# Date 2008-01-16 Time 00:39:12 PST -0800 (1200472752.14 s)
#phil __OFF__

Command line arguments: "../88.param" "adp.set_b_iso=10" "sites.shake=0.5" "main.number_of_macro_cycles=5" "--overwrite"

HOST = thunderbird.lbl.gov
HOSTTYPE = x86_64-linux
USER = phzwart
PID = 2600
JOB_ID = 5158
SGE_ARCH = lx24-amd64
SGE_TASK_FIRST = 1
SGE_TASK_LAST = 1330
SGE_TASK_ID = 88

-------------------------------------------------------------------------------
  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: (68.4938, 47.6339, 84.2302, 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: 3.28, per 1000 atoms: 1.16


================================== 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: (68.4938, 47.6339, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8572 1.95055
Completeness in resolution range: 0.94839
Completeness with d_max=infinity: 0.945506

Number of F-obs in resolution range:                   19589
Number of F-obs <= 0:                                  0
Refinement resolution range: d_max =  14.8572
                             d_min =   1.9505

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: (68.4938, 47.6339, 84.2302, 90, 90, 90)
Space group: P 21 21 21 (No. 19)
Systematic absences: 0
Centric reflections: 2427
Resolution range: 14.8572 1.95055
Completeness in resolution range: 0.94839
Completeness with d_max=infinity: 0.945506

Test (R-free flags) flag value: 1

Number of work/free reflections by resolution:
                                         work  free  %free
  bin  1: 14.8576 -  4.1742 [2169/2198]  1950   219  10.1%
  bin  2:  4.1742 -  3.3254 [2083/2106]  1875   208  10.0%
  bin  3:  3.3254 -  2.9086 [2052/2077]  1847   205  10.0%
  bin  4:  2.9086 -  2.6443 [2026/2045]  1828   198   9.8%
  bin  5:  2.6443 -  2.4557 [2016/2057]  1810   206  10.2%
  bin  6:  2.4557 -  2.3115 [2017/2045]  1823   194   9.6%
  bin  7:  2.3115 -  2.1961 [1987/2023]  1787   200  10.1%
  bin  8:  2.1961 -  2.1008 [2003/2045]  1804   199   9.9%
  bin  9:  2.1008 -  2.0201 [1963/2020]  1762   201  10.2%
  bin 10:  2.0201 -  1.9505 [1273/2039]  1144   129  10.1%
                                overall 17630  1959  10.0%
Writing MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_88/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:
        1.18 -     1.92: 24
        1.92 -     2.67: 161
        2.67 -     3.41: 4501
        3.41 -     4.16: 9562
        4.16 -     4.90: 14689
  Nonbonded interactions sorted by model distance:
             atom i - atom j             model   vdw sym.op. j
  " O   HOH Z  18 " - " O   HOH Z 102 "  1.175 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z  52 " - " O   HOH Z 183 "  1.247 3.040 -x+1,y+1/2,-z+1/2
  " O   HOH Z 178 " - " O   HOH Z 403 "  1.352 3.040 -x+1,y-1/2,-z+1/2
  " CA  GLY A  91 " - " O   HOH Z 401 "  1.364 3.440 -x+1,y-1/2,-z+1/2
  " OD2 ASP A 107 " - " OG BSER A 216 "  1.368 3.040 -x+1/2,-y+1,z+1/2
  ... (remaining 28932 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_88/model_refine_001.eff

Writing geometry restraints to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_88/model_refine_001.geo

CPU time processing inputs: 9.20


============================ 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 = 68.49375 47.63395 84.23025 90 90 90
    space_group = "P 21 21 21"
  }
  input {
    pdb {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/model.pdb"
    }
    xray_data {
      file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
      labels = "FOBS,SIGMA"
      r_free_flags {
        file_name = "/net/cci-filer1/vol1/tmp/phzwart/tassos/trial/1e0w.cns"
        label = "TEST"
        test_flag_value = 1
      }
    }
  }
  output {
    prefix = "model_refine"
    serial = 1
  }
  main {
    number_of_macro_cycles = 5
  }
  modify_start_model {
    adp {
      set_b_iso = 10
    }
    sites {
      shake = 0.5
    }
  }
}
#phil __OFF__


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


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


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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5194   r_free= 0.5122   ksol= 0.00   Bsol= 0.00   scale= 0.777    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.95 A                  |
| x-ray target function (ml) for work reflections: 6.311556                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8576 -  4.6559 0.99   1405  159 0.4364 0.4309       6.662      6.6991|
|  2:  4.6559 -  3.7145 0.99   1354  148 0.4626 0.4459        6.87      6.8732|
|  3:  3.7145 -  3.2506 0.99   1331  149 0.4920 0.4709       6.735      6.7871|
|  4:  3.2506 -  2.9559 0.99   1322  136 0.5002 0.5116      6.5547      6.5438|
|  5:  2.9559 -  2.7455 0.99   1308  151 0.5541 0.5581      6.4041      6.4103|
|  6:  2.7455 -  2.5845 0.99   1304  147 0.5375 0.5492      6.2946      6.2206|
|  7:  2.5845 -  2.4557 0.98   1286  146 0.5613 0.5019      6.2797      6.1907|
|  8:  2.4557 -  2.3492 0.98   1314  138 0.5550 0.5390      6.1917      6.2163|
|  9:  2.3492 -  2.2591 0.99   1276  145 0.5635 0.5616      6.1305      6.1583|
| 10:  2.2591 -  2.1814 0.98   1291  143 0.5556 0.5773      6.1254      6.1392|
| 11:  2.1814 -  2.1134 0.97   1271  144 0.5557 0.5790      6.0413      6.0462|
| 12:  2.1134 -  2.0531 0.98   1287  143 0.5485 0.5583      5.9703      5.9995|
| 13:  2.0531 -  1.9992 0.93   1209  132 0.5638 0.5613      5.8926      5.8983|
| 14:  1.9992 -  1.9505 0.52    672   78 0.5662 0.4698      5.9044      5.6942|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8576 -  4.6559  1405   159  0.62  41.34   0.78     0.64      94501.56|
|  2:  4.6559 -  3.7145  1354   148  0.60  43.49   0.85     0.67     145401.96|
|  3:  3.7145 -  3.2506  1331   149  0.48  53.34   0.82     0.61     155777.88|
|  4:  3.2506 -  2.9559  1322   136  0.38  61.20   0.79     0.49     132115.71|
|  5:  2.9559 -  2.7455  1308   151  0.29  68.46   0.71     0.37     103678.81|
|  6:  2.7455 -  2.5845  1304   147  0.28  69.22   0.71     0.33      82676.48|
|  7:  2.5845 -  2.4557  1286   146  0.27  69.81   0.72     0.31      72727.22|
|  8:  2.4557 -  2.3492  1314   138  0.27  69.85   0.71     0.33      65174.79|
|  9:  2.3492 -  2.2591  1276   145  0.20  74.91   0.71     0.26      63734.93|
| 10:  2.2591 -  2.1814  1291   143  0.15  79.02   0.77     0.18      59792.05|
| 11:  2.1814 -  2.1134  1271   144  0.07  84.95   0.74     0.09      57804.67|
| 12:  2.1134 -  2.0531  1287   143  0.10  82.57   0.74     0.13      52208.29|
| 13:  2.0531 -  1.9992  1209   132  0.20  75.11   0.73     0.26      40728.38|
| 14:  1.9992 -  1.9505   672    78  0.43  57.79   0.72     0.48      25347.33|
|alpha:            min =        0.09 max =            0.67 mean =         0.37|
|beta:             min =    25347.33 max =       155777.88 mean =     85064.57|
|figures of merit: min =        0.00 max =            1.00 mean =         0.31|
|phase err.(work): min =        0.00 max =           89.99 mean =        66.46|
|phase err.(test): min =        0.00 max =           89.96 mean =        66.70|
|-----------------------------------------------------------------------------|

============================== 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 = 30.736934             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 84.268   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 2.107834              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 85.989   (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 |  0.909 -  1.308:        8 |
| 0.140 - 0.280:   585 |   7.457 -  14.906:   711 |  1.308 -  1.707:       12 |
| 0.280 - 0.420:   441 |  14.906 -  22.354:   630 |  1.707 -  2.106:       99 |
| 0.420 - 0.560:   366 |  22.354 -  29.802:   474 |  2.106 -  2.506:      450 |
| 0.560 - 0.700:   237 |  29.802 -  37.251:   338 |  2.506 -  2.905:     1232 |
| 0.700 - 0.840:   127 |  37.251 -  44.699:   241 |  2.905 -  3.304:     2446 |
| 0.840 - 0.980:    59 |  44.699 -  52.147:   125 |  3.304 -  3.703:     3976 |
| 0.980 - 1.120:    17 |  52.147 -  59.595:    51 |  3.703 -  4.102:     5298 |
| 1.120 - 1.260:     9 |  59.595 -  67.044:    13 |  4.102 -  4.501:     7073 |
| 1.260 - 1.400:     1 |  67.044 -  74.492:     3 |  4.501 -  4.900:     8420 |
|-----------------------------------------------------------------------------|
|-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 |       52.827 |
| planarity |      436 |   0.145    0.405  0.000 |     250.485 |              |
|  dihedral |      870 |  33.790  144.062  0.019 |      20.704 |              |
| nonbonded |     2439 |   4.086    4.900  0.909 |       3.631 |              |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.370)------------------------------------------|
|    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 = 11.370)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.01    19.99   9.86     None  None   None       |
|    all(noH): 2823   0      0.01    19.99   9.86     None  None   None       |
|    Sol.    : 438    0      0.06    19.99   10.10    None  None   None       |
|    Mac.    : 2385   0      0.01    19.98   9.82     None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.008 -   2.007:  301   |   5:    10.002 -  12.000:  285        |
|      1:     2.007 -   4.006:  276   |   6:    12.000 -  13.999:  292        |
|      2:     4.006 -   6.004:  309   |   7:    13.999 -  15.998:  289        |
|      3:     6.004 -   8.003:  285   |   8:    15.998 -  17.996:  266        |
|      4:     8.003 -  10.002:  251   |   9:    17.996 -  19.995:  269        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5218   r_free= 0.5173   ksol= 0.00   Bsol= 0.00   scale= 0.747    |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.00,0.00,0.00,0.00,0.00,0.00); trace/3= 0.00                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   1.01 A                  |
| x-ray target function (ml) for work reflections: 6.311625                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.5120   r_free= 0.5049   ksol= 0.38   Bsol= 20.00   scale= 0.954   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.63,8.79,7.72,0.00,0.00,0.00); trace/3= 7.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   1.12 A                  |
| x-ray target function (ml) for work reflections: 6.309094                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 25.328002             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 85.563   (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 1.906035              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 82.172   (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.5120      final r-factor (work) = 0.4480          |
| start r-factor (free) = 0.5049      final r-factor (free) = 0.4713          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 132.7294 = 25.33 * 0.50 * 6.3094 + 1.00 * 52.8270                           |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 79.3956 = 25.33 * 0.50 * 6.2525 + 1.00 * 0.2135                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4480      final r-factor (work) = 0.4150          |
| start r-factor (free) = 0.4713      final r-factor (free) = 0.4672          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.9319 = 1.91 * 1.00 * 6.2525 + 1.00 * 0.0143                              |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 11.8772 = 1.91 * 1.00 * 6.2187 + 1.00 * 0.0241                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.370)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    107.42  16.54    None  None   None       |
|    all(noH): 2823   0      0.00    107.42  16.54    None  None   None       |
|    Sol.    : 438    0      0.00    98.69   24.27    None  None   None       |
|    Mac.    : 2385   0      0.00    107.42  15.13    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 -  10.742: 1082   |   5:    53.709 -  64.451:   29        |
|      1:    10.742 -  21.484:  941   |   6:    64.451 -  75.193:   11        |
|      2:    21.484 -  32.226:  483   |   7:    75.193 -  85.935:    4        |
|      3:    32.226 -  42.967:  182   |   8:    85.935 -  96.677:    2        |
|      4:    42.967 -  53.709:   87   |   9:    96.677 - 107.418:    2        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.4150 r_free = 0.4672             target_work(ml) = 6.208         |
| occupancies: max = 1.00  min = 0.30   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.4143 r_free = 0.4677             target_work(ml) = 6.207         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4143   r_free= 0.4677   ksol= 0.38   Bsol= 20.00   scale= 1.108   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (6.63,8.79,7.72,0.00,0.00,0.00); trace/3= 7.71                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.207078                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.4139   r_free= 0.4626   ksol= 0.36   Bsol= 36.45   scale= 1.038   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.60,5.59,5.46,0.00,0.00,0.00); trace/3= 4.88                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.78 A                  |
| x-ray target function (ml) for work reflections: 6.207304                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 15.698060             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.090  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.905025              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 121.661  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.4139      final r-factor (work) = 0.3528          |
| start r-factor (free) = 0.4626      final r-factor (free) = 0.4116          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 49.0089 = 15.70 * 0.50 * 6.2167 + 1.00 * 0.2135                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 48.4234 = 15.70 * 0.50 * 6.1535 + 1.00 * 0.1244                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3528      final r-factor (work) = 0.3291          |
| start r-factor (free) = 0.4116      final r-factor (free) = 0.3982          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5968 = 0.91 * 1.00 * 6.1535 + 1.00 * 0.0277                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 5.5068 = 0.91 * 1.00 * 6.0684 + 1.00 * 0.0147                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 26     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.370)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    106.58  16.53    None  None   None       |
|    all(noH): 2823   0      0.00    106.58  16.53    None  None   None       |
|    Sol.    : 438    0      0.00    106.58  30.36    None  None   None       |
|    Mac.    : 2385   0      0.00    74.12   13.99    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -  10.658: 1180   |   5:    53.291 -  63.949:   40        |
|      1:    10.658 -  21.316:  862   |   6:    63.949 -  74.607:   22        |
|      2:    21.316 -  31.975:  419   |   7:    74.607 -  85.265:    4        |
|      3:    31.975 -  42.633:  212   |   8:    85.265 -  95.924:    2        |
|      4:    42.633 -  53.291:   81   |   9:    95.924 - 106.582:    1        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.3291 r_free = 0.3982             target_work(ml) = 6.052         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.3291 r_free = 0.3980             target_work(ml) = 6.051         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3291   r_free= 0.3980   ksol= 0.36   Bsol= 36.45   scale= 1.091   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (3.60,5.59,5.46,0.00,0.00,0.00); trace/3= 4.88                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.051318                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.3259   r_free= 0.3953   ksol= 0.34   Bsol= 46.12   scale= 1.030   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.52,3.11,3.01,0.00,0.00,0.00); trace/3= 2.55                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.51 A                  |
| x-ray target function (ml) for work reflections: 6.048574                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 10.196063             wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 100.627  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.448879              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 124.694  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.3259      final r-factor (work) = 0.2495          |
| start r-factor (free) = 0.3953      final r-factor (free) = 0.3169          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 31.0524 = 10.20 * 0.50 * 6.0667 + 1.00 * 0.1244                             |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 30.4679 = 10.20 * 0.50 * 5.9574 + 1.00 * 0.0969                             |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2495      final r-factor (work) = 0.2223          |
| start r-factor (free) = 0.3169      final r-factor (free) = 0.2814          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6892 = 0.45 * 1.00 * 5.9574 + 1.00 * 0.0150                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.6143 = 0.45 * 1.00 * 5.7917 + 1.00 * 0.0146                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.370)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    95.30   15.68    None  None   None       |
|    all(noH): 2823   0      0.00    95.30   15.68    None  None   None       |
|    Sol.    : 438    0      3.60    95.30   36.12    None  None   None       |
|    Mac.    : 2385   0      0.00    86.94   11.93    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.530: 1278   |   5:    47.650 -  57.180:   73        |
|      1:     9.530 -  19.060:  798   |   6:    57.180 -  66.710:   37        |
|      2:    19.060 -  28.590:  294   |   7:    66.710 -  76.240:   13        |
|      3:    28.590 -  38.120:  186   |   8:    76.240 -  85.770:    4        |
|      4:    38.120 -  47.650:  136   |   9:    85.770 -  95.300:    4        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.2223 r_free = 0.2814             target_work(ml) = 5.734         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.2218 r_free = 0.2811             target_work(ml) = 5.733         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2218   r_free= 0.2811   ksol= 0.34   Bsol= 46.12   scale= 1.060   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (1.52,3.11,3.01,0.00,0.00,0.00); trace/3= 2.55                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.732756                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.2208   r_free= 0.2783   ksol= 0.33   Bsol= 41.56   scale= 1.019   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.05,1.66,1.45,0.00,0.00,0.00); trace/3= 1.05                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.30 A                  |
| x-ray target function (ml) for work reflections: 5.729110                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 6.168573              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 102.344  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.400338              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 101.874  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.2208      final r-factor (work) = 0.1618          |
| start r-factor (free) = 0.2783      final r-factor (free) = 0.2154          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.9663 = 6.17 * 0.50 * 5.7937 + 1.00 * 0.0969                              |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 17.3949 = 6.17 * 0.50 * 5.6136 + 1.00 * 0.0810                              |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1618      final r-factor (work) = 0.1449          |
| start r-factor (free) = 0.2154      final r-factor (free) = 0.1982          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.2588 = 0.40 * 1.00 * 5.6136 + 1.00 * 0.0115                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 2.1801 = 0.40 * 1.00 * 5.4209 + 1.00 * 0.0099                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 29     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.370)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    92.05   15.36    None  None   None       |
|    all(noH): 2823   0      0.00    92.05   15.36    None  None   None       |
|    Sol.    : 438    0      2.51    92.05   39.47    None  None   None       |
|    Mac.    : 2385   0      0.00    89.19   10.93    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.205: 1346   |   5:    46.025 -  55.230:  118        |
|      1:     9.205 -  18.410:  834   |   6:    55.230 -  64.435:   50        |
|      2:    18.410 -  27.615:  202   |   7:    64.435 -  73.640:   21        |
|      3:    27.615 -  36.820:  124   |   8:    73.640 -  82.845:    6        |
|      4:    36.820 -  46.025:  116   |   9:    82.845 -  92.050:    6        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1449 r_free = 0.1982             target_work(ml) = 5.368         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       11 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1446 r_free = 0.1978             target_work(ml) = 5.366         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1446   r_free= 0.1978   ksol= 0.33   Bsol= 41.56   scale= 1.034   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (0.05,1.66,1.45,0.00,0.00,0.00); trace/3= 1.05                              |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.18 A                  |
| x-ray target function (ml) for work reflections: 5.366122                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1447   r_free= 0.1964   ksol= 0.33   Bsol= 41.56   scale= 1.012   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.74,0.86,0.62,0.00,0.00,0.00); trace/3= 0.25                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.19 A                  |
| x-ray target function (ml) for work reflections: 5.365056                   |
|-----------------------------------------------------------------------------|

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

|-----------------------------------------------------------------------------|
| XYZ refinement: T = Eexperimental * wxc * wxc_scale + Echem * wc            |
| wxc = 1.866204              wxc_scale = 0.500            wc = 1.000         |
| angle between x-ray and geometry gradient vectors: 114.085  (deg)           |
|                                                                             |
| ADP refinement: T = Eexperimental * wxu * wxu_scale + Eadp  * wu            |
| wxc = 0.147150              wxc_scale = 1.000            wc = 1.000         |
| angle between Xray and ADP gradient vectors: 136.453  (deg)                 |
|-----------------------------------------------------------------------------|


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1447      final r-factor (work) = 0.1334          |
| start r-factor (free) = 0.1964      final r-factor (free) = 0.1811          |
|-----------------------------------------------------------------------------|
| T_start = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.1443 = 1.87 * 0.50 * 5.4263 + 1.00 * 0.0810                               |
|                                                                             |
| T_final = wxc * wxc_scale * Exray + wc * Echem                              |
| 5.0368 = 1.87 * 0.50 * 5.3352 + 1.00 * 0.0585                               |
|-----------------------------------------------------------------------------|
| number of iterations = 25      |    number of function evaluations = 27     |
|-----------------------------------------------------------------------------|

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


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

|-LBFGS minimization----------------------------------------------------------|
| start r-factor (work) = 0.1334      final r-factor (work) = 0.1323          |
| start r-factor (free) = 0.1811      final r-factor (free) = 0.1778          |
|-----------------------------------------------------------------------------|
| T_start = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.7949 = 0.15 * 1.00 * 5.3352 + 1.00 * 0.0099                               |
|                                                                             |
| T_final = wxu * wxu_scale * Exray + wu * Eadp                               |
| 0.8065 = 0.15 * 1.00 * 5.2897 + 1.00 * 0.0281                               |
|-----------------------------------------------------------------------------|
| number of iterations = 8       |    number of function evaluations = 11     |
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.370)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.00    91.55   15.27    None  None   None       |
|    all(noH): 2823   0      0.00    91.55   15.27    None  None   None       |
|    Sol.    : 438    0      3.66    91.55   38.94    None  None   None       |
|    Mac.    : 2385   0      0.00    88.65   10.92    None  None   None       |
|    Hyd.    : 0      0      None    None    None     None  None   None       |
|    - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -      |
|       Distribution of isotropic (or equivalent) ADP for non-H atoms:        |
|    Bin#      value range     #atoms | Bin#      value range     #atoms      |
|      0:     0.000 -   9.155: 1334   |   5:    45.774 -  54.929:  114        |
|      1:     9.155 -  18.310:  862   |   6:    54.929 -  64.083:   52        |
|      2:    18.310 -  27.464:  193   |   7:    64.083 -  73.238:   19        |
|      3:    27.464 -  36.619:  126   |   8:    73.238 -  82.393:    7        |
|      4:    36.619 -  45.774:  111   |   9:    82.393 -  91.548:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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

|-individual occupancy refinement: start--------------------------------------|
| r_work = 0.1323 r_free = 0.1778             target_work(ml) = 5.280         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|
|-individual occupancy refinement: end----------------------------------------|
| r_work = 0.1321 r_free = 0.1776             target_work(ml) = 5.279         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       10 |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1321   r_free= 0.1776   ksol= 0.33   Bsol= 41.56   scale= 1.015   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.74,0.86,0.62,0.00,0.00,0.00); trace/3= 0.25                             |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.279088                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8576 -  4.6559 0.99   1405  159 0.1107 0.1451       5.493      5.6352|
|  2:  4.6559 -  3.7145 0.99   1354  148 0.1013 0.1294      5.5826      5.8323|
|  3:  3.7145 -  3.2506 0.99   1331  149 0.1242 0.1793       5.622      5.9389|
|  4:  3.2506 -  2.9559 0.99   1322  136 0.1480 0.1762      5.5877      5.7358|
|  5:  2.9559 -  2.7455 0.99   1308  151 0.1575 0.1784      5.4589       5.591|
|  6:  2.7455 -  2.5845 0.99   1304  147 0.1512 0.2231       5.357      5.6042|
|  7:  2.5845 -  2.4557 0.98   1286  146 0.1404 0.1839      5.2632      5.4589|
|  8:  2.4557 -  2.3492 0.98   1314  138 0.1394 0.1705      5.2013      5.3699|
|  9:  2.3492 -  2.2591 0.99   1276  145 0.1391 0.2075       5.149      5.4119|
| 10:  2.2591 -  2.1814 0.98   1291  143 0.1317 0.1937      5.1141      5.3603|
| 11:  2.1814 -  2.1134 0.97   1271  144 0.1361 0.2000      5.0491      5.3188|
| 12:  2.1134 -  2.0531 0.98   1287  143 0.1340 0.1877       4.996      5.2176|
| 13:  2.0531 -  1.9992 0.93   1209  132 0.1355 0.2003      4.9097      5.1671|
| 14:  1.9992 -  1.9505 0.52    672   78 0.1227 0.1945      4.8211      5.0477|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8576 -  4.6559  1405   159  0.93  10.62   0.98     0.96       9292.76|
|  2:  4.6559 -  3.7145  1354   148  0.94  10.00   1.03     1.01      12024.66|
|  3:  3.7145 -  3.2506  1331   149  0.92  13.82   1.04     1.03      14030.70|
|  4:  3.2506 -  2.9559  1322   136  0.90  16.02   1.02     1.02      12941.87|
|  5:  2.9559 -  2.7455  1308   151  0.88  18.32   1.00     0.97      10397.03|
|  6:  2.7455 -  2.5845  1304   147  0.88  18.37   0.99     0.96       9069.19|
|  7:  2.5845 -  2.4557  1286   146  0.89  17.61   0.99     0.95       7434.01|
|  8:  2.4557 -  2.3492  1314   138  0.89  17.77   1.02     1.00       6951.89|
|  9:  2.3492 -  2.2591  1276   145  0.89  17.90   1.03     1.01       6259.41|
| 10:  2.2591 -  2.1814  1291   143  0.88  18.11   1.02     0.98       6007.18|
| 11:  2.1814 -  2.1134  1271   144  0.88  18.30   1.02     0.98       5304.88|
| 12:  2.1134 -  2.0531  1287   143  0.89  17.65   1.02     1.01       4862.64|
| 13:  2.0531 -  1.9992  1209   132  0.88  18.40   1.02     1.01       4162.01|
| 14:  1.9992 -  1.9505   672    78  0.89  17.81   1.01     0.97       3553.63|
|alpha:            min =        0.95 max =            1.03 mean =         0.99|
|beta:             min =     3553.63 max =        14030.70 mean =      8247.59|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.98 mean =        16.35|
|phase err.(test): min =        0.00 max =           89.83 mean =        15.99|
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1321   r_free= 0.1776   ksol= 0.33   Bsol= 41.61   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.99,0.61,0.38,0.00,0.00,0.00); trace/3= -0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.278980                   |
|-----------------------------------------------------------------------------|

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

|--(resolution: 1.95 - 14.86 A; n_refl. = 19589)------------------------------|
|                                                                             |
| r_work= 0.1321   r_free= 0.1776   ksol= 0.33   Bsol= 41.61   scale= 1.010   |
|                                                                             |
| overall anisotropic scale matrix (Cartesian basis; B11,B22,B33,B12,B13,B23):|
| (-0.99,0.61,0.38,0.00,0.00,0.00); trace/3= -0.00                            |
|                                                                             |
| maximum likelihood estimate for coordinate error:   0.17 A                  |
| x-ray target function (ml) for work reflections: 5.278980                   |
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
| Bin     Resolution   Compl.  No. Refl.    R-factors          Targets        |
|number     range              work test   work   test        work        test|
|  1: 14.8576 -  4.6559 0.99   1405  159 0.1106 0.1449       5.492      5.6339|
|  2:  4.6559 -  3.7145 0.99   1354  148 0.1013 0.1294      5.5821      5.8324|
|  3:  3.7145 -  3.2506 0.99   1331  149 0.1242 0.1793       5.622       5.939|
|  4:  3.2506 -  2.9559 0.99   1322  136 0.1480 0.1762      5.5879      5.7357|
|  5:  2.9559 -  2.7455 0.99   1308  151 0.1575 0.1784       5.459      5.5912|
|  6:  2.7455 -  2.5845 0.99   1304  147 0.1512 0.2231       5.357      5.6044|
|  7:  2.5845 -  2.4557 0.98   1286  146 0.1404 0.1839      5.2631      5.4587|
|  8:  2.4557 -  2.3492 0.98   1314  138 0.1393 0.1705      5.2013      5.3698|
|  9:  2.3492 -  2.2591 0.99   1276  145 0.1391 0.2075      5.1489       5.412|
| 10:  2.2591 -  2.1814 0.98   1291  143 0.1317 0.1937       5.114      5.3603|
| 11:  2.1814 -  2.1134 0.97   1271  144 0.1361 0.2000       5.049      5.3187|
| 12:  2.1134 -  2.0531 0.98   1287  143 0.1340 0.1878      4.9962      5.2176|
| 13:  2.0531 -  1.9992 0.93   1209  132 0.1355 0.2003      4.9099      5.1674|
| 14:  1.9992 -  1.9505 0.52    672   78 0.1227 0.1945       4.821      5.0476|
|-----------------------------------------------------------------------------|

|-----------------------------------------------------------------------------|
|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: 14.8576 -  4.6559  1405   159  0.93  10.60   0.98     0.96       9269.44|
|  2:  4.6559 -  3.7145  1354   148  0.94   9.99   1.03     1.01      12009.48|
|  3:  3.7145 -  3.2506  1331   149  0.92  13.82   1.04     1.03      14029.90|
|  4:  3.2506 -  2.9559  1322   136  0.90  16.02   1.02     1.01      12943.30|
|  5:  2.9559 -  2.7455  1308   151  0.88  18.31   1.00     0.97      10397.64|
|  6:  2.7455 -  2.5845  1304   147  0.88  18.37   0.98     0.95       9069.39|
|  7:  2.5845 -  2.4557  1286   146  0.89  17.60   0.99     0.94       7433.29|
|  8:  2.4557 -  2.3492  1314   138  0.89  17.77   1.01     0.99       6952.27|
|  9:  2.3492 -  2.2591  1276   145  0.89  17.89   1.02     1.00       6259.03|
| 10:  2.2591 -  2.1814  1291   143  0.88  18.11   1.01     0.97       6007.57|
| 11:  2.1814 -  2.1134  1271   144  0.88  18.30   1.01     0.97       5305.42|
| 12:  2.1134 -  2.0531  1287   143  0.89  17.65   1.01     1.00       4864.27|
| 13:  2.0531 -  1.9992  1209   132  0.88  18.40   1.01     1.00       4163.16|
| 14:  1.9992 -  1.9505   672    78  0.89  17.81   1.00     0.95       3554.02|
|alpha:            min =        0.94 max =            1.03 mean =         0.98|
|beta:             min =     3554.02 max =        14029.90 mean =      8244.91|
|figures of merit: min =        0.00 max =            1.00 mean =         0.90|
|phase err.(work): min =        0.00 max =           89.98 mean =        16.35|
|phase err.(test): min =        0.00 max =           89.83 mean =        15.99|
|-----------------------------------------------------------------------------|

|-ADP statistics (Wilson B = 11.370)------------------------------------------|
|    Atom    | Number of   | Isotropic or equivalent| Anisotropy lmin/max     |
|    type    |iso    aniso | min     max     mean   | min   max    mean       |
|    - - - - |- - - - - - -| - - - - - - - - - - - -| - - - - - - - - - -     |
|    all     : 2823   0      0.05    91.60   15.32    None  None   None       |
|    all(noH): 2823   0      0.05    91.60   15.32    None  None   None       |
|    Sol.    : 438    0      3.71    91.60   39.00    None  None   None       |
|    Mac.    : 2385   0      0.05    88.70   10.97    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:     0.053 -   9.208: 1334   |   5:    45.827 -  54.982:  114        |
|      1:     9.208 -  18.363:  862   |   6:    54.982 -  64.136:   52        |
|      2:    18.363 -  27.517:  193   |   7:    64.136 -  73.291:   19        |
|      3:    27.517 -  36.672:  126   |   8:    73.291 -  82.446:    7        |
|      4:    36.672 -  45.827:  111   |   9:    82.446 -  91.601:    5        |
|                               =>continue=>                                  |
|-----------------------------------------------------------------------------|


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


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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 345         
Filter by distance & map next to the model:
   mapped sites are within: 0.469 - 4.171
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 343 from: 345
   mapped sites are within: 0.710 - 4.171

peak=   10.024 closest distance to " CB  VAL A 230 " =    1.408
peak=    9.551 closest distance to " O   HOH Z 138 " =    1.506
peak=    7.739 closest distance to " O   HOH Z 135 " =    1.553
peak=    6.714 closest distance to " O   HOH Z 178 " =    1.922
peak=    6.394 closest distance to " O   HOH Z 137 " =    1.132
peak=    6.365 closest distance to " O   HOH Z 316 " =    1.228
peak=    6.245 closest distance to " O   HOH Z 403 " =    1.064
peak=    6.138 closest distance to " O   HOH Z 199 " =    2.077
peak=    6.077 closest distance to " CG1 VAL A 296 " =    1.102
peak=    5.983 closest distance to " O   HOH Z 247 " =    1.473
peak=    5.974 closest distance to " O   HOH Z 402 " =    1.705
peak=    5.930 closest distance to " O   HOH Z  92 " =    1.404
peak=    5.812 closest distance to " O   HOH Z 249 " =    1.575
peak=    5.740 closest distance to " CD2 LEU A   5 " =    1.333
peak=    5.442 closest distance to " O   HOH Z 279 " =    1.373
peak=    5.337 closest distance to " O   HOH Z  37 " =    1.146
peak=    5.330 closest distance to " O   HOH Z  45 " =    1.012
peak=    5.323 closest distance to " O   HOH Z 278 " =    2.039
peak=    5.298 closest distance to " O   HOH Z 236 " =    1.727
peak=    5.234 closest distance to " CB  VAL A 296 " =    1.299
peak=    5.201 closest distance to " O   HOH Z 406 " =    1.594
peak=    5.168 closest distance to " O   HOH Z 193 " =    1.787
peak=    5.039 closest distance to " O   HOH Z  78 " =    1.417
peak=    5.002 closest distance to " CG AARG A 275 " =    1.227
peak=    4.996 closest distance to " CD1AILE A 234 " =    1.125
peak=    4.971 closest distance to " O   HOH Z 124 " =    1.834
peak=    4.921 closest distance to " OD1 ASN A  60 " =    0.906
peak=    4.853 closest distance to " CB  ARG A 275 " =    1.045
peak=    4.810 closest distance to " O   HOH Z 406 " =    1.897
peak=    4.780 closest distance to " O   HOH Z 117 " =    1.311
peak=    4.750 closest distance to " O   HOH Z 272 " =    1.946
peak=    4.699 closest distance to " O  BHOH Z  74 " =    1.342
peak=    4.613 closest distance to " CG2 VAL A 296 " =    1.009
peak=    4.604 closest distance to " CB  GLN A 223 " =    1.460
peak=    4.592 closest distance to " O   PRO A 198 " =    1.619
peak=    4.590 closest distance to " O   SER A  87 " =    2.267
peak=    4.588 closest distance to " CG  PRO A  54 " =    1.219
peak=    4.570 closest distance to " O   HOH Z 411 " =    3.606
peak=    4.535 closest distance to " CA  VAL A  41 " =    0.854
peak=    4.517 closest distance to " CB  ARG A 275 " =    1.176
peak=    4.486 closest distance to " CG  PRO A 198 " =    1.232
peak=    4.471 closest distance to " CB  GLN A  73 " =    1.038
peak=    4.461 closest distance to " O   HOH Z 192 " =    1.602
peak=    4.409 closest distance to " CG  LEU A   5 " =    1.446
peak=    4.408 closest distance to " O   HOH Z  92 " =    1.533
peak=    4.398 closest distance to " O   HOH Z 248 " =    1.246
peak=    4.387 closest distance to " O   HOH Z 116 " =    1.182
peak=    4.386 closest distance to " CB  ASN A 187 " =    2.042
peak=    4.368 closest distance to " O   HOH Z 263 " =    1.508
peak=    4.338 closest distance to " CG  GLN A  77 " =    0.909
peak=    4.332 closest distance to " CG  ARG A  66 " =    1.265
peak=    4.326 closest distance to " O   HOH Z  47 " =    1.937
peak=    4.321 closest distance to " CB  VAL A 265 " =    1.290
peak=    4.316 closest distance to " O   HOH Z  68 " =    1.861
peak=    4.297 closest distance to " O   HOH Z 163 " =    1.507
peak=    4.282 closest distance to " O   HOH Z 357 " =    2.067
peak=    4.279 closest distance to " O   HOH Z 108 " =    1.311
peak=    4.276 closest distance to " CD2 LEU A 228 " =    1.239
peak=    4.262 closest distance to " OG  SER A  26 " =    1.523
peak=    4.255 closest distance to " O   HOH Z 156 " =    3.128
peak=    4.241 closest distance to " CA  TYR A  30 " =    1.063
peak=    4.224 closest distance to " NH2 ARG A  56 " =    2.155
peak=    4.224 closest distance to " O   HOH Z  80 " =    2.240
peak=    4.219 closest distance to " O   HOH Z 192 " =    1.509
peak=    4.205 closest distance to " O   HOH Z 232 " =    1.414
peak=    4.204 closest distance to " O   HOH Z 394 " =    1.619
peak=    4.192 closest distance to " O   HOH Z  48 " =    2.029
peak=    4.179 closest distance to " O   HOH Z 345 " =    1.992
peak=    4.171 closest distance to " NZ  LYS A 117 " =    3.243
peak=    4.145 closest distance to " O   HOH Z  43 " =    1.716
peak=    4.125 closest distance to " OE1 GLU A   2 " =    2.071
peak=    4.101 closest distance to " CD  ARG A 269 " =    1.011
peak=    4.080 closest distance to " O   HOH Z  49 " =    1.223
peak=    4.076 closest distance to " O   HOH Z 134 " =    2.409
peak=    4.068 closest distance to " O   HOH Z 124 " =    2.042
peak=    4.066 closest distance to " O   HOH Z 416 " =    1.199
peak=    4.064 closest distance to " O   HOH Z 128 " =    1.703
peak=    4.063 closest distance to " O   HOH Z 316 " =    2.002
peak=    4.048 closest distance to " O   HOH Z 208 " =    1.522
peak=    4.044 closest distance to " O   HOH Z 389 " =    1.614
peak=    4.044 closest distance to " O   HOH Z 365 " =    1.816
peak=    4.036 closest distance to " O   HOH Z 214 " =    2.137
peak=    4.032 closest distance to " O   HOH Z 414 " =    1.992
peak=    4.020 closest distance to " O   HOH Z 327 " =    1.798
peak=    4.014 closest distance to " CG  GLN A  88 " =    0.979
peak=    4.013 closest distance to " O   HOH Z 255 " =    1.279
peak=    3.998 closest distance to " O   HOH Z 423 " =    2.158
peak=    3.997 closest distance to " N   ASN A  39 " =    1.263
peak=    3.996 closest distance to " O   HOH Z 155 " =    2.176
peak=    3.995 closest distance to " O   HOH Z 408 " =    1.973
peak=    3.981 closest distance to " CA  ALA A  21 " =    1.104
peak=    3.974 closest distance to " O   HOH Z  69 " =    1.148
peak=    3.970 closest distance to " NH1 ARG A  14 " =    1.001
peak=    3.966 closest distance to " O   HOH Z 154 " =    1.683
peak=    3.945 closest distance to " O   HOH Z 303 " =    2.198
peak=    3.929 closest distance to " CB  ARG A 102 " =    0.814
peak=    3.928 closest distance to " O   HOH Z 129 " =    3.543
peak=    3.921 closest distance to " O   HOH Z  11 " =    1.213
peak=    3.913 closest distance to " O   HOH Z 276 " =    1.384
peak=    3.897 closest distance to " CB  ALA A 100 " =    1.194
peak=    3.881 closest distance to " O   HOH Z 433 " =    1.608
peak=    3.872 closest distance to " O   HOH Z 238 " =    1.152
peak=    3.863 closest distance to " O   HOH Z 260 " =    1.731
peak=    3.860 closest distance to " O   HOH Z 322 " =    1.607
peak=    3.858 closest distance to " O   HOH Z  60 " =    1.736
peak=    3.850 closest distance to " CB  ASN A 148 " =    1.216
peak=    3.845 closest distance to " CA  ALA A 295 " =    0.885
peak=    3.844 closest distance to " O   HOH Z 234 " =    3.727
peak=    3.842 closest distance to " CD  LYS A  76 " =    1.798
peak=    3.842 closest distance to " O   HOH Z 426 " =    1.475
peak=    3.839 closest distance to " O   HOH Z 203 " =    1.740
peak=    3.839 closest distance to " O   HOH Z 245 " =    1.470
peak=    3.836 closest distance to " CG  PRO A 213 " =    1.277
peak=    3.835 closest distance to " CD2 TRP A 179 " =    1.441
peak=    3.832 closest distance to " O   HOH Z 189 " =    2.274
peak=    3.831 closest distance to " NH2BARG A 145 " =    2.158
peak=    3.829 closest distance to " CD1BILE A 234 " =    1.061
peak=    3.827 closest distance to " O   HOH Z 346 " =    1.455
peak=    3.826 closest distance to " O   HOH Z 214 " =    2.183
peak=    3.825 closest distance to " O   HOH Z 191 " =    1.496
peak=    3.825 closest distance to " O   HOH Z 326 " =    1.519
peak=    3.821 closest distance to " O   HOH Z 214 " =    1.265
peak=    3.815 closest distance to " O   HOH Z   4 " =    1.405
peak=    3.807 closest distance to " CD  ARG A 159 " =    0.782
peak=    3.799 closest distance to " NE1 TRP A 274 " =    0.976
peak=    3.794 closest distance to " CA  PRO A 213 " =    0.934
peak=    3.793 closest distance to " O   HOH Z 425 " =    1.464
peak=    3.791 closest distance to " O   GLY A  91 " =    1.354
peak=    3.783 closest distance to " O   HOH Z 188 " =    1.021
peak=    3.782 closest distance to " CB  SER A  26 " =    1.334
peak=    3.780 closest distance to " O   HOH Z 166 " =    1.594
peak=    3.774 closest distance to " CG  PRO A 243 " =    1.294
peak=    3.772 closest distance to " O   HOH Z 147 " =    0.949
peak=    3.754 closest distance to " CG1 ILE A  33 " =    1.297
peak=    3.753 closest distance to " O   HOH Z 284 " =    1.427
peak=    3.751 closest distance to " O   HOH Z  97 " =    2.145
peak=    3.749 closest distance to " CB  GLU A 152 " =    1.038
peak=    3.737 closest distance to " CB  SER A  26 " =    1.710
peak=    3.728 closest distance to " O   HOH Z 194 " =    2.040
peak=    3.722 closest distance to " CB  VAL A 230 " =    1.179
peak=    3.722 closest distance to " O   HOH Z 136 " =    1.437
peak=    3.718 closest distance to " O   HOH Z 344 " =    1.331
peak=    3.717 closest distance to " O   HOH Z 361 " =    2.810
peak=    3.716 closest distance to " O   HOH Z 383 " =    1.915
peak=    3.714 closest distance to " CG2 ILE A 120 " =    1.484
peak=    3.691 closest distance to " O   HOH Z  59 " =    2.047
peak=    3.689 closest distance to " O   HOH Z  44 " =    2.028
peak=    3.683 closest distance to " O   HOH Z 117 " =    2.070
peak=    3.683 closest distance to " O   HOH Z  40 " =    1.752
peak=    3.682 closest distance to " CB  GLN A  58 " =    0.956
peak=    3.679 closest distance to " O   HOH Z 405 " =    1.977
peak=    3.678 closest distance to " O   HOH Z 138 " =    1.360
peak=    3.676 closest distance to " CE  LYS A 119 " =    1.118
peak=    3.674 closest distance to " CB  ARG A 259 " =    1.885
peak=    3.662 closest distance to " O   HOH Z 162 " =    1.917
peak=    3.652 closest distance to " CD2 LEU A 297 " =    0.944
peak=    3.652 closest distance to " O   HOH Z 369 " =    1.836
peak=    3.650 closest distance to " NH1AARG A 275 " =    1.253
peak=    3.643 closest distance to " CD BLYS A 290 " =    0.865
peak=    3.631 closest distance to " O   HOH Z  46 " =    1.412
peak=    3.622 closest distance to " NE BARG A 190 " =    1.558
peak=    3.612 closest distance to " CB BVAL A  41 " =    1.148
peak=    3.606 closest distance to " O   HOH Z 344 " =    2.351
peak=    3.605 closest distance to " CG  PRO A 280 " =    0.859
peak=    3.602 closest distance to " CA  VAL A 126 " =    0.901
peak=    3.592 closest distance to " O   HOH Z 423 " =    1.521
peak=    3.589 closest distance to " OG BSER A 210 " =    1.337
peak=    3.582 closest distance to " O   HOH Z 381 " =    1.548
peak=    3.579 closest distance to " CB  SER A  63 " =    1.156
peak=    3.575 closest distance to " O   HOH Z 250 " =    1.420
peak=    3.563 closest distance to " O   HOH Z 150 " =    1.612
peak=    3.559 closest distance to " CA  ALA A 299 " =    0.955
peak=    3.553 closest distance to " ND2 ASN A 110 " =    1.550
peak=    3.533 closest distance to " O   HOH Z  54 " =    1.505
peak=    3.528 closest distance to " NZ  LYS A 117 " =    0.959
peak=    3.522 closest distance to " O   HOH Z 368 " =    2.105
peak=    3.521 closest distance to " O   HOH Z 368 " =    1.110
peak=    3.519 closest distance to " CD  PRO A  54 " =    0.910
peak=    3.513 closest distance to " CB  TYR A 169 " =    0.741
peak=    3.512 closest distance to " CG  GLN A  77 " =    2.170
peak=    3.511 closest distance to " NZ  LYS A 119 " =    2.913
peak=    3.510 closest distance to " O   HOH Z 305 " =    1.790
peak=    3.508 closest distance to " O  BHOH Z 338 " =    1.229
peak=    3.502 closest distance to " O   HOH Z 232 " =    1.901
peak=    3.501 closest distance to " O   THR A  82 " =    1.843
peak=    3.495 closest distance to " O   HOH Z  68 " =    2.540
peak=    3.489 closest distance to " O   HOH Z 345 " =    2.161
peak=    3.488 closest distance to " O   HOH Z 380 " =    1.829
peak=    3.487 closest distance to " CB  SER A 141 " =    1.060
peak=    3.487 closest distance to " O   ARG A 102 " =    2.367
peak=    3.483 closest distance to " O   HOH Z  32 " =    1.943
peak=    3.478 closest distance to " O   HOH Z 217 " =    1.826
peak=    3.478 closest distance to " O   HOH Z  30 " =    2.351
peak=    3.475 closest distance to " O   ASN A 217 " =    1.227
peak=    3.470 closest distance to " CA  ASP A 191 " =    1.106
peak=    3.469 closest distance to " NH2 ARG A 219 " =    1.946
peak=    3.467 closest distance to " CG  LEU A 228 " =    1.378
peak=    3.467 closest distance to " OD1 ASN A  45 " =    1.216
peak=    3.460 closest distance to " O   HOH Z 126 " =    2.526
peak=    3.453 closest distance to " O   HOH Z 359 " =    1.533
peak=    3.453 closest distance to " CG1 VAL A 153 " =    0.989
peak=    3.451 closest distance to " O   HOH Z 404 " =    1.567
peak=    3.447 closest distance to " O   HOH Z 433 " =    4.171
peak=    3.447 closest distance to " O   HOH Z 315 " =    1.896
peak=    3.446 closest distance to " O   HOH Z 350 " =    2.073
peak=    3.444 closest distance to " O   HOH Z 364 " =    1.823
peak=    3.440 closest distance to " O   HOH Z  66 " =    2.171
peak=    3.438 closest distance to " OG1 THR A 294 " =    2.287
peak=    3.436 closest distance to " N   TYR A  15 " =    0.907
peak=    3.432 closest distance to " CG1BVAL A  72 " =    1.609
peak=    3.432 closest distance to " O   HOH Z 313 " =    2.006
peak=    3.419 closest distance to " O   HOH Z 130 " =    2.702
peak=    3.419 closest distance to " O   HOH Z 132 " =    1.296
peak=    3.414 closest distance to " CB  TRP A 179 " =    1.059
peak=    3.398 closest distance to " CB  GLN A 194 " =    0.967
peak=    3.389 closest distance to " CA  ILE A  20 " =    0.806
peak=    3.387 closest distance to " O   HOH Z 365 " =    2.879
peak=    3.380 closest distance to " O   HOH Z 253 " =    1.921
peak=    3.377 closest distance to " CD2 HIS A  81 " =    1.542
peak=    3.374 closest distance to " CB  SER A   3 " =    1.233
peak=    3.374 closest distance to " CB  TYR A 247 " =    1.021
peak=    3.372 closest distance to " NH2AARG A 145 " =    2.071
peak=    3.369 closest distance to " O   HOH Z  19 " =    2.307
peak=    3.356 closest distance to " CD  ARG A 195 " =    0.960
peak=    3.355 closest distance to " O   HOH Z 128 " =    1.521
peak=    3.353 closest distance to " CA  ASN A 284 " =    0.961
peak=    3.348 closest distance to " O   HOH Z 236 " =    1.502
peak=    3.346 closest distance to " O   HOH Z 415 " =    3.298
peak=    3.345 closest distance to " CB  PRO A 198 " =    1.158
peak=    3.342 closest distance to " O   HOH Z 343 " =    2.388
peak=    3.340 closest distance to " O   HOH Z 336 " =    3.471
peak=    3.339 closest distance to " O   HOH Z 118 " =    1.834
peak=    3.338 closest distance to " O   TRP A 274 " =    1.558
peak=    3.336 closest distance to " CG2 THR A 251 " =    1.277
peak=    3.331 closest distance to " CD1 PHE A  61 " =    1.033
peak=    3.329 closest distance to " CB  PRO A 213 " =    1.248
peak=    3.326 closest distance to " OG  SER A 245 " =    1.307
peak=    3.326 closest distance to " CZ  PHE A 218 " =    1.229
peak=    3.326 closest distance to " ND1 HIS A  81 " =    1.211
peak=    3.325 closest distance to " O   SER A 164 " =    0.927
peak=    3.325 closest distance to " CA  ILE A 263 " =    0.922
peak=    3.318 closest distance to " CD1 LEU A  96 " =    0.710
peak=    3.318 closest distance to " CE2 TRP A  70 " =    1.335
peak=    3.316 closest distance to " CG2 THR A 294 " =    1.402
peak=    3.316 closest distance to " NZ  LYS A  76 " =    1.033
peak=    3.313 closest distance to " CA  PHE A  59 " =    0.993
peak=    3.313 closest distance to " CG  ARG A 269 " =    0.973
peak=    3.312 closest distance to " O   HOH Z 409 " =    3.422
peak=    3.312 closest distance to " O   HOH Z  54 " =    2.487
peak=    3.310 closest distance to " CB  GLN A 183 " =    1.267
peak=    3.307 closest distance to " CB  ASP A 253 " =    1.056
peak=    3.306 closest distance to " CG  MET A 185 " =    1.253
peak=    3.306 closest distance to " CE  MET A  93 " =    1.211
peak=    3.305 closest distance to " O   HOH Z 412 " =    3.707
peak=    3.303 closest distance to " CA  THR A 221 " =    0.888
peak=    3.299 closest distance to " O   HOH Z 291 " =    1.132
peak=    3.299 closest distance to " O   HOH Z 276 " =    1.551
peak=    3.298 closest distance to " CB  VAL A 202 " =    1.585
peak=    3.298 closest distance to " O   HOH Z 155 " =    2.090
peak=    3.296 closest distance to " O   HOH Z 387 " =    1.991
peak=    3.289 closest distance to " O   HOH Z 173 " =    1.851
peak=    3.284 closest distance to " CB  ALA A 248 " =    1.378
peak=    3.283 closest distance to " O   HOH Z  38 " =    2.145
peak=    3.282 closest distance to " CG2 VAL A 197 " =    1.208
peak=    3.279 closest distance to " O   HOH Z 285 " =    1.471
peak=    3.276 closest distance to " CG2 THR A 220 " =    0.815
peak=    3.276 closest distance to " O   HOH Z  95 " =    1.771
peak=    3.276 closest distance to " NH2 ARG A 156 " =    0.941
peak=    3.275 closest distance to " CG2 THR A  42 " =    0.907
peak=    3.274 closest distance to " O   HOH Z 301 " =    1.545
peak=    3.270 closest distance to " O   HOH Z 215 " =    1.440
peak=    3.270 closest distance to " O   HOH Z 423 " =    1.725
peak=    3.268 closest distance to " CB  SER A  32 " =    1.286
peak=    3.265 closest distance to " CD2 TYR A  30 " =    0.793
peak=    3.265 closest distance to " N   SER A 135 " =    1.161
peak=    3.264 closest distance to " O   HOH Z 389 " =    1.287
peak=    3.261 closest distance to " O   HOH Z 362 " =    3.584
peak=    3.257 closest distance to " CB  TRP A 266 " =    1.148
peak=    3.253 closest distance to " CB  ALA A 256 " =    0.976
peak=    3.251 closest distance to " O   HOH Z 109 " =    1.526
peak=    3.249 closest distance to " O   HOH Z 132 " =    2.084
peak=    3.249 closest distance to " O   HOH Z 393 " =    2.204
peak=    3.245 closest distance to " O   HOH Z 409 " =    2.056
peak=    3.243 closest distance to " CB  SER A  62 " =    1.236
peak=    3.239 closest distance to " O   HOH Z 144 " =    1.869
peak=    3.238 closest distance to " O   PHE A 283 " =    1.496
peak=    3.238 closest distance to " OG  SER A  62 " =    2.895
peak=    3.237 closest distance to " O   HOH Z 313 " =    1.517
peak=    3.228 closest distance to " CA  LEU A 282 " =    1.151
peak=    3.226 closest distance to " CB  SER A 273 " =    0.986
peak=    3.225 closest distance to " CB  ASP A 107 " =    1.148
peak=    3.224 closest distance to " O   HOH Z 402 " =    2.349
peak=    3.221 closest distance to " CB  LEU A 228 " =    1.513
peak=    3.218 closest distance to " O   HOH Z 219 " =    1.807
peak=    3.217 closest distance to " CA  ALA A  51 " =    1.119
peak=    3.213 closest distance to " O   HOH Z  96 " =    2.109
peak=    3.209 closest distance to " OH  TYR A  30 " =    1.005
peak=    3.208 closest distance to " O   HOH Z 278 " =    1.464
peak=    3.208 closest distance to " CB  MET A  47 " =    0.998
peak=    3.205 closest distance to " O   HOH Z 374 " =    2.502
peak=    3.202 closest distance to " O   HOH Z 174 " =    2.393
peak=    3.198 closest distance to " O   HOH Z 108 " =    2.038
peak=    3.191 closest distance to " O   HOH Z 209 " =    2.434
peak=    3.190 closest distance to " O   HOH Z 280 " =    1.433
peak=    3.188 closest distance to " CB  GLN A 278 " =    0.775
peak=    3.184 closest distance to " CD2 LEU A 255 " =    1.142
peak=    3.181 closest distance to " O   HOH Z 130 " =    1.141
peak=    3.179 closest distance to " CB  VAL A 126 " =    1.093
peak=    3.177 closest distance to " CG2 VAL A  78 " =    0.892
peak=    3.176 closest distance to " O   GLY A 147 " =    1.505
peak=    3.175 closest distance to " O   HOH Z 109 " =    2.020
peak=    3.173 closest distance to " CG2 THR A 221 " =    1.235
peak=    3.173 closest distance to " CE1 HIS A 108 " =    1.225
peak=    3.170 closest distance to " CA  ASN A 176 " =    0.923
peak=    3.169 closest distance to " CG  MET A  93 " =    1.081
peak=    3.168 closest distance to " O   HOH Z  20 " =    1.773
peak=    3.164 closest distance to " O   HOH Z 183 " =    1.828
peak=    3.163 closest distance to " O   HOH Z 234 " =    1.979
peak=    3.160 closest distance to " OG1 THR A 294 " =    4.085
peak=    3.160 closest distance to " CB  LEU A 237 " =    0.903
peak=    3.156 closest distance to " O   HOH Z 197 " =    2.033
peak=    3.150 closest distance to " O   HOH Z 427 " =    2.716
peak=    3.148 closest distance to " O   HOH Z 267 " =    2.013
peak=    3.141 closest distance to " O   HOH Z 331 " =    1.371
peak=    3.138 closest distance to " CG AARG A 190 " =    1.312
peak=    3.138 closest distance to " O   HOH Z 298 " =    1.876
peak=    3.136 closest distance to " O   HOH Z 221 " =    1.325
peak=    3.136 closest distance to " O   HOH Z 279 " =    2.031
peak=    3.127 closest distance to " O   HOH Z 273 " =    2.785
peak=    3.121 closest distance to " CA  ARG A 195 " =    1.157
peak=    3.119 closest distance to " O   ALA A 165 " =    1.264
peak=    3.115 closest distance to " O   HOH Z 148 " =    2.606
peak=    3.106 closest distance to " O   HOH Z  15 " =    2.386
peak=    3.104 closest distance to " O   HOH Z 366 " =    2.323
peak=    3.101 closest distance to " O   HOH Z  85 " =    1.552
peak=    3.095 closest distance to " NE2 GLN A  11 " =    1.063
peak=    3.089 closest distance to " CA  LYS A 117 " =    1.291
peak=    3.085 closest distance to " CB  SER A  62 " =    0.795
peak=    3.083 closest distance to " O   HOH Z 436 " =    1.603
peak=    3.059 closest distance to " N   PHE A  61 " =    0.863
peak=    3.057 closest distance to " O   HOH Z 240 " =    2.068
peak=    3.043 closest distance to " CD2 LEU A  83 " =    1.568
peak=    3.035 closest distance to " CB  PRO A  54 " =    0.716

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

Number of peaks found at mFobs-DFmodel map (map cutoff=3.00 sigma)= 192         
Filter by distance & map next to the model:
   mapped sites are within: 0.285 - 5.555
   number of sites selected in [dist_min= 0.70, dist_max= 6.00]: 186 from: 192
   mapped sites are within: 0.727 - 5.555

peak=   -4.626 closest distance to " CG2 VAL A 230 " =    0.727
peak=   -4.250 closest distance to " CD  ARG A  14 " =    3.078
peak=   -4.242 closest distance to " O   HOH Z 290 " =    0.819
peak=   -4.238 closest distance to " OG  SER A  26 " =    1.029
peak=   -4.237 closest distance to " O   HOH Z  13 " =    1.015
peak=   -4.233 closest distance to " CG  ARG A 219 " =    2.345
peak=   -4.229 closest distance to " O   SER A 146 " =    0.838
peak=   -4.197 closest distance to " O   HOH Z  92 " =    1.498
peak=   -4.156 closest distance to " O   ASN A 187 " =    1.460
peak=   -4.131 closest distance to " CD1 PHE A  59 " =    1.835
peak=   -4.124 closest distance to " C   HIS A 108 " =    1.103
peak=   -4.000 closest distance to " O   HOH Z 423 " =    2.546
peak=   -3.969 closest distance to " CD2 LEU A 300 " =    2.485
peak=   -3.969 closest distance to " O   HOH Z 103 " =    1.908
peak=   -3.960 closest distance to " CA  SER A 164 " =    1.893
peak=   -3.936 closest distance to " CB  ALA A 161 " =    2.250
peak=   -3.923 closest distance to " OG ASER A 134 " =    1.262
peak=   -3.921 closest distance to " CG1 VAL A 296 " =    0.974
peak=   -3.889 closest distance to " O   HOH Z 362 " =    5.555
peak=   -3.880 closest distance to " OD1 ASP A 200 " =    1.403
peak=   -3.863 closest distance to " O   HOH Z 351 " =    1.358
peak=   -3.847 closest distance to " C   THR A 279 " =    1.094
peak=   -3.825 closest distance to " CG2 THR A  18 " =    2.767
peak=   -3.825 closest distance to " O   HOH Z 221 " =    1.239
peak=   -3.824 closest distance to " CG BARG A 275 " =    0.860
peak=   -3.823 closest distance to " CG2 VAL A 230 " =    0.839
peak=   -3.805 closest distance to " CE2 TYR A  30 " =    2.819
peak=   -3.759 closest distance to " O   HOH Z 198 " =    1.055
peak=   -3.742 closest distance to " N   ALA A 248 " =    2.008
peak=   -3.742 closest distance to " O   VAL A 197 " =    1.002
peak=   -3.742 closest distance to " O   ALA A 161 " =    1.218
peak=   -3.722 closest distance to " CA  VAL A 296 " =    0.855
peak=   -3.695 closest distance to " N   GLY A  17 " =    1.398
peak=   -3.666 closest distance to " CD  GLN A 223 " =    0.931
peak=   -3.654 closest distance to " O   HOH Z 250 " =    1.366
peak=   -3.646 closest distance to " CD  LYS A 289 " =    2.470
peak=   -3.642 closest distance to " CD1 TRP A 179 " =    1.094
peak=   -3.635 closest distance to " O   ASP A 107 " =    1.033
peak=   -3.625 closest distance to " OXT GLY A 302 " =    2.614
peak=   -3.617 closest distance to " O   HOH Z 126 " =    2.095
peak=   -3.605 closest distance to " O   HOH Z 416 " =    0.794
peak=   -3.603 closest distance to " N   ARG A  66 " =    1.737
peak=   -3.601 closest distance to " O   LEU A 228 " =    2.343
peak=   -3.594 closest distance to " O   SER A  99 " =    1.353
peak=   -3.591 closest distance to " NH2 ARG A  79 " =    1.986
peak=   -3.589 closest distance to " C   TYR A  30 " =    0.888
peak=   -3.582 closest distance to " O   HOH Z 281 " =    3.018
peak=   -3.575 closest distance to " CG2BVAL A  41 " =    2.779
peak=   -3.567 closest distance to " O   HOH Z 313 " =    1.987
peak=   -3.564 closest distance to " O  BHOH Z 338 " =    1.211
peak=   -3.564 closest distance to " O   SER A 273 " =    1.234
peak=   -3.560 closest distance to " NE2 GLN A  88 " =    1.808
peak=   -3.560 closest distance to " O   ALA A  51 " =    1.306
peak=   -3.558 closest distance to " CB  PHE A 208 " =    2.278
peak=   -3.557 closest distance to " CG  ASP A  50 " =    2.029
peak=   -3.555 closest distance to " OG  SER A  63 " =    0.996
peak=   -3.552 closest distance to " C   ALA A 158 " =    1.063
peak=   -3.548 closest distance to " O   HOH Z 166 " =    1.880
peak=   -3.539 closest distance to " O   HOH Z 424 " =    3.158
peak=   -3.533 closest distance to " O   HOH Z 222 " =    3.063
peak=   -3.531 closest distance to " CD1 TRP A  70 " =    1.897
peak=   -3.530 closest distance to " CD1 LEU A 101 " =    2.505
peak=   -3.522 closest distance to " CA  ALA A 227 " =    2.316
peak=   -3.518 closest distance to " O   LEU A 143 " =    1.562
peak=   -3.507 closest distance to " O   HOH Z 196 " =    2.023
peak=   -3.506 closest distance to " O   HOH Z 171 " =    2.211
peak=   -3.497 closest distance to " OG  SER A  32 " =    0.946
peak=   -3.492 closest distance to " C   GLY A  91 " =    1.170
peak=   -3.486 closest distance to " O   HOH Z 172 " =    4.926
peak=   -3.479 closest distance to " CD1 TYR A 247 " =    2.174
peak=   -3.473 closest distance to " O   HOH Z 215 " =    3.472
peak=   -3.473 closest distance to " NH2AARG A 275 " =    4.372
peak=   -3.466 closest distance to " O   HOH Z 227 " =    0.967
peak=   -3.456 closest distance to " O   HOH Z  56 " =    2.237
peak=   -3.451 closest distance to " N   GLN A  58 " =    2.102
peak=   -3.450 closest distance to " O   HOH Z 388 " =    2.108
peak=   -3.445 closest distance to " O   HOH Z  11 " =    1.555
peak=   -3.442 closest distance to " O   HOH Z 174 " =    4.209
peak=   -3.442 closest distance to " CG  LYS A 193 " =    2.031
peak=   -3.439 closest distance to " O   HOH Z 266 " =    4.294
peak=   -3.437 closest distance to " CA  GLN A  58 " =    1.482
peak=   -3.425 closest distance to " O   HOH Z 313 " =    1.301
peak=   -3.424 closest distance to " O   HOH Z 435 " =    2.282
peak=   -3.408 closest distance to " O   HOH Z 138 " =    1.701
peak=   -3.404 closest distance to " O   VAL A 174 " =    1.832
peak=   -3.401 closest distance to " N   SER A 210 " =    1.255
peak=   -3.396 closest distance to " NE1 TRP A  70 " =    2.361
peak=   -3.395 closest distance to " O   HOH Z 252 " =    0.788
peak=   -3.380 closest distance to " NH2 ARG A  66 " =    1.529
peak=   -3.377 closest distance to " CA  GLN A 103 " =    0.962
peak=   -3.376 closest distance to " CD  GLN A 103 " =    1.292
peak=   -3.371 closest distance to " N   ALA A 226 " =    1.865
peak=   -3.361 closest distance to " OG BSER A 134 " =    1.523
peak=   -3.358 closest distance to " CD1 TRP A 266 " =    1.499
peak=   -3.357 closest distance to " O   HOH Z 426 " =    2.345
peak=   -3.353 closest distance to " O   HOH Z 126 " =    1.620
peak=   -3.352 closest distance to " C   ASN A 285 " =    2.099
peak=   -3.348 closest distance to " CG  ASP A 231 " =    0.854
peak=   -3.347 closest distance to " OG  SER A 206 " =    1.319
peak=   -3.346 closest distance to " C   ASN A 142 " =    0.886
peak=   -3.343 closest distance to " OG1 THR A 251 " =    2.768
peak=   -3.341 closest distance to " ND2 ASN A 173 " =    1.283
peak=   -3.334 closest distance to " CE  LYS A  76 " =    2.486
peak=   -3.329 closest distance to " O   HOH Z 166 " =    1.356
peak=   -3.321 closest distance to " CD  ARG A 156 " =    1.952
peak=   -3.319 closest distance to " O   HOH Z 137 " =    1.639
peak=   -3.316 closest distance to " O   PRO A  54 " =    1.350
peak=   -3.315 closest distance to " O   VAL A  67 " =    2.375
peak=   -3.315 closest distance to " CA  ALA A 114 " =    0.988
peak=   -3.309 closest distance to " O   ARG A 275 " =    1.649
peak=   -3.303 closest distance to " O   HOH Z  34 " =    1.938
peak=   -3.300 closest distance to " O   ALA A 160 " =    1.271
peak=   -3.295 closest distance to " O   HOH Z 368 " =    2.353
peak=   -3.285 closest distance to " O   ASP A 191 " =    1.377
peak=   -3.279 closest distance to " OG  SER A  97 " =    1.974
peak=   -3.277 closest distance to " O   HOH Z 165 " =    1.617
peak=   -3.272 closest distance to " CD2 PHE A  59 " =    2.513
peak=   -3.268 closest distance to " C   GLN A 144 " =    0.742
peak=   -3.264 closest distance to " CD  ARG A 259 " =    1.365
peak=   -3.261 closest distance to " CD  PRO A 198 " =    1.568
peak=   -3.258 closest distance to " O   GLN A  58 " =    0.827
peak=   -3.257 closest distance to " CD1 LEU A  96 " =    2.012
peak=   -3.257 closest distance to " O   HOH Z 174 " =    2.160
peak=   -3.256 closest distance to " O   GLN A  11 " =    1.192
peak=   -3.256 closest distance to " O   HOH Z 183 " =    1.434
peak=   -3.254 closest distance to " O   MET A 188 " =    1.514
peak=   -3.251 closest distance to " O   HOH Z 316 " =    1.561
peak=   -3.251 closest distance to " N   VAL A 189 " =    1.597
peak=   -3.250 closest distance to " O   HOH Z 125 " =    3.120
peak=   -3.249 closest distance to " O   TYR A  15 " =    1.683
peak=   -3.241 closest distance to " CG  GLN A  88 " =    1.202
peak=   -3.235 closest distance to " O   HOH Z 297 " =    3.110
peak=   -3.228 closest distance to " O   HOH Z 212 " =    1.323
peak=   -3.226 closest distance to " N   GLY A 302 " =    1.654
peak=   -3.218 closest distance to " O   HOH Z 275 " =    1.234
peak=   -3.210 closest distance to " O   HOH Z 292 " =    2.698
peak=   -3.207 closest distance to " O   HOH Z 147 " =    1.002
peak=   -3.207 closest distance to " OG ASER A 134 " =    0.905
peak=   -3.203 closest distance to " O   HOH Z 414 " =    2.279
peak=   -3.197 closest distance to " OD2 ASP A 191 " =    1.513
peak=   -3.192 closest distance to " CZ2 TRP A  92 " =    2.429
peak=   -3.186 closest distance to " O   PHE A 218 " =    1.442
peak=   -3.186 closest distance to " O   LYS A 289 " =    0.951
peak=   -3.170 closest distance to " CB  SER A  62 " =    5.492
peak=   -3.170 closest distance to " O   HOH Z 138 " =    0.982
peak=   -3.168 closest distance to " CG1BVAL A  41 " =    2.403
peak=   -3.167 closest distance to " CD1 LEU A 228 " =    2.289
peak=   -3.165 closest distance to " CD  GLU A   2 " =    1.692
peak=   -3.163 closest distance to " O   HOH Z 360 " =    2.360
peak=   -3.161 closest distance to " O   HOH Z 297 " =    3.571
peak=   -3.156 closest distance to " O   HOH Z 353 " =    0.966
peak=   -3.152 closest distance to " CG2BVAL A  41 " =    1.769
peak=   -3.151 closest distance to " O   HOH Z 385 " =    3.339
peak=   -3.150 closest distance to " O   ASN A  45 " =    1.692
peak=   -3.149 closest distance to " CB  THR A  31 " =    1.033
peak=   -3.149 closest distance to " O   HOH Z  63 " =    0.961
peak=   -3.142 closest distance to " CB  ALA A 100 " =    1.900
peak=   -3.136 closest distance to " O   VAL A 121 " =    1.058
peak=   -3.136 closest distance to " O   HOH Z 116 " =    0.965
peak=   -3.136 closest distance to " CB  PRO A 213 " =    1.468
peak=   -3.130 closest distance to " CG1 VAL A 296 " =    1.206
peak=   -3.130 closest distance to " O   HOH Z 188 " =    4.460
peak=   -3.129 closest distance to " CE3 TRP A 150 " =    1.773
peak=   -3.125 closest distance to " CG  ASP A 286 " =    1.116
peak=   -3.117 closest distance to " NE2 GLN A 240 " =    1.904
peak=   -3.116 closest distance to " CD  GLN A  11 " =    1.283
peak=   -3.116 closest distance to " CD2 LEU A 143 " =    2.389
peak=   -3.115 closest distance to " O   HOH Z  55 " =    2.348
peak=   -3.114 closest distance to " O   TRP A  85 " =    2.064
peak=   -3.109 closest distance to " ND2 ASN A  45 " =    0.896
peak=   -3.104 closest distance to " CB  CYS A 254 " =    2.607
peak=   -3.089 closest distance to " NH1 ARG A  66 " =    4.471
peak=   -3.088 closest distance to " CB  SER A 273 " =    1.715
peak=   -3.087 closest distance to " O   HOH Z  20 " =    1.275
peak=   -3.080 closest distance to " O   HOH Z 340 " =    1.135
peak=   -3.077 closest distance to " CA  ASP A  27 " =    2.262
peak=   -3.077 closest distance to " OD1 ASP A 191 " =    1.465
peak=   -3.073 closest distance to " CG1AVAL A  72 " =    1.976
peak=   -3.071 closest distance to " O   HOH Z 361 " =    3.443
peak=   -3.067 closest distance to " O   HOH Z 124 " =    1.858
peak=   -3.066 closest distance to " O   HOH Z 422 " =    1.426
peak=   -3.054 closest distance to " CE  MET A 105 " =    1.881
peak=   -3.049 closest distance to " O   HOH Z 202 " =    1.754
peak=   -3.048 closest distance to " CG AARG A 102 " =    1.903
peak=   -3.042 closest distance to " OG  SER A   3 " =    1.224
peak=   -3.026 closest distance to " CD  ARG A 139 " =    1.562

================= 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    :  0.5194 0.5122   6.311556e+00   6.304166e+00
   1_bss:  0.5120 0.5049   6.309094e+00   6.297479e+00
   1_xyz:  0.4480 0.4713   6.244173e+00   6.272895e+00
   1_adp:  0.4150 0.4672   6.208002e+00   6.267633e+00
   1_occ:  0.4143 0.4677   6.207078e+00   6.267022e+00
   2_bss:  0.4139 0.4626   6.207304e+00   6.265923e+00
   2_xyz:  0.3528 0.4116   6.092024e+00   6.191844e+00
   2_adp:  0.3291 0.3982   6.051649e+00   6.167469e+00
   2_occ:  0.3291 0.3980   6.051318e+00   6.167304e+00
   3_bss:  0.3259 0.3953   6.048574e+00   6.166010e+00
   3_xyz:  0.2495 0.3169   5.834837e+00   6.008391e+00
   3_adp:  0.2223 0.2814   5.733608e+00   5.914059e+00
   3_occ:  0.2218 0.2811   5.732756e+00   5.913963e+00
   4_bss:  0.2208 0.2783   5.729110e+00   5.909970e+00
   4_xyz:  0.1618 0.2154   5.467726e+00   5.686939e+00
   4_adp:  0.1449 0.1982   5.367777e+00   5.594928e+00
   4_occ:  0.1446 0.1978   5.366122e+00   5.594094e+00
   5_bss:  0.1447 0.1964   5.365056e+00   5.590683e+00
   5_xyz:  0.1334 0.1811   5.293762e+00   5.516575e+00
   5_adp:  0.1323 0.1778   5.280317e+00   5.498345e+00
   5_occ:  0.1321 0.1776   5.279088e+00   5.497329e+00
   5_bss:  0.1321 0.1776   5.278980e+00   5.497265e+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:  0.384  20.000   6.627   8.792   7.715   0.000   0.000   0.000
   1_xyz:  0.384  20.000   6.627   8.792   7.715   0.000   0.000   0.000
   1_adp:  0.384  20.000   6.627   8.792   7.715   0.000   0.000   0.000
   1_occ:  0.384  20.000   6.627   8.792   7.715   0.000   0.000   0.000
   2_bss:  0.355  36.446   3.596   5.593   5.465   0.000   0.000   0.000
   2_xyz:  0.355  36.446   3.596   5.593   5.465   0.000   0.000   0.000
   2_adp:  0.355  36.446   3.596   5.593   5.465   0.000   0.000   0.000
   2_occ:  0.355  36.446   3.596   5.593   5.465   0.000   0.000   0.000
   3_bss:  0.341  46.120   1.517   3.113   3.005   0.000   0.000   0.000
   3_xyz:  0.341  46.120   1.517   3.113   3.005   0.000   0.000   0.000
   3_adp:  0.341  46.120   1.517   3.113   3.005   0.000   0.000   0.000
   3_occ:  0.341  46.120   1.517   3.113   3.005   0.000   0.000   0.000
   4_bss:  0.335  41.557   0.048   1.657   1.453   0.000   0.000   0.000
   4_xyz:  0.335  41.557   0.048   1.657   1.453   0.000   0.000   0.000
   4_adp:  0.335  41.557   0.048   1.657   1.453   0.000   0.000   0.000
   4_occ:  0.335  41.557   0.048   1.657   1.453   0.000   0.000   0.000
   5_bss:  0.335  41.557  -0.737   0.862   0.621   0.000   0.000   0.000
   5_xyz:  0.335  41.557  -0.737   0.862   0.621   0.000   0.000   0.000
   5_adp:  0.335  41.557  -0.737   0.862   0.621   0.000   0.000   0.000
   5_occ:  0.335  41.557  -0.737   0.862   0.621   0.000   0.000   0.000
   5_bss:  0.335  41.610  -0.992   0.611   0.380   0.000   0.000   0.000
------------------------------------------------------------------------
 stage     <pher>    fom   alpha         beta
   0    :  66.485 0.3094  0.3689    85035.895
   1_bss:  66.251 0.3109  0.4593    82680.686
   1_xyz:  63.882 0.3399  0.4886    72773.908
   1_adp:  59.473 0.3983  0.6549    69831.707
   1_occ:  59.466 0.3983  0.6528    69660.772
   2_bss:  58.998 0.4042  0.6056    68811.561
   2_xyz:  47.928 0.5447  0.8205    49567.301
   2_adp:  45.163 0.5786  0.8728    44953.097
   2_occ:  45.126 0.5790  0.8736    44887.204
   3_bss:  44.846 0.5822  0.8086    44322.234
   3_xyz:  33.853 0.7132  0.9607    27296.696
   3_adp:  28.765 0.7713  0.9984    21267.496
   3_occ:  28.757 0.7713  0.9982    21248.117
   4_bss:  28.578 0.7729  0.9458    20890.433
   4_xyz:  21.199 0.8499  1.0026    12265.822
   4_adp:  18.704 0.8746  1.0112    10229.034
   4_occ:  18.669 0.8749  1.0112    10187.820
   5_bss:  18.591 0.8755  0.9813    10086.305
   5_xyz:  16.791 0.8919  0.9880     8508.748
   5_adp:  16.351 0.8960  0.9905     8272.463
   5_occ:  16.318 0.8963  0.9906     8245.100
   5_bss:  16.314 0.8964  0.9835     8242.411
------------------------------------------------------------------------
 stage       angl   bond   chir   dihe   plan   repu  geom_target
   0    :  24.226  0.414  2.119 33.790  0.145  4.086   5.2827e+01
   1_bss:  24.226  0.414  2.119 33.790  0.145  4.086   5.2827e+01
   1_xyz:   2.106  0.018  0.125 18.860  0.009  4.104   2.1347e-01
   1_adp:   2.106  0.018  0.125 18.860  0.009  4.104   2.1347e-01
   1_occ:   2.106  0.018  0.125 18.860  0.009  4.104   2.1347e-01
   2_bss:   2.106  0.018  0.125 18.860  0.009  4.104   2.1347e-01
   2_xyz:   1.414  0.011  0.090 17.782  0.006  4.103   1.2438e-01
   2_adp:   1.414  0.011  0.090 17.782  0.006  4.103   1.2438e-01
   2_occ:   1.414  0.011  0.090 17.782  0.006  4.103   1.2438e-01
   3_bss:   1.414  0.011  0.090 17.782  0.006  4.103   1.2438e-01
   3_xyz:   1.316  0.009  0.089 16.892  0.005  4.105   9.6857e-02
   3_adp:   1.316  0.009  0.089 16.892  0.005  4.105   9.6857e-02
   3_occ:   1.316  0.009  0.089 16.892  0.005  4.105   9.6857e-02
   4_bss:   1.316  0.009  0.089 16.892  0.005  4.105   9.6857e-02
   4_xyz:   1.188  0.008  0.084 16.166  0.005  4.107   8.0973e-02
   4_adp:   1.188  0.008  0.084 16.166  0.005  4.107   8.0973e-02
   4_occ:   1.188  0.008  0.084 16.166  0.005  4.107   8.0973e-02
   5_bss:   1.188  0.008  0.084 16.166  0.005  4.107   8.0973e-02
   5_xyz:   0.964  0.006  0.069 15.667  0.004  4.111   5.8493e-02
   5_adp:   0.964  0.006  0.069 15.667  0.004  4.111   5.8493e-02
   5_occ:   0.964  0.006  0.069 15.667  0.004  4.111   5.8493e-02
   5_bss:   0.964  0.006  0.069 15.667  0.004  4.111   5.8493e-02
------------------------------------------------------------------------
                      Maximal deviations:
 stage       angl   bond   chir   dihe   plan   repu       |grad|
   0    :  74.492  1.400  6.404144.062  0.405  0.909   6.8344e+00
   1_bss:  74.492  1.400  6.404144.062  0.405  0.909   6.8344e+00
   1_xyz:  18.033  0.235  0.620 88.841  0.067  2.052   1.2958e-01
   1_adp:  18.033  0.235  0.620 88.841  0.067  2.052   1.2958e-01
   1_occ:  18.033  0.235  0.620 88.841  0.067  2.052   1.2958e-01
   2_bss:  18.033  0.235  0.620 88.841  0.067  2.052   1.2958e-01
   2_xyz:  10.523  0.141  0.302 86.461  0.058  2.060   9.0617e-02
   2_adp:  10.523  0.141  0.302 86.461  0.058  2.060   9.0617e-02
   2_occ:  10.523  0.141  0.302 86.461  0.058  2.060   9.0617e-02
   3_bss:  10.523  0.141  0.302 86.461  0.058  2.060   9.0617e-02
   3_xyz:   8.658  0.080  0.377 83.919  0.034  2.218   7.2442e-02
   3_adp:   8.658  0.080  0.377 83.919  0.034  2.218   7.2442e-02
   3_occ:   8.658  0.080  0.377 83.919  0.034  2.218   7.2442e-02
   4_bss:   8.658  0.080  0.377 83.919  0.034  2.218   7.2442e-02
   4_xyz:   8.392  0.049  0.445 81.635  0.031  2.208   6.3421e-02
   4_adp:   8.392  0.049  0.445 81.635  0.031  2.208   6.3421e-02
   4_occ:   8.392  0.049  0.445 81.635  0.031  2.208   6.3421e-02
   5_bss:   8.392  0.049  0.445 81.635  0.031  2.208   6.3421e-02
   5_xyz:   6.276  0.042  0.298 87.102  0.030  2.334   7.0372e-02
   5_adp:   6.276  0.042  0.298 87.102  0.030  2.334   7.0372e-02
   5_occ:   6.276  0.042  0.298 87.102  0.030  2.334   7.0372e-02
   5_bss:   6.276  0.042  0.298 87.102  0.030  2.334   7.0372e-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: 107.42   0.00  16.54 107.42   0.00  15.13  98.69   0.00  24.27
   1_occ: 107.42   0.00  16.54 107.42   0.00  15.13  98.69   0.00  24.27
   2_bss: 107.42   0.00  16.54 107.42   0.00  15.13  98.69   0.00  24.27
   2_xyz: 107.42   0.00  16.54 107.42   0.00  15.13  98.69   0.00  24.27
   2_adp: 106.58   0.00  16.53  74.12   0.00  13.99 106.58   0.00  30.36
   2_occ: 106.58   0.00  16.53  74.12   0.00  13.99 106.58   0.00  30.36
   3_bss: 106.58   0.00  16.53  74.12   0.00  13.99 106.58   0.00  30.36
   3_xyz: 106.58   0.00  16.53  74.12   0.00  13.99 106.58   0.00  30.36
   3_adp:  95.30   0.00  15.68  86.94   0.00  11.93  95.30   3.60  36.12
   3_occ:  95.30   0.00  15.68  86.94   0.00  11.93  95.30   3.60  36.12
   4_bss:  95.30   0.00  15.68  86.94   0.00  11.93  95.30   3.60  36.12
   4_xyz:  95.30   0.00  15.68  86.94   0.00  11.93  95.30   3.60  36.12
   4_adp:  92.05   0.00  15.36  89.19   0.00  10.93  92.05   2.51  39.47
   4_occ:  92.05   0.00  15.36  89.19   0.00  10.93  92.05   2.51  39.47
   5_bss:  92.05   0.00  15.36  89.19   0.00  10.93  92.05   2.51  39.47
   5_xyz:  92.05   0.00  15.36  89.19   0.00  10.93  92.05   2.51  39.47
   5_adp:  91.55   0.00  15.27  88.65   0.00  10.92  91.55   3.66  38.94
   5_occ:  91.55   0.00  15.27  88.65   0.00  10.92  91.55   3.66  38.94
   5_bss:  91.60   0.05  15.32  88.70   0.05  10.97  91.60   3.71  39.00
------------------------------------------------------------------------
 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:    1.258    0.029    0.449
   1_adp:    1.258    0.029    0.449
   1_occ:    1.258    0.029    0.449
   2_bss:    1.258    0.029    0.449
   2_xyz:    1.857    0.010    0.634
   2_adp:    1.857    0.010    0.634
   2_occ:    1.857    0.010    0.634
   3_bss:    1.857    0.010    0.634
   3_xyz:    1.815    0.029    0.797
   3_adp:    1.815    0.029    0.797
   3_occ:    1.815    0.029    0.797
   4_bss:    1.815    0.029    0.797
   4_xyz:    2.124    0.044    0.912
   4_adp:    2.124    0.044    0.912
   4_occ:    2.124    0.044    0.912
   5_bss:    2.124    0.044    0.912
   5_xyz:    2.180    0.060    0.924
   5_adp:    2.180    0.060    0.924
   5_occ:    2.180    0.060    0.924
   5_bss:    2.180    0.060    0.924
------------------------------------------------------------------------

CPU time actual refinement: 361.76


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

Writing refined structure to PDB file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_88/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_88/model_refine_001_2mFobs-DFmodel.map
Writing mFobs-DFmodel XPLOR map to file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_88/model_refine_001_mFobs-DFmodel.map
Writing map coefficients to MTZ file:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_88/model_refine_001_map_coeffs.mtz

Writing default parameters for subsequent refinement:
  /net/cci-filer1/vol1/tmp/phzwart/tassos/trial/run_88/model_refine_002.def


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

Pure refinement (no I/O, processing, etc)= 361.60 
  Macro-tasks:
    bulk solvent and scale       = 42.53  
    individual site refinement   = 157.79 
    weights calculation          = 32.39  
    collect and process          = 6.37   
    model show statistics        = 0.12   
    TOTAL for macro-tasks        = 239.20 
  Micro-tasks:
    mask                            = 2.42   
    f_calc                          = 115.76 
    alpha_beta                      = 8.42   
    target                          = 1.14   
    gradients_wrt_atomic_parameters = 126.52 
    fmodel                         = 6.96   
    r_factors                      = 0.29   
    phase_errors                   = 9.93   
    foms                           = 0.28   
    TOTAL for micro-tasks          = 271.72 
NUMBER OF MASK CALCS=  5
Time per interpreted Python bytecode instruction: 5.053 micro seconds
Total CPU time: 6.26 minutes
from_scatterers_fft:    652 calls, 115.31 s
gradients_fft:          596 calls, 112.94 s

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

# Date 2008-01-16 Time 00:45:27 PST -0800 (1200473127.60 s)
Start R-work = 0.5194, R-free = 0.5122 (no bulk solvent and anisotropic scale)
Final R-work = 0.1495, R-free = 0.1960 (no bulk solvent and anisotropic scale)

Start R-work = 0.5120, R-free = 0.5049
Final R-work = 0.1321, R-free = 0.1776