " O   HOH Z 266 " =    4.413
peak=   -4.416 closest distance to " O   ILE A 109 " =    2.641
peak=   -4.326 closest distance to " O   HOH Z 290 " =    1.071
peak=   -4.196 closest distance to " CG  LEU A 101 " =    2.586
peak=   -4.150 closest distance to " OXT GLY A 302 " =    2.911
peak=   -4.037 closest distance to " O   HOH Z 231 " =    1.876
peak=   -4.032 closest distance to " SG  CYS A 254 " =    3.157
peak=   -4.003 closest distance to " CD  GLN A  88 " =    2.206
peak=   -3.979 closest distance to " OG ASER A 134 " =    1.394
peak=   -3.967 closest distance to " O   HOH Z  92 " =    1.459
peak=   -3.946 closest distance to " O   HOH Z  13 " =    1.377
peak=   -3.937 closest distance to " CG1 VAL A 250 " =    2.768
peak=   -3.904 closest distance to " O   HOH Z  17 " =    1.437
peak=   -3.901 closest distance to " O   HOH Z  52 " =    1.574
peak=   -3.899 closest distance to " CG  GLN A 223 " =    2.163
peak=   -3.859 closest distance to " NH2 ARG A  66 " =    1.745
peak=   -3.848 closest distance to " CE2 TYR A  30 " =    2.775
peak=   -3.832 closest distance to " CG2 THR A   4 " =    1.939
peak=   -3.829 closest distance to " N   GLN A  58 " =    1.727
peak=   -3.825 closest distance to " O   PRO A 163 " =    2.066
peak=   -3.813 closest distance to " O   HOH Z 103 " =    1.838
peak=   -3.773 closest distance to " O   HOH Z  11 " =    1.726
peak=   -3.772 closest distance to " C   ASN A 187 " =    1.798
peak=   -3.771 closest distance to " O   HOH Z 166 " =    1.469
peak=   -3.769 closest distance to " O   HOH Z 377 " =    1.869
peak=   -3.747 closest distance to " OG BSER A 134 " =    1.743
peak=   -3.732 closest distance to " O   HOH Z  43 " =    1.657
peak=   -3.722 closest distance to " C   ALA A 158 " =    1.250
peak=   -3.711 closest distance to " CD2 LEU A 300 " =    2.854
peak=   -3.698 closest distance to " O   HOH Z 166 " =    1.811
peak=   -3.689 closest distance to " OE2 GLU A   2 " =    1.825
peak=   -3.685 closest distance to " N   THR A 157 " =    1.615
peak=   -3.684 closest distance to " CG2 VAL A 296 " =    1.334
peak=   -3.666 closest distance to " N   ALA A 226 " =    2.080
peak=   -3.664 closest distance to " NH2 ARG A  79 " =    1.877
peak=   -3.660 closest distance to " CD1 PHE A  59 " =    1.886
peak=   -3.654 closest distance to " CD  ARG A 139 " =    1.621
peak=   -3.645 closest distance to " CG  ASP A  50 " =    2.516
peak=   -3.633 closest distance to " O   HOH Z 151 " =    1.422
peak=   -3.625 closest distance to " CD1 LEU A 228 " =    2.328
peak=   -3.613 closest distance to " OD1 ASN A 148 " =    1.602
peak=   -3.610 closest distance to " O   HOH Z 388 " =    1.937
peak=   -3.600 closest distance to " O   HOH Z 292 " =    4.460
peak=   -3.596 closest distance to " O   HOH Z 234 " =    4.227
peak=   -3.593 closest distance to " CD1 LEU A 101 " =    2.672
peak=   -3.580 closest distance to " C   HIS A 108 " =    1.182
peak=   -3.575 closest distance to " O   HOH Z  19 " =    2.179
peak=   -3.574 closest distance to " O   HOH Z 241 " =    1.247
peak=   -3.570 closest distance to " CB  PRO A 243 " =    2.591
peak=   -3.570 closest distance to " CD  LYS A 289 " =    2.510
peak=   -3.565 closest distance to " CG  LEU A 228 " =    1.031
peak=   -3.564 closest distance to " CG  TRP A 266 " =    1.692
peak=   -3.559 closest distance to " OG BSER A 134 " =    1.261
peak=   -3.558 closest distance to " OG  SER A  87 " =    1.452
peak=   -3.556 closest distance to " CB  PRO A 163 " =    2.685
peak=   -3.556 closest distance to " NH2 ARG A 159 " =    2.335
peak=   -3.554 closest distance to " O   HOH Z 407 " =    3.244
peak=   -3.551 closest distance to " OG  SER A  26 " =    1.202
peak=   -3.544 closest distance to " CZ3 TRP A 179 " =    1.290
peak=   -3.543 closest distance to " NH2AARG A 275 " =    5.210
peak=   -3.538 closest distance to " CB  TYR A  15 " =    2.227
peak=   -3.536 closest distance to " CG2 VAL A 112 " =    2.600
peak=   -3.529 closest distance to " O   HOH Z  97 " =    1.667
peak=   -3.528 closest distance to " O   HOH Z  71 " =    1.048
peak=   -3.525 closest distance to " O   HOH Z 266 " =    4.401
peak=   -3.517 closest distance to " O   HOH Z  15 " =    1.569
peak=   -3.510 closest distance to " O   HOH Z 275 " =    1.493
peak=   -3.509 closest distance to " OG  SER A  97 " =    2.222
peak=   -3.509 closest distance to " CG  ASP A 231 " =    0.773
peak=   -3.496 closest distance to " CB  ALA A  43 " =    2.368
peak=   -3.489 closest distance to " O   ALA A 161 " =    1.519
peak=   -3.484 closest distance to " CB  PHE A 283 " =    2.833
peak=   -3.481 closest distance to " ND2 ASN A  60 " =    1.528
peak=   -3.474 closest distance to " CZ  TYR A 169 " =    1.779
peak=   -3.470 closest distance to " O   SER A 271 " =    2.109
peak=   -3.464 closest distance to " O   GLY A 211 " =    1.412
peak=   -3.462 closest distance to " CG  LYS A 193 " =    2.423
peak=   -3.457 closest distance to " CB  ALA A 248 " =    1.960
peak=   -3.451 closest distance to " OG  SER A  62 " =    1.498
peak=   -3.450 closest distance to " CB  CYS A 254 " =    2.339
peak=   -3.447 closest distance to " O   HOH Z  38 " =    1.643
peak=   -3.446 closest distance to " CG  GLU A  53 " =    1.610
peak=   -3.443 closest distance to " O   HOH Z 184 " =    1.479
peak=   -3.441 closest distance to " N   SER A 276 " =    1.326
peak=   -3.439 closest distance to " O   HOH Z  10 " =    1.549
peak=   -3.435 closest distance to " O   HOH Z 211 " =    1.562
peak=   -3.429 closest distance to " ND2 ASN A  45 " =    1.026
peak=   -3.428 closest distance to " O   HOH Z  98 " =    1.948
peak=   -3.406 closest distance to " O   HOH Z 389 " =    1.789
peak=   -3.405 closest distance to " O   HOH Z 353 " =    2.223
peak=   -3.401 closest distance to " O   GLY A 196 " =    1.123
peak=   -3.401 closest distance to " CE  MET A 105 " =    2.070
peak=   -3.400 closest distance to " N   ALA A  43 " =    2.473
peak=   -3.400 closest distance to " O   HOH Z 394 " =    1.551
peak=   -3.398 closest distance to " CG1 VAL A 296 " =    1.557
peak=   -3.397 closest distance to " O   HOH Z 426 " =    2.330
peak=   -3.397 closest distance to " O   VAL A  67 " =    2.571
peak=   -3.396 closest distance to " CD2 TYR A 293 " =    2.141
peak=   -3.396 closest distance to " O   HOH Z 185 " =    2.413
peak=   -3.393 closest distance to " CG1 VAL A 112 " =    2.620
peak=   -3.377 closest distance to " O   HOH Z 339 " =    1.849
peak=   -3.374 closest distance to " CG  MET A 105 " =    0.907
peak=   -3.373 closest distance to " CG  PRO A 163 " =    2.585
peak=   -3.371 closest distance to " O   HOH Z 351 " =    1.466
peak=   -3.371 closest distance to " CG2BVAL A  41 " =    2.859
peak=   -3.370 closest distance to " N   THR A 235 " =    1.264
peak=   -3.360 closest distance to " O   HOH Z 189 " =    2.053
peak=   -3.359 closest distance to " O   HOH Z 196 " =    2.264
peak=   -3.353 closest distance to " CA  ASP A 298 " =    1.049
peak=   -3.348 closest distance to " C   GLN A 240 " =    2.224
peak=   -3.345 closest distance to " O   HOH Z 426 " =    1.650
peak=   -3.331 closest distance to " O   HOH Z 252 " =    4.086
peak=   -3.330 closest distance to " OD1 ASP A 191 " =    1.607
peak=   -3.328 closest distance to " O   PRO A 198 " =    1.282
peak=   -3.323 closest distance to " CB  SER A 245 " =    2.323
peak=   -3.323 closest distance to " O   HOH Z 165 " =    2.126
peak=   -3.315 closest distance to " O   HOH Z 311 " =    3.685
peak=   -3.314 closest distance to " CA  SER A  62 " =    2.479
peak=   -3.310 closest distance to " ND2 ASN A 187 " =    1.729
peak=   -3.307 closest distance to " O   PRO A 198 " =    1.287
peak=   -3.304 closest distance to " O   VAL A 125 " =    2.216
peak=   -3.303 closest distance to " N   ALA A 248 " =    2.545
peak=   -3.301 closest distance to " O   HOH Z  63 " =    0.863
peak=   -3.301 closest distance to " C   ASN A 285 " =    2.454
peak=   -3.300 closest distance to " O   HOH Z 431 " =    1.761
peak=   -3.294 closest distance to " O   HOH Z 411 " =    3.678
peak=   -3.291 closest distance to " CD2 LEU A 167 " =    1.716
peak=   -3.282 closest distance to " CA  ASN A 127 " =    1.076
peak=   -3.280 closest distance to " CZ  TYR A 172 " =    1.710
peak=   -3.272 closest distance to " O   HOH Z 385 " =    2.073
peak=   -3.272 closest distance to " CB  ASN A  39 " =    2.047
peak=   -3.270 closest distance to " O   HOH Z 292 " =    2.934
peak=   -3.269 closest distance to " OD2 ASP A 171 " =    2.214
peak=   -3.267 closest distance to " O   SER A 210 " =    1.951
peak=   -3.262 closest distance to " CB  ASP A 132 " =    2.315
peak=   -3.260 closest distance to " O   HOH Z 435 " =    2.712
peak=   -3.257 closest distance to " O   HOH Z 359 " =    2.899
peak=   -3.256 closest distance to " O   HOH Z  60 " =    2.050
peak=   -3.256 closest distance to " SG ACYS A 201 " =    1.981
peak=   -3.255 closest distance to " OXT GLY A 302 " =    3.435
peak=   -3.248 closest distance to " O   HOH Z  98 " =    2.214
peak=   -3.237 closest distance to " CD1 ILE A 199 " =    2.507
peak=   -3.233 closest distance to " CE3 TRP A  70 " =    1.747
peak=   -3.232 closest distance to " N   PHE A  59 " =    2.145
peak=   -3.228 closest distance to " ND2 ASN A  60 " =    1.587
peak=   -3.227 closest distance to " CE BMET A  47 " =    1.810
peak=   -3.222 closest distance to " CD  GLN A  88 " =    0.805
peak=   -3.221 closest distance to " O   HOH Z 423 " =    2.200
peak=   -3.220 closest distance to " O   HOH Z 350 " =    1.748
peak=   -3.210 closest distance to " O   HOH Z 396 " =    1.657
peak=   -3.207 closest distance to " N   ALA A 248 " =    1.599
peak=   -3.202 closest distance to " ND2 ASN A  45 " =    1.205
peak=   -3.202 closest distance to " CE2 PHE A 218 " =    2.600
peak=   -3.199 closest distance to " OD1 ASN A 187 " =    1.652
peak=   -3.197 closest distance to " O   VAL A 174 " =    2.036
peak=   -3.195 closest distance to " CE3 TRP A 150 " =    2.069
peak=   -3.187 closest distance to " O   VAL A 197 " =    1.288
peak=   -3.186 closest distance to " CG  GLU A 277 " =    1.119
peak=   -3.178 closest distance to " O   HOH Z 205 " =    2.448
peak=   -3.177 closest distance to " O   HOH Z  98 " =    1.518
peak=   -3.176 closest distance to " NH1 ARG A 195 " =    2.622
peak=   -3.173 closest distance to " CG1 VAL A 197 " =    2.261
peak=   -3.173 closest distance to " O   ALA A   8 " =    1.867
peak=   -3.173 closest distance to " CG1 VAL A 112 " =    2.725
peak=   -3.172 closest distance to " N   HIS A 115 " =    2.065
peak=   -3.172 closest distance to " CG  ARG A 259 " =    2.866
peak=   -3.170 closest distance to " CA  GLY A 133 " =    2.232
peak=   -3.170 closest distance to " O   HOH Z 377 " =    1.533
peak=   -3.169 closest distance to " O   HOH Z 222 " =    1.426
peak=   -3.167 closest distance to " CG  ARG A 269 " =    2.278
peak=   -3.164 closest distance to " NH1 ARG A 195 " =    2.272
peak=   -3.164 closest distance to " C   LEU A 143 " =    1.184
peak=   -3.159 closest distance to " C   MET A 188 " =    1.492
peak=   -3.155 closest distance to " CZ  PHE A  59 " =    1.629
peak=   -3.153 closest distance to " NE2 GLN A  88 " =    1.093
peak=   -3.153 closest distance to " OD1 ASP A 191 " =    1.533
peak=   -3.140 closest distance to " O   HOH Z 283 " =    1.736
peak=   -3.129 closest distance to " CD2 LEU A   5 " =    1.064
peak=   -3.126 closest distance to " O   HOH Z 417 " =    2.760
peak=   -3.122 closest distance to " O   ASN A 301 " =    1.425
peak=   -3.122 closest distance to " C   GLN A 205 " =    2.009
peak=   -3.117 closest distance to " CD2 TYR A 247 " =    2.396
peak=   -3.098 closest distance to " O   HOH Z 265 " =    1.804
peak=   -3.092 closest distance to " CB  GLN A  55 " =    1.522
peak=   -3.089 closest distance to " CB  ALA A 291 " =    2.155
peak=   -3.087 closest distance to " CB  ALA A 227 " =    2.330
peak=   -3.085 closest distance to " O   HOH Z  47 " =    1.501
peak=   -3.081 closest distance to " O   HOH Z 148 " =    2.895
peak=   -3.077 closest distance to " O   HOH Z 429 " =    1.931
peak=   -3.071 closest distance to " OD1 ASN A 249 " =    1.287
peak=   -3.065 closest distance to " O   HOH Z 310 " =    1.750
peak=   -3.033 closest distance to " O   HOH Z 262 " =    2.524
peak=   -3.033 closest distance to " NH2 ARG A  79 " =    1.746
peak=   -3.030 closest distance to " CB  ASP A 132 " =    2.236

================= 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    :  0.4591 0.4561   6.259453e+00   6.254067e+00
   1_bss:  0.4506 0.4441   6.258245e+00   6.245155e+00
   1_xyz:  0.3612 0.3955   6.114164e+00   6.166014e+00
   1_adp:  0.3133 0.3698   6.017226e+00   6.124117e+00
   1_occ:  0.3129 0.3700   6.016571e+00   6.124045e+00
   2_bss:  0.3091 0.3650   6.015226e+00   6.120445e+00
   2_xyz:  0.2125 0.2743   5.703776e+00   5.885394e+00
   2_adp:  0.1896 0.2464   5.597612e+00   5.797245e+00
   2_occ:  0.1894 0.2465   5.597031e+00   5.797288e+00
   3_bss:  0.1869 0.2437   5.594170e+00   5.793309e+00
   3_xyz:  0.1394 0.1857   5.325334e+00   5.548731e+00
   3_adp:  0.1277 0.1743   5.255783e+00   5.486893e+00
   3_occ:  0.1275 0.1741   5.255164e+00   5.486396e+00
   4_bss:  0.1278 0.1744   5.256535e+00   5.487505e+00
   4_xyz:  0.1222 0.1669   5.223113e+00   5.450691e+00
   4_adp:  0.1207 0.1653   5.213747e+00   5.442080e+00
   4_occ:  0.1206 0.1652   5.213308e+00   5.441743e+00
   5_bss:  0.1206 0.1652   5.213308e+00   5.441743e+00
   5_xyz:  0.1122 0.1596   5.161234e+00   5.406775e+00
   5_adp:  0.1119 0.1585   5.157691e+00   5.402083e+00
   5_occ:  0.1119 0.1584   5.157523e+00   5.402009e+00
   5_bss:  0.1119 0.1584   5.157523e+00   5.402009e+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:  0.344  12.330   7.659   8.156   9.316   0.000   0.000   0.000
   1_xyz:  0.344  12.330   7.659   8.156   9.316   0.000   0.000   0.000
   1_adp:  0.344  12.330   7.659   8.156   9.316   0.000   0.000   0.000
   1_occ:  0.344  12.330   7.659   8.156   9.316   0.000   0.000   0.000
   2_bss:  0.335  50.000   4.059   4.356   6.070   0.000   0.000   0.000
   2_xyz:  0.335  50.000   4.059   4.356   6.070   0.000   0.000   0.000
   2_adp:  0.335  50.000   4.059   4.356   6.070   0.000   0.000   0.000
   2_occ:  0.335  50.000   4.059   4.356   6.070   0.000   0.000   0.000
   3_bss:  0.331  46.140   2.483   2.692   3.472   0.000   0.000   0.000
   3_xyz:  0.331  46.140   2.483   2.692   3.472   0.000   0.000   0.000
   3_adp:  0.331  46.140   2.483   2.692   3.472   0.000   0.000   0.000
   3_occ:  0.331  46.140   2.483   2.692   3.472   0.000   0.000   0.000
   4_bss:  0.324  45.443   2.181   2.366   2.798   0.000   0.000   0.000
   4_xyz:  0.324  45.443   2.181   2.366   2.798   0.000   0.000   0.000
   4_adp:  0.324  45.443   2.181   2.366   2.798   0.000   0.000   0.000
   4_occ:  0.324  45.443   2.181   2.366   2.798   0.000   0.000   0.000
   5_bss:  0.324  45.443   2.181   2.366   2.798   0.000   0.000   0.000
   5_xyz:  0.324  45.443   2.181   2.366   2.798   0.000   0.000   0.000
   5_adp:  0.324  45.443   2.181   2.366   2.798   0.000   0.000   0.000
   5_occ:  0.324  45.443   2.181   2.366   2.798   0.000   0.000   0.000
   5_bss:  0.324  47.891  -0.267  -0.082   0.350   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  54.344 0.4660  0.5421    63599.087
   1_bss:  54.949 0.4552  0.6675    61115.625
   1_xyz:  45.148 0.5779  0.8386    44653.165
   1_adp:  40.936 0.6300  0.9367    38698.145
   1_occ:  40.940 0.6300  0.9364    38742.614
   2_bss:  40.537 0.6347  0.8348    38190.814
   2_xyz:  28.000 0.7787  0.9879    19804.363
   2_adp:  24.313 0.8188  1.0210    15827.640
   2_occ:  24.308 0.8188  1.0207    15811.919
   3_bss:  24.146 0.8203  0.9523    15626.495
   3_xyz:  17.711 0.8826  0.9864     8925.887
   3_adp:  16.295 0.8955  0.9891     7913.838
   3_occ:  16.278 0.8957  0.9890     7903.979
   4_bss:  16.302 0.8955  0.9731     7942.106
   4_xyz:  15.415 0.9034  0.9768     7291.130
   4_adp:  15.153 0.9059  0.9771     7169.659
   4_occ:  15.141 0.9060  0.9771     7165.632
   5_bss:  15.141 0.9060  0.9771     7165.632
   5_xyz:  14.521 0.9108  0.9780     6660.357
   5_adp:  14.399 0.9119  0.9759     6596.592
   5_occ:  14.396 0.9119  0.9758     6598.428
   5_bss:  14.396 0.9119  0.9758     6598.428
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.091   5.3622e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.091   5.3622e+01
   1_xyz:   1.652  0.013  0.106 18.030  0.007  4.111   1.3447e-01
   1_adp:   1.652  0.013  0.106 18.030  0.007  4.111   1.3447e-01
   1_occ:   1.652  0.013  0.106 18.030  0.007  4.111   1.3447e-01
   2_bss:   1.652  0.013  0.106 18.030  0.007  4.111   1.3447e-01
   2_xyz:   1.119  0.009  0.078 15.946  0.005  4.117   7.6604e-02
   2_adp:   1.119  0.009  0.078 15.946  0.005  4.117   7.6604e-02
   2_occ:   1.119  0.009  0.078 15.946  0.005  4.117   7.6604e-02
   3_bss:   1.119  0.009  0.078 15.946  0.005  4.117   7.6604e-02
   3_xyz:   1.116  0.008  0.084 15.719  0.004  4.128   7.0601e-02
   3_adp:   1.116  0.008  0.084 15.719  0.004  4.128   7.0601e-02
   3_occ:   1.116  0.008  0.084 15.719  0.004  4.128   7.0601e-02
   4_bss:   1.116  0.008  0.084 15.719  0.004  4.128   7.0601e-02
   4_xyz:   0.920  0.006  0.071 15.419  0.003  4.113   5.4155e-02
   4_adp:   0.920  0.006  0.071 15.419  0.003  4.113   5.4155e-02
   4_occ:   0.920  0.006  0.071 15.419  0.003  4.113   5.4155e-02
   5_bss:   0.920  0.006  0.071 15.419  0.003  4.113   5.4155e-02
   5_xyz:   1.111  0.008  0.088 15.596  0.004  4.115   7.1240e-02
   5_adp:   1.111  0.008  0.088 15.596  0.004  4.115   7.1240e-02
   5_occ:   1.111  0.008  0.088 15.596  0.004  4.115   7.1240e-02
   5_bss:   1.111  0.008  0.088 15.596  0.004  4.115   7.1240e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.9515e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.9515e+00
   1_xyz:  14.361  0.160  0.471 84.746  0.054  2.174   9.6677e-02
   1_adp:  14.361  0.160  0.471 84.746  0.054  2.174   9.6677e-02
   1_occ:  14.361  0.160  0.471 84.746  0.054  2.174   9.6677e-02
   2_bss:  14.361  0.160  0.471 84.746  0.054  2.174   9.6677e-02
   2_xyz:   6.969  0.095  0.264 83.501  0.034  2.292   6.5967e-02
   2_adp:   6.969  0.095  0.264 83.501  0.034  2.292   6.5967e-02
   2_occ:   6.969  0.095  0.264 83.501  0.034  2.292   6.5967e-02
   3_bss:   6.969  0.095  0.264 83.501  0.034  2.292   6.5967e-02
   3_xyz:   8.669  0.050  0.539 81.790  0.032  2.345   5.8431e-02
   3_adp:   8.669  0.050  0.539 81.790  0.032  2.345   5.8431e-02
   3_occ:   8.669  0.050  0.539 81.790  0.032  2.345   5.8431e-02
   4_bss:   8.669  0.050  0.539 81.790  0.032  2.345   5.8431e-02
   4_xyz:   6.957  0.046  0.408 82.480  0.028  2.369   3.3586e-02
   4_adp:   6.957  0.046  0.408 82.480  0.028  2.369   3.3586e-02
   4_occ:   6.957  0.046  0.408 82.480  0.028  2.369   3.3586e-02
   5_bss:   6.957  0.046  0.408 82.480  0.028  2.369   3.3586e-02
   5_xyz:   7.160  0.046  0.649 82.817  0.030  2.305   5.1825e-02
   5_adp:   7.160  0.046  0.649 82.817  0.030  2.305   5.1825e-02
   5_occ:   7.160  0.046  0.649 82.817  0.030  2.305   5.1825e-02
   5_bss:   7.160  0.046  0.649 82.817  0.030  2.305   5.1825e-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:  78.33   0.00  11.85  68.29   0.00   9.11  78.33   0.00  26.79
   1_occ:  78.33   0.00  11.85  68.29   0.00   9.11  78.33   0.00  26.79
   2_bss:  78.33   0.00  11.85  68.29   0.00   9.11  78.33   0.00  26.79
   2_xyz:  78.33   0.00  11.85  68.29   0.00   9.11  78.33   0.00  26.79
   2_adp:  78.41   0.00  12.27  69.86   0.00   8.56  78.41   1.68  32.47
   2_occ:  78.41   0.00  12.27  69.86   0.00   8.56  78.41   1.68  32.47
   3_bss:  78.41   0.00  12.27  69.86   0.00   8.56  78.41   1.68  32.47
   3_xyz:  78.41   0.00  12.27  69.86   0.00   8.56  78.41   1.68  32.47
   3_adp:  86.10   0.00  12.94  86.10   0.00   8.51  77.73   1.75  37.06
   3_occ:  86.10   0.00  12.94  86.10   0.00   8.51  77.73   1.75  37.06
   4_bss:  86.10   0.00  12.94  86.10   0.00   8.51  77.73   1.75  37.06
   4_xyz:  86.10   0.00  12.94  86.10   0.00   8.51  77.73   1.75  37.06
   4_adp:  90.76   0.00  12.80  90.76   0.00   8.48  76.78   1.63  36.35
   4_occ:  90.76   0.00  12.80  90.76   0.00   8.48  76.78   1.63  36.35
   5_bss:  90.76   0.00  12.80  90.76   0.00   8.48  76.78   1.63  36.35
   5_xyz:  90.76   0.00  12.80  90.76   0.00   8.48  76.78   1.63  36.35
   5_adp:  91.42   0.00  12.58  91.42   0.00   8.35  75.43   1.58  35.60
   5_occ:  91.42   0.00  12.58  91.42   0.00   8.35  75.43   1.58  35.60
   5_bss:  93.87   2.45  15.03  93.87   2.45  10.80  77.88   4.03  38.04
------------------------------------------------------------------------
 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:    1.222    0.023    0.410
   1_adp:    1.222    0.023    0.410
   1_occ:    1.222    0.023    0.410
   2_bss:    1.222    0.023    0.410
   2_xyz:    1.501    0.049    0.574
   2_adp:    1.501    0.049    0.574
   2_occ:    1.501    0.049    0.574
   3_bss:    1.501    0.049    0.574
   3_xyz:    1.560    0.073    0.632
   3_adp:    1.560    0.073    0.632
   3_occ:    1.560    0.073    0.632
   4_bss:    1.560    0.073    0.632
   4_xyz:    1.629    0.053    0.646
   4_adp:    1.629    0.053    0.646
   4_occ:    1.629    0.053    0.646
   5_bss:    1.629    0.053    0.646
   5_xyz:    1.653    0.023    0.661
   5_adp:    1.653    0.023    0.661
   5_occ:    1.653    0.023    0.661
   5_bss:    1.653    0.023    0.661
------------------------------------------------------------------------

CPU time actual refinement: 361.71


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_914/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_914/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_914/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_914/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_914/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 361.55 
  Macro-tasks:
    bulk solvent and scale       = 43.61  
    individual site refinement   = 154.67 
    weights calculation          = 33.03  
    collect and process          = 6.70   
    model show statistics        = 0.15   
    TOTAL for macro-tasks        = 238.16 
  Micro-tasks:
    mask                            = 1.88   
    f_calc                          = 114.03 
    alpha_beta                      = 8.30   
    target                          = 1.19   
    gradients_wrt_atomic_parameters = 124.99 
    fmodel                         = 7.65   
    r_factors                      = 0.24   
    phase_errors                   = 10.74  
    foms                           = 0.23   
    TOTAL for micro-tasks          = 269.25 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 5.013 micro seconds
Total CPU time: 6.26 minutes
from_scatterers_fft:    653 calls, 113.63 s
gradients_fft:          597 calls, 110.82 s

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

# Date 2008-01-16 Time 02:44:28 PST -0800 (1200480268.69 s)
Start R-work = 0.4591, R-free = 0.4561 (no bulk solvent and anisotropic scale)
Final R-work = 0.1286, R-free = 0.1757 (no bulk solvent and anisotropic scale)

Start R-work = 0.4506, R-free = 0.4441
Final R-work = 0.1119, R-free = 0.1584