# Date 2008-01-16 Time 00:51:55 PST -0800 (1200473515.73 s)
#phil __OFF__

Command line arguments: "../190.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = moonbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 22995
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 190

-------------------------------------------------------------------------------
  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: (68.845, 47.1647, 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: 3.30, per 1000 atoms: 1.17


================================== 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: (68.845, 47.1647, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7559 1.96064
Completeness in resolution range: 0.953839
Completeness with d_max=infinity: 0.950876

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.7559
                             d_min =   1.9606

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: (68.845, 47.1647, 85.5261, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.7559 1.96064
Completeness in resolution range: 0.953839
Completeness with d_max=infinity: 0.950876

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.7563 -  4.1948 [2168/2196]  1950   218  10.1%
  bin  2:  4.1948 -  3.3422 [2055/2078]  1851   204   9.9%
  bin  3:  3.3422 -  2.9235 [2051/2073]  1846   205  10.0%
  bin  4:  2.9235 -  2.6579 [2027/2046]  1824   203  10.0%
  bin  5:  2.6579 -  2.4683 [2007/2036]  1797   210  10.5%
  bin  6:  2.4683 -  2.3234 [2003/2045]  1814   189   9.4%
  bin  7:  2.3234 -  2.2074 [1988/2024]  1789   199  10.0%
  bin  8:  2.2074 -  2.1116 [1988/2025]  1785   203  10.2%
  bin  9:  2.1116 -  2.0305 [1969/2001]  1778   191   9.7%
  bin 10:  2.0305 -  1.9606 [1333/2013]  1196   137  10.3%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_190/model_refine_data.mtz


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

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

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

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: " SG  CYS A 168 " - " SG ACYS A 201 " distance=2.08
    Simple disulfide: " SG  CYS A 168 " - " SG BCYS A 201 " distance=1.98
    Simple disulfide: " SG  CYS A 254 " - " SG  CYS A 260 " distance=2.05
  Time building geometry restraints manager: 0.14 seconds
  Histogram of bond lengths:
        1.21 -     1.38: 943
        1.38 -     1.56: 1465
        1.56 -     1.73: 7
        1.73 -     1.90: 21
        1.90 -     2.08: 3
  Bond restraints sorted by residual:
             atom i - atom j            ideal  model  delta   weight residual
  " SG  CYS A 168 " - " SG BCYS A 201 " 2.031  1.983  0.048 2.50e+03 5.87e+00
  " C   GLN A  88 " - " N   GLN A  89 " 1.329  1.360 -0.031 5.10e+03 4.97e+00
  " SG  CYS A 168 " - " SG ACYS A 201 " 2.031  2.075 -0.044 2.50e+03 4.89e+00
  " CB  CYS A 201 " - " SG ACYS A 201 " 1.808  1.738  0.070 9.18e+02 4.46e+00
  " C   PRO A 198 " - " N   ILE A 199 " 1.329  1.301  0.028 5.10e+03 4.10e+00
  ... (remaining 2434 not shown)
  Histogram of nonbonded interaction distances:
        1.35 -     2.06: 13
        2.06 -     2.77: 531
        2.77 -     3.48: 4599
        3.48 -     4.19: 9482
        4.19 -     4.90: 14061
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.351 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.476 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  37 " - " O   HOH Z 416 "  1.527 3.040 -x+1,y-1/2,-z+1/2
  " O   HOH Z 109 " - " O   HOH Z 417 "  1.737 3.040 -x+1,y-1/2,-z+1/2
  " CE BMET A  47 " - " O  BHOH Z  74 "  1.806 3.460
  ... (remaining 28681 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_190/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_190/model_refine_001.geo

CPU time processing inputs: 9.27


============================ 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 = 68.845 47.16465 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: 1.96 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4599   r_free= 0.4504   ksol= 0.00   Bsol= 0.00   scale= 0.816    |
|                                                                             |
| 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:   0.67 A                  |
| x-ray target function (ml) for work reflections: 6.257515                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7563 -  4.6783 0.99   1400  157 0.3784 0.3737      6.5495      6.5837|
|  2:  4.6783 -  3.7331 0.99   1352  150 0.3684 0.3546      6.7122      6.7228|
|  3:  3.7331 -  3.2671 0.99   1326  150 0.4095 0.3978      6.6191      6.6729|
|  4:  3.2671 -  2.9710 0.99   1311  134 0.4354 0.4203      6.4767      6.4225|
|  5:  2.9710 -  2.7596 0.98   1293  149 0.4782 0.4864      6.3514      6.3768|
|  6:  2.7596 -  2.5978 0.98   1294  143 0.4879 0.5371      6.2622      6.2019|
|  7:  2.5978 -  2.4683 0.99   1292  157 0.5020 0.4721      6.2444      6.1598|
|  8:  2.4683 -  2.3613 0.99   1317  129 0.5095 0.4860      6.1637      6.1573|
|  9:  2.3613 -  2.2708 0.98   1275  146 0.5017 0.5205         6.1      6.1556|
| 10:  2.2708 -  2.1927 0.97   1260  144 0.5127 0.4699      6.1099      6.0619|
| 11:  2.1927 -  2.1243 0.98   1286  145 0.5097 0.5248      6.0224      6.0519|
| 12:  2.1243 -  2.0637 0.99   1279  137 0.5296 0.5092      5.9762      6.0095|
| 13:  2.0637 -  2.0096 0.97   1263  134 0.5384 0.5059      5.9002      5.8485|
| 14:  2.0096 -  1.9606 0.54    682   84 0.5190 0.4963      5.8513      5.7456|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7563 -  4.6783  1400   157  0.69  35.31   0.81     0.70      71788.00|
|  2:  4.6783 -  3.7331  1352   150  0.72  33.58   0.91     0.78      95625.89|
|  3:  3.7331 -  3.2671  1326   150  0.64  40.28   0.87     0.75      98389.64|
|  4:  3.2671 -  2.9710  1311   134  0.58  45.73   0.82     0.67      84644.18|
|  5:  2.9710 -  2.7596  1293   149  0.48  53.21   0.75     0.58      73594.28|
|  6:  2.7596 -  2.5978  1294   143  0.45  55.92   0.74     0.52      64586.86|
|  7:  2.5978 -  2.4683  1292   157  0.44  56.84   0.76     0.50      59803.78|
|  8:  2.4683 -  2.3613  1317   129  0.44  56.90   0.75     0.51      51619.73|
|  9:  2.3613 -  2.2708  1275   146  0.43  57.76   0.75     0.51      48541.29|
| 10:  2.2708 -  2.1927  1260   144  0.43  57.76   0.77     0.51      43673.46|
| 11:  2.1927 -  2.1243  1286   145  0.39  60.93   0.75     0.48      43858.21|
| 12:  2.1243 -  2.0637  1279   137  0.36  62.97   0.78     0.47      42127.09|
| 13:  2.0637 -  2.0096  1263   134  0.35  64.15   0.75     0.44      35988.75|
| 14:  2.0096 -  1.9606   682    84  0.42  58.76   0.74     0.44      24454.49|
|alpha:            min =        0.44 max =            0.78 mean =         0.57|
|beta:             min =    24454.49 max =        98389.64 mean =     61516.60|
|figures of merit: min =        0.00 max =            1.00 mean =         0.49|
|phase err.(work): min =        0.00 max =           89.99 mean =        52.42|
|phase err.(test): min =        0.00 max =           89.84 mean =        52.44|
|-----------------------------------------------------------------------------|

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

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

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.657557             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 78.201   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.866503              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 80.403   (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 |  1.139 -  1.515:        4 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.515 -  1.891:       20 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.891 -  2.267:      150 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.267 -  2.643:      664 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.643 -  3.019:     1475 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  3.019 -  3.396:     2575 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.396 -  3.772:     4028 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.772 -  4.148:     5183 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.148 -  4.524:     6715 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.524 -  4.900:     7898 |
|-----------------------------------------------------------------------------|
|-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 |       53.191 |
| 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  1.139 |       2.482 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.557)------------------------------------------|
|    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 = 11.557)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4667   r_free= 0.4588   ksol= 0.00   Bsol= 0.00   scale= 0.784    |
|                                                                             |
| 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:   0.69 A                  |
| x-ray target function (ml) for work reflections: 6.260262                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4507   r_free= 0.4420   ksol= 0.35   Bsol= 11.03   scale= 1.017   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.43,8.39,8.30,0.00,0.00,0.00); trace/3= 8.37                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.68 A                  |
| x-ray target function (ml) for work reflections: 6.249729                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 9.939219              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 79.622   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.929545              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 78.686   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4507      final r-factor (work) = 0.3553          |
| start r-factor (free) = 0.4420      final r-factor (free) = 0.3779          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 84.3208 = 9.94 * 0.50 * 6.2640 + 1.00 * 53.1913                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.6517 = 9.94 * 0.50 * 6.1402 + 1.00 * 0.1372                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3553      final r-factor (work) = 0.3000          |
| start r-factor (free) = 0.3779      final r-factor (free) = 0.3409          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.7219 = 0.93 * 1.00 * 6.1402 + 1.00 * 0.0143                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.6000 = 0.93 * 1.00 * 6.0088 + 1.00 * 0.0145                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.557)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    79.01   11.84    None  None   None       |
|    all(noH): 2823   0      0.00    79.01   11.84    None  None   None       |
|    Sol.    : 438    0      0.00    79.01   27.42    None  None   None       |
|    Mac.    : 2385   0      0.00    67.16   8.98     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 -   7.901: 1403   |   5:    39.506 -  47.407:   71        |
|      1:     7.901 -  15.802:  697   |   6:    47.407 -  55.308:   28        |
|      2:    15.802 -  23.704:  328   |   7:    55.308 -  63.209:   14        |
|      3:    23.704 -  31.605:  172   |   8:    63.209 -  71.111:    5        |
|      4:    31.605 -  39.506:  104   |   9:    71.111 -  79.012:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3000 r_free = 0.3409             target_work(ml) = 5.968         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2994 r_free = 0.3403             target_work(ml) = 5.966         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2994   r_free= 0.3403   ksol= 0.35   Bsol= 11.03   scale= 1.103   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (8.43,8.39,8.30,0.00,0.00,0.00); trace/3= 8.37                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.38 A                  |
| x-ray target function (ml) for work reflections: 5.966340                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2951   r_free= 0.3339   ksol= 0.33   Bsol= 33.53   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.73,4.61,5.18,0.00,0.00,0.00); trace/3= 4.84                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.40 A                  |
| x-ray target function (ml) for work reflections: 5.964302                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 4.588547              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 96.628   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.394896              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 117.227  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2951      final r-factor (work) = 0.2031          |
| start r-factor (free) = 0.3339      final r-factor (free) = 0.2431          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.9224 = 4.59 * 0.50 * 6.0085 + 1.00 * 0.1372                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 13.3830 = 4.59 * 0.50 * 5.8034 + 1.00 * 0.0683                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2031      final r-factor (work) = 0.1802          |
| start r-factor (free) = 0.2431      final r-factor (free) = 0.2235          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.3077 = 0.39 * 1.00 * 5.8034 + 1.00 * 0.0159                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2138 = 0.39 * 1.00 * 5.5779 + 1.00 * 0.0111                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.557)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.83   12.18    None  None   None       |
|    all(noH): 2823   0      0.00    78.83   12.18    None  None   None       |
|    Sol.    : 438    0      1.47    78.83   32.71    None  None   None       |
|    Mac.    : 2385   0      0.00    76.70   8.41     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.883: 1513   |   5:    39.417 -  47.301:   83        |
|      1:     7.883 -  15.767:  658   |   6:    47.301 -  55.184:   64        |
|      2:    15.767 -  23.650:  217   |   7:    55.184 -  63.067:   24        |
|      3:    23.650 -  31.534:  123   |   8:    63.067 -  70.951:    9        |
|      4:    31.534 -  39.417:  128   |   9:    70.951 -  78.834:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1802 r_free = 0.2235             target_work(ml) = 5.536         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1799 r_free = 0.2229             target_work(ml) = 5.535         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1799   r_free= 0.2229   ksol= 0.33   Bsol= 33.53   scale= 1.052   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (4.73,4.61,5.18,0.00,0.00,0.00); trace/3= 4.84                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.534783                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1779   r_free= 0.2216   ksol= 0.32   Bsol= 32.06   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.51,3.33,3.83,0.00,0.00,0.00); trace/3= 3.22                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.20 A                  |
| x-ray target function (ml) for work reflections: 5.531749                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.765344              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 104.005  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.190798              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 129.251  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1779      final r-factor (work) = 0.1405          |
| start r-factor (free) = 0.2216      final r-factor (free) = 0.1808          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.9998 = 1.77 * 0.50 * 5.5870 + 1.00 * 0.0683                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.8458 = 1.77 * 0.50 * 5.4281 + 1.00 * 0.0546                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1405      final r-factor (work) = 0.1352          |
| start r-factor (free) = 0.1808      final r-factor (free) = 0.1722          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0465 = 0.19 * 1.00 * 5.4281 + 1.00 * 0.0109                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 1.0215 = 0.19 * 1.00 * 5.3032 + 1.00 * 0.0097                               |
|-----------------------------------------------------------------------------|
| number of iterations = 21      |    number of function evaluations = 21     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.557)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    75.97   12.15    None  None   None       |
|    all(noH): 2823   0      0.00    75.97   12.15    None  None   None       |
|    Sol.    : 438    0      1.99    75.65   33.30    None  None   None       |
|    Mac.    : 2385   0      0.00    75.97   8.27     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.597: 1533   |   5:    37.984 -  45.580:   96        |
|      1:     7.597 -  15.194:  663   |   6:    45.580 -  53.177:   66        |
|      2:    15.194 -  22.790:  175   |   7:    53.177 -  60.774:   33        |
|      3:    22.790 -  30.387:  117   |   8:    60.774 -  68.371:    8        |
|      4:    30.387 -  37.984:  127   |   9:    68.371 -  75.967:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1352 r_free = 0.1722             target_work(ml) = 5.279         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1350 r_free = 0.1721             target_work(ml) = 5.279         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1350   r_free= 0.1721   ksol= 0.32   Bsol= 32.06   scale= 1.023   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (2.51,3.33,3.83,0.00,0.00,0.00); trace/3= 3.22                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.278699                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1352   r_free= 0.1720   ksol= 0.32   Bsol= 35.33   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.79,2.80,3.30,0.00,0.00,0.00); trace/3= 2.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.279091                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.997328              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 117.250  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.184370              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 109.321  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1352      final r-factor (work) = 0.1188          |
| start r-factor (free) = 0.1720      final r-factor (free) = 0.1583          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.3541 = 2.00 * 0.50 * 5.3066 + 1.00 * 0.0546                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.2719 = 2.00 * 0.50 * 5.2183 + 1.00 * 0.0606                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1188      final r-factor (work) = 0.1170          |
| start r-factor (free) = 0.1583      final r-factor (free) = 0.1576          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9719 = 0.18 * 1.00 * 5.2183 + 1.00 * 0.0098                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.9645 = 0.18 * 1.00 * 5.1712 + 1.00 * 0.0111                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 30     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.557)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    78.05   12.03    None  None   None       |
|    all(noH): 2823   0      0.00    78.05   12.03    None  None   None       |
|    Sol.    : 438    0      1.56    69.48   33.13    None  None   None       |
|    Mac.    : 2385   0      0.00    78.05   8.16     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   7.806: 1573   |   5:    39.027 -  46.833:   96        |
|      1:     7.806 -  15.611:  668   |   6:    46.833 -  54.638:   63        |
|      2:    15.611 -  23.417:  149   |   7:    54.638 -  62.444:   20        |
|      3:    23.417 -  31.222:  123   |   8:    62.444 -  70.249:   10        |
|      4:    31.222 -  39.027:  119   |   9:    70.249 -  78.055:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1170 r_free = 0.1576             target_work(ml) = 5.169         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1169 r_free = 0.1576             target_work(ml) = 5.168         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1169   r_free= 0.1576   ksol= 0.32   Bsol= 35.33   scale= 1.009   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.79,2.80,3.30,0.00,0.00,0.00); trace/3= 2.63                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.167790                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1169   r_free= 0.1576   ksol= 0.32   Bsol= 35.66   scale= 1.005   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.64,2.61,3.21,0.00,0.00,0.00); trace/3= 2.49                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.14 A                  |
| x-ray target function (ml) for work reflections: 5.167657                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.535958              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 149.241  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.752399              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 108.327  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1169      final r-factor (work) = 0.1154          |
| start r-factor (free) = 0.1576      final r-factor (free) = 0.1566          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0317 = 1.54 * 0.50 * 5.1708 + 1.00 * 0.0606                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 4.0184 = 1.54 * 0.50 * 5.1625 + 1.00 * 0.0537                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1154      final r-factor (work) = 0.1134          |
| start r-factor (free) = 0.1566      final r-factor (free) = 0.1578          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.9134 = 0.75 * 1.00 * 5.1625 + 1.00 * 0.0292                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 3.8862 = 0.75 * 1.00 * 5.1504 + 1.00 * 0.0110                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 28     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.557)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    81.32   12.26    None  None   None       |
|    all(noH): 2823   0      0.00    81.32   12.26    None  None   None       |
|    Sol.    : 438    0      1.51    69.47   34.40    None  None   None       |
|    Mac.    : 2385   0      0.00    81.32   8.20     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   8.132: 1616   |   5:    40.662 -  48.794:  108        |
|      1:     8.132 -  16.265:  624   |   6:    48.794 -  56.927:   60        |
|      2:    16.265 -  24.397:  156   |   7:    56.927 -  65.059:   20        |
|      3:    24.397 -  32.530:  113   |   8:    65.059 -  73.191:    9        |
|      4:    32.530 -  40.662:  113   |   9:    73.191 -  81.324:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1134 r_free = 0.1578             target_work(ml) = 5.155         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1134 r_free = 0.1578             target_work(ml) = 5.155         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        5 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1134   r_free= 0.1578   ksol= 0.32   Bsol= 35.66   scale= 1.006   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.64,2.61,3.21,0.00,0.00,0.00); trace/3= 2.49                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.154834                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7563 -  4.6783 0.99   1400  157 0.1048 0.1312      5.4145      5.5546|
|  2:  4.6783 -  3.7331 0.99   1352  150 0.0881 0.1112       5.452      5.6374|
|  3:  3.7331 -  3.2671 0.99   1326  150 0.1070 0.1485      5.4738      5.8096|
|  4:  3.2671 -  2.9710 0.99   1311  134 0.1204 0.1571      5.4442      5.6111|
|  5:  2.9710 -  2.7596 0.98   1293  149 0.1332 0.1639      5.3301      5.4793|
|  6:  2.7596 -  2.5978 0.98   1294  143 0.1264 0.2020       5.225      5.5027|
|  7:  2.5978 -  2.4683 0.99   1292  157 0.1204 0.1589      5.1622      5.3695|
|  8:  2.4683 -  2.3613 0.99   1317  129 0.1184 0.1733       5.091      5.3418|
|  9:  2.3613 -  2.2708 0.98   1275  146 0.1189 0.1874      5.0279       5.319|
| 10:  2.2708 -  2.1927 0.97   1260  144 0.1137 0.1584      4.9655      5.1407|
| 11:  2.1927 -  2.1243 0.98   1286  145 0.1149 0.1741      4.9208      5.2569|
| 12:  2.1243 -  2.0637 0.99   1279  137 0.1107 0.1703      4.8586      5.1482|
| 13:  2.0637 -  2.0096 0.97   1263  134 0.1116 0.1753      4.7995      5.0508|
| 14:  2.0096 -  1.9606 0.54    682   84 0.1134 0.1793      4.7422      4.9629|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7563 -  4.6783  1400   157  0.94   8.97   0.98     0.96       7126.97|
|  2:  4.6783 -  3.7331  1352   150  0.95   7.76   1.02     1.01       8889.07|
|  3:  3.7331 -  3.2671  1326   150  0.94  11.03   1.03     1.03      10205.84|
|  4:  3.2671 -  2.9710  1311   134  0.92  13.30   1.01     1.01      10005.73|
|  5:  2.9710 -  2.7596  1293   149  0.90  15.89   1.00     0.97       8252.52|
|  6:  2.7596 -  2.5978  1294   143  0.90  16.34   0.98     0.95       7120.64|
|  7:  2.5978 -  2.4683  1292   157  0.91  15.37   0.98     0.95       6139.62|
|  8:  2.4683 -  2.3613  1317   129  0.91  15.29   1.00     0.98       5571.41|
|  9:  2.3613 -  2.2708  1275   146  0.91  15.57   1.01     0.98       4964.44|
| 10:  2.2708 -  2.1927  1260   144  0.90  15.78   1.00     0.97       4441.91|
| 11:  2.1927 -  2.1243  1286   145  0.90  15.70   1.00     0.97       4177.14|
| 12:  2.1243 -  2.0637  1279   137  0.91  14.96   1.01     1.00       3779.43|
| 13:  2.0637 -  2.0096  1263   134  0.90  16.03   1.01     1.00       3464.70|
| 14:  2.0096 -  1.9606   682    84  0.90  16.52   0.99     0.94       3019.53|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     3019.53 max =        10205.84 mean =      6373.69|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.98 mean =        14.03|
|phase err.(test): min =        0.00 max =           87.91 mean =        13.62|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1578   ksol= 0.32   Bsol= 39.96   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.85,0.13,0.72,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.154618                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.96 - 14.76 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1133   r_free= 0.1578   ksol= 0.32   Bsol= 39.96   scale= 1.008   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.85,0.13,0.72,0.00,0.00,0.00); trace/3= 0.00                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.15 A                  |
| x-ray target function (ml) for work reflections: 5.154618                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.7563 -  4.6783 0.99   1400  157 0.1048 0.1312       5.414      5.5548|
|  2:  4.6783 -  3.7331 0.99   1352  150 0.0883 0.1115      5.4536      5.6388|
|  3:  3.7331 -  3.2671 0.99   1326  150 0.1071 0.1486      5.4745      5.8101|
|  4:  3.2671 -  2.9710 0.99   1311  134 0.1205 0.1569       5.444      5.6106|
|  5:  2.9710 -  2.7596 0.98   1293  149 0.1331 0.1638      5.3295      5.4788|
|  6:  2.7596 -  2.5978 0.98   1294  143 0.1263 0.2019      5.2243      5.5016|
|  7:  2.5978 -  2.4683 0.99   1292  157 0.1204 0.1590      5.1614      5.3693|
|  8:  2.4683 -  2.3613 0.99   1317  129 0.1183 0.1731      5.0903      5.3407|
|  9:  2.3613 -  2.2708 0.98   1275  146 0.1189 0.1875      5.0276      5.3191|
| 10:  2.2708 -  2.1927 0.97   1260  144 0.1137 0.1585      4.9652      5.1403|
| 11:  2.1927 -  2.1243 0.98   1286  145 0.1148 0.1740      4.9206      5.2568|
| 12:  2.1243 -  2.0637 0.99   1279  137 0.1107 0.1704      4.8584      5.1482|
| 13:  2.0637 -  2.0096 0.97   1263  134 0.1116 0.1752      4.7991      5.0504|
| 14:  2.0096 -  1.9606 0.54    682   84 0.1134 0.1791      4.7415       4.962|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.7563 -  4.6783  1400   157  0.94   8.97   0.98     0.96       7115.96|
|  2:  4.6783 -  3.7331  1352   150  0.95   7.77   1.02     1.01       8900.24|
|  3:  3.7331 -  3.2671  1326   150  0.94  11.05   1.03     1.03      10227.53|
|  4:  3.2671 -  2.9710  1311   134  0.92  13.30   1.01     1.01      10001.03|
|  5:  2.9710 -  2.7596  1293   149  0.90  15.89   1.00     0.97       8241.79|
|  6:  2.7596 -  2.5978  1294   143  0.90  16.33   0.98     0.95       7110.46|
|  7:  2.5978 -  2.4683  1292   157  0.91  15.36   0.99     0.95       6129.72|
|  8:  2.4683 -  2.3613  1317   129  0.91  15.28   1.00     0.98       5563.07|
|  9:  2.3613 -  2.2708  1275   146  0.91  15.56   1.01     0.99       4959.13|
| 10:  2.2708 -  2.1927  1260   144  0.90  15.78   1.01     0.98       4439.99|
| 11:  2.1927 -  2.1243  1286   145  0.90  15.69   1.01     0.97       4175.19|
| 12:  2.1243 -  2.0637  1279   137  0.91  14.96   1.02     1.00       3777.64|
| 13:  2.0637 -  2.0096  1263   134  0.90  16.02   1.01     1.00       3461.02|
| 14:  2.0096 -  1.9606   682    84  0.90  16.51   0.99     0.95       3013.63|
|alpha:            min =        0.95 max =            1.03 mean =         0.98|
|beta:             min =     3013.63 max =        10227.53 mean =      6370.79|
|figures of merit: min =        0.00 max =            1.00 mean =         0.91|
|phase err.(work): min =        0.00 max =           89.94 mean =        14.03|
|phase err.(test): min =        0.00 max =           87.96 mean =        13.61|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.557)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      2.57    83.90   14.84    None  None   None       |
|    all(noH): 2823   0      2.57    83.90   14.84    None  None   None       |
|    Sol.    : 438    0      4.08    72.05   36.97    None  None   None       |
|    Mac.    : 2385   0      2.57    83.90   10.77    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     2.574 -  10.707: 1616   |   5:    43.236 -  51.368:  108        |
|      1:    10.707 -  18.839:  624   |   6:    51.368 -  59.501:   60        |
|      2:    18.839 -  26.971:  156   |   7:    59.501 -  67.633:   20        |
|      3:    26.971 -  35.104:  113   |   8:    67.633 -  75.766:    9        |
|      4:    35.104 -  43.236:  113   |   9:    75.766 -  83.898:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 304         
Filter by distance & map next to the model:
   mapped sites are within: 0.336 - 4.787
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 302 from: 304
   mapped sites are within: 0.725 - 4.787

peak=   11.139 closest distance to " CB  VAL A 230 " =    1.437
peak=    8.999 closest distance to " CG2 VAL A 296 " =    1.305
peak=    6.183 closest distance to " CG  LEU A   5 " =    1.209
peak=    5.468 closest distance to " CD2 LEU A   5 " =    1.137
peak=    5.438 closest distance to " CB  ARG A 275 " =    0.959
peak=    5.291 closest distance to " O   HOH Z 193 " =    1.739
peak=    5.236 closest distance to " O   HOH Z 142 " =    1.816
peak=    5.052 closest distance to " CB  ASN A 187 " =    1.916
peak=    5.035 closest distance to " CB  GLN A 223 " =    1.434
peak=    5.014 closest distance to " CG  PRO A  54 " =    1.295
peak=    4.950 closest distance to " NE2 GLN A  11 " =    1.086
peak=    4.913 closest distance to " O   HOH Z  85 " =    1.627
peak=    4.900 closest distance to " O   HOH Z 402 " =    1.481
peak=    4.891 closest distance to " CG  LEU A 228 " =    1.142
peak=    4.838 closest distance to " NH2 ARG A  56 " =    2.119
peak=    4.801 closest distance to " CB  VAL A 296 " =    0.988
peak=    4.789 closest distance to " CG  PRO A 213 " =    1.279
peak=    4.743 closest distance to " CB  PRO A  54 " =    0.984
peak=    4.739 closest distance to " CB  GLN A 183 " =    1.302
peak=    4.725 closest distance to " O   HOH Z 209 " =    2.321
peak=    4.650 closest distance to " O   HOH Z 124 " =    1.557
peak=    4.640 closest distance to " CB  SER A  63 " =    1.211
peak=    4.602 closest distance to " CG  PRO A 198 " =    1.167
peak=    4.588 closest distance to " CB  VAL A 230 " =    1.153
peak=    4.584 closest distance to " O   HOH Z 232 " =    2.295
peak=    4.527 closest distance to " O   HOH Z 346 " =    1.555
peak=    4.513 closest distance to " O   HOH Z 272 " =    1.923
peak=    4.441 closest distance to " O   SER A  87 " =    2.234
peak=    4.440 closest distance to " CD1AILE A 234 " =    0.930
peak=    4.428 closest distance to " O   HOH Z  59 " =    2.067
peak=    4.428 closest distance to " C   PRO A 198 " =    1.491
peak=    4.395 closest distance to " CG  PRO A 243 " =    1.169
peak=    4.362 closest distance to " O   HOH Z 234 " =    3.587
peak=    4.359 closest distance to " CD2 LEU A 228 " =    1.234
peak=    4.332 closest distance to " CB  SER A   3 " =    1.251
peak=    4.315 closest distance to " CA  TYR A  30 " =    0.955
peak=    4.304 closest distance to " O   HOH Z 298 " =    1.827
peak=    4.278 closest distance to " CB  GLU A 152 " =    1.134
peak=    4.275 closest distance to " O   HOH Z 403 " =    1.875
peak=    4.257 closest distance to " O   HOH Z  97 " =    1.967
peak=    4.250 closest distance to " N   ASN A  39 " =    1.175
peak=    4.235 closest distance to " O   HOH Z 128 " =    2.189
peak=    4.205 closest distance to " O   HOH Z 368 " =    2.136
peak=    4.204 closest distance to " O   HOH Z 423 " =    1.823
peak=    4.188 closest distance to " CA  VAL A  41 " =    0.830
peak=    4.174 closest distance to " O   HOH Z 102 " =    1.268
peak=    4.171 closest distance to " CB  ASN A 148 " =    1.389
peak=    4.160 closest distance to " O   HOH Z  97 " =    2.369
peak=    4.155 closest distance to " O   HOH Z 369 " =    2.402
peak=    4.150 closest distance to " CD2 TRP A 179 " =    1.419
peak=    4.141 closest distance to " O   HOH Z  54 " =    1.569
peak=    4.125 closest distance to " O   HOH Z 345 " =    2.914
peak=    4.091 closest distance to " O   HOH Z  42 " =    2.313
peak=    4.080 closest distance to " CB  TYR A 169 " =    0.811
peak=    4.077 closest distance to " CB  ARG A  79 " =    1.336
peak=    4.071 closest distance to " O   HOH Z 316 " =    2.833
peak=    4.062 closest distance to " O   HOH Z  63 " =    2.287
peak=    4.046 closest distance to " O   HOH Z 327 " =    1.632
peak=    4.033 closest distance to " O   HOH Z 303 " =    2.011
peak=    4.027 closest distance to " CA  ALA A  21 " =    1.138
peak=    4.025 closest distance to " O   HOH Z  61 " =    1.672
peak=    4.002 closest distance to " O   HOH Z 411 " =    3.705
peak=    4.001 closest distance to " CB  VAL A 265 " =    1.211
peak=    4.000 closest distance to " O   HOH Z 322 " =    2.077
peak=    3.981 closest distance to " ND2 ASN A 187 " =    1.541
peak=    3.977 closest distance to " CD  ARG A 269 " =    1.069
peak=    3.977 closest distance to " O   HOH Z 287 " =    1.789
peak=    3.970 closest distance to " NZ  LYS A 117 " =    2.946
peak=    3.957 closest distance to " O   HOH Z  78 " =    1.638
peak=    3.943 closest distance to " O   HOH Z 130 " =    2.751
peak=    3.931 closest distance to " CB  ALA A 295 " =    1.092
peak=    3.930 closest distance to " O   TRP A 274 " =    1.927
peak=    3.918 closest distance to " CB  GLU A 128 " =    1.088
peak=    3.916 closest distance to " O   HOH Z  44 " =    1.952
peak=    3.910 closest distance to " CA  ALA A  51 " =    1.037
peak=    3.900 closest distance to " O   HOH Z 344 " =    2.726
peak=    3.896 closest distance to " O   HOH Z  48 " =    1.706
peak=    3.892 closest distance to " CB  ALA A   9 " =    1.602
peak=    3.891 closest distance to " CG  ARG A  66 " =    1.002
peak=    3.888 closest distance to " O   HOH Z 357 " =    1.902
peak=    3.886 closest distance to " CB  TRP A 179 " =    1.152
peak=    3.874 closest distance to " O   HOH Z 189 " =    2.523
peak=    3.868 closest distance to " O   HOH Z  80 " =    1.683
peak=    3.855 closest distance to " OE1 GLU A   2 " =    2.126
peak=    3.851 closest distance to " O   HOH Z 414 " =    1.491
peak=    3.850 closest distance to " CA  LYS A 117 " =    1.272
peak=    3.850 closest distance to " O   HOH Z 130 " =    2.401
peak=    3.850 closest distance to " CB  GLU A 277 " =    3.529
peak=    3.846 closest distance to " O   HOH Z 427 " =    2.651
peak=    3.842 closest distance to " O   HOH Z 250 " =    1.400
peak=    3.824 closest distance to " CA  ASP A 140 " =    1.148
peak=    3.821 closest distance to " CB  ALA A 248 " =    1.379
peak=    3.821 closest distance to " CG AARG A 275 " =    1.144
peak=    3.819 closest distance to " CG2 ILE A 120 " =    1.232
peak=    3.816 closest distance to " O   HOH Z 371 " =    3.222
peak=    3.791 closest distance to " CB  SER A  26 " =    1.701
peak=    3.790 closest distance to " CG1 ILE A  33 " =    1.324
peak=    3.786 closest distance to " CB  ARG A 139 " =    0.909
peak=    3.778 closest distance to " O   HOH Z 245 " =    1.379
peak=    3.772 closest distance to " O   HOH Z 227 " =    1.605
peak=    3.762 closest distance to " CG2 ILE A  20 " =    1.479
peak=    3.759 closest distance to " O   HOH Z 426 " =    1.473
peak=    3.757 closest distance to " O   HOH Z 416 " =    2.772
peak=    3.745 closest distance to " O   HOH Z 389 " =    1.798
peak=    3.733 closest distance to " O   HOH Z 284 " =    2.908
peak=    3.731 closest distance to " O   HOH Z 406 " =    1.212
peak=    3.725 closest distance to " CG1BVAL A  72 " =    1.554
peak=    3.719 closest distance to " CG2 VAL A 257 " =    0.841
peak=    3.710 closest distance to " O   HOH Z 404 " =    2.158
peak=    3.704 closest distance to " O   HOH Z 197 " =    3.019
peak=    3.697 closest distance to " O   HOH Z 203 " =    1.622
peak=    3.694 closest distance to " O   HOH Z  66 " =    2.204
peak=    3.693 closest distance to " O   ASP A 124 " =    1.243
peak=    3.692 closest distance to " O   HOH Z  54 " =    2.378
peak=    3.691 closest distance to " CB  TRP A 266 " =    1.076
peak=    3.673 closest distance to " O   HOH Z 273 " =    2.779
peak=    3.666 closest distance to " CG  GLN A  77 " =    2.270
peak=    3.662 closest distance to " O   HOH Z 408 " =    1.586
peak=    3.650 closest distance to " O   HOH Z 137 " =    1.696
peak=    3.642 closest distance to " O   HOH Z 134 " =    1.443
peak=    3.633 closest distance to " O   HOH Z 417 " =    3.291
peak=    3.630 closest distance to " CB  VAL A 202 " =    1.537
peak=    3.621 closest distance to " OD2 ASP A 298 " =    3.944
peak=    3.613 closest distance to " O   HOH Z 422 " =    2.527
peak=    3.612 closest distance to " CD1 LEU A  96 " =    0.740
peak=    3.609 closest distance to " O   HOH Z 263 " =    1.574
peak=    3.608 closest distance to " O   HOH Z 236 " =    1.341
peak=    3.586 closest distance to " O   HOH Z 118 " =    1.491
peak=    3.585 closest distance to " O   HOH Z  40 " =    1.615
peak=    3.584 closest distance to " O   HOH Z 313 " =    1.839
peak=    3.584 closest distance to " O   HOH Z  15 " =    2.058
peak=    3.584 closest distance to " O   HOH Z 128 " =    1.875
peak=    3.582 closest distance to " CB  ASN A  39 " =    0.831
peak=    3.582 closest distance to " O   HOH Z 366 " =    2.827
peak=    3.576 closest distance to " CG BARG A 102 " =    1.796
peak=    3.574 closest distance to " OD1 ASN A  69 " =    2.624
peak=    3.565 closest distance to " O   HOH Z 421 " =    1.629
peak=    3.562 closest distance to " O   ARG A  56 " =    2.747
peak=    3.561 closest distance to " O   HOH Z 425 " =    1.353
peak=    3.556 closest distance to " CD  ARG A 159 " =    0.725
peak=    3.552 closest distance to " O   HOH Z 248 " =    1.686
peak=    3.548 closest distance to " CB  THR A  31 " =    1.581
peak=    3.547 closest distance to " O   HOH Z  47 " =    1.757
peak=    3.545 closest distance to " OD1 ASP A 286 " =    1.743
peak=    3.543 closest distance to " O   HOH Z 109 " =    2.164
peak=    3.542 closest distance to " OD2 ASP A 286 " =    2.639
peak=    3.540 closest distance to " CA  ARG A  36 " =    1.009
peak=    3.538 closest distance to " CD2 TYR A  30 " =    0.863
peak=    3.538 closest distance to " NH2BARG A 145 " =    2.337
peak=    3.537 closest distance to " CB  HIS A 108 " =    0.876
peak=    3.519 closest distance to " OH  TYR A 116 " =    1.109
peak=    3.515 closest distance to " CB AVAL A  41 " =    1.279
peak=    3.514 closest distance to " O   HOH Z 261 " =    1.805
peak=    3.502 closest distance to " O   HOH Z 425 " =    1.970
peak=    3.501 closest distance to " CG  MET A 185 " =    1.142
peak=    3.496 closest distance to " O   HOH Z 367 " =    3.455
peak=    3.496 closest distance to " O   HOH Z 435 " =    1.958
peak=    3.495 closest distance to " CB  ASN A 110 " =    1.093
peak=    3.487 closest distance to " CB  PRO A 198 " =    1.005
peak=    3.486 closest distance to " O   HOH Z 193 " =    2.031
peak=    3.483 closest distance to " CA  ASN A 215 " =    1.142
peak=    3.479 closest distance to " CB  GLN A 278 " =    0.943
peak=    3.465 closest distance to " O   HOH Z 209 " =    2.333
peak=    3.456 closest distance to " O   HOH Z 406 " =    1.346
peak=    3.456 closest distance to " CE1 TYR A 186 " =    1.301
peak=    3.452 closest distance to " O   HOH Z 261 " =    2.178
peak=    3.452 closest distance to " CZ  PHE A 218 " =    1.139
peak=    3.449 closest distance to " OG1 THR A 294 " =    2.296
peak=    3.444 closest distance to " O   HOH Z 261 " =    2.010
peak=    3.444 closest distance to " O   HOH Z 214 " =    2.536
peak=    3.442 closest distance to " O   HOH Z 419 " =    1.666
peak=    3.440 closest distance to " CE1 HIS A 108 " =    1.162
peak=    3.426 closest distance to " O   HOH Z 374 " =    2.379
peak=    3.424 closest distance to " CD  GLN A 194 " =    1.483
peak=    3.418 closest distance to " O   HOH Z 118 " =    1.201
peak=    3.415 closest distance to " O   HOH Z 158 " =    3.015
peak=    3.409 closest distance to " O   HOH Z 154 " =    1.416
peak=    3.403 closest distance to " CD2 LEU A 297 " =    0.904
peak=    3.400 closest distance to " O   HOH Z 250 " =    1.481
peak=    3.399 closest distance to " O   HOH Z 227 " =    2.140
peak=    3.395 closest distance to " CA  ASN A 176 " =    1.028
peak=    3.385 closest distance to " O   HOH Z 303 " =    1.531
peak=    3.372 closest distance to " CA  GLN A 194 " =    1.120
peak=    3.371 closest distance to " O   HOH Z 247 " =    1.302
peak=    3.369 closest distance to " O   HOH Z 423 " =    3.258
peak=    3.369 closest distance to " CD2 HIS A  81 " =    1.057
peak=    3.368 closest distance to " N   PHE A 130 " =    1.312
peak=    3.365 closest distance to " CB  GLN A 205 " =    1.189
peak=    3.364 closest distance to " O   HOH Z 148 " =    3.246
peak=    3.360 closest distance to " CB  ALA A   1 " =    1.195
peak=    3.359 closest distance to " CA  VAL A 126 " =    1.100
peak=    3.354 closest distance to " ND2 ASN A 110 " =    1.621
peak=    3.354 closest distance to " CB  SER A 273 " =    0.881
peak=    3.353 closest distance to " CG  LEU A 167 " =    1.127
peak=    3.352 closest distance to " CD  LYS A 119 " =    1.940
peak=    3.350 closest distance to " O   HOH Z 286 " =    2.281
peak=    3.349 closest distance to " CB  ALA A 291 " =    1.284
peak=    3.344 closest distance to " NZ  LYS A  76 " =    1.866
peak=    3.343 closest distance to " OG BSER A 164 " =    2.124
peak=    3.342 closest distance to " CA  GLY A  80 " =    1.066
peak=    3.341 closest distance to " O   GLY A  91 " =    1.763
peak=    3.338 closest distance to " CD1 ILE A 106 " =    1.226
peak=    3.333 closest distance to " O   HOH Z 222 " =    2.405
peak=    3.329 closest distance to " O   HOH Z 244 " =    1.602
peak=    3.327 closest distance to " O   HOH Z   3 " =    1.638
peak=    3.320 closest distance to " O   HOH Z 145 " =    3.729
peak=    3.320 closest distance to " CA  LYS A 290 " =    1.175
peak=    3.319 closest distance to " O   HOH Z 344 " =    1.849
peak=    3.317 closest distance to " O   HOH Z  88 " =    2.938
peak=    3.315 closest distance to " O   HOH Z 383 " =    1.883
peak=    3.314 closest distance to " O   HOH Z 280 " =    2.528
peak=    3.313 closest distance to " O   HOH Z 147 " =    1.697
peak=    3.312 closest distance to " N   SER A 135 " =    1.268
peak=    3.310 closest distance to " O   HOH Z  21 " =    1.769
peak=    3.307 closest distance to " CG2 THR A 294 " =    1.630
peak=    3.307 closest distance to " C   ALA A 299 " =    0.896
peak=    3.307 closest distance to " CD  LYS A 166 " =    1.354
peak=    3.307 closest distance to " NH2 ARG A 156 " =    1.026
peak=    3.307 closest distance to " CB  ASN A 215 " =    1.072
peak=    3.301 closest distance to " CA  SER A 146 " =    1.926
peak=    3.299 closest distance to " CE  LYS A 119 " =    1.025
peak=    3.293 closest distance to " O   HOH Z 411 " =    1.792
peak=    3.292 closest distance to " O   HOH Z 299 " =    4.319
peak=    3.291 closest distance to " CG1 VAL A 296 " =    1.218
peak=    3.289 closest distance to " O   HOH Z 345 " =    1.555
peak=    3.288 closest distance to " O   HOH Z   9 " =    2.113
peak=    3.288 closest distance to " O   HOH Z 380 " =    1.977
peak=    3.283 closest distance to " CZ2 TRP A 179 " =    1.836
peak=    3.283 closest distance to " O   HOH Z 253 " =    1.441
peak=    3.281 closest distance to " O   HOH Z 132 " =    2.462
peak=    3.277 closest distance to " CB  THR A  52 " =    1.141
peak=    3.277 closest distance to " O   HOH Z 329 " =    3.776
peak=    3.275 closest distance to " N   TYR A 116 " =    1.598
peak=    3.274 closest distance to " CG2 ILE A 106 " =    0.847
peak=    3.273 closest distance to " O   HOH Z 359 " =    1.362
peak=    3.270 closest distance to " N   ARG A 190 " =    1.027
peak=    3.269 closest distance to " CG2 ILE A 234 " =    2.017
peak=    3.266 closest distance to " O   HOH Z 412 " =    2.045
peak=    3.264 closest distance to " NH1 ARG A 138 " =    1.276
peak=    3.262 closest distance to " CB  ARG A 190 " =    1.729
peak=    3.259 closest distance to " CD BLYS A 290 " =    1.159
peak=    3.258 closest distance to " OG  SER A  97 " =    2.557
peak=    3.256 closest distance to " NH2 ARG A  79 " =    1.290
peak=    3.255 closest distance to " OG  SER A  62 " =    2.800
peak=    3.254 closest distance to " O   HOH Z  89 " =    1.517
peak=    3.253 closest distance to " CB  ARG A 138 " =    0.791
peak=    3.252 closest distance to " O   HOH Z 251 " =    1.672
peak=    3.250 closest distance to " O   HOH Z 108 " =    2.432
peak=    3.249 closest distance to " C   ILE A 106 " =    1.901
peak=    3.241 closest distance to " CB  TYR A 247 " =    0.942
peak=    3.241 closest distance to " O   HOH Z 438 " =    1.962
peak=    3.240 closest distance to " CG1 ILE A  49 " =    1.388
peak=    3.226 closest distance to " O   HOH Z 388 " =    2.023
peak=    3.224 closest distance to " CA  ASP A 162 " =    1.104
peak=    3.222 closest distance to " C   PHE A  59 " =    0.916
peak=    3.220 closest distance to " O   HOH Z  61 " =    1.450
peak=    3.216 closest distance to " O   HOH Z  71 " =    1.931
peak=    3.216 closest distance to " O   HOH Z  59 " =    2.092
peak=    3.215 closest distance to " CB  SER A 141 " =    1.086
peak=    3.210 closest distance to " NZ  LYS A 119 " =    1.611
peak=    3.207 closest distance to " CG2 THR A 221 " =    1.234
peak=    3.202 closest distance to " CE  LYS A  48 " =    1.196
peak=    3.195 closest distance to " O   HOH Z 352 " =    1.272
peak=    3.195 closest distance to " CG  LYS A  76 " =    1.098
peak=    3.194 closest distance to " C   ALA A   1 " =    1.761
peak=    3.191 closest distance to " N   ARG A 156 " =    1.358
peak=    3.190 closest distance to " O   HOH Z 113 " =    1.922
peak=    3.182 closest distance to " O   HOH Z 361 " =    3.154
peak=    3.171 closest distance to " O   HOH Z  88 " =    2.584
peak=    3.160 closest distance to " O   HOH Z 185 " =    1.641
peak=    3.159 closest distance to " O   HOH Z 183 " =    1.711
peak=    3.159 closest distance to " CA  MET A 105 " =    1.081
peak=    3.158 closest distance to " O   HOH Z 337 " =    3.478
peak=    3.152 closest distance to " O   HOH Z 291 " =    1.645
peak=    3.151 closest distance to " O   HOH Z 298 " =    4.787
peak=    3.150 closest distance to " O   HOH Z 175 " =    2.087
peak=    3.147 closest distance to " O   HOH Z  50 " =    2.067
peak=    3.147 closest distance to " O   HOH Z  35 " =    2.265
peak=    3.137 closest distance to " CB  LYS A 290 " =    1.106
peak=    3.135 closest distance to " O   HOH Z 178 " =    1.704
peak=    3.134 closest distance to " NH1AARG A 145 " =    1.111
peak=    3.134 closest distance to " CZ2 TRP A 150 " =    1.141
peak=    3.126 closest distance to " CA  ALA A  84 " =    1.284
peak=    3.125 closest distance to " O   HOH Z 188 " =    2.220
peak=    3.121 closest distance to " CG1 ILE A 120 " =    1.158
peak=    3.119 closest distance to " CB  ASN A 142 " =    1.156
peak=    3.113 closest distance to " CB  VAL A 268 " =    0.829
peak=    3.112 closest distance to " CB  SER A 216 " =    0.799
peak=    3.107 closest distance to " O   HOH Z  11 " =    2.385
peak=    3.100 closest distance to " O   HOH Z 215 " =    1.399
peak=    3.098 closest distance to " CB  LEU A 255 " =    0.762
peak=    3.094 closest distance to " CB  PRO A 243 " =    1.142
peak=    3.092 closest distance to " O   HOH Z 368 " =    3.600
peak=    3.092 closest distance to " NH2BARG A 190 " =    1.882
peak=    3.088 closest distance to " O   HOH Z  46 " =    1.481
peak=    3.080 closest distance to " CB  ALA A 242 " =    1.001
peak=    3.071 closest distance to " O   HOH Z  39 " =    2.625
peak=    3.067 closest distance to " O   HOH Z 192 " =    1.789
peak=    3.066 closest distance to " O  BHOH Z  74 " =    1.468
peak=    3.053 closest distance to " CD1 LEU A 228 " =    1.760
peak=    3.041 closest distance to " CB  ARG A 259 " =    1.923
peak=    3.030 closest distance to " CZ2 TRP A 274 " =    1.563

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 203         
Filter by distance & map next to the model:
   mapped sites are within: 0.667 - 5.904
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 202 from: 203
   mapped sites are within: 0.723 - 5.904

peak=   -4.947 closest distance to " CG2 VAL A 230 " =    0.730
peak=   -4.600 closest distance to " SG  CYS A 254 " =    3.188
peak=   -4.448 closest distance to " CD  ARG A 156 " =    2.066
peak=   -4.395 closest distance to " O   HOH Z 290 " =    1.001
peak=   -4.388 closest distance to " O   HOH Z 266 " =    4.799
peak=   -4.388 closest distance to " OXT GLY A 302 " =    2.739
peak=   -4.385 closest distance to " CD1 LEU A 101 " =    2.421
peak=   -4.347 closest distance to " CG2BVAL A  41 " =    2.600
peak=   -4.275 closest distance to " C   HIS A 108 " =    1.203
peak=   -4.259 closest distance to " CE2 TYR A  30 " =    2.812
peak=   -4.255 closest distance to " CD  GLN A  58 " =    1.218
peak=   -4.221 closest distance to " N   ALA A 248 " =    1.702
peak=   -4.165 closest distance to " O   PRO A 163 " =    2.030
peak=   -4.154 closest distance to " O   HOH Z 166 " =    1.931
peak=   -4.075 closest distance to " OG BSER A 134 " =    1.269
peak=   -4.074 closest distance to " O   HOH Z 351 " =    1.471
peak=   -4.027 closest distance to " ND2 ASN A  45 " =    0.989
peak=   -3.993 closest distance to " CG  GLN A 223 " =    2.218
peak=   -3.968 closest distance to " CB  ALA A 161 " =    2.533
peak=   -3.946 closest distance to " CB  PHE A 192 " =    1.990
peak=   -3.944 closest distance to " ND2 ASN A 187 " =    1.603
peak=   -3.898 closest distance to " OG  SER A   3 " =    1.615
peak=   -3.885 closest distance to " O   ASN A  45 " =    1.841
peak=   -3.871 closest distance to " CA  VAL A  67 " =    2.679
peak=   -3.864 closest distance to " CG  ASP A 231 " =    0.846
peak=   -3.845 closest distance to " O   HOH Z 114 " =    3.150
peak=   -3.834 closest distance to " CB  GLN A  11 " =    1.861
peak=   -3.825 closest distance to " O   HOH Z 423 " =    2.191
peak=   -3.796 closest distance to " O   VAL A  67 " =    1.866
peak=   -3.794 closest distance to " C   THR A 279 " =    1.205
peak=   -3.753 closest distance to " O   HOH Z 102 " =    1.742
peak=   -3.738 closest distance to " N   ALA A 226 " =    1.943
peak=   -3.724 closest distance to " O   HOH Z  37 " =    1.801
peak=   -3.711 closest distance to " CB  ALA A 291 " =    2.375
peak=   -3.711 closest distance to " CB  ALA A 248 " =    2.021
peak=   -3.697 closest distance to " CG2 VAL A 296 " =    1.677
peak=   -3.694 closest distance to " O   HOH Z  13 " =    1.678
peak=   -3.690 closest distance to " O   MET A  40 " =    2.670
peak=   -3.678 closest distance to " OD1 ASN A  39 " =    2.115
peak=   -3.672 closest distance to " NE2 GLN A  88 " =    1.103
peak=   -3.660 closest distance to " OG ASER A 134 " =    1.238
peak=   -3.650 closest distance to " CD  ARG A 139 " =    1.607
peak=   -3.647 closest distance to " N   GLN A  58 " =    1.885
peak=   -3.641 closest distance to " O   ALA A 256 " =    1.522
peak=   -3.632 closest distance to " CG1 VAL A 112 " =    2.634
peak=   -3.631 closest distance to " ND2 ASN A  45 " =    1.112
peak=   -3.619 closest distance to " O   PHE A 218 " =    1.749
peak=   -3.611 closest distance to " OG  SER A  97 " =    2.251
peak=   -3.609 closest distance to " C   ASP A 231 " =    2.494
peak=   -3.606 closest distance to " O   HOH Z 431 " =    1.762
peak=   -3.606 closest distance to " O   HOH Z 165 " =    1.907
peak=   -3.598 closest distance to " O   HOH Z 166 " =    1.674
peak=   -3.596 closest distance to " CZ  TYR A 169 " =    1.808
peak=   -3.595 closest distance to " CE  MET A 105 " =    2.233
peak=   -3.592 closest distance to " O   SER A 210 " =    1.894
peak=   -3.591 closest distance to " O   HOH Z 362 " =    5.904
peak=   -3.588 closest distance to " O   ALA A 161 " =    1.714
peak=   -3.587 closest distance to " NE2 GLN A  88 " =    1.921
peak=   -3.582 closest distance to " ND2 ASN A  39 " =    1.156
peak=   -3.578 closest distance to " N   THR A 157 " =    1.488
peak=   -3.574 closest distance to " C   MET A 188 " =    1.495
peak=   -3.556 closest distance to " O   HOH Z 407 " =    2.738
peak=   -3.550 closest distance to " O   HOH Z  11 " =    1.786
peak=   -3.545 closest distance to " OD2 ASP A 191 " =    1.447
peak=   -3.524 closest distance to " CB  PRO A 163 " =    2.613
peak=   -3.522 closest distance to " CB  ASP A 132 " =    2.250
peak=   -3.520 closest distance to " N   VAL A 230 " =    1.123
peak=   -3.513 closest distance to " CB  PRO A 243 " =    2.624
peak=   -3.512 closest distance to " CD1 PHE A  59 " =    2.153
peak=   -3.509 closest distance to " CD1 LEU A 255 " =    2.684
peak=   -3.502 closest distance to " O   HOH Z 231 " =    2.278
peak=   -3.497 closest distance to " O   ASN A 187 " =    1.490
peak=   -3.495 closest distance to " CD2 LEU A 300 " =    2.804
peak=   -3.495 closest distance to " CE  LYS A 166 " =    3.055
peak=   -3.492 closest distance to " NH2AARG A 275 " =    4.738
peak=   -3.486 closest distance to " O   PRO A 198 " =    1.199
peak=   -3.475 closest distance to " CA  GLY A 133 " =    1.929
peak=   -3.467 closest distance to " N   THR A 235 " =    1.286
peak=   -3.457 closest distance to " O   GLY A  80 " =    2.352
peak=   -3.456 closest distance to " O   HOH Z 426 " =    1.736
peak=   -3.456 closest distance to " O   HOH Z 389 " =    1.785
peak=   -3.450 closest distance to " CB  ASN A  39 " =    2.212
peak=   -3.447 closest distance to " CB  ASP A 132 " =    2.324
peak=   -3.443 closest distance to " CG2 THR A 178 " =    2.221
peak=   -3.441 closest distance to " CG  PHE A 283 " =    2.770
peak=   -3.439 closest distance to " O   HOH Z 250 " =    1.348
peak=   -3.431 closest distance to " CG  GLU A 277 " =    1.112
peak=   -3.429 closest distance to " O   HOH Z 196 " =    2.202
peak=   -3.428 closest distance to " NH2 ARG A  66 " =    1.712
peak=   -3.415 closest distance to " O   HOH Z 353 " =    2.115
peak=   -3.405 closest distance to " O   HOH Z 372 " =    2.106
peak=   -3.398 closest distance to " O   HOH Z 126 " =    1.840
peak=   -3.397 closest distance to " CZ  PHE A 130 " =    0.946
peak=   -3.397 closest distance to " CB  PRO A 280 " =    2.037
peak=   -3.391 closest distance to " N   SER A 206 " =    1.800
peak=   -3.386 closest distance to " O   HOH Z 197 " =    5.059
peak=   -3.380 closest distance to " O   GLY A  75 " =    1.627
peak=   -3.379 closest distance to " CB  ALA A 248 " =    2.307
peak=   -3.374 closest distance to " NH2 ARG A  79 " =    1.969
peak=   -3.371 closest distance to " CD1 TYR A 247 " =    2.491
peak=   -3.369 closest distance to " O   HOH Z 427 " =    1.514
peak=   -3.368 closest distance to " CA  GLY A  23 " =    1.814
peak=   -3.366 closest distance to " CG1 VAL A  78 " =    2.520
peak=   -3.365 closest distance to " OG BSER A 134 " =    1.655
peak=   -3.359 closest distance to " O   HOH Z  17 " =    1.337
peak=   -3.357 closest distance to " NE2 GLN A 194 " =    1.714
peak=   -3.356 closest distance to " O   HOH Z 191 " =    5.287
peak=   -3.347 closest distance to " O   VAL A 197 " =    1.345
peak=   -3.345 closest distance to " OXT GLY A 302 " =    3.419
peak=   -3.343 closest distance to " O   HOH Z 174 " =    4.227
peak=   -3.326 closest distance to " CD2 TYR A 293 " =    2.083
peak=   -3.326 closest distance to " ND2 ASN A  69 " =    1.622
peak=   -3.323 closest distance to " CA  ASP A 298 " =    1.050
peak=   -3.322 closest distance to " CD  LYS A 289 " =    2.508
peak=   -3.306 closest distance to " O   HOH Z  71 " =    1.396
peak=   -3.305 closest distance to " N   HIS A 115 " =    2.049
peak=   -3.303 closest distance to " CH2 TRP A 179 " =    1.351
peak=   -3.300 closest distance to " CG  GLU A  53 " =    1.503
peak=   -3.300 closest distance to " CG2 ILE A 263 " =    2.222
peak=   -3.296 closest distance to " CB  PHE A 208 " =    2.303
peak=   -3.296 closest distance to " NH1 ARG A  66 " =    0.723
peak=   -3.291 closest distance to " O   SER A 146 " =    1.012
peak=   -3.287 closest distance to " O   HOH Z 131 " =    4.015
peak=   -3.287 closest distance to " O   HOH Z 111 " =    4.782
peak=   -3.285 closest distance to " CG  TRP A 266 " =    2.091
peak=   -3.283 closest distance to " OD2 ASP A  50 " =    1.338
peak=   -3.282 closest distance to " O   ALA A  51 " =    1.317
peak=   -3.280 closest distance to " O   HOH Z 397 " =    1.208
peak=   -3.279 closest distance to " CB  ALA A 291 " =    2.147
peak=   -3.273 closest distance to " O   HOH Z 385 " =    2.100
peak=   -3.270 closest distance to " CG  ASP A  50 " =    2.502
peak=   -3.270 closest distance to " O   HOH Z 377 " =    1.617
peak=   -3.269 closest distance to " O   HOH Z 256 " =    1.199
peak=   -3.268 closest distance to " CA  GLY A 241 " =    2.320
peak=   -3.264 closest distance to " CB  ALA A  43 " =    2.299
peak=   -3.264 closest distance to " O   GLU A 277 " =    0.924
peak=   -3.263 closest distance to " N   SER A 276 " =    1.220
peak=   -3.259 closest distance to " O   HOH Z 211 " =    1.624
peak=   -3.256 closest distance to " C   ALA A 158 " =    1.297
peak=   -3.255 closest distance to " O   TRP A  92 " =    1.830
peak=   -3.247 closest distance to " CB  SER A 210 " =    1.228
peak=   -3.244 closest distance to " OG BSER A 210 " =    1.356
peak=   -3.239 closest distance to " O   HOH Z 301 " =    2.282
peak=   -3.235 closest distance to " O   HOH Z 295 " =    1.428
peak=   -3.234 closest distance to " CB  LEU A  83 " =    2.347
peak=   -3.234 closest distance to " O   ILE A 120 " =    1.269
peak=   -3.233 closest distance to " CD2 LEU A 167 " =    1.738
peak=   -3.233 closest distance to " O   HOH Z 185 " =    2.364
peak=   -3.233 closest distance to " OG1 THR A  82 " =    1.304
peak=   -3.231 closest distance to " O   GLY A 196 " =    1.078
peak=   -3.225 closest distance to " O   ALA A 160 " =    1.415
peak=   -3.225 closest distance to " CG1 VAL A 112 " =    2.813
peak=   -3.225 closest distance to " O   LEU A 167 " =    1.566
peak=   -3.222 closest distance to " CG1 VAL A 296 " =    1.233
peak=   -3.220 closest distance to " O   HOH Z 339 " =    1.714
peak=   -3.220 closest distance to " CE BMET A  47 " =    1.590
peak=   -3.219 closest distance to " CD1 LEU A  25 " =    2.515
peak=   -3.199 closest distance to " O   HOH Z  60 " =    2.062
peak=   -3.193 closest distance to " CA  ASN A 127 " =    1.108
peak=   -3.192 closest distance to " OD1 ASN A 301 " =    2.001
peak=   -3.191 closest distance to " CD1 ILE A 199 " =    2.364
peak=   -3.189 closest distance to " O   HOH Z 198 " =    1.846
peak=   -3.188 closest distance to " OD2 ASP A 171 " =    2.385
peak=   -3.186 closest distance to " CE1 TYR A 169 " =    2.215
peak=   -3.177 closest distance to " OD1 ASP A 200 " =    1.322
peak=   -3.166 closest distance to " O   THR A 182 " =    1.301
peak=   -3.164 closest distance to " CD2 LEU A 237 " =    2.640
peak=   -3.163 closest distance to " CD2 LEU A 237 " =    2.758
peak=   -3.163 closest distance to " O   HOH Z  56 " =    2.239
peak=   -3.160 closest distance to " N   ALA A  43 " =    2.477
peak=   -3.160 closest distance to " CB  ASP A 132 " =    2.225
peak=   -3.157 closest distance to " CG  GLU A   2 " =    1.901
peak=   -3.152 closest distance to " CD  GLN A  11 " =    0.856
peak=   -3.149 closest distance to " O   HOH Z  11 " =    1.924
peak=   -3.144 closest distance to " O   HOH Z 193 " =    1.607
peak=   -3.144 closest distance to " O   HOH Z 234 " =    3.946
peak=   -3.143 closest distance to " OD1 ASN A 249 " =    2.004
peak=   -3.137 closest distance to " O   HOH Z 193 " =    1.802
peak=   -3.125 closest distance to " O   HOH Z 139 " =    5.052
peak=   -3.125 closest distance to " O   HOH Z 313 " =    1.752
peak=   -3.123 closest distance to " O   HOH Z  97 " =    1.204
peak=   -3.123 closest distance to " O   HOH Z 139 " =    3.294
peak=   -3.123 closest distance to " O   HOH Z 369 " =    2.192
peak=   -3.117 closest distance to " O   HOH Z 388 " =    2.107
peak=   -3.111 closest distance to " CG  ARG A 269 " =    2.209
peak=   -3.104 closest distance to " O   VAL A 174 " =    1.897
peak=   -3.103 closest distance to " CZ  PHE A  38 " =    2.086
peak=   -3.101 closest distance to " N   THR A  52 " =    1.696
peak=   -3.100 closest distance to " N   LYS A 289 " =    1.601
peak=   -3.099 closest distance to " O   HOH Z 134 " =    2.712
peak=   -3.099 closest distance to " CG  LEU A 228 " =    1.116
peak=   -3.096 closest distance to " O   PRO A 198 " =    1.238
peak=   -3.095 closest distance to " OD1 ASN A 249 " =    1.425
peak=   -3.094 closest distance to " CB  TYR A 172 " =    2.273
peak=   -3.076 closest distance to " C   ASN A 148 " =    1.033
peak=   -3.053 closest distance to " O   SER A   3 " =    1.046
peak=   -3.045 closest distance to " NH1 ARG A 195 " =    2.534
peak=   -3.042 closest distance to " O   HOH Z  47 " =    1.622
peak=   -3.034 closest distance to " CG  GLU A 152 " =    2.179
peak=   -3.033 closest distance to " O   HOH Z 407 " =    3.385
peak=   -3.021 closest distance to " NH1 ARG A  66 " =    4.955
peak=   -3.012 closest distance to " O   HOH Z 113 " =    2.075

================= 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    :  0.4599 0.4504   6.257515e+00   6.248494e+00
   1_bss:  0.4507 0.4420   6.249729e+00   6.238433e+00
   1_xyz:  0.3553 0.3779   6.094382e+00   6.139947e+00
   1_adp:  0.3000 0.3409   5.967661e+00   6.068314e+00
   1_occ:  0.2994 0.3403   5.966340e+00   6.067506e+00
   2_bss:  0.2951 0.3339   5.964302e+00   6.064372e+00
   2_xyz:  0.2031 0.2431   5.637979e+00   5.801440e+00
   2_adp:  0.1802 0.2235   5.535684e+00   5.714886e+00
   2_occ:  0.1799 0.2229   5.534783e+00   5.713965e+00
   3_bss:  0.1779 0.2216   5.531749e+00   5.710367e+00
   3_xyz:  0.1405 0.1808   5.322317e+00   5.520529e+00
   3_adp:  0.1352 0.1722   5.279314e+00   5.470356e+00
   3_occ:  0.1350 0.1721   5.278699e+00   5.469983e+00
   4_bss:  0.1352 0.1720   5.279091e+00   5.467729e+00
   4_xyz:  0.1188 0.1583   5.178933e+00   5.392874e+00
   4_adp:  0.1170 0.1576   5.168578e+00   5.386766e+00
   4_occ:  0.1169 0.1576   5.167790e+00   5.386217e+00
   5_bss:  0.1169 0.1576   5.167657e+00   5.386084e+00
   5_xyz:  0.1154 0.1566   5.159025e+00   5.381103e+00
   5_adp:  0.1134 0.1578   5.154966e+00   5.387761e+00
   5_occ:  0.1134 0.1578   5.154834e+00   5.387703e+00
   5_bss:  0.1133 0.1578   5.154618e+00   5.387525e+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:  0.353  11.032   8.431   8.393   8.299   0.000   0.000   0.000
   1_xyz:  0.353  11.032   8.431   8.393   8.299   0.000   0.000   0.000
   1_adp:  0.353  11.032   8.431   8.393   8.299   0.000   0.000   0.000
   1_occ:  0.353  11.032   8.431   8.393   8.299   0.000   0.000   0.000
   2_bss:  0.328  33.534   4.726   4.610   5.179   0.000   0.000   0.000
   2_xyz:  0.328  33.534   4.726   4.610   5.179   0.000   0.000   0.000
   2_adp:  0.328  33.534   4.726   4.610   5.179   0.000   0.000   0.000
   2_occ:  0.328  33.534   4.726   4.610   5.179   0.000   0.000   0.000
   3_bss:  0.322  32.059   2.506   3.327   3.828   0.000   0.000   0.000
   3_xyz:  0.322  32.059   2.506   3.327   3.828   0.000   0.000   0.000
   3_adp:  0.322  32.059   2.506   3.327   3.828   0.000   0.000   0.000
   3_occ:  0.322  32.059   2.506   3.327   3.828   0.000   0.000   0.000
   4_bss:  0.324  35.326   1.790   2.798   3.303   0.000   0.000   0.000
   4_xyz:  0.324  35.326   1.790   2.798   3.303   0.000   0.000   0.000
   4_adp:  0.324  35.326   1.790   2.798   3.303   0.000   0.000   0.000
   4_occ:  0.324  35.326   1.790   2.798   3.303   0.000   0.000   0.000
   5_bss:  0.323  35.659   1.642   2.612   3.210   0.000   0.000   0.000
   5_xyz:  0.323  35.659   1.642   2.612   3.210   0.000   0.000   0.000
   5_adp:  0.323  35.659   1.642   2.612   3.210   0.000   0.000   0.000
   5_occ:  0.323  35.659   1.642   2.612   3.210   0.000   0.000   0.000
   5_bss:  0.322  39.956  -0.853   0.129   0.724   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  52.421 0.4916  0.5674    61508.306
   1_bss:  53.072 0.4808  0.7107    59372.390
   1_xyz:  42.508 0.6113  0.8864    40693.332
   1_adp:  36.116 0.6886  1.0065    31917.080
   1_occ:  36.033 0.6896  1.0064    31794.914
   2_bss:  35.616 0.6943  0.8927    31149.122
   2_xyz:  24.613 0.8147  1.0069    15502.590
   2_adp:  21.700 0.8450  1.0339    12785.584
   2_occ:  21.675 0.8453  1.0338    12751.377
   3_bss:  21.553 0.8463  0.9736    12595.171
   3_xyz:  16.900 0.8902  0.9984     8286.815
   3_adp:  15.733 0.9009  1.0063     7586.935
   3_occ:  15.720 0.9010  1.0062     7581.189
   4_bss:  15.675 0.9013  0.9848     7546.054
   4_xyz:  14.174 0.9138  0.9891     6494.733
   4_adp:  14.024 0.9152  0.9890     6426.460
   4_occ:  14.006 0.9153  0.9889     6419.199
   5_bss:  14.002 0.9153  0.9838     6416.006
   5_xyz:  13.867 0.9165  0.9835     6319.182
   5_adp:  13.994 0.9155  0.9802     6372.736
   5_occ:  13.990 0.9155  0.9801     6372.375
   5_bss:  13.986 0.9155  0.9833     6369.472
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.088   5.3191e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.088   5.3191e+01
   1_xyz:   1.664  0.013  0.107 18.023  0.006  4.107   1.3719e-01
   1_adp:   1.664  0.013  0.107 18.023  0.006  4.107   1.3719e-01
   1_occ:   1.664  0.013  0.107 18.023  0.006  4.107   1.3719e-01
   2_bss:   1.664  0.013  0.107 18.023  0.006  4.107   1.3719e-01
   2_xyz:   1.049  0.007  0.077 16.088  0.004  4.119   6.8343e-02
   2_adp:   1.049  0.007  0.077 16.088  0.004  4.119   6.8343e-02
   2_occ:   1.049  0.007  0.077 16.088  0.004  4.119   6.8343e-02
   3_bss:   1.049  0.007  0.077 16.088  0.004  4.119   6.8343e-02
   3_xyz:   0.942  0.005  0.070 15.519  0.003  4.109   5.4625e-02
   3_adp:   0.942  0.005  0.070 15.519  0.003  4.109   5.4625e-02
   3_occ:   0.942  0.005  0.070 15.519  0.003  4.109   5.4625e-02
   4_bss:   0.942  0.005  0.070 15.519  0.003  4.109   5.4625e-02
   4_xyz:   1.012  0.006  0.078 15.553  0.004  4.110   6.0643e-02
   4_adp:   1.012  0.006  0.078 15.553  0.004  4.110   6.0643e-02
   4_occ:   1.012  0.006  0.078 15.553  0.004  4.110   6.0643e-02
   5_bss:   1.012  0.006  0.078 15.553  0.004  4.110   6.0643e-02
   5_xyz:   0.928  0.005  0.073 15.251  0.003  4.110   5.3716e-02
   5_adp:   0.928  0.005  0.073 15.251  0.003  4.110   5.3716e-02
   5_occ:   0.928  0.005  0.073 15.251  0.003  4.110   5.3716e-02
   5_bss:   0.928  0.005  0.073 15.251  0.003  4.110   5.3716e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  1.139   6.8906e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  1.139   6.8906e+00
   1_xyz:  15.136  0.165  0.511 85.222  0.044  2.240   9.8947e-02
   1_adp:  15.136  0.165  0.511 85.222  0.044  2.240   9.8947e-02
   1_occ:  15.136  0.165  0.511 85.222  0.044  2.240   9.8947e-02
   2_bss:  15.136  0.165  0.511 85.222  0.044  2.240   9.8947e-02
   2_xyz:   6.905  0.074  0.296 82.632  0.034  2.340   5.0575e-02
   2_adp:   6.905  0.074  0.296 82.632  0.034  2.340   5.0575e-02
   2_occ:   6.905  0.074  0.296 82.632  0.034  2.340   5.0575e-02
   3_bss:   6.905  0.074  0.296 82.632  0.034  2.340   5.0575e-02
   3_xyz:   6.609  0.049  0.393 82.076  0.033  2.349   3.5062e-02
   3_adp:   6.609  0.049  0.393 82.076  0.033  2.349   3.5062e-02
   3_occ:   6.609  0.049  0.393 82.076  0.033  2.349   3.5062e-02
   4_bss:   6.609  0.049  0.393 82.076  0.033  2.349   3.5062e-02
   4_xyz:   6.786  0.034  0.504 83.272  0.035  2.321   3.8809e-02
   4_adp:   6.786  0.034  0.504 83.272  0.035  2.321   3.8809e-02
   4_occ:   6.786  0.034  0.504 83.272  0.035  2.321   3.8809e-02
   5_bss:   6.786  0.034  0.504 83.272  0.035  2.321   3.8809e-02
   5_xyz:   6.331  0.039  0.435 81.714  0.030  2.356   3.0337e-02
   5_adp:   6.331  0.039  0.435 81.714  0.030  2.356   3.0337e-02
   5_occ:   6.331  0.039  0.435 81.714  0.030  2.356   3.0337e-02
   5_bss:   6.331  0.039  0.435 81.714  0.030  2.356   3.0337e-02
------------------------------------------------------------------------
           |-----overall-----|---macromolecule----|------solvent-------|
  stage    b_max  b_min  b_ave  b_max  b_min  b_ave  b_max  b_min  b_ave
   0    :  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00  10.00
   1_bss:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_xyz:  19.99   0.01   9.86  19.98   0.01   9.82  19.99   0.06  10.10
   1_adp:  79.01   0.00  11.84  67.16   0.00   8.98  79.01   0.00  27.42
   1_occ:  79.01   0.00  11.84  67.16   0.00   8.98  79.01   0.00  27.42
   2_bss:  79.01   0.00  11.84  67.16   0.00   8.98  79.01   0.00  27.42
   2_xyz:  79.01   0.00  11.84  67.16   0.00   8.98  79.01   0.00  27.42
   2_adp:  78.83   0.00  12.18  76.70   0.00   8.41  78.83   1.47  32.71
   2_occ:  78.83   0.00  12.18  76.70   0.00   8.41  78.83   1.47  32.71
   3_bss:  78.83   0.00  12.18  76.70   0.00   8.41  78.83   1.47  32.71
   3_xyz:  78.83   0.00  12.18  76.70   0.00   8.41  78.83   1.47  32.71
   3_adp:  75.97   0.00  12.15  75.97   0.00   8.27  75.65   1.99  33.30
   3_occ:  75.97   0.00  12.15  75.97   0.00   8.27  75.65   1.99  33.30
   4_bss:  75.97   0.00  12.15  75.97   0.00   8.27  75.65   1.99  33.30
   4_xyz:  75.97   0.00  12.15  75.97   0.00   8.27  75.65   1.99  33.30
   4_adp:  78.05   0.00  12.03  78.05   0.00   8.16  69.48   1.56  33.13
   4_occ:  78.05   0.00  12.03  78.05   0.00   8.16  69.48   1.56  33.13
   5_bss:  78.05   0.00  12.03  78.05   0.00   8.16  69.48   1.56  33.13
   5_xyz:  78.05   0.00  12.03  78.05   0.00   8.16  69.48   1.56  33.13
   5_adp:  81.32   0.00  12.26  81.32   0.00   8.20  69.47   1.51  34.40
   5_occ:  81.32   0.00  12.26  81.32   0.00   8.20  69.47   1.51  34.40
   5_bss:  83.90   2.57  14.84  83.90   2.57  10.77  72.05   4.08  36.97
------------------------------------------------------------------------
 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:    1.218    0.012    0.413
   1_adp:    1.218    0.012    0.413
   1_occ:    1.218    0.012    0.413
   2_bss:    1.218    0.012    0.413
   2_xyz:    1.581    0.011    0.554
   2_adp:    1.581    0.011    0.554
   2_occ:    1.581    0.011    0.554
   3_bss:    1.581    0.011    0.554
   3_xyz:    1.548    0.036    0.589
   3_adp:    1.548    0.036    0.589
   3_occ:    1.548    0.036    0.589
   4_bss:    1.548    0.036    0.589
   4_xyz:    1.666    0.046    0.626
   4_adp:    1.666    0.046    0.626
   4_occ:    1.666    0.046    0.626
   5_bss:    1.666    0.046    0.626
   5_xyz:    1.702    0.047    0.635
   5_adp:    1.702    0.047    0.635
   5_occ:    1.702    0.047    0.635
   5_bss:    1.702    0.047    0.635
------------------------------------------------------------------------

CPU time actual refinement: 329.99


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_190/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_190/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_190/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_190/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_190/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 329.84 
  Macro-tasks:
    bulk solvent and scale       = 40.05  
    individual site refinement   = 135.49 
    weights calculation          = 31.80  
    collect and process          = 6.50   
    model show statistics        = 0.15   
    TOTAL for macro-tasks        = 213.99 
  Micro-tasks:
    mask                            = 1.84   
    f_calc                          = 102.34 
    alpha_beta                      = 7.99   
    target                          = 1.13   
    gradients_wrt_atomic_parameters = 112.01 
    fmodel                         = 7.13   
    r_factors                      = 0.27   
    phase_errors                   = 10.71  
    foms                           = 0.25   
    TOTAL for micro-tasks          = 243.67 
NUMBER OF MASK CALCS=  4
Time per interpreted Python bytecode instruction: 4.672 micro seconds
Total CPU time: 5.73 minutes
from_scatterers_fft:    634 calls, 101.96 s
gradients_fft:          578 calls,  99.01 s

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

# Date 2008-01-16 Time 00:57:38 PST -0800 (1200473858.35 s)
Start R-work = 0.4599, R-free = 0.4504 (no bulk solvent and anisotropic scale)
Final R-work = 0.1312, R-free = 0.1735 (no bulk solvent and anisotropic scale)

Start R-work = 0.4507, R-free = 0.4420
Final R-work = 0.1133, R-free = 0.1578