# Date 2008-01-16 Time 01:52:34 PST -0800 (1200477154.18 s)
#phil __OFF__

Command line arguments: "../608.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 = 11815
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 608

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

              phenix.refine: Macromolecular Structure Refinement

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

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

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

Processing inputs. This may take a minute or two.

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

  refinement.modify_start_model.sites.shake = 0.5

  refinement.main.number_of_macro_cycles = 5

Working crystal symmetry after inspecting all inputs:
  Unit cell: (70.25, 45.7567, 85.5261, 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: (70.25, 45.7567, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9529 1.95311
Completeness in resolution range: 0.951615
Completeness with d_max=infinity: 0.948804

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.9529
                             d_min =   1.9531

Miller array info: /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns:TEST
Observation type: None
Type of data: int, size=19589
Type of sigmas: None
Number of Miller indices: 19589
Anomalous flag: False
Unit cell: (70.25, 45.7567, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.9529 1.95311
Completeness in resolution range: 0.951615
Completeness with d_max=infinity: 0.948804

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.9533 -  4.1801 [2163/2189]  1947   216  10.0%
  bin  2:  4.1801 -  3.3299 [2070/2090]  1864   206  10.0%
  bin  3:  3.3299 -  2.9125 [2062/2081]  1853   209  10.1%
  bin  4:  2.9125 -  2.6478 [2024/2054]  1821   203  10.0%
  bin  5:  2.6478 -  2.4589 [2021/2040]  1826   195   9.6%
  bin  6:  2.4589 -  2.3145 [2010/2035]  1798   212  10.5%
  bin  7:  2.3145 -  2.1990 [2003/2031]  1807   196   9.8%
  bin  8:  2.1990 -  2.1035 [1993/2029]  1796   197   9.9%
  bin  9:  2.1035 -  2.0228 [1968/2010]  1771   197  10.0%
  bin 10:  2.0228 -  1.9531 [1275/2026]  1147   128  10.0%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_608/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:
        1.68 -     2.32: 33
        2.32 -     2.97: 1818
        2.97 -     3.61: 4652
        3.61 -     4.26: 9321
        4.26 -     4.90: 12972
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " OG1 THR A  29 " - " O   HOH Z 245 "  1.681 3.040 x,y+1,z
  " O   HOH Z 204 " - " O   HOH Z 296 "  1.731 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z  61 " - " O   HOH Z 246 "  1.742 3.040 x,y+1,z
  " O   HOH Z  70 " - " O   HOH Z 302 "  1.766 3.040 -x+1/2,-y+1,z+1/2
  " O   HOH Z 302 " - " O   HOH Z  70 "  1.766 3.040 -x+1/2,-y+1,z-1/2
  ... (remaining 28791 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_608/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_608/model_refine_001.geo

CPU time processing inputs: 9.13


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

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

#phil __ON__
refinement {
  crystal_symmetry {
    unit_cell = 70.25 45.75675 85.5261 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: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4932   r_free= 0.4914   ksol= 0.00   Bsol= 0.00   scale= 0.790    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.83 A                  |
| x-ray target function (ml) for work reflections: 6.298392                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9533 -  4.6627 0.99   1402  157 0.4302 0.4372      6.6396      6.7193|
|  2:  4.6627 -  3.7197 0.99   1348  150 0.4357 0.3964      6.8484      6.7677|
|  3:  3.7197 -  3.2550 0.99   1330  143 0.4578 0.4380      6.7085       6.739|
|  4:  3.2550 -  2.9599 0.99   1321  152 0.4853 0.4667      6.5653      6.4912|
|  5:  2.9599 -  2.7492 0.99   1317  147 0.5148 0.5538      6.3792      6.4176|
|  6:  2.7492 -  2.5880 0.99   1299  138 0.5157 0.5539      6.2903      6.2203|
|  7:  2.5880 -  2.4589 0.99   1294  142 0.5240 0.4924      6.2605       6.217|
|  8:  2.4589 -  2.3523 0.98   1271  145 0.5410 0.4997      6.1807      6.1665|
|  9:  2.3523 -  2.2621 0.98   1282  151 0.5202 0.5506       6.127      6.2082|
| 10:  2.2621 -  2.1843 1.00   1306  148 0.5216 0.5337      6.1098      6.0778|
| 11:  2.1843 -  2.1162 0.98   1284  132 0.5119 0.4933      6.0358      6.0435|
| 12:  2.1162 -  2.0558 0.98   1259  142 0.5091 0.5756      5.9704       6.028|
| 13:  2.0558 -  2.0018 0.99   1284  138 0.5476 0.5258      5.8839      5.8111|
| 14:  2.0018 -  1.9531 0.48    633   74 0.5628 0.4762      5.8773      5.8244|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9533 -  4.6627  1402   157  0.59  43.92   0.78     0.65     107870.75|
|  2:  4.6627 -  3.7197  1348   150  0.65  39.77   0.85     0.74     132083.90|
|  3:  3.7197 -  3.2550  1330   143  0.55  47.85   0.85     0.70     132013.47|
|  4:  3.2550 -  2.9599  1321   152  0.46  55.19   0.80     0.56     115295.67|
|  5:  2.9599 -  2.7492  1317   147  0.34  64.44   0.74     0.43      93818.17|
|  6:  2.7492 -  2.5880  1299   138  0.30  67.25   0.72     0.36      82681.37|
|  7:  2.5880 -  2.4589  1294   142  0.27  70.12   0.75     0.31      73751.54|
|  8:  2.4589 -  2.3523  1271   145  0.25  71.60   0.72     0.30      67454.87|
|  9:  2.3523 -  2.2621  1282   151  0.27  70.03   0.73     0.31      59403.82|
| 10:  2.2621 -  2.1843  1306   148  0.29  68.21   0.77     0.36      52512.70|
| 11:  2.1843 -  2.1162  1284   132  0.27  69.63   0.78     0.35      51160.32|
| 12:  2.1162 -  2.0558  1259   142  0.25  71.78   0.79     0.32      47800.20|
| 13:  2.0558 -  2.0018  1284   138  0.22  73.67   0.73     0.30      41575.70|
| 14:  2.0018 -  1.9531   633    74  0.31  66.82   0.72     0.35      30376.15|
|alpha:            min =        0.30 max =            0.74 mean =         0.44|
|beta:             min =    30376.15 max =       132083.90 mean =     80120.11|
|figures of merit: min =        0.00 max =            1.00 mean =         0.36|
|phase err.(work): min =        0.00 max =           89.99 mean =        62.46|
|phase err.(test): min =        0.00 max =           89.95 mean =        62.66|
|-----------------------------------------------------------------------------|

============================== 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 = 21.456295             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 82.566   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.964406              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 81.515   (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:        5 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.566 -  1.937:       35 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.937 -  2.307:      176 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.307 -  2.677:      720 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.677 -  3.048:     1547 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.048 -  3.418:     2686 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.418 -  3.789:     4004 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.789 -  4.159:     5161 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.159 -  4.530:     6640 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.530 -  4.900:     7864 |
|-----------------------------------------------------------------------------|
|-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 |       53.002 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.088    4.900  1.196 |       2.424 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.473)------------------------------------------|
|    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 = 11.473)------------------------------------------|
|    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: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4978   r_free= 0.4930   ksol= 0.00   Bsol= 0.00   scale= 0.760    |
|                                                                             |
| 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:   0.82 A                  |
| x-ray target function (ml) for work reflections: 6.299311                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4843   r_free= 0.4790   ksol= 0.41   Bsol= 20.00   scale= 0.966   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.95,9.45,7.03,0.00,0.00,0.00); trace/3= 7.48                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.82 A                  |
| x-ray target function (ml) for work reflections: 6.292896                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 17.431051             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 83.328   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.799889              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.728   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4843      final r-factor (work) = 0.4231          |
| start r-factor (free) = 0.4790      final r-factor (free) = 0.4539          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 107.8630 = 17.43 * 0.50 * 6.2946 + 1.00 * 53.0024                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 54.5597 = 17.43 * 0.50 * 6.2435 + 1.00 * 0.1443                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4231      final r-factor (work) = 0.3864          |
| start r-factor (free) = 0.4539      final r-factor (free) = 0.4473          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.2520 = 1.80 * 1.00 * 6.2435 + 1.00 * 0.0144                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.1658 = 1.80 * 1.00 * 6.1926 + 1.00 * 0.0198                              |
|-----------------------------------------------------------------------------|
| number of iterations = 15      |    number of function evaluations = 20     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.473)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    64.44   13.42    None  None   None       |
|    all(noH): 2823   0      0.00    64.44   13.42    None  None   None       |
|    Sol.    : 438    0      0.00    64.44   20.56    None  None   None       |
|    Mac.    : 2385   0      0.00    61.87   12.11    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 -   6.444:  788   |   5:    32.219 -  38.662:   95        |
|      1:     6.444 -  12.887:  781   |   6:    38.662 -  45.106:   36        |
|      2:    12.887 -  19.331:  553   |   7:    45.106 -  51.550:   16        |
|      3:    19.331 -  25.775:  340   |   8:    51.550 -  57.993:    3        |
|      4:    25.775 -  32.219:  206   |   9:    57.993 -  64.437:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3864 r_free = 0.4473             target_work(ml) = 6.185         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3858 r_free = 0.4476             target_work(ml) = 6.184         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3858   r_free= 0.4476   ksol= 0.41   Bsol= 20.00   scale= 1.074   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (5.95,9.45,7.03,0.00,0.00,0.00); trace/3= 7.48                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.184458                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3848   r_free= 0.4439   ksol= 0.37   Bsol= 37.79   scale= 0.991   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.02,5.67,4.12,0.00,0.00,0.00); trace/3= 4.27                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.185183                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 8.925984              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.438  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.923559              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 138.632  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3848      final r-factor (work) = 0.3410          |
| start r-factor (free) = 0.4439      final r-factor (free) = 0.4085          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.7648 = 8.93 * 0.50 * 6.1888 + 1.00 * 0.1443                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.4695 = 8.93 * 0.50 * 6.1357 + 1.00 * 0.0858                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3410      final r-factor (work) = 0.3257          |
| start r-factor (free) = 0.4085      final r-factor (free) = 0.4003          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6919 = 0.92 * 1.00 * 6.1357 + 1.00 * 0.0252                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6301 = 0.92 * 1.00 * 6.0805 + 1.00 * 0.0143                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.473)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    85.52   13.96    None  None   None       |
|    all(noH): 2823   0      0.00    85.52   13.96    None  None   None       |
|    Sol.    : 438    0      0.00    85.52   24.74    None  None   None       |
|    Mac.    : 2385   0      0.00    79.92   11.98    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 -   8.552: 1110   |   5:    42.758 -  51.310:   46        |
|      1:     8.552 -  17.103:  828   |   6:    51.310 -  59.862:   13        |
|      2:    17.103 -  25.655:  475   |   7:    59.862 -  68.413:    8        |
|      3:    25.655 -  34.207:  234   |   8:    68.413 -  76.965:    0        |
|      4:    34.207 -  42.758:  106   |   9:    76.965 -  85.517:    3        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3257 r_free = 0.4003             target_work(ml) = 6.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3256 r_free = 0.4002             target_work(ml) = 6.070         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3256   r_free= 0.4002   ksol= 0.37   Bsol= 37.79   scale= 1.033   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.02,5.67,4.12,0.00,0.00,0.00); trace/3= 4.27                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.069918                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3262   r_free= 0.3995   ksol= 0.37   Bsol= 56.71   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.73,4.08,3.60,0.00,0.00,0.00); trace/3= 3.47                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.54 A                  |
| x-ray target function (ml) for work reflections: 6.071412                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.161606              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.901  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.945254              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 155.579  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3262      final r-factor (work) = 0.2665          |
| start r-factor (free) = 0.3995      final r-factor (free) = 0.3402          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.9400 = 9.16 * 0.50 * 6.0807 + 1.00 * 0.0855                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 27.5628 = 9.16 * 0.50 * 5.9951 + 1.00 * 0.1003                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2665      final r-factor (work) = 0.2456          |
| start r-factor (free) = 0.3402      final r-factor (free) = 0.3281          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6812 = 0.95 * 1.00 * 5.9951 + 1.00 * 0.0142                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5710 = 0.95 * 1.00 * 5.8773 + 1.00 * 0.0155                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.473)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    93.87   14.59    None  None   None       |
|    all(noH): 2823   0      0.00    93.87   14.59    None  None   None       |
|    Sol.    : 438    0      0.00    93.87   32.89    None  None   None       |
|    Mac.    : 2385   0      0.00    85.08   11.23    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 -   9.387: 1315   |   5:    46.936 -  56.324:   57        |
|      1:     9.387 -  18.775:  741   |   6:    56.324 -  65.711:   26        |
|      2:    18.775 -  28.162:  368   |   7:    65.711 -  75.098:   11        |
|      3:    28.162 -  37.549:  175   |   8:    75.098 -  84.485:    1        |
|      4:    37.549 -  46.936:  125   |   9:    84.485 -  93.873:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2456 r_free = 0.3281             target_work(ml) = 5.856         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2451 r_free = 0.3280             target_work(ml) = 5.855         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2451   r_free= 0.3280   ksol= 0.37   Bsol= 56.71   scale= 1.046   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.73,4.08,3.60,0.00,0.00,0.00); trace/3= 3.47                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.855400                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2446   r_free= 0.3267   ksol= 0.35   Bsol= 50.28   scale= 1.018   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.98,2.42,2.79,0.00,0.00,0.00); trace/3= 2.40                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.852563                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 5.290316              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 97.659   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.377149              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 148.708  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2446      final r-factor (work) = 0.2014          |
| start r-factor (free) = 0.3267      final r-factor (free) = 0.2672          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.6425 = 5.29 * 0.50 * 5.8757 + 1.00 * 0.1003                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 15.3456 = 5.29 * 0.50 * 5.7766 + 1.00 * 0.0655                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2014      final r-factor (work) = 0.1837          |
| start r-factor (free) = 0.2672      final r-factor (free) = 0.2404          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1939 = 0.38 * 1.00 * 5.7766 + 1.00 * 0.0153                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1333 = 0.38 * 1.00 * 5.6217 + 1.00 * 0.0131                               |
|-----------------------------------------------------------------------------|
| number of iterations = 23      |    number of function evaluations = 25     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.473)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.54   14.09    None  None   None       |
|    all(noH): 2823   0      0.00    89.54   14.09    None  None   None       |
|    Sol.    : 438    0      1.99    89.54   36.83    None  None   None       |
|    Mac.    : 2385   0      0.00    85.64   9.92     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 -   8.955: 1459   |   5:    44.772 -  53.727:   99        |
|      1:     8.955 -  17.909:  703   |   6:    53.727 -  62.681:   52        |
|      2:    17.909 -  26.863:  218   |   7:    62.681 -  71.636:   12        |
|      3:    26.863 -  35.818:  157   |   8:    71.636 -  80.590:    1        |
|      4:    35.818 -  44.772:  117   |   9:    80.590 -  89.544:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1837 r_free = 0.2404             target_work(ml) = 5.573         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1832 r_free = 0.2391             target_work(ml) = 5.571         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1832   r_free= 0.2391   ksol= 0.35   Bsol= 50.28   scale= 1.032   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.98,2.42,2.79,0.00,0.00,0.00); trace/3= 2.40                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.570956                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1833   r_free= 0.2383   ksol= 0.34   Bsol= 50.28   scale= 1.011   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.33,1.28,2.34,0.00,0.00,0.00); trace/3= 1.65                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.25 A                  |
| x-ray target function (ml) for work reflections: 5.569780                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 3.136221              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 110.560  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.288706              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 92.362   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1833      final r-factor (work) = 0.1472          |
| start r-factor (free) = 0.2383      final r-factor (free) = 0.1990          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.8816 = 3.14 * 0.50 * 5.6221 + 1.00 * 0.0655                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 8.6487 = 3.14 * 0.50 * 5.4772 + 1.00 * 0.0599                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1472      final r-factor (work) = 0.1394          |
| start r-factor (free) = 0.1990      final r-factor (free) = 0.1910          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5926 = 0.29 * 1.00 * 5.4772 + 1.00 * 0.0113                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.5639 = 0.29 * 1.00 * 5.3589 + 1.00 * 0.0168                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.473)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    89.29   13.92    None  None   None       |
|    all(noH): 2823   0      0.00    89.29   13.92    None  None   None       |
|    Sol.    : 438    0      3.67    89.29   38.07    None  None   None       |
|    Mac.    : 2385   0      0.00    85.89   9.48     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 -   8.929: 1533   |   5:    44.643 -  53.572:  106        |
|      1:     8.929 -  17.857:  680   |   6:    53.572 -  62.500:   62        |
|      2:    17.857 -  26.786:  190   |   7:    62.500 -  71.429:   19        |
|      3:    26.786 -  35.714:  123   |   8:    71.429 -  80.357:    8        |
|      4:    35.714 -  44.643:   97   |   9:    80.357 -  89.286:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1394 r_free = 0.1910             target_work(ml) = 5.334         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1392 r_free = 0.1905             target_work(ml) = 5.333         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1392   r_free= 0.1905   ksol= 0.34   Bsol= 50.28   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.33,1.28,2.34,0.00,0.00,0.00); trace/3= 1.65                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.333157                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9533 -  4.6627 0.99   1402  157 0.1113 0.1527      5.5085      5.7223|
|  2:  4.6627 -  3.7197 0.99   1348  150 0.1036 0.1433      5.6215      5.8755|
|  3:  3.7197 -  3.2550 0.99   1330  143 0.1356 0.1665      5.6801      5.9472|
|  4:  3.2550 -  2.9599 0.99   1321  152 0.1565 0.2091      5.6712      5.8211|
|  5:  2.9599 -  2.7492 0.99   1317  147 0.1666 0.2273      5.5317      5.7786|
|  6:  2.7492 -  2.5880 0.99   1299  138 0.1485 0.2090      5.3916      5.5593|
|  7:  2.5880 -  2.4589 0.99   1294  142 0.1534 0.1969      5.3402      5.5254|
|  8:  2.4589 -  2.3523 0.98   1271  145 0.1529 0.2334      5.2839      5.5848|
|  9:  2.3523 -  2.2621 0.98   1282  151 0.1510 0.2053      5.2389      5.4751|
| 10:  2.2621 -  2.1843 1.00   1306  148 0.1409 0.2223       5.156      5.4265|
| 11:  2.1843 -  2.1162 0.98   1284  132 0.1398 0.2024      5.1189      5.3471|
| 12:  2.1162 -  2.0558 0.98   1259  142 0.1406 0.2040      5.0587      5.3688|
| 13:  2.0558 -  2.0018 0.99   1284  138 0.1455 0.2000      4.9402      5.1466|
| 14:  2.0018 -  1.9531 0.48    633   74 0.1251 0.1610      4.7818      4.9812|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9533 -  4.6627  1402   157  0.92  11.77   0.98     0.96      10296.59|
|  2:  4.6627 -  3.7197  1348   150  0.93  10.79   1.03     1.01      13387.48|
|  3:  3.7197 -  3.2550  1330   143  0.90  15.37   1.05     1.03      15879.27|
|  4:  3.2550 -  2.9599  1321   152  0.88  18.14   1.03     0.99      16206.89|
|  5:  2.9599 -  2.7492  1317   147  0.86  20.17   1.00     0.96      12622.37|
|  6:  2.7492 -  2.5880  1299   138  0.86  20.16   1.00     0.95      10266.56|
|  7:  2.5880 -  2.4589  1294   142  0.86  20.23   1.01     0.98       9251.22|
|  8:  2.4589 -  2.3523  1271   145  0.86  20.20   1.00     0.97       8305.18|
|  9:  2.3523 -  2.2621  1282   151  0.87  20.10   1.02     0.97       7781.92|
| 10:  2.2621 -  2.1843  1306   148  0.86  20.37   1.01     0.96       6727.12|
| 11:  2.1843 -  2.1162  1284   132  0.87  19.70   1.03     0.97       6295.18|
| 12:  2.1162 -  2.0558  1259   142  0.87  19.71   1.03     1.02       5815.43|
| 13:  2.0558 -  2.0018  1284   138  0.88  19.10   1.02     1.00       4226.34|
| 14:  2.0018 -  1.9531   633    74  0.91  15.64   1.01     0.98       2925.31|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     2925.31 max =        16206.89 mean =      9582.69|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           89.99 mean =        17.98|
|phase err.(test): min =        0.00 max =           89.38 mean =        17.10|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1392   r_free= 0.1902   ksol= 0.32   Bsol= 41.12   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.24,-0.53,0.77,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.331235                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.95 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1392   r_free= 0.1902   ksol= 0.32   Bsol= 41.12   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.24,-0.53,0.77,0.00,0.00,0.00); trace/3= 0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.331235                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.9533 -  4.6627 0.99   1402  157 0.1102 0.1467      5.4851      5.6882|
|  2:  4.6627 -  3.7197 0.99   1348  150 0.1039 0.1425      5.6131      5.8693|
|  3:  3.7197 -  3.2550 0.99   1330  143 0.1355 0.1655      5.6761       5.943|
|  4:  3.2550 -  2.9599 0.99   1321  152 0.1562 0.2095      5.6695      5.8211|
|  5:  2.9599 -  2.7492 0.99   1317  147 0.1667 0.2274      5.5325      5.7788|
|  6:  2.7492 -  2.5880 0.99   1299  138 0.1486 0.2096      5.3939      5.5615|
|  7:  2.5880 -  2.4589 0.99   1294  142 0.1536 0.1972      5.3431      5.5287|
|  8:  2.4589 -  2.3523 0.98   1271  145 0.1530 0.2347      5.2856       5.589|
|  9:  2.3523 -  2.2621 0.98   1282  151 0.1508 0.2044      5.2403      5.4733|
| 10:  2.2621 -  2.1843 1.00   1306  148 0.1408 0.2244      5.1577      5.4329|
| 11:  2.1843 -  2.1162 0.98   1284  132 0.1397 0.2028      5.1206      5.3502|
| 12:  2.1162 -  2.0558 0.98   1259  142 0.1405 0.2043      5.0598      5.3699|
| 13:  2.0558 -  2.0018 0.99   1284  138 0.1456 0.1991      4.9408      5.1437|
| 14:  2.0018 -  1.9531 0.48    633   74 0.1248 0.1617      4.7809      4.9833|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.9533 -  4.6627  1402   157  0.92  11.20   0.98     0.96       9451.22|
|  2:  4.6627 -  3.7197  1348   150  0.94  10.49   1.03     1.01      12827.50|
|  3:  3.7197 -  3.2550  1330   143  0.90  15.23   1.05     1.03      15699.22|
|  4:  3.2550 -  2.9599  1321   152  0.88  18.08   1.02     0.99      16103.59|
|  5:  2.9599 -  2.7492  1317   147  0.86  20.15   1.00     0.96      12612.05|
|  6:  2.7492 -  2.5880  1299   138  0.86  20.19   0.99     0.94      10312.52|
|  7:  2.5880 -  2.4589  1294   142  0.86  20.28   1.01     0.97       9320.14|
|  8:  2.4589 -  2.3523  1271   145  0.86  20.31   0.99     0.96       8373.05|
|  9:  2.3523 -  2.2621  1282   151  0.87  20.16   1.01     0.96       7827.18|
| 10:  2.2621 -  2.1843  1306   148  0.86  20.44   1.00     0.94       6770.54|
| 11:  2.1843 -  2.1162  1284   132  0.87  19.77   1.02     0.96       6335.37|
| 12:  2.1162 -  2.0558  1259   142  0.87  19.76   1.02     1.01       5838.17|
| 13:  2.0558 -  2.0018  1284   138  0.88  19.11   1.01     0.99       4230.45|
| 14:  2.0018 -  1.9531   633    74  0.91  15.60   0.99     0.97       2916.84|
|alpha:            min =        0.94 max =            1.03 mean =         0.97|
|beta:             min =     2916.84 max =        16103.59 mean =      9474.94|
|figures of merit: min =        0.00 max =            1.00 mean =         0.88|
|phase err.(work): min =        0.00 max =           90.00 mean =        17.93|
|phase err.(test): min =        0.00 max =           89.36 mean =        17.05|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.473)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      1.42    90.71   15.34    None  None   None       |
|    all(noH): 2823   0      1.42    90.71   15.34    None  None   None       |
|    Sol.    : 438    0      5.09    90.71   39.50    None  None   None       |
|    Mac.    : 2385   0      1.42    87.32   10.91    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     1.422 -  10.351: 1533   |   5:    46.065 -  54.994:  106        |
|      1:    10.351 -  19.279:  680   |   6:    54.994 -  63.922:   62        |
|      2:    19.279 -  28.208:  190   |   7:    63.922 -  72.851:   19        |
|      3:    28.208 -  37.137:  123   |   8:    72.851 -  81.780:    8        |
|      4:    37.137 -  46.065:   97   |   9:    81.780 -  90.708:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 340         
Filter by distance & map next to the model:
   mapped sites are within: 0.387 - 5.756
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 334 from: 340
   mapped sites are within: 0.751 - 5.756

peak=    9.587 closest distance to " CB  VAL A 296 " =    1.444
peak=    8.200 closest distance to " O   HOH Z 390 " =    1.285
peak=    7.863 closest distance to " CG2 VAL A 230 " =    1.377
peak=    6.877 closest distance to " O   HOH Z 268 " =    1.230
peak=    6.766 closest distance to " O   HOH Z 130 " =    1.984
peak=    6.732 closest distance to " O   HOH Z  15 " =    1.148
peak=    6.542 closest distance to " O   HOH Z 415 " =    1.401
peak=    6.274 closest distance to " CG  ARG A 138 " =    1.294
peak=    6.184 closest distance to " CD2 LEU A   5 " =    1.539
peak=    6.126 closest distance to " O   HOH Z 387 " =    1.616
peak=    6.041 closest distance to " CD1AILE A 234 " =    1.087
peak=    5.878 closest distance to " O   HOH Z 289 " =    1.511
peak=    5.687 closest distance to " O   HOH Z 424 " =    1.895
peak=    5.674 closest distance to " O   HOH Z  65 " =    1.745
peak=    5.573 closest distance to " O   HOH Z 124 " =    1.873
peak=    5.418 closest distance to " O   HOH Z   7 " =    1.979
peak=    5.379 closest distance to " NE2 GLN A  11 " =    1.344
peak=    5.337 closest distance to " O   HOH Z 350 " =    1.419
peak=    5.307 closest distance to " O   HOH Z   9 " =    1.719
peak=    5.229 closest distance to " O   HOH Z  46 " =    1.273
peak=    5.189 closest distance to " NH2 ARG A  56 " =    1.968
peak=    5.178 closest distance to " O   HOH Z 222 " =    1.491
peak=    5.164 closest distance to " O   PRO A 198 " =    1.453
peak=    5.162 closest distance to " O   HOH Z 375 " =    1.311
peak=    5.119 closest distance to " O   HOH Z 403 " =    1.693
peak=    5.081 closest distance to " NH1 ARG A 138 " =    1.001
peak=    4.944 closest distance to " O   HOH Z  27 " =    1.191
peak=    4.934 closest distance to " O   HOH Z 363 " =    1.242
peak=    4.877 closest distance to " O   HOH Z 127 " =    1.205
peak=    4.867 closest distance to " O   HOH Z 142 " =    2.095
peak=    4.843 closest distance to " CB  PRO A  54 " =    1.124
peak=    4.816 closest distance to " O   HOH Z  54 " =    1.308
peak=    4.812 closest distance to " O   HOH Z 358 " =    1.376
peak=    4.747 closest distance to " O   HOH Z 112 " =    1.436
peak=    4.735 closest distance to " CB  ARG A 275 " =    1.162
peak=    4.730 closest distance to " CB  SER A   3 " =    1.410
peak=    4.727 closest distance to " O   HOH Z 410 " =    1.471
peak=    4.723 closest distance to " O   HOH Z  28 " =    1.744
peak=    4.687 closest distance to " O   HOH Z 105 " =    1.219
peak=    4.653 closest distance to " O   HOH Z 214 " =    1.507
peak=    4.628 closest distance to " O   HOH Z 400 " =    0.872
peak=    4.610 closest distance to " NZ BLYS A 290 " =    1.061
peak=    4.540 closest distance to " NE1 TRP A 266 " =    1.889
peak=    4.519 closest distance to " O   HOH Z 239 " =    1.696
peak=    4.515 closest distance to " CB  VAL A 230 " =    1.242
peak=    4.475 closest distance to " O   HOH Z 250 " =    2.204
peak=    4.463 closest distance to " O   HOH Z 139 " =    1.844
peak=    4.458 closest distance to " O   HOH Z 417 " =    1.603
peak=    4.421 closest distance to " OE1 GLU A   2 " =    1.945
peak=    4.420 closest distance to " O   HOH Z 418 " =    1.376
peak=    4.404 closest distance to " O   HOH Z 123 " =    1.192
peak=    4.390 closest distance to " O   HOH Z 426 " =    1.163
peak=    4.346 closest distance to " O   HOH Z  69 " =    2.321
peak=    4.310 closest distance to " O   HOH Z 381 " =    1.059
peak=    4.275 closest distance to " O   HOH Z 215 " =    1.400
peak=    4.272 closest distance to " O   HOH Z 416 " =    1.436
peak=    4.268 closest distance to " O   HOH Z 263 " =    1.617
peak=    4.256 closest distance to " O   HOH Z  63 " =    1.791
peak=    4.251 closest distance to " OG ASER A 258 " =    3.052
peak=    4.242 closest distance to " O   HOH Z 120 " =    0.992
peak=    4.241 closest distance to " O   HOH Z 402 " =    1.590
peak=    4.237 closest distance to " CE  MET A  93 " =    1.453
peak=    4.224 closest distance to " O   HOH Z 293 " =    1.463
peak=    4.208 closest distance to " O   HOH Z 132 " =    1.128
peak=    4.207 closest distance to " O   HOH Z 147 " =    1.594
peak=    4.201 closest distance to " O   HOH Z  24 " =    2.139
peak=    4.194 closest distance to " O   HOH Z 371 " =    3.085
peak=    4.191 closest distance to " CG  TRP A 179 " =    2.261
peak=    4.183 closest distance to " OG ASER A 134 " =    1.382
peak=    4.181 closest distance to " O   HOH Z 422 " =    1.036
peak=    4.176 closest distance to " N   GLN A 278 " =    0.939
peak=    4.156 closest distance to " O   HOH Z 225 " =    1.627
peak=    4.150 closest distance to " O   HOH Z 427 " =    1.297
peak=    4.149 closest distance to " O   HOH Z 389 " =    1.664
peak=    4.145 closest distance to " O   HOH Z 193 " =    1.660
peak=    4.143 closest distance to " CD2 LEU A 228 " =    1.368
peak=    4.136 closest distance to " O   HOH Z 423 " =    1.758
peak=    4.133 closest distance to " NE1 TRP A 274 " =    1.097
peak=    4.130 closest distance to " NH2BARG A 145 " =    1.451
peak=    4.121 closest distance to " O   HOH Z 130 " =    2.281
peak=    4.109 closest distance to " O   HOH Z 369 " =    2.083
peak=    4.105 closest distance to " O   HOH Z 414 " =    1.702
peak=    4.078 closest distance to " CD  ARG A 138 " =    0.825
peak=    4.075 closest distance to " O   HOH Z 427 " =    2.176
peak=    4.072 closest distance to " O   HOH Z 119 " =    1.464
peak=    4.071 closest distance to " O   HOH Z 361 " =    1.588
peak=    4.048 closest distance to " CA  ASN A 127 " =    1.077
peak=    4.042 closest distance to " CG1AVAL A 121 " =    0.892
peak=    4.023 closest distance to " O   HOH Z   1 " =    1.799
peak=    4.015 closest distance to " O   HOH Z 236 " =    1.938
peak=    4.014 closest distance to " CG  LEU A   5 " =    1.187
peak=    4.002 closest distance to " O   HOH Z 126 " =    1.738
peak=    3.999 closest distance to " O   HOH Z 258 " =    2.287
peak=    3.981 closest distance to " O   HOH Z 356 " =    1.773
peak=    3.979 closest distance to " O   HOH Z 233 " =    1.417
peak=    3.972 closest distance to " O   HOH Z 344 " =    1.177
peak=    3.956 closest distance to " CB  ASP A 124 " =    1.002
peak=    3.951 closest distance to " O   HOH Z  48 " =    1.787
peak=    3.933 closest distance to " CG  GLN A  88 " =    1.045
peak=    3.932 closest distance to " O   HOH Z 353 " =    2.093
peak=    3.931 closest distance to " NZ  LYS A 117 " =    1.206
peak=    3.926 closest distance to " CB  LEU A 300 " =    0.955
peak=    3.915 closest distance to " CG1 ILE A 120 " =    1.573
peak=    3.910 closest distance to " O   HOH Z 357 " =    1.486
peak=    3.891 closest distance to " CG2 ILE A 234 " =    0.863
peak=    3.883 closest distance to " CB  ASN A 148 " =    1.437
peak=    3.872 closest distance to " O   HOH Z  57 " =    2.182
peak=    3.870 closest distance to " CA  ILE A 234 " =    1.097
peak=    3.853 closest distance to " CG  PRO A 280 " =    0.932
peak=    3.849 closest distance to " CB  SER A  62 " =    1.166
peak=    3.843 closest distance to " O   HOH Z 392 " =    1.655
peak=    3.829 closest distance to " O   HOH Z 193 " =    1.991
peak=    3.822 closest distance to " O   HOH Z 133 " =    1.591
peak=    3.808 closest distance to " OG  SER A 276 " =    0.946
peak=    3.808 closest distance to " CG1BVAL A 121 " =    2.232
peak=    3.804 closest distance to " CB  SER A 216 " =    0.975
peak=    3.779 closest distance to " O   HOH Z 359 " =    1.482
peak=    3.776 closest distance to " CB  ALA A 104 " =    0.867
peak=    3.765 closest distance to " O   VAL A  72 " =    0.930
peak=    3.750 closest distance to " N   GLU A   2 " =    1.348
peak=    3.743 closest distance to " O   HOH Z 287 " =    1.777
peak=    3.739 closest distance to " CG  PRO A 213 " =    1.234
peak=    3.735 closest distance to " O   HOH Z 422 " =    2.454
peak=    3.722 closest distance to " O   HOH Z 291 " =    1.421
peak=    3.716 closest distance to " O   HOH Z 294 " =    1.633
peak=    3.710 closest distance to " O   HOH Z  48 " =    1.601
peak=    3.708 closest distance to " O   HOH Z 143 " =    1.234
peak=    3.702 closest distance to " CG  PRO A  54 " =    1.292
peak=    3.692 closest distance to " O   HOH Z  59 " =    1.327
peak=    3.692 closest distance to " NE2 GLN A  58 " =    5.479
peak=    3.688 closest distance to " CG  LEU A 228 " =    1.053
peak=    3.688 closest distance to " O   HOH Z 363 " =    2.717
peak=    3.686 closest distance to " O   HOH Z  22 " =    1.980
peak=    3.684 closest distance to " O   HOH Z 380 " =    2.180
peak=    3.677 closest distance to " O   ASN A 285 " =    0.944
peak=    3.673 closest distance to " O   HOH Z  57 " =    1.123
peak=    3.666 closest distance to " CB  ASN A 187 " =    0.995
peak=    3.661 closest distance to " CB  TRP A 266 " =    0.898
peak=    3.661 closest distance to " CB  GLN A 223 " =    1.351
peak=    3.661 closest distance to " OG BSER A 258 " =    1.063
peak=    3.657 closest distance to " O   HOH Z 374 " =    1.221
peak=    3.655 closest distance to " O   HOH Z  91 " =    2.361
peak=    3.649 closest distance to " O   HOH Z  61 " =    1.521
peak=    3.643 closest distance to " O   HOH Z 108 " =    1.887
peak=    3.639 closest distance to " O   HOH Z 151 " =    1.725
peak=    3.638 closest distance to " CB  ASN A  39 " =    0.821
peak=    3.636 closest distance to " CB  GLN A 183 " =    1.054
peak=    3.629 closest distance to " O   HOH Z 240 " =    2.214
peak=    3.611 closest distance to " CB  VAL A 265 " =    1.361
peak=    3.605 closest distance to " O   HOH Z   6 " =    2.018
peak=    3.599 closest distance to " NH2AARG A 145 " =    2.319
peak=    3.593 closest distance to " NE AARG A 275 " =    1.522
peak=    3.592 closest distance to " O   HOH Z  30 " =    1.346
peak=    3.588 closest distance to " O   HOH Z 128 " =    2.080
peak=    3.578 closest distance to " O   GLY A 302 " =    2.245
peak=    3.576 closest distance to " O   HOH Z 384 " =    1.752
peak=    3.568 closest distance to " CB  GLU A 277 " =    1.083
peak=    3.568 closest distance to " OG  SER A  62 " =    3.180
peak=    3.564 closest distance to " NH1AARG A 145 " =    1.040
peak=    3.560 closest distance to " CA  SER A  87 " =    0.990
peak=    3.548 closest distance to " CA  LEU A 282 " =    1.045
peak=    3.543 closest distance to " O   HOH Z 362 " =    1.836
peak=    3.540 closest distance to " CB  GLU A 152 " =    1.235
peak=    3.535 closest distance to " O   HOH Z 245 " =    1.423
peak=    3.531 closest distance to " OG BSER A 212 " =    2.720
peak=    3.524 closest distance to " O   HOH Z 406 " =    1.811
peak=    3.520 closest distance to " O   HOH Z 272 " =    1.812
peak=    3.516 closest distance to " OD1 ASP A 286 " =    1.118
peak=    3.511 closest distance to " CD BLYS A 290 " =    1.067
peak=    3.510 closest distance to " O   HOH Z 298 " =    1.812
peak=    3.510 closest distance to " O   HOH Z 278 " =    1.220
peak=    3.508 closest distance to " CB  ALA A 114 " =    1.237
peak=    3.506 closest distance to " O   HOH Z 227 " =    1.707
peak=    3.487 closest distance to " CB  GLU A 277 " =    3.677
peak=    3.484 closest distance to " O   HOH Z 217 " =    1.577
peak=    3.482 closest distance to " CG2 THR A 220 " =    1.083
peak=    3.481 closest distance to " O   HOH Z  65 " =    1.330
peak=    3.481 closest distance to " O   HOH Z   1 " =    1.658
peak=    3.479 closest distance to " N   SER A  97 " =    0.844
peak=    3.478 closest distance to " NH2BARG A 190 " =    1.489
peak=    3.478 closest distance to " CG  GLN A 278 " =    3.967
peak=    3.471 closest distance to " O   HOH Z   7 " =    3.430
peak=    3.463 closest distance to " CE3 TRP A 274 " =    2.134
peak=    3.462 closest distance to " CD1 LEU A   5 " =    1.395
peak=    3.461 closest distance to " CG  ASN A 301 " =    1.090
peak=    3.459 closest distance to " OG BSER A  12 " =    0.929
peak=    3.456 closest distance to " O   HOH Z 302 " =    1.652
peak=    3.447 closest distance to " O   HOH Z 371 " =    2.026
peak=    3.444 closest distance to " CG2 THR A 221 " =    1.338
peak=    3.437 closest distance to " CB  PHE A 204 " =    0.754
peak=    3.432 closest distance to " O   HOH Z 226 " =    1.166
peak=    3.427 closest distance to " O   HOH Z 405 " =    1.870
peak=    3.424 closest distance to " CB  ASN A 142 " =    1.004
peak=    3.421 closest distance to " CA  ALA A 295 " =    0.927
peak=    3.415 closest distance to " OD1 ASN A 217 " =    1.594
peak=    3.414 closest distance to " O   HOH Z 172 " =    1.517
peak=    3.410 closest distance to " O   HOH Z 244 " =    1.419
peak=    3.409 closest distance to " ND1 HIS A  86 " =    1.854
peak=    3.409 closest distance to " O   HOH Z 276 " =    1.399
peak=    3.406 closest distance to " CB  ALA A 233 " =    1.212
peak=    3.401 closest distance to " CG2 THR A 294 " =    1.171
peak=    3.400 closest distance to " O   HOH Z  28 " =    1.969
peak=    3.399 closest distance to " O   HOH Z  51 " =    1.513
peak=    3.399 closest distance to " NH2 ARG A 269 " =    0.891
peak=    3.398 closest distance to " CB  VAL A 202 " =    1.722
peak=    3.396 closest distance to " CD2 LEU A 297 " =    0.930
peak=    3.395 closest distance to " NH2 ARG A 219 " =    1.743
peak=    3.393 closest distance to " OD1 ASN A  45 " =    1.105
peak=    3.387 closest distance to " N   ALA A   1 " =    1.400
peak=    3.383 closest distance to " CB  SER A 276 " =    1.336
peak=    3.378 closest distance to " O   HOH Z  61 " =    1.861
peak=    3.378 closest distance to " OD1 ASP A 200 " =    1.506
peak=    3.371 closest distance to " CG2 ILE A  49 " =    1.115
peak=    3.370 closest distance to " CB  TRP A 179 " =    1.390
peak=    3.359 closest distance to " O   HOH Z 285 " =    2.185
peak=    3.357 closest distance to " CZ3 TRP A 274 " =    1.430
peak=    3.354 closest distance to " O   HOH Z 388 " =    2.096
peak=    3.354 closest distance to " CB  GLU A 128 " =    0.923
peak=    3.351 closest distance to " O   HOH Z 207 " =    2.394
peak=    3.349 closest distance to " CB  MET A  40 " =    0.792
peak=    3.345 closest distance to " O   HOH Z 158 " =    2.411
peak=    3.337 closest distance to " N   GLY A 136 " =    1.134
peak=    3.337 closest distance to " CG  PRO A 243 " =    1.114
peak=    3.331 closest distance to " CG  LEU A 167 " =    1.321
peak=    3.330 closest distance to " CD  PRO A 243 " =    1.437
peak=    3.327 closest distance to " O   HOH Z 389 " =    1.410
peak=    3.325 closest distance to " CA  ALA A  21 " =    1.083
peak=    3.322 closest distance to " CA  ALA A 158 " =    1.060
peak=    3.322 closest distance to " ND2BASN A 224 " =    0.774
peak=    3.320 closest distance to " O   HOH Z 217 " =    3.065
peak=    3.315 closest distance to " CG  GLN A  11 " =    2.177
peak=    3.315 closest distance to " CB  ASP A 132 " =    3.743
peak=    3.314 closest distance to " N   TYR A  15 " =    1.042
peak=    3.313 closest distance to " OD2 ASP A 286 " =    2.332
peak=    3.312 closest distance to " NH2 ARG A 138 " =    1.554
peak=    3.312 closest distance to " CB  ASP A 200 " =    0.861
peak=    3.311 closest distance to " ND1 HIS A  81 " =    1.478
peak=    3.309 closest distance to " O   HOH Z  59 " =    1.924
peak=    3.308 closest distance to " CA  ARG A  36 " =    1.074
peak=    3.306 closest distance to " CB  SER A 210 " =    0.997
peak=    3.301 closest distance to " CB  ASN A 148 " =    1.892
peak=    3.295 closest distance to " O   HOH Z 284 " =    1.524
peak=    3.288 closest distance to " O   HOH Z 114 " =    2.108
peak=    3.287 closest distance to " O   HOH Z 368 " =    3.108
peak=    3.286 closest distance to " OG  SER A  26 " =    1.372
peak=    3.285 closest distance to " O   HOH Z 280 " =    1.586
peak=    3.281 closest distance to " CB  ASP A 140 " =    0.854
peak=    3.280 closest distance to " O   HOH Z  97 " =    1.908
peak=    3.278 closest distance to " NE2 GLN A  73 " =    1.607
peak=    3.275 closest distance to " O   HOH Z 248 " =    2.184
peak=    3.275 closest distance to " O   HOH Z 184 " =    1.505
peak=    3.269 closest distance to " CB  PHE A 225 " =    1.497
peak=    3.268 closest distance to " CG  PRO A 198 " =    1.422
peak=    3.267 closest distance to " CB  PRO A 163 " =    3.985
peak=    3.266 closest distance to " O   ARG A 275 " =    0.968
peak=    3.263 closest distance to " O   HOH Z 434 " =    5.756
peak=    3.262 closest distance to " OD1 ASP A 238 " =    0.836
peak=    3.262 closest distance to " O   HOH Z 303 " =    1.703
peak=    3.261 closest distance to " O   HOH Z 158 " =    1.281
peak=    3.260 closest distance to " O   HOH Z  88 " =    2.865
peak=    3.257 closest distance to " O   HOH Z 178 " =    1.221
peak=    3.252 closest distance to " CA  ALA A  51 " =    1.117
peak=    3.251 closest distance to " O   HOH Z 412 " =    2.047
peak=    3.251 closest distance to " O   HOH Z 213 " =    1.705
peak=    3.246 closest distance to " CA  TYR A  30 " =    1.101
peak=    3.244 closest distance to " CD2 LEU A 300 " =    1.134
peak=    3.243 closest distance to " CD  ARG A 159 " =    0.815
peak=    3.242 closest distance to " CD2 LEU A 167 " =    1.142
peak=    3.239 closest distance to " NH1 ARG A  14 " =    1.049
peak=    3.239 closest distance to " CD1 ILE A  33 " =    1.710
peak=    3.239 closest distance to " O   HOH Z 434 " =    1.418
peak=    3.239 closest distance to " CG2 THR A 235 " =    0.780
peak=    3.238 closest distance to " O   HOH Z 366 " =    2.630
peak=    3.238 closest distance to " CB  SER A  63 " =    1.270
peak=    3.236 closest distance to " CA  ARG A 195 " =    1.259
peak=    3.229 closest distance to " NE2 GLN A  58 " =    3.512
peak=    3.228 closest distance to " O   HOH Z 153 " =    3.525
peak=    3.219 closest distance to " O   HOH Z 287 " =    1.811
peak=    3.218 closest distance to " CE AMET A  47 " =    1.370
peak=    3.208 closest distance to " O   HOH Z 176 " =    2.117
peak=    3.208 closest distance to " O   HOH Z 148 " =    1.650
peak=    3.207 closest distance to " CB  GLU A   2 " =    0.983
peak=    3.207 closest distance to " O   HOH Z 214 " =    1.801
peak=    3.205 closest distance to " CG  ASN A  60 " =    1.580
peak=    3.204 closest distance to " CA  ASN A 284 " =    1.044
peak=    3.197 closest distance to " O   HOH Z 166 " =    1.571
peak=    3.197 closest distance to " CG2 THR A 251 " =    1.809
peak=    3.193 closest distance to " O   HOH Z  64 " =    2.022
peak=    3.192 closest distance to " CB  TYR A 169 " =    0.751
peak=    3.186 closest distance to " O   HOH Z 334 " =    2.680
peak=    3.183 closest distance to " CD  LYS A 119 " =    2.147
peak=    3.182 closest distance to " O   HOH Z  44 " =    2.671
peak=    3.182 closest distance to " CA  ARG A 159 " =    1.216
peak=    3.180 closest distance to " O   HOH Z 279 " =    2.347
peak=    3.179 closest distance to " O   HOH Z 368 " =    1.754
peak=    3.175 closest distance to " O   HOH Z 222 " =    1.697
peak=    3.174 closest distance to " CZ3 TRP A 274 " =    2.064
peak=    3.172 closest distance to " CD2 LEU A  25 " =    1.148
peak=    3.170 closest distance to " O   HOH Z 222 " =    2.155
peak=    3.170 closest distance to " O   HOH Z 145 " =    2.632
peak=    3.166 closest distance to " O   HOH Z 281 " =    2.095
peak=    3.165 closest distance to " OE1 GLN A 240 " =    1.707
peak=    3.163 closest distance to " O   HOH Z 128 " =    2.047
peak=    3.156 closest distance to " O   HOH Z 110 " =    1.818
peak=    3.156 closest distance to " N   GLN A  73 " =    1.244
peak=    3.156 closest distance to " CB  ARG A  79 " =    1.450
peak=    3.155 closest distance to " NE BARG A 275 " =    1.028
peak=    3.154 closest distance to " O   HOH Z  32 " =    2.145
peak=    3.152 closest distance to " O   HOH Z 353 " =    1.855
peak=    3.150 closest distance to " CB  PHE A  16 " =    0.921
peak=    3.150 closest distance to " O   HOH Z 425 " =    1.854
peak=    3.150 closest distance to " O   HOH Z 124 " =    2.161
peak=    3.150 closest distance to " O   HOH Z 247 " =    1.276
peak=    3.149 closest distance to " O   HOH Z 188 " =    4.467
peak=    3.147 closest distance to " O   HOH Z 204 " =    1.221
peak=    3.146 closest distance to " CG  ARG A 159 " =    0.887
peak=    3.145 closest distance to " CB  LYS A 290 " =    1.344
peak=    3.141 closest distance to " O   HOH Z 180 " =    2.127
peak=    3.141 closest distance to " O   HOH Z  95 " =    1.491
peak=    3.141 closest distance to " OG1 THR A 246 " =    1.391
peak=    3.137 closest distance to " O   HOH Z 413 " =    1.698
peak=    3.131 closest distance to " CB  ALA A  34 " =    1.121
peak=    3.128 closest distance to " CD1 TYR A  15 " =    1.122
peak=    3.128 closest distance to " N   PHE A 130 " =    1.152
peak=    3.107 closest distance to " CB  ALA A   1 " =    1.023
peak=    3.107 closest distance to " CD1 LEU A 228 " =    1.697
peak=    3.107 closest distance to " CG2 ILE A  20 " =    1.202
peak=    3.098 closest distance to " O   HOH Z 220 " =    1.533
peak=    3.097 closest distance to " C   ASN A 215 " =    1.227
peak=    3.081 closest distance to " CG  LYS A 166 " =    1.364
peak=    3.070 closest distance to " O   HOH Z  11 " =    1.620
peak=    3.061 closest distance to " CA  GLY A 241 " =    4.424
peak=    3.058 closest distance to " CE  LYS A  48 " =    1.067
peak=    3.039 closest distance to " O   HOH Z 282 " =    1.626

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 207         
Filter by distance & map next to the model:
   mapped sites are within: 0.635 - 5.315
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 205 from: 207
   mapped sites are within: 0.702 - 5.315

peak=   -5.023 closest distance to " CG2 VAL A 230 " =    0.827
peak=   -4.611 closest distance to " CD  ARG A 138 " =    1.178
peak=   -4.610 closest distance to " CD  ARG A  14 " =    2.958
peak=   -4.480 closest distance to " CG1 VAL A 296 " =    0.702
peak=   -4.464 closest distance to " OG ASER A 134 " =    1.006
peak=   -4.391 closest distance to " O   HOH Z 231 " =    0.795
peak=   -4.369 closest distance to " O   HOH Z  76 " =    1.061
peak=   -4.317 closest distance to " O   PRO A 198 " =    1.105
peak=   -4.297 closest distance to " O   HOH Z  52 " =    0.860
peak=   -4.271 closest distance to " O   HOH Z  95 " =    0.985
peak=   -4.257 closest distance to " O   HOH Z 385 " =    0.908
peak=   -4.204 closest distance to " O   HOH Z 163 " =    1.569
peak=   -4.200 closest distance to " O   HOH Z  54 " =    0.778
peak=   -4.143 closest distance to " O   HOH Z 268 " =    0.832
peak=   -4.085 closest distance to " CA  GLY A  98 " =    1.798
peak=   -4.063 closest distance to " CD  GLU A 277 " =    2.544
peak=   -4.024 closest distance to " NH2 ARG A  79 " =    2.038
peak=   -4.015 closest distance to " CD1 TRP A 179 " =    1.105
peak=   -4.013 closest distance to " CD2 LEU A   5 " =    0.886
peak=   -4.004 closest distance to " CG  PRO A 163 " =    2.423
peak=   -3.977 closest distance to " O   HOH Z 290 " =    1.042
peak=   -3.970 closest distance to " O   HOH Z 347 " =    0.789
peak=   -3.967 closest distance to " O   GLN A  11 " =    1.631
peak=   -3.954 closest distance to " O   HOH Z  24 " =    1.242
peak=   -3.946 closest distance to " C   PHE A 155 " =    0.816
peak=   -3.893 closest distance to " O   HOH Z 377 " =    1.147
peak=   -3.886 closest distance to " O   HOH Z 298 " =    0.873
peak=   -3.861 closest distance to " CA  GLY A 133 " =    2.100
peak=   -3.819 closest distance to " O   HOH Z 111 " =    0.996
peak=   -3.808 closest distance to " ND2BASN A 224 " =    1.461
peak=   -3.799 closest distance to " O   HOH Z 264 " =    1.098
peak=   -3.790 closest distance to " O   HOH Z 359 " =    1.473
peak=   -3.778 closest distance to " O   GLY A  98 " =    2.030
peak=   -3.777 closest distance to " OG  SER A  97 " =    2.209
peak=   -3.775 closest distance to " CB  PRO A 243 " =    2.504
peak=   -3.774 closest distance to " CG  MET A 105 " =    0.869
peak=   -3.771 closest distance to " O   HOH Z 242 " =    1.680
peak=   -3.741 closest distance to " O   TRP A 179 " =    1.759
peak=   -3.732 closest distance to " O   HOH Z 286 " =    1.573
peak=   -3.711 closest distance to " CD  GLN A  77 " =    1.158
peak=   -3.674 closest distance to " O   HOH Z 235 " =    1.002
peak=   -3.672 closest distance to " OG  SER A 206 " =    1.904
peak=   -3.670 closest distance to " O   HOH Z 313 " =    0.953
peak=   -3.667 closest distance to " CB  ASP A  27 " =    2.394
peak=   -3.647 closest distance to " O   HOH Z 381 " =    0.929
peak=   -3.642 closest distance to " N   THR A 157 " =    1.704
peak=   -3.619 closest distance to " O   HOH Z  60 " =    1.591
peak=   -3.616 closest distance to " N   GLN A  58 " =    1.120
peak=   -3.610 closest distance to " CD1 TRP A 274 " =    1.033
peak=   -3.608 closest distance to " O   ASN A 301 " =    1.595
peak=   -3.605 closest distance to " O   HOH Z 413 " =    4.204
peak=   -3.602 closest distance to " OG1 THR A 264 " =    2.185
peak=   -3.589 closest distance to " N   PRO A 163 " =    1.468
peak=   -3.588 closest distance to " OG BSER A 134 " =    1.524
peak=   -3.588 closest distance to " O   ALA A  51 " =    1.325
peak=   -3.577 closest distance to " O   HOH Z 140 " =    1.241
peak=   -3.564 closest distance to " NE1 TRP A 177 " =    1.746
peak=   -3.561 closest distance to " O   HOH Z 300 " =    0.914
peak=   -3.559 closest distance to " O   HOH Z 431 " =    1.080
peak=   -3.527 closest distance to " CB  ALA A 248 " =    2.006
peak=   -3.525 closest distance to " CD2 TRP A 150 " =    1.322
peak=   -3.521 closest distance to " CD1 LEU A   5 " =    2.617
peak=   -3.517 closest distance to " O   HOH Z  39 " =    1.074
peak=   -3.511 closest distance to " O   HOH Z 197 " =    3.199
peak=   -3.509 closest distance to " CA  GLY A  35 " =    1.908
peak=   -3.501 closest distance to " CB  ASN A  39 " =    2.349
peak=   -3.496 closest distance to " N   VAL A  72 " =    1.976
peak=   -3.484 closest distance to " CG  GLU A 277 " =    1.174
peak=   -3.484 closest distance to " O   HOH Z  43 " =    1.824
peak=   -3.472 closest distance to " O   HOH Z 186 " =    1.393
peak=   -3.464 closest distance to " OG  SER A   3 " =    0.942
peak=   -3.464 closest distance to " O   ALA A  10 " =    1.763
peak=   -3.463 closest distance to " O   HOH Z 376 " =    2.392
peak=   -3.462 closest distance to " O   HOH Z 397 " =    1.406
peak=   -3.461 closest distance to " O   GLY A 118 " =    1.233
peak=   -3.460 closest distance to " O   HOH Z 426 " =    1.467
peak=   -3.459 closest distance to " O   HOH Z 350 " =    1.997
peak=   -3.455 closest distance to " O   HOH Z 404 " =    1.236
peak=   -3.453 closest distance to " O   HOH Z 415 " =    0.893
peak=   -3.446 closest distance to " O   HOH Z 407 " =    3.035
peak=   -3.441 closest distance to " CG  ARG A 138 " =    0.934
peak=   -3.438 closest distance to " CB  TYR A  15 " =    2.112
peak=   -3.424 closest distance to " O   HOH Z  68 " =    1.140
peak=   -3.422 closest distance to " OG  SER A  87 " =    1.595
peak=   -3.415 closest distance to " O   HOH Z 416 " =    1.075
peak=   -3.414 closest distance to " ND2 ASN A 285 " =    2.070
peak=   -3.413 closest distance to " CG2 ILE A  20 " =    2.872
peak=   -3.412 closest distance to " O   ILE A  49 " =    1.709
peak=   -3.412 closest distance to " O   HOH Z 134 " =    2.579
peak=   -3.407 closest distance to " N   ALA A   1 " =    1.018
peak=   -3.391 closest distance to " O   HOH Z 389 " =    2.078
peak=   -3.386 closest distance to " N   VAL A 125 " =    1.098
peak=   -3.383 closest distance to " OE1 GLN A 223 " =    2.400
peak=   -3.381 closest distance to " CG  TRP A 266 " =    1.717
peak=   -3.376 closest distance to " CD  LYS A 289 " =    2.371
peak=   -3.369 closest distance to " N   ARG A 275 " =    0.841
peak=   -3.366 closest distance to " O   HOH Z  47 " =    1.489
peak=   -3.365 closest distance to " CA  TYR A  68 " =    2.777
peak=   -3.353 closest distance to " O   HOH Z 148 " =    2.604
peak=   -3.350 closest distance to " O   HOH Z  71 " =    1.198
peak=   -3.348 closest distance to " O   HOH Z 222 " =    4.730
peak=   -3.345 closest distance to " OE2 GLU A 152 " =    0.966
peak=   -3.344 closest distance to " O   HOH Z  40 " =    4.288
peak=   -3.337 closest distance to " O   HOH Z 129 " =    0.705
peak=   -3.337 closest distance to " NE2 GLN A 223 " =    1.526
peak=   -3.330 closest distance to " C   ARG A  79 " =    2.478
peak=   -3.327 closest distance to " CE2 PHE A 218 " =    2.508
peak=   -3.325 closest distance to " O   HOH Z  56 " =    0.829
peak=   -3.316 closest distance to " O   VAL A  72 " =    0.902
peak=   -3.314 closest distance to " N   ASN A 127 " =    1.294
peak=   -3.314 closest distance to " NH2 ARG A 159 " =    2.299
peak=   -3.308 closest distance to " O   HOH Z 244 " =    1.563
peak=   -3.307 closest distance to " O   HOH Z 231 " =    1.747
peak=   -3.307 closest distance to " O   HOH Z 390 " =    2.423
peak=   -3.301 closest distance to " O   HOH Z 414 " =    3.069
peak=   -3.298 closest distance to " CG  ARG A 219 " =    2.350
peak=   -3.297 closest distance to " O   HOH Z 352 " =    1.918
peak=   -3.297 closest distance to " O   HOH Z 143 " =    0.755
peak=   -3.297 closest distance to " OG  SER A  26 " =    0.869
peak=   -3.297 closest distance to " O   HOH Z 429 " =    1.528
peak=   -3.297 closest distance to " OE2 GLU A   2 " =    0.787
peak=   -3.295 closest distance to " O   HOH Z 102 " =    1.572
peak=   -3.294 closest distance to " O   HOH Z 131 " =    3.802
peak=   -3.294 closest distance to " O   HOH Z 353 " =    1.293
peak=   -3.293 closest distance to " CG  ASP A 231 " =    0.742
peak=   -3.291 closest distance to " OG  SER A  63 " =    1.623
peak=   -3.291 closest distance to " CB  ALA A 291 " =    1.771
peak=   -3.291 closest distance to " C   ASN A 217 " =    1.722
peak=   -3.291 closest distance to " O   HOH Z 414 " =    1.991
peak=   -3.290 closest distance to " CE2 TYR A  30 " =    2.680
peak=   -3.290 closest distance to " CB  SER A 273 " =    1.807
peak=   -3.285 closest distance to " O   GLU A  44 " =    1.900
peak=   -3.284 closest distance to " CB  ALA A 100 " =    2.545
peak=   -3.284 closest distance to " CG  GLN A  88 " =    0.820
peak=   -3.283 closest distance to " O   GLY A 211 " =    1.090
peak=   -3.280 closest distance to " O   ILE A 106 " =    2.143
peak=   -3.279 closest distance to " O   THR A  42 " =    2.526
peak=   -3.270 closest distance to " O   HOH Z 189 " =    2.937
peak=   -3.269 closest distance to " O   HOH Z 383 " =    0.768
peak=   -3.268 closest distance to " C   ILE A 239 " =    1.792
peak=   -3.267 closest distance to " CD  GLU A 277 " =    0.805
peak=   -3.266 closest distance to " O   HOH Z 275 " =    1.906
peak=   -3.265 closest distance to " N   ARG A 138 " =    1.549
peak=   -3.261 closest distance to " CD  GLN A  58 " =    0.941
peak=   -3.259 closest distance to " O   HOH Z 174 " =    2.946
peak=   -3.254 closest distance to " CA  TYR A  68 " =    1.089
peak=   -3.251 closest distance to " O   HOH Z  77 " =    1.524
peak=   -3.249 closest distance to " CB  ALA A 129 " =    2.455
peak=   -3.249 closest distance to " O   HOH Z 236 " =    1.883
peak=   -3.247 closest distance to " CG1 ILE A 263 " =    2.047
peak=   -3.247 closest distance to " CG2 THR A  31 " =    2.179
peak=   -3.239 closest distance to " N   LYS A 166 " =    1.914
peak=   -3.235 closest distance to " CD  GLN A  11 " =    0.912
peak=   -3.232 closest distance to " CG  PHE A  59 " =    1.522
peak=   -3.218 closest distance to " OD2 ASP A 171 " =    1.567
peak=   -3.214 closest distance to " O   HOH Z 126 " =    1.656
peak=   -3.214 closest distance to " NE2 GLN A  55 " =    0.873
peak=   -3.209 closest distance to " CB  PHE A 130 " =    1.162
peak=   -3.208 closest distance to " O   HOH Z 426 " =    1.908
peak=   -3.208 closest distance to " O   ASP A 191 " =    1.961
peak=   -3.205 closest distance to " O   SER A  22 " =    2.599
peak=   -3.200 closest distance to " O   HOH Z 166 " =    2.038
peak=   -3.198 closest distance to " O   HOH Z   1 " =    3.653
peak=   -3.197 closest distance to " O   HOH Z  22 " =    2.872
peak=   -3.196 closest distance to " N   GLN A  58 " =    2.045
peak=   -3.196 closest distance to " O   GLY A  57 " =    1.382
peak=   -3.190 closest distance to " O   HOH Z  69 " =    2.014
peak=   -3.188 closest distance to " O   HOH Z 429 " =    2.125
peak=   -3.181 closest distance to " NE2 GLN A 194 " =    2.928
peak=   -3.179 closest distance to " O   GLY A  80 " =    2.527
peak=   -3.178 closest distance to " CE3 TRP A 274 " =    2.413
peak=   -3.175 closest distance to " O   HOH Z 402 " =    1.558
peak=   -3.172 closest distance to " CD1 LEU A 101 " =    2.259
peak=   -3.171 closest distance to " CD2 LEU A 237 " =    2.228
peak=   -3.169 closest distance to " O   HOH Z 435 " =    2.239
peak=   -3.165 closest distance to " CZ  ARG A  56 " =    0.725
peak=   -3.162 closest distance to " C   SER A 206 " =    1.452
peak=   -3.160 closest distance to " O   HOH Z 298 " =    2.573
peak=   -3.157 closest distance to " O   HOH Z 124 " =    3.966
peak=   -3.156 closest distance to " CD  LYS A 166 " =    2.623
peak=   -3.147 closest distance to " ND2 ASN A 173 " =    1.611
peak=   -3.142 closest distance to " O   HOH Z  30 " =    0.987
peak=   -3.140 closest distance to " C   VAL A 265 " =    0.964
peak=   -3.128 closest distance to " O   PRO A 243 " =    2.540
peak=   -3.128 closest distance to " O   HOH Z 266 " =    4.642
peak=   -3.127 closest distance to " CG  PHE A 283 " =    2.472
peak=   -3.125 closest distance to " CE3 TRP A 179 " =    2.388
peak=   -3.124 closest distance to " O   HOH Z 132 " =    4.372
peak=   -3.123 closest distance to " C   MET A 188 " =    1.684
peak=   -3.114 closest distance to " C   GLN A 205 " =    1.955
peak=   -3.112 closest distance to " O   HOH Z 207 " =    2.133
peak=   -3.109 closest distance to " O   HOH Z 198 " =    2.260
peak=   -3.107 closest distance to " O   HOH Z 368 " =    2.734
peak=   -3.103 closest distance to " CG  ASP A  50 " =    1.162
peak=   -3.096 closest distance to " O   HOH Z 313 " =    1.670
peak=   -3.096 closest distance to " O   HOH Z  73 " =    1.978
peak=   -3.094 closest distance to " O   HOH Z  95 " =    1.491
peak=   -3.093 closest distance to " CD  ARG A 139 " =    1.583
peak=   -3.092 closest distance to " O   HOH Z  64 " =    1.802
peak=   -3.091 closest distance to " CA  ASN A 142 " =    2.022
peak=   -3.081 closest distance to " O   HOH Z 214 " =    1.070
peak=   -3.080 closest distance to " NH2AARG A 275 " =    5.315
peak=   -3.076 closest distance to " O  BHOH Z  74 " =    2.075
peak=   -3.066 closest distance to " CG2 THR A   4 " =    2.022
peak=   -3.050 closest distance to " CB  ASN A  45 " =    1.991

================= 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    :  0.4932 0.4914   6.298392e+00   6.290353e+00
   1_bss:  0.4843 0.4790   6.292896e+00   6.281513e+00
   1_xyz:  0.4231 0.4539   6.227851e+00   6.255970e+00
   1_adp:  0.3864 0.4473   6.184951e+00   6.250440e+00
   1_occ:  0.3858 0.4476   6.184458e+00   6.250864e+00
   2_bss:  0.3848 0.4439   6.185183e+00   6.249387e+00
   2_xyz:  0.3410 0.4085   6.091336e+00   6.201663e+00
   2_adp:  0.3257 0.4003   6.070207e+00   6.186465e+00
   2_occ:  0.3256 0.4002   6.069918e+00   6.186142e+00
   3_bss:  0.3262 0.3995   6.071412e+00   6.186337e+00
   3_xyz:  0.2665 0.3402   5.910582e+00   6.069478e+00
   3_adp:  0.2456 0.3281   5.855942e+00   6.037078e+00
   3_occ:  0.2451 0.3280   5.855400e+00   6.037378e+00
   4_bss:  0.2446 0.3267   5.852563e+00   6.034079e+00
   4_xyz:  0.2014 0.2672   5.662295e+00   5.863424e+00
   4_adp:  0.1837 0.2404   5.573182e+00   5.779146e+00
   4_occ:  0.1832 0.2391   5.570956e+00   5.776146e+00
   5_bss:  0.1833 0.2383   5.569780e+00   5.774764e+00
   5_xyz:  0.1472 0.1990   5.381556e+00   5.612018e+00
   5_adp:  0.1394 0.1910   5.334346e+00   5.566730e+00
   5_occ:  0.1392 0.1905   5.333157e+00   5.565547e+00
   5_bss:  0.1392 0.1902   5.331235e+00   5.563267e+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:  0.409  19.999   5.947   9.454   7.031   0.000   0.000   0.000
   1_xyz:  0.409  19.999   5.947   9.454   7.031   0.000   0.000   0.000
   1_adp:  0.409  19.999   5.947   9.454   7.031   0.000   0.000   0.000
   1_occ:  0.409  19.999   5.947   9.454   7.031   0.000   0.000   0.000
   2_bss:  0.372  37.787   3.022   5.671   4.121   0.000   0.000   0.000
   2_xyz:  0.372  37.787   3.022   5.671   4.121   0.000   0.000   0.000
   2_adp:  0.372  37.787   3.022   5.671   4.121   0.000   0.000   0.000
   2_occ:  0.372  37.787   3.022   5.671   4.121   0.000   0.000   0.000
   3_bss:  0.365  56.713   2.725   4.083   3.599   0.000   0.000   0.000
   3_xyz:  0.365  56.713   2.725   4.083   3.599   0.000   0.000   0.000
   3_adp:  0.365  56.713   2.725   4.083   3.599   0.000   0.000   0.000
   3_occ:  0.365  56.713   2.725   4.083   3.599   0.000   0.000   0.000
   4_bss:  0.349  50.283   1.980   2.417   2.791   0.000   0.000   0.000
   4_xyz:  0.349  50.283   1.980   2.417   2.791   0.000   0.000   0.000
   4_adp:  0.349  50.283   1.980   2.417   2.791   0.000   0.000   0.000
   4_occ:  0.349  50.283   1.980   2.417   2.791   0.000   0.000   0.000
   5_bss:  0.337  50.283   1.334   1.278   2.345   0.000   0.000   0.000
   5_xyz:  0.337  50.283   1.334   1.278   2.345   0.000   0.000   0.000
   5_adp:  0.337  50.283   1.334   1.278   2.345   0.000   0.000   0.000
   5_occ:  0.337  50.283   1.334   1.278   2.345   0.000   0.000   0.000
   5_bss:  0.321  41.119  -0.242  -0.529   0.771   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  62.482 0.3621  0.4375    80115.964
   1_bss:  61.324 0.3763  0.5630    77042.592
   1_xyz:  54.824 0.4595  0.6759    65717.822
   1_adp:  53.746 0.4731  0.7403    64263.639
   1_occ:  53.771 0.4729  0.7394    64460.912
   2_bss:  53.470 0.4765  0.6678    63766.531
   2_xyz:  46.973 0.5570  0.7738    50818.925
   2_adp:  44.984 0.5821  0.8177    48495.776
   2_occ:  44.973 0.5823  0.8178    48479.431
   3_bss:  44.848 0.5837  0.7972    48311.924
   3_xyz:  36.412 0.6848  0.9155    33001.936
   3_adp:  34.182 0.7109  0.9384    30020.238
   3_occ:  34.207 0.7106  0.9373    29993.082
   4_bss:  34.024 0.7125  0.9035    29603.377
   4_xyz:  26.582 0.7946  0.9728    18442.669
   4_adp:  23.374 0.8287  0.9874    14946.203
   4_occ:  23.271 0.8297  0.9874    14801.123
   5_bss:  23.223 0.8301  0.9610    14706.218
   5_xyz:  19.084 0.8704  0.9846    10390.358
   5_adp:  17.922 0.8817  0.9841     9634.945
   5_occ:  17.892 0.8819  0.9837     9582.878
   5_bss:  17.839 0.8822  0.9749     9475.087
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.3002e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.3002e+01
   1_xyz:   1.695  0.013  0.105 18.313  0.006  4.105   1.4428e-01
   1_adp:   1.695  0.013  0.105 18.313  0.006  4.105   1.4428e-01
   1_occ:   1.695  0.013  0.105 18.313  0.006  4.105   1.4428e-01
   2_bss:   1.695  0.013  0.105 18.313  0.006  4.105   1.4428e-01
   2_xyz:   1.167  0.008  0.076 16.067  0.005  4.118   8.5807e-02
   2_adp:   1.167  0.008  0.076 16.067  0.005  4.118   8.5807e-02
   2_occ:   1.167  0.008  0.076 16.067  0.005  4.118   8.5807e-02
   3_bss:   1.167  0.008  0.076 16.067  0.005  4.118   8.5807e-02
   3_xyz:   1.282  0.011  0.090 16.142  0.005  4.116   1.0027e-01
   3_adp:   1.282  0.011  0.090 16.142  0.005  4.116   1.0027e-01
   3_occ:   1.282  0.011  0.090 16.142  0.005  4.116   1.0027e-01
   4_bss:   1.282  0.011  0.090 16.142  0.005  4.116   1.0027e-01
   4_xyz:   1.006  0.007  0.071 15.503  0.004  4.106   6.5524e-02
   4_adp:   1.006  0.007  0.071 15.503  0.004  4.106   6.5524e-02
   4_occ:   1.006  0.007  0.071 15.503  0.004  4.106   6.5524e-02
   5_bss:   1.006  0.007  0.071 15.503  0.004  4.106   6.5524e-02
   5_xyz:   0.986  0.006  0.068 15.448  0.003  4.112   5.9876e-02
   5_adp:   0.986  0.006  0.068 15.448  0.003  4.112   5.9876e-02
   5_occ:   0.986  0.006  0.068 15.448  0.003  4.112   5.9876e-02
   5_bss:   0.986  0.006  0.068 15.448  0.003  4.112   5.9876e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.196   6.8667e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.196   6.8667e+00
   1_xyz:  13.024  0.191  0.423 84.820  0.047  2.162   9.7965e-02
   1_adp:  13.024  0.191  0.423 84.820  0.047  2.162   9.7965e-02
   1_occ:  13.024  0.191  0.423 84.820  0.047  2.162   9.7965e-02
   2_bss:  13.024  0.191  0.423 84.820  0.047  2.162   9.7965e-02
   2_xyz:   6.842  0.087  0.277 78.224  0.051  2.052   6.2652e-02
   2_adp:   6.842  0.087  0.277 78.224  0.051  2.052   6.2652e-02
   2_occ:   6.842  0.087  0.277 78.224  0.051  2.052   6.2652e-02
   3_bss:   6.842  0.087  0.277 78.224  0.051  2.052   6.2652e-02
   3_xyz:   8.474  0.076  0.302 75.824  0.033  2.128   1.1072e-01
   3_adp:   8.474  0.076  0.302 75.824  0.033  2.128   1.1072e-01
   3_occ:   8.474  0.076  0.302 75.824  0.033  2.128   1.1072e-01
   4_bss:   8.474  0.076  0.302 75.824  0.033  2.128   1.1072e-01
   4_xyz:   8.194  0.052  0.300 76.392  0.030  2.314   4.8543e-02
   4_adp:   8.194  0.052  0.300 76.392  0.030  2.314   4.8543e-02
   4_occ:   8.194  0.052  0.300 76.392  0.030  2.314   4.8543e-02
   5_bss:   8.194  0.052  0.300 76.392  0.030  2.314   4.8543e-02
   5_xyz:   7.704  0.055  0.238 83.074  0.031  2.316   3.7391e-02
   5_adp:   7.704  0.055  0.238 83.074  0.031  2.316   3.7391e-02
   5_occ:   7.704  0.055  0.238 83.074  0.031  2.316   3.7391e-02
   5_bss:   7.704  0.055  0.238 83.074  0.031  2.316   3.7391e-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:  64.44   0.00  13.42  61.87   0.00  12.11  64.44   0.00  20.56
   1_occ:  64.44   0.00  13.42  61.87   0.00  12.11  64.44   0.00  20.56
   2_bss:  64.44   0.00  13.42  61.87   0.00  12.11  64.44   0.00  20.56
   2_xyz:  64.44   0.00  13.42  61.87   0.00  12.11  64.44   0.00  20.56
   2_adp:  85.52   0.00  13.96  79.92   0.00  11.98  85.52   0.00  24.74
   2_occ:  85.52   0.00  13.96  79.92   0.00  11.98  85.52   0.00  24.74
   3_bss:  85.52   0.00  13.96  79.92   0.00  11.98  85.52   0.00  24.74
   3_xyz:  85.52   0.00  13.96  79.92   0.00  11.98  85.52   0.00  24.74
   3_adp:  93.87   0.00  14.59  85.08   0.00  11.23  93.87   0.00  32.89
   3_occ:  93.87   0.00  14.59  85.08   0.00  11.23  93.87   0.00  32.89
   4_bss:  93.87   0.00  14.59  85.08   0.00  11.23  93.87   0.00  32.89
   4_xyz:  93.87   0.00  14.59  85.08   0.00  11.23  93.87   0.00  32.89
   4_adp:  89.54   0.00  14.09  85.64   0.00   9.92  89.54   1.99  36.83
   4_occ:  89.54   0.00  14.09  85.64   0.00   9.92  89.54   1.99  36.83
   5_bss:  89.54   0.00  14.09  85.64   0.00   9.92  89.54   1.99  36.83
   5_xyz:  89.54   0.00  14.09  85.64   0.00   9.92  89.54   1.99  36.83
   5_adp:  89.29   0.00  13.92  85.89   0.00   9.48  89.29   3.67  38.07
   5_occ:  89.29   0.00  13.92  85.89   0.00   9.48  89.29   3.67  38.07
   5_bss:  90.71   1.42  15.34  87.32   1.42  10.91  90.71   5.09  39.50
------------------------------------------------------------------------
 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:    1.251    0.013    0.410
   1_adp:    1.251    0.013    0.410
   1_occ:    1.251    0.013    0.410
   2_bss:    1.251    0.013    0.410
   2_xyz:    1.667    0.023    0.550
   2_adp:    1.667    0.023    0.550
   2_occ:    1.667    0.023    0.550
   3_bss:    1.667    0.023    0.550
   3_xyz:    1.692    0.031    0.691
   3_adp:    1.692    0.031    0.691
   3_occ:    1.692    0.031    0.691
   4_bss:    1.692    0.031    0.691
   4_xyz:    1.973    0.045    0.804
   4_adp:    1.973    0.045    0.804
   4_occ:    1.973    0.045    0.804
   5_bss:    1.973    0.045    0.804
   5_xyz:    2.066    0.054    0.867
   5_adp:    2.066    0.054    0.867
   5_occ:    2.066    0.054    0.867
   5_bss:    2.066    0.054    0.867
------------------------------------------------------------------------

CPU time actual refinement: 346.43


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_608/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_608/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_608/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_608/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_608/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 346.26 
  Macro-tasks:
    bulk solvent and scale       = 42.07  
    individual site refinement   = 149.31 
    weights calculation          = 32.61  
    collect and process          = 6.45   
    model show statistics        = 0.15   
    TOTAL for macro-tasks        = 230.59 
  Micro-tasks:
    mask                            = 2.95   
    f_calc                          = 107.05 
    alpha_beta                      = 8.23   
    target                          = 1.15   
    gradients_wrt_atomic_parameters = 119.23 
    fmodel                         = 7.26   
    r_factors                      = 0.27   
    phase_errors                   = 10.03  
    foms                           = 0.24   
    TOTAL for micro-tasks          = 256.41 
NUMBER OF MASK CALCS=  6
Time per interpreted Python bytecode instruction: 4.798 micro seconds
Total CPU time: 6.00 minutes
from_scatterers_fft:    655 calls, 106.70 s
gradients_fft:          600 calls, 105.29 s

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

# Date 2008-01-16 Time 01:58:34 PST -0800 (1200477514.00 s)
Start R-work = 0.4932, R-free = 0.4914 (no bulk solvent and anisotropic scale)
Final R-work = 0.1542, R-free = 0.2036 (no bulk solvent and anisotropic scale)

Start R-work = 0.4843, R-free = 0.4790
Final R-work = 0.1392, R-free = 0.1902